1
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Happi AN, Ogunsanya OA, Ayinla AO, Sijuwola AE, Saibu FM, Akano K, Nwofoke C, Elias OT, Achonduh-Atijegbe O, Daodu RO, Adedokun OA, Adeyemo A, Ogundana KE, Lawal OZ, Parker E, Nosamiefan I, Okolie J, Parker ZF, McCauley MD, Eller LA, Lombardi K, Tiamiyu AB, Iroezindu M, Akinwale E, Njatou TLFA, Mebrahtu T, Broach E, Zuppe A, Prins P, Lay J, Amare M, Modjarrad K, Collins ND, Vasan S, Tucker C, Daye S, Happi CT. Lassa virus in novel hosts: insights into the epidemiology of lassa virus infections in southern Nigeria. Emerg Microbes Infect 2024; 13:2294859. [PMID: 38088796 PMCID: PMC10810657 DOI: 10.1080/22221751.2023.2294859] [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: 10/03/2023] [Accepted: 12/11/2023] [Indexed: 01/24/2024]
Abstract
Identification of the diverse animal hosts responsible for spill-over events from animals to humans is crucial for comprehending the transmission patterns of emerging infectious diseases, which pose significant public health risks. To better characterize potential animal hosts of Lassa virus (LASV), we assessed domestic and non-domestic animals from 2021-2022 in four locations in southern Nigeria with reported cases of Lassa fever (LF). Birds, lizards, and domestic mammals (dogs, pigs, cattle and goats) were screened using RT-qPCR, and whole genome sequencing was performed for lineage identification on selected LASV positive samples. Animals were also screened for exposure to LASV by enzyme-linked immunosorbent assay (ELISA). Among these animals, lizards had the highest positivity rate by PCR. Genomic sequencing of samples in most infected animals showed sub-lineage 2 g of LASV. Seropositivity was highest among cattle and lowest in pigs. Though the specific impact these additional hosts may have in the broader virus-host context are still unknown - specifically relating to pathogen diversity, evolution, and transmission - the detection of LASV in non-rodent hosts living in proximity to confirmed human LF cases suggests their involvement during transmission as potential reservoirs. Additional epidemiological data comparing viral genomes from humans and animals, as well as those circulating within the environment will be critical in understanding LASV transmission dynamics and will ultimately guide the development of countermeasures for this zoonotic health threat.
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Affiliation(s)
- Anise Nkenjop Happi
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
| | - Olusola Akinola Ogunsanya
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
| | - Akeemat Opeyemi Ayinla
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
| | - Ayotunde Elijah Sijuwola
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
| | - Femi Mudasiru Saibu
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
| | - Kazeem Akano
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
- Redeemer’s University, Ede, Osun, Nigeria
| | - Cecilia Nwofoke
- Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi State, Nigeria
| | | | | | - Richard Olumide Daodu
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
| | - Oluwatobi Abel Adedokun
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
| | - Abraham Adeyemo
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
| | | | | | - Edyth Parker
- Scripps Translational Science Institute, La Jolla, CA, USA
| | - Iguosadolo Nosamiefan
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
| | - Johnson Okolie
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
| | - Zahra F. Parker
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Melanie D. McCauley
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Leigh Anne Eller
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Kara Lombardi
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Abdulwasiu Bolaji Tiamiyu
- Henry M. Jackson Foundation Medical Research International Ltd/Gte, Abuja, Nigeria
- Emerging Infectious Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Michael Iroezindu
- Henry M. Jackson Foundation Medical Research International Ltd/Gte, Abuja, Nigeria
- Emerging Infectious Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Edward Akinwale
- Henry M. Jackson Foundation Medical Research International Ltd/Gte, Abuja, Nigeria
- Emerging Infectious Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | | | - Tsedal Mebrahtu
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Erica Broach
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Anastasia Zuppe
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Petra Prins
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Jenny Lay
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Mihret Amare
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Kayvon Modjarrad
- Emerging Infectious Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Natalie D. Collins
- Viral Diseases Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Sandhya Vasan
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Cynthia Tucker
- One Health Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Sharon Daye
- One Health Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Christian Tientcha Happi
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
- Redeemer’s University, Ede, Osun, Nigeria
- Department of Immunology and Infectious Diseases, Harvard T H Chan School of Public Health, Boston, MA, USA
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2
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Bangura U, Davis C, Lamin J, Bangura J, Soropogui B, Davison AJ, Nichols J, Vucak M, Dawson M, Ansumana R, Sondufu D, Cadar D, Rieger T, Thomson E, Sahr F, Magassouba N, Ghersi B, Bird BH, Fichet-Calvet E. Spatio-temporal spread of Lassa virus and a new rodent host in the Mano River Union area, West Africa. Emerg Microbes Infect 2024; 13:2290834. [PMID: 38047354 PMCID: PMC10919312 DOI: 10.1080/22221751.2023.2290834] [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: 09/13/2023] [Accepted: 11/29/2023] [Indexed: 12/05/2023]
Abstract
The spread of Lassa virus (LASV) in Guinea, Liberia and Sierra Leone, which together are named the Mano River Union (MRU) area, was examined phylogeographically. To provide a reliable evolutionary scenario, new rodent-derived, whole LASV sequences were included. These were generated by metatranscriptomic next-generation sequencing from rodents sampled between 2003 and 2020 in 21 localities of Guinea and Sierra Leone. An analysis was performed using BEAST to perform continuous phylogeographic inference and EvoLaps v36 to visualize spatio-temporal spread. LASV was identified as expected in its primary host reservoir, the Natal multimammate mouse (Mastomys natalensis), and also in two Guinean multimammate mice (Mastomys erythroleucus) in northern Sierra Leone and two rusty-bellied brush-furred mice (Lophuromys sikapusi) in southern Sierra Leone. This finding is consistent with the latter two species being secondary host reservoirs. The strains in these three species were very closely related in LASV lineage IV. Phylogenetic analysis indicated that the most recent common ancestor of lineage IV existed 316-374 years ago and revealed distinct, well-supported clades from Sierra Leone (Bo, Kabala and Kenema), Guinea (Faranah, Kissidougou-Guekedou and Macenta) and Liberia (Phebe-Ganta). The phylogeographic scenario suggests southern Guinea as the point of origin of LASV in the MRU area, with subsequent spread to towards Mali, Liberia and Sierra Leone at a mean speed of 1.6 to 1.1 km/year.
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Affiliation(s)
- Umaru Bangura
- Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Hemorrhagic Fever Reference and Research, Hamburg, Germany
| | | | - Joyce Lamin
- Mercy Hospital Research Laboratory, Bo, Sierra Leone
| | - James Bangura
- University of Makeni and University of California, Davis One Health Program, Makeni, Sierra Leone
| | - Barré Soropogui
- Laboratoire des Fièvres Hémorragiques en Guinée, Conakry, Guinea
| | | | - Jenna Nichols
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Matej Vucak
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | | | | | - Dániel Cadar
- Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Hemorrhagic Fever Reference and Research, Hamburg, Germany
| | - Toni Rieger
- Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Hemorrhagic Fever Reference and Research, Hamburg, Germany
| | - Emma Thomson
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Foday Sahr
- College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
| | | | - Bruno Ghersi
- One Health Institute, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Brian H. Bird
- One Health Institute, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Elisabeth Fichet-Calvet
- Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Hemorrhagic Fever Reference and Research, Hamburg, Germany
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3
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Eskew EA, Bird BH, Ghersi BM, Bangura J, Basinski AJ, Amara E, Bah MA, Kanu MC, Kanu OT, Lavalie EG, Lungay V, Robert W, Vandi MA, Fichet-Calvet E, Nuismer SL. Reservoir displacement by an invasive rodent reduces Lassa virus zoonotic spillover risk. Nat Commun 2024; 15:3589. [PMID: 38678025 PMCID: PMC11055883 DOI: 10.1038/s41467-024-47991-1] [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: 08/04/2023] [Accepted: 04/17/2024] [Indexed: 04/29/2024] Open
Abstract
The black rat (Rattus rattus) is a globally invasive species that has been widely introduced across Africa. Within its invasive range in West Africa, R. rattus may compete with the native rodent Mastomys natalensis, the primary reservoir host of Lassa virus, a zoonotic pathogen that kills thousands annually. Here, we use rodent trapping data from Sierra Leone and Guinea to show that R. rattus presence reduces M. natalensis density within the human dwellings where Lassa virus exposure is most likely to occur. Further, we integrate infection data from M. natalensis to demonstrate that Lassa virus zoonotic spillover risk is lower at sites with R. rattus. While non-native species can have numerous negative effects on ecosystems, our results suggest that R. rattus invasion has the indirect benefit of decreasing zoonotic spillover of an endemic pathogen, with important implications for invasive species control across West Africa.
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Affiliation(s)
- Evan A Eskew
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, USA.
| | - Brian H Bird
- One Health Institute, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA
| | - Bruno M Ghersi
- One Health Institute, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA
- Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, USA
| | | | - Andrew J Basinski
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, USA
| | | | - Mohamed A Bah
- Ministry of Agriculture and Forestry, Freetown, Sierra Leone
| | | | | | | | | | | | | | | | - Scott L Nuismer
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA.
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4
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Wang X, Ye X, Li R, Zai X, Hu M, Wang S, Ren H, Jin Y, Xu J, Yue J. Spatio-temporal spread and evolution of Lassa virus in West Africa. BMC Infect Dis 2024; 24:314. [PMID: 38486143 PMCID: PMC10941413 DOI: 10.1186/s12879-024-09200-8] [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: 09/21/2023] [Accepted: 03/06/2024] [Indexed: 03/17/2024] Open
Abstract
BACKGROUND Lassa fever is a hemorrhagic disease caused by Lassa virus (LASV), which has been classified by the World Health Organization as one of the top infectious diseases requiring prioritized research. Previous studies have provided insights into the classification and geographic characteristics of LASV lineages. However, the factor of the distribution and evolution characteristics and phylodynamics of the virus was still limited. METHODS To enhance comprehensive understanding of LASV, we employed phylogenetic analysis, reassortment and recombination detection, and variation evaluation utilizing publicly available viral genome sequences. RESULTS The results showed the estimated the root of time of the most recent common ancestor (TMRCA) for large (L) segment was approximately 634 (95% HPD: [385879]), whereas the TMRCA for small (S) segment was around 1224 (95% HPD: [10301401]). LASV primarily spread from east to west in West Africa through two routes, and in route 2, the virus independently spread to surrounding countries through Liberia, resulting in a wider spread of LASV. From 1969 to 2018, the effective population size experienced two significant increased, indicating the enhanced genetic diversity of LASV. We also found the evolution rate of L segment was faster than S segment, further results showed zinc-binding protein had the fastest evolution rate. Reassortment events were detected in multiple lineages including sub-lineage IIg, while recombination events were observed within lineage V. Significant amino acid changes in the glycoprotein precursor of LASV were identified, demonstrating sequence diversity among lineages in LASV. CONCLUSION This study comprehensively elucidated the transmission and evolution of LASV in West Africa, providing detailed insights into reassortment events, recombination events, and amino acid variations.
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Affiliation(s)
- Xia Wang
- Laboratory of Advanced Biotechnology & State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, China
- Medical College of Guizhou University, Guiyang, 550025, China
| | - Xianwei Ye
- Medical College of Guizhou University, Guiyang, 550025, China
- Guizhou Provincial People's Hospital, Guiyang, 550002, China
| | - Ruihua Li
- Laboratory of Advanced Biotechnology & State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, China
| | - Xiaodong Zai
- Laboratory of Advanced Biotechnology & State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, China
| | - Mingda Hu
- Laboratory of Advanced Biotechnology & State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, China
| | - Shaoyan Wang
- Laboratory of Advanced Biotechnology & State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, China
| | - Hongguang Ren
- Laboratory of Advanced Biotechnology & State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, China
| | - Yuan Jin
- Laboratory of Advanced Biotechnology & State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, China.
| | - Junjie Xu
- Laboratory of Advanced Biotechnology & State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, China.
| | - Junjie Yue
- Laboratory of Advanced Biotechnology & State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, China.
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5
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Kotliar D, Raju S, Tabrizi S, Odia I, Goba A, Momoh M, Sandi JD, Nair P, Phelan E, Tariyal R, Eromon PE, Mehta S, Robles-Sikisaka R, Siddle KJ, Stremlau M, Jalloh S, Gire SK, Winnicki S, Chak B, Schaffner SF, Pauthner M, Karlsson EK, Chapin SR, Kennedy SG, Branco LM, Kanneh L, Vitti JJ, Broodie N, Gladden-Young A, Omoniwa O, Jiang PP, Yozwiak N, Heuklom S, Moses LM, Akpede GO, Asogun DA, Rubins K, Kales S, Happi AN, Iruolagbe CO, Dic-Ijiewere M, Iraoyah K, Osazuwa OO, Okonkwo AK, Kunz S, McCormick JB, Khan SH, Honko AN, Lander ES, Oldstone MBA, Hensley L, Folarin OA, Okogbenin SA, Günther S, Ollila HM, Tewhey R, Okokhere PO, Schieffelin JS, Andersen KG, Reilly SK, Grant DS, Garry RF, Barnes KG, Happi CT, Sabeti PC. Genome-wide association study identifies human genetic variants associated with fatal outcome from Lassa fever. Nat Microbiol 2024; 9:751-762. [PMID: 38326571 PMCID: PMC10914620 DOI: 10.1038/s41564-023-01589-3] [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: 09/30/2022] [Accepted: 12/14/2023] [Indexed: 02/09/2024]
Abstract
Infection with Lassa virus (LASV) can cause Lassa fever, a haemorrhagic illness with an estimated fatality rate of 29.7%, but causes no or mild symptoms in many individuals. Here, to investigate whether human genetic variation underlies the heterogeneity of LASV infection, we carried out genome-wide association studies (GWAS) as well as seroprevalence surveys, human leukocyte antigen typing and high-throughput variant functional characterization assays. We analysed Lassa fever susceptibility and fatal outcomes in 533 cases of Lassa fever and 1,986 population controls recruited over a 7 year period in Nigeria and Sierra Leone. We detected genome-wide significant variant associations with Lassa fever fatal outcomes near GRM7 and LIF in the Nigerian cohort. We also show that a haplotype bearing signatures of positive selection and overlapping LARGE1, a required LASV entry factor, is associated with decreased risk of Lassa fever in the Nigerian cohort but not in the Sierra Leone cohort. Overall, we identified variants and genes that may impact the risk of severe Lassa fever, demonstrating how GWAS can provide insight into viral pathogenesis.
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Affiliation(s)
- Dylan Kotliar
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
- Department of Internal Medicine, Brigham and Women's Hospital, Boston, MA, USA.
| | - Siddharth Raju
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Shervin Tabrizi
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ikponmwosa Odia
- Institute of Lassa Fever, Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Augustine Goba
- College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
| | - Mambu Momoh
- College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
- Eastern Polytechnic College, Kenema, Sierra Leone
| | - John Demby Sandi
- College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
| | - Parvathy Nair
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | | | - Philomena E Eromon
- Institute of Lassa Fever, Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Nigeria
| | - Samar Mehta
- Department of Critical Care Medicine, University of Maryland Medical Center, Baltimore, MA, USA
| | - Refugio Robles-Sikisaka
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Katherine J Siddle
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | | | - Simbirie Jalloh
- College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
| | | | - Sarah Winnicki
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Bridget Chak
- Biological Sciences Division, University of Chicago, Chicago, IL, USA
| | - Stephen F Schaffner
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | | | - Elinor K Karlsson
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA, USA
- Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA, USA
| | - Sarah R Chapin
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Sharon G Kennedy
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Lansana Kanneh
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Joseph J Vitti
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Nisha Broodie
- New York-Presbyterian Hospital-Columbia and Cornell, New York, NY, USA
| | - Adrianne Gladden-Young
- Molecular Microbiology, Graduate School of Biomedical Sciences, Tufts University, Boston, MA, USA
| | | | | | - Nathan Yozwiak
- Gene and Cell Therapy Institute, Mass General Brigham, Cambridge, MA, USA
| | - Shannon Heuklom
- San Francisco Community Health Center, San Francisco, CA, USA
| | - Lina M Moses
- Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - George O Akpede
- Institute of Lassa Fever, Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
- Department of Medicine, Ambrose Alli University, Ekpoma, Nigeria
| | - Danny A Asogun
- Department of Community Medicine, Ambrose Alli University, Ekpoma, Nigeria
| | - Kathleen Rubins
- National Aeronautics and Space Administration, Houston, TX, USA
| | | | - Anise N Happi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Nigeria
| | | | - Mercy Dic-Ijiewere
- Department of Medicine, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Kelly Iraoyah
- Department of Medicine, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Omoregie O Osazuwa
- Department of Medicine, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | | | - Stefan Kunz
- Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
| | - Joseph B McCormick
- UTHealth Houston School of Public Health, Brownsville Campus, Brownsville, TX, USA
| | - S Humarr Khan
- College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
| | - Anna N Honko
- Boston University School of Medicine, Boston, MA, USA
| | - Eric S Lander
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Michael B A Oldstone
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Lisa Hensley
- National Institutes of Health Integrated Research Facility, Frederick, MA, USA
| | - Onikepe A Folarin
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Nigeria
- Department of Biological Sciences, Redeemer's University, Ede, Nigeria
| | - Sylvanus A Okogbenin
- Institute of Lassa Fever, Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Stephan Günther
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Hanna M Ollila
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Peter O Okokhere
- Institute of Lassa Fever, Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
- Department of Medicine, Ambrose Alli University, Ekpoma, Nigeria
- Department of Medicine, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - John S Schieffelin
- Section of Infectious Disease, Department of Pediatrics, Tulane University School of Medicine, New Orleans, LA, USA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Steven K Reilly
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Donald S Grant
- College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Robert F Garry
- Tulane University School of Medicine, New Orleans, LA, USA
| | - Kayla G Barnes
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Department of Vector Biology and Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Christian T Happi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Nigeria.
