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Windah ALL, Tallei TE, AlShehail BM, Suoth EJ, Fatimawali, Alhashem YN, Halwani MA, AlShakhal MM, Aljeldah M, Alissa M, Alsuwat MA, Almanaa TN, Alshehri AA, Rabaan AA. Immunoinformatics-Driven Strategies for Advancing Epitope-Based Vaccine Design for West Nile Virus. J Pharm Sci 2024; 113:906-917. [PMID: 38042341 DOI: 10.1016/j.xphs.2023.11.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 12/04/2023]
Abstract
The West Nile virus (WNV) is the causative agent of West Nile disease (WND), which poses a potential risk of meningitis or encephalitis. The aim of the study was to design an epitope-based vaccine for WNV by utilizing computational analyses. The epitope-based vaccine design process encompassed WNV sequence collection, phylogenetic tree construction, and sequence alignment. Computational models identified B-cell and T-cell epitopes, followed by immunological property analysis. Epitopes were then modeled and docked with B-cell receptors, MHC I, and MHC II. Molecular dynamics simulations further explored dynamic interactions between epitopes and receptors. The findings indicated that the B-cell epitope QINHHWHKSGSSIG, along with three T-cell epitopes (FLVHREWFM for MHC I, NPFVSVATANAKVLI for MHC II, and NAYYVMTVGTKTFLV for MHC II), successfully passed the immunological evaluations. These four epitopes were further subjected to docking and molecular dynamics simulation studies. Although each demonstrated favorable affinities with their respective receptors, only NAYYVMTVGTKTFLV displayed a stable interaction with MHC II during MDS analysis, hence emerging as a potential candidate for a WNV epitope-based vaccine. This study demonstrates a comprehensive approach to epitope vaccine design, combining computational analyses, molecular modeling, and simulation techniques to identify potential vaccine candidates for WNV.
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Affiliation(s)
- Axl Laurens Lukas Windah
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, Surabaya 60115, East Java, Indonesia
| | - Trina Ekawati Tallei
- Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, North Sulawesi, Indonesia.
| | - Bashayer M AlShehail
- Pharmacy Practice Department, College of Clinical Pharmacy, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Elly Juliana Suoth
- Pharmacy Study Program, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Mana-do 95115, North Sulawesi, Indonesia
| | - Fatimawali
- Pharmacy Study Program, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Mana-do 95115, North Sulawesi, Indonesia
| | - Yousef N Alhashem
- Clinical Laboratory Science Department, Mohammed Al-Mana College for Medical Sciences, Dammam 34222, Saudi Arabia
| | - Muhammad A Halwani
- Department of Medical Microbiology, Faculty of Medicine, Al Baha University. Al Baha 4781, Saudi Arabia
| | - Mouayd M AlShakhal
- Internal Medicine Department, Qatif Central Hospital, Qatif 32654, Saudi Arabia
| | - Mohammed Aljeldah
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hafr Al Batin, Hafr Al Batin 39831, Saudi Arabia
| | - Mohammed Alissa
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Meshari A Alsuwat
- Clinical Laboratory Sciences Department, College of Applied Medical Sciences, Taif University, Al-Taif 21974, Saudi Arabia
| | - Taghreed N Almanaa
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ahmad A Alshehri
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia
| | - Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia; College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan
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2
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Talmi-Frank D, Byas AD, Murrieta R, Weger-Lucarelli J, Rückert C, Gallichotte EN, Yoshimoto JA, Allen C, Bosco-Lauth AM, Graham B, Felix TA, Brault AC, Ebel GD. Intracellular Diversity of WNV within Circulating Avian Peripheral Blood Mononuclear Cells Reveals Host-Dependent Patterns of Polyinfection. Pathogens 2023; 12:767. [PMID: 37375457 DOI: 10.3390/pathogens12060767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/12/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
Arthropod-borne virus (arbovirus) populations exist as mutant swarms that are maintained between arthropods and vertebrates. West Nile virus (WNV) population dynamics are host-dependent. In American crows, purifying selection is weak and population diversity is high compared to American robins, which have 100- to 1000-fold lower viremia. WNV passed in robins leads to fitness gains, whereas that passed in crows does not. Therefore, we tested the hypothesis that high crow viremia allows for higher genetic diversity within individual avian peripheral blood mononuclear cells (PBMCs), reasoning that this could have produced the previously observed host-specific differences in genetic diversity and fitness. Specifically, we infected cells and birds with a molecularly barcoded WNV and sequenced viral RNA from single cells to quantify the number of WNV barcodes in each. Our results demonstrate that the richness of WNV populations within crows far exceeds that in robins. Similarly, rare WNV variants were maintained by crows more frequently than by robins. Our results suggest that increased viremia in crows relative to robins leads to the maintenance of defective genomes and less prevalent variants, presumably through complementation. Our findings further suggest that weaker purifying selection in highly susceptible crows is attributable to this higher viremia, polyinfections and complementation.
