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Narayanan SA, Jamison DA, Guarnieri JW, Zaksas V, Topper M, Koutnik AP, Park J, Clark KB, Enguita FJ, Leitão AL, Das S, Moraes-Vieira PM, Galeano D, Mason CE, Trovão NS, Schwartz RE, Schisler JC, Coelho-Dos-Reis JGA, Wurtele ES, Beheshti A. A comprehensive SARS-CoV-2 and COVID-19 review, Part 2: host extracellular to systemic effects of SARS-CoV-2 infection. Eur J Hum Genet 2024; 32:10-20. [PMID: 37938797 PMCID: PMC10772081 DOI: 10.1038/s41431-023-01462-1] [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: 01/16/2023] [Revised: 09/01/2023] [Accepted: 09/13/2023] [Indexed: 11/09/2023] Open
Abstract
COVID-19, the disease caused by SARS-CoV-2, has caused significant morbidity and mortality worldwide. The betacoronavirus continues to evolve with global health implications as we race to learn more to curb its transmission, evolution, and sequelae. The focus of this review, the second of a three-part series, is on the biological effects of the SARS-CoV-2 virus on post-acute disease in the context of tissue and organ adaptations and damage. We highlight the current knowledge and describe how virological, animal, and clinical studies have shed light on the mechanisms driving the varied clinical diagnoses and observations of COVID-19 patients. Moreover, we describe how investigations into SARS-CoV-2 effects have informed the understanding of viral pathogenesis and provide innovative pathways for future research on the mechanisms of viral diseases.
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Affiliation(s)
- S Anand Narayanan
- COVID-19 International Research Team, Medford, MA, 02155, USA.
- Department of Health, Nutrition and Food Sciences, Florida State University, Tallahassee, FL, 32301, USA.
| | - David A Jamison
- COVID-19 International Research Team, Medford, MA, 02155, USA
| | - Joseph W Guarnieri
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Victoria Zaksas
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Center for Translational Data Science, University of Chicago, Chicago, IL, 60637, USA
- Clever Research Lab, Springfield, IL, 62704, USA
| | - Michael Topper
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Departments of Oncology and Medicine and the Sidney Comprehensive Cancer Center, The Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Andrew P Koutnik
- Human Healthspan, Resilience, and Performance, Florida Institute for Human and Machine Cognition, Pensacola, FL, 32502, USA
- Sansum Diabetes Research Institute, Santa Barbara, CA, 93015, USA
| | - Jiwoon Park
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, 10065, USA
| | - Kevin B Clark
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Cures Within Reach, Chicago, IL, 60602, USA
- Campus and Domain Champions Program, Multi-Tier Assistance, Training, and Computational Help (MATCH) Track, National Science Foundation's Advanced Cyberinfrastructure Coordination Ecosystem: Services and Support (ACCESS), Philadelphia, PA, USA
- Expert Network, Penn Center for Innovation, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Biometrics and Nanotechnology Councils, Institute for Electrical and Electronics Engineers, New York, NY, 10016, USA
- Peace Innovation Institute, The Hague 2511, Netherlands and Stanford University, Palo Alto, 94305, CA, USA
| | - Francisco J Enguita
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028, Lisboa, Portugal
| | - Ana Lúcia Leitão
- MEtRICs, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
| | - Saswati Das
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Atal Bihari Vajpayee Institute of Medical Sciences and Dr Ram Mannohar Lohia Hospital, New Delhi, 110001, India
| | - Pedro M Moraes-Vieira
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
- Experimental Medicine Research Cluster (EMRC) and Obesity and Comorbidities Research Center (OCRC), University of Campinas, Campinas, Brazil
| | - Diego Galeano
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Facultad de Ingeniería, Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | - Christopher E Mason
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- New York Genome Center, New York, NY, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Nídia S Trovão
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Fogarty International Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Robert E Schwartz
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Jonathan C Schisler
- COVID-19 International Research Team, Medford, MA, 02155, USA
- McAllister Heart Institute and Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jordana G A Coelho-Dos-Reis
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Basic and Applied Virology Lab, Department of Microbiology, Institute for Biological Sciences (ICB), Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Eve Syrkin Wurtele
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Genetics Program, Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 90011, USA
- Bioinformatics and Computational Biology Program, Center for Metabolomics, Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 90011, USA
| | - Afshin Beheshti
- COVID-19 International Research Team, Medford, MA, 02155, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Blue Marble Space Institute of Science, Space Biosciences Division, NASA Ames Research Center, Moffett Field, Santa Clara, CA, 94035, USA.
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Li X, Trovão NS, Wertheim JO, Baele G, de Bernardi Schneider A. Optimizing ancestral trait reconstruction of large HIV Subtype C datasets through multiple-trait subsampling. Virus Evol 2023; 9:vead069. [PMID: 38046219 PMCID: PMC10691791 DOI: 10.1093/ve/vead069] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/29/2023] [Accepted: 11/20/2023] [Indexed: 12/05/2023] Open
Abstract
Large datasets along with sampling bias represent a challenge for phylodynamic reconstructions, particularly when the study data are obtained from various heterogeneous sources and/or through convenience sampling. In this study, we evaluate the presence of unbalanced sampled distribution by collection date, location, and risk group of human immunodeficiency virus Type 1 Subtype C using a comprehensive subsampling strategy and assess their impact on the reconstruction of the viral spatial and risk group dynamics using phylogenetic comparative methods. Our study shows that a most suitable dataset for ancestral trait reconstruction can be obtained through subsampling by all available traits, particularly using multigene datasets. We also demonstrate that sampling bias is inflated when considerable information for a given trait is unavailable or of poor quality, as we observed for the trait risk group. In conclusion, we suggest that, even if traits are not well recorded, including them deliberately optimizes the representativeness of the original dataset rather than completely excluding them. Therefore, we advise the inclusion of as many traits as possible with the aid of subsampling approaches in order to optimize the dataset for phylodynamic analysis while reducing the computational burden. This will benefit research communities investigating the evolutionary and spatio-temporal patterns of infectious diseases.
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Affiliation(s)
| | - Nídia S Trovão
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, 31 Center Dr, Bethesda, MA 20892, USA
| | - Joel O Wertheim
- Department of Medicine, University of California, La Jolla, San Diego, CA 92093, USA
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven BE-3000, Belgium
| | - Adriano de Bernardi Schneider
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Ningbo No.2 Hospital, Ningbo 315010, China
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo 315000, China
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3
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Bukhari AR, Ashraf J, Kanji A, Rahman YA, Trovão NS, Thielen PM, Yameen M, Kanwar S, Khan W, Kabir F, Nisar MI, Merritt B, Hasan R, Spiro D, Rasmussen Z, Aamir UB, Hasan Z. Sequential viral introductions and spread of BA.1 across Pakistan provinces during the Omicron wave. BMC Genomics 2023; 24:432. [PMID: 37532989 PMCID: PMC10399012 DOI: 10.1186/s12864-023-09539-3] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 07/27/2023] [Indexed: 08/04/2023] Open
Abstract
BACKGROUND COVID-19 waves caused by specific SARS-CoV-2 variants have occurred globally at different times. We focused on Omicron variants to understand the genomic diversity and phylogenetic relatedness of SARS-CoV-2 strains in various regions of Pakistan. METHODS We studied 276,525 COVID-19 cases and 1,031 genomes sequenced from December 2021 to August 2022. Sequences were analyzed and visualized using phylogenetic trees. RESULTS The highest case numbers and deaths were recorded in Sindh and Punjab, the most populous provinces in Pakistan. Omicron variants comprised 93% of all genomes, with BA.2 (32.6%) and BA.5 (38.4%) predominating. The first Omicron wave was associated with the sequential identification of BA.1 in Sindh, then Islamabad Capital Territory, Punjab, Khyber Pakhtunkhwa (KP), Azad Jammu Kashmir (AJK), Gilgit-Baltistan (GB) and Balochistan. Phylogenetic analysis revealed Sindh to be the source of BA.1 and BA.2 introductions into Punjab and Balochistan during early 2022. BA.4 was first introduced in AJK and BA.5 in Punjab. Most recent common ancestor (MRCA) analysis revealed relatedness between the earliest BA.1 genome from Sindh with Balochistan, AJK, Punjab and ICT, and that of first BA.1 from Punjab with strains from KPK and GB. CONCLUSIONS Phylogenetic analysis provides insights into the introduction and transmission dynamics of the Omicron variant in Pakistan, identifying Sindh as a hotspot for viral dissemination. Such data linked with public health efforts can help limit surges of new infections.