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.
- Department of Biological Sciences, Redeemer's University, Ede, Nigeria.
| | - Pardis C Sabeti
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA.
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6
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Zhan L, Luo X, Xie W, Zhu XA, Xie Z, Lin J, Li L, Tang W, Wang R, Deng L, Liao Y, Liu B, Cai Y, Wang Q, Xu S, Yu G. shinyTempSignal: an R shiny application for exploring temporal and other phylogenetic signals. J Genet Genomics 2024:S1673-8527(24)00033-X. [PMID: 38417547 DOI: 10.1016/j.jgg.2024.02.004] [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: 12/14/2023] [Revised: 02/20/2024] [Accepted: 02/22/2024] [Indexed: 03/01/2024]
Abstract
The molecular clock model is fundamental for inferring species divergence times from molecular sequences. However, its direct application may introduce significant biases due to sequencing errors, recombination events, and inaccurately labeled sampling times. Improving accuracy necessitates rigorous quality control measures to identify and remove potentially erroneous sequences. Furthermore, while not all branches of a phylogenetic tree may exhibit a clear temporal signal, specific branches may still adhere to the assumptions, with varying evolutionary rates. Supporting a relaxed molecular clock model better aligns with the complexities of evolution. The root-to-tip regression method has been widely used to analyze the temporal signal in phylogenetic studies and can be generalized for detecting other phylogenetic signals. Despite its utility, there remains a lack of corresponding software implementations for broader applications. To address this gap, we present shinyTempSignal, an interactive web application implemented with the shiny framework, available as an R package and publicly accessible at https://github.com/YuLab-SMU/shinyTempSignal. This tool facilitates the analysis of temporal and other phylogenetic signals under both strict and relaxed models. By extending the root-to-tip regression method to diverse signals, shinyTempSignal helps in the detection of evolving features or traits, thereby laying the foundation for deeper insights and subsequent analyses.
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Affiliation(s)
- Li Zhan
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Xiao Luo
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Wenqin Xie
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Xuan-An Zhu
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China; Faculty of Computers, Guangdong University of Technology, Guangzhou, Guangdong 510006, China
| | - Zijing Xie
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Jianfeng Lin
- Ubigene Biosciences Co., Ltd., Guangzhou, Guangdong 510530, China
| | - Lin Li
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Wenli Tang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Rui Wang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Lin Deng
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Yufan Liao
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Bingdong Liu
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China; State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong 510070, China
| | - Yantong Cai
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Qianwen Wang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Shuangbin Xu
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China.
| | - Guangchuang Yu
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China.
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7
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Reyna RA, Littlefield KE, Shehu N, Makishima T, Maruyama J, Paessler S. The Importance of Lassa Fever and Its Disease Management in West Africa. Viruses 2024; 16:266. [PMID: 38400041 PMCID: PMC10892767 DOI: 10.3390/v16020266] [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: 12/11/2023] [Revised: 01/21/2024] [Accepted: 02/02/2024] [Indexed: 02/25/2024] Open
Abstract
Lassa virus (LASV) is a zoonotic pathogen endemic throughout western Africa and is responsible for a human disease known as Lassa fever (LF). Historically, LASV has been emphasized as one of the greatest public health threats in West Africa, with up to 300,000 cases and 5000 associated deaths per year. This, and the fact that the disease has been reported in travelers, has driven a rapid production of various vaccine candidates. Several of these vaccines are currently in clinical development, despite limitations in understanding the immune response to infection. Alarmingly, the host immune response has been implicated in the induction of sensorineural hearing loss in LF survivors, legitimately raising safety questions about any future vaccines as well as efficacy in preventing potential hearing loss. The objective of this article is to revisit the importance and prevalence of LF in West Africa, with focus on Nigeria, and discuss current therapeutic approaches and ongoing vaccine development. In addition, we aim to emphasize the need for more scientific studies relating to LF-associated hearing loss, and to promote critical discussion about potential risks and benefits of vaccinating the population in endemic regions of West Africa.
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Affiliation(s)
- Rachel A. Reyna
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Kirsten E. Littlefield
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Nathan Shehu
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Infectious Disease Unit, Department of Medicine, Jos University Teaching Hospital, Jos P.M.B. 2076, Nigeria
| | - Tomoko Makishima
- Department of Otolaryngology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Junki Maruyama
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Slobodan Paessler
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
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8
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Carr CR, Crawford KHD, Murphy M, Galloway JG, Haddox HK, Matsen FA, Andersen KG, King NP, Bloom JD. Deep mutational scanning reveals functional constraints and antigenic variability of Lassa virus glycoprotein complex. bioRxiv 2024:2024.02.05.579020. [PMID: 38370709 PMCID: PMC10871245 DOI: 10.1101/2024.02.05.579020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Lassa virus is estimated to cause thousands of human deaths per year, primarily due to spillovers from its natural host, Mastomys rodents. Efforts to create vaccines and antibody therapeutics must account for the evolutionary variability of Lassa virus's glycoprotein complex (GPC), which mediates viral entry into cells and is the target of neutralizing antibodies. To map the evolutionary space accessible to GPC, we use pseudovirus deep mutational scanning to measure how nearly all GPC amino-acid mutations affect cell entry and antibody neutralization. Our experiments define functional constraints throughout GPC. We quantify how GPC mutations affect neutralization by a panel of monoclonal antibodies and show that all antibodies are escaped by mutations that exist among natural Lassa virus lineages. Overall, our work describes a biosafety-level-2 method to elucidate the mutational space accessible to GPC and shows how prospective characterization of antigenic variation could aid design of therapeutics and vaccines.
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Affiliation(s)
- Caleb R. Carr
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA 98109, USA
| | - Katharine H. D. Crawford
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA 98109, USA
| | - Michael Murphy
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Jared G. Galloway
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Hugh K. Haddox
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Frederick A. Matsen
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Department of Statistics, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98109, USA
| | - Kristian G. Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Scripps Research Translational Institute, La Jolla, CA 92037, USA
| | - Neil P. King
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Jesse D. Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA
- Howard Hughes Medical Institute, Seattle, WA 98109, USA
- Lead contact
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9
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Kim J, Park K, Kim K, Noh J, Kim SG, Yang E, Cho HK, Lee SH, No JS, Lee GY, Lee D, Song DH, Gu SH, Park MS, Cho NH, Jeong ST, Kim WK, Song JW. High-resolution phylogeographical surveillance of Hantaan orthohantavirus using rapid amplicon-based Flongle sequencing, Republic of Korea. J Med Virol 2024; 96:e29346. [PMID: 38178580 DOI: 10.1002/jmv.29346] [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: 10/20/2023] [Revised: 12/04/2023] [Accepted: 12/14/2023] [Indexed: 01/06/2024]
Abstract
Orthohantaviruses, etiological agents of hemorrhagic fever with renal syndrome (HFRS) and hantavirus cardiopulmonary syndrome, pose a critical public health threat worldwide. Hantaan orthohantavirus (HTNV) outbreaks are particularly endemic in Gyeonggi Province in northern area of the Republic of Korea (ROK). Small mammals were collected from three regions in the Gyeonggi Province during 2017 and 2018. Serological and molecular prevalence of HTNV was 25/201 (12.4%) and 10/25 (40%), respectively. A novel nanopore-based diagnostic assay using a cost-efficient Flongle chip was developed to rapidly and sensitively detect HTNV infection in rodent specimens within 3 h. A rapid phylogeographical surveillance of HTNV at high-resolution phylogeny was established using the amplicon-based Flongle sequencing. In total, seven whole-genome sequences of HTNV were newly obtained from wild rodents collected in Paju-si (Gaekhyeon-ri) and Yeoncheon-gun (Hyeonga-ri and Wangnim-ri), Gyeonggi Province. Phylogenetic analyses revealed well-supported evolutionary divergence and genetic diversity, enhancing the resolution of the phylogeographic map of orthohantaviruses in the ROK. Incongruences in phylogenetic patterns were identified among HTNV tripartite genomes, suggesting differential evolution for each segment. These findings provide crucial insights into on-site diagnostics, genome-based surveillance, and the evolutionary dynamics of orthohantaviruses to mitigate hantaviral outbreaks in HFRS-endemic areas in the ROK.
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Affiliation(s)
- Jongwoo Kim
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Korea University College of Medicine, Seoul, Republic of Korea
| | - Kyungmin Park
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Korea University College of Medicine, Seoul, Republic of Korea
| | - Kijin Kim
- Centre for Infectious Disease Genomics and One Health, Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Juyoung Noh
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Korea University College of Medicine, Seoul, Republic of Korea
| | - Seong-Gyu Kim
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Korea University College of Medicine, Seoul, Republic of Korea
| | - Eunyoung Yang
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Korea University College of Medicine, Seoul, Republic of Korea
| | - Hee-Kyung Cho
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Korea University College of Medicine, Seoul, Republic of Korea
| | - Seung-Ho Lee
- Chem-Bio Technology Center, Agency for Defense Development, Daejeon, Republic of Korea
| | - Jin Sun No
- Division of High-Risk Pathogens, Bureau of Infectious Diseases Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Geum-Young Lee
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
| | - Daesang Lee
- Chem-Bio Technology Center, Agency for Defense Development, Daejeon, Republic of Korea
| | - Dong-Hyun Song
- Chem-Bio Technology Center, Agency for Defense Development, Daejeon, Republic of Korea
| | - Se Hun Gu
- Chem-Bio Technology Center, Agency for Defense Development, Daejeon, Republic of Korea
| | - Man-Seong Park
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Korea University College of Medicine, Seoul, Republic of Korea
- Department of Microbiology, Institute for Viral Diseases, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Nam-Hyuk Cho
- Department of Microbiology and Immunology, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Seong Tae Jeong
- Chem-Bio Technology Center, Agency for Defense Development, Daejeon, Republic of Korea
| | - Won-Keun Kim
- Department of Microbiology, Hallym University, Chuncheon, Republic of Korea
- Institute of Medical Research, Hallym University, Chuncheon, Republic of Korea
| | - Jin-Won Song
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Korea University College of Medicine, Seoul, Republic of Korea
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10
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Adesina AS, Oyeyiola A, Obadare A, Igbokwe J, Abejegah C, Akhilomen P, Bangura U, Asogun D, Tobin E, Ayodeji O, Osoniyi O, Davis C, Thomson EC, Pahlmann M, Günther S, Fichet-Calvet E, Olayemi A. Circulation of Lassa virus across the endemic Edo-Ondo axis, Nigeria, with cross-species transmission between multimammate mice. Emerg Microbes Infect 2023; 12:2219350. [PMID: 37288752 PMCID: PMC10251791 DOI: 10.1080/22221751.2023.2219350] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 05/24/2023] [Indexed: 06/09/2023]
Abstract
We phylogenetically compared sequences of the zoonotic Lassa virus (LASV) obtained from Mastomys rodents in seven localities across the highly endemic Edo and Ondo States within Nigeria. Sequencing 1641 nt from the S segment of the virus genome, we resolved clades within lineage II that were either limited to Ebudin and Okhuesan in Edo state (2g-beta) or along Owo-Okeluse-Ifon in Ondo state (2g-gamma). We also found clades within Ekpoma, a relatively large cosmopolitan town in Edo state, that extended into other localities within Edo (2g-alpha) and Ondo (2g-delta). LASV variants from M. natalensis within Ebudin and Ekpoma in Edo State (dated approximately 1961) were more ancient compared to those from Ondo state (approximately 1977), suggesting a broadly east-west virus migration across south-western Nigeria; a pattern not always consistent with LASV sequences derived from humans in the same localities. Additionally, in Ebudin and Ekpoma, LASV sequences between M. natalensis and M. erythroleucus were interspersed on the phylogenetic tree, but those from M. erythroleucus were estimated to emerge more recently (approximately 2005). Overall, our results show that LASV amplification in certain localities (reaching a prevalence as high as 76% in Okeluse), anthropogenically-aided spread of rodent-borne variants amidst the larger towns (involving communal accommodation such as student hostels), and virus-exchange between syntopic M. natalensis and M. erythroleucus rodents (as the latter, a savanna species, encroaches southward into the degraded forest) pose perpetual zoonotic hazard across the Edo-Ondo Lassa fever belt, threatening to accelerate the dissemination of the virus into non endemic areas.
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Affiliation(s)
- Adetunji Samuel Adesina
- Department of Biochemistry and Molecular Biology, Obafemi Awolowo University, Ile Ife, Osun State, Nigeria
| | - Akinlabi Oyeyiola
- Natural History Museum, Obafemi Awolowo University, Ile Ife, Osun State, Nigeria
| | - Adeoba Obadare
- Natural History Museum, Obafemi Awolowo University, Ile Ife, Osun State, Nigeria
| | - Joseph Igbokwe
- Department of Zoology, Obafemi Awolowo University, Ile Ife, Osun State, Nigeria
| | | | | | - Umaru Bangura
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Danny Asogun
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Ekaete Tobin
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | | | - Omolaja Osoniyi
- Department of Biochemistry and Molecular Biology, Obafemi Awolowo University, Ile Ife, Osun State, Nigeria
| | - Chris Davis
- Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Emma C Thomson
- Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Meike Pahlmann
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Stephan Günther
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | | | - Ayodeji Olayemi
- Natural History Museum, Obafemi Awolowo University, Ile Ife, Osun State, Nigeria
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11
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Ji X, Fisher AA, Su S, Thorne JL, Potter B, Lemey P, Baele G, Suchard MA. Scalable Bayesian Divergence Time Estimation With Ratio Transformations. Syst Biol 2023; 72:1136-1153. [PMID: 37458991 PMCID: PMC10636426 DOI: 10.1093/sysbio/syad039] [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: 01/02/2022] [Revised: 06/13/2023] [Accepted: 06/30/2023] [Indexed: 11/08/2023] Open
Abstract
Divergence time estimation is crucial to provide temporal signals for dating biologically important events from species divergence to viral transmissions in space and time. With the advent of high-throughput sequencing, recent Bayesian phylogenetic studies have analyzed hundreds to thousands of sequences. Such large-scale analyses challenge divergence time reconstruction by requiring inference on highly correlated internal node heights that often become computationally infeasible. To overcome this limitation, we explore a ratio transformation that maps the original $N-1$ internal node heights into a space of one height parameter and $N-2$ ratio parameters. To make the analyses scalable, we develop a collection of linear-time algorithms to compute the gradient and Jacobian-associated terms of the log-likelihood with respect to these ratios. We then apply Hamiltonian Monte Carlo sampling with the ratio transform in a Bayesian framework to learn the divergence times in 4 pathogenic viruses (West Nile virus, rabies virus, Lassa virus, and Ebola virus) and the coralline red algae. Our method both resolves a mixing issue in the West Nile virus example and improves inference efficiency by at least 5-fold for the Lassa and rabies virus examples as well as for the algae example. Our method now also makes it computationally feasible to incorporate mixed-effects molecular clock models for the Ebola virus example, confirms the findings from the original study, and reveals clearer multimodal distributions of the divergence times of some clades of interest.
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Affiliation(s)
- Xiang Ji
- Department of Mathematics, School of Science & Engineering, Tulane University, 6823 St. Charles Avenue, New Orleans, LA 70118, USA
| | - Alexander A Fisher
- Department of Statistical Science, Duke University, 214 Old Chemistry, Durham, NC 27708, USA
| | - Shuo Su
- MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, No. 1 Weigang, Xiaolingwei District, Nanjing, Jiangsu 210095, China
| | - Jeffrey L Thorne
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
- Department of Statistics, North Carolina State University, Raleigh, NC, USA
- Department of Biological Sciences, North Carolina State University, Ricks Hall, 1 Lampe Dr, Raleigh, NC 27607, USA
| | - Barney Potter
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Herestraat 49, 3000 Leuven, Belgium
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Herestraat 49, 3000 Leuven, Belgium
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Herestraat 49, 3000 Leuven, Belgium
| | - Marc A Suchard
- Department of Biomathematics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, 695 Charles E Young Dr S, Los Angeles, CA 90095, USA
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12
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Senghore M, Read H, Oza P, Johnson S, Passarelli-Araujo H, Taylor BP, Ashley S, Grey A, Callendrello A, Lee R, Goddard MR, Lumley T, Hanage WP, Wiles S. Inferring bacterial transmission dynamics using deep sequencing genomic surveillance data. Nat Commun 2023; 14:6397. [PMID: 37907520 PMCID: PMC10618251 DOI: 10.1038/s41467-023-42211-8] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 09/27/2023] [Indexed: 11/02/2023] Open
Abstract
Identifying and interrupting transmission chains is important for controlling infectious diseases. One way to identify transmission pairs - two hosts in which infection was transmitted from one to the other - is using the variation of the pathogen within each single host (within-host variation). However, the role of such variation in transmission is understudied due to a lack of experimental and clinical datasets that capture pathogen diversity in both donor and recipient hosts. In this work, we assess the utility of deep-sequenced genomic surveillance (where genomic regions are sequenced hundreds to thousands of times) using a mouse transmission model involving controlled spread of the pathogenic bacterium Citrobacter rodentium from infected to naïve female animals. We observe that within-host single nucleotide variants (iSNVs) are maintained over multiple transmission steps and present a model for inferring the likelihood that a given pair of sequenced samples are linked by transmission. In this work we show that, beyond the presence and absence of within-host variants, differences arising in the relative abundance of iSNVs (allelic frequency) can infer transmission pairs more precisely. Our approach further highlights the critical role bottlenecks play in reserving the within-host diversity during transmission.
