1
|
Khawaja T, Kajova M, Levonen I, Pietilä JP, Välimaa H, Paajanen J, Pakkanen SH, Patjas A, Montonen R, Miettinen S, Virtanen J, Smura T, Sironen T, Fagerlund R, Ugurlu H, Iheozor-Ejiofor R, Saksela K, Vahlberg T, Ranki A, Vierikko A, Ihalainen J, Vapalahti O, Kantele A. Double-blinded, randomised, placebo-controlled trial of convalescent plasma for COVID-19: analyses by neutralising antibodies homologous to recipients' variants. Infect Dis (Lond) 2024; 56:423-433. [PMID: 38513074 DOI: 10.1080/23744235.2024.2329957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 03/08/2024] [Indexed: 03/23/2024] Open
Abstract
INTRODUCTION Convalescent plasma (CP) emerged as potential treatment for COVID-19 early in the pandemic. While efficacy in hospitalised patients has been lacklustre, CP may be beneficial at the first stages of disease. Despite multiple new variants emerging, no trials have involved analyses on variant-specific antibody titres of CP. METHODS We recruited hospitalised COVID-19 patients within 10 days of symptom onset and, employing a double-blinded approach, randomised them to receive 200 ml convalescent plasma with high (HCP) or low (LCP) neutralising antibody (NAb) titre against the ancestral strain (Wuhan-like variant) or placebo in 1:1:1 ratio. Primary endpoints comprised intubation, corticosteroids for symptom aggravation, and safety assessed as serious adverse events. For a preplanned ad hoc analysis, the patients were regrouped by infused CP's NAb titers to variants infecting the recipients i.e. by titres of homologous HCP (hHCP) or LCP (hLCP). RESULTS Of the 57 patients, 18 received HCP, 19 LCP and 20 placebo, all groups smaller than planned. No significant differences were found for primary endpoints. In ad hoc analysis, hHCPrecipients needed significantly less respiratory support, and appeared to be given corticosteroids less frequently (1/14; 7.1%) than those receiving hLCP (9/23; 39.1%) or placebo (8/20; 40%), (p = 0.077). DISCUSSION Our double-blinded, placebo-controlled CP therapy trial remained underpowered and does not allow any firm conclusions for early-stage hospitalised COVID-19 patients. Interestingly, however, regrouping by homologous - recipients' variant-specific - CP titres suggested benefits for hHCP. We encourage similar re-analysis of ongoing/previous larger CP studies. TRIAL REGISTRATION ClinTrials.gov identifier: NCT0473040.
Collapse
Affiliation(s)
- T Khawaja
- Meilahti Vaccine Research Center, MeVac, Department of Infectious Diseases, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Infectious Diseases, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- FIMAR, Multidisciplinary Center of Excellence in Antimicrobial Resistance Research, University of Helsinki, Helsinki, Finland
| | - M Kajova
- Meilahti Vaccine Research Center, MeVac, Department of Infectious Diseases, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Infectious Diseases, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- FIMAR, Multidisciplinary Center of Excellence in Antimicrobial Resistance Research, University of Helsinki, Helsinki, Finland
| | - I Levonen
- Meilahti Vaccine Research Center, MeVac, Department of Infectious Diseases, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - J P Pietilä
- Meilahti Vaccine Research Center, MeVac, Department of Infectious Diseases, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- FIMAR, Multidisciplinary Center of Excellence in Antimicrobial Resistance Research, University of Helsinki, Helsinki, Finland
| | - H Välimaa
- Meilahti Vaccine Research Center, MeVac, Department of Infectious Diseases, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, University of Helsinki, Helsinki, Finland
| | - J Paajanen
- Meilahti Vaccine Research Center, MeVac, Department of Infectious Diseases, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Pulmonary Medicine, Heart and Lung Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - S H Pakkanen
- Meilahti Vaccine Research Center, MeVac, Department of Infectious Diseases, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- FIMAR, Multidisciplinary Center of Excellence in Antimicrobial Resistance Research, University of Helsinki, Helsinki, Finland
| | - A Patjas
- Meilahti Vaccine Research Center, MeVac, Department of Infectious Diseases, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- FIMAR, Multidisciplinary Center of Excellence in Antimicrobial Resistance Research, University of Helsinki, Helsinki, Finland
| | - R Montonen
- Department of Virology, University of Helsinki, Helsinki, Finland
| | - S Miettinen
- Department of Virology, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - J Virtanen
- Department of Virology, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - T Smura
- Department of Virology, University of Helsinki, Helsinki, Finland
| | - T Sironen
- Department of Virology, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - R Fagerlund
- Department of Virology, University of Helsinki, Helsinki, Finland
| | - H Ugurlu
- Department of Virology, University of Helsinki, Helsinki, Finland
| | - R Iheozor-Ejiofor
- Department of Virology, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - K Saksela
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Centre, HUSLAB, Clinical Microbiology, Helsinki University Hospital, Helsinki, Finland
| | - T Vahlberg
- Department of Biostatistics, University of Turku and Turku University Hospital, Turku, Finland
| | - A Ranki
- Department of Dermatology, Allergology and Venereology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - A Vierikko
- Finnish Red Cross Blood Service, Helsinki, Finland
| | - J Ihalainen
- Finnish Red Cross Blood Service, Helsinki, Finland
| | - O Vapalahti
- Department of Virology, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Centre, HUSLAB, Clinical Microbiology, Helsinki University Hospital, Helsinki, Finland
| | - A Kantele
- Meilahti Vaccine Research Center, MeVac, Department of Infectious Diseases, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Infectious Diseases, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- FIMAR, Multidisciplinary Center of Excellence in Antimicrobial Resistance Research, University of Helsinki, Helsinki, Finland
| |
Collapse
|
2
|
Lehikoinen J, Nurmi K, Ainola M, Clancy J, Nieminen JK, Jansson L, Vauhkonen H, Vaheri A, Smura T, Laakso SM, Eklund KK, Tienari PJ. Epstein-Barr Virus in the Cerebrospinal Fluid and Blood Compartments of Patients With Multiple Sclerosis and Controls. Neurol Neuroimmunol Neuroinflamm 2024; 11:e200226. [PMID: 38608226 DOI: 10.1212/nxi.0000000000200226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2024]
Abstract
BACKGROUND AND OBJECTIVES Epstein-Barr virus (EBV) infection is a major risk factor of multiple sclerosis (MS). We examined the presence of EBV DNA in the CSF and blood of patients with MS and controls. We analyzed whether EBV DNA is more common in the CSF of patients with MS than in controls and estimated the proportions of EBV-positive B cells in the CSF and blood. METHODS CSF supernatants and cells were collected at diagnostic lumbar punctures from 45 patients with MS and 45 HLA-DR15 matched controls with other conditions, all participants were EBV seropositive. Cellular DNA was amplified by Phi polymerase targeting both host and viral DNA, and representative samples were obtained in 28 cases and 28 controls. Nonamplified DNA from CSF cells (14 cases, 14 controls) and blood B cells (10 cases, 10 controls) were analyzed in a subset of participants. Multiple droplet digital PCR (ddPCR) runs were performed per sample to assess the cumulative EBV positivity rate. To detect viral RNA as a sign of activation, RNA sequencing was performed in blood CD4-positive, CD8-positive, and CD19-positive cells from 21 patients with MS and 3 controls. RESULTS One of the 45 patients with MS and none of the 45 controls were positive for EBV DNA in CSF supernatants (1 mL). CSF cellular DNA was analyzed in 8 independent ddPCRs: EBV DNA was detected at least once in 18 (64%) of the 28 patients with MS and in 15 (54%) of the 28 controls (p = 0.59, Fisher test). The cumulative EBV positivity increased steadily up to 59% in the successive ddPCRs, suggesting that all individuals would have reached EBV positivity in the CSF cells, if more DNA would have been analyzed. The estimated proportion of EBV-positive B cells was >1/10,000 in both the CSF and blood. We did not detect viral RNA, except from endogenous retroviruses, in the blood lymphocyte subpopulations. DISCUSSION EBV-DNA is equally detectable in the CSF cells of both patients with MS and controls with ddPCR, and the probabilistic approach indicates that the true positivity rate approaches 100% in EBV-positive individuals. The proportion of EBV-positive B cells seems higher than previously estimated.
Collapse
Affiliation(s)
- Joonas Lehikoinen
- From the Translational Immunology Research Program (J.L., K.N., M.A., J.K.N., L.J., S.M.L., K.K.E., P.J.T.), University of Helsinki; Departments of Neurology (J.L., J.K.N., L.J., S.M.L., P.J.T.), Neurocenter, and Rheumatology (K.N., M.A., K.K.E.), Helsinki University Hospital; Research and Development (J.C.), Finnish Red Cross Blood Service, Helsinki; and Department of Virology (H.V., A.V., T.S.), Medicum, University of Helsinki, Finland
| | - Katariina Nurmi
- From the Translational Immunology Research Program (J.L., K.N., M.A., J.K.N., L.J., S.M.L., K.K.E., P.J.T.), University of Helsinki; Departments of Neurology (J.L., J.K.N., L.J., S.M.L., P.J.T.), Neurocenter, and Rheumatology (K.N., M.A., K.K.E.), Helsinki University Hospital; Research and Development (J.C.), Finnish Red Cross Blood Service, Helsinki; and Department of Virology (H.V., A.V., T.S.), Medicum, University of Helsinki, Finland
| | - Mari Ainola
- From the Translational Immunology Research Program (J.L., K.N., M.A., J.K.N., L.J., S.M.L., K.K.E., P.J.T.), University of Helsinki; Departments of Neurology (J.L., J.K.N., L.J., S.M.L., P.J.T.), Neurocenter, and Rheumatology (K.N., M.A., K.K.E.), Helsinki University Hospital; Research and Development (J.C.), Finnish Red Cross Blood Service, Helsinki; and Department of Virology (H.V., A.V., T.S.), Medicum, University of Helsinki, Finland
| | - Jonna Clancy
- From the Translational Immunology Research Program (J.L., K.N., M.A., J.K.N., L.J., S.M.L., K.K.E., P.J.T.), University of Helsinki; Departments of Neurology (J.L., J.K.N., L.J., S.M.L., P.J.T.), Neurocenter, and Rheumatology (K.N., M.A., K.K.E.), Helsinki University Hospital; Research and Development (J.C.), Finnish Red Cross Blood Service, Helsinki; and Department of Virology (H.V., A.V., T.S.), Medicum, University of Helsinki, Finland
| | - Janne K Nieminen
- From the Translational Immunology Research Program (J.L., K.N., M.A., J.K.N., L.J., S.M.L., K.K.E., P.J.T.), University of Helsinki; Departments of Neurology (J.L., J.K.N., L.J., S.M.L., P.J.T.), Neurocenter, and Rheumatology (K.N., M.A., K.K.E.), Helsinki University Hospital; Research and Development (J.C.), Finnish Red Cross Blood Service, Helsinki; and Department of Virology (H.V., A.V., T.S.), Medicum, University of Helsinki, Finland
| | - Lilja Jansson
- From the Translational Immunology Research Program (J.L., K.N., M.A., J.K.N., L.J., S.M.L., K.K.E., P.J.T.), University of Helsinki; Departments of Neurology (J.L., J.K.N., L.J., S.M.L., P.J.T.), Neurocenter, and Rheumatology (K.N., M.A., K.K.E.), Helsinki University Hospital; Research and Development (J.C.), Finnish Red Cross Blood Service, Helsinki; and Department of Virology (H.V., A.V., T.S.), Medicum, University of Helsinki, Finland
| | - Hanna Vauhkonen
- From the Translational Immunology Research Program (J.L., K.N., M.A., J.K.N., L.J., S.M.L., K.K.E., P.J.T.), University of Helsinki; Departments of Neurology (J.L., J.K.N., L.J., S.M.L., P.J.T.), Neurocenter, and Rheumatology (K.N., M.A., K.K.E.), Helsinki University Hospital; Research and Development (J.C.), Finnish Red Cross Blood Service, Helsinki; and Department of Virology (H.V., A.V., T.S.), Medicum, University of Helsinki, Finland
| | - Antti Vaheri
- From the Translational Immunology Research Program (J.L., K.N., M.A., J.K.N., L.J., S.M.L., K.K.E., P.J.T.), University of Helsinki; Departments of Neurology (J.L., J.K.N., L.J., S.M.L., P.J.T.), Neurocenter, and Rheumatology (K.N., M.A., K.K.E.), Helsinki University Hospital; Research and Development (J.C.), Finnish Red Cross Blood Service, Helsinki; and Department of Virology (H.V., A.V., T.S.), Medicum, University of Helsinki, Finland
| | - Teemu Smura
- From the Translational Immunology Research Program (J.L., K.N., M.A., J.K.N., L.J., S.M.L., K.K.E., P.J.T.), University of Helsinki; Departments of Neurology (J.L., J.K.N., L.J., S.M.L., P.J.T.), Neurocenter, and Rheumatology (K.N., M.A., K.K.E.), Helsinki University Hospital; Research and Development (J.C.), Finnish Red Cross Blood Service, Helsinki; and Department of Virology (H.V., A.V., T.S.), Medicum, University of Helsinki, Finland
| | - Sini M Laakso
- From the Translational Immunology Research Program (J.L., K.N., M.A., J.K.N., L.J., S.M.L., K.K.E., P.J.T.), University of Helsinki; Departments of Neurology (J.L., J.K.N., L.J., S.M.L., P.J.T.), Neurocenter, and Rheumatology (K.N., M.A., K.K.E.), Helsinki University Hospital; Research and Development (J.C.), Finnish Red Cross Blood Service, Helsinki; and Department of Virology (H.V., A.V., T.S.), Medicum, University of Helsinki, Finland
| | - Kari K Eklund
- From the Translational Immunology Research Program (J.L., K.N., M.A., J.K.N., L.J., S.M.L., K.K.E., P.J.T.), University of Helsinki; Departments of Neurology (J.L., J.K.N., L.J., S.M.L., P.J.T.), Neurocenter, and Rheumatology (K.N., M.A., K.K.E.), Helsinki University Hospital; Research and Development (J.C.), Finnish Red Cross Blood Service, Helsinki; and Department of Virology (H.V., A.V., T.S.), Medicum, University of Helsinki, Finland
| | - Pentti J Tienari
- From the Translational Immunology Research Program (J.L., K.N., M.A., J.K.N., L.J., S.M.L., K.K.E., P.J.T.), University of Helsinki; Departments of Neurology (J.L., J.K.N., L.J., S.M.L., P.J.T.), Neurocenter, and Rheumatology (K.N., M.A., K.K.E.), Helsinki University Hospital; Research and Development (J.C.), Finnish Red Cross Blood Service, Helsinki; and Department of Virology (H.V., A.V., T.S.), Medicum, University of Helsinki, Finland
| |
Collapse
|
3
|
Lipponen A, Kolehmainen A, Oikarinen S, Hokajärvi AM, Lehto KM, Heikinheimo A, Halkilahti J, Juutinen A, Luomala O, Smura T, Liitsola K, Blomqvist S, Savolainen-Kopra C, Pitkänen T. Detection of SARS-COV-2 variants and their proportions in wastewater samples using next-generation sequencing in Finland. Sci Rep 2024; 14:7751. [PMID: 38565591 PMCID: PMC10987589 DOI: 10.1038/s41598-024-58113-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 03/25/2024] [Indexed: 04/04/2024] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants may have different characteristics, e.g., in transmission, mortality, and the effectiveness of vaccines, indicating the importance of variant detection at the population level. Wastewater-based surveillance of SARS-CoV-2 RNA fragments has been shown to be an effective way to monitor the COVID-19 pandemic at the population level. Wastewater is a complex sample matrix affected by environmental factors and PCR inhibitors, causing insufficient coverage in sequencing, for example. Subsequently, results where part of the genome does not have sufficient coverage are not uncommon. To identify variants and their proportions in wastewater over time, we utilized next-generation sequencing with the ARTIC Network's primer set and bioinformatics pipeline to evaluate the presence of variants in partial genome data. Based on the wastewater data from November 2021 to February 2022, the Delta variant was dominant until mid-December in Helsinki, Finland's capital, and thereafter in late December 2022 Omicron became the most common variant. At the same time, the Omicron variant of SARS-CoV-2 outcompeted the previous Delta variant in Finland in new COVID-19 cases. The SARS-CoV-2 variant findings from wastewater are in agreement with the variant information obtained from the patient samples when visually comparing trends in the sewerage network area. This indicates that the sequencing of wastewater is an effective way to monitor temporal and spatial trends of SARS-CoV-2 variants at the population level.
Collapse
Affiliation(s)
- Anssi Lipponen
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Kuopio, Finland.
- Institute of Biomedicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland.
| | - Aleksi Kolehmainen
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Kuopio, Finland
| | - Sami Oikarinen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Anna-Maria Hokajärvi
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Kuopio, Finland
| | - Kirsi-Maarit Lehto
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Annamari Heikinheimo
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- Microbiology Unit, Laboratory and Research Division, Finnish Food Authority, Helsinki, Finland
| | - Jani Halkilahti
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Aapo Juutinen
- Infectious Disease Control and Vaccinations Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Oskari Luomala
- Infectious Disease Control and Vaccinations Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Teemu Smura
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Kirsi Liitsola
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Soile Blomqvist
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Carita Savolainen-Kopra
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Tarja Pitkänen
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Kuopio, Finland
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| |
Collapse
|
4
|
Ianevski A, Frøysa IT, Lysvand H, Calitz C, Smura T, Schjelderup Nilsen HJ, Høyer E, Afset JE, Sridhar A, Wolthers KC, Zusinaite E, Tenson T, Kurg R, Oksenych V, Galabov AS, Stoyanova A, Bjørås M, Kainov DE. The combination of pleconaril, rupintrivir, and remdesivir efficiently inhibits enterovirus infections in vitro, delaying the development of drug-resistant virus variants. Antiviral Res 2024; 224:105842. [PMID: 38417531 DOI: 10.1016/j.antiviral.2024.105842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/10/2024] [Accepted: 02/24/2024] [Indexed: 03/01/2024]
Abstract
Enteroviruses are a significant global health concern, causing a spectrum of diseases from the common cold to more severe conditions like hand-foot-and-mouth disease, meningitis, myocarditis, pancreatitis, and poliomyelitis. Current treatment options for these infections are limited, underscoring the urgent need for effective therapeutic strategies. To find better treatment option we analyzed toxicity and efficacy of 12 known broad-spectrum anti-enterovirals both individually and in combinations against different enteroviruses in vitro. We identified several novel, synergistic two-drug and three-drug combinations that demonstrated significant inhibition of enterovirus infections in vitro. Specifically, the triple-drug combination of pleconaril, rupintrivir, and remdesivir exhibited remarkable efficacy against echovirus (EV) 1, EV6, EV11, and coxsackievirus (CV) B5, in human lung epithelial A549 cells. This combination surpassed the effectiveness of single-agent or dual-drug treatments, as evidenced by its ability to protect A549 cells from EV1-induced cytotoxicity across seven passages. Additionally, this triple-drug cocktail showed potent antiviral activity against EV-A71 in human intestinal organoids. Thus, our findings highlight the therapeutic potential of the pleconaril-rupintrivir-remdesivir combination as a broad-spectrum treatment option against a range of enterovirus infections. The study also paves the way towards development of strategic antiviral drug combinations with virus family coverage and high-resistance barriers.