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Affiliation(s)
- Dalit Talmi-Frank
- Center for Vector-Borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Alex D Byas
- Center for Vector-Borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Reyes Murrieta
- Center for Vector-Borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - James Weger-Lucarelli
- Center for Vector-Borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Claudia Rückert
- Department of Biochemistry and Molecular Biology, College of Agriculture, Biotechnology & Natural Resources, University of Nevada, Reno, NV 89557, USA
| | - Emily N Gallichotte
- Center for Vector-Borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Janna A Yoshimoto
- Center for Vector-Borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Chris Allen
- Center for Vector-Borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Angela M Bosco-Lauth
- Center for Vector-Borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Barbara Graham
- Center for Vector-Borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Todd A Felix
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, Lakewood, CO 80228, USA
| | - Aaron C Brault
- Division of Vector-Borne Diseases, National Center for Emerging Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA
| | - Gregory D Ebel
- Center for Vector-Borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
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Foss L, Feiszli T, Kramer VL, Reisen WK, Padgett K. Epidemic versus endemic West Nile virus dead bird surveillance in California: Changes in sensitivity and focus. PLoS One 2023; 18:e0284039. [PMID: 37023091 PMCID: PMC10079120 DOI: 10.1371/journal.pone.0284039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 03/21/2023] [Indexed: 04/07/2023] Open
Abstract
Since 2003, the California West Nile virus (WNV) dead bird surveillance program (DBSP) has monitored publicly reported dead birds for WNV surveillance and response. In the current paper, we compared DBSP data from early epidemic years (2004-2006) with recent endemic years (2018-2020), with a focus on specimen collection criteria, county report incidence, bird species selection, WNV prevalence in dead birds, and utility of the DBSP as an early environmental indicator of WNV. Although fewer agencies collected dead birds in recent years, most vector control agencies with consistent WNV activity continued to use dead birds as a surveillance tool, with streamlined operations enhancing efficiency. The number of dead bird reports was approximately ten times greater during 2004-2006 compared to 2018-2020, with reports from the Central Valley and portions of Southern California decreasing substantially in recent years; reports from the San Francisco Bay Area decreased less dramatically. Seven of ten counties with high numbers of dead bird reports were also high human WNV case burden areas. Dead corvid, sparrow, and quail reports decreased the most compared to other bird species reports. West Nile virus positive dead birds were the most frequent first indicators of WNV activity by county in 2004-2006, followed by positive mosquitoes; in contrast, during 2018-2020 mosquitoes were the most frequent first indicators followed by dead birds, and initial environmental WNV detections occurred later in the season during 2018-2020. Evidence for WNV impacts on avian populations and susceptibility are discussed. Although patterns of dead bird reports and WNV prevalence in tested dead birds have changed, dead birds have endured as a useful element within our multi-faceted WNV surveillance program.
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Affiliation(s)
- Leslie Foss
- Vector-Borne Disease Section, California Department of Public Health, Richmond, California, United States of America
| | - Tina Feiszli
- Vector-Borne Disease Section, California Department of Public Health, Richmond, California, United States of America
| | - Vicki L. Kramer
- Vector-Borne Disease Section, California Department of Public Health, Sacramento, California, United States of America
| | - William K. Reisen
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, CA, United States of America
| | - Kerry Padgett
- Vector-Borne Disease Section, California Department of Public Health, Richmond, California, United States of America
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Frank DT, Byas AD, Murrieta R, Weger-Lucarelli J, Rückert C, Gallichotte E, Yoshimoto JA, Allen C, Bosco-Lauth AM, Graham B, Felix TA, Brault A, Ebel GD. Intracellular diversity of WNV within circulating avian peripheral blood mononuclear cells reveals host-dependent patterns of polyinfection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.27.525959. [PMID: 36747638 PMCID: PMC9900929 DOI: 10.1101/2023.01.27.525959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Error-prone replication of RNA viruses generates the genetic diversity required for adaptation within rapidly changing environments. Thus, arthropod-borne virus (arbovirus) populations exist in nature as mutant swarms that are maintained between arthropods and vertebrates. Previous studies have demonstrated that West Nile virus (WNV) population dynamics are host dependent: In American crows, which experience extremely high viremia, purifying selection is weak and population diversity is high compared to American robins, which have 100 to 1000-fold lower viremia. WNV passed in robins experiences fitness gains, whereas that passed in crows does not. Therefore, we tested the hypothesis that high crow viremia allows higher genetic diversity within individual avian peripheral-blood mononuclear cells (PBMCs), reasoning that this could have produced the previously observed host-specific differences in genetic diversity and fitness. Specifically, we infected cells and birds with a novel, barcoded version of WNV and sequenced viral RNA from single cells to quantify the number of WNV barcodes that each contained. Our results demonstrate that the richness of WNV populations within crows far exceeds that in robins. Similarly, rare WNV variants were maintained by crows more frequently than by robins. Our results suggest that increased viremia in crows relative to robins leads to maintenance of defective genomes and less prevalent variants, presumably through complementation. Our findings further suggest that weaker purifying selection in highly susceptible crows is attributable to this higher viremia, polyinfections and complementation. These studies further document the role of particular, ecologically relevant hosts in shaping virus population structure. Author Summary WNV mutational diversity in vertebrates is species-dependent. In crows, low frequency variants are common, and viral populations are more diverse. In robins, fewer mutations become permanent fixtures of the overall viral population. We infected crows, robins and a chicken cell line with a genetically marked (barcoded) WNV. Higher levels of virus led to multiple unique WNV genomes infecting individual cells, even when a genotype was present at low levels in the input viral stock. Our findings suggest that higher levels of circulating virus in natural hosts allow less fit viruses to survive in RNA virus populations through complementation by more fit viruses. This is significant as it allows less represented and less fit viruses to be maintained at low levels until they potentially emerge when virus environments change. Overall our data reveal new insights on the relationships between host susceptibility to high viremia and virus evolution.