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Affiliation(s)
- Ali Raza Bukhari
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, 74800, Pakistan
| | - Javaria Ashraf
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, 74800, Pakistan
| | - Akbar Kanji
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, 74800, Pakistan
| | - Yusra Abdul Rahman
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, 74800, Pakistan
| | - Nídia S Trovão
- Fogarty International Center, U.S. National Institutes of Health, 16 Center Drive, Bethesda, MD, 20892, USA
| | - Peter M Thielen
- Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, MD, 20723, USA
| | - Maliha Yameen
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, 74800, Pakistan
| | - Samiah Kanwar
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, 74800, Pakistan
| | - Waqasuddin Khan
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, 74800, Pakistan
| | - Furqan Kabir
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, 74800, Pakistan
| | - Muhammad Imran Nisar
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, 74800, Pakistan
| | - Brian Merritt
- Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, MD, 20723, USA
| | - Rumina Hasan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, 74800, Pakistan
| | - David Spiro
- Fogarty International Center, U.S. National Institutes of Health, 16 Center Drive, Bethesda, MD, 20892, USA
| | - Zeba Rasmussen
- Fogarty International Center, U.S. National Institutes of Health, 16 Center Drive, Bethesda, MD, 20892, USA
| | - Uzma Bashir Aamir
- World Health Organization Country Office, Park Road, Chak Shahzad, Islamabad, Pakistan
| | - Zahra Hasan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, 74800, Pakistan.
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4
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Zhang Z, Nishimura A, Trovão NS, Cherry JL, Holbrook AJ, Ji X, Lemey P, Suchard MA. Accelerating Bayesian inference of dependency between mixed-type biological traits. PLoS Comput Biol 2023; 19:e1011419. [PMID: 37639445 PMCID: PMC10491301 DOI: 10.1371/journal.pcbi.1011419] [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] [Received: 07/20/2022] [Revised: 09/08/2023] [Accepted: 08/09/2023] [Indexed: 08/31/2023] Open
Abstract
Inferring dependencies between mixed-type biological traits while accounting for evolutionary relationships between specimens is of great scientific interest yet remains infeasible when trait and specimen counts grow large. The state-of-the-art approach uses a phylogenetic multivariate probit model to accommodate binary and continuous traits via a latent variable framework, and utilizes an efficient bouncy particle sampler (BPS) to tackle the computational bottleneck-integrating many latent variables from a high-dimensional truncated normal distribution. This approach breaks down as the number of specimens grows and fails to reliably characterize conditional dependencies between traits. Here, we propose an inference pipeline for phylogenetic probit models that greatly outperforms BPS. The novelty lies in 1) a combination of the recent Zigzag Hamiltonian Monte Carlo (Zigzag-HMC) with linear-time gradient evaluations and 2) a joint sampling scheme for highly correlated latent variables and correlation matrix elements. In an application exploring HIV-1 evolution from 535 viruses, the inference requires joint sampling from an 11,235-dimensional truncated normal and a 24-dimensional covariance matrix. Our method yields a 5-fold speedup compared to BPS and makes it possible to learn partial correlations between candidate viral mutations and virulence. Computational speedup now enables us to tackle even larger problems: we study the evolution of influenza H1N1 glycosylations on around 900 viruses. For broader applicability, we extend the phylogenetic probit model to incorporate categorical traits, and demonstrate its use to study Aquilegia flower and pollinator co-evolution.
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Affiliation(s)
- Zhenyu Zhang
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, California, United States of America
| | - Akihiko Nishimura
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Nídia S. Trovão
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Joshua L. Cherry
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Andrew J. Holbrook
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, California, United States of America
| | - Xiang Ji
- Department of Mathematics, Tulane University, New Orleans, Louisiana, United States of America
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Marc A. Suchard
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Biomathematics, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Human Genetics, University of California Los Angeles, Los Angeles, California, United States of America
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5
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Gass JD, Dusek RJ, Hall JS, Hallgrimsson GT, Halldórsson HP, Vignisson SR, Ragnarsdottir SB, Jónsson JE, Krauss S, Wong SS, Wan XF, Akter S, Sreevatsan S, Trovão NS, Nutter FB, Runstadler JA, Hill NJ. Global dissemination of influenza A virus is driven by wild bird migration through arctic and subarctic zones. Mol Ecol 2023; 32:198-213. [PMID: 36239465 PMCID: PMC9797457 DOI: 10.1111/mec.16738] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [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: 08/20/2021] [Revised: 10/03/2022] [Accepted: 10/07/2022] [Indexed: 12/31/2022]
Abstract
Influenza A viruses (IAV) circulate endemically among many wild aquatic bird populations that seasonally migrate between wintering grounds in southern latitudes to breeding ranges along the perimeter of the circumpolar arctic. Arctic and subarctic zones are hypothesized to serve as ecologic drivers of the intercontinental movement and reassortment of IAVs due to high densities of disparate populations of long distance migratory and native bird species present during breeding seasons. Iceland is a staging ground that connects the East Atlantic and North Atlantic American flyways, providing a unique study system for characterizing viral flow between eastern and western hemispheres. Using Bayesian phylodynamic analyses, we sought to evaluate the viral connectivity of Iceland to proximal regions and how inter-species transmission and reassortment dynamics in this region influence the geographic spread of low and highly pathogenic IAVs. Findings demonstrate that IAV movement in the arctic and subarctic reflects wild bird migration around the perimeter of the circumpolar north, favouring short-distance flights between proximal regions rather than long distance flights over the polar interior. Iceland connects virus movement between mainland Europe and North America, consistent with the westward migration of wild birds from mainland Europe to Northeastern Canada and Greenland. Though virus diffusion rates were similar among avian taxonomic groups in Iceland, gulls play an outsized role as sinks of IAVs from other avian hosts prior to onward migration. These data identify patterns of virus movement in northern latitudes and inform future surveillance strategies related to seasonal and emergent IAVs with potential public health concern.
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Affiliation(s)
- Jonathon D. Gass
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University
| | | | | | | | | | - Solvi Runar Vignisson
- University of Iceland’s Research Centre in Suðurnes
- Suðurnes Science and Learning Center
| | | | | | - Scott Krauss
- Department of Infectious Diseases, St. Jude Children’s Research Hospital
| | - Sook-San Wong
- Department of Infectious Diseases, St. Jude Children’s Research Hospital
| | - Xiu-Feng Wan
- Center for Influenza and Emerging Infectious Diseases (CIEID), University of Missouri, Columbia
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia
- Bond Life Sciences Center, University of Missouri, Columbia
- Department of Electronic Engineering and Computer Science, University of Missouri, Columbia
| | - Sadia Akter
- Center for Influenza and Emerging Infectious Diseases (CIEID), University of Missouri, Columbia
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia
- Bond Life Sciences Center, University of Missouri, Columbia
- Department of Electronic Engineering and Computer Science, University of Missouri, Columbia
| | | | - Nídia S. Trovão
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health
| | - Felicia B. Nutter
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University
| | - Jonathan A. Runstadler
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University
| | - Nichola J. Hill
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University
- Department of Biology, University of Massachusetts, Boston
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Schimmoller BJ, Trovão NS, Isbell M, Goel C, Heck BF, Archer TC, Cardinal KD, Naik NB, Dutta S, Rohr Daniel A, Beheshti A. COVID-19 Exposure Assessment Tool (CEAT): Exposure quantification based on ventilation, infection prevalence, group characteristics, and behavior. Sci Adv 2022; 8:eabq0593. [PMID: 36179034 PMCID: PMC9524836 DOI: 10.1126/sciadv.abq0593] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 08/17/2022] [Indexed: 06/16/2023]
Abstract
The coronavirus disease 2019 (COVID-19) Exposure Assessment Tool (CEAT) allows users to compare respiratory relative risk to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) for various scenarios, providing understanding of how combinations of protective measures affect risk. CEAT incorporates mechanistic, stochastic, and epidemiological factors including the (i) emission rate of virus, (ii) viral aerosol degradation and removal, (iii) duration of activity/exposure, (iv) inhalation rates, (v) ventilation rates (indoors/outdoors), (vi) volume of indoor space, (vii) filtration, (viii) mask use and effectiveness, (ix) distance between people (taking into account both near-field and far-field effects of proximity), (x) group size, (xi) current infection rates by variant, (xii) prevalence of infection and immunity in the community, (xiii) vaccination rates, and (xiv) implementation of COVID-19 testing procedures. CEAT applied to published studies of COVID-19 transmission events demonstrates the model's accuracy. We also show how health and safety professionals at NASA Ames Research Center used CEAT to manage potential risks posed by SARS-CoV-2 exposures.
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Affiliation(s)
- Brian J. Schimmoller
- Signature Science LLC, Austin, TX 78759, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Nídia S. Trovão
- COVID-19 International Research Team, Medford, MA 02155, USA
- Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Chirag Goel
- COVID-19 International Research Team, Medford, MA 02155, USA
- Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Benjamin F. Heck
- Bastion Technologies, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Tenley C. Archer
- COVID-19 International Research Team, Medford, MA 02155, USA
- Biomea Fusion Inc., Redwood City, CA 94063, USA
| | - Klint D. Cardinal
- Leidos Inc., NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Neil B. Naik
- Leidos Inc., NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Som Dutta
- COVID-19 International Research Team, Medford, MA 02155, USA
- Mechanical and Aerospace Engineering, Utah State University, Logan, UT 84332, USA
| | - Ahleah Rohr Daniel
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Afshin Beheshti
- COVID-19 International Research Team, Medford, MA 02155, USA
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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7
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Otieno JR, Cherry JL, Spiro DJ, Nelson MI, Trovão NS. Origins and Evolution of Seasonal Human Coronaviruses. Viruses 2022; 14:1551. [PMID: 35891531 PMCID: PMC9320361 DOI: 10.3390/v14071551] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/11/2022] [Accepted: 07/11/2022] [Indexed: 11/16/2022] Open
Abstract
Four seasonal human coronaviruses (sHCoVs) are endemic globally (229E, NL63, OC43, and HKU1), accounting for 5-30% of human respiratory infections. However, the epidemiology and evolution of these CoVs remain understudied due to their association with mild symptomatology. Using a multigene and complete genome analysis approach, we find the evolutionary histories of sHCoVs to be highly complex, owing to frequent recombination of CoVs including within and between sHCoVs, and uncertain, due to the under sampling of non-human viruses. The recombination rate was highest for 229E and OC43 whereas substitutions per recombination event were highest in NL63 and HKU1. Depending on the gene studied, OC43 may have ungulate, canine, or rabbit CoV ancestors. 229E may have origins in a bat, camel, or an unsampled intermediate host. HKU1 had the earliest common ancestor (1809-1899) but fell into two distinct clades (genotypes A and B), possibly representing two independent transmission events from murine-origin CoVs that appear to be a single introduction due to large gaps in the sampling of CoVs in animals. In fact, genotype B was genetically more diverse than all the other sHCoVs. Finally, we found shared amino acid substitutions in multiple proteins along the non-human to sHCoV host-jump branches. The complex evolution of CoVs and their frequent host switches could benefit from continued surveillance of CoVs across non-human hosts.