Collapse
Affiliation(s)
- Aleksandr Ianevski
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7028 Trondheim, Norway
| | - Irene Trøen Frøysa
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7028 Trondheim, Norway
| | - Hilde Lysvand
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7028 Trondheim, Norway
| | - Carlemi Calitz
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
| | - Teemu Smura
- Department of Virology, University of Helsinki, 00014 Helsinki, Finland; HUS Diagnostic Center, Clinical Microbiology, Helsinki University Hospital, University of Helsinki, 00029 Helsinki, Finland
| | | | - Erling Høyer
- Department of Medical Microbiology, Clinic for Laboratory Medicine, St. Olavs Hospital, 7028 Trondheim, Norway
| | - Jan Egil Afset
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7028 Trondheim, Norway; Department of Medical Microbiology, Clinic for Laboratory Medicine, St. Olavs Hospital, 7028 Trondheim, Norway
| | - Adithya Sridhar
- OrganoVIR Labs, Dept of Pediatric Infectious Diseases, Emma Children's Hospital, Amsterdam University Centers, University of Amsterdam, Amsterdam, the Netherlands
| | - Katja C Wolthers
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
| | - Eva Zusinaite
- Institute of Technology, University of Tartu, 50411 Tartu, Estonia
| | - Tanel Tenson
- Institute of Technology, University of Tartu, 50411 Tartu, Estonia
| | - Reet Kurg
- Institute of Technology, University of Tartu, 50411 Tartu, Estonia
| | - Valentyn Oksenych
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Angel S Galabov
- The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Adelina Stoyanova
- The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Magnar Bjørås
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7028 Trondheim, Norway; Department of Microbiology, Oslo University Hospital and University of Oslo, 0372 Oslo, Norway
| | - Denis E Kainov
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7028 Trondheim, Norway; Institute for Molecular Medicine Finland, University of Helsinki, 00014, Helsinki, Finland.
| |
Collapse
|
5
|
Erdin M, Polat C, Smura T, Irmak S, Cetintas O, Cogal M, Colak F, Karatas A, Sozen M, Matur F, Vapalahti O, Sironen T, Oktem IMA. Phylogenetic Characterization of Orthohantavirus dobravaense (Dobrava Virus). Emerg Infect Dis 2024; 30:779-782. [PMID: 38526228 PMCID: PMC10977844 DOI: 10.3201/eid3004.230912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024] Open
Abstract
We report complete coding sequences of Orthohantavirus dobravaense (Dobrava virus) Igneada strains and phylogenetic characterization of all available complete coding sequences. Our analyses suggested separation of host-dependent lineages, followed by geographic clustering. Surveillance of orthohantaviruses using complete genomes would be useful for assessing public health threats from Dobrava virus.
Collapse
|
6
|
Kuhn JH, Babaian A, Bergner LM, Dény P, Glebe D, Horie M, Koonin EV, Krupovic M, Paraskevopoulou S, de la Peña M, Smura T, Hepojoki J. ICTV Virus Taxonomy Profile: Kolmioviridae 2024. J Gen Virol 2024; 105. [PMID: 38421275 DOI: 10.1099/jgv.0.001963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024] Open
Abstract
Kolmioviridae is a family for negative-sense RNA viruses with circular, viroid-like genomes of about 1.5-1.7 kb that are maintained in mammals, amphibians, birds, fish, insects and reptiles. Deltaviruses, for instance, can cause severe hepatitis in humans. Kolmiovirids encode delta antigen (DAg) and replicate using host-cell DNA-directed RNA polymerase II and ribozymes encoded in their genome and antigenome. They require evolutionary unrelated helper viruses to provide envelopes and incorporate helper virus proteins for infectious particle formation. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Kolmioviridae, which is available at ictv.global/report/kolmioviridae.
Collapse
Affiliation(s)
- Jens H Kuhn
- Integrated Research Facility at Fort Detrick, Frederick, Maryland, USA
| | | | - Laura M Bergner
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Paul Dény
- University Sorbonne Paris Nord, Bobigny, France
| | | | | | - Eugene V Koonin
- National Center for Biotechnology Information, Bethesda, Maryland, USA
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, Paris, France
| | | | | | | | | |
Collapse
|
7
|
Mull N, Erdin M, Smura T, Sironen T, Forbes KM. Novel Ozark Orthohantavirus in Hispid Cotton Rats (Sigmodon hispidus), Arkansas, USA. Emerg Infect Dis 2023; 29:2576-2578. [PMID: 37987606 PMCID: PMC10683798 DOI: 10.3201/eid2912.230549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023] Open
Abstract
We report a novel orthohantavirus, putatively named Ozark orthohantavirus, in hispid cotton rats captured within the Ozark Plateau in Arkansas, USA. This virus phylogenetically clusters with other orthohantaviruses that cause severe human disease. Continued orthohantavirus surveillance and virus sequencing are needed to address the potential public health threat of this virus.
Collapse
Affiliation(s)
| | - Mert Erdin
- University of Arkansas, Fayetteville, Arkansas, USA (N. Mull, K.M. Forbes)
- University of Helsinki, Helsinki, Finland (M. Erdin, T. Smura, T. Sironen)
| | - Teemu Smura
- University of Arkansas, Fayetteville, Arkansas, USA (N. Mull, K.M. Forbes)
- University of Helsinki, Helsinki, Finland (M. Erdin, T. Smura, T. Sironen)
| | - Tarja Sironen
- University of Arkansas, Fayetteville, Arkansas, USA (N. Mull, K.M. Forbes)
- University of Helsinki, Helsinki, Finland (M. Erdin, T. Smura, T. Sironen)
| | - Kristian M. Forbes
- University of Arkansas, Fayetteville, Arkansas, USA (N. Mull, K.M. Forbes)
- University of Helsinki, Helsinki, Finland (M. Erdin, T. Smura, T. Sironen)
| |
Collapse
|
8
|
Virtanen J, Hautala K, Utriainen M, Dutra L, Eskola K, Airas N, Uusitalo R, Ahvenainen E, Smura T, Sironen T, Vapalahti O, Kant R, Virtala AMK, Kinnunen PM. Equine dermatitis outbreak associated with parapoxvirus. J Gen Virol 2023; 104. [PMID: 38117290 DOI: 10.1099/jgv.0.001940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023] Open
Abstract
Parapoxviruses (PPV) cause skin and mucous membrane lesions in several animal species, and of the five recognized PPVs, at least three are zoonotic. Equine PPV (EqPPV) is the sixth one initially described in humans in the United States and later in a severely sick horse in Finland in 2013-2015. In 2021-2022, a large-scale pustulo-vesicular pastern dermatitis outbreak occurred in horses all over Finland. This study aimed at analysing the outbreak, identifying and describing the causative agent, describing clinical signs, and searching for risk factors. EqPPV was identified as a probable causative agent and co-infections with several potentially pathogenic and zoonotic bacteria were observed. Histopathologically, suppurative and ulcerative dermatitis was diagnosed. Due to the lack of specific tests for this virus, we developed a novel diagnostic EqPPV-PCR with sensitivity of 10 copies/reaction. Based on a large proportion of the genome sequenced directly from clinical samples, very little variation was detected between the sequences of the case from 2013 and the cases from 2021 to 2022. Based on an epidemiological survey, the main risk factor for pastern dermatitis was having racehorses. Approximately one third of the horses at each affected stable got clinical dermatitis, manifesting as severe skin lesions. Skin lesions were also occasionally reported in humans, indicating potential zoonotic transmission. Case stables commonly reported attendance at race events before acquiring the disease. Survey also identified differences in practises between case and control stables. Taken together, these results enable a better preparedness, diagnostics, and guidelines for future outbreaks.
Collapse
Affiliation(s)
- Jenni Virtanen
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Katja Hautala
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Mira Utriainen
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Lara Dutra
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Katarina Eskola
- Department of Equine and Small Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- Animal Health and Welfare Department, Finnish Food Authority, Helsinki, Finland
| | - Niina Airas
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Ruut Uusitalo
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Geosciences and Geography, Faculty of Science, University of Helsinki, Helsinki, Finland
| | - Ella Ahvenainen
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Teemu Smura
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Tarja Sironen
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Olli Vapalahti
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Ravi Kant
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Anna-Maija K Virtala
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Paula M Kinnunen
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| |
Collapse
|
9
|
Ravlo E, Ianevski A, Starheim E, Wang W, Ji P, Lysvand H, Smura T, Kivi G, Voolaid ML, Plaan K, Ustav M, Ustav M, Zusinaite E, Tenson T, Kurg R, Oksenych V, Walstad K, Nordbø SA, Kaarbø M, Ernits K, Bjørås M, Kainov DE, Fenstad MH. Boosted production of antibodies that neutralized different SARS-CoV-2 variants in a COVID-19 convalescent following messenger RNA vaccination - a case study. Int J Infect Dis 2023; 137:75-78. [PMID: 37852599 DOI: 10.1016/j.ijid.2023.10.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 10/20/2023] Open
Abstract
Vaccinated convalescents do not develop severe COVID-19 after infection with new SARS-CoV-2 variants. We questioned how messenger RNA (mRNA) vaccination of convalescents provides protection from emerging virus variants. From the cohort of 71 convalescent plasma donors, we identified a patient who developed immune response to infection with SARS-CoV-2 variant of 20A clade and who subsequently received mRNA vaccine encoding spike (S) protein of strain of 19A clade. We showed that vaccination increased the production of immune cells and anti-S antibodies in the serum. Serum antibodies neutralized not only 19A and 20A, but also 20B, 20H, 21J, and 21K virus variants. One of the serum antibodies (100F8) completely neutralized 20A, 21J, and partially 21K strains. 100F8 was structurally similar to published Ab188 antibody, which recognized non-conserved epitope on the S protein. We proposed that 100F8 and other serum antibodies of the patient which recognized non- and conserved epitopes of the S protein, could have additive or synergistic effects to neutralize various virus variants. Thus, mRNA vaccination could be beneficial for convalescents because it boosts production of neutralizing antibodies with broad-spectrum activity.
Collapse
Affiliation(s)
- Erlend Ravlo
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, Trondheim, Norway
| | - Aleksandr Ianevski
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, Trondheim, Norway
| | - Eirin Starheim
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, Trondheim, Norway
| | - Wei Wang
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, Trondheim, Norway
| | - Ping Ji
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, Trondheim, Norway
| | - Hilde Lysvand
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, Trondheim, Norway
| | - Teemu Smura
- Department of Virology, University of Helsinki, Helsinki, Finland; HUS Diagnostic Center, Clinical Microbiology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Gaily Kivi
- Icosagen Cell Factory OÜ, Tartu, Estonia
| | | | - Kati Plaan
- Icosagen Cell Factory OÜ, Tartu, Estonia
| | - Mart Ustav
- Icosagen Cell Factory OÜ, Tartu, Estonia
| | - Mart Ustav
- Icosagen Cell Factory OÜ, Tartu, Estonia
| | - Eva Zusinaite
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Tanel Tenson
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Reet Kurg
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Valentyn Oksenych
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Kirsti Walstad
- Department of Immunology and Transfusion Medicine, St. Olavs Hospital, Trondheim, Norway
| | - Svein Arne Nordbø
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, Trondheim, Norway; Department of Immunology and Transfusion Medicine, St. Olavs Hospital, Trondheim, Norway
| | - Mari Kaarbø
- Department of Microbiology, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Karin Ernits
- Department of Experimental Medicine, University of Lund, Lund, Sweden
| | - Magnar Bjørås
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, Trondheim, Norway; Department of Microbiology, Oslo University Hospital and University of Oslo, Oslo, Norway; Centre for Embryology and Healthy Development, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Denis E Kainov
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, Trondheim, Norway; Institute of Technology, University of Tartu, Tartu, Estonia; Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland.
| | - Mona Høysæter Fenstad
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, Trondheim, Norway; Department of Immunology and Transfusion Medicine, St. Olavs Hospital, Trondheim, Norway
| |
Collapse
|
10
|
Zakham F, Korhonen EM, Puonti PT, Castrén RS, Uusitalo R, Smura T, Kant R, Vapalahti O, Sironen T, Kinnunen PM. Molecular detection of pathogens from ticks collected from dogs and cats at veterinary clinics in Finland. Parasit Vectors 2023; 16:327. [PMID: 37704990 PMCID: PMC10498522 DOI: 10.1186/s13071-023-05864-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 07/04/2023] [Indexed: 09/15/2023] Open
Abstract
BACKGROUND Ticks carry microbes, some of which are pathogenic for humans and animals. To assess this One Health challenge, 342 ticks were collected from pet dogs and cats at 10 veterinary clinics in Finland as part of the European project "Protect Our Future Too". METHODS The tick species were identified, and ticks were screened with quantitative PCR (qPCR) for tick-borne pathogens, including Borrelia burgdorferi sensu lato, Borrelia miyamotoi, Ehrlichia canis, Anaplasma spp., Candidatus Neoehrlichia mikurensis, tick-borne encephalitis virus (TBEV), and Babesia spp. For comparison, a subset of tick DNA (20 qPCR-positive samples) was analysed with 16S next-generation sequencing (NGS). RESULTS Most ticks were Ixodes ricinus (289, 84.5%), followed by Ixodes persulcatus (51, 14.9%). One hybrid tick (I. ricinus/I. persulcatus, 0.3%) and one Rhipicephalus sanguineus tick (0.3%) were identified. We found one or more of the analysed pathogens in 17% (59/342) of the ticks. The most prevalent pathogen was B. burgdorferi s.l. (36, 10.5%), followed by Anaplasma phagocytophilum (12, 3.5%), B. miyamotoi (5, 1.5%), Babesia venatorum (4, 1.2%), and TBEV (1, 0.3%). Candidatus Neoehrlichia mikurensis DNA was amplified from three (0.9%) ticks. Ehrlichia canis was not detected. In the 16S NGS, six samples produced enough reads for the analysis. In these six samples, we confirmed all the positive qPCR findings of Borrelia spp. and Ca. N. mikurensis. CONCLUSIONS The high prevalence of pathogenic microorganisms in the ticks of this study emphasizes the importance of awareness of ticks and tick-borne diseases and prevention. Furthermore, the results show that veterinary surveillance can facilitate early detection of tick-borne pathogens and new tick species and draw attention to possible co-infections that should be considered both in symptomatic humans and animals after tick bites.
Collapse
Affiliation(s)
- Fathiah Zakham
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Essi M Korhonen
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Petteri T Puonti
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Robert S Castrén
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Ruut Uusitalo
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland
| | - Teemu Smura
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Clinical Microbiology, HUS Diagnostic Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Ravi Kant
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Olli Vapalahti
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- Clinical Microbiology, HUS Diagnostic Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Tarja Sironen
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Paula M Kinnunen
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland.
- Companion Animal Business Unit, Nordic Cluster, MSD Animal Health, Espoo, Finland.
| |
Collapse
|
11
|
Virtanen J, Hautaniemi M, Dutra L, Plyusnin I, Hautala K, Smura T, Vapalahti O, Sironen T, Kant R, Kinnunen PM. Partial Genome Characterization of Novel Parapoxvirus in Horse, Finland. Emerg Infect Dis 2023; 29:1941-1944. [PMID: 37610155 PMCID: PMC10461679 DOI: 10.3201/eid2909.230049] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023] Open
Abstract
We report a sequencing protocol and 121-kb poxvirus sequence from a clinical sample from a horse in Finland with dermatitis. Based on phylogenetic analyses, the virus is a novel parapoxvirus associated with a recent epidemic; previous data suggest zoonotic potential. Increased awareness of this virus and specific diagnostic protocols are needed.
Collapse
|
12
|
Riekkinen M, Kajova M, Eriksson M, Luukkainen A, Holmberg V, Aro T, Pakkanen SH, Miettinen S, Montonen R, Smura T, Lääveri T, Kantele A. Superspreading of SARS-CoV-2 Omicron BA.2.23 among vaccinated Finnish adults: symptomatic COVID-19 only contracted by those without recent infection. Epidemiol Infect 2023:1-23. [PMID: 37401478 PMCID: PMC10368952 DOI: 10.1017/s0950268823001024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2023] Open
Abstract
An outbreak of SARS-CoV-2 was confirmed after an academic party in Helsinki, Finland, in 2022. All 70 guests were requested to fill in follow-up questionnaires; serologic analyses and whole-genome sequencing (WGS) were conducted when possible.Of those participating - all but one with ≥3 vaccine doses - 21/53 (40%) had test-confirmed symptomatic COVID-19: 7% of those with earlier episodes and 76% of those without. Half (11/21) were febrile, but none needed hospitalisation. WGS revealed subvariant BA.2.23.Compared to vaccination alone, our data suggest remarkable protection by hybrid immunity against symptomatic infection, particularly in instances of recent infections with homologous variants.
Collapse
|
13
|
Vaheri A, Smura T, Vauhkonen H, Hepojoki J, Sironen T, Strandin T, Tietäväinen J, Outinen T, Mäkelä S, Pörsti I, Mustonen J. Puumala Hantavirus Infections Show Extensive Variation in Clinical Outcome. Viruses 2023; 15:v15030805. [PMID: 36992513 PMCID: PMC10054505 DOI: 10.3390/v15030805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 03/31/2023] Open
Abstract
The clinical outcome of Puumala hantavirus (PUUV) infection shows extensive variation, ranging from inapparent subclinical infection (70-80%) to severe hemorrhagic fever with renal syndrome (HFRS), with about 0.1% of cases being fatal. Most hospitalized patients experience acute kidney injury (AKI), histologically known as acute hemorrhagic tubulointerstitial nephritis. Why this variation? There is no evidence that there would be more virulent and less virulent variants infecting humans, although this has not been extensively studied. Individuals with the human leukocyte antigen (HLA) alleles B*08 and DRB1*0301 are likely to have a severe form of the PUUV infection, and those with B*27 are likely to have a benign clinical course. Other genetic factors, related to the tumor necrosis factor (TNF) gene and the C4A component of the complement system, may be involved. Various autoimmune phenomena and Epstein-Barr virus infection are associated with PUUV infection, but hantavirus-neutralizing antibodies are not associated with lower disease severity in PUUV HFRS. Wide individual differences occur in ocular and central nervous system (CNS) manifestations and in the long-term consequences of nephropathia epidemica (NE). Numerous biomarkers have been detected, and some are clinically used to assess and predict the severity of PUUV infection. A new addition is the plasma glucose concentration associated with the severity of both capillary leakage, thrombocytopenia, inflammation, and AKI in PUUV infection. Our question, "Why this variation?" remains largely unanswered.
Collapse
Affiliation(s)
- Antti Vaheri
- Department of Virology, Medicum, University of Helsinki, 00290 Helsinki, Finland
| | - Teemu Smura
- Department of Virology, Medicum, University of Helsinki, 00290 Helsinki, Finland
| | - Hanna Vauhkonen
- Department of Virology, Medicum, University of Helsinki, 00290 Helsinki, Finland
| | - Jussi Hepojoki
- Department of Virology, Medicum, University of Helsinki, 00290 Helsinki, Finland
| | - Tarja Sironen
- Department of Virology, Medicum, University of Helsinki, 00290 Helsinki, Finland
| | - Tomas Strandin
- Department of Virology, Medicum, University of Helsinki, 00290 Helsinki, Finland
| | - Johanna Tietäväinen
- Faculty of Medicine and Health Technology, Tampere University, 33014 Tampere, Finland
- Department of Internal Medicine, Tampere University Hospital, 33520 Tampere, Finland
| | - Tuula Outinen
- Department of Internal Medicine, Tampere University Hospital, 33520 Tampere, Finland
| | - Satu Mäkelä
- Department of Internal Medicine, Tampere University Hospital, 33520 Tampere, Finland
| | - Ilkka Pörsti
- Faculty of Medicine and Health Technology, Tampere University, 33014 Tampere, Finland
- Department of Internal Medicine, Tampere University Hospital, 33520 Tampere, Finland
| | - Jukka Mustonen
- Faculty of Medicine and Health Technology, Tampere University, 33014 Tampere, Finland
- Department of Internal Medicine, Tampere University Hospital, 33520 Tampere, Finland
| |
Collapse
|
14
|
Vauhkonen H, Kallio-Kokko H, Hiltunen-Back E, Lönnqvist L, Leppäaho-Lakka J, Mannonen L, Kant R, Sironen T, Kurkela S, Lappalainen M, Zorec TM, Zakotnik S, Vlaj D, Korva M, Avšič-Županc T, Poljak M, Smura T, Vapalahti O. Intrahost Monkeypox Virus Genome Variation in Patient with Early Infection, Finland, 2022. Emerg Infect Dis 2023; 29:649-652. [PMID: 36703245 PMCID: PMC9973688 DOI: 10.3201/eid2903.221388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Monkeypox virus was imported into Finland during late May-early June 2022. Intrahost viral genome variation in a sample from 1 patient comprised a major variant with 3 lineage B.1.3-specific mutations and a minor variant with ancestral B.1 nucleotides. Results suggest either ongoing APOBEC3 enzyme-mediated evolution or co-infection.