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Affiliation(s)
- Madikay Senghore
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA.
| | - Hannah Read
- Bioluminescent Superbugs Lab, Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Priyali Oza
- Bioluminescent Superbugs Lab, Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Sarah Johnson
- Bioluminescent Superbugs Lab, Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Hemanoel Passarelli-Araujo
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Minas Gerais, Brazil
| | - Bradford P Taylor
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Stephen Ashley
- Bioluminescent Superbugs Lab, Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Alex Grey
- Bioluminescent Superbugs Lab, Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Alanna Callendrello
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Robyn Lee
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA
- University of Toronto Dalla Lana School of Public Health, Toronto, ON, Canada
| | - Matthew R Goddard
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- School of Life and Environmental Sciences, University of Lincoln, Lincoln, UK
| | - Thomas Lumley
- Department of Statistics, University of Auckland, Auckland, New Zealand
| | - William P Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Siouxsie Wiles
- Bioluminescent Superbugs Lab, Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand.
- Te Pūnaha Matatini, Centre of Research Excellence in Complex Systems, Auckland, New Zealand.
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13
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N’Guessan A, Kailasam S, Mostefai F, Poujol R, Grenier JC, Ismailova N, Contini P, De Palma R, Haber C, Stadler V, Bourque G, Hussin JG, Shapiro BJ, Fritz JH, Piccirillo CA. Selection for immune evasion in SARS-CoV-2 revealed by high-resolution epitope mapping and sequence analysis. iScience 2023; 26:107394. [PMID: 37599818 PMCID: PMC10433132 DOI: 10.1016/j.isci.2023.107394] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 02/10/2023] [Accepted: 07/10/2023] [Indexed: 08/22/2023] Open
Abstract
Here, we exploit a deep serological profiling strategy coupled with an integrated, computational framework for the analysis of SARS-CoV-2 humoral immune responses. Applying a high-density peptide array (HDPA) spanning the entire proteomes of SARS-CoV-2 and endemic human coronaviruses allowed identification of B cell epitopes and relate them to their evolutionary and structural properties. We identify hotspots of pre-existing immunity and identify cross-reactive epitopes that contribute to increasing the overall humoral immune response to SARS-CoV-2. Using a public dataset of over 38,000 viral genomes from the early phase of the pandemic, capturing both inter- and within-host genetic viral diversity, we determined the evolutionary profile of epitopes and the differences across proteins, waves, and SARS-CoV-2 variants. Lastly, we show that mutations in spike and nucleocapsid epitopes are under stronger selection between than within patients, suggesting that most of the selective pressure for immune evasion occurs upon transmission between hosts.
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Affiliation(s)
- Arnaud N’Guessan
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
- McGill Genome Centre, McGill University, Montréal, QC, Canada
| | - Senthilkumar Kailasam
- Canadian Center for Computational Genomics, Montréal, QC, Canada
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Dahdaleh Institute of Genomic Medicine (DIgM), McGill University, Montréal, QC, Canada
| | - Fatima Mostefai
- Research Centre, Montreal Heart Institute, Montreal, QC, Canada
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC, Canada
| | - Raphaël Poujol
- Research Centre, Montreal Heart Institute, Montreal, QC, Canada
| | | | - Nailya Ismailova
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
- McGill University Research Center on Complex Traits (MRCCT), McGill University, Montréal, QC, Canada
- Dahdaleh Institute of Genomic Medicine (DIgM), McGill University, Montréal, QC, Canada
| | - Paola Contini
- Department of Internal Medicine, University of Genoa and IRCCS IST-Ospedale San Martino, Genoa, Italy
| | - Raffaele De Palma
- Department of Internal Medicine, University of Genoa and IRCCS IST-Ospedale San Martino, Genoa, Italy
| | | | | | - Guillaume Bourque
- Canadian Center for Computational Genomics, Montréal, QC, Canada
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Dahdaleh Institute of Genomic Medicine (DIgM), McGill University, Montréal, QC, Canada
| | - Julie G. Hussin
- Research Centre, Montreal Heart Institute, Montreal, QC, Canada
- Département de Médecine, Université de Montréal, Montréal, QC, Canada
| | - B. Jesse Shapiro
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
- McGill Genome Centre, McGill University, Montréal, QC, Canada
- Dahdaleh Institute of Genomic Medicine (DIgM), McGill University, Montréal, QC, Canada
| | - Jörg H. Fritz
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
- McGill University Research Center on Complex Traits (MRCCT), McGill University, Montréal, QC, Canada
- Dahdaleh Institute of Genomic Medicine (DIgM), McGill University, Montréal, QC, Canada
| | - Ciriaco A. Piccirillo
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
- McGill University Research Center on Complex Traits (MRCCT), McGill University, Montréal, QC, Canada
- Infectious Diseases and Immunity in Global Health Program of the Research Institute of McGill Health Center, Montréal, QC, Canada
- Dahdaleh Institute of Genomic Medicine (DIgM), McGill University, Montréal, QC, Canada
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14
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Isibor PO, Onwaeze OO, Kayode-Edwards II, Agbontaen DO, Ifebem-Ezima IAM, Bilewu O, Onuselogu C, Akinniyi AP, Obafemi YD, Oniha MI. Investigating and combatting the key drivers of viral zoonoses in Africa: an analysis of eight epidemics. BRAZ J BIOL 2023; 84:e270857. [PMID: 37531478 DOI: 10.1590/1519-6984.270857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 03/02/2023] [Indexed: 08/04/2023] Open
Abstract
Investigating the interplay of factors that result in a viral zoonotic outbreak is difficult, though it is increasingly important. As anthropogenic influences shift the delicate balance of ecosystems, new zoonoses emerge in humans. Sub-Saharan Africa is a notable hotspot for zoonotic disease due to abundant competent mammalian reservoir hosts. Furthermore, poverty, corruption, and an overreliance on natural resources play considerable roles in depleting biological resources, exacerbating the population's susceptibility. Unsurprisingly, viral zoonoses have emerged in Africa, including HIV/AIDS, Ebola, Avian influenza, Lassa fever, Zika, and Monkeypox. These diseases are among the principal causes of death in endemic areas. Though typically distinct in their manifestations, viral zoonoses are connected by underlying, definitive factors. This review summarises vital findings on viral zoonoses in Africa using nine notable case studies as a benchmark for future studies. We discuss the importance of ecological recuperation and protection as a central strategy to control zoonotic diseases. Emphasis was made on moderating key drivers of zoonotic diseases to forestall future pandemics. This is in conjunction with attempts to redirect efforts from reactive to pre-emptive through a multidisciplinary "one health" approach.
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Affiliation(s)
- P O Isibor
- Covenant University, Department of Biological Sciences, Ota, Ogun State, Nigeria
| | - O O Onwaeze
- Covenant University, Department of Biological Sciences, Ota, Ogun State, Nigeria
| | - I I Kayode-Edwards
- Covenant University, Department of Biological Sciences, Ota, Ogun State, Nigeria
| | - D O Agbontaen
- University of South Wales, Department of Public Health, Pontypridd, United Kingdom
| | - I-A M Ifebem-Ezima
- Covenant University, Department of Biological Sciences, Ota, Ogun State, Nigeria
| | - O Bilewu
- Covenant University, Department of Biological Sciences, Ota, Ogun State, Nigeria
| | - C Onuselogu
- Covenant University, Department of Biological Sciences, Ota, Ogun State, Nigeria
| | - A P Akinniyi
- Covenant University, Department of Biological Sciences, Ota, Ogun State, Nigeria
| | - Y D Obafemi
- Covenant University, Department of Biological Sciences, Ota, Ogun State, Nigeria
| | - M I Oniha
- Covenant University, Department of Biological Sciences, Ota, Ogun State, Nigeria
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15
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Akash S, Baeza J, Mahmood S, Mukerjee N, Subramaniyan V, Islam MR, Gupta G, Rajakumari V, Chinni SV, Ramachawolran G, Saleh FM, Albadrani GM, Sayed AA, Abdel-Daim MM. Development of a new drug candidate for the inhibition of Lassa virus glycoprotein and nucleoprotein by modification of evodiamine as promising therapeutic agents. Front Microbiol 2023; 14:1206872. [PMID: 37497547 PMCID: PMC10366616 DOI: 10.3389/fmicb.2023.1206872] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 06/15/2023] [Indexed: 07/28/2023] Open
Abstract
The Lassa virus (LASV), an RNA virus prevalent in West and Central Africa, causes severe hemorrhagic fever with a high fatality rate. However, no FDA-approved treatments or vaccines exist. Two crucial proteins, LASV glycoprotein and nucleoprotein, play vital roles in pathogenesis and are potential therapeutic targets. As effective treatments for many emerging infections remain elusive, cutting-edge drug development approaches are essential, such as identifying molecular targets, screening lead molecules, and repurposing existing drugs. Bioinformatics and computational biology expedite drug discovery pipelines, using data science to identify targets, predict structures, and model interactions. These techniques also facilitate screening leads with optimal drug-like properties, reducing time, cost, and complexities associated with traditional drug development. Researchers have employed advanced computational drug design methods such as molecular docking, pharmacokinetics, drug-likeness, and molecular dynamics simulation to investigate evodiamine derivatives as potential LASV inhibitors. The results revealed remarkable binding affinities, with many outperforming standard compounds. Additionally, molecular active simulation data suggest stability when bound to target receptors. These promising findings indicate that evodiamine derivatives may offer superior pharmacokinetics and drug-likeness properties, serving as a valuable resource for professionals developing synthetic drugs to combat the Lassa virus.
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Affiliation(s)
- Shopnil Akash
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International, University, Dhaka, Bangladesh
| | - Javiera Baeza
- Center for Bioinformatics and Molecular Simulation, Universidad de Talca, Talca, Chile
- Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Universidad de Chile, Santiago, Chile
| | - Sajjat Mahmood
- Department of Microbiology, Jagannath University, Dhaka, Bangladesh
| | - Nobendu Mukerjee
- Department of Microbiology, West Bengal State University, West Bengal, Kolkata, India
- Department of Health Sciences, Novel Global Community Educational Foundation, Hebersham, NSW, Australia
| | - Vetriselvan Subramaniyan
- Pharmacology Unit, Jeffrey Cheah School of Medicine and Health Sciences, MONASH University, Jalan Lagoon Selatan, Bandar Sunway, Selangor, Malaysia
- Center for Transdisciplinary Research, Department of Pharmacology, Saveetha Institute of Medical and Technical Sciences, Saveetha Dental College and Hospital, Saveetha University, Chennai, Tamil Nadu, India
| | - Md. Rezaul Islam
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International, University, Dhaka, Bangladesh
| | - Gaurav Gupta
- School of Pharmacy, Suresh Gyan Vihar University, Jagatpura, Jaipur, India
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India
| | | | - Suresh V. Chinni
- Department of Biochemistry, Faculty of Medicine, Bioscience, and Nursing, MAHSA University, Selangor, Malaysia
- Department of Periodontics, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
| | | | - Fayez M. Saleh
- Department of Medical Microbiology, Faculty of Medicine, University of Tabuk, Tabuk, Saudi Arabia
| | - Ghadeer M. Albadrani
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Amany A. Sayed
- Department of Zoology, Faculty of Science, Cairo University, Giza, Egypt
| | - Mohamed M. Abdel-Daim
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, Jeddah, Saudi Arabia
- Department of Pharmacology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
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16
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Perrett HR, Brouwer PJM, Hurtado J, Newby ML, Liu L, Müller-Kräuter H, Müller Aguirre S, Burger JA, Bouhuijs JH, Gibson G, Messmer T, Schieffelin JS, Antanasijevic A, Boons GJ, Strecker T, Crispin M, Sanders RW, Briney B, Ward AB. Structural conservation of Lassa virus glycoproteins and recognition by neutralizing antibodies. Cell Rep 2023; 42:112524. [PMID: 37209096 PMCID: PMC10242449 DOI: 10.1016/j.celrep.2023.112524] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 03/07/2023] [Accepted: 05/01/2023] [Indexed: 05/22/2023] Open
Abstract
Lassa fever is an acute hemorrhagic fever caused by the zoonotic Lassa virus (LASV). The LASV glycoprotein complex (GPC) mediates viral entry and is the sole target for neutralizing antibodies. Immunogen design is complicated by the metastable nature of recombinant GPCs and the antigenic differences among phylogenetically distinct LASV lineages. Despite the sequence diversity of the GPC, structures of most lineages are lacking. We present the development and characterization of prefusion-stabilized, trimeric GPCs of LASV lineages II, V, and VII, revealing structural conservation despite sequence diversity. High-resolution structures and biophysical characterization of the GPC in complex with GP1-A-specific antibodies suggest their neutralization mechanisms. Finally, we present the isolation and characterization of a trimer-preferring neutralizing antibody belonging to the GPC-B competition group with an epitope that spans adjacent protomers and includes the fusion peptide. Our work provides molecular detail information on LASV antigenic diversity and will guide efforts to design pan-LASV vaccines.
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Affiliation(s)
- Hailee R Perrett
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Philip J M Brouwer
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jonathan Hurtado
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA; Center for Viral Systems Biology, Scripps Research, La Jolla, CA 92037, USA
| | - Maddy L Newby
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Lin Liu
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | | | | | - Judith A Burger
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers. Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, Amsterdam 1105 AZ, the Netherlands
| | - Joey H Bouhuijs
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers. Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, Amsterdam 1105 AZ, the Netherlands
| | - Grace Gibson
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Terrence Messmer
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA
| | - John S Schieffelin
- Department of Pediatrics, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Aleksandar Antanasijevic
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Geert-Jan Boons
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA; Department of Chemical Biology and Drug Discovery, Utrecht University, Utrecht 3584 CG, the Netherlands
| | - Thomas Strecker
- Institute of Virology, Philipps University Marburg, 35043 Marburg, Germany
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Rogier W Sanders
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers. Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, Amsterdam 1105 AZ, the Netherlands; Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Bryan Briney
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA; Center for Viral Systems Biology, Scripps Research, La Jolla, CA 92037, USA
| | - Andrew B Ward
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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17
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Grant DS, Samuels RJ, Garry RF, Schieffelin JS. Lassa Fever Natural History and Clinical Management. Curr Top Microbiol Immunol 2023. [PMID: 37106159 DOI: 10.1007/82_2023_263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Lassa fever is caused by Lassa virus (LASV), an Old World Mammarenavirus that is carried by Mastomys natalensis and other rodents. It is endemic in Sierra Leone, Nigeria, and other countries in West Africa. The clinical presentation of LASV infection is heterogenous varying from an inapparent or mild illness to a fatal hemorrhagic fever. Exposure to LASV is usually through contact with rodent excreta. After an incubation period of 1-3 weeks, initial symptoms such as fever, headache, and fatigue develop that may progress to sore throat, retrosternal chest pain, conjunctival injection, vomiting, diarrhea, and abdominal pain. Severe illness, including hypotension, shock, and multiorgan failure, develops in a minority of patients. Patient demographics and case fatality rates are distinctly different in Sierra Leone and Nigeria. Laboratory diagnosis relies on the detection of LASV antigens or genomic RNA. LASV-specific immunoglobulin G and M assays can also contribute to clinical management. The mainstay of treatment for Lassa fever is supportive care. The nucleoside analog ribavirin is commonly used to treat acute Lassa fever but is considered useful only if treatment is begun early in the disease course. Drugs in development, including a monoclonal antibody cocktail, have the potential to impact the management of Lassa fever.
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Affiliation(s)
- Donald S Grant
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health, Kenema, Sierra Leone
- College of Medicine and Allied Health Sciences (COMAHS), University of Sierra Leone, Freetown, Sierra Leone
| | - Robert J Samuels
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health, Kenema, Sierra Leone
| | - Robert F Garry
- School of Medicine, Department of Microbiology and Immunology, Tulane University, New Orleans, LA, 70112, USA
- Zalgen Labs, Frederick, MD, 21703, USA
- Global Virus Network (GVN), Baltimore, MD, 21201, USA
| | - John S Schieffelin
- School of Medicine, Department of Pediatrics, Tulane University, New Orleans, LA, 70112, USA.
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18
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Garry RF. Lassa Virus Structural Biology and Replication. Curr Top Microbiol Immunol 2023. [PMID: 37100973 DOI: 10.1007/82_2023_262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Lassa virus (LASV) is the causative agent of Lassa fever, an often-fatal hemorrhagic fever that is endemic in West Africa. LASV virions are enveloped and contain two single-stranded RNA genome segments. Both segments are ambisense and encode two proteins. The nucleoprotein associates with viral RNAs forming ribonucleoprotein complexes. The glycoprotein complex mediates viral attachment and entry. The Zinc protein serves as the matrix protein. Large is a polymerase that catalyzes viral RNA transcription and replication. LASV virion entry occurs via a clathrin-independent endocytic pathway usually involving alpha-dystroglycan and lysosomal associated membrane protein 1 as surface and intracellular receptors, respectively. Advances in understanding LASV structural biology and replication have facilitated development of promising vaccine and drug candidates.
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Affiliation(s)
- Robert F Garry
- School of Medicine, Department of Microbiology and Immunology, Tulane University, New Orleans, LA, 70112, USA.
- Zalgen Labs, Frederick, MD, 21703, USA.
- Global Virus Network (GVN), Baltimore, MD, 21201, USA.