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Affiliation(s)
- Dalit Talmi Frank
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Alex D. Byas
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Reyes Murrieta
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - James Weger-Lucarelli
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Claudia Rückert
- Department of Biochemistry and Molecular Biology, College of Agriculture, Biotechnology & Natural Resources, University of Nevada, Reno, Nevada, USA
| | - Emily Gallichotte
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Janna A. Yoshimoto
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Chris Allen
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Angela M. Bosco-Lauth
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Barbara Graham
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Todd A. Felix
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, Golden, CO, USA
| | - Aaron Brault
- Division of Vector-borne Diseases, National Center for Emerging Zoonotic Infectious Diseases, Centers for Disease Control and Prevention Fort Collins, Colorado, USA
| | - Gregory D. Ebel
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
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Saiz JC, Martín-Acebes MA, Blázquez AB, Escribano-Romero E, Poderoso T, Jiménez de Oya N. Pathogenicity and virulence of West Nile virus revisited eight decades after its first isolation. Virulence 2021; 12:1145-1173. [PMID: 33843445 PMCID: PMC8043182 DOI: 10.1080/21505594.2021.1908740] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
West Nile virus (WNV) is a flavivirus which transmission cycle is maintained between mosquitoes and birds, although it occasionally causes sporadic outbreaks in horses and humans that can result in serious diseases and even death. Since its first isolation in Africa in 1937, WNV had been considered a neglected pathogen until its recent spread throughout Europe and the colonization of America, regions where it continues to cause outbreaks with severe neurological consequences in humans and horses. Although our knowledge about the characteristics and consequences of the virus has increased enormously lately, many questions remain to be resolved. Here, we thoroughly update our knowledge of different aspects of the WNV life cycle: virology and molecular classification, host cell interactions, transmission dynamics, host range, epidemiology and surveillance, immune response, clinical presentations, pathogenesis, diagnosis, prophylaxis (antivirals and vaccines), and prevention, and we highlight those aspects that are still unknown and that undoubtedly require further investigation.
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Affiliation(s)
- Juan-Carlos Saiz
- Department of Biotechnology, National Institute for Agricultural and Food Research and Technology (INIA), Madrid, Spain
| | - Miguel A Martín-Acebes
- Department of Biotechnology, National Institute for Agricultural and Food Research and Technology (INIA), Madrid, Spain
| | - Ana B Blázquez
- Department of Biotechnology, National Institute for Agricultural and Food Research and Technology (INIA), Madrid, Spain
| | - Estela Escribano-Romero
- Department of Biotechnology, National Institute for Agricultural and Food Research and Technology (INIA), Madrid, Spain
| | - Teresa Poderoso
- Molecular Virology Group, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Nereida Jiménez de Oya
- Department of Biotechnology, National Institute for Agricultural and Food Research and Technology (INIA), Madrid, Spain
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Dellicour S, Lequime S, Vrancken B, Gill MS, Bastide P, Gangavarapu K, Matteson NL, Tan Y, du Plessis L, Fisher AA, Nelson MI, Gilbert M, Suchard MA, Andersen KG, Grubaugh ND, Pybus OG, Lemey P. Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework. Nat Commun 2020; 11:5620. [PMID: 33159066 PMCID: PMC7648063 DOI: 10.1038/s41467-020-19122-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 09/30/2020] [Indexed: 01/05/2023] Open
Abstract
Computational analyses of pathogen genomes are increasingly used to unravel the dispersal history and transmission dynamics of epidemics. Here, we show how to go beyond historical reconstructions and use spatially-explicit phylogeographic and phylodynamic approaches to formally test epidemiological hypotheses. We illustrate our approach by focusing on the West Nile virus (WNV) spread in North America that has substantially impacted public, veterinary, and wildlife health. We apply an analytical workflow to a comprehensive WNV genome collection to test the impact of environmental factors on the dispersal of viral lineages and on viral population genetic diversity through time. We find that WNV lineages tend to disperse faster in areas with higher temperatures and we identify temporal variation in temperature as a main predictor of viral genetic diversity through time. By contrasting inference with simulation, we find no evidence for viral lineages to preferentially circulate within the same migratory bird flyway, suggesting a substantial role for non-migratory birds or mosquito dispersal along the longitudinal gradient.
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Affiliation(s)
- Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, CP160/12, 50 Avenue FD Roosevelt, 1050, Bruxelles, Belgium.