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Affiliation(s)
- James R. Otieno
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA; (J.L.C.); (D.J.S.); (M.I.N.)
| | - Joshua L. Cherry
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA; (J.L.C.); (D.J.S.); (M.I.N.)
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - David J. Spiro
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA; (J.L.C.); (D.J.S.); (M.I.N.)
| | - Martha I. Nelson
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA; (J.L.C.); (D.J.S.); (M.I.N.)
| | - Nídia S. Trovão
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA; (J.L.C.); (D.J.S.); (M.I.N.)
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8
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Ayora-Talavera G, Kirstein OD, Puerta-Guardo H, Barrera-Fuentes GA, Ortegòn-Abud D, Che-Mendoza A, Parra M, Peña-Miranda F, Culquichicon C, Pavia-Ruz N, Beheshti A, Trovão NS, Granja-Pérez P, Manrique-Saide P, Vazquez-Prokopec GM, Earnest JT. SARS-CoV-2 antibody prevalence in a pediatric cohort of unvaccinated children in Mérida, Yucatán, México. PLOS Glob Public Health 2022; 2:e0000354. [PMID: 36962356 PMCID: PMC10021704 DOI: 10.1371/journal.pgph.0000354] [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] [Received: 11/24/2021] [Accepted: 05/25/2022] [Indexed: 11/18/2022]
Abstract
The prevalence of SARS-CoV-2 exposure in children during the global COVID-19 pandemic has been underestimated due to lack of testing and the relatively mild symptoms in adolescents. Understanding the exposure rates in the pediatric population is essential as children are the last to receive vaccines and can act as a source for SARS-CoV-2 mutants that may threaten vaccine escape. This cross-sectional study aims to quantify the prevalence of anti-SARS-CoV-2 serum antibodies in children in a major city in México in the Spring of 2021 and determine if there are any demographic or socioeconomic correlating factors. We obtained socioeconomic information and blood samples from 1,005 children from 50 neighborhood clusters in Mérida, Yucatán, México. We then tested the sera of these participants for anti-SARS-CoV-2 IgG and IgM antibodies using lateral flow immunochromatography. We found that 25.5% of children in our cohort were positive for anti-SARS-CoV-2 antibodies and there was no correlation between age and antibody prevalence. Children that lived with large families were statistically more likely to have antibodies against SARS-CoV-2. Spatial analyses identified two hotspots of high SARS-CoV-2 seroprevalence in the west of the city. These results indicate that a large urban population of unvaccinated children has been exposed to SARS-CoV-2 and that a major correlating factor was the number of people within the child's household with a minor correlation with particular geographical hotspots. There is also a larger population of children that may be susceptible to future infection upon easing of social distancing measures. These findings suggest that in future pandemic scenarios, limited public health resources can be best utilized on children living in large households in urban areas.
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Affiliation(s)
- Guadalupe Ayora-Talavera
- Virology Laboratory, Centro de Investigaciones Regionales Dr. Hideyo Noguchi, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
| | - Oscar D. Kirstein
- Department of Environmental Sciences, Emory University, Atlanta, GA, United States of America
| | - Henry Puerta-Guardo
- Virology Laboratory, Centro de Investigaciones Regionales Dr. Hideyo Noguchi, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
- Campus de Ciencias Biológicas y Agropecuarias, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
| | - Gloria A. Barrera-Fuentes
- Campus de Ciencias Biológicas y Agropecuarias, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
- Hematology Laboratory, Centro de Investigaciones Regionales Dr. Hideyo Noguchi, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
| | - Desiree Ortegòn-Abud
- Campus de Ciencias Biológicas y Agropecuarias, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
- Hematology Laboratory, Centro de Investigaciones Regionales Dr. Hideyo Noguchi, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
| | - Azael Che-Mendoza
- Campus de Ciencias Biológicas y Agropecuarias, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
| | - Manuel Parra
- Virology Laboratory, Centro de Investigaciones Regionales Dr. Hideyo Noguchi, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
- Campus de Ciencias Biológicas y Agropecuarias, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
| | | | - Carlos Culquichicon
- Department of Environmental Sciences, Emory University, Atlanta, GA, United States of America
- Rollins School of Public Health, Emory University, Atlanta, GA, United States of America
| | - Norma Pavia-Ruz
- Hematology Laboratory, Centro de Investigaciones Regionales Dr. Hideyo Noguchi, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
| | - Afshin Beheshti
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, United States of America
- COVID-19 International Research Team, Medford, MA, United States of America
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, United States of America
| | - Nídia S. Trovão
- COVID-19 International Research Team, Medford, MA, United States of America
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | | | - Pablo Manrique-Saide
- Campus de Ciencias Biológicas y Agropecuarias, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
| | | | - James T. Earnest
- Department of Environmental Sciences, Emory University, Atlanta, GA, United States of America
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9
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Hill NJ, Bishop MA, Trovão NS, Ineson KM, Schaefer AL, Puryear WB, Zhou K, Foss AD, Clark DE, MacKenzie KG, Gass JD, Borkenhagen LK, Hall JS, Runstadler JA. Ecological divergence of wild birds drives avian influenza spillover and global spread. PLoS Pathog 2022; 18:e1010062. [PMID: 35588106 PMCID: PMC9119557 DOI: 10.1371/journal.ppat.1010062] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [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: 10/26/2021] [Accepted: 04/01/2022] [Indexed: 01/21/2023] Open
Abstract
The diversity of influenza A viruses (IAV) is primarily hosted by two highly divergent avian orders: Anseriformes (ducks, swans and geese) and Charadriiformes (gulls, terns and shorebirds). Studies of IAV have historically focused on Anseriformes, specifically dabbling ducks, overlooking the diversity of hosts in nature, including gull and goose species that have successfully adapted to human habitats. This study sought to address this imbalance by characterizing spillover dynamics and global transmission patterns of IAV over 10 years at greater taxonomic resolution than previously considered. Furthermore, the circulation of viral subtypes in birds that are either host-adapted (low pathogenic H13, H16) or host-generalist (highly pathogenic avian influenza—HPAI H5) provided a unique opportunity to test and extend models of viral evolution. Using Bayesian phylodynamic modelling we uncovered a complex transmission network that relied on ecologically divergent bird hosts. The generalist subtype, HPAI H5 was driven largely by wild geese and swans that acted as a source for wild ducks, gulls, land birds, and domestic geese. Gulls were responsible for moving HPAI H5 more rapidly than any other host, a finding that may reflect their long-distance, pelagic movements and their immuno-naïve status against this subtype. Wild ducks, long viewed as primary hosts for spillover, occupied an optimal space for viral transmission, contributing to geographic expansion and rapid dispersal of HPAI H5. Evidence of inter-hemispheric dispersal via both the Pacific and Atlantic Rims was detected, supporting surveillance at high latitudes along continental margins to achieve early detection. Both neutral (geographic expansion) and non-neutral (antigenic selection) evolutionary processes were found to shape subtype evolution which manifested as unique geographic hotspots for each subtype at the global scale. This study reveals how a diversity of avian hosts contribute to viral spread and spillover with the potential to improve surveillance in an era of rapid global change. Our study provides novel insights into the biology of influenza A virus (IAV), which is timely in view of the unusually large number of animal and human cases of highly pathogenic avian influenza (HPAI) H5 across Europe, Asia, Africa and North America. Currently we face challenges with predicting how the avian reservoir will influence IAV spread because the mechanisms by which different subtypes disperse are not well understood. Our study sought to address this knowledge gap by systematically comparing the evolutionary dynamics that drive IAV transmission across subtypes and bird hosts with the goal of identifying spillover pathways at the wild-domestic interface. By analyzing the evolution of IAV over 10 years at greater taxonomic resolution than previously considered, we uncovered a complex transmission network that relied on ecologically divergent bird hosts. Domestic birds were responsible for slow but steady range expansion of HPAI H5, while wild birds such as geese, swans, gulls and ducks contibuted to rapid but episodic dispersal via uniquely different pathways. By assessing how virus-host systems are coupled, findings from this study have the potential to refine and enhance global surveillance and outbreak prediction.
