1
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Gladkikh AS, Cao TM, Klyuchnikova EO, Dao MH, Sharova AA, Melnichenko VD, Popova MR, Arbuzova TV, Sbarzaglia VA, Tsyganova NA, Ramsay E, Dedkov VG. Near complete genome sequences from Southern Vietnam revealed local features of genetic diversity and intergenerational changes in SARS- CoV-2 variants in 2020-2021. BMC Infect Dis 2023; 23:806. [PMID: 37974125 PMCID: PMC10655423 DOI: 10.1186/s12879-023-08814-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND Since its beginnings in 2019, the COVID-19 pandemic is still a problem of global medical concern. Southern Vietnam is one of the country's vast regions, including 20 provinces and the densely populated metropolis Ho Chi Minh City. A randomized retrospective study was performed to investigate the epidemiology and genetic diversity of COVID-19. Whole-genome sequencing of 126 SARS-CoV-2 samples collected from Southern Vietnam between January 2020 and December 2021 revealed the main circulating variants and their distribution. METHODS Epidemiological data were obtained from the Department of Preventive Medicine of the Vietnamese Ministry of Health. To identify circulating variants, RNA, extracted from 126 nasopharyngeal swabs of patients with suspected COVID-19 were sequenced on Illunina MiSeq to obtain near complete genomes SARS-CoV-2. RESULTS Due to the effectiveness of restrictive measures in Vietnam, it was possible to keep incidence at a low level. The partial relaxation of restrictive measures, and the spread of Delta lineages, contributed to the beginning of a logarithmic increase in incidence. Lineages 20A-H circulated in Southern Vietnam during 2020. Spread of the Delta lineage in Southern Vietnam began in March 2021, causing a logarithmic rise in the number of COVID-19 cases. CONCLUSIONS Pandemic dynamics in Southern Vietnam feature specific variations in incidence, and these reflect the success of the restrictive measures put in place during the early stages of the pandemic.
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Affiliation(s)
- Anna S Gladkikh
- Saint Petersburg Pasteur Institute, 14 Mira Street, Saint Petersburg, 197101, Russia
| | - Thang M Cao
- Pasteur Institute in Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | | | - Manh H Dao
- Pasteur Institute in Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Alena A Sharova
- Saint Petersburg Pasteur Institute, 14 Mira Street, Saint Petersburg, 197101, Russia
| | | | - Margarita R Popova
- Saint Petersburg Pasteur Institute, 14 Mira Street, Saint Petersburg, 197101, Russia
| | - Tatiana V Arbuzova
- Saint Petersburg Pasteur Institute, 14 Mira Street, Saint Petersburg, 197101, Russia
| | - Valeriya A Sbarzaglia
- Saint Petersburg Pasteur Institute, 14 Mira Street, Saint Petersburg, 197101, Russia
| | - Nadezhda A Tsyganova
- Saint Petersburg Pasteur Institute, 14 Mira Street, Saint Petersburg, 197101, Russia
| | - Edward Ramsay
- Saint Petersburg Pasteur Institute, 14 Mira Street, Saint Petersburg, 197101, Russia
| | - Vladimir G Dedkov
- Saint Petersburg Pasteur Institute, 14 Mira Street, Saint Petersburg, 197101, Russia
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, Moscow, Russia
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2
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Simas MCDC, Costa SM, Gomes PDSFC, Cruz NVGD, Corrêa IA, de Souza MRM, Dornelas-Ribeiro M, Nogueira TLS, Santos CGMD, Hoffmann L, Tanuri A, Moura-Neto RSD, Damaso CR, Costa LJD, Silva R. Evaluation of SARS-CoV-2 ORF7a Deletions from COVID-19-Positive Individuals and Its Impact on Virus Spread in Cell Culture. Viruses 2023; 15:v15030801. [PMID: 36992509 PMCID: PMC10051148 DOI: 10.3390/v15030801] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/16/2023] [Accepted: 03/16/2023] [Indexed: 03/31/2023] Open
Abstract
The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing the COVID-19 outbreak, posed a primary concern of public health worldwide. The most common changes in SARS-CoV-2 are single nucleotide substitutions, also reported insertions and deletions. This work investigates the presence of SARS-CoV-2 ORF7a deletions identified in COVID-19-positive individuals. Sequencing of SARS-CoV-2 complete genomes showed three different ORF7a size deletions (190-nt, 339-nt and 365-nt). Deletions were confirmed through Sanger sequencing. The ORF7a∆190 was detected in a group of five relatives with mild symptoms of COVID-19, and the ORF7a∆339 and ORF7a∆365 in a couple of co-workers. These deletions did not affect subgenomic RNAs (sgRNA) production downstream of ORF7a. Still, fragments associated with sgRNA of genes upstream of ORF7a showed a decrease in size when corresponding to samples with deletions. In silico analysis suggests that the deletions impair protein proper function; however, isolated viruses with partial deletion of ORF7a can replicate in culture cells similarly to wild-type viruses at 24 hpi, but with less infectious particles after 48 hpi. These findings on deleted ORF7a accessory protein gene, contribute to understanding SARS-CoV-2 phenotypes such as replication, immune evasion and evolutionary fitness as well insights into the role of SARS-CoV-2_ORF7a in the mechanism of virus-host interactions.