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Herestraat 49, 3000, Leuven, Belgium.
| | - Sebastian Lequime
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Bram Vrancken
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Mandev S Gill
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Paul Bastide
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Karthik Gangavarapu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Nathaniel L Matteson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Yi Tan
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Infectious Diseases Group, J. Craig Venter Institute, Rockville, MD, USA
| | | | - Alexander A Fisher
- Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Martha I Nelson
- Fogarty International Center, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Marius Gilbert
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, CP160/12, 50 Avenue FD Roosevelt, 1050, Bruxelles, Belgium
| | - Marc A Suchard
- Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Scripps Research Translational Institute, La Jolla, CA, 92037, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | | | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
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Snyder RE, Feiszli T, Foss L, Messenger S, Fang Y, Barker CM, Reisen WK, Vugia DJ, Padgett KA, Kramer VL. West Nile virus in California, 2003-2018: A persistent threat. PLoS Negl Trop Dis 2020; 14:e0008841. [PMID: 33206634 PMCID: PMC7710070 DOI: 10.1371/journal.pntd.0008841] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 12/02/2020] [Accepted: 09/24/2020] [Indexed: 02/06/2023] Open
Abstract
The California Arbovirus Surveillance Program was initiated over 50 years ago to track endemic encephalitides and was enhanced in 2000 to include West Nile virus (WNV) infections in humans, mosquitoes, sentinel chickens, dead birds and horses. This comprehensive statewide program is a function of strong partnerships among the California Department of Public Health (CDPH), the University of California, and local vector control and public health agencies. This manuscript summarizes WNV surveillance data in California since WNV was first detected in 2003 in southern California. From 2003 through 2018, 6,909 human cases of WNV disease, inclusive of 326 deaths, were reported to CDPH, as well as 730 asymptomatic WNV infections identified during screening of blood and organ donors. Of these, 4,073 (59.0%) were reported as West Nile neuroinvasive disease. California's WNV disease burden comprised 15% of all cases that were reported to the U.S. Centers for Disease Control and Prevention during this time, more than any other state. Additionally, 1,299 equine WNV cases were identified, along with detections of WNV in 23,322 dead birds, 31,695 mosquito pools, and 7,340 sentinel chickens. Annual enzootic detection of WNV typically preceded detection in humans and prompted enhanced intervention to reduce the risk of WNV transmission. Peak WNV activity occurred from July through October in the Central Valley and southern California. Less than five percent of WNV activity occurred in other regions of the state or outside of this time. WNV continues to be a major threat to public and wild avian health in California, particularly in southern California and the Central Valley during summer and early fall months. Local and state public health partners must continue statewide human and mosquito surveillance and facilitate effective mosquito control and bite prevention measures.
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Affiliation(s)
- Robert E. Snyder
- California Department of Public Health, Vector-Borne Disease Section, Richmond and Sacramento, California, United States of America
| | - Tina Feiszli
- California Department of Public Health, Vector-Borne Disease Section, Richmond and Sacramento, California, United States of America
| | - Leslie Foss
- California Department of Public Health, Vector-Borne Disease Section, Richmond and Sacramento, California, United States of America
| | - Sharon Messenger
- California Department of Public Health, Division of Communicable Disease Control, Richmond, California, United States of America
| | - Ying Fang
- Department of Pathology, Microbiology & Immunology, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Christopher M. Barker
- Department of Pathology, Microbiology & Immunology, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - William K. Reisen
- Department of Pathology, Microbiology & Immunology, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Duc J. Vugia
- California Department of Public Health, Division of Communicable Disease Control, Richmond, California, United States of America
| | - Kerry A. Padgett
- California Department of Public Health, Vector-Borne Disease Section, Richmond and Sacramento, California, United States of America
| | - Vicki L. Kramer
- California Department of Public Health, Vector-Borne Disease Section, Richmond and Sacramento, California, United States of America
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8
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Ferreira PG, Tesla B, Horácio ECA, Nahum LA, Brindley MA, de Oliveira Mendes TA, Murdock CC. Temperature Dramatically Shapes Mosquito Gene Expression With Consequences for Mosquito-Zika Virus Interactions. Front Microbiol 2020; 11:901. [PMID: 32595607 PMCID: PMC7303344 DOI: 10.3389/fmicb.2020.00901] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 04/16/2020] [Indexed: 12/20/2022] Open
Abstract
Vector-borne flaviviruses are emerging threats to human health. For successful transmission, the virus needs to efficiently enter mosquito cells and replicate within and escape several tissue barriers while mosquitoes elicit major transcriptional responses to flavivirus infection. This process will be affected not only by the specific mosquito-pathogen pairing but also by variation in key environmental variables such as temperature. Thus far, few studies have examined the molecular responses triggered by temperature and how these responses modify infection outcomes, despite substantial evidence showing strong relationships between temperature and transmission in a diversity of systems. To define the host transcriptional changes associated with temperature variation during the early infection process, we compared the transcriptome of mosquito midgut samples from mosquitoes exposed to Zika virus (ZIKV) and non-exposed mosquitoes housed at three different temperatures (20, 28, and 36°C). While the high-temperature samples did not show significant changes from those with standard rearing conditions (28°C) 48 h post-exposure, the transcriptome profile of mosquitoes housed at 20°C was dramatically different. The expression of genes most altered by the cooler temperature involved aspects of blood-meal digestion, ROS metabolism, and mosquito innate immunity. Further, we did not find significant differences in the viral RNA copy number between 24 and 48 h post-exposure at 20°C, suggesting that ZIKV replication is limited by cold-induced changes to the mosquito midgut environment. In ZIKV-exposed mosquitoes, vitellogenin, a lipid carrier protein, was most up-regulated at 20°C. Our results provide a deeper understanding of the temperature-triggered transcriptional changes in Aedes aegypti and can be used to further define the molecular mechanisms driven by environmental temperature variation.