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Affiliation(s)
- Nichola J. Hill
- Department of Biology, University of Massachusetts, Boston, Massachusetts, United States of America
- * E-mail:
| | - Mary Anne Bishop
- Prince William Sound Science Center, Cordova, Alaska, United States of America
| | - Nídia S. Trovão
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Katherine M. Ineson
- U.S. Fish and Wildlife Service, Hadley, Massachusetts, United States of America
| | - Anne L. Schaefer
- Prince William Sound Science Center, Cordova, Alaska, United States of America
| | - Wendy B. Puryear
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine Tufts University, North Grafton, Massachusetts, United States of America
| | - Katherine Zhou
- College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Alexa D. Foss
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine Tufts University, North Grafton, Massachusetts, United States of America
| | - Daniel E. Clark
- Division of Water Supply Protection, Massachusetts Department of Conservation and Recreation, West Boylston, Massachusetts, United States of America
| | - Kenneth G. MacKenzie
- Division of Water Supply Protection, Massachusetts Department of Conservation and Recreation, West Boylston, Massachusetts, United States of America
| | - Jonathon D. Gass
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine Tufts University, North Grafton, Massachusetts, United States of America
| | - Laura K. Borkenhagen
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine Tufts University, North Grafton, Massachusetts, United States of America
| | - Jeffrey S. Hall
- U.S. Geological Survey, National Wildlife Health Center, Madison, Wisconsin, United States of America
| | - Jonathan A. Runstadler
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine Tufts University, North Grafton, Massachusetts, United States of America
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10
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Jamison DA, Anand Narayanan S, Trovão NS, Guarnieri JW, Topper MJ, Moraes-Vieira PM, Zaksas V, Singh KK, Wurtele ES, Beheshti A. A comprehensive SARS-CoV-2 and COVID-19 review, Part 1: Intracellular overdrive for SARS-CoV-2 infection. Eur J Hum Genet 2022; 30:889-898. [PMID: 35577935 PMCID: PMC9108708 DOI: 10.1038/s41431-022-01108-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [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: 11/24/2021] [Revised: 03/20/2022] [Accepted: 04/12/2022] [Indexed: 12/15/2022] Open
Abstract
COVID-19, the disease caused by SARS-CoV-2, has claimed approximately 5 million lives and 257 million cases reported globally. This virus and disease have significantly affected people worldwide, whether directly and/or indirectly, with a virulent pathogen that continues to evolve as we race to learn how to prevent, control, or cure COVID-19. The focus of this review is on the SARS-CoV-2 virus' mechanism of infection and its proclivity at adapting and restructuring the intracellular environment to support viral replication. We highlight current knowledge and how scientific communities with expertize in viral, cellular, and clinical biology have contributed to increase our understanding of SARS-CoV-2, and how these findings may help explain the widely varied clinical observations of COVID-19 patients.
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Affiliation(s)
| | - S Anand Narayanan
- COVID-19 International Research Team, Medford, MA, USA. .,Department of Nutrition & Integrative Physiology, Florida State University, Tallahassee, FL, USA.
| | - Nídia S Trovão
- COVID-19 International Research Team, Medford, MA, USA.,Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Joseph W Guarnieri
- COVID-19 International Research Team, Medford, MA, USA.,Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Michael J Topper
- COVID-19 International Research Team, Medford, MA, USA.,Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA
| | - Pedro M Moraes-Vieira
- COVID-19 International Research Team, Medford, MA, USA.,Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, SP, Brazil.,Obesity and Comorbidities research Center (OCRC), University of Campinas, Campinas, SP, Brazil.,Experimental Medicine Research Cluster, University of Campinas, Campinas, Brazil
| | - Viktorija Zaksas
- COVID-19 International Research Team, Medford, MA, USA.,Center for Translational Data Science, University of Chicago, Chicago, IL, USA
| | - Keshav K Singh
- COVID-19 International Research Team, Medford, MA, USA.,Department of Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Eve Syrkin Wurtele
- COVID-19 International Research Team, Medford, MA, USA.,Center for Metabolic Biology, Bioinformatics and Computational Biology, and Genetics Development, and Cell Biology, Iowa State University, Ames, IA, USA
| | - Afshin Beheshti
- COVID-19 International Research Team, Medford, MA, USA. .,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA.
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11
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Okoh OS, Nii-Trebi NI, Jakkari A, Olaniran TT, Senbadejo TY, Kafintu-Kwashie AA, Dairo EO, Ganiyu TO, Akaninyene IE, Ezediuno LO, Adeosun IJ, Ockiya MA, Jimah EM, Spiro DJ, Oladipo EK, Trovão NS. Epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in Africa. iScience 2022; 25:103880. [PMID: 35156006 PMCID: PMC8817759 DOI: 10.1016/j.isci.2022.103880] [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] [Received: 08/03/2021] [Revised: 11/29/2021] [Accepted: 02/03/2022] [Indexed: 12/15/2022] Open
Abstract
There is a dearth of information on COVID-19 disease dynamics in Africa. To fill this gap, we investigated the epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in the continent. We retrieved 5229 complete genomes collected in 33 African countries from the GISAID database. We investigated the circulating diversity, reconstructed the viral evolutionary divergence and history, and studied the case and death trends in the continent. Almost a fifth (144/782, 18.4%) of Pango lineages found worldwide circulated in Africa, with five different lineages dominating over time. Phylogenetic analysis revealed that African viruses cluster more closely with those from Europe. We also identified two motifs that could function as integrin-binding sites and N-glycosylation domains. These results shed light on the epidemiological and evolutionary dynamics of the circulating viral diversity in Africa. They also emphasize the need to expand surveillance efforts in Africa to help inform and implement better public health measures. SARS-CoV-2 viruses from Africa cluster predominantly with European strains Lower viral diversity observed in Africa is likely due to genomic under-surveillance Number of cases, deaths, and testing show substantial heterogeneity across Africa Two motifs could function as integrin-binding sites and N-glycosylation domains
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Affiliation(s)
| | - Nicholas Israel Nii-Trebi
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana, Accra, Ghana
| | - Abdulrokeeb Jakkari
- Department of Microbiology, Faculty of Science, Lagos State University, Ojo, Lagos, Nigeria
| | - Tosin Titus Olaniran
- Department of Pure and Applied Biology (Microbiology Unit), Ladoke Akintola University of Technology, Ogbomoso, Nigeria.,Helix Biogen Institute, Ogbomoso, Nigeria
| | - Tosin Yetunde Senbadejo
- Department of Biological Sciences, College of Natural and Applied Sciences, Fountain University, Osogbo, Nigeria
| | - Anna Aba Kafintu-Kwashie
- Department of Medical Microbiology, Clinical Virology Unit, University of Ghana Medical School, Accra, Ghana
| | - Emmanuel Oluwatobi Dairo
- Helix Biogen Institute, Ogbomoso, Nigeria.,Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Tajudeen Oladunni Ganiyu
- Department of Biological Sciences, College of Natural and Applied Sciences, Fountain University, Osogbo, Nigeria
| | - Ifiokakaninyene Ekpo Akaninyene
- Department of Pure and Applied Biology (Microbiology Unit), Ladoke Akintola University of Technology, Ogbomoso, Nigeria.,Helix Biogen Institute, Ogbomoso, Nigeria
| | - Louis Odinakaose Ezediuno
- Department of Microbiology, Faculty of Life Sciences, University of Ilorin,1515 P.M.B, Ilorin, Nigeria
| | - Idowu Jesulayomi Adeosun
- Department of Microbiology, Laboratory of Molecular Biology, Immunology and Bioinformatics, Adeleke University, Ede, Osun, Nigeria.,Division of Microbiology, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Private Bag X20, Hatfield Pretoria 0028, South Africa
| | - Michael Asebake Ockiya
- Department of Animal Science, Niger Delta University, Wilberforce Island, Bayelsa, Nigeria
| | - Esther Moradeyo Jimah
- Helix Biogen Institute, Ogbomoso, Nigeria.,Department of Medical Microbiology and Parasitology, University of Ilorin 1515, P.M.B, Ilorin, Nigeria
| | - David J Spiro
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Elijah Kolawole Oladipo
- Helix Biogen Institute, Ogbomoso, Nigeria.,Department of Microbiology, Laboratory of Molecular Biology, Immunology and Bioinformatics, Adeleke University, Ede, Osun, Nigeria
| | - Nídia S Trovão
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
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12
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Nasir A, Bukhari AR, Trovão NS, Thielen PM, Kanji A, Mahmood SF, Ghanchi NK, Ansar Z, Merritt B, Mehoke T, Razzak SA, Syed MA, Shaikh SR, Wassan M, Bashir Aamir U, Baele G, Rasmussen Z, Spiro D, Hasan R, Hasan Z. Evolutionary History and Introduction of SARS-CoV-2 Alpha VOC/B.1.1.7 in Pakistan Through International Travelers. Virus Evol 2022; 8:veac020. [PMID: 35462736 PMCID: PMC9021734 DOI: 10.1093/ve/veac020] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 02/18/2022] [Accepted: 03/14/2022] [Indexed: 11/12/2022] Open
Abstract
Abstract
SARS-CoV-2 variants continue to emerge, and their identification is important for the public health response to COVID-19. Genomic sequencing provides robust information but may not always be accessible and therefore rapid mutation-based PCR approaches can be used to identify known variants. International travelers arriving in Karachi between December 2020 and February 2021 were tested for SARS-CoV-2 by PCR. A subset of positive samples was tested for S-Gene Target Failure (SGTF) on TaqPathTM COVID-19 (Thermo Fisher Scientific) and for mutations using the GSD NovaType SARS-CoV-2 (Eurofins Technologies) assays. Sequencing was conducted on the MinION platform (Oxford Nanopore Technologies (ONT). Bayesian phylogeographic inference was performed integrating the patients’ travel history information. Of the thirty-five COVID-19 cases screened, thirteen had isolates with SGTF. The travelers transmitted infection to sixty-eight contact cases. The B.1.1.7 lineage was confirmed through sequencing and PCR. Phylogenetic analysis of sequence data available for six cases included four B.1.1.7 strains and one B.1.36 and B.1.1.212 lineage isolate, respectively. Phylogeographic modeling estimated at least three independent B.1.1.7 introductions into Karachi, Pakistan, originating from the UK. B.1.1.212 and B.1.36 were inferred to be introduced either from the UK or the travelers’ layover location. We report the introduction of SARS-CoV-2 B.1.1.7 and other lineages in Pakistan by international travelers arriving via different flight routes. This highlights SARS-CoV-2 transmission through travel, importance of testing and quarantine post-travel to prevent transmission of new strains, as well as recording detailed patients’ metadata. Such results help inform policies on restricting travel from destinations where new highly transmissible variants have emerged.