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Affiliation(s)
- Maria Clara da Costa Simas
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Sara Mesquita Costa
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Priscila da Silva Figueiredo Celestino Gomes
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
- Physics Department, Auburn University, Auburn, AL 36849, USA
| | | | - Isadora Alonso Corrêa
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | | | - Marcos Dornelas-Ribeiro
- Laboratório de Biodefesa, Instituto de Biologia do Exército, Rio de Janeiro 20911-270, Brazil
| | | | | | - Luísa Hoffmann
- Instituto Federal de Educação, Ciência e Tecnologia do Rio de Janeiro, Rio de Janeiro 20270-021, Brazil
| | - Amilcar Tanuri
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | | | - Clarissa R Damaso
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Luciana Jesus da Costa
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Rosane Silva
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
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3
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Foster CSP, Bull RA, Tedla N, Santiago F, Agapiou D, Adhikari A, Walker GJ, Shrestha LB, Van Hal SJ, Kim KW, Rawlinson WD. Persistence of a Frameshifting Deletion in SARS-CoV-2 ORF7a for the Duration of a Major Outbreak. Viruses 2023; 15:v15020522. [PMID: 36851735 PMCID: PMC9966144 DOI: 10.3390/v15020522] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/08/2023] [Accepted: 02/10/2023] [Indexed: 02/15/2023] Open
Abstract
Australia experienced widespread COVID-19 outbreaks from infection with the SARS-CoV-2 Delta variant between June 2021 and February 2022. A 17-nucleotide frameshift-inducing deletion in ORF7a rapidly became represented at the consensus level (Delta-ORF7aΔ17del) in most Australian outbreak cases. Studies from early in the COVID-19 pandemic suggest that frameshift-inducing deletions in ORF7a do not persist for long in the population; therefore, Delta-ORF7aΔ17del genomes should have disappeared early in the Australian outbreak. In this study, we conducted a retrospective analysis of global Delta genomes to characterise the dynamics of Delta-ORF7aΔ17del over time, determined the frequency of all ORF7a deletions worldwide, and compared global trends with those of the Australian Delta outbreak. We downloaded all GISAID clade GK Delta genomes and scanned them for deletions in ORF7a. For each deletion we identified, we characterised its frequency, the number of countries it was found in, and how long it persisted. Of the 4,018,216 Delta genomes identified globally, 134,751 (~3.35%) possessed an ORF7a deletion, and ORF7aΔ17del was the most common. ORF7aΔ17del was the sole deletion in 28,014 genomes, of which 27,912 (~99.6%) originated from the Australian outbreak. During the outbreak, ~87% of genomes were Delta-ORF7aΔ17del, and genomes with this deletion were sampled until the outbreak's end. These data demonstrate that, contrary to suggestions early in the COVID-19 pandemic, genomes with frameshifting deletions in ORF7a can persist over long time periods. We suggest that the proliferation of Delta-ORF7aΔ17del genomes was likely a chance founder effect. Nonetheless, the frequency of ORF7a deletions in SARS-CoV-2 genomes worldwide suggests they might have some benefit for virus transmission.
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Affiliation(s)
- Charles S. P. Foster
- Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
- School of Biomedical Sciences, Faculty of Medicine & Health, University of New South Wales, Sydney, NSW 2052, Australia
- Correspondence:
| | - Rowena A. Bull
- School of Biomedical Sciences, Faculty of Medicine & Health, University of New South Wales, Sydney, NSW 2052, Australia
- The Kirby Institute for Infection and Immunity, University of New South Wales, Sydney, NSW 2052, Australia
| | - Nicodemus Tedla
- School of Biomedical Sciences, Faculty of Medicine & Health, University of New South Wales, Sydney, NSW 2052, Australia
| | - Fernando Santiago
- School of Biomedical Sciences, Faculty of Medicine & Health, University of New South Wales, Sydney, NSW 2052, Australia
| | - David Agapiou
- The Kirby Institute for Infection and Immunity, University of New South Wales, Sydney, NSW 2052, Australia
| | - Anurag Adhikari
- School of Biomedical Sciences, Faculty of Medicine & Health, University of New South Wales, Sydney, NSW 2052, Australia
- The Kirby Institute for Infection and Immunity, University of New South Wales, Sydney, NSW 2052, Australia
- Department of Infection and Immunology, Kathmandu Research Institute for Biological Sciences, Lalitpur 44700, Province Bagmati, Nepal
| | - Gregory J. Walker
- Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
- School of Biomedical Sciences, Faculty of Medicine & Health, University of New South Wales, Sydney, NSW 2052, Australia
| | - Lok Bahadur Shrestha
- School of Biomedical Sciences, Faculty of Medicine & Health, University of New South Wales, Sydney, NSW 2052, Australia
- The Kirby Institute for Infection and Immunity, University of New South Wales, Sydney, NSW 2052, Australia
| | - Sebastiaan J. Van Hal
- Department of Infectious Diseases and Microbiology, NSW Health Pathology, Royal Prince Alfred Hospital, Sydney, NSW 2050, Australia
- Central Clinical School, University of Sydney, Sydney, NSW 2006, Australia
| | - Ki Wook Kim
- Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
- School of Women’s and Children’s Health, Faculty of Medicine & Health, University of New South Wales, Sydney, NSW 2052, Australia
| | - William D. Rawlinson
- Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
- School of Biomedical Sciences, Faculty of Medicine & Health, University of New South Wales, Sydney, NSW 2052, Australia
- School of Women’s and Children’s Health, Faculty of Medicine & Health, University of New South Wales, Sydney, NSW 2052, Australia
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW 2052, Australia
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4
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Panzera Y, Cortinas MN, Marandino A, Calleros L, Bormida V, Goñi N, Techera C, Grecco S, Williman J, Ramas V, Coppola L, Mogdasy C, Chiparelli H, Pérez R. Emergence and spreading of the largest SARS-CoV-2 deletion in the Delta AY.20 lineage from Uruguay. GENE REPORTS 2022; 29:101703. [PMID: 36338321 PMCID: PMC9617655 DOI: 10.1016/j.genrep.2022.101703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/24/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022]
Abstract
The genetic variability of SARS-CoV-2 (genus Betacoronavirus, family Coronaviridae) has been scrutinized since its first detection in December 2019. Although the role of structural variants, particularly deletions, in virus evolution is little explored, these genome changes are extremely frequent. They are associated with relevant processes, including immune escape and attenuation. Deletions commonly occur in accessory ORFs and might even lead to the complete loss of one or more ORFs. This scenario poses an interesting question about the origin and spreading of extreme structural rearrangements that persist without compromising virus viability. Here, we analyze the genome of SARS-CoV-2 in late 2021 in Uruguay and identify a Delta lineage (AY.20) that experienced a large deletion (872 nucleotides according to the reference Wuhan strain) that removes the 7a, 7b, and 8 ORFs. Deleted viruses coexist with wild-type (without deletion) AY.20 and AY.43 strains. The Uruguayan deletion is like those identified in Delta strains from Poland and Japan but occurs in a different Delta clade. Besides providing proof of the circulation of this large deletion in America, we infer that the 872-deletion arises by the consecutive occurrence of a 6-nucleotide deletion, characteristic of delta strains, and an 866-nucleotide deletion that arose independently in the AY.20 Uruguayan lineage. The largest deletion occurs adjacent to transcription regulatory sequences needed to synthesize the nested set of subgenomic mRNAs that serve as templates for transcription. Our findings support the role of transcription sequences as a hotspot for copy-choice recombination and highlight the remarkable dynamic of SARS-CoV-2 genomes.