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Affiliation(s)
| | - Blanka Tesla
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Elvira Cynthia Alves Horácio
- René Rachou Institute, Oswaldo Cruz Foundation, Belo Horizonte, Brazil.,Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Laila Alves Nahum
- René Rachou Institute, Oswaldo Cruz Foundation, Belo Horizonte, Brazil.,Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil.,Promove College of Technology, Belo Horizonte, Brazil
| | - Melinda Ann Brindley
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States.,Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, United States.,Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States
| | | | - Courtney Cuinn Murdock
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States.,Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States.,Odum School of Ecology, University of Georgia, Athens, GA, United States.,Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA, United States.,Center for Emerging and Global Tropical Diseases, University of Georgia, Athens, GA, United States.,River Basin Center, University of Georgia, Athens, GA, United States.,Department of Entomology, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, United States
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9
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Swetnam DM, Stuart JB, Young K, Maharaj PD, Fang Y, Garcia S, Barker CM, Smith K, Godsey MS, Savage HM, Barton V, Bolling BG, Duggal N, Brault AC, Coffey LL. Movement of St. Louis encephalitis virus in the Western United States, 2014- 2018. PLoS Negl Trop Dis 2020; 14:e0008343. [PMID: 32520944 PMCID: PMC7307790 DOI: 10.1371/journal.pntd.0008343] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 06/22/2020] [Accepted: 05/02/2020] [Indexed: 11/22/2022] Open
Abstract
St. Louis encephalitis virus (SLEV) is a flavivirus that circulates in an enzootic cycle between birds and mosquitoes and can also infect humans to cause febrile disease and sometimes encephalitis. Although SLEV is endemic to the United States, no activity was detected in California during the years 2004 through 2014, despite continuous surveillance in mosquitoes and sentinel chickens. In 2015, SLEV-positive mosquito pools were detected in Maricopa County, Arizona, concurrent with an outbreak of human SLEV disease. SLEV-positive mosquito pools were also detected in southeastern California and Nevada in summer 2015. From 2016 to 2018, SLEV was detected in mosquito pools throughout southern and central California, Oregon, Idaho, and Texas. To understand genetic relatedness and geographic dispersal of SLEV in the western United States since 2015, we sequenced four historical genomes (3 from California and 1 from Louisiana) and 26 contemporary SLEV genomes from mosquito pools from locations across the western US. Bayesian phylogeographic approaches were then applied to map the recent spread of SLEV. Three routes of SLEV dispersal in the western United States were identified: Arizona to southern California, Arizona to Central California, and Arizona to all locations east of the Sierra Nevada mountains. Given the topography of the Western United States, these routes may have been limited by mountain ranges that influence the movement of avian reservoirs and mosquito vectors, which probably represents the primary mechanism of SLEV dispersal. Our analysis detected repeated SLEV introductions from Arizona into southern California and limited evidence of year-to-year persistence of genomes of the same ancestry. By contrast, genetic tracing suggests that all SLEV activity since 2015 in central California is the result of a single persistent SLEV introduction. The identification of natural barriers that influence SLEV dispersal enhances our understanding of arbovirus ecology in the western United States and may also support regional public health agencies in implementing more targeted vector mitigation efforts to protect their communities more effectively. Following the detection of West Nile virus in the United States, evidence of the historically endemic and closely related virus, St. Louis encephalitis virus (SLEV), dropped nationwide. However, in 2015, a novel genotype of SLEV, previously restricted to Argentina, was identified as the etiological agent of an outbreak of neurological disease in Arizona, United States. Since that time, the genotype has expanded throughout the Western United States, including into California, Nevada, Texas, Idaho, and Oregon. In this study, samples containing SLEV, provided by public health and mosquito abatement agencies, were sequenced and used in phylogenetic analyses to infer patterns of SLEV movement. Three independent routes of SLEV dispersal were identified: Arizona to Southern California, Arizona to Central California, and Arizona to all locations east of the Sierra Nevada mountains. The Sierra Nevada mountains and the Transverse Ranges appear to separate the three routes of SLEV movement, suggesting that geographic features may act as barriers to virus dispersal. Identification of patterns of SLEV dispersal can support regional public health agencies in improving vector mitigation efforts to protect their communities more effectively.