Collapse
|
15
|
Plyusnin I, Vapalahti O, Sironen T, Kant R, Smura T. Enhanced Viral Metagenomics with Lazypipe 2. Viruses 2023; 15:v15020431. [PMID: 36851645 PMCID: PMC9960287 DOI: 10.3390/v15020431] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/29/2023] [Accepted: 01/31/2023] [Indexed: 02/08/2023] Open
Abstract
Viruses are the main agents causing emerging and re-emerging infectious diseases. It is therefore important to screen for and detect them and uncover the evolutionary processes that support their ability to jump species boundaries and establish themselves in new hosts. Metagenomic next-generation sequencing (mNGS) is a high-throughput, impartial technology that has enabled virologists to detect either known or novel, divergent viruses from clinical, animal, wildlife and environmental samples, with little a priori assumptions. mNGS is heavily dependent on bioinformatic analysis, with an emerging demand for integrated bioinformatic workflows. Here, we present Lazypipe 2, an updated mNGS pipeline with, as compared to Lazypipe1, significant improvements in code stability and transparency, with added functionality and support for new software components. We also present extensive benchmarking results, including evaluation of a novel canine simulated metagenome, precision and recall of virus detection at varying sequencing depth, and a low to extremely low proportion of viral genetic material. Additionally, we report accuracy of virus detection with two strategies: homology searches using nucleotide or amino acid sequences. We show that Lazypipe 2 with nucleotide-based annotation approaches near perfect detection for eukaryotic viruses and, in terms of accuracy, outperforms the compared pipelines. We also discuss the importance of homology searches with amino acid sequences for the detection of highly divergent novel viruses.
Collapse
Affiliation(s)
- Ilya Plyusnin
- Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland
- Department of Virology, University of Helsinki, 00014 Helsinki, Finland
- Correspondence:
| | - Olli Vapalahti
- Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland
- Department of Virology, University of Helsinki, 00014 Helsinki, Finland
- HUS Diagnostic Center, Clinical Microbiology, Helsinki University Hospital, University of Helsinki, 00029 Helsinki, Finland
| | - Tarja Sironen
- Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland
- Department of Virology, University of Helsinki, 00014 Helsinki, Finland
| | - Ravi Kant
- Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland
- Department of Virology, University of Helsinki, 00014 Helsinki, Finland
- Department of Tropical Parasitology, Institute of Maritime and Tropical Medicine, Medical University of Gdansk, 81-519 Gdynia, Poland
| | - Teemu Smura
- Department of Virology, University of Helsinki, 00014 Helsinki, Finland
- HUS Diagnostic Center, Clinical Microbiology, Helsinki University Hospital, University of Helsinki, 00029 Helsinki, Finland
| |
Collapse
|
16
|
Alfaro-Alarcón A, Hetzel U, Smura T, Baggio F, Morales JA, Kipar A, Hepojoki J. Boid Inclusion Body Disease Is Also a Disease of Wild Boa Constrictors. Microbiol Spectr 2022; 10:e0170522. [PMID: 36094085 PMCID: PMC9602588 DOI: 10.1128/spectrum.01705-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 08/05/2022] [Indexed: 12/31/2022] Open
Abstract
Reptarenaviruses cause boid inclusion body disease (BIBD), a potentially fatal disease, occurring in captive constrictor snakes boas and pythons worldwide. Classical BIBD, characterized by the formation of pathognomonic cytoplasmic inclusion bodies (IBs), occurs mainly in boas, whereas in pythons, for example, reptarenavirus infection most often manifests as central nervous system signs with limited IB formation. The natural hosts of reptarenaviruses are unknown, although free-ranging/wild constrictor snakes are among the suspects. Here, we report BIBD with reptarenavirus infection in indigenous captive and wild boid snakes in Costa Rica using histology, immunohistology, transmission electron microscopy, and next-generation sequencing (NGS). The snakes studied represented diagnostic postmortem cases of captive and wild-caught snakes since 1989. The results from NGS on archival paraffin blocks confirm that reptarenaviruses were already present in wild boa constrictors in Costa Rica in the 1980s. Continuous sequences that were de novo assembled from the low-quality RNA obtained from paraffin-embedded tissue allowed the identification of a distinct pair of reptarenavirus S and L segments in all studied animals; in most cases, reference assembly could recover almost complete segments. Sampling of three prospective cases in 2018 allowed an examination of fresh blood or tissues and resulted in the identification of additional reptarenavirus segments and hartmanivirus coinfection. Our results show that BIBD is not only a disease of captive snakes but also occurs in indigenous wild constrictor snakes in Costa Rica, suggesting boa constrictors to play a role in natural reptarenavirus circulation. IMPORTANCE The literature describes cases of boid inclusion body disease (BIBD) in captive snakes since the 1970s, and in the 2010s, others and ourselves identified reptarenaviruses as the causative agent. BIBD affects captive snakes globally, but the origin and the natural host of reptarenaviruses remain unknown. In this report, we show BIBD and reptarenavirus infections in two native Costa Rican constrictor snake species, and by studying archival samples, we show that both the viruses and the disease have been present in free-ranging/wild snakes in Costa Rica at least since the 1980s. The diagnosis of BIBD in wild boa constrictors suggests that this species plays a role in the circulation of reptarenaviruses. Additional sample collection and analysis would help to clarify this role further and the possibility of, e.g., vector transmission from an arthropod host.
Collapse
Affiliation(s)
- Alejandro Alfaro-Alarcón
- Departamento de Patología, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
| | - Udo Hetzel
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
- University of Helsinki, Faculty of Veterinary Medicine, Department of Veterinary Biosciences, Helsinki, Finland
| | - Teemu Smura
- University of Helsinki, Faculty of Medicine, Medicum, Department of Virology, Helsinki, Finland
| | - Francesca Baggio
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Juan Alberto Morales
- Departamento de Patología, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
| | - Anja Kipar
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
- University of Helsinki, Faculty of Veterinary Medicine, Department of Veterinary Biosciences, Helsinki, Finland
| | - Jussi Hepojoki
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
- University of Helsinki, Faculty of Medicine, Medicum, Department of Virology, Helsinki, Finland
| |
Collapse
|
17
|
Truong Nguyen PT, Culverwell CL, Suvanto MT, Korhonen EM, Uusitalo R, Vapalahti O, Smura T, Huhtamo E. Characterisation of the RNA Virome of Nine Ochlerotatus Species in Finland. Viruses 2022; 14:1489. [PMID: 35891469 PMCID: PMC9324324 DOI: 10.3390/v14071489] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/19/2022] [Accepted: 06/19/2022] [Indexed: 02/01/2023] Open
Abstract
RNA viromes of nine commonly encountered Ochlerotatus mosquito species collected around Finland in 2015 and 2017 were studied using next-generation sequencing. Mosquito homogenates were sequenced from 91 pools comprising 16-60 morphologically identified adult females of Oc. cantans, Oc. caspius, Oc. communis, Oc. diantaeus, Oc. excrucians, Oc. hexodontus, Oc. intrudens, Oc. pullatus and Oc. punctor/punctodes. In total 514 viral Reverse dependent RNA polymerase (RdRp) sequences of 159 virus species were recovered, belonging to 25 families or equivalent rank, as follows: Aliusviridae, Aspiviridae, Botybirnavirus, Chrysoviridae, Chuviridae, Endornaviridae, Flaviviridae, Iflaviridae, Negevirus, Partitiviridae, Permutotetraviridae, Phasmaviridae, Phenuiviridae, Picornaviridae, Qinviridae, Quenyavirus, Rhabdoviridae, Sedoreoviridae, Solemoviridae, Spinareoviridae, Togaviridae, Totiviridae, Virgaviridae, Xinmoviridae and Yueviridae. Of these, 147 are tentatively novel viruses. One sequence of Sindbis virus, which causes Pogosta disease in humans, was detected from Oc. communis from Pohjois-Karjala. This study greatly increases the number of mosquito-associated viruses known from Finland and presents the northern-most mosquito-associated viruses in Europe to date.
Collapse
Affiliation(s)
- Phuoc T. Truong Nguyen
- Department of Virology, Medicum, University of Helsinki, Haartmaninkatu 3, FI-00290 Helsinki, Finland; (C.L.C.); (M.T.S.); (E.M.K.); (R.U.); (O.V.); (T.S.); (E.H.)
| | - C. Lorna Culverwell
- Department of Virology, Medicum, University of Helsinki, Haartmaninkatu 3, FI-00290 Helsinki, Finland; (C.L.C.); (M.T.S.); (E.M.K.); (R.U.); (O.V.); (T.S.); (E.H.)
- The Natural History Museum, Cromwell Road, South Kensington, London SW5 7BD, UK
| | - Maija T. Suvanto
- Department of Virology, Medicum, University of Helsinki, Haartmaninkatu 3, FI-00290 Helsinki, Finland; (C.L.C.); (M.T.S.); (E.M.K.); (R.U.); (O.V.); (T.S.); (E.H.)
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Agnes Sjöbergin Katu 2, P.O. Box 66, FI-00014 Helsinki, Finland
| | - Essi M. Korhonen
- Department of Virology, Medicum, University of Helsinki, Haartmaninkatu 3, FI-00290 Helsinki, Finland; (C.L.C.); (M.T.S.); (E.M.K.); (R.U.); (O.V.); (T.S.); (E.H.)
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Agnes Sjöbergin Katu 2, P.O. Box 66, FI-00014 Helsinki, Finland
| | - Ruut Uusitalo
- Department of Virology, Medicum, University of Helsinki, Haartmaninkatu 3, FI-00290 Helsinki, Finland; (C.L.C.); (M.T.S.); (E.M.K.); (R.U.); (O.V.); (T.S.); (E.H.)
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Agnes Sjöbergin Katu 2, P.O. Box 66, FI-00014 Helsinki, Finland
- Department of Geosciences and Geography, Faculty of Science, University of Helsinki, Gustaf Hällströmin Katu 2, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Olli Vapalahti
- Department of Virology, Medicum, University of Helsinki, Haartmaninkatu 3, FI-00290 Helsinki, Finland; (C.L.C.); (M.T.S.); (E.M.K.); (R.U.); (O.V.); (T.S.); (E.H.)
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Agnes Sjöbergin Katu 2, P.O. Box 66, FI-00014 Helsinki, Finland
- Virology and Immunology, Diagnostic Center, HUSLAB, Helsinki University Hospital, FI-00029 Helsinki, Finland
| | - Teemu Smura
- Department of Virology, Medicum, University of Helsinki, Haartmaninkatu 3, FI-00290 Helsinki, Finland; (C.L.C.); (M.T.S.); (E.M.K.); (R.U.); (O.V.); (T.S.); (E.H.)
| | - Eili Huhtamo
- Department of Virology, Medicum, University of Helsinki, Haartmaninkatu 3, FI-00290 Helsinki, Finland; (C.L.C.); (M.T.S.); (E.M.K.); (R.U.); (O.V.); (T.S.); (E.H.)
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Agnes Sjöbergin Katu 2, P.O. Box 66, FI-00014 Helsinki, Finland
| |
Collapse
|
18
|
Kolehmainen P, Heroum J, Jalkanen P, Huttunen M, Toivonen L, Marjomäki V, Waris M, Smura T, Kakkola L, Tauriainen S, Peltola V, Julkunen I. Serological Follow-Up Study Indicates High Seasonal Coronavirus Infection and Reinfection Rates in Early Childhood. Microbiol Spectr 2022; 10:e0196721. [PMID: 35481830 PMCID: PMC9241850 DOI: 10.1128/spectrum.01967-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 02/17/2022] [Indexed: 11/20/2022] Open
Abstract
Seasonal human coronaviruses (HCoVs) cause respiratory infections, especially in children. Currently, the knowledge on early childhood seasonal coronavirus infections and the duration of antibody levels following the first infections is limited. Here we analyzed serological follow-up samples to estimate the rate of primary infection and reinfection(s) caused by seasonal coronaviruses in early childhood. Serum specimens were collected from 140 children at ages of 13, 24, and 36 months (1, 2, and 3 years), and IgG antibody levels against recombinant HCoV nucleoproteins (N) were measured by enzyme immunoassay (EIA). Altogether, 84% (118/140) of the children were seropositive for at least one seasonal coronavirus N by the age of 3 years. Cumulative seroprevalences for HCoVs 229E, HKU1, NL63, and OC43 increased by age, and they were 45%, 27%, 70%, and 44%, respectively, at the age of 3 years. Increased antibody levels between yearly samples indicated reinfections by 229E, NL63, and OC43 viruses in 20-48% of previously seropositive children by the age of 3 years. Antibody levels declined 54-73% or 31-77% during the year after seropositivity in children initially seropositive at 1 or 2 years of age, respectively, in case there was no reinfection. The correlation of 229E and NL63, and OC43 and HKU1 EIA results, suggested potential cross-reactivity between the N specific antibodies inside the coronavirus genera. The data shows that seasonal coronavirus infections and reinfections are common in early childhood and the antibody levels decline relatively rapidly. IMPORTANCE The rapid spread of COVID-19 requires better knowledge on the rate of coronavirus infections and coronavirus specific antibody responses in different population groups. In this work we analyzed changes in seasonal human coronavirus specific antibodies in young children participating in a prospective 3-year serological follow-up study. We show that based on seropositivity and changes in serum coronavirus antibody levels, coronavirus infections and reinfections are common in early childhood and the antibodies elicited by the infection decline relatively rapidly. These observations provide further information on the characteristics of humoral immune responses of coronavirus infections in children.
Collapse
Affiliation(s)
| | - Jemna Heroum
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Pinja Jalkanen
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Moona Huttunen
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Laura Toivonen
- Department of Paediatrics and Adolescent Medicine, Turku University Hospital and University of Turku, Turku, Finland
| | - Varpu Marjomäki
- Department of Biological and Environmental Sciences/Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Matti Waris
- Institute of Biomedicine, University of Turku, Turku, Finland
- Clinical Microbiology, Turku University Hospital, Turku, Finland
| | - Teemu Smura
- Department of Virology, University of Helsinki, Helsinki, Finland
| | - Laura Kakkola
- Institute of Biomedicine, University of Turku, Turku, Finland
| | | | - Ville Peltola
- Department of Paediatrics and Adolescent Medicine, Turku University Hospital and University of Turku, Turku, Finland
| | - Ilkka Julkunen
- Institute of Biomedicine, University of Turku, Turku, Finland
- Clinical Microbiology, Turku University Hospital, Turku, Finland
| |
Collapse
|
19
|
Masika MM, Korhonen EM, Smura T, Uusitalo R, Ogola J, Mwaengo D, Jääskeläinen AJ, Alburkat H, Gwon YD, Evander M, Anzala O, Vapalahti O, Huhtamo E. Serological Evidence of Exposure to Onyong-Nyong and Chikungunya Viruses in Febrile Patients of Rural Taita-Taveta County and Urban Kibera Informal Settlement in Nairobi, Kenya. Viruses 2022; 14:v14061286. [PMID: 35746757 PMCID: PMC9230508 DOI: 10.3390/v14061286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/28/2022] [Accepted: 06/08/2022] [Indexed: 02/01/2023] Open
Abstract
Several alphaviruses, such as chikungunya (CHIKV) and Onyong-nyong (ONNV), are endemic in Kenya and often cause outbreaks in different parts of the country. We assessed the seroprevalence of alphaviruses in patients with acute febrile illness in two geographically distant areas in Kenya with no previous record of alphavirus outbreaks. Blood samples were collected from febrile patients in health facilities located in the rural Taita-Taveta County in 2016 and urban Kibera informal settlement in Nairobi in 2017 and tested for CHIKV IgG and IgM antibodies using an in-house immunofluorescence assay (IFA) and a commercial ELISA test, respectively. A subset of CHIKV IgG or IgM antibody-positive samples were further analyzed using plaque reduction neutralization tests (PRNT) for CHIKV, ONNV, and Sindbis virus. Out of 537 patients, 4 (0.7%) and 28 (5.2%) had alphavirus IgM and IgG antibodies, respectively, confirmed on PRNT. We show evidence of previous and current exposure to alphaviruses based on serological testing in areas with no recorded history of outbreaks.
Collapse
Affiliation(s)
- Moses Muia Masika
- KAVI Institute of Clinical Research, University of Nairobi, POB 19676, Nairobi 00202, Kenya; (J.O.); (O.A.)
- Department of Medical Microbiology, University of Nairobi, POB 19676, Nairobi 00202, Kenya;
- Correspondence: ; Tel.: +254-721770306
| | - Essi M. Korhonen
- Department of Virology, University of Helsinki, 00014 Helsinki, Finland; (E.M.K.); (T.S.); (R.U.); (A.J.J.); (H.A.); (O.V.); (E.H.)
- Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland
| | - Teemu Smura
- Department of Virology, University of Helsinki, 00014 Helsinki, Finland; (E.M.K.); (T.S.); (R.U.); (A.J.J.); (H.A.); (O.V.); (E.H.)
- HUS Diagnostic Center, HUSLAB, Virology and Immunology, Helsinki University Hospital, 00029 Helsinki, Finland
| | - Ruut Uusitalo
- Department of Virology, University of Helsinki, 00014 Helsinki, Finland; (E.M.K.); (T.S.); (R.U.); (A.J.J.); (H.A.); (O.V.); (E.H.)
- Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland
- Department of Geosciences and Geography, University of Helsinki, 00014 Helsinki, Finland
| | - Joseph Ogola
- KAVI Institute of Clinical Research, University of Nairobi, POB 19676, Nairobi 00202, Kenya; (J.O.); (O.A.)
- Department of Medical Microbiology, University of Nairobi, POB 19676, Nairobi 00202, Kenya;
| | - Dufton Mwaengo
- Department of Medical Microbiology, University of Nairobi, POB 19676, Nairobi 00202, Kenya;
| | - Anne J. Jääskeläinen
- Department of Virology, University of Helsinki, 00014 Helsinki, Finland; (E.M.K.); (T.S.); (R.U.); (A.J.J.); (H.A.); (O.V.); (E.H.)
- HUS Diagnostic Center, HUSLAB, Virology and Immunology, Helsinki University Hospital, 00029 Helsinki, Finland
| | - Hussein Alburkat
- Department of Virology, University of Helsinki, 00014 Helsinki, Finland; (E.M.K.); (T.S.); (R.U.); (A.J.J.); (H.A.); (O.V.); (E.H.)
| | - Yong-Dae Gwon
- Department of Clinical Microbiology, Umeå University, 90185 SE Umeå, Sweden; (Y.-D.G.); (M.E.)
| | - Magnus Evander
- Department of Clinical Microbiology, Umeå University, 90185 SE Umeå, Sweden; (Y.-D.G.); (M.E.)
| | - Omu Anzala
- KAVI Institute of Clinical Research, University of Nairobi, POB 19676, Nairobi 00202, Kenya; (J.O.); (O.A.)
- Department of Medical Microbiology, University of Nairobi, POB 19676, Nairobi 00202, Kenya;
| | - Olli Vapalahti
- Department of Virology, University of Helsinki, 00014 Helsinki, Finland; (E.M.K.); (T.S.); (R.U.); (A.J.J.); (H.A.); (O.V.); (E.H.)
- Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Virology and Immunology, Helsinki University Hospital, 00029 Helsinki, Finland
| | - Eili Huhtamo
- Department of Virology, University of Helsinki, 00014 Helsinki, Finland; (E.M.K.); (T.S.); (R.U.); (A.J.J.); (H.A.); (O.V.); (E.H.)
- Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland
| |
Collapse
|
20
|
Truong Nguyen P, Kant R, Van den Broeck F, Suvanto MT, Alburkat H, Virtanen J, Ahvenainen E, Castren R, Hong SL, Baele G, Ahava MJ, Jarva H, Jokiranta ST, Kallio-Kokko H, Kekäläinen E, Kirjavainen V, Kortela E, Kurkela S, Lappalainen M, Liimatainen H, Suchard MA, Hannula S, Ellonen P, Sironen T, Lemey P, Vapalahti O, Smura T. The phylodynamics of SARS-CoV-2 during 2020 in Finland. Commun Med (Lond) 2022; 2:65. [PMID: 35698660 PMCID: PMC9187640 DOI: 10.1038/s43856-022-00130-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 05/23/2022] [Indexed: 02/01/2023] Open
Abstract
Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused millions of infections and fatalities globally since its emergence in late 2019. The virus was first detected in Finland in January 2020, after which it rapidly spread among the populace in spring. However, compared to other European nations, Finland has had a low incidence of SARS-CoV-2. To gain insight into the origins and turnover of SARS-CoV-2 lineages circulating in Finland in 2020, we investigated the phylogeographic and -dynamic history of the virus. Methods The origins of SARS-CoV-2 introductions were inferred via Travel-aware Bayesian time-measured phylogeographic analyses. Sequences for the analyses included virus genomes belonging to the B.1 lineage and with the D614G mutation from countries of likely origin, which were determined utilizing Google mobility data. We collected all available sequences from spring and fall peaks to study lineage dynamics. Results We observed rapid turnover among Finnish lineages during this period. Clade 20C became the most prevalent among sequenced cases and was replaced by other strains in fall 2020. Bayesian phylogeographic reconstructions suggested 42 independent introductions into Finland during spring 2020, mainly from Italy, Austria, and Spain. Conclusions A single introduction from Spain might have seeded one-third of cases in Finland during spring in 2020. The investigations of the original introductions of SARS-CoV-2 to Finland during the early stages of the pandemic and of the subsequent lineage dynamics could be utilized to assess the role of transboundary movements and the effects of early intervention and public health measures.
Collapse
Affiliation(s)
- Phuoc Truong Nguyen
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Ravi Kant
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Frederik Van den Broeck
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Maija T. Suvanto
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Hussein Alburkat
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jenni Virtanen
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Ella Ahvenainen
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Robert Castren
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Samuel L. Hong
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Maarit J. Ahava
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Hanna Jarva
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
- Department of Bacteriology and Immunology, University of Helsinki, Helsinki, Finland
| | - Suvi Tuulia Jokiranta
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
- Department of Bacteriology and Immunology, University of Helsinki, Helsinki, Finland
| | - Hannimari Kallio-Kokko
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Eliisa Kekäläinen
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
| | - Vesa Kirjavainen
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Elisa Kortela
- Infectious Diseases, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Satu Kurkela
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Maija Lappalainen
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Hanna Liimatainen
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Marc A. Suchard
- Departments of Biomathematics, Biostatistics and Human Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA USA
| | - Sari Hannula
- Institute for Molecular Medicine Finland (FIMM), Helsinki, Finland
| | - Pekka Ellonen
- Institute for Molecular Medicine Finland (FIMM), Helsinki, Finland
| | - Tarja Sironen
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Olli Vapalahti
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Teemu Smura
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| |
Collapse
|
21
|
Virtanen J, Aaltonen K, Kegler K, Venkat V, Niamsap T, Kareinen L, Malmgren R, Kivelä O, Atanasova N, Österlund P, Smura T, Sukura A, Strandin T, Dutra L, Vapalahti O, Nordgren H, Kant R, Sironen T. Experimental Infection of Mink with SARS-COV-2 Omicron Variant and Subsequent Clinical Disease. Emerg Infect Dis 2022; 28:1286-1288. [PMID: 35608951 PMCID: PMC9155874 DOI: 10.3201/eid2806.220328] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
We report an experimental infection of American mink with SARS-CoV-2 Omicron variant and show that mink remain positive for viral RNA for days, experience clinical signs and histopathologic changes, and transmit the virus to uninfected recipients. Preparedness is crucial to avoid spread among mink and spillover to human populations.
Collapse
|
22
|
Plyusnin I, Truong Nguyen PT, Sironen T, Vapalahti O, Smura T, Kant R. ClusTRace, a bioinformatic pipeline for analyzing clusters in virus phylogenies. BMC Bioinformatics 2022; 23:196. [PMID: 35643449 PMCID: PMC9143711 DOI: 10.1186/s12859-022-04709-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/04/2022] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND SARS-CoV-2 is the highly transmissible etiologic agent of coronavirus disease 2019 (COVID-19) and has become a global scientific and public health challenge since December 2019. Several new variants of SARS-CoV-2 have emerged globally raising concern about prevention and treatment of COVID-19. Early detection and in-depth analysis of the emerging variants allowing pre-emptive alert and mitigation efforts are thus of paramount importance. RESULTS Here we present ClusTRace, a novel bioinformatic pipeline for a fast and scalable analysis of sequence clusters or clades in large viral phylogenies. ClusTRace offers several high-level functionalities including lineage assignment, outlier filtering, aligning, phylogenetic tree reconstruction, cluster extraction, variant calling, visualization and reporting. ClusTRace was developed as an aid for COVID-19 transmission chain tracing in Finland with the main emphasis on fast screening of phylogenies for markers of super-spreading events and other features of concern, such as high rates of cluster growth and/or accumulation of novel mutations. CONCLUSIONS ClusTRace provides an effective interface that can significantly cut down learning and operating costs related to complex bioinformatic analysis of large viral sequence sets and phylogenies. All code is freely available from https://bitbucket.org/plyusnin/clustrace/.
Collapse
Affiliation(s)
- Ilya Plyusnin
- Department of Veterinary Bioscience, University of Helsinki, 00014, Helsinki, Finland.
- Department of Virology, University of Helsinki, 00014, Helsinki, Finland.
| | | | - Tarja Sironen
- Department of Veterinary Bioscience, University of Helsinki, 00014, Helsinki, Finland
- Department of Virology, University of Helsinki, 00014, Helsinki, Finland
| | - Olli Vapalahti
- Department of Veterinary Bioscience, University of Helsinki, 00014, Helsinki, Finland
- Department of Virology, University of Helsinki, 00014, Helsinki, Finland
- Department of Virology and Immunology, Helsinki University Hospital, Diagnostic Center, 00029, Helsinki, Finland
| | - Teemu Smura
- Department of Virology, University of Helsinki, 00014, Helsinki, Finland
- Department of Virology and Immunology, Helsinki University Hospital, Diagnostic Center, 00029, Helsinki, Finland
| | - Ravi Kant
- Department of Veterinary Bioscience, University of Helsinki, 00014, Helsinki, Finland
- Department of Virology, University of Helsinki, 00014, Helsinki, Finland
| |
Collapse
|
23
|
Al-Rashedi NAM, Alburkat H, Hadi AO, Munahi MG, Jasim A, Hameed A, Oda BS, Lilo KM, AlObaidi LAH, Vapalahti O, Sironen T, Smura T. High prevalence of an alpha variant lineage with a premature stop codon in ORF7a in Iraq, winter 2020-2021. PLoS One 2022; 17:e0267295. [PMID: 35617193 PMCID: PMC9135184 DOI: 10.1371/journal.pone.0267295] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 04/06/2022] [Indexed: 01/08/2023] Open
Abstract
Since the first reported case of coronavirus disease 2019 (COVID-19) in China, SARS-CoV-2 has been spreading worldwide. Genomic surveillance of SARS-CoV-2 has had a critical role in tracking the emergence, introduction, and spread of new variants, which may affect transmissibility, pathogenicity, and escape from infection or vaccine-induced immunity. As anticipated, the rapid increase in COVID-19 infections in Iraq in February 2021 is due to the introduction of variants of concern during the second wave of the COVID-19 pandemic. To understand the molecular epidemiology of SARS-CoV-2 during the second wave in Iraq (2021), we sequenced 76 complete SARS-CoV-2 genomes using NGS technology and identified genomic mutations and proportions of circulating variants among these. Also, we performed an in silico study to predict the effect of the truncation of NS7a protein (ORF7a) on its function. We detected nine different lineages of SARS-CoV-2. The B.1.1.7 lineage was predominant (80.20%) from February to May 2021, while only one B.1.351 strain was detected. Interestingly, the phylogenetic analysis showed that multiple strains of the B.1.1.7 lineage clustered closely with those from European countries. A notable frequency (43.33%) of stop codon mutation (NS7a Q62stop) was detected among the B.1.1.7 lineage sequences. In silico analysis of NS7a with Q62stop found that this stop codon had no considerable effect on the function of NS7a. This work provides molecular epidemiological insights into the spread variants of SARS-CoV-2 in Iraq, which are most likely imported from Europe.
Collapse
Affiliation(s)
| | - Hussein Alburkat
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Abas O. Hadi
- Department of Health Administration, College of Health & Medical Technology, Sawa University, Samawah, Iraq
- Department of Public Health, Al-Muthanna Health Directorate, Samawah, Iraq
| | - Murad G. Munahi
- Department of Chemistry, College of Science, Al-Muthanna University, Samawah, Iraq
| | - Ali Jasim
- Department of Public Health, Al-Muthanna Health Directorate, Samawah, Iraq
| | - Alaa Hameed
- Department of Health Administration, College of Health & Medical Technology, Sawa University, Samawah, Iraq
| | - Basel Saber Oda
- Department of Public Health, Al-Muthanna Health Directorate, Samawah, Iraq
| | | | - Laith A. H. AlObaidi
- Department of Biology, College of Science, Al-Muthanna University, Samawah, Iraq
| | - Olli Vapalahti
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Tarja Sironen
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Teemu Smura
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| |
Collapse
|
24
|
Jalkanen P, Kolehmainen P, Haveri A, Huttunen M, Laine L, Österlund P, Tähtinen PA, Ivaska L, Maljanen S, Reinholm A, Belik M, Smura T, Häkkinen HK, Ortamo E, Kantele A, Julkunen I, Lempainen J, Kakkola L. Vaccine-Induced Antibody Responses against SARS-CoV-2 Variants-Of-Concern Six Months after the BNT162b2 COVID-19 mRNA Vaccination. Microbiol Spectr 2022; 10:e0225221. [PMID: 35262410 PMCID: PMC9045126 DOI: 10.1128/spectrum.02252-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 02/06/2022] [Indexed: 01/11/2023] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants has raised concern about increased transmissibility, infectivity, and immune evasion from a vaccine and infection-induced immune responses. Although COVID-19 mRNA vaccines have proven to be highly effective against severe COVID-19 disease, the decrease in vaccine efficacy against emerged Beta and Delta variants emphasizes the need for constant monitoring of new virus lineages and studies on the persistence of vaccine-induced neutralizing antibodies. To analyze the dynamics of COVID-19 mRNA vaccine-induced antibody responses, we followed 52 health care workers in Finland for 6 months after receiving two doses of BNT162b2 vaccine with a 3-week interval. We demonstrate that, although anti-S1 antibody levels decrease 2.3-fold compared to peak antibody levels, anti-SARS-CoV-2 antibodies persist for months after BNT162b2 vaccination. Variants D614G, Alpha, and Eta are neutralized by sera of 100% of vaccinees, whereas neutralization of Delta is 3.8-fold reduced and neutralization of Beta is 5.8-fold reduced compared to D614G. Despite this reduction, 85% of sera collected 6 months postvaccination neutralizes Delta variant. IMPORTANCE A decrease in vaccine efficacy against emerging SARS-CoV-2 variants has increased the importance of assessing the persistence of SARS-CoV-2 spike protein-specific antibodies and neutralizing antibodies. Our data show that after 6 months post two doses of BNT162b2 vaccine, antibody levels decrease yet remain detectable and capable of neutralizing emerging variants. By monitoring the vaccine-induced antibody responses, vaccination strategies and administration of booster doses can be optimized.
Collapse
Affiliation(s)
- Pinja Jalkanen
- Institute of Biomedicine, University of Turku, Turku, Finland
| | | | - Anu Haveri
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Moona Huttunen
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Larissa Laine
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | | | - Paula A. Tähtinen
- Department of Paediatrics and Adolescent Medicine, Turku University Hospital and University of Turku, Turku, Finland
| | - Lauri Ivaska
- Department of Paediatrics and Adolescent Medicine, Turku University Hospital and University of Turku, Turku, Finland
| | - Sari Maljanen
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Arttu Reinholm
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Milja Belik
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Teemu Smura
- Department of Virology, University of Helsinki, Helsinki, Finland
| | - Hanni K. Häkkinen
- Meilahti Infectious Diseases and Vaccine Research Center, MeiVac, Department of Infectious Diseases, University Hospital and University of Helsinki, Helsinki, Finland
| | - Eeva Ortamo
- Meilahti Infectious Diseases and Vaccine Research Center, MeiVac, Department of Infectious Diseases, University Hospital and University of Helsinki, Helsinki, Finland
| | - Anu Kantele
- Meilahti Infectious Diseases and Vaccine Research Center, MeiVac, Department of Infectious Diseases, University Hospital and University of Helsinki, Helsinki, Finland
| | - Ilkka Julkunen
- Institute of Biomedicine, University of Turku, Turku, Finland
- Clinical Microbiology, Turku University Hospital, Turku, Finland
| | - Johanna Lempainen
- Department of Paediatrics and Adolescent Medicine, Turku University Hospital and University of Turku, Turku, Finland
- Clinical Microbiology, Turku University Hospital, Turku, Finland
- Immunogenetics Laboratory, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Laura Kakkola
- Institute of Biomedicine, University of Turku, Turku, Finland
| |
Collapse
|
25
|
Lindh E, Smura T, Blomqvist S, Liitsola K, Vauhkonen H, Savolainen L, Ikonen J, Ronkainen J, Taskila J, Taskila T, Sakaranaho P, Savolainen-Kopra C, Vapalahti O, Ikonen N. Genomic and epidemiological report of the recombinant XJ lineage SARS-CoV-2 variant, detected in northern Finland, January 2022. Euro Surveill 2022; 27. [PMID: 35451361 PMCID: PMC9027151 DOI: 10.2807/1560-7917.es.2022.27.16.2200257] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recombinant sequences of the SARS-CoV-2 Omicron variant were detected in surveillance samples collected in north-western Finland in January 2022. We detected 191 samples with an identical genome arrangement in weeks 3 to 11, indicating sustained community transmission. The recombinant lineage has a 5’-end of BA.1, a recombination breakpoint between orf1a and orf1b (nucleotide position 13,296–15,240) and a 3’-end of BA.2 including the S gene. We describe the available genomic and epidemiological data about this currently circulating recombinant XJ lineage.
Collapse
Affiliation(s)
- Erika Lindh
- Department of Health Security, Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Teemu Smura
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,HUS Diagnostic Center, HUSLAB, Clinical Microbiology, Helsinki University Hospital, Finland
| | - Soile Blomqvist
- Department of Health Security, Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Kirsi Liitsola
- Department of Health Security, Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Hanna Vauhkonen
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | | | - Jaana Ikonen
- Northern Finland Laboratory Center, Nordlab, Länsi-Pohja, Finland
| | - Jukka Ronkainen
- Primary Health Care Center City of Tornio, Finland and Center for Life Course Health Research, University of Oulu, Finland
| | | | - Tea Taskila
- Primary Health Care Center City of Kemi, Kemi, Finland
| | | | - Carita Savolainen-Kopra
- Department of Health Security, Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Olli Vapalahti
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland.,Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,HUS Diagnostic Center, HUSLAB, Clinical Microbiology, Helsinki University Hospital, Finland
| | - Niina Ikonen
- Department of Health Security, Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| |
Collapse
|
26
|
Malik A, Lehtola L, Isosomppi S, Smura T, Saarenheimo J, Anttila VJ, Särelä E. Outbreak of delta variant SARS-CoV-2 virus on a psychogeriatric ward in Helsinki, Finland, August 2021; two-dose vaccination reduces mortality and disease severity amongst the elderly. Epidemiol Infect 2022; 150:1-14. [PMID: 35440347 PMCID: PMC9114754 DOI: 10.1017/s0950268822000589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 03/04/2022] [Accepted: 03/13/2022] [Indexed: 11/26/2022] Open
Abstract
We describe an outbreak of delta variant SARS-CoV-2 on a psychogeriatric ward of elderly patients. Retrospectively collected data was analysed using Fisher's exact test to assess the association between patients’ vaccination status and infection rates, severity of disease and mortality. Vaccination with two doses was shown to reduce severity of disease (5% vs. 75%, p < 0.001) and mortality (5% vs. 50%, p < 0.018) amongst an elderly inpatient population during an outbreak of delta variant SARS-CoV-2. Vaccination should be encouraged in elderly care institutions. Furthermore, adequate vaccination in elderly care institutions is an important consideration in current booster (third/fourth) dose schedules.
Collapse
Affiliation(s)
- Adnan Malik
- Suursuo Hospital, Social Services and Healthcare Division, Helsinki, Finland
| | - Laura Lehtola
- Infectious Diseases Unit, Helsinki University Hospitals, Helsinki, Finland
| | - Sanna Isosomppi
- Epidemiological Operations Unit, Social Services and Healthcare Division, Helsinki, Finland
| | - Teemu Smura
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jaana Saarenheimo
- Suursuo Hospital, Social Services and Healthcare Division, Helsinki, Finland
| | - Veli-Jukka Anttila
- Infectious Diseases Unit, Helsinki University Hospitals, Helsinki, Finland
| | - Eeva Särelä
- Epidemiological Operations Unit, Social Services and Healthcare Division, Helsinki, Finland
| |
Collapse
|
27
|
Vauhkonen H, Nguyen PT, Kant R, Plyusnin I, Erdin M, Kurkela S, Liimatainen H, Ikonen N, Blomqvist S, Liitsola K, Lindh E, Helve O, Jarva H, Loginov R, Palva A, Hannunen T, Hannula S, Parry M, Kauppi P, Vaheri A, Sironen T, Lappalainen M, Savolainen-Kopra C, Smura T, Vapalahti O. Introduction and Rapid Spread of SARS-CoV-2 Omicron Variant and Dynamics of BA.1 and BA.1.1 Sublineages, Finland, December 2021. Emerg Infect Dis 2022; 28:1229-1232. [PMID: 35378057 PMCID: PMC9155872 DOI: 10.3201/eid2806.220515] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Multiple introductions of SARS-COV-2 Omicron variant BA.1 and BA.1.1. lineages to Finland were detected in early December 2021. Within 3 weeks, Omicron overtook Delta as the most common variant in the capital region. Sequence analysis demonstrated the emergence and spread through community transmission of a large cluster of BA.1.1 virus.