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19
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Terbot JW, Johri P, Liphardt SW, Soni V, Pfeifer SP, Cooper BS, Good JM, Jensen JD. Developing an appropriate evolutionary baseline model for the study of SARS-CoV-2 patient samples. PLoS Pathog 2023; 19:e1011265. [PMID: 37018331 PMCID: PMC10075409 DOI: 10.1371/journal.ppat.1011265] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023] Open
Abstract
Over the past 3 years, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has spread through human populations in several waves, resulting in a global health crisis. In response, genomic surveillance efforts have proliferated in the hopes of tracking and anticipating the evolution of this virus, resulting in millions of patient isolates now being available in public databases. Yet, while there is a tremendous focus on identifying newly emerging adaptive viral variants, this quantification is far from trivial. Specifically, multiple co-occurring and interacting evolutionary processes are constantly in operation and must be jointly considered and modeled in order to perform accurate inference. We here outline critical individual components of such an evolutionary baseline model-mutation rates, recombination rates, the distribution of fitness effects, infection dynamics, and compartmentalization-and describe the current state of knowledge pertaining to the related parameters of each in SARS-CoV-2. We close with a series of recommendations for future clinical sampling, model construction, and statistical analysis.
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Affiliation(s)
- John W Terbot
- University of Montana, Division of Biological Sciences, Missoula, Montana, United States of America
- Arizona State University, School of Life Sciences, Center for Evolution & Medicine, Tempe, Arizona, United States of America
| | - Parul Johri
- Arizona State University, School of Life Sciences, Center for Evolution & Medicine, Tempe, Arizona, United States of America
| | - Schuyler W Liphardt
- University of Montana, Division of Biological Sciences, Missoula, Montana, United States of America
| | - Vivak Soni
- Arizona State University, School of Life Sciences, Center for Evolution & Medicine, Tempe, Arizona, United States of America
| | - Susanne P Pfeifer
- Arizona State University, School of Life Sciences, Center for Evolution & Medicine, Tempe, Arizona, United States of America
| | - Brandon S Cooper
- University of Montana, Division of Biological Sciences, Missoula, Montana, United States of America
| | - Jeffrey M Good
- University of Montana, Division of Biological Sciences, Missoula, Montana, United States of America
| | - Jeffrey D Jensen
- Arizona State University, School of Life Sciences, Center for Evolution & Medicine, Tempe, Arizona, United States of America
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20
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Okokhere PO. Finding a safe and effective vaccine for the Lassa virus. Lancet 2023; 401:1242-1243. [PMID: 36934735 DOI: 10.1016/s0140-6736(23)00093-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 01/10/2023] [Indexed: 03/18/2023]
Affiliation(s)
- Peter O Okokhere
- Department of Medicine, Irrua Specialist Teaching Hospital, Irrua, Nigeria; Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma 310103, Nigeria.
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21
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Cuypers LN, Gryseels S, Van Houtte N, Baird SJE, Sabuni CA, Katakweba AS, van den Burg SRM, Bryja J, Leirs H, Goüy de Bellocq J. Subspecific rodent taxa as the relevant host taxonomic level for mammarenavirus host specificity. Virology 2023; 581:116-127. [PMID: 36958216 DOI: 10.1016/j.virol.2023.02.014] [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: 12/22/2022] [Revised: 02/19/2023] [Accepted: 02/23/2023] [Indexed: 03/10/2023]
Abstract
Mastomys natalensis-borne mammarenaviruses appear specific to subspecific M. natalensis taxa rather than to the whole species. Yet mammarenaviruses carried by M. natalensis are known to spill over and jump hosts in northern sub-Saharan Africa. Phylogeographic studies increasingly show that, like M. natalensis, small mammals in sub-Saharan Africa are often genetically structured into several subspecific taxa. Other mammarenaviruses may thus also form virus-subspecific host taxon associations. To investigate this, and if mammarenaviruses carried by M. natalensis in southern Africa are less prone to spill-over, we screened 1225 non-M. natalensis samples from Tanzania where many small mammal taxa meet. We found mammarenavirus RNA in 6 samples. Genetic/genomic characterisation confirmed they were not spill-over from M. natalensis. We detected host jumps among rodent tribe members and an association between mammarenaviruses and subspecific taxa of Mus minutoides and Grammomys surdaster, indicating host genetic structure may be crucial to understand virus distribution and host specificity.
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Affiliation(s)
- Laura N Cuypers
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium.
| | - Sophie Gryseels
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium; OD Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Vautierstraat 29, 1000, Brussels, Belgium
| | - Natalie Van Houtte
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium
| | - Stuart J E Baird
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Květná 8, 603 65, Brno, Czech Republic
| | - Christopher A Sabuni
- Institute of Pest Management, Sokoine University of Agriculture, P.O. Box 3110 Chuo Kikuu, Morogoro, Tanzania
| | - Abdul S Katakweba
- Institute of Pest Management, Sokoine University of Agriculture, P.O. Box 3110 Chuo Kikuu, Morogoro, Tanzania
| | - Sebastiaan R M van den Burg
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium
| | - Josef Bryja
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Květná 8, 603 65, Brno, Czech Republic; Department of Botany and Zoology, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - Herwig Leirs
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium
| | - Joëlle Goüy de Bellocq
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Květná 8, 603 65, Brno, Czech Republic
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22
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Whitlock AOB, Bird BH, Ghersi B, Davison AJ, Hughes J, Nichols J, Vučak M, Amara E, Bangura J, Lavalie EG, Kanu MC, Kanu OT, Sjodin A, Remien CH, Nuismer SL. Identifying the genetic basis of viral spillover using Lassa virus as a test case. R Soc Open Sci 2023; 10:221503. [PMID: 36968239 PMCID: PMC10031424 DOI: 10.1098/rsos.221503] [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] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 02/27/2023] [Indexed: 06/18/2023]
Abstract
The rate at which zoonotic viruses spill over into the human population varies significantly over space and time. Remarkably, we do not yet know how much of this variation is attributable to genetic variation within viral populations. This gap in understanding arises because we lack methods of genetic analysis that can be easily applied to zoonotic viruses, where the number of available viral sequences is often limited, and opportunistic sampling introduces significant population stratification. Here, we explore the feasibility of using patterns of shared ancestry to correct for population stratification, enabling genome-wide association methods to identify genetic substitutions associated with spillover into the human population. Using a combination of phylogenetically structured simulations and Lassa virus sequences collected from humans and rodents in Sierra Leone, we demonstrate that existing methods do not fully correct for stratification, leading to elevated error rates. We also demonstrate, however, that the Type I error rate can be substantially reduced by confining the analysis to a less-stratified region of the phylogeny, even in an already-small dataset. Using this method, we detect two candidate single-nucleotide polymorphisms associated with spillover in the Lassa virus polymerase gene and provide generalized recommendations for the collection and analysis of zoonotic viruses.
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Affiliation(s)
| | - Brian H. Bird
- One Health Institute, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Bruno Ghersi
- One Health Institute, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | | | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Jenna Nichols
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Matej Vučak
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Emmanuel Amara
- University of Makeni and University of California, Davis One Health Program, Makeni, Sierra Leone
| | - James Bangura
- University of Makeni and University of California, Davis One Health Program, Makeni, Sierra Leone
| | - Edwin G. Lavalie
- University of Makeni and University of California, Davis One Health Program, Makeni, Sierra Leone
| | - Marilyn C. Kanu
- University of Makeni and University of California, Davis One Health Program, Makeni, Sierra Leone
| | - Osman T. Kanu
- University of Makeni and University of California, Davis One Health Program, Makeni, Sierra Leone
| | - Anna Sjodin
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Christopher H. Remien
- Department of Mathematics and Statistical Science, University of Idaho, Moscow, ID, USA
| | - Scott L. Nuismer
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
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23
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Grant DS, Engel EJ, Roberts Yerkes N, Kanneh L, Koninga J, Gbakie MA, Alhasan F, Kanneh FB, Kanneh IM, Kamara FK, Momoh M, Yillah MS, Foday M, Okoli A, Zeoli A, Weldon C, Bishop CM, Zheng C, Hartnett J, Chao K, Shore K, Melnik LI, Mucci M, Bond NG, Doyle P, Yenni R, Podgorski R, Ficenec SC, Moses L, Shaffer JG, Garry RF, Schieffelin JS. Seroprevalence of anti-Lassa Virus IgG antibodies in three districts of Sierra Leone: A cross-sectional, population-based study. PLoS Negl Trop Dis 2023; 17:e0010938. [PMID: 36758101 PMCID: PMC9946222 DOI: 10.1371/journal.pntd.0010938] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 02/22/2023] [Accepted: 11/09/2022] [Indexed: 02/11/2023] Open
Abstract
BACKGROUND Lassa virus (LASV), the cause of the acute viral hemorrhagic illness Lassa fever (LF), is endemic in West Africa. Infections in humans occur mainly after exposure to infected excrement or urine of the rodent-host, Mastomys natalensis. The prevalence of exposure to LASV in Sierra Leone is crudely estimated and largely unknown. This cross-sectional study aimed to establish a baseline point seroprevalence of IgG antibodies to LASV in three administrative districts of Sierra Leone and identify potential risk factors for seropositivity and LASV exposure. METHODOLOGY AND PRINCIPAL FINDINGS Between 2015 and 2018, over 10,642 participants from Kenema, Tonkolili, and Port Loko Districts were enrolled in this cross-sectional study. Previous LASV and LF epidemiological studies support classification of these districts as "endemic," "emerging," and "non-endemic", respectively. Dried blood spot samples were tested for LASV antibodies by ELISA to determine the seropositivity of participants, indicating previous exposure to LASV. Surveys were administered to each participant to assess demographic and environmental factors associated with a higher risk of exposure to LASV. Overall seroprevalence for antibodies to LASV was 16.0%. In Kenema, Port Loko, and Tonkolili Districts, seroprevalences were 20.1%, 14.1%, and 10.6%, respectively. In a multivariate analysis, individuals were more likely to be LASV seropositive if they were living in Kenema District, regardless of sex, age, or occupation. Environmental factors contributed to an increased risk of LASV exposure, including poor housing construction and proximity to bushland, forested areas, and refuse. CONCLUSIONS AND SIGNIFICANCE In this study we determine a baseline LASV seroprevalence in three districts which will inform future epidemiological, ecological, and clinical studies on LF and the LASV in Sierra Leone. The heterogeneity of the distribution of LASV and LF over both space, and time, can make the design of efficacy trials and intervention programs difficult. Having more studies on the prevalence of LASV and identifying potential hyper-endemic areas will greatly increase the awareness of LF and improve targeted control programs related to LASV.
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Affiliation(s)
- Donald S. Grant
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
- College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
| | - Emily J. Engel
- Department of Pediatrics, Sections of Pediatric Infectious Diseases, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Nicole Roberts Yerkes
- Department of Pediatrics, Sections of Pediatric Infectious Diseases, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Lansana Kanneh
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - James Koninga
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Michael A. Gbakie
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Foday Alhasan
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Franklyn B. Kanneh
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Ibrahim Mustapha Kanneh
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Fatima K. Kamara
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Mambu Momoh
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
- Eastern Technical University of Sierra Leone, Kenema, Sierra Leone
| | - Mohamed S. Yillah
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Momoh Foday
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Adaora Okoli
- Department of Tropical Medicine, Tulane University School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Ashley Zeoli
- Department of Pediatrics, Sections of Pediatric Infectious Diseases, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Caroline Weldon
- Department of Tropical Medicine, Tulane University School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Christopher M. Bishop
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Crystal Zheng
- Department of Internal Medicine, Section of Infectious Diseases, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Jessica Hartnett
- Department of Pediatrics, Sections of Pediatric Infectious Diseases, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Karissa Chao
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Kayla Shore
- Department of Tropical Medicine, Tulane University School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Lilia I. Melnik
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Mallory Mucci
- Department of Tropical Medicine, Tulane University School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Nell G. Bond
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Philip Doyle
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Rachael Yenni
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Rachel Podgorski
- Department of Tropical Medicine, Tulane University School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Samuel C. Ficenec
- Department of Internal Medicine, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Lina Moses
- Department of Tropical Medicine, Tulane University School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Jeffrey G. Shaffer
- Department of Biostatistics and Data Science, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana, United States of America
| | - Robert F. Garry
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - John S. Schieffelin
- Department of Pediatrics, Sections of Pediatric Infectious Diseases, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
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Gladden-young A. Diverse pathways toward a cure. iScience 2023. [PMID: 36994187 PMCID: PMC10040886 DOI: 10.1016/j.isci.2023.106052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023] Open
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25
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Abstract
Lassa virus (LASV) is endemic in the rodent populations of Sierra Leone, Nigeria and other countries in West Africa. Spillover to humans occurs frequently and results in Lassa fever, a viral haemorrhagic fever (VHF) associated with a high case fatality rate. Despite advances, fundamental gaps in knowledge of the immunology, epidemiology, ecology and pathogenesis of Lassa fever persist. More frequent outbreaks, the potential for further geographic expansion of Mastomys natalensis and other rodent reservoirs, the ease of procurement and possible use and weaponization of LASV, the frequent importation of LASV to North America and Europe, and the emergence of novel LASV strains in densely populated West Africa have driven new initiatives to develop countermeasures for LASV. Although promising candidates are being evaluated, as yet there are no approved vaccines or therapeutics for human use. This Review discusses the virology of LASV, the clinical course of Lassa fever and the progress towards developing medical countermeasures.
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Affiliation(s)
- Robert F Garry
- Department of Microbiology and Immunology, Tulane University, New Orleans, LA, USA.
- Zalgen Labs, Frederick, MD, USA.
- Global Viral Network, Baltimore, MD, USA.
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26
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Aloke C, Obasi NA, Aja PM, Emelike CU, Egwu CO, Jeje O, Edeogu CO, Onisuru OO, Orji OU, Achilonu I. Combating Lassa Fever in West African Sub-Region: Progress, Challenges, and Future Perspectives. Viruses 2023; 15:146. [PMID: 36680186 PMCID: PMC9864412 DOI: 10.3390/v15010146] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 12/28/2022] [Accepted: 12/28/2022] [Indexed: 01/05/2023] Open
Abstract
Lassa fever (LF) is a rodent-borne disease that threatens human health in the sub-region of West Africa where the zoonotic host of Lassa virus (LASV) is predominant. Currently, treatment options for LF are limited and since no preventive vaccine is approved for its infectivity, there is a high mortality rate in endemic areas. This narrative review explores the transmission, pathogenicity of LASV, advances, and challenges of different treatment options. Our findings indicate that genetic diversity among the different strains of LASV and their ability to circumvent the immune system poses a critical challenge to the development of LASV vaccines/therapeutics. Thus, understanding the biochemistry, physiology and genetic polymorphism of LASV, mechanism of evading host immunity are essential for development of effective LASV vaccines/therapeutics to combat this lethal viral disease. The LASV nucleoprotein (NP) is a novel target for therapeutics as it functions significantly in several aspects of the viral life cycle. Consequently, LASV NP inhibitors could be employed as effective therapeutics as they will potentially inhibit LASV replication. Effective preventive control measures, vaccine development, target validation, and repurposing of existing drugs, such as ribavirin, using activity or in silico-based and computational bioinformatics, would aid in the development of novel drugs for LF management.
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Affiliation(s)
- Chinyere Aloke
- Protein Structure-Function and Research Unit, School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Braamfontein, Johannesburg 2050, South Africa
- Department of Medical Biochemistry, Alex Ekwueme Federal University Ndufu-Alike, Abakaliki PMB 1010, Ebonyi State, Nigeria
| | - Nwogo Ajuka Obasi
- Department of Medical Biochemistry, Alex Ekwueme Federal University Ndufu-Alike, Abakaliki PMB 1010, Ebonyi State, Nigeria
| | - Patrick Maduabuchi Aja
- Department of Biochemistry, Faculty of Biological Sciences, Ebonyi State University, Abakaliki PMB 053, Ebonyi State, Nigeria
- Department of Biochemistry, Faculty of Medicine, Mbarara University of Science and Technology (MUST), Mbarara P.O. Box 1410, Uganda
- Department of Medical Biochemistry, Kampala International University, Bushenyi, Ishaka P.O. Box 71, Uganda
| | - Chinedum Uche Emelike
- Department of Physiology, Alex Ekwueme Federal University Ndufu-Alike, Abakaliki PMB 1010, Ebonyi State, Nigeria
| | - Chinedu Ogbonnia Egwu
- Department of Medical Biochemistry, Alex Ekwueme Federal University Ndufu-Alike, Abakaliki PMB 1010, Ebonyi State, Nigeria
| | - Olamide Jeje
- Protein Structure-Function and Research Unit, School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Braamfontein, Johannesburg 2050, South Africa
| | - Chuks Oswald Edeogu
- Department of Medical Biochemistry, Faculty of Basic Medical Sciences, Ebonyi State University, Abakaliki PMB 053, Ebonyi State, Nigeria
| | - Olalekan Olugbenga Onisuru
- Protein Structure-Function and Research Unit, School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Braamfontein, Johannesburg 2050, South Africa
| | - Obasi Uche Orji
- Department of Biochemistry, Faculty of Biological Sciences, Ebonyi State University, Abakaliki PMB 053, Ebonyi State, Nigeria
| | - Ikechukwu Achilonu
- Protein Structure-Function and Research Unit, School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Braamfontein, Johannesburg 2050, South Africa
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Sironi M, Forni D, de la Torre JC. Mammarenavirus Genetic Diversity and Its Biological Implications. Curr Top Microbiol Immunol 2023; 439:265-303. [PMID: 36592249 DOI: 10.1007/978-3-031-15640-3_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Members of the family Arenaviridae are classified into four genera: Antennavirus, Hartmanivirus, Mammarenavirus, and Reptarenavirus. Reptarenaviruses and hartmaniviruses infect (captive) snakes and have been shown to cause boid inclusion body disease (BIBD). Antennaviruses have genomes consisting of 3, rather than 2, segments, and were discovered in actinopterygian fish by next-generation sequencing but no biological isolate has been reported yet. The hosts of mammarenaviruses are mainly rodents and infections are generally asymptomatic. Current knowledge about the biology of reptarenaviruses, hartmaniviruses, and antennaviruses is very limited and their zoonotic potential is unknown. In contrast, some mammarenaviruses are associated with zoonotic events that pose a threat to human health. This review will focus on mammarenavirus genetic diversity and its biological implications. Some mammarenaviruses including lymphocytic choriomeningitis virus (LCMV) are excellent experimental model systems for the investigation of acute and persistent viral infections, whereas others including Lassa (LASV) and Junin (JUNV) viruses, the causative agents of Lassa fever (LF) and Argentine hemorrhagic fever (AHF), respectively, are important human pathogens. Mammarenaviruses were thought to have high degree of intra-and inter-species amino acid sequence identities, but recent evidence has revealed a high degree of mammarenavirus genetic diversity in the field. Moreover, closely related mammarenavirus can display dramatic phenotypic differences in vivo. These findings support a role of genetic variability in mammarenavirus adaptability and pathogenesis. Here, we will review the molecular biology of mammarenaviruses, phylogeny, and evolution, as well as the quasispecies dynamics of mammarenavirus populations and their biological implications.