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Affiliation(s)
- Yanina Panzera
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - María Noel Cortinas
- Genómica, Departamento de Laboratorios de Salud Pública, Ministerio de Salud Pública, Alfredo Navarro 3051 (entrada N), 11600 Montevideo, Uruguay
| | - Ana Marandino
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Lucía Calleros
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Victoria Bormida
- Genómica, Departamento de Laboratorios de Salud Pública, Ministerio de Salud Pública, Alfredo Navarro 3051 (entrada N), 11600 Montevideo, Uruguay
| | - Natalia Goñi
- Centro Nacional de Referencia de Influenza y otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Ministerio de Salud Pública, Alfredo Navarro 3051 (entrada N), 11600 Montevideo, Uruguay
| | - Claudia Techera
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Sofía Grecco
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Joaquín Williman
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Viviana Ramas
- Centro Nacional de Referencia de Influenza y otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Ministerio de Salud Pública, Alfredo Navarro 3051 (entrada N), 11600 Montevideo, Uruguay
| | - Leticia Coppola
- Centro Nacional de Referencia de Influenza y otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Ministerio de Salud Pública, Alfredo Navarro 3051 (entrada N), 11600 Montevideo, Uruguay
| | - Cristina Mogdasy
- Centro Nacional de Referencia de Influenza y otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Ministerio de Salud Pública, Alfredo Navarro 3051 (entrada N), 11600 Montevideo, Uruguay
| | - Héctor Chiparelli
- Centro Nacional de Referencia de Influenza y otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Ministerio de Salud Pública, Alfredo Navarro 3051 (entrada N), 11600 Montevideo, Uruguay
| | - Ruben Pérez
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
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5
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García-García T, Fernández-Rodríguez R, Redondo N, de Lucas-Rius A, Zaldívar-López S, López-Ayllón BD, Suárez-Cárdenas JM, Jiménez-Marín Á, Montoya M, Garrido JJ. Impairment of antiviral immune response and disruption of cellular functions by SARS-CoV-2 ORF7a and ORF7b. iScience 2022; 25:105444. [PMID: 36310646 PMCID: PMC9597514 DOI: 10.1016/j.isci.2022.105444] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 09/20/2022] [Accepted: 10/21/2022] [Indexed: 11/09/2022] Open
Abstract
SARS-CoV-2, the causative agent of the present COVID-19 pandemic, possesses eleven accessory proteins encoded in its genome, and some have been implicated in facilitating infection and pathogenesis through their interaction with cellular components. Among these proteins, accessory protein ORF7a and ORF7b functions are poorly understood. In this study, A549 cells were transduced to express ORF7a and ORF7b, respectively, to explore more in depth the role of each accessory protein in the pathological manifestation leading to COVID-19. Bioinformatic analysis and integration of transcriptome results identified defined canonical pathways and functional groupings revealing that after expression of ORF7a or ORF7b, the lung cells are potentially altered to create conditions more favorable for SARS-CoV-2, by inhibiting the IFN-I response, increasing proinflammatory cytokines release, and altering cell metabolic activity and adhesion. Based on these results, it is plausible to suggest that ORF7a or ORF7b could be used as biomarkers of progression in this pandemic.
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Affiliation(s)
- Tránsito García-García
- Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), GA-14 Research Group, Córdoba, Spain
| | - Raúl Fernández-Rodríguez
- Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), GA-14 Research Group, Córdoba, Spain
| | - Natalia Redondo
- Molecular Biomedicine Department, Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid 28040, Spain
| | - Ana de Lucas-Rius
- Molecular Biomedicine Department, Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid 28040, Spain
| | - Sara Zaldívar-López
- Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), GA-14 Research Group, Córdoba, Spain
| | - Blanca Dies López-Ayllón
- Molecular Biomedicine Department, Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid 28040, Spain
| | - José M. Suárez-Cárdenas
- Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), GA-14 Research Group, Córdoba, Spain
| | - Ángeles Jiménez-Marín
- Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), GA-14 Research Group, Córdoba, Spain
| | - María Montoya
- Molecular Biomedicine Department, Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid 28040, Spain
- Corresponding author
| | - Juan J. Garrido
- Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), GA-14 Research Group, Córdoba, Spain
- Corresponding author
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6
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Brandolini M, Dirani G, Taddei F, Zannoli S, Denicolò A, Arfilli V, Battisti A, Manera M, Mancini A, Grumiro L, Marino MM, Gatti G, Fantini M, Semprini S, Sambri V. Mutational induction in SARS-CoV-2 major lineages by experimental exposure to neutralising sera. Sci Rep 2022; 12:12479. [PMID: 35864211 PMCID: PMC9302871 DOI: 10.1038/s41598-022-16533-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 07/12/2022] [Indexed: 11/24/2022] Open
Abstract
The ongoing evolution of SARS-CoV-2 and the emergence of new viral variants bearing specific escape mutations responsible for immune evasion from antibody neutralisation has required a more accurate characterisation of the immune response as one of the evolutive forces behind viral adaptation to a largely immunised human population. In this work, culturing in the presence of neutralising sera vigorously promoted mutagenesis leading to the acquisition of known escape mutations on the spike as well as new presumptive escape mutations on structural proteins whose role as target of the neutralizing antibody response might have been thus far widely neglected. From this perspective, this study, in addition to tracing the past evolution of the species back to interactions with neutralising antibody immune response, also offers a glimpse into future evolutive scenarios.
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Affiliation(s)
- Martina Brandolini
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522, Cesena, Italy
| | - Giorgio Dirani
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522, Cesena, Italy
| | - Francesca Taddei
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522, Cesena, Italy
| | - Silvia Zannoli
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522, Cesena, Italy
| | - Agnese Denicolò
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522, Cesena, Italy
| | - Valentina Arfilli
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522, Cesena, Italy
| | - Arianna Battisti
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522, Cesena, Italy
| | - Martina Manera
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522, Cesena, Italy
| | - Andrea Mancini
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522, Cesena, Italy
| | - Laura Grumiro
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522, Cesena, Italy
| | - Maria Michela Marino
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522, Cesena, Italy
| | - Giulia Gatti
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522, Cesena, Italy
| | - Michela Fantini
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522, Cesena, Italy
| | - Simona Semprini
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522, Cesena, Italy
| | - Vittorio Sambri
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522, Cesena, Italy.
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES)-Alma Mater Studiorum, University of Bologna, 40138, Bologna, Italy.