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Affiliation(s)
- Daniele M. Swetnam
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, Davis, California, United States of America
| | - Jackson B. Stuart
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, Davis, California, United States of America
| | - Katherine Young
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, Davis, California, United States of America
| | - Payal D. Maharaj
- Division of Vector-borne Diseases, Centers for Disease Control, Fort Collins, Colorado, United States of America
| | - Ying Fang
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, Davis, California, United States of America
| | - Sandra Garcia
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, Davis, California, United States of America
| | - Christopher M. Barker
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, Davis, California, United States of America
| | - Kirk Smith
- Maricopa County Environmental Services Department, Phoenix, Arizona, United States of America
| | - Marvin S. Godsey
- Division of Vector-borne Diseases, Centers for Disease Control, Fort Collins, Colorado, United States of America
| | - Harry M. Savage
- Division of Vector-borne Diseases, Centers for Disease Control, Fort Collins, Colorado, United States of America
| | - Vonnita Barton
- Idaho Bureau of Laboratories, Boise, Idaho, United States of America
| | - Bethany G. Bolling
- Laboratory Services Section, Texas Department of State Health Services, Austin, Texas, United States of America
| | - Nisha Duggal
- Department of Molecular Biology, College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Aaron C. Brault
- Division of Vector-borne Diseases, Centers for Disease Control, Fort Collins, Colorado, United States of America
| | - Lark L. Coffey
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, Davis, California, United States of America
- * E-mail:
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10
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Duggal NK, Langwig KE, Ebel GD, Brault AC. On the Fly: Interactions Between Birds, Mosquitoes, and Environment That Have Molded West Nile Virus Genomic Structure Over Two Decades. JOURNAL OF MEDICAL ENTOMOLOGY 2019; 56:1467-1474. [PMID: 31549720 PMCID: PMC7182917 DOI: 10.1093/jme/tjz112] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Indexed: 05/15/2023]
Abstract
West Nile virus (WNV) was first identified in North America almost 20 yr ago. In that time, WNV has crossed the continent and established enzootic transmission cycles, resulting in intermittent outbreaks of human disease that have largely been linked with climatic variables and waning avian seroprevalence. During the transcontinental dissemination of WNV, the original genotype has been displaced by two principal extant genotypes which contain an envelope mutation that has been associated with enhanced vector competence by Culex pipiens L. (Diptera: Culicidae) and Culex tarsalis Coquillett vectors. Analyses of retrospective avian host competence data generated using the founding NY99 genotype strain have demonstrated a steady reduction in viremias of house sparrows over time. Reciprocally, the current genotype strains WN02 and SW03 have demonstrated an inverse correlation between house sparrow viremia magnitude and the time since isolation. These data collectively indicate that WNV has evolved for increased avian viremia while house sparrows have evolved resistance to the virus such that the relative host competence has remained constant. Intrahost analyses of WNV evolution demonstrate that selection pressures are avian species-specific and purifying selection is greater in individual birds compared with individual mosquitoes, suggesting that the avian adaptive and/or innate immune response may impose a selection pressure on WNV. Phylogenomic, experimental evolutionary systems, and models that link viral evolution with climate, host, and vector competence studies will be needed to identify the relative effect of different selective and stochastic mechanisms on viral phenotypes and the capacity of newly evolved WNV genotypes for transmission in continuously changing landscapes.
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Affiliation(s)
- Nisha K Duggal
- Department of Biomedical Sciences and Pathobiology, Virginia Polytechnic Institute and State University, Blacksburg, VA
| | - Kate E Langwig
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA
| | - Gregory D Ebel
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO
| | - Aaron C Brault
- Division of Vector-borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO
- Corresponding author, e-mail:
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11
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Reisen WK, Wheeler SS. Overwintering of West Nile Virus in the United States. JOURNAL OF MEDICAL ENTOMOLOGY 2019; 56:1498-1507. [PMID: 31549726 DOI: 10.1093/jme/tjz070] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Indexed: 06/10/2023]
Abstract
The establishment of a tropical virus such as West Nile (WNV; Flaviviridae: Flavivirus) within the temperate latitudes of the continental United States was unexpected and perhaps contingent, in part, upon the ability of this invasive virus to persist during winter when temperatures become too cold for replication and vector mosquito gonotrophic activity. Our Forum article reviews research examining possible overwintering mechanisms that include consistent reintroduction and local persistence in vector mosquitoes and avian hosts, mostly using examples from research conducted in California. We conclude that the transmission of WNV involves so many vectors and hosts within different landscapes that multiple overwintering pathways are possible and collectively may be necessary to allow this virus to overwinter consistently within the United States.