Collapse
|
28
|
Kant R, Kareinen L, Smura T, Freitag TL, Jha SK, Alitalo K, Meri S, Sironen T, Saksela K, Strandin T, Kipar A, Vapalahti O. Common Laboratory Mice Are Susceptible to Infection with the SARS-CoV-2 Beta Variant. Viruses 2021; 13:2263. [PMID: 34835069 PMCID: PMC8619350 DOI: 10.3390/v13112263] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/02/2021] [Accepted: 11/09/2021] [Indexed: 01/25/2023] Open
Abstract
Small animal models are of crucial importance for assessing COVID-19 countermeasures. Common laboratory mice would be well-suited for this purpose but are not susceptible to infection with wild-type SARS-CoV-2. However, the development of mouse-adapted virus strains has revealed key mutations in the SARS-CoV-2 spike protein that increase infectivity, and interestingly, many of these mutations are also present in naturally occurring SARS-CoV-2 variants of concern. This suggests that these variants might have the ability to infect common laboratory mice. Herein we show that the SARS-CoV-2 beta variant attains infectibility to BALB/c mice and causes pulmonary changes within 2-3 days post infection, consistent with results seen in other murine models of COVID-19, at a reasonable virus dose (2 × 105 PFU). The findings suggest that common laboratory mice can serve as the animal model of choice for testing the effectiveness of antiviral drugs and vaccines against SARS-CoV-2.
Collapse
Affiliation(s)
- Ravi Kant
- Zoonosis Unit, Department of Virology, Medicum, University of Helsinki, 00290 Helsinki, Finland; (L.K.); (T.S.); (T.S.); (K.S.); (O.V.)
- Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine, University of Helsinki, 00790 Helsinki, Finland;
| | - Lauri Kareinen
- Zoonosis Unit, Department of Virology, Medicum, University of Helsinki, 00290 Helsinki, Finland; (L.K.); (T.S.); (T.S.); (K.S.); (O.V.)
- Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine, University of Helsinki, 00790 Helsinki, Finland;
| | - Teemu Smura
- Zoonosis Unit, Department of Virology, Medicum, University of Helsinki, 00290 Helsinki, Finland; (L.K.); (T.S.); (T.S.); (K.S.); (O.V.)
| | - Tobias L. Freitag
- Research Programs Unit, Immunobiology, University of Helsinki, 00290 Helsinki, Finland;
| | - Sawan Kumar Jha
- Translational Cancer Medicine Program, Faculty of Medicine and Helsinki Institute of Life Science, University of Helsinki, 00290 Helsinki, Finland; (S.K.J.); (K.A.)
| | - Kari Alitalo
- Translational Cancer Medicine Program, Faculty of Medicine and Helsinki Institute of Life Science, University of Helsinki, 00290 Helsinki, Finland; (S.K.J.); (K.A.)
| | - Seppo Meri
- Department of Bacteriology and Immunology and Translational Immunology Research Program, University of Helsinki, 00290 Helsinki, Finland;
| | - Tarja Sironen
- Zoonosis Unit, Department of Virology, Medicum, University of Helsinki, 00290 Helsinki, Finland; (L.K.); (T.S.); (T.S.); (K.S.); (O.V.)
- Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine, University of Helsinki, 00790 Helsinki, Finland;
| | - Kalle Saksela
- Zoonosis Unit, Department of Virology, Medicum, University of Helsinki, 00290 Helsinki, Finland; (L.K.); (T.S.); (T.S.); (K.S.); (O.V.)
| | - Tomas Strandin
- Zoonosis Unit, Department of Virology, Medicum, University of Helsinki, 00290 Helsinki, Finland; (L.K.); (T.S.); (T.S.); (K.S.); (O.V.)
| | - Anja Kipar
- Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine, University of Helsinki, 00790 Helsinki, Finland;
- Laboratory for Animal Model Pathology, Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L3 3RF, UK
| | - Olli Vapalahti
- Zoonosis Unit, Department of Virology, Medicum, University of Helsinki, 00290 Helsinki, Finland; (L.K.); (T.S.); (T.S.); (K.S.); (O.V.)
- Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine, University of Helsinki, 00790 Helsinki, Finland;
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, Helsinki University Hospital, 00290 Helsinki, Finland
| |
Collapse
|
29
|
Kant R, Nguyen PT, Blomqvist S, Erdin M, Alburkat H, Suvanto M, Zakham F, Salminen V, Olander V, Paloniemi M, Huhti L, Lehtinen S, Luukinen B, Jarva H, Kallio-Kokko H, Kurkela S, Lappalainen M, Liimatainen H, Hannula S, Halkilahti J, Ikonen J, Ikonen N, Helve O, Gunell M, Vuorinen T, Plyusnin I, Lindh E, Ellonen P, Sironen T, Savolainen-Kopra C, Smura T, Vapalahti O. Incidence Trends for SARS-CoV-2 Alpha and Beta Variants, Finland, Spring 2021. Emerg Infect Dis 2021; 27:3137-3141. [PMID: 34708686 PMCID: PMC8632157 DOI: 10.3201/eid2712.211631] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 Alpha and Beta variants became dominant in Finland in spring 2021 but had diminished by summer. We used phylogenetic clustering to identify sources of spreading. We found that outbreaks were mostly seeded by a few introductions, highlighting the importance of surveillance and prevention policies.
Collapse
|
30
|
Virtanen J, Zalewski A, Kołodziej-Sobocińska M, Brzeziński M, Smura T, Sironen T. Diversity and transmission of Aleutian mink disease virus in feral and farmed American mink and native mustelids. Virus Evol 2021; 7:veab075. [PMID: 34548930 PMCID: PMC8449508 DOI: 10.1093/ve/veab075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 08/25/2021] [Accepted: 08/27/2021] [Indexed: 12/11/2022] Open
Abstract
Aleutian mink disease virus (AMDV), which causes Aleutian disease, is widely spread both in farmed mink and wild mustelids. However, only limited data are available on the role of wild animals in AMDV transmission and spread. Our aim was to shed light on AMDV transmission among wild mustelids and estimate the effect of intense farming practices on the virus circulation by studying AMDV prevalence and genetic diversity among wild mustelids in Poland. We compared AMDV seroprevalence and proportion of PCR-positive individuals in American mink, polecats, otters, stone martens, and pine martens and used the phylogenetic analysis of the NS1 region to study transmission. In addition, we used a metagenomic approach to sequence complete AMDV genomes from tissue samples. In eastern Poland, AMDV seroprevalence in wild mustelids varied from 22 per cent in otters to 62 per cent and 64 per cent in stone martens and feral mink, respectively. All studied antibody-positive mink were also PCR positive, whereas only 10, 15, and 18 per cent of antibody-positive polecats, pine martens, and stone martens, respectively, were PCR positive, suggesting lower virus persistence among these animal species as compared to feral mink. In phylogenetic analysis, most sequences from feral mink formed region-specific clusters that have most likely emerged through multiple introductions of AMDV to feral mink population over decades. However, virus spread between regions was also observed. Virus sequences derived from farmed and wild animals formed separate subclusters in the phylogenetic tree, and no signs of recent virus transmission between farmed and wild animals were observed despite the frequent inflow of farmed mink escapees to wild populations. These results provide new information about the role of different mustelid species in AMDV transmission and about virus circulation among the wild mustelids. In addition, we pinpoint gaps of knowledge, where more studies are needed to achieve a comprehensive picture of AMDV transmission.
Collapse
Affiliation(s)
| | | | | | - Marcin Brzeziński
- Faculty of Biology, University of Warsaw, ul. Miecznikowa 1, Warszawa 02-096, Poland
| | - Teemu Smura
- Department of Virology, Faculty of Medicine, University of Helsinki, Haartmaninkatu 3, Helsinki 00290, Finland
| | - Tarja Sironen
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Agnes Sjöbergin katu 2, Helsinki 00790, Finland
- Department of Virology, Faculty of Medicine, University of Helsinki, Haartmaninkatu 3, Helsinki 00290, Finland
| |
Collapse
|
31
|
Castel G, Kant R, Badou S, Etougbétché J, Dossou HJ, Gauthier P, Houéménou G, Smura T, Sironen T, Dobigny G. Genetic Characterization of Seoul Virus in the Seaport of Cotonou, Benin. Emerg Infect Dis 2021; 27:2704-2706. [PMID: 34545795 PMCID: PMC8462318 DOI: 10.3201/eid2710.210268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Seoul virus is a zoonotic pathogen carried by the brown rat Rattus norvegicus. Information on its circulation in Africa is limited. In this study, the virus was detected in 37.5% of brown rats captured in the Autonomous Port of Cotonou, Benin. Phylogenetic analyses place this virus in Seoul virus lineage 7.
Collapse
|
32
|
O'Toole Á, Hill V, Pybus OG, Watts A, Bogoch II, Khan K, Messina JP, Tegally H, Lessells RR, Giandhari J, Pillay S, Tumedi KA, Nyepetsi G, Kebabonye M, Matsheka M, Mine M, Tokajian S, Hassan H, Salloum T, Merhi G, Koweyes J, Geoghegan JL, de Ligt J, Ren X, Storey M, Freed NE, Pattabiraman C, Prasad P, Desai AS, Vasanthapuram R, Schulz TF, Steinbrück L, Stadler T, Parisi A, Bianco A, García de Viedma D, Buenestado-Serrano S, Borges V, Isidro J, Duarte S, Gomes JP, Zuckerman NS, Mandelboim M, Mor O, Seemann T, Arnott A, Draper J, Gall M, Rawlinson W, Deveson I, Schlebusch S, McMahon J, Leong L, Lim CK, Chironna M, Loconsole D, Bal A, Josset L, Holmes E, St. George K, Lasek-Nesselquist E, Sikkema RS, Oude Munnink B, Koopmans M, Brytting M, Sudha rani V, Pavani S, Smura T, Heim A, Kurkela S, Umair M, Salman M, Bartolini B, Rueca M, Drosten C, Wolff T, Silander O, Eggink D, Reusken C, Vennema H, Park A, Carrington C, Sahadeo N, Carr M, Gonzalez G, de Oliveira T, Faria N, Rambaut A, Kraemer MUG. Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch. Wellcome Open Res 2021; 6:121. [PMID: 34095513 PMCID: PMC8176267 DOI: 10.12688/wellcomeopenres.16661.2] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2021] [Indexed: 11/20/2022] Open
Abstract
Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected.
Collapse
Affiliation(s)
- Áine O'Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Verity Hill
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | | | - Alexander Watts
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
| | - Issac I. Bogoch
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
| | - Kamran Khan
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
| | | | - The COVID-19 Genomics UK (COG-UK) consortium
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Network for Genomic Surveillance in South Africa (NGS-SA)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Brazil-UK CADDE Genomic Network
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Richard R. Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | | | | | | | | | - Madisa Mine
- National Health Laboratory, Gaborone, Botswana
| | - Sima Tokajian
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Hamad Hassan
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
| | - Tamara Salloum
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Georgi Merhi
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Jad Koweyes
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Jemma L. Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Joep de Ligt
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Xiaoyun Ren
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Matthew Storey
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Nikki E. Freed
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | - Chitra Pattabiraman
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Pramada Prasad
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Anita S. Desai
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Ravi Vasanthapuram
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Thomas F. Schulz
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Lars Steinbrück
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
| | - Swiss Viollier Sequencing Consortium
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Antonio Parisi
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
| | - Angelica Bianco
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
| | - Darío García de Viedma
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
| | - Sergio Buenestado-Serrano
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Joana Isidro
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Sílvia Duarte
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Neta S. Zuckerman
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Michal Mandelboim
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Orna Mor
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Torsten Seemann
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
| | - Alicia Arnott
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
| | - Jenny Draper
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
| | - Mailie Gall
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
| | - William Rawlinson
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
| | - Ira Deveson
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
| | - Sanmarié Schlebusch
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
| | - Jamie McMahon
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
| | - Lex Leong
- South Australia Pathology, Adelaide, Australia
| | | | - Maria Chironna
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
| | - Daniela Loconsole
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
| | - Antonin Bal
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
| | - Laurence Josset
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
| | | | - Kirsten St. George
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | | | - Reina S. Sikkema
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
| | - Bas Oude Munnink
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
| | - Marion Koopmans
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
| | - Mia Brytting
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
| | - V. Sudha rani
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
| | - S. Pavani
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
| | - Teemu Smura
- Department of Virology, University of Helsinki, Helsinki, Finland
| | - Albert Heim
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Satu Kurkela
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Massab Umair
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Muhammad Salman
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Barbara Bartolini
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
| | - Martina Rueca
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
| | - Christian Drosten
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
| | - Thorsten Wolff
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
| | - Olin Silander
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | - Dirk Eggink
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Chantal Reusken
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Harry Vennema
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Aekyung Park
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
| | | | - Nikita Sahadeo
- University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Michael Carr
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Gabo Gonzalez
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - SEARCH Alliance San Diego
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - National Virus Reference Laboratory
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - SeqCOVID-Spain
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Danish Covid-19 Genome Consortium (DCGC)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Communicable Diseases Genomic Network (CDGN)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Dutch National SARS-CoV-2 surveillance program
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Division of Emerging Infectious Diseases (KDCA)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Nuno Faria
- Department of Zoology, University of Oxford, Oxford, UK
- Imperial College London, London, UK
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | | |
Collapse
|
33
|
Rabalski L, Kosinski M, Smura T, Aaltonen K, Kant R, Sironen T, Szewczyk B, Grzybek M. Severe Acute Respiratory Syndrome Coronavirus 2 in Farmed Mink (Neovison vison), Poland. Emerg Infect Dis 2021; 27:2333-2339. [PMID: 34423763 PMCID: PMC8386773 DOI: 10.3201/eid2709.210286] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent of coronavirus disease and has been spreading worldwide since December 2019. The virus can infect different animal species under experimental conditions, and mink on fur farms in Europe and other areas are susceptible to SARS-CoV-2 infection. We investigated SARS-CoV-2 infection in 91 mink from a farm in northern Poland. Using reverse transcription PCR, antigen detection, and next-generation sequencing, we confirmed that 15 animals were positive for SARS-CoV-2. We verified this finding by sequencing full viral genomes and confirmed a virus variant that has sporadic mutations through the full genome sequence in the spike protein (G75V and C1247F). We were unable to find other SARS-CoV-2 sequences simultaneously containing these 2 mutations. Country-scale monitoring by veterinary inspection should be implemented to detect SARS-CoV-2 in other mink farms.
Collapse
|
34
|
Truong Nguyen PT, Plyusnin I, Sironen T, Vapalahti O, Kant R, Smura T. HAVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences. BMC Bioinformatics 2021; 22:373. [PMID: 34273961 PMCID: PMC8285700 DOI: 10.1186/s12859-021-04294-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 07/08/2021] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND SARS-CoV-2 related research has increased in importance worldwide since December 2019. Several new variants of SARS-CoV-2 have emerged globally, of which the most notable and concerning currently are the UK variant B.1.1.7, the South African variant B1.351 and the Brazilian variant P.1. Detecting and monitoring novel variants is essential in SARS-CoV-2 surveillance. While there are several tools for assembling virus genomes and performing lineage analyses to investigate SARS-CoV-2, each is limited to performing singular or a few functions separately. RESULTS Due to the lack of publicly available pipelines, which could perform fast reference-based assemblies on raw SARS-CoV-2 sequences in addition to identifying lineages to detect variants of concern, we have developed an open source bioinformatic pipeline called HAVoC (Helsinki university Analyzer for Variants of Concern). HAVoC can reference assemble raw sequence reads and assign the corresponding lineages to SARS-CoV-2 sequences. CONCLUSIONS HAVoC is a pipeline utilizing several bioinformatic tools to perform multiple necessary analyses for investigating genetic variance among SARS-CoV-2 samples. The pipeline is particularly useful for those who need a more accessible and fast tool to detect and monitor the spread of SARS-CoV-2 variants of concern during local outbreaks. HAVoC is currently being used in Finland for monitoring the spread of SARS-CoV-2 variants. HAVoC user manual and source code are available at https://www.helsinki.fi/en/projects/havoc and https://bitbucket.org/auto_cov_pipeline/havoc , respectively.
Collapse
Affiliation(s)
| | - Ilya Plyusnin
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Tarja Sironen
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Olli Vapalahti
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Ravi Kant
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Teemu Smura
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| |
Collapse
|
35
|
Kareinen L, Ogola J, Kivistö I, Smura T, Aaltonen K, Jääskeläinen AJ, Kibiwot S, Masika MM, Nyaga P, Mwaengo D, Anzala O, Vapalahti O, Webala PW, Forbes KM, Sironen T. Range Expansion of Bombali Virus in Mops condylurus Bats, Kenya, 2019. Emerg Infect Dis 2021; 26:3007-3010. [PMID: 33219788 PMCID: PMC7706938 DOI: 10.3201/eid2612.202925] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Previously identified only in Sierra Leone, Guinea, and southeastern Kenya, Bombali virus–infected Mops condylurus bats were recently found »750 km away in western Kenya. This finding supports the role of M. condylurus bats as hosts and the potential for Bombali virus circulation across the bats’ range in sub-Saharan Africa.
Collapse
|
36
|
Alburkat H, Jääskeläinen AJ, Barakat AM, Hasony HJ, Sironen T, Al-Hello H, Smura T, Vapalahti O. Lymphocytic Choriomeningitis Virus Infections and Seroprevalence, Southern Iraq. Emerg Infect Dis 2021; 26:3002-3006. [PMID: 33219805 PMCID: PMC7706927 DOI: 10.3201/eid2612.201792] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Acute febrile neurological infection cases in southern Iraq (N = 212) were screened for lymphocytic choriomeningitis virus (LCMV). Two LCMV IgM-positive serum samples and 2 cerebrospinal fluid samples with phylogenetically distinct LCMV strains were found. The overall LCMV seroprevalence was 8.8%. LCMV infections are common and associated with acute neurological disease in Iraq.
Collapse
|
37
|
O'Toole Á, Hill V, Pybus OG, Watts A, Bogoch II, Khan K, Messina JP, Tegally H, Lessells RR, Giandhari J, Pillay S, Tumedi KA, Nyepetsi G, Kebabonye M, Matsheka M, Mine M, Tokajian S, Hassan H, Salloum T, Merhi G, Koweyes J, Geoghegan JL, de Ligt J, Ren X, Storey M, Freed NE, Pattabiraman C, Prasad P, Desai AS, Vasanthapuram R, Schulz TF, Steinbrück L, Stadler T, Parisi A, Bianco A, García de Viedma D, Buenestado-Serrano S, Borges V, Isidro J, Duarte S, Gomes JP, Zuckerman NS, Mandelboim M, Mor O, Seemann T, Arnott A, Draper J, Gall M, Rawlinson W, Deveson I, Schlebusch S, McMahon J, Leong L, Lim CK, Chironna M, Loconsole D, Bal A, Josset L, Holmes E, St. George K, Lasek-Nesselquist E, Sikkema RS, Oude Munnink B, Koopmans M, Brytting M, Sudha rani V, Pavani S, Smura T, Heim A, Kurkela S, Umair M, Salman M, Bartolini B, Rueca M, Drosten C, Wolff T, Silander O, Eggink D, Reusken C, Vennema H, Park A, Carrington C, Sahadeo N, Carr M, Gonzalez G, de Oliveira T, Faria N, Rambaut A, Kraemer MUG. Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2. Wellcome Open Res 2021; 6:121. [PMID: 34095513 PMCID: PMC8176267 DOI: 10.12688/wellcomeopenres.16661.1] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2021] [Indexed: 12/13/2022] Open
Abstract
Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected.