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7
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Jelley L, Douglas J, Ren X, Winter D, McNeill A, Huang S, French N, Welch D, Hadfield J, de Ligt J, Geoghegan JL. Genomic epidemiology of Delta SARS-CoV-2 during transition from elimination to suppression in Aotearoa New Zealand. Nat Commun 2022; 13:4035. [PMID: 35821124 PMCID: PMC9274967 DOI: 10.1038/s41467-022-31784-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/30/2022] [Indexed: 12/12/2022] Open
Abstract
New Zealand’s COVID-19 elimination strategy heavily relied on the use of genomics to inform contact tracing, linking cases to the border and to clusters during community outbreaks. In August 2021, New Zealand entered its second nationwide lockdown after the detection of a single community case with no immediately apparent epidemiological link to the border. This incursion resulted in the largest outbreak seen in New Zealand caused by the Delta Variant of Concern. Here we generated 3806 high quality SARS-CoV-2 genomes from cases reported in New Zealand between 17 August and 1 December 2021, representing 43% of reported cases. We detected wide geographical spread coupled with undetected community transmission, characterised by the apparent extinction and reappearance of genomically linked clusters. We also identified the emergence, and near replacement, of genomes possessing a 10-nucleotide frameshift deletion that caused the likely truncation of accessory protein ORF7a. By early October, New Zealand moved from an elimination strategy to a suppression strategy and the role of genomics changed markedly from being used to track and trace, towards population-level surveillance. Aotearoa New Zealand pursued a COVID-19 elimination strategy until October 2021 when it moved to a suppression strategy. In this genomic surveillance study, the authors describe spread of the virus during the transition between these strategies, with evidence of substantial undetected community transmission.
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Affiliation(s)
- Lauren Jelley
- Institute of Environmental Science and Research, Wellington, New Zealand.,Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Jordan Douglas
- Centre for Computational Evolution, School of Computer Science, University of Auckland, Auckland, New Zealand
| | - Xiaoyun Ren
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - David Winter
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Andrea McNeill
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Sue Huang
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Nigel French
- Tāwharau Ora/School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - David Welch
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - James Hadfield
- Fred Hutchinson Cancer Research Centre, Seattle, Washington, USA
| | - Joep de Ligt
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Jemma L Geoghegan
- Institute of Environmental Science and Research, Wellington, New Zealand. .,Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.
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8
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Saravanan KA, Panigrahi M, Kumar H, Rajawat D, Nayak SS, Bhushan B, Dutt T. Role of genomics in combating COVID-19 pandemic. Gene 2022; 823:146387. [PMID: 35248659 PMCID: PMC8894692 DOI: 10.1016/j.gene.2022.146387] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/17/2022] [Accepted: 02/28/2022] [Indexed: 12/20/2022]
Abstract
The coronavirus disease 2019 (COVID-19) quickly swept over the world, becoming one of the most devastating outbreaks in human history. Being the first pandemic in the post-genomic era, advancements in genomics contributed significantly to scientific understanding and public health response to COVID-19. Genomic technologies have been employed by researchers all over the world to better understand the biology of SARS-CoV-2 and its origin, genomic diversity, and evolution. Worldwide genomic resources have greatly aided in the investigation of the COVID-19 pandemic. The pandemic has ushered in a new era of genomic surveillance, wherein scientists are tracking the changes of the SARS-CoV-2 genome in real-time at the international and national levels. Availability of genomic and proteomic information enables the rapid development of molecular diagnostics and therapeutics. The advent of high-throughput sequencing and genome editing technologies led to the development of modern vaccines. We briefly discuss the impact of genomics in the ongoing COVID-19 pandemic in this review.
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Affiliation(s)
- K A Saravanan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India.
| | - Harshit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
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9
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Consecutive deletions in a unique Uruguayan SARS-CoV-2 lineage evidence the genetic variability potential of accessory genes. PLoS One 2022; 17:e0263563. [PMID: 35176063 PMCID: PMC8853529 DOI: 10.1371/journal.pone.0263563] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 01/24/2022] [Indexed: 11/19/2022] Open
Abstract
Deletions frequently occur in the six accessory genes of SARS-CoV-2, but most genomes with deletions are sporadic and have limited spreading capability. Here, we analyze deletions in the ORF7a of the N.7 lineage, a unique Uruguayan clade from the Brazilian B.1.1.33 lineage. Thirteen samples collected during the early SARS-CoV-2 wave in Uruguay had deletions in the ORF7a. Complete genomes were obtained by Illumina next-generation sequencing, and deletions were confirmed by Sanger sequencing and capillary electrophoresis. The N.7 lineage includes several individuals with a 12-nucleotide deletion that removes four amino acids of the ORF7a. Notably, four individuals underwent an additional 68-nucleotide novel deletion that locates 44 nucleotides downstream in the terminal region of the same ORF7a. The simultaneous occurrence of the 12 and 68-nucleotide deletions fuses the ORF7a and ORF7b, two contiguous accessory genes that encode transmembrane proteins with immune-modulation activity. The fused ORF retains the signal peptide and the complete Ig-like fold of the 7a protein and the transmembrane domain of the 7b protein, suggesting that the fused protein plays similar functions to original proteins in a single format. Our findings evidence the remarkable dynamics of SARS-CoV-2 and the possibility that single and consecutive deletions occur in accessory genes and promote changes in the genomic organization that help the virus explore genetic variations and select for new, higher fit changes.