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Affiliation(s)
- William K Reisen
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, CA
| | - Sarah S Wheeler
- Sacramento-Yolo Mosquito and Vector Control District, Elk Grove, CA
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12
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Hadfield J, Brito AF, Swetnam DM, Vogels CBF, Tokarz RE, Andersen KG, Smith RC, Bedford T, Grubaugh ND. Twenty years of West Nile virus spread and evolution in the Americas visualized by Nextstrain. PLoS Pathog 2019; 15:e1008042. [PMID: 31671157 PMCID: PMC6822705 DOI: 10.1371/journal.ppat.1008042] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
It has been 20 years since West Nile virus first emerged in the Americas, and since then, little progress has been made to control outbreaks caused by this virus. After its first detection in New York in 1999, West Nile virus quickly spread across the continent, causing an epidemic of human disease and massive bird die-offs. Now the virus has become endemic to the United States, where an estimated 7 million human infections have occurred, making it the leading mosquito-borne virus infection and the most common cause of viral encephalitis in the country. To bring new attention to one of the most important mosquito-borne viruses in the Americas, we provide an interactive review using Nextstrain: a visualization tool for real-time tracking of pathogen evolution (nextstrain.org/WNV/NA). Nextstrain utilizes a growing database of more than 2,000 West Nile virus genomes and harnesses the power of phylogenetics for students, educators, public health workers, and researchers to visualize key aspects of virus spread and evolution. Using Nextstrain, we use virus genomics to investigate the emergence of West Nile virus in the U S, followed by its rapid spread, evolution in a new environment, establishment of endemic transmission, and subsequent international spread. For each figure, we include a link to Nextstrain to allow the readers to directly interact with and explore the underlying data in new ways. We also provide a brief online narrative that parallels this review to further explain the data and highlight key epidemiological and evolutionary features (nextstrain.org/narratives/twenty-years-of-WNV). Mirroring the dynamic nature of outbreaks, the Nextstrain links provided within this paper are constantly updated as new West Nile virus genomes are shared publicly, helping to stay current with the research. Overall, our review showcases how genomics can track West Nile virus spread and evolution, as well as potentially uncover novel targeted control measures to help alleviate its public health burden.
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Affiliation(s)
- James Hadfield
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Anderson F. Brito
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Daniele M. Swetnam
- Department of Pathology, Microbiology and Immunology, University of California, Davis, Davis, California, United States of America
| | - Chantal B. F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Ryan E. Tokarz
- Department of Entomology, Iowa State University, Ames, Iowa, United States of America
| | - Kristian G. Andersen
- Department of Immunology and Microbiology, Scripps Research, La Jolla, California, United States of America
- Scripps Research Translational Institute, La Jolla, California, United States of America
| | - Ryan C. Smith
- Department of Entomology, Iowa State University, Ames, Iowa, United States of America
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
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13
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Therrien C, Fournier É, Ludwig A, Ménard J, Charest H, Martineau C. Phylogenetic analysis of West Nile virus in Quebec, Canada, 2004-2016: Co-circulation of distinct variants harbouring conserved amino acid motifs in North America. Virology 2019; 537:65-73. [PMID: 31465892 DOI: 10.1016/j.virol.2019.08.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/16/2019] [Accepted: 08/19/2019] [Indexed: 11/18/2022]
Abstract
West Nile virus (WNV) was introduced for the first time in the western hemisphere in 1999 in New York City. In 2002, a phenotype-modifying mutation (Env-V159A) defined the first North American genotype WN02. So far, three genotypes has been described in North America but little is known about WNV evolution in Canada. We report the phylogenetic characterization of twenty-six WNV genomes isolated from mosquitoes in the province of Quebec. WNV strains found in Quebec are phylogenetically related to American strains collected in northern and southern regions. We also noted the presence of two robust monophyletic groups of isolates characterized by distinct conserved amino acid motifs. These emerging genotypes were detected for several years in different ecosystems. These results highlight the need for the maintenance of a nationwide surveillance to follow the dispersion of emergent WNV genotypes.
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Affiliation(s)
- Christian Therrien
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec. 20045 Chemin Sainte-Marie, Saint-Anne-de-Bellevue, H9X 3Y3, QC, Canada.
| | - Éric Fournier
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec. 20045 Chemin Sainte-Marie, Saint-Anne-de-Bellevue, H9X 3Y3, QC, Canada
| | - Antoinette Ludwig
- Laboratoire National de microbiologie, Agence de santé publique du Canada, 3200 Sicotte, Saint-Hyacinthe, QC, J2S 2M2, Canada
| | - Joel Ménard
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec. 20045 Chemin Sainte-Marie, Saint-Anne-de-Bellevue, H9X 3Y3, QC, Canada
| | - Hugues Charest
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec. 20045 Chemin Sainte-Marie, Saint-Anne-de-Bellevue, H9X 3Y3, QC, Canada
| | - Christine Martineau
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec. 20045 Chemin Sainte-Marie, Saint-Anne-de-Bellevue, H9X 3Y3, QC, Canada
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14
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Swetnam D, Widen SG, Wood TG, Reyna M, Wilkerson L, Debboun M, Symonds DA, Mead DG, Beaty BJ, Guzman H, Tesh RB, Barrett ADT. Terrestrial Bird Migration and West Nile Virus Circulation, United States. Emerg Infect Dis 2019; 24:2184-2194. [PMID: 30457531 PMCID: PMC6256381 DOI: 10.3201/eid2412.180382] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Host migration and emerging pathogens are strongly associated, especially with regard to zoonotic diseases. West Nile virus (WNV), a mosquitoborne pathogen capable of causing severe, sometimes fatal, neuroinvasive disease in humans, is maintained in highly mobile avian hosts. Using phylogeographic approaches, we investigated the relationship between WNV circulation in the United States and the flight paths of terrestrial birds. We demonstrated southward migration of WNV in the eastern flyway and northward migration in the central flyway, which is consistent with the looped flight paths of many terrestrial birds. We also identified 3 optimal locations for targeted WNV surveillance campaigns in the United States—Illinois, New York, and Texas. These results illustrate the value of multidisciplinary approaches to surveillance of infectious diseases, especially zoonotic diseases.