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28
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Abstract
Individuals living in endemic hotspots of Lassa fever have recurrent exposure to Lassa virus (LASV) via spillover from the primary host reservoir Mastomys natalensis. Despite M. natalensis being broadly distributed across sub-Saharan Africa, Lassa fever is only found in West Africa. In recent years, new LASV reservoirs have been identified. Erudition of rodent habitats, reproduction and fecundity, movement patterns, and spatial preferences are essential to institute preventative measures against Lassa fever. Evolutionary insights have also added to our knowledge of closely related mammarenavirus distribution amongst rodents throughout the continent.
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Affiliation(s)
- Allison R Smither
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA, USA.
| | - Antoinette R Bell-Kareem
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA, USA
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29
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Li Q, Huang W, Wang Y. Pseudotyped Viruses for Mammarenavirus. Adv Exp Med Biol 2023; 1407:279-97. [PMID: 36920703 DOI: 10.1007/978-981-99-0113-5_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Mammarenaviruses are classified into New World arenaviruses (NW) and Old World arenaviruses (OW). The OW arenaviruses include the first discovered mammarenavirus-lymphocytic choriomeningitis virus (LCMV) and the highly lethal Lassa virus (LASV). Mammarenaviruses are transmitted to human by rodents, resulting in severe acute infections and hemorrhagic fever. Pseudotyped viruses have been widely used as a tool in the study of mammarenaviruses. HIV-1, SIV, FIV-based lentiviral vectors, VSV-based vectors, MLV-based vectors, and reverse genetic approaches have been applied in the construction of pseudotyped mammarenaviruses. Pseudotyped mammarenaviruses are commonly used in receptor research, neutralizing antibody detection, inhibitor screening, viral virulence studies, functional analysis of N-linked glycans, and studies of viral infection, endocytosis, and fusion mechanisms.
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30
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Ugwu C, Olumade T, Nwakpakpa E, Onyia V, Odeh E, Duruiheoma RO, Ojide CK, Eke MA, Nwafor IE, Chika-Igwenyi N, Abu AM, Azuogu B, Ajayi N, Ogah E, Ayodeji O, Abejegah C, Adedosu N, Oyejide N, Abah S, Omidele A, Ingbian W, Osoba E, Eromon P, Oluniyi P, Ogunsanya O, Happi A, Otuh P, Nadesalingam A, Carnell G, Krause N, Aguinam E, Kinsley R, Storisteanu DML, Tonks P, Nelson D, McAlister C, Boisen M, Garry R, Wright E, Temperton N, Frost S, Heeney JL, Happi C. Humoral and cellular immune responses to Lassa fever virus in Lassa fever survivors and their exposed contacts in Southern Nigeria. Sci Rep 2022; 12:22330. [PMID: 36567369 DOI: 10.1038/s41598-022-26045-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 12/08/2022] [Indexed: 12/26/2022] Open
Abstract
Elucidating the adaptive immune characteristics of natural protection to Lassa fever (LF) is vital in designing and selecting optimal vaccine candidates. With rejuvenated interest in LF and a call for accelerated research on the Lassa virus (LASV) vaccine, there is a need to define the correlates of natural protective immune responses to LF. Here, we describe cellular and antibody immune responses present in survivors of LF (N = 370) and their exposed contacts (N = 170) in a LASV endemic region in Nigeria. Interestingly, our data showed comparable T cell and binding antibody responses from both survivors and their contacts, while neutralizing antibody responses were primarily seen in the LF survivors and not their contacts. Neutralizing antibody responses were found to be cross-reactive against all five lineages of LASV with a strong bias to Lineage II, the prevalent strain in southern Nigeria. We demonstrated that both T cell and antibody responses were not detectable in peripheral blood after a decade in LF survivors. Notably LF survivors maintained high levels of detectable binding antibody response for six months while their contacts did not. Lastly, as potential vaccine targets, we identified the regions of the LASV Glycoprotein (GP) and Nucleoprotein (NP) that induced the broadest peptide-specific T cell responses. Taken together this data informs immunological readouts and potential benchmarks for clinical trials evaluating LASV vaccine candidates.
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31
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Brouwer PJ, Antanasijevic A, Ronk AJ, Müller-Kräuter H, Watanabe Y, Claireaux M, Perrett HR, Bijl TP, Grobben M, Umotoy JC, Schriek AI, Burger JA, Tejjani K, Lloyd NM, Steijaert TH, van Haaren MM, Sliepen K, de Taeye SW, van Gils MJ, Crispin M, Strecker T, Bukreyev A, Ward AB, Sanders RW. Lassa virus glycoprotein nanoparticles elicit neutralizing antibody responses and protection. Cell Host Microbe 2022; 30:1759-1772.e12. [PMID: 36400021 PMCID: PMC9794196 DOI: 10.1016/j.chom.2022.10.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 09/07/2022] [Accepted: 10/25/2022] [Indexed: 11/18/2022]
Abstract
The Lassa virus is endemic in parts of West Africa, and it causes hemorrhagic fever with high mortality. The development of a recombinant protein vaccine has been hampered by the instability of soluble Lassa virus glycoprotein complex (GPC) trimers, which disassemble into monomeric subunits after expression. Here, we use two-component protein nanoparticles consisting of trimeric and pentameric subunits to stabilize GPC in a trimeric conformation. These GPC nanoparticles present twenty prefusion GPC trimers on the surface of an icosahedral particle. Cryo-EM studies of GPC nanoparticles demonstrated a well-ordered structure and yielded a high-resolution structure of an unliganded GPC. These nanoparticles induced potent humoral immune responses in rabbits and protective immunity against the lethal Lassa virus challenge in guinea pigs. Additionally, we isolated a neutralizing antibody that mapped to the putative receptor-binding site, revealing a previously undefined site of vulnerability. Collectively, these findings offer potential approaches to vaccine and therapeutic design for the Lassa virus.
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Affiliation(s)
- Philip J.M. Brouwer
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands,Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Aleksandar Antanasijevic
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Adam J. Ronk
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77550, USA,Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77550, USA
| | | | - Yasunori Watanabe
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Mathieu Claireaux
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Hailee R. Perrett
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tom P.L. Bijl
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Marloes Grobben
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Jeffrey C. Umotoy
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Angela I. Schriek
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Judith A. Burger
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Khadija Tejjani
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Nicole M. Lloyd
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77550, USA,Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77550, USA
| | - Thijs H. Steijaert
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Marlies M. van Haaren
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Kwinten Sliepen
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Steven W. de Taeye
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Marit J. van Gils
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Thomas Strecker
- Institute of Virology, Philipps University Marburg, 35043 Marburg, Germany
| | - Alexander Bukreyev
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77550, USA,Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77550, USA
| | - Andrew B. Ward
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA,Corresponding author
| | - Rogier W. Sanders
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands,Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA,Corresponding author
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32
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Li H, Buck T, Zandonatti M, Yin J, Moon-Walker A, Fang J, Koval A, Heinrich ML, Rowland MM, Avalos RD, Schendel SL, Parekh D, Zyla D, Enriquez A, Harkins S, Sullivan B, Smith V, Chukwudozie O, Watanabe R, Robinson JE, Garry RF, Branco LM, Hastie KM, Saphire EO. A cocktail of protective antibodies subverts the dense glycan shield of Lassa virus. Sci Transl Med 2022; 14:eabq0991. [PMID: 36288283 PMCID: PMC10084740 DOI: 10.1126/scitranslmed.abq0991] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Developing potent therapeutics and effective vaccines are the ultimate goals in controlling infectious diseases. Lassa virus (LASV), the causative pathogen of Lassa fever (LF), infects hundreds of thousands annually, but effective antivirals or vaccines against LASV infection are still lacking. Furthermore, neutralizing antibodies against LASV are rare. Here, we describe biochemical analyses and high-resolution cryo-electron microscopy structures of a therapeutic cocktail of three broadly protective antibodies that target the LASV glycoprotein complex (GPC), previously identified from survivors of multiple LASV infections. Structural and mechanistic analyses reveal compatible neutralizing epitopes and complementary neutralization mechanisms that offer high potency, broad range, and resistance to escape. These antibodies either circumvent or exploit specific glycans comprising the extensive glycan shield of GPC. Further, they require mammalian glycosylation, native GPC cleavage, and proper GPC trimerization. These findings guided engineering of a next-generation GPC antigen suitable for future neutralizing antibody and vaccine discovery. Together, these results explain protective mechanisms of rare, broad, and potent antibodies and identify a strategy for the rational design of therapeutic modalities against LF and related infectious diseases.
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Affiliation(s)
- Haoyang Li
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle La Jolla, CA 92037 USA
| | - Tierra Buck
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle La Jolla, CA 92037 USA
| | - Michelle Zandonatti
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle La Jolla, CA 92037 USA
| | - Jieyun Yin
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle La Jolla, CA 92037 USA
| | - Alex Moon-Walker
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle La Jolla, CA 92037 USA
| | - Jingru Fang
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle La Jolla, CA 92037 USA
| | - Anatoliy Koval
- Zalgen Labs LLC, 7495 New Horizon Way, Suite 120, Frederick, MD 21703 USA
| | - Megan L. Heinrich
- Zalgen Labs LLC, 7495 New Horizon Way, Suite 120, Frederick, MD 21703 USA
| | - Megan M. Rowland
- Zalgen Labs LLC, 7495 New Horizon Way, Suite 120, Frederick, MD 21703 USA
| | - Ruben Diaz Avalos
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle La Jolla, CA 92037 USA
| | - Sharon L. Schendel
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle La Jolla, CA 92037 USA
| | - Diptiben Parekh
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle La Jolla, CA 92037 USA
| | - Dawid Zyla
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle La Jolla, CA 92037 USA
| | - Adrian Enriquez
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle La Jolla, CA 92037 USA
| | - Stephanie Harkins
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle La Jolla, CA 92037 USA
| | - Brian Sullivan
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle La Jolla, CA 92037 USA
| | - Victoria Smith
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle La Jolla, CA 92037 USA
- Department of Medicine, University of California San Diego, La Jolla, CA 92037 USA
| | - Onyeka Chukwudozie
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle La Jolla, CA 92037 USA
- Department of Medicine, University of California San Diego, La Jolla, CA 92037 USA
| | - Reika Watanabe
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle La Jolla, CA 92037 USA
| | - James E. Robinson
- Department of Microbiology and Immunology, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, LA 70118 USA
| | - Robert F. Garry
- Zalgen Labs LLC, 7495 New Horizon Way, Suite 120, Frederick, MD 21703 USA
- Department of Microbiology and Immunology, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, LA 70118 USA
| | - Luis M. Branco
- Zalgen Labs LLC, 7495 New Horizon Way, Suite 120, Frederick, MD 21703 USA
| | - Kathryn M. Hastie
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle La Jolla, CA 92037 USA
| | - Erica Ollmann Saphire
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle La Jolla, CA 92037 USA
- Department of Medicine, University of California San Diego, La Jolla, CA 92037 USA
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33
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Klitting R, Kafetzopoulou LE, Thiery W, Dudas G, Gryseels S, Kotamarthi A, Vrancken B, Gangavarapu K, Momoh M, Sandi JD, Goba A, Alhasan F, Grant DS, Okogbenin S, Ogbaini-Emovo E, Garry RF, Smither AR, Zeller M, Pauthner MG, McGraw M, Hughes LD, Duraffour S, Günther S, Suchard MA, Lemey P, Andersen KG, Dellicour S. Predicting the evolution of the Lassa virus endemic area and population at risk over the next decades. Nat Commun 2022; 13:5596. [PMID: 36167835 PMCID: PMC9515147 DOI: 10.1038/s41467-022-33112-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [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] [Received: 09/30/2021] [Accepted: 09/02/2022] [Indexed: 01/27/2023] Open
Abstract
Lassa fever is a severe viral hemorrhagic fever caused by a zoonotic virus that repeatedly spills over to humans from its rodent reservoirs. It is currently not known how climate and land use changes could affect the endemic area of this virus, currently limited to parts of West Africa. By exploring the environmental data associated with virus occurrence using ecological niche modelling, we show how temperature, precipitation and the presence of pastures determine ecological suitability for virus circulation. Based on projections of climate, land use, and population changes, we find that regions in Central and East Africa will likely become suitable for Lassa virus over the next decades and estimate that the total population living in ecological conditions that are suitable for Lassa virus circulation may drastically increase by 2070. By analysing geotagged viral genomes using spatially-explicit phylogeography and simulating virus dispersal, we find that in the event of Lassa virus being introduced into a new suitable region, its spread might remain spatially limited over the first decades.
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Affiliation(s)
- Raphaëlle Klitting
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
| | - Liana E. Kafetzopoulou
- grid.5596.f0000 0001 0668 7884Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven - University of Leuven, Leuven, Belgium ,grid.424065.10000 0001 0701 3136Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Wim Thiery
- grid.8767.e0000 0001 2290 8069Department of Hydrology and Hydraulic Engineering, Vrije Universiteit Brussel, Brussels, Belgium
| | - Gytis Dudas
- grid.6441.70000 0001 2243 2806Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Sophie Gryseels
- grid.5284.b0000 0001 0790 3681Evolutionary Ecology group, Department of Biology, University of Antwerp, 2610 Antwerp, Belgium ,grid.20478.390000 0001 2171 9581Vertebrate group, Directorate Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, 1000 Brussels, Belgium
| | - Anjali Kotamarthi
- grid.214007.00000000122199231Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Bram Vrancken
- grid.5596.f0000 0001 0668 7884Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven - University of Leuven, Leuven, Belgium
| | - Karthik Gangavarapu
- grid.214007.00000000122199231Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Mambu Momoh
- grid.442296.f0000 0001 2290 9707Eastern Technical University of Sierra Leone, Kenema, Sierra Leone ,grid.463455.50000 0004 1799 2069Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - John Demby Sandi
- grid.463455.50000 0004 1799 2069Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Augustine Goba
- grid.463455.50000 0004 1799 2069Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Foday Alhasan
- grid.463455.50000 0004 1799 2069Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Donald S. Grant
- grid.463455.50000 0004 1799 2069Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone ,grid.442296.f0000 0001 2290 9707College of Medicine and Allied Health Sciences, University of Sierra Leone, Kenema, Sierra Leone
| | - Sylvanus Okogbenin
- grid.508091.5Irrua Specialist Teaching Hospital, Irrua, Nigeria ,grid.411357.50000 0000 9018 355XFaculty of Clinical Sciences, College of Medicine, Ambrose Alli University, Ekpoma, Nigeria
| | | | - Robert F. Garry
- grid.265219.b0000 0001 2217 8588Department of Microbiology and Immunology, Tulane University, School of Medicine, New Orleans, LA 70112 USA ,grid.505518.c0000 0004 5901 1919Zalgen Labs, LCC, Frederick, MD 21703 USA ,grid.475149.aGlobal Virus Network (GVN), Baltimore, MD 21201 USA
| | - Allison R. Smither
- grid.265219.b0000 0001 2217 8588Department of Microbiology and Immunology, Tulane University, School of Medicine, New Orleans, LA 70112 USA
| | - Mark Zeller
- grid.214007.00000000122199231Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Matthias G. Pauthner
- grid.214007.00000000122199231Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Michelle McGraw
- grid.214007.00000000122199231Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Laura D. Hughes
- grid.214007.00000000122199231Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Sophie Duraffour
- grid.424065.10000 0001 0701 3136Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany ,grid.452463.2German Center for Infection Research (DZIF), Partner site Hamburg–Lübeck–Borstel–Riems, Hamburg, Germany
| | - Stephan Günther
- grid.424065.10000 0001 0701 3136Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany ,grid.452463.2German Center for Infection Research (DZIF), Partner site Hamburg–Lübeck–Borstel–Riems, Hamburg, Germany
| | - Marc A. Suchard
- grid.19006.3e0000 0000 9632 6718Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA USA
| | - Philippe Lemey
- grid.5596.f0000 0001 0668 7884Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven - University of Leuven, Leuven, Belgium
| | - Kristian G. Andersen
- grid.214007.00000000122199231Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037 USA ,grid.214007.00000000122199231Scripps Research Translational Institute, La Jolla, CA 92037 USA
| | - Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven - University of Leuven, Leuven, Belgium. .,Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, CP160/12 50, av. FD Roosevelt, 1050, Bruxelles, Belgium.