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Lucas S, Jones M, Kothari S, Madlambayan A, Ngo C, Chan C, Goraichuk IV. A 336-Nucleotide In-Frame Deletion in ORF7a Gene of SARS-CoV-2 Identified in Genomic Surveillance by Next-Generation Sequencing. J Clin Virol 2022; 148:105105. [PMID: 35220006 PMCID: PMC8842577 DOI: 10.1016/j.jcv.2022.105105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 02/09/2022] [Accepted: 02/13/2022] [Indexed: 10/25/2022]
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11
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Quéromès G, Destras G, Bal A, Regue H, Burfin G, Brun S, Fanget R, Morfin F, Valette M, Trouillet-Assant S, Lina B, Frobert E, Josset L. Characterization of SARS-CoV-2 ORF6 deletion variants detected in a nosocomial cluster during routine genomic surveillance, Lyon, France. Emerg Microbes Infect 2021; 10:167-177. [PMID: 33399033 PMCID: PMC7850418 DOI: 10.1080/22221751.2021.1872351] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 12/10/2020] [Accepted: 12/30/2020] [Indexed: 12/21/2022]
Abstract
During routine molecular surveillance of SARS-CoV-2 performed at the National Reference Center of Respiratory Viruses (Lyon, France) (n = 229 sequences collected February-April 2020), two frameshifting deletions were detected in the open reading frame 6, at the same position (27267). While a 26-nucleotide deletion variant (D26) was only found in one nasopharyngeal sample in March 2020, the 34-nucleotide deletion (D34) was found within a single geriatric hospital unit in 5/9 patients and one health care worker in April 2020. Phylogeny analysis strongly suggested a nosocomial transmission of D34, with potential fecal transmission, as also identified in a stool sample. No difference in disease severity was observed between patients hospitalized in the geriatric unit infected with WT or D34. In vitro D26 and D34 characterization revealed comparable replication kinetics with the wild-type (WT), but differential host immune responses. While interferon-stimulated genes were similarly upregulated after infection with WT and ORF6 variants, the latter specifically induced overexpression of 9 genes coding for inflammatory cytokines in the NF-kB pathway, including CCL2/MCP1, PTX3, and TNFα, for which high plasma levels have been associated with severe COVID-19. Our findings emphasize the need to monitor the occurrence of ORF6 deletions and assess their impact on the host immune response.
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Affiliation(s)
- Grégory Quéromès
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Lyon, Fracne
| | - Grégory Destras
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Lyon, Fracne
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Lyon, France
| | - Antonin Bal
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Lyon, Fracne
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Lyon, France
| | - Hadrien Regue
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Lyon, France
| | - Gwendolyne Burfin
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Lyon, France
- Centre National de Référence des virus des infections respiratoires, Lyon, Fracne
| | - Solenne Brun
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Lyon, France
- Centre National de Référence des virus des infections respiratoires, Lyon, Fracne
| | - Rémi Fanget
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Lyon, France
- Centre National de Référence des virus des infections respiratoires, Lyon, Fracne
| | - Florence Morfin
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Lyon, Fracne
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Lyon, France
| | - Martine Valette
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Lyon, Fracne
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Lyon, France
- Centre National de Référence des virus des infections respiratoires, Lyon, Fracne
| | | | - Bruno Lina
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Lyon, Fracne
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Lyon, France
- Centre National de Référence des virus des infections respiratoires, Lyon, Fracne
| | - Emilie Frobert
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Lyon, Fracne
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Lyon, France
| | - Laurence Josset
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Lyon, Fracne
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Lyon, France
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12
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Yek C, Nam VS, Leang R, Parker DM, Heng S, Souv K, Sovannaroth S, Mayxay M, AbuBakar S, Sasmono RT, Tran ND, Le Nguyen HK, Lon C, Boonnak K, Huy R, Sovann L, Manning JE. The Pandemic Experience in Southeast Asia: Interface Between SARS-CoV-2, Malaria, and Dengue. FRONTIERS IN TROPICAL DISEASES 2021; 2:788590. [PMID: 35373190 PMCID: PMC8975143 DOI: 10.3389/fitd.2021.788590] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Southeast Asia (SEA) emerged relatively unscathed from the first year of the global SARS-CoV-2 pandemic, but as of July 2021 the region is experiencing a surge in case numbers primarily driven by Alpha (B.1.1.7) and subsequently the more transmissible Delta (B.1.617.2) variants. While initial disease burden was mitigated by swift government responses, favorable cultural and societal factors, the more recent rise in cases suggests an under-appreciation of prior prevalence and over-appreciation of possible cross-protective immunity from exposure to endemic viruses, and highlights the effects of vaccine rollout at varying tempos and of variable efficacy. This burgeoning crisis is further complicated by co-existence of malaria and dengue in the region, with implications of serological cross-reactivity on interpretation of SARS-CoV-2 assays and competing resource demands impacting efforts to contain both endemic and pandemic disease.
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Affiliation(s)
- Christina Yek
- Department of Critical Care Medicine, National Institutes of Health Clinical Center, Bethesda, MD, United States
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, United States
| | - Vu Sinh Nam
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | | | - Daniel M. Parker
- Department of Population Health and Disease Prevention, University of California, Irvine, Irvine, CA, United States
- Department of Epidemiology, University of California, Irvine, Irvine, CA, United States
| | - Seng Heng
- Ministry of Health, Phnom Penh, Cambodia
| | | | | | - Mayfong Mayxay
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
- Institute of Research and Education Development, University of Health Sciences, Vientiane, Laos
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Sazaly AbuBakar
- WHO Collaborating Center for Arbovirus Reference and Research (Dengue) and Tropical Infectious Diseases Research and Education Center, Universiti Malaya, Kuala Lumpur, Malaysia
| | | | - Nhu Duong Tran
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | | | - Chanthap Lon
- International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Phnom Penh, Cambodia
| | - Kobporn Boonnak
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Rekol Huy
- Ministry of Health, Phnom Penh, Cambodia
| | - Ly Sovann
- Ministry of Health, Phnom Penh, Cambodia
| | - Jessica E. Manning
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, United States
- International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Phnom Penh, Cambodia
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13
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Mazur-Panasiuk N, Rabalski L, Gromowski T, Nowicki G, Kowalski M, Wydmanski W, Szulc P, Kosinski M, Gackowska K, Drweska-Matelska N, Grabowski J, Piotrowska-Mietelska A, Szewczyk B, Bienkowska-Szewczyk K, Swadzba J, Labaj P, Grzybek M, Pyrc K. Expansion of a SARS-CoV-2 Delta variant with an 872 nt deletion encompassing ORF7a, ORF7b and ORF8, Poland, July to August 2021. ACTA ACUST UNITED AC 2021; 26. [PMID: 34596017 PMCID: PMC8485581 DOI: 10.2807/1560-7917.es.2021.26.39.2100902] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Routine genomic surveillance on samples from COVID-19 patients collected in Poland during summer 2021 revealed the emergence of a SARS-CoV-2 Delta variant with a large 872 nt deletion. This change, confirmed by Sanger and deep sequencing, causes complete loss of ORF7a, ORF7b, and ORF8 genes. The index case carrying the deletion is unknown. The standard pipeline for sequencing may mask this deletion with a long stretch of N’s. Effects of this deletion on phenotype or immune evasion needs further study.