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Affiliation(s)
- Asghar Nasir
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan
| | - Ali Raza Bukhari
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan
| | - Nídia S Trovão
- Fogarty International Center, National Institute of Health, Bethesda, Maryland, USA
| | - Peter M Thielen
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland, USA
| | - Akbar Kanji
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan
| | | | - Najia Karim Ghanchi
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan
| | - Zeeshan Ansar
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan
| | - Brian Merritt
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland, USA
| | - Thomas Mehoke
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland, USA
| | - Safina Abdul Razzak
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan
| | | | | | - Mansoor Wassan
- Department of Medicine, The Aga Khan University, Karachi, Pakistan
| | | | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Zeba Rasmussen
- Fogarty International Center, National Institute of Health, Bethesda, Maryland, USA
| | - David Spiro
- Fogarty International Center, National Institute of Health, Bethesda, Maryland, USA
| | - Rumina Hasan
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan
| | - Zahra Hasan
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan
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13
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Schimmoller BJ, Trovão NS, Isbell M, Goel C, Heck BF, Archer TC, Cardinal KD, Naik NB, Dutta S, Daniel AR, Beheshti A. Covid-19 Exposure Assessment Tool (CEAT): Easy-to-use tool to quantify exposure based on airflow, group behavior, and infection prevalence in the community.. [PMID: 35291295 PMCID: PMC8923112 DOI: 10.1101/2022.03.02.22271806] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The COVID-19 Exposure Assessment Tool (CEAT) allows users to compare respiratory relative risk to SARS-CoV-2 for various scenarios, providing understanding of how combinations of protective measures affect exposure, dose, and risk. CEAT incorporates mechanistic, stochastic and epidemiological factors including the: 1) emission rate of virus, 2) viral aerosol degradation and removal, 3) duration of activity/exposure, 4) inhalation rates, 5) ventilation rates (indoors/outdoors), 6) volume of indoor space, 7) filtration, 8) mask use and effectiveness, 9) distance between people, 10) group size, 11) current infection rates by variant, 12) prevalence of infection and immunity in the community, 13) vaccination rates of the community, and 14) implementation of COVID-19 testing procedures. Demonstration of CEAT, from published studies of COVID-19 transmission events, shows the model accurately predicts transmission. We also show how health and safety professionals at NASA Ames Research Center used CEAT to manage potential risks posed by SARS-CoV-2 exposures. Given its accuracy and flexibility, the wide use of CEAT will have a long lasting beneficial impact in managing both the current COVID-19 pandemic as well as a variety of other scenarios.
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14
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Li X, Li Y, Liu H, Trovão NS, Foley BT. The Emergence and Transmission Dynamics of HIV-1 CRF07_BC in Mainland China. Virus Evol 2022; 8:veac014. [PMID: 35350472 PMCID: PMC8946679 DOI: 10.1093/ve/veac014] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 02/03/2022] [Accepted: 02/17/2022] [Indexed: 11/16/2022] Open
Abstract
A total of 1155 partial pol gene sequences of human immunodeficiency virus (HIV)-1 CRF07_BC were sampled between 1997 and 2015, spanning 13 provinces in Mainland China and risk groups [heterosexual, injecting drug users (IDU), and men who have sex with men (MSM)] to investigate the evolution, adaptation, spatiotemporal and risk group dynamics, migration patterns, and protein structure of HIV-1 CRF07_BC. Due to the unequal distribution of sequences across time, location, and risk group in the complete dataset (‘full1155’), subsampling methods were used. Maximum-likelihood and Bayesian phylogenetic analysis as well as discrete trait analysis of geographical location and risk group were carried out. To study mutations of a cluster of HIV-1 CRF07_BC (CRF07-1), we performed a comparative analysis of this cluster to the other CRF07_BC sequences (‘backbone_295’) and mapped the mutations observed in the respective protein structure. Our findings showed that HIV-1 CRF07_BC most likely originated among IDU in Yunnan Province between October 1992 to July 1993 [95 per cent hightest posterior density (HPD): May 1989–August 1995] and that IDU in Yunnan Province and MSM in Guangdong Province likely served as the viral sources during the early and more recent spread in Mainland China. We also revealed that HIV-1 CRF07-1 has been spreading for roughly 20 years and continues to cause local transmission in Mainland China and worldwide. Overall, our study sheds light on the dynamics of HIV-1 CRF07_BC distribution patterns in Mainland China. Our research may also be useful in formulating public health policies aimed at controlling acquired immune deficiency syndrome in Mainland China and globally.
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Affiliation(s)
- Xingguang Li
- Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, 315010, China
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, 315000, China
| | - Yanping Li
- College of Chemistry Biology and Environment, Yuxi Normal University, Yuxi, 653100, China
| | - Haizhou Liu
- National Virus Resource Center, Wuhan Institute of Virology, University of Chinese Academy of Sciences, Wuhan, 430071, China
| | - Nídia S Trovão
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Brian T Foley
- HIV Databases, Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, USA
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15
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Morais P, Trovão NS, Abecasis AB, Parreira R. Genetic lineage characterization and spatiotemporal dynamics of classical insect-specific flaviviruses: outcomes and limitations. Virus Res 2021; 303:198507. [PMID: 34271039 DOI: 10.1016/j.virusres.2021.198507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 07/06/2021] [Accepted: 07/07/2021] [Indexed: 12/28/2022]
Abstract
The genus Flavivirus incorporates bona fide arboviruses, as well as others viruses with restricted replication in insect cells. Among the latter, a large monophyletic cluster of viruses, known as cISF (classical insect-specific flaviviruses), has been sampled in many species of mosquitoes collected over a large geographic range. In this study, we investigated nucleotide and protein sequences with a suite of molecular characterization approaches including genetic distance, Shannon entropy, selective pressure analysis, polymorphism identification, principal coordinate analysis, likelihood mapping, phylodynamic reconstruction, and spatiotemporal dispersal, to further characterize this diverse group of insect-viruses. The different lineages and sub-lineages of viral sequences presented low sequence diversity and entropy (though some displayed lineage-specific polymorphisms), did not show evidence of frequent recombination and evolved under strong purifying selection. Moreover, the reconstruction of the evolutionary history and spatiotemporal dispersal was highly impacted by overall low signals of sequence divergence throughout time but suggested that cISF distribution in space and time is dynamic and may be dependent on human activities, including commercial trading and traveling.
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Affiliation(s)
- Paulo Morais
- Unidade de Microbiologia Médica, Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (NOVA), Lisboa, Portugal/Global Health and Tropical Medicine (GHTM), Lisboa, Portugal
| | - Nídia S Trovão
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Ana B Abecasis
- Unidade de Saúde Pública Internacional e Bioestatística, Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (NOVA), Lisboa, Portugal/Global Health and Tropical Medicine (GHTM), Lisboa, Portugal
| | - Ricardo Parreira
- Unidade de Microbiologia Médica, Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (NOVA), Lisboa, Portugal/Global Health and Tropical Medicine (GHTM), Lisboa, Portugal.