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34
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Xu ZY, Gao H, Kuang QY, Xing JB, Wang ZY, Cao XY, Xu SJ, Liu J, Huang Z, Zheng ZZ, Gong L, Wang H, Shi M, Zhang GH, Sun YK. Clinical sequencing uncovers the genomic characteristics and mutation spectrum of the 2018 African swine fever virus in Guangdong, China. Front Vet Sci 2022; 9:978243. [PMID: 36061106 PMCID: PMC9437553 DOI: 10.3389/fvets.2022.978243] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 06/25/2022] [Accepted: 08/02/2022] [Indexed: 11/24/2022] Open
Abstract
African swine fever (ASF) outbreak have caused tremendous economic loss to the pig industry in China since its emergence in August 2018. Previous studies revealed that many published sequences are not suitable for detailed analyses due to the lack of data regarding quality parameters and methodology, and outdated annotations. Thus, high-quality genomes of highly pathogenic strains that can be used as references for early Chinese ASF outbreaks are still lacking, and little is known about the features of intra-host variants of ASF virus (ASFV). In this study, a full genome sequencing of clinical samples from the first ASF outbreak in Guangdong in 2018 was performed using MGI (MGI Tech Co., Ltd., Shenzhen, China) and Nanopore sequencing platforms, followed by Sanger sequencing to verify the variations. With 22 sequencing corrections, we obtained a high-quality genome of one of the earliest virulent isolates, GZ201801_2. After proofreading, we improved (add or modify) the annotations of this isolate using the whole genome alignment with Georgia 2007/1. Based on the complete genome sequence, we constructed the methylation profiles of early ASFV strains in China and predicted the potential 5mC and 6mA methylation sites, which are likely involved in metabolism, transcription, and replication. Additionally, the intra-host single nucleotide variant distribution and mutant allele frequency in the clinical samples of early strain were determined for the first time and found a strong preference for A and T substitution mutation, non-synonymous mutations, and mutations that resulted in amino acid substitutions into Lysine. In conclusion, this study provides a high-quality genome sequence, updated genome annotation, methylation profile, and mutation spectrum of early ASFV strains in China, thereby providing a reference basis for further studies on the evolution, transmission, and virulence of ASFV.
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Affiliation(s)
- Zhi-ying Xu
- African Swine Fever Regional Laboratory of China, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Han Gao
- African Swine Fever Regional Laboratory of China, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Qi-yuan Kuang
- African Swine Fever Regional Laboratory of China, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Jia-bao Xing
- African Swine Fever Regional Laboratory of China, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Zhi-yuan Wang
- African Swine Fever Regional Laboratory of China, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Xin-yu Cao
- African Swine Fever Regional Laboratory of China, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Si-jia Xu
- African Swine Fever Regional Laboratory of China, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Jing Liu
- African Swine Fever Regional Laboratory of China, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Zhao Huang
- African Swine Fever Regional Laboratory of China, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Ze-zhong Zheng
- African Swine Fever Regional Laboratory of China, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Lang Gong
- African Swine Fever Regional Laboratory of China, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Heng Wang
- African Swine Fever Regional Laboratory of China, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Mang Shi
- School of Medicine, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Mang Shi
| | - Gui-hong Zhang
- African Swine Fever Regional Laboratory of China, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
- Gui-hong Zhang
| | - Yan-kuo Sun
- African Swine Fever Regional Laboratory of China, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
- Yan-kuo Sun
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35
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Grimaldi A, Panariello F, Annunziata P, Giuliano T, Daniele M, Pierri B, Colantuono C, Salvi M, Bouché V, Manfredi A, Cuomo MC, Di Concilio D, Tiberio C, Fiorenza M, Portella G, Cimmino I, Sorrentino A, Fusco G, Granata MR, Cerino P, Limone A, Atripaldi L, Ballabio A, Cacchiarelli D. Improved SARS-CoV-2 sequencing surveillance allows the identification of new variants and signatures in infected patients. Genome Med 2022; 14:90. [PMID: 35962405 PMCID: PMC9372932 DOI: 10.1186/s13073-022-01098-8] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/29/2022] [Indexed: 12/12/2022] Open
Abstract
Background Genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the only approach to rapidly monitor and tackle emerging variants of concern (VOC) of the COVID-19 pandemic. Such scrutiny is crucial to limit the spread of VOC that might escape the immune protection conferred by vaccination strategies or previous virus exposure. It is also becoming clear now that efficient genomic surveillance would require monitoring of the host gene expression to identify prognostic biomarkers of treatment efficacy and disease progression. Here we propose an integrative workflow to both generate thousands of SARS-CoV-2 genome sequences per week and analyze host gene expression upon infection. Methods In this study we applied an integrated workflow for RNA extracted from nasal swabs to obtain in parallel the full genome of SARS-CoV-2 and transcriptome of host respiratory epithelium. The RNA extracted from each sample was reverse transcribed and the viral genome was specifically enriched through an amplicon-based approach. The very same RNA was then used for patient transcriptome analysis. Samples were collected in the Campania region, Italy, for viral genome sequencing. Patient transcriptome analysis was performed on about 700 samples divided into two cohorts of patients, depending on the viral variant detected (B.1 or delta). Results We sequenced over 20,000 viral genomes since the beginning of the pandemic, producing the highest number of sequences in Italy. We thus reconstructed the pandemic dynamics in the regional territory from March 2020 to December 2021. In addition, we have matured and applied novel proof-of-principle approaches to prioritize possible gain-of-function mutations by leveraging patients’ metadata and isolated patient-specific signatures of SARS-CoV-2 infection. This allowed us to (i) identify three new viral variants that specifically originated in the Campania region, (ii) map SARS-CoV-2 intrahost variability during long-term infections and in one case identify an increase in the number of mutations in the viral genome, and (iii) identify host gene expression signatures correlated with viral load in upper respiratory ways. Conclusion In conclusion, we have successfully generated an optimized and cost-effective strategy to monitor SARS-CoV-2 genetic variability, without the need of automation. Thus, our approach is suitable for any lab with a benchtop sequencer and a limited budget, allowing an integrated genomic surveillance on premises. Finally, we have also identified a gene expression signature defining SARS-CoV-2 infection in real-world patients’ upper respiratory ways. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01098-8.
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Affiliation(s)
- Antonio Grimaldi
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | - Francesco Panariello
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | - Patrizia Annunziata
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy.,Next Generation Diagnostic srl, Pozzuoli, Italy
| | - Teresa Giuliano
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | - Michela Daniele
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy.,Next Generation Diagnostic srl, Pozzuoli, Italy
| | - Biancamaria Pierri
- Centro di Referenza Nazionale per l'analisi e studio di correlazione tra ambiente, animale e uomo. Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Chiara Colantuono
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy.,Next Generation Diagnostic srl, Pozzuoli, Italy
| | - Marcello Salvi
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy.,Next Generation Diagnostic srl, Pozzuoli, Italy
| | - Valentina Bouché
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | - Anna Manfredi
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy.,Next Generation Diagnostic srl, Pozzuoli, Italy
| | - Maria Concetta Cuomo
- Centro di Referenza Nazionale per l'analisi e studio di correlazione tra ambiente, animale e uomo. Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Denise Di Concilio
- Centro di Referenza Nazionale per l'analisi e studio di correlazione tra ambiente, animale e uomo. Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Claudia Tiberio
- UOC Microbiologia e Virologia, P.O. Cotugno A.O. dei Colli, Naples, Italy
| | - Mariano Fiorenza
- Department of Translational Medicine, University of Naples Federico II, Naples, Italy
| | - Giuseppe Portella
- Department of Translational Medicine, University of Naples Federico II, Naples, Italy
| | - Ilaria Cimmino
- Department of Translational Medicine, University of Naples Federico II, Naples, Italy.,UOC Epidemiologia e Prevenzione, ASL Napoli 2 Nord, Dipartimento di Prevenzione, Casavatore, Italy
| | - Antonio Sorrentino
- UOC Epidemiologia e Prevenzione, ASL Napoli 2 Nord, Dipartimento di Prevenzione, Casavatore, Italy
| | - Giovanna Fusco
- Centro di Referenza Nazionale per l'analisi e studio di correlazione tra ambiente, animale e uomo. Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Maria Rosaria Granata
- UOC Epidemiologia e Prevenzione, ASL Napoli 2 Nord, Dipartimento di Prevenzione, Casavatore, Italy
| | - Pellegrino Cerino
- Centro di Referenza Nazionale per l'analisi e studio di correlazione tra ambiente, animale e uomo. Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Antonio Limone
- Centro di Referenza Nazionale per l'analisi e studio di correlazione tra ambiente, animale e uomo. Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Luigi Atripaldi
- UOC Microbiologia e Virologia, P.O. Cotugno A.O. dei Colli, Naples, Italy
| | - Andrea Ballabio
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy.,Department of Translational Medicine, University of Naples Federico II, Naples, Italy.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children Hospital, Houston, TX, USA.,SSM School for Advanced Studies, University of Naples Federico II, Naples, Italy
| | - Davide Cacchiarelli
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy. .,Department of Translational Medicine, University of Naples Federico II, Naples, Italy. .,SSM School for Advanced Studies, University of Naples Federico II, Naples, Italy.
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36
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Cuypers LN, Čížková D, Goüy de Bellocq J. Co-Infection of Mammarenaviruses in a Wild Mouse, Tanzania. Virus Evol 2022; 8:veac065. [DOI: 10.1093/ve/veac065] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/03/2022] [Accepted: 07/20/2022] [Indexed: 11/14/2022] Open
Abstract
Abstract
Mammarenaviruses are bi-segmented RNA viruses. They encompass viruses responsible for several severe diseases in humans. While performing a de novo assembly of a new virus found in a wild single-striped grass mouse in Tanzania, we found a single S but two divergent L segments. Natural co-infections, common within reptarenaviruses in captivity, were never reported for mammarenaviruses and never in a wild sample. This finding can have implications for virus evolution as co-infection could trigger viral recombination/reassortment in natural reservoirs.
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Affiliation(s)
- Laura N Cuypers
- University of Antwerp , Universiteitsplein 1, 2610 Antwerp, Belgium
| | - Dagmar Čížková
- Institute of Vertebrate Biology of the Czech Academy of Sciences , Kvetna 8, 603 65 Brno, Czech Republic
| | - Joëlle Goüy de Bellocq
- Institute of Vertebrate Biology of the Czech Academy of Sciences , Kvetna 8, 603 65 Brno, Czech Republic
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37
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Li B, Wu H, Miao Z, Lu Y. Using codon usage analysis to speculate potential animal hosts of hepatitis E virus: An exploratory study. Infect Genet Evol 2022; 101:105284. [PMID: 35439638 DOI: 10.1016/j.meegid.2022.105284] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/10/2022] [Accepted: 04/12/2022] [Indexed: 06/14/2023]
Abstract
There has been an increase in the reported number of animals worldwide that carry the hepatitis E virus (HEV). This study aimed to explore potential animal hosts for HEV through codon usage analysis. Full-length HEV sequences of six genotypes as well as codon usage of potential animal hosts were collected. Moreover, nucleotide composition and codon usage bias were compared across HEV genotypes and animal hosts. Based on the analysis for human HEV-1 and humans, the results were basically consistent with epidemiology evidence. Among 17 potential animal hosts, all HEV genotypes exhibited a preference for guanine/cytosine in the third position of synonymous codons. Furthermore, non-human primates and humans have large high-frequency codons identical to HEV in addition to a high correlation of codon fraction with HEV. Some animals in close contact with humans showed high preference for HEV, including cattle, dogs, and rats with HEV-A, cats, dogs, and swine with HEV-C1. Codon usage bias has limited efficiency in determining the hosts for HEV, but it may provide indicative clues for potential animal hosts when combined with experimental and epidemiological evidence.
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Affiliation(s)
- Bingzhe Li
- Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Shanghai 200032, China.
| | - Han Wu
- Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Shanghai 200032, China.
| | - Ziping Miao
- Institute of Communicable Diseases Prevention and Control, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310052, Zhejiang, China.
| | - Yihan Lu
- Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Shanghai 200032, China.
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38
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Buck TK, Enriquez AS, Schendel SL, Zandonatti MA, Harkins SS, Li H, Moon-Walker A, Robinson JE, Branco LM, Garry RF, Saphire EO, Hastie KM. Neutralizing Antibodies against Lassa Virus Lineage I. mBio 2022;:e0127822. [PMID: 35730904 DOI: 10.1128/mbio.01278-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Lassa virus (LASV) is the causative agent of the deadly Lassa fever (LF). Seven distinct LASV lineages circulate through western Africa, among which lineage I (LI), the first to be identified, is particularly resistant to antibody neutralization. Lineage I LASV evades neutralization by half of known antibodies in the GPC-A antibody competition group and all but one of the antibodies in the GPC-B competition group. Here, we solve two cryo-electron microscopy (cryo-EM) structures of LI GP in complex with a GPC-A and a GPC-B antibody. We used complementary structural and biochemical techniques to identify single-amino-acid substitutions in LI that are responsible for immune evasion by each antibody group. Further, we show that LI infection is more dependent on the endosomal receptor lysosome-associated membrane protein 1 (LAMP1) for viral entry relative to LIV. In the absence of LAMP1, LI requires a more acidic fusion pH to initiate membrane fusion with the host cell relative to LIV.
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39
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Enriquez AS, Buck TK, Li H, Norris MJ, Moon-Walker A, Zandonatti MA, Harkins SS, Robinson JE, Branco LM, Garry RF, Saphire EO, Hastie KM. Delineating the mechanism of anti-Lassa virus GPC-A neutralizing antibodies. Cell Rep 2022; 39:110841. [PMID: 35613585 PMCID: PMC9258627 DOI: 10.1016/j.celrep.2022.110841] [Citation(s) in RCA: 11] [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] [Received: 10/11/2021] [Revised: 03/16/2022] [Accepted: 04/28/2022] [Indexed: 12/16/2022] Open
Abstract
Lassa virus (LASV) is the etiologic agent of Lassa Fever, a hemorrhagic disease that is endemic to West Africa. During LASV infection, LASV glycoprotein (GP) engages with multiple host receptors for cell entry. Neutralizing antibodies against GP are rare and principally target quaternary epitopes displayed only on the metastable, pre-fusion conformation of GP. Currently, the structural features of the neutralizing GPC-A antibody competition group are understudied. Structures of two GPC-A antibodies presented here demonstrate that they bind the side of the pre-fusion GP trimer, bridging the GP1 and GP2 subunits. Complementary biochemical analyses indicate that antibody 25.10C, which is broadly specific, neutralizes by inhibiting binding of the endosomal receptor LAMP1 and also by blocking membrane fusion. The other GPC-A antibody, 36.1F, which is lineage-specific, prevents LAMP1 association only. These data illuminate a site of vulnerability on LASV GP and will guide efforts to elicit broadly reactive therapeutics and vaccines. Enriquez et al. present two structures of GPC-A antibody Fab fragments bound to Lassa virus glycoprotein. Complementary biochemical analyses illuminate mechanistic differences between pan-Lassa 25.10C and lineage-specific 36.1F. 25.10C inhibits two steps of Lassa virus infection, LAMP1 binding and membrane fusion, while 36.1F only blocks LAMP1.
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Affiliation(s)
| | - Tierra K Buck
- La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Haoyang Li
- La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | | | - Alex Moon-Walker
- La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Program in Virology, Harvard University, Boston, MA 02115, USA; Department of Molecular Microbiology, Washington University in Saint Louis, St. Louis, MO 63130, USA
| | | | | | - James E Robinson
- Department of Pediatrics, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | | | - Robert F Garry
- Zalgen Labs, LLC, Germantown, MD 20876, USA; Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
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40
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Mateo M, Hortion J, Perthame E, Picard C, Reynard S, Journeaux A, Germain C, Carnec X, Baillet N, Borges-Cardoso V, Pietrosemoli N, Vallve A, Barron S, Jourjon O, Lacroix O, Duthey A, Dirheimer M, Daniau M, Legras-Lachuer C, Jouvion G, Carbonnelle C, Raoul H, Baize S. Pathogenesis of recent Lassa virus isolates from lineages II and VII in cynomolgus monkeys. Virulence 2022; 13:654-669. [PMID: 35437094 PMCID: PMC9037461 DOI: 10.1080/21505594.2022.2060170] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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] [Indexed: 11/28/2022] Open
Abstract
The area of Lassa virus (LASV) circulation is expanding, with the emergence of highly pathogenic new LASV lineages. Benin recently became an endemic country for LASV and has seen the emergence of a new LASV lineage (VII). The first two outbreaks in 2014 and 2016 showed a relatively high mortality rate compared to other outbreaks. We infected cynomolgus monkeys with two strains belonging to lineage II and lineage VII that were isolated from deceased patients during the 2016 outbreak in Benin. The lineage VII strain (L7) caused uniform mortality. Death was associated with uncontrolled viral replication, unbalanced inflammatory responses characterized by increased concentrations of pro- and anti-inflammatory mediators, and the absence of efficient immune responses, resembling the pathogenesis associated with the prototypic Josiah strain in monkeys. The lineage II strain (L2) showed apparently lower virulence than its counterpart, with a prolonged time to death and a lower mortality rate. Prolonged survival was associated with better control of viral replication, a moderate inflammatory response, and efficient T-cell responses. Transcriptomic analyses also highlighted important differences in the immune responses associated with the outcome. Both strains caused strong inflammation in several organs. Notably, meningitis and encephalitis were observed in the cerebral cortex and cerebellum in all monkeys, independently of the outcome. Due to their apparently high pathogenicity, emerging strains from lineage VII should be considered in preclinical vaccine testing. Lineage II would also be beneficial in pathogenesis studies to study the entire spectrum of Lassa fever severity.