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Affiliation(s)
- Natalia Mazur-Panasiuk
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Lukasz Rabalski
- Laboratory of Recombinant Vaccines, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Tomasz Gromowski
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.,Human Genome Research Variation Group, Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Grzegorz Nowicki
- genXone SA, Research & Development Laboratory, Suchy Las, Poland
| | - Michal Kowalski
- Bioinformatics Research Group, Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Witold Wydmanski
- Bioinformatics Research Group, Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Piotr Szulc
- Bioinformatics Research Group, Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Maciej Kosinski
- Laboratory of Recombinant Vaccines, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Karolina Gackowska
- Laboratory of Recombinant Vaccines, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | | | - Jakub Grabowski
- genXone SA, Research & Development Laboratory, Suchy Las, Poland
| | | | - Boguslaw Szewczyk
- Laboratory of Recombinant Vaccines, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Krystyna Bienkowska-Szewczyk
- Laboratory of Virus Molecular Biology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | | | - Pawel Labaj
- Bioinformatics Research Group, Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Maciej Grzybek
- Department of Tropical Parasitology, Institute of Maritime and Tropical Medicine, Medical University of Gdansk, Gdynia, Poland
| | - Krzysztof Pyrc
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
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14
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15
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Ongaro A, Oselladore E, Memo M, Ribaudo G, Gianoncelli A. Insight into the LFA-1/SARS-CoV-2 Orf7a Complex by Protein-Protein Docking, Molecular Dynamics, and MM-GBSA Calculations. J Chem Inf Model 2021; 61:2780-2787. [PMID: 34043356 PMCID: PMC8189040 DOI: 10.1021/acs.jcim.1c00198] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) genome, open reading frames (ORFs) encode for viral accessory proteins. Among these, Orf7a structurally resembles the members of the immunoglobulin (Ig) superfamily and intracellular adhesion molecules (ICAMs), in particular. ICAMs are involved in integrin binding through lymphocyte function-associated antigen 1 (LFA-1). Based on such considerations and on previous findings on SARS-CoV, it has been postulated that the formation of the LFA-1/Orf7a complex could contribute to SARS-CoV-2 infectivity and pathogenicity. With the current work, we aim at providing insight into this macromolecular assembly, taking advantage of the recently reported SARS-CoV-2 Orf7a structure. Protein-protein docking, molecular dynamics (MD) simulations, and a Molecular Mechanical-Generalized Born Surface Area (MM-GBSA)-based stage were enrolled to provide refined models.
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Affiliation(s)
- Alberto Ongaro
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Erika Oselladore
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Maurizio Memo
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Giovanni Ribaudo
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Alessandra Gianoncelli
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
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16
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Peacock TP, Penrice-Randal R, Hiscox JA, Barclay WS. SARS-CoV-2 one year on: evidence for ongoing viral adaptation. J Gen Virol 2021; 102:001584. [PMID: 33855951 PMCID: PMC8290271 DOI: 10.1099/jgv.0.001584] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 03/16/2021] [Indexed: 12/23/2022] Open
Abstract
SARS-CoV-2 is thought to have originated in the human population from a zoonotic spillover event. Infection in humans results in a variety of outcomes ranging from asymptomatic cases to the disease COVID-19, which can have significant morbidity and mortality, with over two million confirmed deaths worldwide as of January 2021. Over a year into the pandemic, sequencing analysis has shown that variants of SARS-CoV-2 are being selected as the virus continues to circulate widely within the human population. The predominant drivers of genetic variation within SARS-CoV-2 are single nucleotide polymorphisms (SNPs) caused by polymerase error, potential host factor driven RNA modification, and insertion/deletions (indels) resulting from the discontinuous nature of viral RNA synthesis. While many mutations represent neutral 'genetic drift' or have quickly died out, a subset may be affecting viral traits such as transmissibility, pathogenicity, host range, and antigenicity of the virus. In this review, we summarise the current extent of genetic change in SARS-CoV-2, particularly recently emerging variants of concern, and consider the phenotypic consequences of this viral evolution that may impact the future trajectory of the pandemic.
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Affiliation(s)
- Thomas P. Peacock
- Department of Infectious Diseases, St Marys Medical School, Imperial College London, UK
| | | | - Julian A. Hiscox
- Institute of Infection, Veterinary and Ecology Sciences, University of Liverpool, UK
- A*STAR Infectious Diseases Laboratories (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Wendy S. Barclay
- Department of Infectious Diseases, St Marys Medical School, Imperial College London, UK
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17
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Mungaomklang A, Atsawawaranunt K, Kochakarn T, Batty EM, Kaewmalang P, Kongklieng A, Panwijitkul P, Joonlasak K, Kotanan N, Loesbanluechai D, Pawun V, Chantratita W, Chookajorn T. Pitfalls of exceptions for COVID-19 travel quarantine: lessons from a dignitary visit to Thailand. J Travel Med 2021; 28:taab010. [PMID: 33506268 PMCID: PMC7901055 DOI: 10.1093/jtm/taab010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 01/11/2021] [Accepted: 01/12/2021] [Indexed: 12/04/2022]
Abstract
A dignitary from a European country made an official visit to Thailand in November 2020. Due to the nature of this visit, a standard 14-day quarantine was not implemented. After a series of meetings with diplomats and hotel staffers, the dignitary was diagnosed with COVID-19. Here, we detailed the transmission and the genomic investigation from the visit, presenting the factors that need to be considered when a standard quarantine was waivered.