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16
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Trovão NS, Khuri-Bulos N, Tan Y, Puri V, Shilts MH, Halpin RA, Fedorova NB, Nelson MI, Halasa N, Das SR. Molecular characterization of respiratory syncytial viruses circulating in a paediatric cohort in Amman, Jordan. Microb Genom 2021; 7:000292. [PMID: 31532357 PMCID: PMC8627666 DOI: 10.1099/mgen.0.000292] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 08/15/2019] [Indexed: 12/20/2022] Open
Abstract
Respiratory syncytial viruses (RSVs) are an important cause of mortality worldwide and a major cause of respiratory tract infections in children, driving development of vaccine candidates. However, there are large gaps in our knowledge of the local evolutionary and transmission dynamics of RSVs, particularly in understudied regions such as the Middle East. To address this gap, we sequenced the complete genomes of 58 RSVA and 27 RSVB samples collected in a paediatric cohort in Amman, Jordan, between 2010 and 2013. RSVA and RSVB co-circulated during each winter epidemic of RSV in Amman, and each epidemic comprised multiple independent viral introductions of RSVA and RSVB. However, RSVA and RSVB alternated in dominance across years, potential evidence of immunological interactions. Children infected with RSVA tended to be older than RSVB-infected children [30 months versus 22.4 months, respectively (P value = 0.02)], and tended to developed bronchopneumonia less frequently than those with RSVB, although the difference was not statistically significant (P value = 0.06). Differences in spatial patterns were investigated, and RSVA lineages were often identified in multiple regions in Amman, whereas RSVB introductions did not spread beyond a single region of the city, although these findings were based on small sample sizes. Multiple RSVA genotypes were identified in Amman, including GA2 viruses as well as three viruses from the ON1 sub-genotype that emerged in 2009 and are now the dominant genotype circulating worldwide. As vaccine development advances, further sequencing of RSV is needed to understand viral ecology and transmission, particularly in under-studied locations.
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Affiliation(s)
- Nídia S. Trovão
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Najwa Khuri-Bulos
- Division of Infectious Diseases, Department of Pediatrics, University of Jordan, Amman, Jordan
| | - Yi Tan
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Infectious Disease Group, J. Craig Venter Institute, Rockville, MD, USA
| | - Vinita Puri
- Infectious Disease Group, J. Craig Venter Institute, Rockville, MD, USA
| | - Meghan H. Shilts
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Infectious Disease Group, J. Craig Venter Institute, Rockville, MD, USA
| | - Rebecca A. Halpin
- Infectious Disease Group, J. Craig Venter Institute, Rockville, MD, USA
| | - Nadia B. Fedorova
- Infectious Disease Group, J. Craig Venter Institute, Rockville, MD, USA
| | - Martha I. Nelson
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Natasha Halasa
- Departments of Pediatrics, Vanderbilt University, Nashville, TN, USA
| | - Suman R. Das
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Infectious Disease Group, J. Craig Venter Institute, Rockville, MD, USA
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17
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Okoh OS, Nii-Trebi NI, Jakkari A, Olaniran TT, Senbadejo TY, Kafintu-kwashie AA, Dairo EO, Ganiyu TO, Akaninyene IE, Ezediuno LO, Adeosun IJ, Ockiya MA, Jimah EM, Spiro DJ, Oladipo EK, Trovão NS. Epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in Africa. medRxiv 2021:2021.05.17.21257341. [PMID: 34031660 PMCID: PMC8142660 DOI: 10.1101/2021.05.17.21257341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
COVID-19 disease dynamics have been widely studied in different settings around the globe, but little is known about these patterns in the African continent. To investigate the epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in Africa, more than 2400 complete genomes from 33 African countries were retrieved from the GISAID database and analyzed. We investigated their diversity using various clade and lineage nomenclature systems, reconstructed their evolutionary divergence and history using maximum likelihood inference methods, and studied the case and death trends in the continent. We also examined potential repeat patterns and motifs across the sequences. In this study, we show that after almost one year of the COVID-19 pandemic, only 143 out of the 782 Pango lineages found worldwide circulated in Africa, with five different lineages dominating in distinct periods of the pandemic. Analysis of the number of reported deaths in Africa also revealed large heterogeneity across the continent. Phylogenetic analysis revealed that African viruses cluster closely with those from all continents but more notably with viruses from Europe. However, the extent of viral diversity observed among African genomes is closest to that of the Oceania outbreak, most likely due to genomic under-surveillance in Africa. We also identified two motifs that could function as integrin-binding sites and N-glycosylation domains. These results shed light on the evolutionary dynamics of the circulating viral strains in Africa, elucidate the functions of protein motifs present in the genome sequences, and emphasize the need to expand genomic surveillance efforts in the continent to better understand the molecular, evolutionary, epidemiological, and spatiotemporal dynamics of the COVID-19 pandemic in Africa.
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Affiliation(s)
| | - Nicholas Israel Nii-Trebi
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana, Accra, Ghana
| | - Abdulrokeeb Jakkari
- Department of Microbiology, Faculty of Science, Lagos State University, Ojo, Lagos, Nigeria
| | - Tosin Titus Olaniran
- Department of Pure and Applied Biology (Microbiology Unit), Ladoke Akintola University of Technology, Ogbomoso, Nigeria
- Helix Biogen Institute, Ogbomoso, Nigeria
| | - Tosin Yetunde Senbadejo
- Department of Biological Sciences, College of Natural and Applied Sciences, Fountain University, Osogbo, Nigeria
| | - Anna Aba Kafintu-kwashie
- Department of Medical Microbiology Clinical Virology unit, University of Ghana Medical School, Accra, Ghana
| | - Emmanuel Oluwatobi Dairo
- Helix Biogen Institute, Ogbomoso, Nigeria
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Tajudeen Oladunni Ganiyu
- Department of Biological Sciences, College of Natural and Applied Sciences, Fountain University, Osogbo, Nigeria
| | - Ifiokakaninyene Ekpo Akaninyene
- Department of Pure and Applied Biology (Microbiology Unit), Ladoke Akintola University of Technology, Ogbomoso, Nigeria
- Helix Biogen Institute, Ogbomoso, Nigeria
| | | | - Idowu Jesulayomi Adeosun
- Department of Microbiology, Laboratory of Molecular Biology, Immunology and Bioinformatics, Adeleke University, Ede, Osun State, Nigeria
| | - Michael Asebake Ockiya
- Department of Animal Science, Niger Delta University, Wilberforce Island, Bayelsa State, Nigeria
| | - Esther Moradeyo Jimah
- Helix Biogen Institute, Ogbomoso, Nigeria
- Department of Medical Microbiology and Parasitology, University of Ilorin, Nigeria
| | - David J. Spiro
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Elijah Kolawole Oladipo
- Helix Biogen Institute, Ogbomoso, Nigeria
- Department of Microbiology, Laboratory of Molecular Biology, Immunology and Bioinformatics, Adeleke University, Ede, Osun State, Nigeria
| | - Nídia S. Trovão
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA
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18
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Thielen PM, Wohl S, Mehoke T, Ramakrishnan S, Kirsche M, Falade-Nwulia O, Trovão NS, Ernlund A, Howser C, Sadowski N, Morris CP, Hopkins M, Schwartz M, Fan Y, Gniazdowski V, Lessler J, Sauer L, Schatz MC, Evans JD, Ray SC, Timp W, Mostafa HH. Genomic diversity of SARS-CoV-2 during early introduction into the Baltimore-Washington metropolitan area. JCI Insight 2021; 6:144350. [PMID: 33749660 PMCID: PMC8026189 DOI: 10.1172/jci.insight.144350] [Citation(s) in RCA: 21] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 02/10/2021] [Indexed: 01/19/2023] Open
Abstract
The early COVID-19 pandemic was characterized by rapid global spread. In Maryland and Washington, DC, United States, more than 2500 cases were reported within 3 weeks of the first COVID-19 detection in March 2020. We aimed to use genomic sequencing to understand the initial spread of SARS-CoV-2 — the virus that causes COVID-19 — in the region. We analyzed 620 samples collected from the Johns Hopkins Health System during March 11–31, 2020, comprising 28.6% of the total cases in Maryland and Washington, DC. From these samples, we generated 114 complete viral genomes. Analysis of these genomes alongside a subsampling of over 1000 previously published sequences showed that the diversity in this region rivaled global SARS-CoV-2 genetic diversity at that time and that the sequences belong to all of the major globally circulating lineages, suggesting multiple introductions into the region. We also analyzed these regional SARS-CoV-2 genomes alongside detailed clinical metadata and found that clinically severe cases had viral genomes belonging to all major viral lineages. We conclude that efforts to control local spread of the virus were likely confounded by the number of introductions into the region early in the epidemic and the interconnectedness of the region as a whole.