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Affiliation(s)
- Mathieu Mateo
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, Lyon, France.,Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS UMR5308, Lyon France
| | - Jimmy Hortion
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, Lyon, France.,Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS UMR5308, Lyon France
| | - Emeline Perthame
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Université de Paris, Paris, France
| | - Caroline Picard
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, Lyon, France.,Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS UMR5308, Lyon France
| | - Stéphanie Reynard
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, Lyon, France.,Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS UMR5308, Lyon France
| | - Alexandra Journeaux
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, Lyon, France.,Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS UMR5308, Lyon France
| | - Clara Germain
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, Lyon, France.,Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS UMR5308, Lyon France
| | - Xavier Carnec
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, Lyon, France.,Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS UMR5308, Lyon France
| | - Nicolas Baillet
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, Lyon, France.,Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS UMR5308, Lyon France
| | - Virginie Borges-Cardoso
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, Lyon, France.,Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS UMR5308, Lyon France
| | - Natalia Pietrosemoli
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Université de Paris, Paris, France
| | - Audrey Vallve
- Laboratoire P4 INSERM-Jean Mérieux, INSERM US003, 69007 Lyon, France
| | - Stéphane Barron
- Laboratoire P4 INSERM-Jean Mérieux, INSERM US003, 69007 Lyon, France
| | - Ophélie Jourjon
- Laboratoire P4 INSERM-Jean Mérieux, INSERM US003, 69007 Lyon, France
| | - Orianne Lacroix
- Laboratoire P4 INSERM-Jean Mérieux, INSERM US003, 69007 Lyon, France
| | - Aurélie Duthey
- Laboratoire P4 INSERM-Jean Mérieux, INSERM US003, 69007 Lyon, France
| | - Manon Dirheimer
- INSERM, Délégation Régionale Auvergne Rhône-Alpes, Bron, France
| | | | | | - Gregory Jouvion
- Ecole Nationale Vétérinaire d'Alfort, Unité d'Histologie et d'Anatomie Pathologique, Maisons-Alfort, France.,Dynamic Research Group, Ecole Nationale Vétérinaired'Alfort, USC ANSES, Université Paris Est Créteil, Maisons-Alfort, France
| | | | - Hervé Raoul
- Laboratoire P4 INSERM-Jean Mérieux, INSERM US003, 69007 Lyon, France
| | - Sylvain Baize
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, Lyon, France.,Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS UMR5308, Lyon France
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41
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Raabe V, Mehta AK, Evans JD. Lassa Virus Infection: a Summary for Clinicians. Int J Infect Dis 2022; 119:187-200. [PMID: 35395384 DOI: 10.1016/j.ijid.2022.04.004] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/01/2022] [Accepted: 04/03/2022] [Indexed: 11/25/2022] Open
Abstract
OBJECTIVES This summary on Lassa virus (LASV) infection and Lassa fever disease (LF) was developed from a clinical perspective to provide clinicians a condensed, accessible understanding of the current literature. The information provided highlights pathogenesis, clinical features, and diagnostics with an emphasis on therapies and vaccines that have demonstrated potential value for use in clinical or research environments. METHODS An integrative literature review was conducted on the clinical and pathological features, vaccines, and treatments for LASV infection, with a focus on recent studies and in vivo evidence from humans and/or non-human primates (NHPs), when available. RESULTS Two antiviral medications with potential benefit for the treatment of LASV infection and one for post-exposure prophylaxis were identified, although a larger number of potential candidates are currently being evaluated. Multiple vaccine platforms are in pre-clinical development for LASV prevention, but data from human clinical trials are not yet available. CONCLUSION We provide succinct summaries of medical countermeasures against LASV to give the busy clinician a rapid reference. Although there are no approved drugs or vaccines for LF, we provide condensed information from a literature review for measures that can be taken when faced with a suspected infection, including investigational treatment options and hospital engineering controls.
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Affiliation(s)
- Vanessa Raabe
- New York University Grossman School of Medicine, New York, NY.
| | | | - Jared D Evans
- Johns Hopkins Applied Physics Laboratory, Laurel, MD.
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42
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Merabet O, Pietrosemoli N, Perthame E, Armengaud J, Gaillard JC, Borges-Cardoso V, Daniau M, Legras-Lachuer C, Carnec X, Baize S. Infection of Human Endothelial Cells with Lassa Virus Induces Early but Transient Activation and Low Type I IFN Response Compared to the Closely-Related Nonpathogenic Mopeia Virus. Viruses 2022; 14:v14030652. [PMID: 35337059 PMCID: PMC8953476 DOI: 10.3390/v14030652] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/10/2022] [Accepted: 03/16/2022] [Indexed: 02/01/2023] Open
Abstract
Lassa virus (LASV), an Old World arenavirus, is responsible for hemorrhagic fevers in western Africa. The privileged tropism of LASV for endothelial cells combined with a dysregulated inflammatory response are the main cause of the increase in vascular permeability observed during the disease. Mopeia virus (MOPV) is another arenavirus closely related to LASV but nonpathogenic for non-human primates (NHPs) and has never been described in humans. MOPV is more immunogenic than LASV in NHPs and in vitro in human immune cell models, with more intense type I IFN and adaptive cellular responses. Here, we compared the transcriptomic and proteomic responses of human umbilical vein endothelial cells (HUVECs) to infection with the two viruses to further decipher the mechanisms involved in their differences in immunogenicity and pathogenicity. Both viruses replicated durably and efficiently in HUVECs, but the responses they induced were strikingly different. Modest activation was observed at an early stage of LASV infection and then rapidly shut down. By contrast, MOPV induced a late but more intense response, characterized by the expression of genes and proteins mainly associated with the type I IFN response and antigen processing/presentation. Such a response is consistent with the higher immunogenicity of MOPV relative to LASV, whereas the lack of an innate response induced in HUVECs by LASV is consistent with its uncontrolled systemic dissemination through the vascular endothelium.
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Affiliation(s)
- Othmann Merabet
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, 69007 Lyon, France; (O.M.); (V.B.-C.); (X.C.)
- Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, UMR5308, 69007 Lyon, France
| | - Natalia Pietrosemoli
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Université de Paris, 75015 Paris, France; (N.P.); (E.P.)
| | - Emeline Perthame
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Université de Paris, 75015 Paris, France; (N.P.); (E.P.)
| | - Jean Armengaud
- Laboratoire Innovations Technologiques pour la Détection et le Diagnostic (LI2D), Service de Pharmacologie et Immunoanalyse (SPI), Commissariat à l’Energie Atomique, 30200 Bagnols-sur-Cèze, France; (J.A.); (J.-C.G.)
| | - Jean-Charles Gaillard
- Laboratoire Innovations Technologiques pour la Détection et le Diagnostic (LI2D), Service de Pharmacologie et Immunoanalyse (SPI), Commissariat à l’Energie Atomique, 30200 Bagnols-sur-Cèze, France; (J.A.); (J.-C.G.)
| | - Virginie Borges-Cardoso
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, 69007 Lyon, France; (O.M.); (V.B.-C.); (X.C.)
- Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, UMR5308, 69007 Lyon, France
| | - Maïlys Daniau
- ViroScan3D SAS, 01600 Trévoux, France; (M.D.); (C.L.-L.)
| | | | - Xavier Carnec
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, 69007 Lyon, France; (O.M.); (V.B.-C.); (X.C.)
- Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, UMR5308, 69007 Lyon, France
| | - Sylvain Baize
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, 69007 Lyon, France; (O.M.); (V.B.-C.); (X.C.)
- Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, UMR5308, 69007 Lyon, France
- Correspondence: ; Tel.: +33-4-3728-2440
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43
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Salam AP, Duvignaud A, Jaspard M, Malvy D, Carroll M, Tarning J, Olliaro PL, Horby PW. Ribavirin for treating Lassa fever: A systematic review of pre-clinical studies and implications for human dosing. PLoS Negl Trop Dis 2022; 16:e0010289. [PMID: 35353804 PMCID: PMC9000057 DOI: 10.1371/journal.pntd.0010289] [Citation(s) in RCA: 4] [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: 11/11/2021] [Revised: 04/11/2022] [Accepted: 02/28/2022] [Indexed: 12/24/2022] Open
Abstract
Ribavirin is currently the standard of care for treating Lassa fever. However, the human clinical trial data supporting its use suffer from several serious flaws that render the results and conclusions unreliable. We performed a systematic review of available pre-clinical data and human pharmacokinetic data on ribavirin in Lassa. In in-vitro studies, the EC50 of ribavirin ranged from 0.6 μg/ml to 21.72 μg/ml and the EC90 ranged from 1.5 μg/ml to 29 μg/ml. The mean EC50 was 7 μg/ml and the mean EC90 was 15 μg/ml. Human PK data in patients with Lassa fever was sparse and did not allow for estimation of concentration profiles or pharmacokinetic parameters. Pharmacokinetic modelling based on healthy human data suggests that the concentration profiles of current ribavirin regimes only exceed the mean EC50 for less than 20% of the time and the mean EC90 for less than 10% of the time, raising the possibility that the current ribavirin regimens in clinical use are unlikely to reliably achieve serum concentrations required to inhibit Lassa virus replication. The results of this review highlight serious issues with the evidence, which, by today standards, would be unlikely to support the transition of ribavirin from pre-clinical studies to human clinical trials. Additional pre-clinical studies are needed before embarking on expensive and challenging clinical trials of ribavirin in Lassa fever.
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Affiliation(s)
- Alex P. Salam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- United Kingdom Public Health Rapid Support Team, London, United Kingdom
| | - Alexandre Duvignaud
- Department of Infectious Diseases and Tropical Medicine, Division of Tropical Medicine and Clinical International Health, CHU de Bordeaux, Bordeaux, France
- UMR1219, INSERM, French National Research Institute for Sustainable Development (IRD), and University of Bordeaux, Bordeaux, France
- Programme PAC-CI/ANRS Research Center, CHU de Treichville, Abidjan, Côte d’Ivoire
| | - Marie Jaspard
- UMR1219, INSERM, French National Research Institute for Sustainable Development (IRD), and University of Bordeaux, Bordeaux, France
- Programme PAC-CI/ANRS Research Center, CHU de Treichville, Abidjan, Côte d’Ivoire
- Alliance for International Medical Action, Dakar, Senegal
| | - Denis Malvy
- Department of Infectious Diseases and Tropical Medicine, Division of Tropical Medicine and Clinical International Health, CHU de Bordeaux, Bordeaux, France
- UMR1219, INSERM, French National Research Institute for Sustainable Development (IRD), and University of Bordeaux, Bordeaux, France
- Programme PAC-CI/ANRS Research Center, CHU de Treichville, Abidjan, Côte d’Ivoire
| | - Miles Carroll
- Wellcome Center for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Joel Tarning
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Piero L. Olliaro
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Peter W. Horby
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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44
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Li J, Du P, Yang L, Zhang J, Song C, Chen D, Song Y, Ding N, Hua M, Han K, Song R, Xie W, Chen Z, Wang X, Liu J, Xu Y, Gao G, Wang Q, Pu L, Di L, Li J, Yue J, Han J, Zhao X, Yan Y, Yu F, Wu AR, Zhang F, Gao YQ, Huang Y, Wang J, Zeng H, Chen C. Two-step fitness selection for intra-host variations in SARS-CoV-2. Cell Rep 2022; 38:110205. [PMID: 34982968 PMCID: PMC8674508 DOI: 10.1016/j.celrep.2021.110205] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [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: 06/08/2021] [Revised: 10/10/2021] [Accepted: 12/13/2021] [Indexed: 12/30/2022] Open
Abstract
Spontaneous mutations introduce uncertainty into coronavirus disease 2019 (COVID-19) control procedures and vaccine development. Here, we perform a spatiotemporal analysis on intra-host single-nucleotide variants (iSNVs) in 402 clinical samples from 170 affected individuals, which reveals an increase in genetic diversity over time after symptom onset in individuals. Nonsynonymous mutations are overrepresented in the pool of iSNVs but underrepresented at the single-nucleotide polymorphism (SNP) level, suggesting a two-step fitness selection process: a large number of nonsynonymous substitutions are generated in the host (positive selection), and these substitutions tend to be unfixed as SNPs in the population (negative selection). Dynamic iSNV changes in subpopulations with different gender, age, illness severity, and viral shedding time displayed a varied fitness selection process among populations. Our study highlights that iSNVs provide a mutational pool shaping the rapid global evolution of the virus.
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Affiliation(s)
- Jiarui Li
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, P. R. China
| | - Pengcheng Du
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, P. R. China
| | - Lijiang Yang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Beijing Advanced Innovation Center for Genomics, Biomedical Pioneering Innovation Center, Peking University, Beijing 100871, China
| | - Ju Zhang
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, P. R. China
| | - Chuan Song
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, P. R. China
| | - Danying Chen
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, P. R. China
| | - Yangzi Song
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, P. R. China
| | - Nan Ding
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, P. R. China
| | - Mingxi Hua
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, P. R. China
| | - Kai Han
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, P. R. China
| | - Rui Song
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China
| | - Wen Xie
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China
| | - Zhihai Chen
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China
| | - Xianbo Wang
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China
| | - Jingyuan Liu
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China
| | - Yanli Xu
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China
| | - Guiju Gao
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China
| | - Qi Wang
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China
| | - Lin Pu
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China
| | - Lin Di
- Beijing Advanced Innovation Center for Genomics, Biomedical Pioneering Innovation Center, Peking University, Beijing 100871, China; School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Jie Li
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China
| | - Jinglin Yue
- Peking University Ditan Teaching Hospital, Beijing 100015, China
| | - Junyan Han
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, P. R. China
| | - Xuesen Zhao
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, P. R. China
| | - Yonghong Yan
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, P. R. China
| | - Fengting Yu
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China
| | - Angela R Wu
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong SAR, P.R. China; Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Hong Kong SAR, P.R. China
| | - Fujie Zhang
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, P. R. China.
| | - Yi Qin Gao
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Beijing Advanced Innovation Center for Genomics, Biomedical Pioneering Innovation Center, Peking University, Beijing 100871, China; Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China.
| | - Yanyi Huang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Beijing Advanced Innovation Center for Genomics, Biomedical Pioneering Innovation Center, Peking University, Beijing 100871, China; School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 518055, China; Chinese Institute for Brain Research, Beijing 102206, China.
| | - Jianbin Wang
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China; Chinese Institute for Brain Research, Beijing 102206, China.
| | - Hui Zeng
- Biomedical Innovation Center, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China.
| | - Chen Chen
- Biomedical Innovation Center, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China.
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45
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Goodman JR, Wohns N. AIM and Evolutionary Theory. Artif Intell Med 2022. [DOI: 10.1007/978-3-030-64573-1_41] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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46
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Thielebein A, Ighodalo Y, Taju A, Olokor T, Omiunu R, Esumeh R, Ebhodaghe P, Ekanem A, Igenegbale G, Giwa R, Renevey A, Hinzmann J, Müller J, Pallasch E, Pahlmann M, Guedj J, Nwatuzor J, Femi Babatunde O, Adomeh DI, Asogun D, Akpede N, Okogbenin S, Günther S, Oestereich L, Duraffour S, Ogbaini-Emovon E. Virus persistence after recovery from acute Lassa fever in Nigeria: a 2-year interim analysis of a prospective longitudinal cohort study. The Lancet Microbe 2022; 3:e32-e40. [DOI: 10.1016/s2666-5247(21)00178-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 05/22/2021] [Accepted: 06/30/2021] [Indexed: 12/13/2022] Open
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47
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Borrega R, Nelson DKS, Koval AP, Bond NG, Heinrich ML, Rowland MM, Lathigra R, Bush DJ, Aimukanova I, Phinney WN, Koval SA, Hoffmann AR, Smither AR, Bell-Kareem AR, Melnik LI, Genemaras KJ, Chao K, Snarski P, Melton AB, Harrell JE, Smira AA, Elliott DH, Rouelle JA, Sabino-Santos G, Drouin AC, Momoh M, Sandi JD, Goba A, Samuels RJ, Kanneh L, Gbakie M, Branco ZL, Shaffer JG, Schieffelin JS, Robinson JE, Fusco DN, Sabeti PC, Andersen KG, Grant DS, Boisen ML, Branco LM, Garry RF. Cross-Reactive Antibodies to SARS-CoV-2 and MERS-CoV in Pre-COVID-19 Blood Samples from Sierra Leoneans. Viruses 2021; 13:2325. [PMID: 34835131 PMCID: PMC8625389 DOI: 10.3390/v13112325] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [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: 09/29/2021] [Revised: 11/14/2021] [Accepted: 11/17/2021] [Indexed: 12/15/2022] Open
Abstract
Many countries in sub-Saharan Africa have experienced lower COVID-19 caseloads and fewer deaths than countries in other regions worldwide. Under-reporting of cases and a younger population could partly account for these differences, but pre-existing immunity to coronaviruses is another potential factor. Blood samples from Sierra Leonean Lassa fever and Ebola survivors and their contacts collected before the first reported COVID-19 cases were assessed using enzyme-linked immunosorbent assays for the presence of antibodies binding to proteins of coronaviruses that infect humans. Results were compared to COVID-19 subjects and healthy blood donors from the United States. Prior to the pandemic, Sierra Leoneans had more frequent exposures than Americans to coronaviruses with epitopes that cross-react with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), SARS-CoV, and Middle Eastern respiratory syndrome coronavirus (MERS-CoV). The percentage of Sierra Leoneans with antibodies reacting to seasonal coronaviruses was also higher than for American blood donors. Serological responses to coronaviruses by Sierra Leoneans did not differ by age or sex. Approximately a quarter of Sierra Leonian pre-pandemic blood samples had neutralizing antibodies against SARS-CoV-2 pseudovirus, while about a third neutralized MERS-CoV pseudovirus. Prior exposures to coronaviruses that induce cross-protective immunity may contribute to reduced COVID-19 cases and deaths in Sierra Leone.