Collapse
Affiliation(s)
- Áine O'Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Verity Hill
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | | | - Alexander Watts
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
| | - Issac I. Bogoch
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
| | - Kamran Khan
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
| | | | - The COVID-19 Genomics UK (COG-UK) consortium
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Network for Genomic Surveillance in South Africa (NGS-SA)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Brazil-UK CADDE Genomic Network
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Richard R. Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | | | | | | | | | - Madisa Mine
- National Health Laboratory, Gaborone, Botswana
| | - Sima Tokajian
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Hamad Hassan
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
| | - Tamara Salloum
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Georgi Merhi
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Jad Koweyes
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Jemma L. Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Joep de Ligt
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Xiaoyun Ren
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Matthew Storey
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Nikki E. Freed
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | - Chitra Pattabiraman
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Pramada Prasad
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Anita S. Desai
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Ravi Vasanthapuram
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Thomas F. Schulz
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Lars Steinbrück
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
| | - Swiss Viollier Sequencing Consortium
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Antonio Parisi
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
| | - Angelica Bianco
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
| | - Darío García de Viedma
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
| | - Sergio Buenestado-Serrano
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Joana Isidro
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Sílvia Duarte
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Neta S. Zuckerman
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Michal Mandelboim
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Orna Mor
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Torsten Seemann
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
| | - Alicia Arnott
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
| | - Jenny Draper
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
| | - Mailie Gall
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
| | - William Rawlinson
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
| | - Ira Deveson
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
| | - Sanmarié Schlebusch
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
| | - Jamie McMahon
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
| | - Lex Leong
- South Australia Pathology, Adelaide, Australia
| | | | - Maria Chironna
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
| | - Daniela Loconsole
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
| | - Antonin Bal
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
| | - Laurence Josset
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
| | | | - Kirsten St. George
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | | | - Reina S. Sikkema
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
| | - Bas Oude Munnink
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
| | - Marion Koopmans
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
| | - Mia Brytting
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
| | - V. Sudha rani
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
| | - S. Pavani
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
| | - Teemu Smura
- Department of Virology, University of Helsinki, Helsinki, Finland
| | - Albert Heim
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Satu Kurkela
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Massab Umair
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Muhammad Salman
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Barbara Bartolini
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
| | - Martina Rueca
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
| | - Christian Drosten
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
| | - Thorsten Wolff
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
| | - Olin Silander
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | - Dirk Eggink
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Chantal Reusken
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Harry Vennema
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Aekyung Park
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
| | | | - Nikita Sahadeo
- University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Michael Carr
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Gabo Gonzalez
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - SEARCH Alliance San Diego
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - National Virus Reference Laboratory
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - SeqCOVID-Spain
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Danish Covid-19 Genome Consortium (DCGC)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Communicable Diseases Genomic Network (CDGN)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Dutch National SARS-CoV-2 surveillance program
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Division of Emerging Infectious Diseases (KDCA)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Nuno Faria
- Department of Zoology, University of Oxford, Oxford, UK
- Imperial College London, London, UK
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | | |
Collapse
|
38
|
Lin JW, Tang C, Wei HC, Du B, Chen C, Wang M, Zhou Y, Yu MX, Cheng L, Kuivanen S, Ogando NS, Levanov L, Zhao Y, Li CL, Zhou R, Li Z, Zhang Y, Sun K, Wang C, Chen L, Xiao X, Zheng X, Chen SS, Zhou Z, Yang R, Zhang D, Xu M, Song J, Wang D, Li Y, Lei S, Zeng W, Yang Q, He P, Zhang Y, Zhou L, Cao L, Luo F, Liu H, Wang L, Ye F, Zhang M, Li M, Fan W, Li X, Li K, Ke B, Xu J, Yang H, He S, Pan M, Yan Y, Zha Y, Jiang L, Yu C, Liu Y, Xu Z, Li Q, Jiang Y, Sun J, Hong W, Wei H, Lu G, Vapalahti O, Luo Y, Wei Y, Connor T, Tan W, Snijder EJ, Smura T, Li W, Geng J, Ying B, Chen L. Genomic monitoring of SARS-CoV-2 uncovers an Nsp1 deletion variant that modulates type I interferon response. Cell Host Microbe 2021; 29:489-502.e8. [PMID: 33548198 PMCID: PMC7846228 DOI: 10.1016/j.chom.2021.01.015] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/07/2021] [Accepted: 01/26/2021] [Indexed: 02/05/2023]
Abstract
The SARS-CoV-2 virus, the causative agent of COVID-19, is undergoing constant mutation. Here, we utilized an integrative approach combining epidemiology, virus genome sequencing, clinical phenotyping, and experimental validation to locate mutations of clinical importance. We identified 35 recurrent variants, some of which are associated with clinical phenotypes related to severity. One variant, containing a deletion in the Nsp1-coding region (Δ500-532), was found in more than 20% of our sequenced samples and associates with higher RT-PCR cycle thresholds and lower serum IFN-β levels of infected patients. Deletion variants in this locus were found in 37 countries worldwide, and viruses isolated from clinical samples or engineered by reverse genetics with related deletions in Nsp1 also induce lower IFN-β responses in infected Calu-3 cells. Taken together, our virologic surveillance characterizes recurrent genetic diversity and identified mutations in Nsp1 of biological and clinical importance, which collectively may aid molecular diagnostics and drug design.
Collapse
Affiliation(s)
- Jing-Wen Lin
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China.
| | - Chao Tang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Han-Cheng Wei
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Baowen Du
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Chuan Chen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Minjin Wang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Yongzhao Zhou
- Department of Respiratory and Critical Care Medicine, Frontier Science Center of Disease Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ming-Xia Yu
- Department of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Lu Cheng
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK; Department of Computer Science, School of Science, Aalto University, Aalto FI-00076, Finland
| | - Suvi Kuivanen
- University of Helsinki, Medicum, Department of Virology, Helsinki, Finland
| | - Natacha S Ogando
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Lev Levanov
- University of Helsinki, Medicum, Department of Virology, Helsinki, Finland
| | - Yuancun Zhao
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Chang-Ling Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Ran Zhou
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Zhidan Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Yiming Zhang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Ke Sun
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Chengdi Wang
- Department of Respiratory and Critical Care Medicine, Frontier Science Center of Disease Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Li Chen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Xia Xiao
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Xiuran Zheng
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Sha-Sha Chen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Zhen Zhou
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Ruirui Yang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Dan Zhang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Mengying Xu
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Junwei Song
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Danrui Wang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Yupeng Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - ShiKun Lei
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Wanqin Zeng
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Qingxin Yang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Ping He
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Yaoyao Zhang
- Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Lifang Zhou
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Ling Cao
- Department of Clinical Laboratory, Public Health Clinical Center of Chengdu, Chengdu, Sichuan 610041, China
| | - Feng Luo
- Wuhan Chain Medical Labs, Wuhan, Hubei 430011, China
| | - Huayi Liu
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Liping Wang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Fei Ye
- NHC Key Laboratory, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Ming Zhang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Mengjiao Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Wei Fan
- Department of Respiratory and Critical Care Medicine, Frontier Science Center of Disease Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xinqiong Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Kaiju Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Bowen Ke
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Jiannan Xu
- Sichuan Center for Disease Control and Prevention, No. 6 Zhongxue Rd, Chengdu 610041, China
| | - Huiping Yang
- Sichuan Center for Disease Control and Prevention, No. 6 Zhongxue Rd, Chengdu 610041, China
| | - Shusen He
- Sichuan Center for Disease Control and Prevention, No. 6 Zhongxue Rd, Chengdu 610041, China
| | - Ming Pan
- Sichuan Center for Disease Control and Prevention, No. 6 Zhongxue Rd, Chengdu 610041, China
| | - Yichen Yan
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Yi Zha
- Department of Clinical Laboratory, Public Health Clinical Center of Chengdu, Chengdu, Sichuan 610041, China
| | - Lingyu Jiang
- Department of Clinical Laboratory, Public Health Clinical Center of Chengdu, Chengdu, Sichuan 610041, China
| | - Changxiu Yu
- Department of Clinical Laboratory, Public Health Clinical Center of Chengdu, Chengdu, Sichuan 610041, China
| | - Yingfen Liu
- Department of Clinical Laboratory, Public Health Clinical Center of Chengdu, Chengdu, Sichuan 610041, China
| | - Zhiyong Xu
- Department of Clinical Laboratory, Public Health Clinical Center of Chengdu, Chengdu, Sichuan 610041, China
| | - Qingfeng Li
- Department of Clinical Laboratory, Public Health Clinical Center of Chengdu, Chengdu, Sichuan 610041, China
| | - Yongmei Jiang
- Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Jiufeng Sun
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong 511430, China
| | - Wei Hong
- CAS Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongping Wei
- CAS Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guangwen Lu
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Olli Vapalahti
- University of Helsinki, Medicum, Department of Virology, Helsinki, Finland; University of Helsinki and Helsinki University Hospital, Department of Virology, Helsinki, Finland; Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Yunzi Luo
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yuquan Wei
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Thomas Connor
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
| | - Wenjie Tan
- NHC Key Laboratory, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Eric J Snijder
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Teemu Smura
- University of Helsinki, Medicum, Department of Virology, Helsinki, Finland; University of Helsinki and Helsinki University Hospital, Department of Virology, Helsinki, Finland.
| | - Weimin Li
- Department of Respiratory and Critical Care Medicine, Frontier Science Center of Disease Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Jia Geng
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China.
| | - Binwu Ying
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China.
| | - Lu Chen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China.
| |
Collapse
|
39
|
Plyusnin I, Kant R, Jääskeläinen AJ, Sironen T, Holm L, Vapalahti O, Smura T. Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types. Virus Evol 2020; 6:veaa091. [PMID: 33408878 PMCID: PMC7772471 DOI: 10.1093/ve/veaa091] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The study of the microbiome data holds great potential for elucidating the biological and metabolic functioning of living organisms and their role in the environment. Metagenomic analyses have shown that humans, along with for example, domestic animals, wildlife and arthropods, are colonized by an immense community of viruses. The current Coronavirus pandemic (COVID-19) heightens the need to rapidly detect previously unknown viruses in an unbiased way. The increasing availability of metagenomic data in this era of next-generation sequencing (NGS), along with increasingly affordable sequencing technologies, highlight the need for reliable and comprehensive methods to manage such data. In this article, we present a novel bioinformatics pipeline called LAZYPIPE for identifying both previously known and novel viruses in host associated or environmental samples and give examples of virus discovery based on it. LAZYPIPE is a Unix-based pipeline for automated assembling and taxonomic profiling of NGS libraries implemented as a collection of C++, Perl, and R scripts.
Collapse
Affiliation(s)
- Ilya Plyusnin
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Ravi Kant
- Department of Veterinary Bioscience, University of Helsinki, Helsinki 00014, Finland
| | - Anne J Jääskeläinen
- Department of Virology and Immunology, University of Helsinki and Helsinki University Hospital, Helsinki 00014, Finland
| | - Tarja Sironen
- Department of Veterinary Bioscience, University of Helsinki, Helsinki 00014, Finland
| | - Liisa Holm
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Olli Vapalahti
- Department of Veterinary Bioscience, University of Helsinki, Helsinki 00014, Finland
| | - Teemu Smura
- Department of Virology, University of Helsinki, Helsinki 00014, Finland
| |
Collapse
|
40
|
Alburkat H, Jääskeläinen AJ, Barakat AM, Hasony HJ, Sironen T, Al-hello H, Smura T, Vapalahti O. Lymphocytic Choriomeningitis Virus Infections and Seroprevalence, Southern Iraq. Emerg Infect Dis 2020. [DOI: 10.3201/eid2612/201792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
|
41
|
Kuhn JH, Adkins S, Alioto D, Alkhovsky SV, Amarasinghe GK, Anthony SJ, Avšič-Županc T, Ayllón MA, Bahl J, Balkema-Buschmann A, Ballinger MJ, Bartonička T, Basler C, Bavari S, Beer M, Bente DA, Bergeron É, Bird BH, Blair C, Blasdell KR, Bradfute SB, Breyta R, Briese T, Brown PA, Buchholz UJ, Buchmeier MJ, Bukreyev A, Burt F, Buzkan N, Calisher CH, Cao M, Casas I, Chamberlain J, Chandran K, Charrel RN, Chen B, Chiumenti M, Choi IR, Clegg JCS, Crozier I, da Graça JV, Dal Bó E, Dávila AMR, de la Torre JC, de Lamballerie X, de Swart RL, Di Bello PL, Di Paola N, Di Serio F, Dietzgen RG, Digiaro M, Dolja VV, Dolnik O, Drebot MA, Drexler JF, Dürrwald R, Dufkova L, Dundon WG, Duprex WP, Dye JM, Easton AJ, Ebihara H, Elbeaino T, Ergünay K, Fernandes J, Fooks AR, Formenty PBH, Forth LF, Fouchier RAM, Freitas-Astúa J, Gago-Zachert S, Gāo GF, García ML, García-Sastre A, Garrison AR, Gbakima A, Goldstein T, Gonzalez JPJ, Griffiths A, Groschup MH, Günther S, Guterres A, Hall RA, Hammond J, Hassan M, Hepojoki J, Hepojoki S, Hetzel U, Hewson R, Hoffmann B, Hongo S, Höper D, Horie M, Hughes HR, Hyndman TH, Jambai A, Jardim R, Jiāng D, Jin Q, Jonson GB, Junglen S, Karadağ S, Keller KE, Klempa B, Klingström J, Kobinger G, Kondō H, Koonin EV, Krupovic M, Kurath G, Kuzmin IV, Laenen L, Lamb RA, Lambert AJ, Langevin SL, Lee B, Lemos ERS, Leroy EM, Li D, Lǐ J, Liang M, Liú W, Liú Y, Lukashevich IS, Maes P, Marciel de Souza W, Marklewitz M, Marshall SH, Martelli GP, Martin RR, Marzano SYL, Massart S, McCauley JW, Mielke-Ehret N, Minafra A, Minutolo M, Mirazimi A, Mühlbach HP, Mühlberger E, Naidu R, Natsuaki T, Navarro B, Navarro JA, Netesov SV, Neumann G, Nowotny N, Nunes MRT, Nylund A, Økland AL, Oliveira RC, Palacios G, Pallas V, Pályi B, Papa A, Parrish CR, Pauvolid-Corrêa A, Pawęska JT, Payne S, Pérez DR, Pfaff F, Radoshitzky SR, Rahman AU, Ramos-González PL, Resende RO, Reyes CA, Rima BK, Romanowski V, Robles Luna G, Rota P, Rubbenstroth D, Runstadler JA, Ruzek D, Sabanadzovic S, Salát J, Sall AA, Salvato MS, Sarpkaya K, Sasaya T, Schwemmle M, Shabbir MZ, Shí X, Shí Z, Shirako Y, Simmonds P, Širmarová J, Sironi M, Smither S, Smura T, Song JW, Spann KM, Spengler JR, Stenglein MD, Stone DM, Straková P, Takada A, Tesh RB, Thornburg NJ, Tomonaga K, Tordo N, Towner JS, Turina M, Tzanetakis I, Ulrich RG, Vaira AM, van den Hoogen B, Varsani A, Vasilakis N, Verbeek M, Wahl V, Walker PJ, Wang H, Wang J, Wang X, Wang LF, Wèi T, Wells H, Whitfield AE, Williams JV, Wolf YI, Wú Z, Yang X, Yáng X, Yu X, Yutin N, Zerbini FM, Zhang T, Zhang YZ, Zhou G, Zhou X. 2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales. Arch Virol 2020; 165:3023-3072. [PMID: 32888050 PMCID: PMC7606449 DOI: 10.1007/s00705-020-04731-2] [Citation(s) in RCA: 134] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 07/04/2020] [Indexed: 12/13/2022]
Abstract
In March 2020, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. At the genus rank, 20 new genera were added, two were deleted, one was moved, and three were renamed. At the species rank, 160 species were added, four were deleted, ten were moved and renamed, and 30 species were renamed. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.
Collapse
Affiliation(s)
- Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA.