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Affiliation(s)
- Peter M Thielen
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland, USA
| | - Shirlee Wohl
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Thomas Mehoke
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland, USA
| | | | - Melanie Kirsche
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA
| | - Oluwaseun Falade-Nwulia
- Department of Medicine, Division of Infectious Disease, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Nídia S Trovão
- NIH, Fogarty International Center, Bethesda, Maryland, USA
| | - Amanda Ernlund
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland, USA
| | - Craig Howser
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland, USA
| | - Norah Sadowski
- Department of Emergency Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - C Paul Morris
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Mark Hopkins
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Matthew Schwartz
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yunfan Fan
- Departments of Biomedical Engineering and Molecular Biology and Genetics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Victoria Gniazdowski
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Justin Lessler
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Lauren Sauer
- Department of Medicine, Division of Infectious Disease, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Emergency Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Michael C Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA
| | - Jared D Evans
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland, USA
| | - Stuart C Ray
- Department of Medicine, Division of Infectious Disease, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Winston Timp
- Department of Medicine, Division of Infectious Disease, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Departments of Biomedical Engineering and Molecular Biology and Genetics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Heba H Mostafa
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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19
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Trovão NS, Nolting JM, Slemons RD, Nelson MI, Bowman AS. The Evolutionary Dynamics of Influenza A Viruses Circulating in Mallards in Duck Hunting Preserves in Maryland, USA. Microorganisms 2020; 9:microorganisms9010040. [PMID: 33375548 PMCID: PMC7823399 DOI: 10.3390/microorganisms9010040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 12/21/2020] [Accepted: 12/23/2020] [Indexed: 11/16/2022] Open
Abstract
Duck hunting preserves (DHP) have resident populations of farm-raised mallard ducks, which create potential foci for the evolution of novel influenza A viruses (IAVs). Through an eleven-year (2003–2013) IAV surveillance project in seven DHPs in Maryland, USA, we frequently identified IAVs in the resident, free-flying mallard ducks (5.8% of cloacal samples were IAV-positive). The IAV population had high genetic diversity, including 12 HA subtypes and 9 NA subtypes. By sequencing the complete genomes of 290 viruses, we determined that genetically diverse IAVs were introduced annually into DHP ducks, predominantly from wild birds in the Anatidae family that inhabit the Atlantic and Mississippi flyways. The relatively low viral gene flow observed out of DHPs suggests that raised mallards do not sustain long-term viral persistence nor do they serve as important sources of new viruses in wild birds. Overall, our findings indicate that DHPs offer reliable samples of the diversity of IAV subtypes, and could serve as regional sentinel sites that mimic the viral diversity found in local wild duck populations, which would provide a cost-efficient strategy for long-term IAV monitoring. Such monitoring could allow for early identification and characterization of viruses that threaten bird species of high economic and environmental interest.
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Affiliation(s)
- Nídia S. Trovão
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20814, USA; (N.S.T.); (M.I.N.)
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jacqueline M. Nolting
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH 43210, USA; (J.M.N.); (R.D.S.)
| | - Richard D. Slemons
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH 43210, USA; (J.M.N.); (R.D.S.)
| | - Martha I. Nelson
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20814, USA; (N.S.T.); (M.I.N.)
| | - Andrew S. Bowman
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH 43210, USA; (J.M.N.); (R.D.S.)
- Correspondence:
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20
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Thielen PM, Wohl S, Mehoke T, Ramakrishnan S, Kirsche M, Falade-Nwulia O, Trovão NS, Ernlund A, Howser C, Sadowski N, Morris P, Hopkins M, Schwartz M, Fan Y, Gniazdowski V, Lessler J, Sauer L, Schatz MC, Evans JD, Ray SC, Timp W, Mostafa HH. Genomic Diversity of SARS-CoV-2 During Early Introduction into the United States National Capital Region. medRxiv 2020:2020.08.13.20174136. [PMID: 32817965 PMCID: PMC7430609 DOI: 10.1101/2020.08.13.20174136] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
BACKGROUND The early COVID-19 pandemic has been characterized by rapid global spread. In the United States National Capital Region, over 2,000 cases were reported within three weeks of its first detection in March 2020. We aimed to use genomic sequencing to understand the initial spread of SARS-CoV-2, the virus that causes COVID-19, in the region. By correlating genetic information to disease phenotype, we also aimed to gain insight into any correlation between viral genotype and case severity or transmissibility. METHODS We performed whole genome sequencing of clinical SARS-CoV-2 samples collected in March 2020 by the Johns Hopkins Health System. We analyzed these regional SARS-CoV-2 genomes alongside detailed clinical metadata and the global phylogeny to understand early establishment of the virus within the region. RESULTS We analyzed 620 samples from the Johns Hopkins Health System collected between March 11-31, 2020, comprising 37.3% of the total cases in Maryland during this period. We selected 143 of these samples for sequencing, generating 114 complete viral genomes. These genomes belong to all five major Nextstrain-defined clades, suggesting multiple introductions into the region and underscoring the diversity of the regional epidemic. We also found that clinically severe cases had genomes belonging to all of these clades. CONCLUSIONS We established a pipeline for SARS-CoV-2 sequencing within the Johns Hopkins Health system, which enabled us to capture the significant viral diversity present in the region as early as March 2020. Efforts to control local spread of the virus were likely confounded by the number of introductions into the region early in the epidemic and interconnectedness of the region as a whole.
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Affiliation(s)
- Peter M. Thielen
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland 20723
| | - Shirlee Wohl
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205
| | - Thomas Mehoke
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland 20723
| | | | - Melanie Kirsche
- Johns Hopkins University Department of Computer Science, Baltimore, Maryland 21218
| | - Oluwaseun Falade-Nwulia
- Johns Hopkins University School of Medicine, Department of Medicine, Division of Infectious Disease, Baltimore, Maryland 21205
| | - Nídia S. Trovão
- National Institutes of Health, Fogarty International Center, Bethesda, Maryland 20892
| | - Amanda Ernlund
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland 20723
| | - Craig Howser
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland 20723
| | - Norah Sadowski
- Johns Hopkins University Department of Emergency Medicine, Baltimore, Maryland 21205
| | - Paul Morris
- Johns Hopkins University School of Medicine, Department of Pathology, Division of Medical Microbiology, Baltimore, Maryland 21205
| | - Mark Hopkins
- Johns Hopkins University School of Medicine, Department of Pathology, Division of Medical Microbiology, Baltimore, Maryland 21205
| | - Matthew Schwartz
- Johns Hopkins University School of Medicine, Department of Pathology, Division of Medical Microbiology, Baltimore, Maryland 21205
| | - Yunfan Fan
- Johns Hopkins University Departments of Biomedical Engineering and Molecular Biology and Genetics, Baltimore, Maryland 21205
| | - Victoria Gniazdowski
- Johns Hopkins University School of Medicine, Department of Pathology, Division of Medical Microbiology, Baltimore, Maryland 21205
| | - Justin Lessler
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205
| | - Lauren Sauer
- Johns Hopkins University School of Medicine, Department of Medicine, Division of Infectious Disease, Baltimore, Maryland 21205
- Johns Hopkins University Department of Emergency Medicine, Baltimore, Maryland 21205
| | - Michael C. Schatz
- Johns Hopkins University Department of Computer Science, Baltimore, Maryland 21218
| | - Jared D. Evans
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland 20723
| | - Stuart C. Ray
- Johns Hopkins University School of Medicine, Department of Medicine, Division of Infectious Disease, Baltimore, Maryland 21205
| | - Winston Timp
- Johns Hopkins University School of Medicine, Department of Medicine, Division of Infectious Disease, Baltimore, Maryland 21205
- Johns Hopkins University Departments of Biomedical Engineering and Molecular Biology and Genetics, Baltimore, Maryland 21205
| | - Heba H. Mostafa
- Johns Hopkins University School of Medicine, Department of Pathology, Division of Medical Microbiology, Baltimore, Maryland 21205
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21
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Affiliation(s)
- Nídia S. Trovão
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Martha I. Nelson
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
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22
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Trovão NS, Shepherd FK, Herzberg K, Jarvis MC, Lam HC, Rovira A, Culhane MR, Nelson MI, Marthaler DG. Cover Image, Volume 66, Issue 5. Zoonoses Public Health 2019. [DOI: 10.1111/zph.12636] [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: 11/30/2022]
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23
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Nelson MI, Souza CK, Trovão NS, Diaz A, Mena I, Rovira A, Vincent AL, Torremorell M, Marthaler D, Culhane MR. Human-Origin Influenza A(H3N2) Reassortant Viruses in Swine, Southeast Mexico. Emerg Infect Dis 2019; 25:691-700. [PMID: 30730827 PMCID: PMC6433011 DOI: 10.3201/eid2504.180779] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The genetic diversity of influenza A viruses circulating in swine in Mexico complicates control efforts in animals and presents a threat to humans, as shown by influenza A(H1N1)pdm09 virus. To describe evolution of swine influenza A viruses in Mexico and evaluate strains for vaccine development, we sequenced the genomes of 59 viruses and performed antigenic cartography on strains from 5 regions. We found that genetic and antigenic diversity were particularly high in southeast Mexico because of repeated introductions of viruses from humans and swine in other regions in Mexico. We identified novel reassortant H3N2 viruses with genome segments derived from 2 different viruses that were independently introduced from humans into swine: pandemic H1N1 viruses and seasonal H3N2 viruses. The Mexico swine viruses are antigenically distinct from US swine lineages. Protection against these viruses is unlikely to be afforded by US virus vaccines and would require development of new vaccines specifically targeting these diverse strains.