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Affiliation(s)
- Anek Mungaomklang
- Department of Disease Control, Ministry of Public Health, Institute for Urban Disease Control and Prevention, Bang Khen, Bangkok 10220, Thailand
| | - Kamolthip Atsawawaranunt
- Department of Disease Control, Ministry of Public Health, Institute for Urban Disease Control and Prevention, Bang Khen, Bangkok 10220, Thailand
| | - Theerarat Kochakarn
- COVID-19 Network Investigations Alliance (CONI), Mahidol University, Rajthevi, Bangkok 10400, Thailand
- Genomics and Evolutionary Medicine Unit, Center of Excellence in Malaria Research, Faculty of Tropical Medicine, Rajthevi, Mahidol University, Bangkok 10400,Thailand
| | - Elizabeth M Batty
- COVID-19 Network Investigations Alliance (CONI), Mahidol University, Rajthevi, Bangkok 10400, Thailand
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Rajthevi, Mahidol University, Bangkok 10400, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, New Richards Building, Old Road Campus, Roosevelt Drive, Oxford, OX3 7LG, UK
| | - Prayuth Kaewmalang
- Department of Disease Control, Ministry of Public Health, Institute for Urban Disease Control and Prevention, Bang Khen, Bangkok 10220, Thailand
| | - Amornmas Kongklieng
- Department of Disease Control, Ministry of Public Health, Institute for Urban Disease Control and Prevention, Bang Khen, Bangkok 10220, Thailand
| | - Pukkaporn Panwijitkul
- Department of Disease Control, Ministry of Public Health, Institute for Urban Disease Control and Prevention, Bang Khen, Bangkok 10220, Thailand
| | - Khajohn Joonlasak
- COVID-19 Network Investigations Alliance (CONI), Mahidol University, Rajthevi, Bangkok 10400, Thailand
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Rajthevi, Bangkok 10400, Thailand
| | - Namfon Kotanan
- COVID-19 Network Investigations Alliance (CONI), Mahidol University, Rajthevi, Bangkok 10400, Thailand
- Genomics and Evolutionary Medicine Unit, Center of Excellence in Malaria Research, Faculty of Tropical Medicine, Rajthevi, Mahidol University, Bangkok 10400,Thailand
| | - Duangkamon Loesbanluechai
- COVID-19 Network Investigations Alliance (CONI), Mahidol University, Rajthevi, Bangkok 10400, Thailand
- Genomics and Evolutionary Medicine Unit, Center of Excellence in Malaria Research, Faculty of Tropical Medicine, Rajthevi, Mahidol University, Bangkok 10400,Thailand
| | - Vichan Pawun
- Department of Disease Control, Ministry of Public Health, Institute for Urban Disease Control and Prevention, Bang Khen, Bangkok 10220, Thailand
| | - Wasun Chantratita
- COVID-19 Network Investigations Alliance (CONI), Mahidol University, Rajthevi, Bangkok 10400, Thailand
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Rajthevi, Bangkok 10400, Thailand
| | - Thanat Chookajorn
- COVID-19 Network Investigations Alliance (CONI), Mahidol University, Rajthevi, Bangkok 10400, Thailand
- Genomics and Evolutionary Medicine Unit, Center of Excellence in Malaria Research, Faculty of Tropical Medicine, Rajthevi, Mahidol University, Bangkok 10400,Thailand
- Center for Medical Genomics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Payathai, Bangkok 10400, Thailand
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18
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Neches RY, Kyrpides NC, Ouzounis CA. Atypical Divergence of SARS-CoV-2 Orf8 from Orf7a within the Coronavirus Lineage Suggests Potential Stealthy Viral Strategies in Immune Evasion. mBio 2021; 12:e03014-20. [PMID: 33468697 PMCID: PMC7845636 DOI: 10.1128/mbio.03014-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 12/11/2020] [Indexed: 01/19/2023] Open
Abstract
Orf8, one of the most puzzling genes in the SARS lineage of coronaviruses, marks a unique and striking difference in genome organization between SARS-CoV-2 and SARS-CoV-1. Here, using sequence comparisons, we unequivocally reveal the distant sequence similarities between SARS-CoV-2 Orf8 with its SARS-CoV-1 counterparts and the X4-like genes of coronaviruses, including its highly divergent "paralog" gene Orf7a, whose product is a potential immune antagonist of known structure. Supervised sequence space walks unravel identity levels that drop below 10% and yet exhibit subtle conservation patterns in this novel superfamily, characterized by an immunoglobulin-like beta sandwich topology. We document the high accuracy of the sequence space walk process in detail and characterize the subgroups of the superfamily in sequence space by systematic annotation of gene and taxon groups. While SARS-CoV-1 Orf7a and Orf8 genes are most similar to bat virus sequences, their SARS-CoV-2 counterparts are closer to pangolin virus homologs, reflecting the fine structure of conservation patterns within the SARS-CoV-2 genomes. The divergence between Orf7a and Orf8 is exceptionally idiosyncratic, since Orf7a is more constrained, whereas Orf8 is subject to rampant change, a peculiar feature that may be related to hitherto-unknown viral infection strategies. Despite their common origin, the Orf7a and Orf8 protein families exhibit different modes of evolutionary trajectories within the coronavirus lineage, which might be partly attributable to their complex interactions with the mammalian host cell, reflected by a multitude of functional associations of Orf8 in SARS-CoV-2 compared to a very small number of interactions discovered for Orf7a.IMPORTANCE Orf8 is one of the most puzzling genes in the SARS lineage of coronaviruses, including SARS-CoV-2. Using sophisticated sequence comparisons, we confirm its origins from Orf7a, another gene in the lineage that appears as more conserved, compared to Orf8. Orf7a is a potential immune antagonist of known structure, while a deletion of Orf8 was shown to decrease the severity of the infection in a cohort study. The subtle sequence similarities imply that Orf8 has the same immunoglobulin-like fold as Orf7a, confirmed by structure determination. We characterize the subgroups of this superfamily and demonstrate the highly idiosyncratic divergence patterns during the evolution of the virus.
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Affiliation(s)
- Russell Y Neches
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
| | - Nikos C Kyrpides
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
| | - Christos A Ouzounis
- Biological Computation and Process Laboratory, Chemical Process and Energy Resources Institute, Centre for Research and Technology Hellas, Thessalonica, Greece
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19
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Paniz-Mondolfi A, Muñoz M, Florez C, Gomez S, Rico A, Pardo L, Barros EC, Hernández C, Delgado L, Jaimes JE, Pérez L, Teherán AA, Alshammary HA, Obla A, Khan Z, Dutta J, van de Guchte A, Gonzalez-Reiche AS, Hernandez MM, Sordillo EM, Simon V, van Bakel H, Llewellyn MS, Ramírez JD. SARS-CoV-2 spread across the Colombian-Venezuelan border. INFECTION GENETICS AND EVOLUTION 2020; 86:104616. [PMID: 33157300 PMCID: PMC7609240 DOI: 10.1016/j.meegid.2020.104616] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/20/2020] [Accepted: 10/31/2020] [Indexed: 01/01/2023]
Abstract
INTRODUCTION Venezuela and Colombia both adopted measures of containment early in response to the COVID-19 pandemic. However, Venezuela's ongoing humanitarian crisis has decimated its health care system, and forced millions of Venezuelans to flee through its porous border with Colombia. The extensive shared border, and illegal cross-border transit through improvised trails between the two countries are major challenges for public health authorities. We report the first SARS-CoV-2 genomes from Venezuela, and present a snapshot of the SARS-CoV-2 epidemiologic landscape in the Colombian-Venezuelan border region. METHODS We sequenced and assembled viral genomes from total RNA extracted from nasopharyngeal (NP) clinical specimens using a custom reference-based analysis pipeline. Three assemblies obtained were subjected to typing using the Phylogenetic Assignment of Named Global Outbreak LINeages 'Pangolin' tool. A total of 376 publicly available SARS-CoV-2 genomes from South America were obtained from the GISAID database to perform comparative genomic analyses. Additionally, the Wuhan-1 strain was used as reference. RESULTS We found that two of the SARS-CoV-2 genomes from Venezuela belonged to the B1 lineage, and the third to the B.1.13 lineage. We observed a point mutation in the Spike protein gene (D614G substitution), previously reported to be associated with increased infectivity, in all three Venezuelan genomes. Additionally, three mutations (R203K/G204R substitution) were present in the nucleocapsid (N) gene of one Venezuelan genome. CONCLUSIONS Genomic sequencing demonstrates similarity between SARS-CoV-2 lineages from Venezuela and viruses collected from patients in bordering areas in Colombia and from Brazil, consistent with cross-border transit despite administrative measures including lockdowns. The presence of mutations associated with increased infectivity in the 3 Venezuelan genomes we report and Colombian SARS-CoV-2 genomes from neighboring borders areas may pose additional challenges for control of SARS-CoV-2 spread in the complex epidemiological landscape in Latin American countries. Public health authorities should carefully follow the progress of the pandemic and its impact on displaced populations within the region.