| | - Scott Adkins
- United States Department of Agriculture, Agricultural Research Service, US Horticultural Research Laboratory, Fort Pierce, FL, USA
| | - Daniela Alioto
- Dipartimento di Agraria, Università degli Studi di Napoli Federico II, Portici, Italy
| | - Sergey V Alkhovsky
- D.I. Ivanovsky Institute of Virology of N.F. Gamaleya National Center on Epidemiology and Microbiology of Ministry of Health of Russian Federation, Moscow, Russia
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Simon J Anthony
- Mailman School of Public Health, Columbia University, New York, NY, USA
- EcoHealth Alliance, New York, NY, USA
| | | | - María A Ayllón
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Justin Bahl
- Department of Infectious Diseases, Department of Epidemiology and Biostatistics, Institute of Bioinformatics, Center for Ecology of Infectious Diseases, University of Georgia, Athens, GA, USA
| | - Anne Balkema-Buschmann
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, Greifswald-Insel Riems, Germany
| | - Matthew J Ballinger
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Tomáš Bartonička
- Department of Botany and Zoology, Masaryk University, Brno, Czech Republic
| | - Christopher Basler
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Sina Bavari
- Edge BioInnovation Consulting and Mgt, Frederick, MD, USA
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Dennis A Bente
- Galveston National Laboratory, The University of Texas, Medical Branch at Galveston, Galveston, TX, USA
| | - Éric Bergeron
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Brian H Bird
- School of Veterinary Medicine, One Health Institute, University of California, Davis, CA, USA
| | - Carol Blair
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Kim R Blasdell
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Steven B Bradfute
- University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Rachel Breyta
- US Geological Survey, Western Fisheries Research Center, Seattle, WA, USA
| | - Thomas Briese
- Department of Epidemiology, Mailman School of Public Health, Center for Infection and Immunity, Columbia University, New York, NY, USA
| | - Paul A Brown
- Laboratory of Ploufragan-Plouzané-Niort, French Agency for Food, Environmental and Occupational Heath Safety ANSES, Ploufragan, France
| | - Ursula J Buchholz
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michael J Buchmeier
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
| | - Alexander Bukreyev
- Galveston National Laboratory, The University of Texas, Medical Branch at Galveston, Galveston, TX, USA
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Felicity Burt
- Division of Virology, National Health Laboratory Service, University of the Free State, Bloemfontein, Republic of South Africa
| | - Nihal Buzkan
- Department of Plant Protection, Faculty of Agriculture, Kahramanmaras Sütçü Imam University, Avsar Campus, 46060, Kahramanmaras, Turkey
| | | | - Mengji Cao
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Inmaculada Casas
- Respiratory Virus and Influenza Unit, National Microbiology Center, Instituto de Salud Carlos III, Madrid, Spain
| | - John Chamberlain
- Virology and Pathogenesis Group, National Infection Service, Public Health England, Porton Down, UK
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Rémi N Charrel
- Unité des Virus Emergents (Aix-Marseille Univ-IRD 190-Inserm 1207-IHU Méditerranée Infection), Marseille, France
| | - Biao Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangdong, China
| | - Michela Chiumenti
- Istituto per la Protezione Sostenibile delle Piante-Consiglio Nazionale delle ricerche (Institute for Sustainable Plant Protection-National Research Council), Bari, Italy
| | - Il-Ryong Choi
- Plant Breeding Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
| | | | - Ian Crozier
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - John V da Graça
- Texas A&M University-Kingsville Citrus Center, Weslaco, TX, USA
| | - Elena Dal Bó
- CIDEFI. Facultad de Ciencias Agrarias y Forestales, Universidad de La Plata, La Plata, Argentina
| | - Alberto M R Dávila
- Laboratório de Biologia Computacional e Sistemas, Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | - Juan Carlos de la Torre
- Department of Immunology and Microbiology IMM-6, The Scripps Research Institute, La Jolla, CA, USA
| | - Xavier de Lamballerie
- Unité des Virus Emergents (Aix-Marseille Univ-IRD 190-Inserm 1207-IHU Méditerranée Infection), Marseille, France
| | - Rik L de Swart
- Department Viroscience, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Patrick L Di Bello
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Nicholas Di Paola
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante-Consiglio Nazionale delle ricerche (Institute for Sustainable Plant Protection-National Research Council), Bari, Italy
| | - Ralf G Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Michele Digiaro
- CIHEAM, Istituto Agronomico Mediterraneo di Bari, Valenzano, Italy
| | - Valerian V Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Olga Dolnik
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Michael A Drebot
- Zoonotic Diseases and Special Pathogens, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Jan Felix Drexler
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
| | | | | | - William G Dundon
- Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Vienna, Austria
| | - W Paul Duprex
- School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - John M Dye
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Andrew J Easton
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Hideki Ebihara
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Koray Ergünay
- Virology Unit, Department of Medical Microbiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Jorlan Fernandes
- Laboratório de Hantaviroses e Rickettsioses, Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | | | | | - Leonie F Forth
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Ron A M Fouchier
- Department Viroscience, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | | | - Selma Gago-Zachert
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle/Saale, Germany
| | - George Fú Gāo
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - María Laura García
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, CONICET UNLP, La Plata, Argentina
| | | | - Aura R Garrison
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Aiah Gbakima
- Metabiota, Inc. Sierra Leone, Freetown, Sierra Leone
| | - Tracey Goldstein
- One Health Institute, Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Jean-Paul J Gonzalez
- Department of Microbiology and Immunology, Division of Biomedical Graduate Research Organization, School of Medicine, Georgetown University, Washington, DC, 20057, USA
- Centaurus Biotechnologies, CTP, Manassas, VA, USA
| | - Anthony Griffiths
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA, USA
| | - Martin H Groschup
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, Greifswald-Insel Riems, Germany
| | - Stephan Günther
- Department of Virology, Bernhard-Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arboviruses and Hemorrhagic Fever Reference and Research, Hamburg, Germany
| | - Alexandro Guterres
- Laboratório de Hantaviroses e Rickettsioses, Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | - Roy A Hall
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - John Hammond
- United States Department of Agriculture, Agricultural Research Service, USNA, Floral and Nursery Plants Research Unit, Beltsville, MD, USA
| | - Mohamed Hassan
- Department of Agricultural Botany, Faculty of Agriculture, Fayoum University, Fayoum, Egypt
| | - Jussi Hepojoki
- Department of Virology, University of Helsinki, Medicum, Helsinki, Finland
- Vetsuisse Faculty, Institute of Veterinary Pathology, University of Zurich, Zurich, Switzerland
| | - Satu Hepojoki
- Department of Virology, University of Helsinki, Medicum, Helsinki, Finland
- Mobidiag Ltd, Espoo, Finland
| | - Udo Hetzel
- Institute of Veterinary Pathology, University of Zuerich, Zurich, Switzerland
| | - Roger Hewson
- Public Health England, Porton Down, Salisbury, Wiltshire, UK
| | - Bernd Hoffmann
- Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Seiji Hongo
- Department of Infectious Diseases, Faculty of Medicine, Yamagata University, Yamagata, Japan
| | - Dirk Höper
- Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Masayuki Horie
- Hakubi Center for Advanced Research, Kyoto University, Kyoto, Japan
| | - Holly R Hughes
- Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | - Timothy H Hyndman
- School of Veterinary Medicine, Murdoch University, Murdoch, WA, Australia
| | - Amara Jambai
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Rodrigo Jardim
- Laboratório de Biologia Computacional e Sistemas, Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | - Dàohóng Jiāng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Qi Jin
- Ministry of Health Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Gilda B Jonson
- Department of Agricultural Biotechnology, Center for Fungal Pathogenesis, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
- German Center for Infection Research (DZIF), Berlin, Germany
| | - Serpil Karadağ
- Republic Of Turkey Ministry Of Agriculture And Forestry, Pistachio Research Institute, Gaziantep, Turkey
| | - Karen E Keller
- United States Department of Agriculture, Agricultural Research Service, Horticulture Crops Research Unit, Corvallis, OR, USA
| | - Boris Klempa
- Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Jonas Klingström
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Gary Kobinger
- Department of Microbiology, Immunology and Infectious Diseases, Université Laval, Quebec City, Canada
| | - Hideki Kondō
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Paris, France
| | - Gael Kurath
- US Geological Survey Western Fisheries Research Center, Seattle, WA, USA
| | - Ivan V Kuzmin
- US Department of Agriculture, Animal and Plant Health Inspection, National Veterinary Services Laboratories, Diagnostic Virology Laboratory, Ames, USA
| | - Lies Laenen
- Zoonotic Infectious Diseases Unit, KU Leuven, Rega Institute, Leuven, Belgium
- Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Robert A Lamb
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
- Howard Hughes Medical Institute, Northwestern University, Evanston, IL, USA
| | - Amy J Lambert
- Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | | | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elba R S Lemos
- Laboratório de Hantaviroses e Rickettsioses, Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | - Eric M Leroy
- MIVEGEC (IRD-CNRS-Montpellier university) Unit, French National Research Institute for Sustainable Development (IRD), Montpellier, France
| | - Dexin Li
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jiànróng Lǐ
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Mifang Liang
- Key Laboratory for Medical Virology, NHFPC, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Wénwén Liú
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yàn Liú
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Igor S Lukashevich
- Department of Pharmacology and Toxicology, School of Medicine, The Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, University of Louisville, Louisville, KY, USA
| | - Piet Maes
- Department of Agricultural Biotechnology, Center for Fungal Pathogenesis, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | | | - Marco Marklewitz
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
- German Center for Infection Research (DZIF), Berlin, Germany
| | - Sergio H Marshall
- Pontificia Universidad Católica de Valparaíso, Campus Curauma, Valparaíso, Chile
| | - Giovanni P Martelli
- Department of Plant, Soil and Food Sciences, University "Aldo Moro", Bari, Italy
| | - Robert R Martin
- United States Department of Agriculture, Horticultural Crops Research Unit, Corvallis, OR, USA
| | - Shin-Yi L Marzano
- Department of Biology and Microbiology, Department of Plant Sciences, South Dakota State University, Brookings, SD, USA
| | - Sébastien Massart
- Gembloux Agro-Bio Tech, TERRA, Plant Pathology Laboratory, Liège University, Liège, Belgium
| | - John W McCauley
- Worldwide Influenza Centre, Francis Crick Institute, London, UK
| | | | - Angelantonio Minafra
- Istituto per la Protezione Sostenibile delle Piante-Consiglio Nazionale delle ricerche (Institute for Sustainable Plant Protection-National Research Council), Bari, Italy
| | - Maria Minutolo
- Dipartimento di Agraria, Università degli Studi di Napoli Federico II, Portici, Italy
| | | | | | - Elke Mühlberger
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA, USA
| | - Rayapati Naidu
- Department of Plant Pathology, Irrigated Agricultural Research and Extension Center, Washington State University, Prosser, WA, USA
| | - Tomohide Natsuaki
- School of Agriculture, Utsunomiya University, Utsunomiya, Tochigi, Japan
| | - Beatriz Navarro
- Istituto per la Protezione Sostenibile delle Piante-Consiglio Nazionale delle ricerche (Institute for Sustainable Plant Protection-National Research Council), Bari, Italy
| | - José A Navarro
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Sergey V Netesov
- Novosibirsk State University, Novosibirsk, Novosibirsk Oblast, Russia
| | - Gabriele Neumann
- Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, Madison, USA
| | - Norbert Nowotny
- Institute of Virology, University of Veterinary Medicine Vienna, Vienna, Austria
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | | | - Are Nylund
- Fish Disease Research Group, Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Arnfinn L Økland
- Fish Disease Research Group, Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Renata C Oliveira
- Laboratório de Hantaviroses e Rickettsioses, Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | - Gustavo Palacios
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Vicente Pallas
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Cientificas-Universidad Politécnica de Valencia, Valencia, Spain
| | - Bernadett Pályi
- National Biosafety Laboratory, National Public Health Center, Budapest, Hungary
| | - Anna Papa
- National Reference Centre for Arboviruses and Haemorrhagic Fever Viruses, Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Thessaloníki, Greece
| | - Colin R Parrish
- College of Veterinary Medicine, Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
| | - Alex Pauvolid-Corrêa
- Department of Veterinary Integrated Biosciences and Department of Entomology, Texas A&M University, College Station, USA
| | - Janusz T Pawęska
- Center for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham-Johannesburg, Gauteng, South Africa
| | - Susan Payne
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Daniel R Pérez
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Florian Pfaff
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Sheli R Radoshitzky
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Aziz-Ul Rahman
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | | | - Renato O Resende
- Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
| | - Carina A Reyes
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET-UNLP, La Plata, Buenos Aires, Argentina
| | - Bertus K Rima
- Centre for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, The Queen's University of Belfast, Belfast, Northern Ireland, UK
| | - Víctor Romanowski
- Instituto de Biotecnología y Biología Molecular, Centro Cientifico Technológico-La Plata, Consejo Nacional de Investigaciones Científico Tecnológico-Universidad Nacional de La Plata, La Plata, Argentina
| | - Gabriel Robles Luna
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET-UNLP, La Plata, Buenos Aires, Argentina
| | - Paul Rota
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Dennis Rubbenstroth
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Jonathan A Runstadler
- Department of Infectious Disease and Global Health, Tufts University Cummings School of Veterinary Medicine, 200 Westboro Road, North Grafton, MA, 01536, USA
| | - Daniel Ruzek
- Veterinary Research Institute, Brno, Czech Republic
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, 37005, Ceske Budejovice, Czech Republic
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, USA
| | - Jiří Salát
- Veterinary Research Institute, Brno, Czech Republic
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, 37005, Ceske Budejovice, Czech Republic
| | | | - Maria S Salvato
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Kamil Sarpkaya
- Department of Forestry Engineering, Faculty of Forestry, Karabuk University (UNIKA), Karabük, Turkey
| | - Takahide Sasaya
- Western Region Agricultural Research Center, National Agriculture and Food Research Organization, Fukuyama, Japan
| | - Martin Schwemmle
- Faculty of Medicine, University Medical Center-University Freiburg, Freiburg, Germany
| | - Muhammad Z Shabbir
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Xiǎohóng Shí
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, UK
| | - Zhènglì Shí
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, People's Republic of China
| | - Yukio Shirako
- Asian Center for Bioresources and Environmental Sciences, University of Tokyo, Tokyo, Japan
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Manuela Sironi
- Bioinformatics Unit, Scientific Institute IRCCS "E. Medea", Bosisio Parini, Italy
| | - Sophie Smither
- CBR Division, Dstl, Porton Down, Salisbury, Wiltshire, UK
| | - Teemu Smura
- Department of Virology, University of Helsinki, Medicum, Helsinki, Finland
| | - Jin-Won Song
- Department of Microbiology, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Kirsten M Spann
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Jessica R Spengler
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mark D Stenglein
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - David M Stone
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, Dorset, UK
| | | | - Ayato Takada
- Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Robert B Tesh
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX, USA
| | | | - Keizō Tomonaga
- Institute for Frontier Life and Medical Sciences (inFront), Kyoto University, Kyoto, Japan
| | - Noël Tordo
- Institut Pasteur, Unité des Stratégies Antivirales, WHO Collaborative Centre for Viral Haemorrhagic Fevers and Arboviruses, OIE Reference Laboratory for RVFV and CCHFV, Paris, France
- Institut Pasteur de Guinée, Conakry, Guinea
| | - Jonathan S Towner
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Massimo Turina
- Institute for Sustainable Plant Protection, National Research Council of Italy (CNR), Strada delle Cacce 73, 10135, Turin, Italy
| | - Ioannis Tzanetakis
- Division of Agriculture, Department of Entomology and Plant Pathology, University of Arkansas System, Fayetteville, AR, 72701, USA
| | - Rainer G Ulrich
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, Südufer 10, 17493, Greifswald-Insel Riems, Germany
- German Center of Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Insel Riems, Greifswald-Insel Riems, Germany
| | - Anna Maria Vaira
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), 73 Strada delle Cacce, 10135, Turin, Italy
| | - Bernadette van den Hoogen
- Department of Viroscience, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Nikos Vasilakis
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Martin Verbeek
- Wageningen University and Research, Biointeractions and Plant Health, Wageningen, The Netherlands
| | - Victoria Wahl
- National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD, USA
| | - Peter J Walker
- School of Biological Sciences, University of Queensland, St. Lucia, Queensland, Australia
| | - Hui Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianwei Wang
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, IPB-Fondation Mérieux, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xifeng Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Tàiyún Wèi
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Heather Wells
- Mailman School of Public Health, Center for Infection and Immunity, Columbia University, New York, USA
| | - Anna E Whitfield
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - John V Williams
- School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Zhìqiáng Wú
- MOH Key Laboratory of Systems Biology of Pathogens, IPB, CAMS, Beijing, China
| | - Xin Yang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangdong, China
| | - Xīnglóu Yáng
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, People's Republic of China
| | - Xuejie Yu
- Wuhan University School of Health Sciences, Wuhan, China
| | - Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - F Murilo Zerbini
- Departamento de Fitopatologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Tong Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangdong, China
| | - Yong-Zhen Zhang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
- Shanghai Public Health Clinical Center, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Guohui Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangdong, China
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
42
|
Zakham F, Jääskeläinen AJ, Castrén J, Sormunen JJ, Uusitalo R, Smura T, Von Troil G, Kuivanen S, Sironen T, Vapalahti O. Molecular detection and phylogenetic analysis of Borrelia miyamotoi strains from ticks collected in the capital region of Finland. Ticks Tick Borne Dis 2020; 12:101608. [PMID: 33249364 DOI: 10.1016/j.ttbdis.2020.101608] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/31/2020] [Accepted: 11/03/2020] [Indexed: 11/16/2022]
Abstract
Borrelia miyamotoi is an emerging pathogen that shares high similarity with relapsing fever Borrelia, but has an atypical clinical presentation. Within the framework of tick-borne disease surveillance in Finland, human serum samples suspected for tick-borne encephalitis (n=974) and questing ticks (n=739) were collected from the capital region in Finland to determine the prevalence of B. miyamotoi. All tested human samples were negative and 5 (0.68 %) Ixodes ricinus ticks were positive for B. miyamotoi. Partial sequencing of the flagellin (flaB) gene of 3 positive samples and 27 B. miyamotoi-positive tick samples obtained from previous studies across Finland were amplified, sequenced, and included in the phylogenetic analysis. The phylogenetic tree revealed that most B. miyamotoi strains isolated from ticks in Finland share high similarity with other European strains, including strains related to human infection. Possible disease transmission may occur during exposure to tick bites. A single strain collected from an I. persulcatus tick in Pajujärvi grouped with an outlier of B. miyamotoi strains isolated from Russia and Far East Asian countries. Further studies should investigate the pathogen's role in human infection in Finland. Another important finding is the occurrence of I. persulcatus ticks (8%) collected by crowdsourcing from the coastal southern part of Finland. This suggests a regular introduction and a possible wide expansion of this tick species in the country. This could be associated with transmission of new pathogens.
Collapse
Affiliation(s)
- Fathiah Zakham
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland.
| | - Anne J Jääskeläinen
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Finland
| | | | | | - Ruut Uusitalo
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Department of Geosciences and Geography, Faculty of Science, University of Helsinki, Helsinki, Finland
| | - Teemu Smura
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Gabriel Von Troil
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Archipelago Doctors Ltd, Helsinki Area, Finland
| | - Suvi Kuivanen
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Tarja Sironen
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Olli Vapalahti
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland; HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Finland
| |
Collapse
|
43
|
Cantuti-Castelvetri L, Ojha R, Pedro LD, Djannatian M, Franz J, Kuivanen S, van der Meer F, Kallio K, Kaya T, Anastasina M, Smura T, Levanov L, Szirovicza L, Tobi A, Kallio-Kokko H, Österlund P, Joensuu M, Meunier FA, Butcher SJ, Winkler MS, Mollenhauer B, Helenius A, Gokce O, Teesalu T, Hepojoki J, Vapalahti O, Stadelmann C, Balistreri G, Simons M. Neuropilin-1 facilitates SARS-CoV-2 cell entry and infectivity. Science 2020; 370:856-860. [PMID: 33082293 PMCID: PMC7857391 DOI: 10.1126/science.abd2985] [Citation(s) in RCA: 1227] [Impact Index Per Article: 306.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 10/12/2020] [Indexed: 12/11/2022]
Abstract
Virus-host interactions determine cellular entry and spreading in tissues. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the earlier SARS-CoV use angiotensin-converting enzyme 2 (ACE2) as a receptor; however, their tissue tropism differs, raising the possibility that additional host factors are involved. The spike protein of SARS-CoV-2 contains a cleavage site for the protease furin that is absent from SARS-CoV (see the Perspective by Kielian). Cantuti-Castelvetri et al. now show that neuropilin-1 (NRP1), which is known to bind furin-cleaved substrates, potentiates SARS-CoV-2 infectivity. NRP1 is abundantly expressed in the respiratory and olfactory epithelium, with highest expression in endothelial and epithelial cells. Daly et al. found that the furin-cleaved S1 fragment of the spike protein binds directly to cell surface NRP1 and blocking this interaction with a small-molecule inhibitor or monoclonal antibodies reduced viral infection in cell culture. Understanding the role of NRP1 in SARS-CoV-2 infection may suggest potential targets for future antiviral therapeutics. Science, this issue p. 856, p. 861; see also p. 765 The causative agent of coronavirus disease 2019 (COVID-19) is the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). For many viruses, tissue tropism is determined by the availability of virus receptors and entry cofactors on the surface of host cells. In this study, we found that neuropilin-1 (NRP1), known to bind furin-cleaved substrates, significantly potentiates SARS-CoV-2 infectivity, an effect blocked by a monoclonal blocking antibody against NRP1. A SARS-CoV-2 mutant with an altered furin cleavage site did not depend on NRP1 for infectivity. Pathological analysis of olfactory epithelium obtained from human COVID-19 autopsies revealed that SARS-CoV-2 infected NRP1-positive cells facing the nasal cavity. Our data provide insight into SARS-CoV-2 cell infectivity and define a potential target for antiviral intervention.
Collapse
Affiliation(s)
- Ludovico Cantuti-Castelvetri
- Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany.,German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Ravi Ojha
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Biosciences Research Program, University of Helsinki, Helsinki, Finland
| | - Liliana D Pedro
- Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany.,German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Minou Djannatian
- Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany.,German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Jonas Franz
- Department of Neuropathology, University Medical Center Göttingen, Göttingen, Germany.,Campus Institute for Dynamics of Biological Networks, University of Göttingen, Göttingen, Germany.,Max Planck Institute for Experimental Medicine, Göttingen, Germany
| | - Suvi Kuivanen
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland
| | | | - Katri Kallio
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Biosciences Research Program, University of Helsinki, Helsinki, Finland
| | - Tuğberk Kaya
- Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany.,German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.,Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
| | - Maria Anastasina
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Biosciences Research Program, University of Helsinki, Helsinki, Finland.,Helsinki Institute of Life Sciences-Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Teemu Smura
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland
| | - Lev Levanov
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland
| | - Leonora Szirovicza
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland
| | - Allan Tobi
- Laboratory of Cancer Biology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Hannimari Kallio-Kokko
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Pamela Österlund
- Department of Health Security, Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Merja Joensuu
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Frédéric A Meunier
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Sarah J Butcher
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Biosciences Research Program, University of Helsinki, Helsinki, Finland.,Helsinki Institute of Life Sciences-Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Martin Sebastian Winkler
- Department of Anesthesiology and Intensive Care Medicine, University Medical Center Göttingen, Göttingen, Germany
| | - Brit Mollenhauer
- Department of Neurology, University Medical Center Göttingen, Göttingen, Germany.,Paracelsus-Elena-Klinik Kassel, Kassel, Germany
| | - Ari Helenius
- Institute of Biochemistry, ETH Zürich, Zürich, Switzerland
| | - Ozgun Gokce
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
| | - Tambet Teesalu
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Biosciences Research Program, University of Helsinki, Helsinki, Finland.,Cancer Research Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.,Center for Nanomedicine and Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Jussi Hepojoki
- Campus Institute for Dynamics of Biological Networks, University of Göttingen, Göttingen, Germany.,Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zürich, Zürich, Switzerland
| | - Olli Vapalahti
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland.,Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Christine Stadelmann
- Department of Neuropathology, University Medical Center Göttingen, Göttingen, Germany
| | - Giuseppe Balistreri
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Biosciences Research Program, University of Helsinki, Helsinki, Finland. .,The Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Mikael Simons
- Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany. .,German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.,Munich Cluster of Systems Neurology (SyNergy), Munich, Germany
| |
Collapse
|
44
|
Paulsen KM, Lamsal A, Bastakoti S, Pettersson JHO, Pedersen BN, Stiasny K, Haglund M, Smura T, Vapalahti O, Vikse R, Alfsnes K, Andreassen ÅK. High-throughput sequencing of two European strains of tick-borne encephalitis virus (TBEV), Hochosterwitz and 1993/783. Ticks Tick Borne Dis 2020; 12:101557. [PMID: 33080519 DOI: 10.1016/j.ttbdis.2020.101557] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 08/28/2020] [Accepted: 09/01/2020] [Indexed: 12/22/2022]
Abstract
Tick-borne encephalitis virus (TBEV) is a medically important arbovirus, widespread in Europe and Asia. The virus is primarily transmitted to humans and animals by bites from ticks and, in rare cases, by consumption of unpasteurized dairy products. The aim of this study was to sequence and characterize two TBEV strains with amplicon sequencing by designing overlapping primers. The amplicon sequencing, via Illumina MiSeq, covering nearly the entire TBEV genome, was successful: We retrieved and characterized the complete polyprotein sequence of two TBEV strains, Hochosterwitz and 1993/783 from Austria and Sweden, respectively. In this study the previous phylogenetic analysis of both strains was confirmed to be of the European subtypes of TBEV (TBEV-Eu) by whole genome sequencing. The Hochosterwitz strain clustered with the two strains KrM 93 and KrM 213 from South Korea, and the 1993/783 strain clustered together with the NL/UH strain from the Netherlands. Our study confirms the suitability and rapidness of the high-throughput sequencing method used to produce complete TBEV genomes from TBEV samples of high viral load giving high-molecular-weight cDNA with large overlapping amplicons.