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24
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Nelson MI, Souza C, Trovão NS, Diaz A, Mena I, Rovira A, Vincent AL, Torremorell M, Marthaler D, Culhane MR. Human-Origin Influenza A(H3N2) Reassortant Viruses in Swine, Southeast Mexico. Emerg Infect Dis 2019. [DOI: 10.3201/eid2503.180779] [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: 11/19/2022] Open
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25
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Trovão NS, Shepherd FK, Herzberg K, Jarvis MC, Lam HC, Rovira A, Culhane MR, Nelson MI, Marthaler DG. Evolution of rotavirus C in humans and several domestic animal species. Zoonoses Public Health 2019; 66:546-557. [PMID: 30848076 DOI: 10.1111/zph.12575] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [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: 07/10/2018] [Revised: 12/21/2018] [Accepted: 02/10/2019] [Indexed: 12/19/2022]
Abstract
Rotavirus C (RVC) causes enteric disease in multiple species, including humans, swine, bovines, and canines. To date, the evolutionary relationships of RVC populations circulating in different host species are poorly understood, owing to the low availability of genetic sequence data. To address this gap, we sequenced 45 RVC complete genomes from swine samples collected in the United States and Mexico. A phylogenetic analysis of each genome segment indicates that RVC populations have been evolving independently in human, swine, canine, and bovine hosts for at least the last century, with inter-species transmission events occurring deep in the phylogenetic tree, and none in the last 100 years. Bovine and canine RVC populations clustered together nine of the 11 gene segments, indicating a shared common ancestor centuries ago. The evolutionary relationships of RVC in humans and swine were more complex, due to the extensive genetic diversity and multiple RVC clades identified in pigs, which were not structured geographically. Topological differences between trees inferred for different genome segments occurred frequently, including at nodes deep in the tree, indicating that RVC's evolutionary history includes multiple reassortment events that occurred a long time ago. Overall, we find that RVC is evolving within host-defined lineages, but the evolutionary history of RVC is more complex than previously recognized due to the high genetic diversity of RVC in swine, with a common ancestor dating back centuries. Pigs may act as a reservoir host for RVC, and a source of the lineages identified in other species, including humans, but additional sequencing is needed to understand the full diversity of this understudied pathogen across multiple host species.
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Affiliation(s)
- Nídia S Trovão
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland.,Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Frances K Shepherd
- Comparative and Molecular Biosciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota
| | - Katerina Herzberg
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota
| | - Matthew C Jarvis
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota.,Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota
| | - Ham C Lam
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota.,Minnesota Supercomputing Institute, University of Minnesota, Saint Paul, Minnesota
| | - Albert Rovira
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota
| | - Marie R Culhane
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota
| | - Martha I Nelson
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland
| | - Douglas G Marthaler
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas.,Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota
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26
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Abstract
Phylogeographic reconstructions are becoming an established procedure to evaluate the factors that could impact virus spread. While a discrete phylogeographic approach can be used to test predictors of transition rates among discrete locations, alternative continuous phylogeographic reconstructions can also be exploited to investigate the impact of underlying environmental layers on the dispersal velocity of a virus. The two approaches are complementary tools for studying pathogens' spread, but in both cases, care must be taken to avoid misinterpretations. Here, we analyse rice yellow mottle virus (RYMV) sequence data from West and East Africa to illustrate how both approaches can be used to study the impact of environmental factors on the virus’ dispersal frequency and velocity. While it was previously reported that host connectivity was a major determinant of RYMV spread, we show that this was a false positive result due to the lack of appropriate negative controls. We also discuss and compare the phylodynamic tools currently available for investigating the impact of environmental factors on virus spread.
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Affiliation(s)
- Simon Dellicour
- Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium.,Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, CP160/12 50, av. FD Roosevelt, 1050 Bruxelles, Belgium
| | - Bram Vrancken
- Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Nídia S Trovão
- Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Denis Fargette
- Institut de Recherche pour le Développement (IRD), UMR IPME (IRD, CIRAD, Université de Montpellier), BP 64051 34394 Montpellier cedex 5, France
| | - Philippe Lemey
- Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium
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Nelson MI, Culhane MR, Trovão NS, Patnayak DP, Halpin RA, Lin X, Shilts MH, Das SR, Detmer SE. The emergence and evolution of influenza A (H1α) viruses in swine in Canada and the United States. J Gen Virol 2017; 98:2663-2675. [PMID: 29058649 DOI: 10.1099/jgv.0.000924] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Swine are a key reservoir host for influenza A viruses (IAVs), with the potential to cause global pandemics in humans. Gaps in surveillance in many of the world's largest swine populations impede our understanding of how novel viruses emerge and expand their spatial range in pigs. Although US swine are intensively sampled, little is known about IAV diversity in Canada's population of ~12 million pigs. By sequencing 168 viruses from multiple regions of Canada, our study reveals that IAV diversity has been underestimated in Canadian pigs for many years. Critically, a new H1 clade has emerged in Canada (H1α-3), with a two-amino acid deletion at H1 positions 146-147, that experienced rapid growth in Manitoba's swine herds during 2014-2015. H1α-3 viruses also exhibit a higher capacity to invade US swine herds, resulting in multiple recent introductions of the virus into the US Heartland following large-scale movements of pigs in this direction. From the Heartland, H1α-3 viruses have disseminated onward to both the east and west coasts of the United States, and may become established in Appalachia. These findings demonstrate how long-distance trading of live pigs facilitates the spread of IAVs, increasing viral genetic diversity and complicating pathogen control. The proliferation of novel H1α-3 viruses also highlights the need for expanded surveillance in a Canadian swine population that has long been overlooked, and may have implications for vaccine design.
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Affiliation(s)
- Martha I Nelson
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | | | - Nídia S Trovão
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA.,Icahn School of Medicine at Mount Sinai University, New York, USA
| | | | | | - Xudong Lin
- J. Craig Venter Institute, Rockville, MD, USA
| | - Meghan H Shilts
- J. Craig Venter Institute, Rockville, MD, USA.,Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Suman R Das
- J. Craig Venter Institute, Rockville, MD, USA.,Vanderbilt University School of Medicine, Nashville, TN, USA
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Mena I, Nelson MI, Quezada-Monroy F, Dutta J, Cortes-Fernández R, Lara-Puente JH, Castro-Peralta F, Cunha LF, Trovão NS, Lozano-Dubernard B, Rambaut A, van Bakel H, García-Sastre A. Origins of the 2009 H1N1 influenza pandemic in swine in Mexico. eLife 2016; 5. [PMID: 27350259 PMCID: PMC4957980 DOI: 10.7554/elife.16777] [Citation(s) in RCA: 182] [Impact Index Per Article: 22.8] [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: 04/08/2016] [Accepted: 06/13/2016] [Indexed: 12/21/2022] Open
Abstract
Asia is considered an important source of influenza A virus (IAV) pandemics, owing to large, diverse viral reservoirs in poultry and swine. However, the zoonotic origins of the 2009 A/H1N1 influenza pandemic virus (pdmH1N1) remain unclear, due to conflicting evidence from swine and humans. There is strong evidence that the first human outbreak of pdmH1N1 occurred in Mexico in early 2009. However, no related swine viruses have been detected in Mexico or any part of the Americas, and to date the most closely related ancestor viruses were identified in Asian swine. Here, we use 58 new whole-genome sequences from IAVs collected in Mexican swine to establish that the swine virus responsible for the 2009 pandemic evolved in central Mexico. This finding highlights how the 2009 pandemic arose from a region not considered a pandemic risk, owing to an expansion of IAV diversity in swine resulting from long-distance live swine trade. DOI:http://dx.doi.org/10.7554/eLife.16777.001 In 2009 a new influenza virus jumped from pigs to humans and spread very rapidly, causing an initial outbreak in Mexico and becoming a global pandemic in just a few months. Although the most straightforward explanation is that the virus originated in swine in Mexico, several studies suggested that this was unlikely because key genetic components of the virus had never been detected in the Americas. Determining the source of the disease is critical for predicting and preparing for future influenza pandemics. Mena, Nelson et al. sought to better characterize the genetic diversity of influenza viruses in Mexican swine by obtaining the entire genetic sequences of 58 viruses collected from swine in Mexico, including some from previously unsampled regions in central Mexico. The sequences revealed extensive diversity among the influenza viruses circulating in Mexican swine. Several viruses included genetic segments that originated from viruses from Eurasia (the landmass containing Europe and Asia) and had not previously been detected in the Americas. The new sequences contained key genetic components of the 2009 pandemic virus. Furthermore, the sequences suggest that viruses with a similar genetic composition to the 2009 pandemic virus have been circulating in pigs in central-west Mexico for more than a decade. Thus, this region is the most likely source of the virus that started the 2009 pandemic. Mena, Nelson et al. also found that the movement of viruses from Eurasia and the United States into Mexico closely follows the direction of the global trade of live swine. This highlights the critical role that animal trading plays in bringing together diverse viruses from different continents, which can then combine and generate new pandemic viruses. A potential next step is to perform experiments that investigate how well the swine viruses can replicate and pass between different animal models. Comparing the results of such experiments with the findings presented by Mena, Nelson et al. could identify factors that make the viruses more likely to spread to humans and produce a pandemic. DOI:http://dx.doi.org/10.7554/eLife.16777.002
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Affiliation(s)
- Ignacio Mena
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, United States.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Martha I Nelson
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, United States
| | | | - Jayeeta Dutta
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | | | | | | | - Luis F Cunha
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Nídia S Trovão
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, United States.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, United States.,Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, United States.,Department of Microbiology and Immunology, Rega Institute, University of Leuven, Leuven, Belgium
| | | | - Andrew Rambaut
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, United States.,Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom.,Centre for Immunology, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Harm van Bakel
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, United States.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, United States.,Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, United States
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