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Affiliation(s)
- Alberto Paniz-Mondolfi
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Marina Muñoz
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | | | | | | | | | | | - Carolina Hernández
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Lourdes Delgado
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Jesús E Jaimes
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Luis Pérez
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | | | - Hala Alejel Alshammary
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ajay Obla
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zenab Khan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jayeeta Dutta
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Adriana van de Guchte
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ana S Gonzalez-Reiche
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Matthew M Hernandez
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Emilia Mia Sordillo
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Martin S Llewellyn
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - Juan David Ramírez
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
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20
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Charre C, Ginevra C, Sabatier M, Regue H, Destras G, Brun S, Burfin G, Scholtes C, Morfin F, Valette M, Lina B, Bal A, Josset L. Evaluation of NGS-based approaches for SARS-CoV-2 whole genome characterisation. Virus Evol 2020; 6:veaa075. [PMID: 33318859 PMCID: PMC7665770 DOI: 10.1093/ve/veaa075] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Since the beginning of the COVID-19 outbreak, SARS-CoV-2 whole-genome sequencing (WGS) has been performed at unprecedented rate worldwide with the use of very diverse Next-Generation Sequencing (NGS) methods. Herein, we compare the performance of four NGS-based approaches for SARS-CoV-2 WGS. Twenty-four clinical respiratory samples with a large scale of Ct values (from 10.7 to 33.9) were sequenced with four methods. Three used Illumina sequencing: an in-house metagenomic NGS (mNGS) protocol and two newly commercialised kits including a hybridisation capture method developed by Illumina (DNA Prep with Enrichment kit and Respiratory Virus Oligo Panel, RVOP), and an amplicon sequencing method developed by Paragon Genomics (CleanPlex SARS-CoV-2 kit). We also evaluated the widely used amplicon sequencing protocol developed by ARTIC Network and combined with Oxford Nanopore Technologies (ONT) sequencing. All four methods yielded near-complete genomes (>99%) for high viral loads samples (n = 8), with mNGS and RVOP producing the most complete genomes. For mid viral loads (Ct 20–25), amplicon-based enrichment methods led to genome coverage >99 per cent for all samples while 1/8 sample sequenced with RVOP and 2/8 samples sequenced with mNGS had a genome coverage below 99 per cent. For low viral loads (Ct ≥25), amplicon-based enrichment methods were the most sensitive techniques. All methods were highly concordant in terms of identity in complete consensus sequence. Just one mismatch in three samples was observed in CleanPlex vs the other methods, due to the dedicated bioinformatics pipeline setting a high threshold to call SNP compared to reference sequence. Importantly, all methods correctly identified a newly observed 34nt-deletion in ORF6 but required specific bioinformatic validation for RVOP. Finally, as a major warning for targeted techniques, a loss of coverage in any given region of the genome should alert to a potential rearrangement or a SNP in primer-annealing or probe-hybridizing regions and would require further validation using unbiased metagenomic sequencing.
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Affiliation(s)
- Caroline Charre
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Université de Lyon, Université Claude Bernard Lyon 1 (UCBL1), Lyon, France.,Centre de recherche en cancérologie (CRCL), INSERM U1052- 69008, Lyon, France
| | - Christophe Ginevra
- CIRI, Centre International de Recherche en Infectiologie, (Team pathogenesis of Legionella), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon 69007, France.,Hospices Civils de Lyon, Centre National de Référence des Légionelles, Lyon, France
| | - Marina Sabatier
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Université de Lyon, Université Claude Bernard Lyon 1 (UCBL1), Lyon, France.,Université de Lyon, Virpath, CIRI, INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Hadrien Regue
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Université de Lyon, Université Claude Bernard Lyon 1 (UCBL1), Lyon, France
| | - Grégory Destras
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Université de Lyon, Université Claude Bernard Lyon 1 (UCBL1), Lyon, France.,Université de Lyon, Virpath, CIRI, INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France.,Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France
| | - Solenne Brun
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France
| | - Gwendolyne Burfin
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France
| | - Caroline Scholtes
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Université de Lyon, Université Claude Bernard Lyon 1 (UCBL1), Lyon, France.,Centre de recherche en cancérologie (CRCL), INSERM U1052- 69008, Lyon, France
| | - Florence Morfin
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Université de Lyon, Université Claude Bernard Lyon 1 (UCBL1), Lyon, France.,Université de Lyon, Virpath, CIRI, INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France.,Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France
| | - Martine Valette
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France
| | - Bruno Lina
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Université de Lyon, Université Claude Bernard Lyon 1 (UCBL1), Lyon, France.,Université de Lyon, Virpath, CIRI, INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France.,Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France
| | - Antonin Bal
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Université de Lyon, Université Claude Bernard Lyon 1 (UCBL1), Lyon, France.,Université de Lyon, Virpath, CIRI, INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France.,Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France
| | - Laurence Josset
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Université de Lyon, Université Claude Bernard Lyon 1 (UCBL1), Lyon, France.,Université de Lyon, Virpath, CIRI, INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France.,Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France
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