Collapse
Affiliation(s)
- Katrine M Paulsen
- Norwegian Institute of Public Health, Division for Infection Control and Environmental Health, Department of Virology, PO-Box 222 Skøyen, NO-0213, Oslo, Norway
| | - Alaka Lamsal
- Norwegian Institute of Public Health, Division for Infection Control and Environmental Health, Department of Virology, PO-Box 222 Skøyen, NO-0213, Oslo, Norway; University of South-Eastern Norway, Department of Natural Science and Environmental Health, Gullbringvegen 36, NO-3800, Bø, Norway
| | - Srijana Bastakoti
- Norwegian Institute of Public Health, Division for Infection Control and Environmental Health, Department of Virology, PO-Box 222 Skøyen, NO-0213, Oslo, Norway
| | - John H-O Pettersson
- Uppsala University, Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala, Sweden; The University of Sydney, Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, Sydney, Australia
| | - Benedikte N Pedersen
- University of South-Eastern Norway, Department of Natural Science and Environmental Health, Gullbringvegen 36, NO-3800, Bø, Norway
| | - Karin Stiasny
- Medical University of Vienna, Center for Virology, Kinderspitalgasse 15, 1090, Vienna, Austria
| | - Mats Haglund
- Kalmar County Hospital, Department of Infectious Diseases, SE-391 85, Kalmar, Sweden
| | - Teemu Smura
- University of Helsinki, Department of Virology, Medicum, Helsinki, Finland
| | - Olli Vapalahti
- University of Helsinki, Department of Virology, Medicum, Helsinki, Finland; University of Helsinki, Department of Veterinary Biosciences, Helsinki, Finland; University of Helsinki and Helsinki University Hospital, Department of Virology and Immunology, Helsinki, Finland
| | - Rose Vikse
- Norwegian Institute of Public Health, Division for Infection Control and Environmental Health, Department of Virology, PO-Box 222 Skøyen, NO-0213, Oslo, Norway
| | - Kristian Alfsnes
- Norwegian Institute of Public Health, Division for Infection Control and Environmental Health, Department of Bacteriology, PO-Box 222 Skøyen, NO-0213, Oslo, Norway
| | - Åshild K Andreassen
- Norwegian Institute of Public Health, Division for Infection Control and Environmental Health, Department of Virology, PO-Box 222 Skøyen, NO-0213, Oslo, Norway; University of South-Eastern Norway, Department of Natural Science and Environmental Health, Gullbringvegen 36, NO-3800, Bø, Norway.
| |
Collapse
|
45
|
Suvanto MT, Truong Nguyen P, Uusitalo R, Korhonen EM, Faolotto G, Vapalahti O, Huhtamo E, Smura T. A novel negevirus isolated from Aedes vexans mosquitoes in Finland. Arch Virol 2020; 165:2989-2992. [PMID: 32951134 PMCID: PMC7588393 DOI: 10.1007/s00705-020-04810-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 08/13/2020] [Indexed: 12/31/2022]
Abstract
Negeviruses are insect-specific enveloped RNA viruses that have been detected in mosquitoes and sandflies from various geographical locations. Here, we describe a new negevirus from Northern Europe, isolated from pool of Aedes vexans mosquitoes collected in Finland, designated as Mekrijärvi negevirus (MEJNV). MEJNV had a typical negevirus genome organization, is 9,740 nucleotides in length, and has a GC content of 47.53%. The MEJNV genome contains three ORFs, each containing the following identified conserved domains: ORF1 (7,068 nt) encodes a viral methyltransferase, an FtsJ-like methyltransferase, a viral RNA helicase, and an RNA-dependent RNA polymerase, ORF2 (1,242 nt) encodes a putative virion glycoprotein, and ORF3 (660 nt) encodes a putative virion membrane protein. A distinctive feature relative to other currently known negeviruses is a 7-nucleotide-long overlap between ORF1 and ORF2. MEJNV shares the highest sequence identity with Ying Kou virus from China, with 67.71% nucleotide and 75.19% and 59.00% amino acid sequence identity in ORF 1 and ORF 2, respectively. ORF3 had the highest amino acid sequence similarity to Daeseongdong virus 1 and negevirus Nona 1, both with 77.61% identity, and to Ying Kou virus, with 71.22% identity. MEJNV is currently the northernmost negevirus described. Our report supports the view that negeviruses are a globally distributed, diverse group of viruses that can be found from mosquitoes in a wide range of terrestrial biomes from tropical to boreal forests.
Collapse
Affiliation(s)
- Maija T Suvanto
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland. .,Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland.
| | | | - Ruut Uusitalo
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland.,Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland.,Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland
| | - Essi M Korhonen
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland.,Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Giulia Faolotto
- Laboratory of Microbiology and Virology, University Hospital Maggiore Della Carità Di Novara, Piemonte, Novara, Italy
| | - Olli Vapalahti
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland.,Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland.,Department of Virology and Immunology, Helsinki University Hospital, HUSLAB, Helsinki, Finland
| | - Eili Huhtamo
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland.,Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Teemu Smura
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland.,Department of Virology and Immunology, Helsinki University Hospital, HUSLAB, Helsinki, Finland
| |
Collapse
|
46
|
Korhonen EM, Suvanto MT, Uusitalo R, Faolotto G, Smura T, Sane J, Vapalahti O, Huhtamo E. Sindbis Virus Strains of Divergent Origin Isolated from Humans and Mosquitoes During a Recent Outbreak in Finland. Vector Borne Zoonotic Dis 2020; 20:843-849. [PMID: 32898458 PMCID: PMC7699012 DOI: 10.1089/vbz.2019.2562] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Sindbis virus (SINV) is a mosquito-borne avian hosted virus that is widely distributed in Europe, Africa, Asia, and Oceania. Disease in humans is documented mainly from Northern Europe and South Africa and associated with genotype I. In 2018 under extremely warm climatic conditions, a small outbreak of 71 diagnosed SINV infections was recorded in Finland. We screened 52 mosquito pools (570 mosquitoes) and 223 human sera for SINV with real-time RT-PCR and the positive samples with virus isolation. One SINV strain was isolated from a pool (n = 13) of genus Ochlerotatus mosquitoes and three strains from patient serum samples. Complete genome analysis suggested all the isolates to be divergent from one another and related to previous Finnish, Swedish, and German strains. The study provides evidence of SINV strain transfer within Europe across regions with different epidemiological characteristics. Whether these are influenced by different mosquito genera involved in the transmission remains to be studied.
Collapse
Affiliation(s)
- Essi M Korhonen
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland.,Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Maija T Suvanto
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland.,Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Ruut Uusitalo
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland.,Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland.,Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland
| | - Giulia Faolotto
- Laboratory of Molecular Virology, University Hospital Maggiore Della Carita Novara, Piemonte, Novara, Italy
| | - Teemu Smura
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Jussi Sane
- Department of Health Security, Infectious Disease Control and Vaccinations Unit, National Institute for Health and Welfare, Helsinki, Finland
| | - Olli Vapalahti
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland.,Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland.,Department of Virology and Immunology, University of Helsinki and Helsinki University Hospital, HUSLAB, Helsinki, Finland
| | - Eili Huhtamo
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland.,Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| |
Collapse
|
47
|
Abstract
The mosquito-borne chikungunya virus (CHIKV) causes an acute febrile illness with rash, joint and muscle pain.A realtime RT-PCR assay for CHIKV detecting non-structural protein (nsP2; CHIKV nsP2-RT-qPCR) was set up. All the serodiagnosed CHIKV cases detected during 2009-2019 in Finland were screened with the assay, followed by isolations attempts and sequencing using Sanger and next generation sequencing (NGS). To validate the assay external and in-house quality control samples were used and all were correctly identified. Specificity of the assay was 100%. Assay was sensitive to detect CHIKV RNA in dilution of 10-8.During years 2009-2019 34 patients were diagnosed for acute CHIKV infection. Twelve out of 34 cases were positive by CHIKV nsP2-RT-qPCR.Two CHIKV isolations succeeded from two individuals infected originally in Thailand, 2019. From 12 CHIKV nsP2-RT-qPCR positive samples, five (42%) CHIKVs were successfully sequenced. In this study, CHIKVs from year 2019 clustered with CHIKV ECSA-lineage forming sub-cluster with strains from ones detected in Bangladesh 2017, and the ones from Jamaica (2014) within Asian lineage showing highest similarity to strains detected in Caribbean outbreak 2013-15. Majority of the CHIKV infections detected in Finland originates from Asia and virus lineages reflect the global circulation of the pathogen.
Collapse
Affiliation(s)
- A J Jääskeläinen
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Helsinki, Finland
| | - L Kareinen
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - T Smura
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - H Kallio-Kokko
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Helsinki, Finland
| | - O Vapalahti
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Helsinki, Finland.,Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| |
Collapse
|
48
|
Kuivanen S, Levanov L, Kareinen L, Sironen T, Jääskeläinen AJ, Plyusnin I, Zakham F, Emmerich P, Schmidt-Chanasit J, Hepojoki J, Smura T, Vapalahti O. Detection of novel tick-borne pathogen, Alongshan virus, in Ixodes ricinus ticks, south-eastern Finland, 2019. ACTA ACUST UNITED AC 2020; 24. [PMID: 31290392 PMCID: PMC6628756 DOI: 10.2807/1560-7917.es.2019.24.27.1900394] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The newly identified tick-borne Alongshan virus (ALSV), a segmented Jingmen virus group flavivirus, was recently associated with human disease in China. We report the detection of ALSV RNA in Ixodes ricinus ticks in south-eastern Finland. Screening of sera from patients suspected for tick-borne encephalitis for Jingmen tick virus-like virus RNA and antibodies revealed no human cases. The presence of ALSV in common European ticks warrants further investigations on its role as a human pathogen.
Collapse
Affiliation(s)
- Suvi Kuivanen
- Authors contributed equally.,Department of Virology, University of Helsinki, Helsinki, Finland
| | - Lev Levanov
- Authors contributed equally.,Department of Virology, University of Helsinki, Helsinki, Finland
| | - Lauri Kareinen
- Department of Virology, University of Helsinki, Helsinki, Finland
| | - Tarja Sironen
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland.,Department of Virology, University of Helsinki, Helsinki, Finland
| | - Anne J Jääskeläinen
- Division of Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Ilya Plyusnin
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Fathiah Zakham
- Department of Virology, University of Helsinki, Helsinki, Finland
| | - Petra Emmerich
- University of Rostock, Rostock, Germany.,Departments of Virology and Arbovirology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Jonas Schmidt-Chanasit
- German Centre for Infection Research (DZIF), Hamburg, Germany.,Departments of Virology and Arbovirology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Jussi Hepojoki
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland.,Department of Virology, University of Helsinki, Helsinki, Finland
| | - Teemu Smura
- Authors contributed equally.,Division of Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Department of Virology, University of Helsinki, Helsinki, Finland
| | - Olli Vapalahti
- Authors contributed equally.,Division of Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland.,Department of Virology, University of Helsinki, Helsinki, Finland
| |
Collapse
|
49
|
Smura T, Blomqvist S, Kolehmainen P, Schuffenecker I, Lina B, Böttcher S, Diedrich S, Löve A, Brytting M, Hauzenberger E, Dudman S, Ivanova O, Lukasev A, Fischer TK, Midgley S, Susi P, Savolainen-Kopra C, Lappalainen M, Jääskeläinen AJ. Aseptic meningitis outbreak associated with echovirus 4 in Northern Europe in 2013-2014. J Clin Virol 2020; 129:104535. [PMID: 32652478 DOI: 10.1016/j.jcv.2020.104535] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 06/29/2020] [Accepted: 07/05/2020] [Indexed: 01/23/2023]
Abstract
Picornaviruses (family Picornaviridae) are small, nonenveloped, positive-sense, single-stranded RNA viruses. The members of this family are currently classified into 47 genera and 110 species. Of picornaviruses, entero- and parechoviruses are associated with aseptic meningitis. They are transmitted via fecal-oral and respiratory routes, and occasionally, these viruses may cause a brief viremia and gain access to central nervous system (CNS). During the diagnostic screening of entero- and parechovirus types in Finland in year 2013-14, we detected a cluster of echovirus 4 (E4) infections in young adults and adolescents. As E4 is infrequently detected in Finland, we contacted several Northern and Central European laboratories that conduct routine surveillance for enteroviruses and, for those who have had E4 cases, we send a query for E4 sequences and data. Here we report CNS infections caused by E4 in Finland, Sweden, Norway, Denmark, Iceland and Germany in 2013 and 2014, and show that the E4 detected in these countries form a single lineage. In contrast, E4 strains circulating in these countries preceding the year 2013, and those circulating elsewhere in Europe during 2013-2014, formed several independent clusters.
Collapse
Affiliation(s)
- Teemu Smura
- University of Helsinki and Helsinki University Hospital, Virology and Immunology, Helsinki, Finland
| | - Soile Blomqvist
- National Institute for Health and Welfare (THL), Department of Health Security, Helsinki, Finland
| | | | - Isabelle Schuffenecker
- Institut des Agents infectieux des HCL, CNR des enterovirus, Hôpital de la Croix-Rousse & Université de Lyon, CIRI INSERM U1111, UCBL, Lyon, France
| | - Bruno Lina
- Institut des Agents infectieux des HCL, CNR des enterovirus, Hôpital de la Croix-Rousse & Université de Lyon, CIRI INSERM U1111, UCBL, Lyon, France
| | | | | | - Arthur Löve
- Landspitali, National University Hospital, Reykjavik, Iceland
| | - Mia Brytting
- Folkhälsomyndigheten, Public Health Agency of Sweden, Solna, Sweden
| | | | | | - Olga Ivanova
- Chumakov Federal Scientific Center for Research and Development, Moscow, Russia; Sechenov First Moscow State Medical University, Moscow, Russian Federation
| | - Alexander Lukasev
- Chumakov Federal Scientific Center for Research and Development, Moscow, Russia; Sechenov First Moscow State Medical University, Moscow, Russian Federation
| | | | | | - Petri Susi
- University of Turku, Institute of Biomedicine, Turku, Finland
| | - Carita Savolainen-Kopra
- National Institute for Health and Welfare (THL), Department of Health Security, Helsinki, Finland
| | - Maija Lappalainen
- University of Helsinki and Helsinki University Hospital, Virology and Immunology, Helsinki, Finland
| | - Anne J Jääskeläinen
- University of Helsinki and Helsinki University Hospital, Virology and Immunology, Helsinki, Finland.
| |
Collapse
|
50
|
Masika MM, Korhonen EM, Smura T, Uusitalo R, Vapalahti K, Mwaengo D, Jääskeläinen AJ, Anzala O, Vapalahti O, Huhtamo E. Detection of dengue virus type 2 of Indian origin in acute febrile patients in rural Kenya. PLoS Negl Trop Dis 2020; 14:e0008099. [PMID: 32126086 PMCID: PMC7069648 DOI: 10.1371/journal.pntd.0008099] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 03/13/2020] [Accepted: 01/29/2020] [Indexed: 01/25/2023] Open
Abstract
Dengue virus (DENV) has caused recent outbreaks in coastal cities of Kenya, but the epidemiological situation in other areas of Kenya is largely unknown. We investigated the role of DENV infection as a cause of acute febrile disease in non-epidemic settings in rural and urban study areas in Kenya. Altogether, 560 patients were sampled in 2016–2017 in rural Taita–Taveta County (n = 327) and urban slums of Kibera, Nairobi (n = 233). The samples were studied for DENV IgM, IgG, NS1 antigen and flaviviral RNA. IgG seroprevalence was found to be higher in Taita–Taveta (14%) than in Nairobi (3%). Five Taita–Taveta patients were positive for flaviviral RNA, all identified as DENV-2, cosmopolitan genotype. Local transmission in Taita–Taveta was suspected in a patient without travel history. The sequence analysis suggested that DENV-2 strains circulating in coastal and southern Kenya likely arose from a single introduction from India. The molecular clock analyses dated the most recent ancestor to the Kenyan strains a year before the large 2013 outbreak in Mombasa. After this, the virus has been detected in Kilifi in 2014, from our patients in Taita–Taveta in 2016, and in an outbreak in Malindi in 2017. The results highlight that silent transmission occurs between epidemics and also affects rural areas. More information is needed to understand the local epidemiological characteristics and future risks of dengue in Kenya. Dengue virus (DENV) is an emerging mosquito-borne global health threat in the tropics and subtropics. The majority of the world’s population live in areas at risk of dengue that can cause a wide variety of symptoms from febrile illness to haemorrhagic fever. Information of DENV in Africa is limited and fragmented. In Kenya, dengue is a recognized disease in coastal cities that have experienced recent outbreaks. We investigated the role of DENV infection as a cause of acute febrile disease in non-epidemic settings in rural and urban study areas in Kenya. We found DENV-2 in five febrile patients from rural Taita–Taveta, where no dengue has been reported before. Genetic analysis of the virus suggests it to be most likely of Indian origin. This Indian origin DENV-2 was detected in the Mombasa outbreak in 2013, in Kilifi in 2014, in Taita–Taveta in 2016 (our study samples) and again in the Malindi outbreak in 2017. The results suggest that dengue is unrecognized in rural Kenya and more studies are needed for local risk assessment. Our findings of virus transmission between epidemics contribute to better understanding of the epidemiological situation and origins of DENV in Kenya.
Collapse
Affiliation(s)
- Moses Muia Masika
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
- KAVI Institute of Clinical Research, University of Nairobi, Nairobi, Kenya
| | - Essi M. Korhonen
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- * E-mail:
| | - Teemu Smura
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland
| | - Ruut Uusitalo
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland
| | - Katariina Vapalahti
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Dufton Mwaengo
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
- Institute of Tropical and Infectious Diseases, University of Nairobi, Nairobi, Kenya
| | - Anne J. Jääskeläinen
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland
- Department of Virology and Immunology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Omu Anzala
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
- KAVI Institute of Clinical Research, University of Nairobi, Nairobi, Kenya
| | - Olli Vapalahti
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Department of Virology and Immunology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Eili Huhtamo
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| |
Collapse
|