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Affiliation(s)
- Rodrigo Borrega
- Zalgen Labs, LCC, Germantown, MD 20876, USA; (R.B.); (A.P.K.); (M.L.H.); (M.M.R.); (R.L.); (S.A.K.); (Z.L.B.)
| | - Diana K. S. Nelson
- Zalgen Labs, LCC, Broomfield, CO 80045, USA; (D.K.S.N.); (D.J.B.); (I.A.); (W.N.P.)
| | - Anatoliy P. Koval
- Zalgen Labs, LCC, Germantown, MD 20876, USA; (R.B.); (A.P.K.); (M.L.H.); (M.M.R.); (R.L.); (S.A.K.); (Z.L.B.)
| | - Nell G. Bond
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (N.G.B.); (A.R.H.); (A.R.S.); (A.R.B.-K.); (L.I.M.); (K.J.G.); (K.C.); (J.E.H.)
| | - Megan L. Heinrich
- Zalgen Labs, LCC, Germantown, MD 20876, USA; (R.B.); (A.P.K.); (M.L.H.); (M.M.R.); (R.L.); (S.A.K.); (Z.L.B.)
| | - Megan M. Rowland
- Zalgen Labs, LCC, Germantown, MD 20876, USA; (R.B.); (A.P.K.); (M.L.H.); (M.M.R.); (R.L.); (S.A.K.); (Z.L.B.)
| | - Raju Lathigra
- Zalgen Labs, LCC, Germantown, MD 20876, USA; (R.B.); (A.P.K.); (M.L.H.); (M.M.R.); (R.L.); (S.A.K.); (Z.L.B.)
| | - Duane J. Bush
- Zalgen Labs, LCC, Broomfield, CO 80045, USA; (D.K.S.N.); (D.J.B.); (I.A.); (W.N.P.)
| | - Irina Aimukanova
- Zalgen Labs, LCC, Broomfield, CO 80045, USA; (D.K.S.N.); (D.J.B.); (I.A.); (W.N.P.)
| | - Whitney N. Phinney
- Zalgen Labs, LCC, Broomfield, CO 80045, USA; (D.K.S.N.); (D.J.B.); (I.A.); (W.N.P.)
| | - Sophia A. Koval
- Zalgen Labs, LCC, Germantown, MD 20876, USA; (R.B.); (A.P.K.); (M.L.H.); (M.M.R.); (R.L.); (S.A.K.); (Z.L.B.)
| | - Andrew R. Hoffmann
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (N.G.B.); (A.R.H.); (A.R.S.); (A.R.B.-K.); (L.I.M.); (K.J.G.); (K.C.); (J.E.H.)
| | - Allison R. Smither
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (N.G.B.); (A.R.H.); (A.R.S.); (A.R.B.-K.); (L.I.M.); (K.J.G.); (K.C.); (J.E.H.)
| | - Antoinette R. Bell-Kareem
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (N.G.B.); (A.R.H.); (A.R.S.); (A.R.B.-K.); (L.I.M.); (K.J.G.); (K.C.); (J.E.H.)
| | - Lilia I. Melnik
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (N.G.B.); (A.R.H.); (A.R.S.); (A.R.B.-K.); (L.I.M.); (K.J.G.); (K.C.); (J.E.H.)
| | - Kaylynn J. Genemaras
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (N.G.B.); (A.R.H.); (A.R.S.); (A.R.B.-K.); (L.I.M.); (K.J.G.); (K.C.); (J.E.H.)
- Bioinnovation Program, Tulane University, New Orleans, LA 70118, USA
| | - Karissa Chao
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (N.G.B.); (A.R.H.); (A.R.S.); (A.R.B.-K.); (L.I.M.); (K.J.G.); (K.C.); (J.E.H.)
- Bioinnovation Program, Tulane University, New Orleans, LA 70118, USA
| | - Patricia Snarski
- Heart and Vascular Institute, John W. Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA;
- Department of Physiology, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Alexandra B. Melton
- Department of Microbiology, Tulane National Primate Research Center, Covington, LA 70433, USA;
| | - Jaikin E. Harrell
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (N.G.B.); (A.R.H.); (A.R.S.); (A.R.B.-K.); (L.I.M.); (K.J.G.); (K.C.); (J.E.H.)
| | - Ashley A. Smira
- Department of Pediatrics, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (A.A.S.); (D.H.E.); (J.A.R.); (J.S.S.); (J.E.R.)
| | - Debra H. Elliott
- Department of Pediatrics, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (A.A.S.); (D.H.E.); (J.A.R.); (J.S.S.); (J.E.R.)
| | - Julie A. Rouelle
- Department of Pediatrics, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (A.A.S.); (D.H.E.); (J.A.R.); (J.S.S.); (J.E.R.)
| | - Gilberto Sabino-Santos
- Department of Tropical Medicine, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA;
- Centre for Virology Research, Ribeirão Preto Medical School, University of Sao Paulo, Ribeirao Preto 14049-900, SP, Brazil
| | - Arnaud C. Drouin
- Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (A.C.D.); (D.N.F.)
| | - Mambu Momoh
- Eastern Polytechnic Institute, Kenema, Sierra Leone;
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone; (J.D.S.); (A.G.); (R.J.S.); (L.K.); (M.G.)
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - John Demby Sandi
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone; (J.D.S.); (A.G.); (R.J.S.); (L.K.); (M.G.)
| | - Augustine Goba
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone; (J.D.S.); (A.G.); (R.J.S.); (L.K.); (M.G.)
| | - Robert J. Samuels
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone; (J.D.S.); (A.G.); (R.J.S.); (L.K.); (M.G.)
| | - Lansana Kanneh
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone; (J.D.S.); (A.G.); (R.J.S.); (L.K.); (M.G.)
| | - Michael Gbakie
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone; (J.D.S.); (A.G.); (R.J.S.); (L.K.); (M.G.)
| | - Zoe L. Branco
- Zalgen Labs, LCC, Germantown, MD 20876, USA; (R.B.); (A.P.K.); (M.L.H.); (M.M.R.); (R.L.); (S.A.K.); (Z.L.B.)
| | - Jeffrey G. Shaffer
- Department of Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA;
| | - John S. Schieffelin
- Department of Pediatrics, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (A.A.S.); (D.H.E.); (J.A.R.); (J.S.S.); (J.E.R.)
- Department of Internal Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - James E. Robinson
- Department of Pediatrics, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (A.A.S.); (D.H.E.); (J.A.R.); (J.S.S.); (J.E.R.)
| | - Dahlene N. Fusco
- Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (A.C.D.); (D.N.F.)
| | - Pardis C. Sabeti
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA;
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA
| | - Kristian G. Andersen
- Department of Immunology and Microbial Science, Scripps Research, La Jolla, CA 92037, USA;
- Scripps Research Translational Institute, La Jolla, CA 92037, USA
| | - Donald S. Grant
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone; (J.D.S.); (A.G.); (R.J.S.); (L.K.); (M.G.)
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Matthew L. Boisen
- Zalgen Labs, LCC, Broomfield, CO 80045, USA; (D.K.S.N.); (D.J.B.); (I.A.); (W.N.P.)
| | - Luis M. Branco
- Zalgen Labs, LCC, Germantown, MD 20876, USA; (R.B.); (A.P.K.); (M.L.H.); (M.M.R.); (R.L.); (S.A.K.); (Z.L.B.)
| | - Robert F. Garry
- Zalgen Labs, LCC, Germantown, MD 20876, USA; (R.B.); (A.P.K.); (M.L.H.); (M.M.R.); (R.L.); (S.A.K.); (Z.L.B.)
- Zalgen Labs, LCC, Broomfield, CO 80045, USA; (D.K.S.N.); (D.J.B.); (I.A.); (W.N.P.)
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (N.G.B.); (A.R.H.); (A.R.S.); (A.R.B.-K.); (L.I.M.); (K.J.G.); (K.C.); (J.E.H.)
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Arefin A, Ismail Ema T, Islam T, Hossen S, Islam T, Al Azad S, Uddin Badal N, Islam A, Biswas P, Alam NU, Islam E, Anjum M, Masud A, Kamran S, Rahman A, Kumar Paul P. Target specificity of selective bioactive compounds in blocking α-dystroglycan receptor to suppress Lassa virus infection: an in silico approach. J Biomed Res 2021; 35:459-473. [PMID: 34857680 PMCID: PMC8637655 DOI: 10.7555/jbr.35.20210111] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 12/16/2022] Open
Abstract
Lassa hemorrhagic fever, caused by Lassa mammarenavirus (LASV) infection, accumulates up to 5000 deaths every year. Currently, there is no vaccine available to combat this disease. In this study, a library of 200 bioactive compounds was virtually screened to study their drug-likeness with the capacity to block the α-dystroglycan (α-DG) receptor and prevent LASV influx. Following rigorous absorption, distribution, metabolism, and excretion (ADME) and quantitative structure-activity relationship (QSAR) profiling, molecular docking was conducted with the top ligands against the α-DG receptor. The compounds chrysin, reticuline, and 3-caffeoylshikimic acid emerged as the top three ligands in terms of binding affinity. Post-docking analysis revealed that interactions with Arg76, Asn224, Ser259, and Lys302 amino acid residues of the receptor protein were important for the optimum binding affinity of ligands. Molecular dynamics simulation was performed comprehensively to study the stability of the protein-ligand complexes. In-depth assessment of root-mean-square deviation (RMSD), root mean square fluctuation (RMSF), polar surface area (PSA), B-Factor, radius of gyration (Rg), solvent accessible surface area (SASA), and molecular surface area (MolSA) values of the protein-ligand complexes affirmed that the candidates with the best binding affinity formed the most stable protein-ligand complexes. To authenticate the potentialities of the ligands as target-specific drugs, an in vivo study is underway in real time as the continuation of the research.
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Affiliation(s)
- Adittya Arefin
- Wolfson Institute for Biomedical Research, Division of Medicine, University College London, London WC1E6AE, UK
| | - Tanzila Ismail Ema
- Department of Biochemistry and Microbiology, North South University, Dhaka 1229, Bangladesh
| | - Tamnia Islam
- Wolfson Institute for Biomedical Research, Division of Medicine, University College London, London WC1E6AE, UK
| | - Saddam Hossen
- Faculty of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang 310018, China
| | - Tariqul Islam
- Faculty of Pharmacy, International Islamic University Malaysia, Kuantan, Pahang 25200, Malaysia
| | - Salauddin Al Azad
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Nasir Uddin Badal
- Department of Biomedical Technology, Tampere University, Tampere 33014, Finland
| | - Aminul Islam
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Partha Biswas
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Nafee Ul Alam
- Faculty of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang 310018, China
| | - Enayetul Islam
- Department of Genetic Engineering and Biotechnology, University of Chittagong, Chittagong 4331, Bangladesh
| | - Maliha Anjum
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Afsana Masud
- Department of Biochemistry and Microbiology, North South University, Dhaka 1229, Bangladesh
| | - Shaikh Kamran
- Applied Statistics and Data Science, Jahangirnagar University, Dhaka 1342, Bangladesh
| | - Ahsab Rahman
- Department of Mathematics and Natural Sciences, Brac University, Dhaka 1212, Bangladesh
| | - Parag Kumar Paul
- Department of Electrical and Electronic Engineering, United International University, Dhaka 1212, Bangladesh
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49
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Stein DR, Warner BM, Audet J, Soule G, Siragam V, Sroga P, Griffin BD, Leung A, Grolla A, Tierney K, Albietz A, Kobasa D, Musa AS, Ahmad A, Akinpelu AM, Mba N, Rosenke R, Scott DP, Saturday G, Ihekweazu C, Safronetz D. Differential pathogenesis of closely related 2018 Nigerian outbreak clade III Lassa virus isolates. PLoS Pathog 2021; 17:e1009966. [PMID: 34634087 PMCID: PMC8530337 DOI: 10.1371/journal.ppat.1009966] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 10/21/2021] [Accepted: 09/23/2021] [Indexed: 12/21/2022] Open
Abstract
Nigeria continues to experience ever increasing annual outbreaks of Lassa fever (LF). The World Health Organization has recently declared Lassa virus (LASV) as a priority pathogen for accelerated research leading to a renewed international effort to develop relevant animal models of disease and effective countermeasures to reduce LF morbidity and mortality in endemic West African countries. A limiting factor in evaluating medical countermeasures against LF is a lack of well characterized animal models outside of those based on infection with LASV strain Josiah originating form Sierra Leone, circa 1976. Here we genetically characterize five recent LASV isolates collected from the 2018 outbreak in Nigeria. Three isolates were further evaluated in vivo and despite being closely related and from the same spatial / geographic region of Nigeria, only one of the three isolates proved lethal in strain 13 guinea pigs and non-human primates (NHP). Additionally, this isolate exhibited atypical pathogenesis characteristics in the NHP model, most notably respiratory failure, not commonly described in hemorrhagic cases of LF. These results suggest that there is considerable phenotypic heterogeneity in LASV infections in Nigeria, which leads to a multitude of pathogenesis characteristics that could account for differences between subclinical and lethal LF infections. Most importantly, the development of disease models using currently circulating LASV strains in West Africa are critical for the evaluation of potential vaccines and medical countermeasures. Lassa fever is a severe viral hemorrhagic fever of humans caused by infection with Lassa virus, which is endemic in many countries in West Africa. Annually, an estimated 300,000–500,000 people are infected with Lassa virus, making it one of the most prominent agents responsible for hemorrhagic disease in humans. Despite this significant burden of disease, to date, no approved therapeutic or prophylactic vaccine exists for Lassa fever, due in part to a lack of characterized animal models for studying the disease. Here, we describe guinea pig and non-human primate models for Lassa fever using recently isolated viruses from a 2018 outbreak of Lassa fever in Nigeria. Despite similar collection locations and dates, the isolates obtained from human infections demonstrated a high degree of genotypic heterogeneity and phenotypic characteristics in animal models resulting in both lethal and non-lethal infections. Of interest, one isolate resulted in significant respiratory manifestations, an under-reported disease manifestation in humans. These models will provide comparative models to those already characterized and aid in elucidating disease characteristics of Lassa fever. In addition, they will serve the immediate purpose of evaluating known and novel medical countermeasures to treat and prevent disease in West Africa.
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Affiliation(s)
- Derek R. Stein
- Zoonotic Diseases and Special Pathogens, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Bryce M. Warner
- Zoonotic Diseases and Special Pathogens, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Jonathan Audet
- Zoonotic Diseases and Special Pathogens, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Geoff Soule
- Zoonotic Diseases and Special Pathogens, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Vinayakumar Siragam
- Zoonotic Diseases and Special Pathogens, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Patrycja Sroga
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Canada
| | - Bryan D. Griffin
- Zoonotic Diseases and Special Pathogens, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Anders Leung
- Zoonotic Diseases and Special Pathogens, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Allen Grolla
- Zoonotic Diseases and Special Pathogens, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Kevin Tierney
- Zoonotic Diseases and Special Pathogens, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Alix Albietz
- Zoonotic Diseases and Special Pathogens, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Darwyn Kobasa
- Zoonotic Diseases and Special Pathogens, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Canada
| | | | - Adama Ahmad
- Nigerian Centre for Disease Control, Jabi, Abuja, Nigeria
| | | | - Nwando Mba
- Nigerian Centre for Disease Control, Jabi, Abuja, Nigeria
| | - Rebecca Rosenke
- Rocky Mountain Veterinary Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton Montana, United States of America
| | - Dana P. Scott
- Rocky Mountain Veterinary Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton Montana, United States of America
| | - Greg Saturday
- Rocky Mountain Veterinary Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton Montana, United States of America
| | | | - David Safronetz
- Zoonotic Diseases and Special Pathogens, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Canada
- * E-mail:
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50
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Redding DW, Gibb R, Dan-Nwafor CC, Ilori EA, Yashe RU, Oladele SH, Amedu MO, Iniobong A, Attfield LA, Donnelly CA, Abubakar I, Jones KE, Ihekweazu C. Geographical drivers and climate-linked dynamics of Lassa fever in Nigeria. Nat Commun 2021; 12:5759. [PMID: 34599162 DOI: 10.1038/s41467-021-25910-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 09/08/2021] [Indexed: 02/08/2023] Open
Abstract
Lassa fever is a longstanding public health concern in West Africa. Recent molecular studies have confirmed the fundamental role of the rodent host (Mastomys natalensis) in driving human infections, but control and prevention efforts remain hampered by a limited baseline understanding of the disease's true incidence, geographical distribution and underlying drivers. Here, we show that Lassa fever occurrence and incidence is influenced by climate, poverty, agriculture and urbanisation factors. However, heterogeneous reporting processes and diagnostic laboratory access also appear to be important drivers of the patchy distribution of observed disease incidence. Using spatiotemporal predictive models we show that including climatic variability added retrospective predictive value over a baseline model (11% decrease in out-of-sample predictive error). However, predictions for 2020 show that a climate-driven model performs similarly overall to the baseline model. Overall, with ongoing improvements in surveillance there may be potential for forecasting Lassa fever incidence to inform health planning.
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