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15
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Hepp CM, Cocking JH, Valentine M, Young SJ, Damian D, Samuels-Crow KE, Sheridan K, Fofanov VY, Furstenau TN, Busch JD, Erickson DE, Lancione RC, Smith K, Will J, Townsend J, Keim PS, Engelthaler DM. Phylogenetic analysis of West Nile Virus in Maricopa County, Arizona: Evidence for dynamic behavior of strains in two major lineages in the American Southwest. PLoS One 2018; 13:e0205801. [PMID: 30475820 PMCID: PMC6261030 DOI: 10.1371/journal.pone.0205801] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 10/02/2018] [Indexed: 01/08/2023] Open
Abstract
West Nile Virus (WNV) has been detected annually in Maricopa County, Arizona, since 2003. With this in mind, we sought to determine if contemporary strains are endemic to the county or are annually imported. As part of this effort, we developed a new protocol for tiled amplicon sequencing of WNV to efficiently attain greater than 99% coverage of 14 WNV genomes collected directly from positive mosquito pools distributed throughout Maricopa County between 2014 and 2017. Bayesian phylogenetic analyses revealed that contemporary genomes fall within two major lineages; NA/WN02 and SW/WN03. We found that all of the Arizona strains possessed an amino acid substitution known to be under positive selection, which has arisen independently at least four times in Arizona. The SW/WN03 strains exhibited transient behavior, with at least 10 separate introductions into Arizona when considering both historical and contemporary strains. However, NA/WN02 strains are geographically differentiated and appear to be endemic in Arizona, with two clades that have been circulating for four and seven years. This establishment in Maricopa County provides the first evidence of local overwintering by a WNV strain over the course of several years in Arizona. Within a national context, the placement of eleven contemporary Arizona strains in the NA/WN02 lineage indicates while WNV first entered the northeastern United States in 1999, the most ancestral extant strains of WNV are now circulating in the American southwest.
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Affiliation(s)
- Crystal M. Hepp
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United Sates of America
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jill Hager Cocking
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United Sates of America
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Michael Valentine
- Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Steven J. Young
- Maricopa County Environmental Services Department Vector Control Division, Phoenix, Arizona, United States of America
| | - Dan Damian
- Maricopa County Environmental Services Department Office of Enterprise Technology, Phoenix, Arizona, United States of America
| | - Kimberly E. Samuels-Crow
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United Sates of America
| | - Krystal Sheridan
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
- Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Viacheslav Y. Fofanov
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United Sates of America
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Tara N. Furstenau
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United Sates of America
| | - Joseph D. Busch
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Daryn E. Erickson
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United Sates of America
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Ryan C. Lancione
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United Sates of America
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Kirk Smith
- Maricopa County Environmental Services Department Vector Control Division, Phoenix, Arizona, United States of America
| | - James Will
- Maricopa County Environmental Services Department Vector Control Division, Phoenix, Arizona, United States of America
| | - John Townsend
- Maricopa County Environmental Services Department Vector Control Division, Phoenix, Arizona, United States of America
| | - Paul S. Keim
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
- Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - David M. Engelthaler
- Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
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16
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Aroh C, Liang C, Raj P, Wakeland B, Yan N, Wakeland E. Co-circulation dynamics and persistence of newly introduced clades of 2012 outbreak associated West Nile Virus in Texas, 2012-2015. INFECTION GENETICS AND EVOLUTION 2018; 66:13-17. [PMID: 30153478 DOI: 10.1016/j.meegid.2018.08.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 08/20/2018] [Accepted: 08/23/2018] [Indexed: 11/16/2022]
Abstract
The second largest outbreak of West Nile encephalitis and West Nile fever ever recorded occurred in the United States (U.S) in the summer of 2012. The outbreak was related to the widespread circulation of closely related clades, or groups, of West Nile virus (WNV) into multiple states where they were not previously found. Whether the invading 2012 strains were able to circulate and overwinter in states with their own endemic population of WNV is unknown and the effect of viral genetics on adaptation and persistence in a new ecological niche is unclear. In this study, we sequenced 70 mosquito isolates from multiple counties throughout Texas in 2012-2015. We identified isolates representative of previously described 2012 WNV groups (Groups 8-10) and discovered a novel group which we called Group 11. Although we identified isolates representative of WNV endemic (2/70) to Texas, most isolates (68/70) were related to the invading 2012 strains, and of these Group 10 (45/68) was predominant. We also observed differences among the 2012 WNV groups correlating to their genotype. Group 10 WNV in Texas, which carry two putative positively selected variants, had limited introductions into Texas, wide circulation, and strong evidence of continued persistence perhaps indicative of overwintering. In contrast, Groups 8 and 11, without positively selected variants, had multiple introductions into Texas, limited circulation, and limited persistence. Lastly, we identified a potential transmission source in New York for incoming Group 8 WNV into Texas. Altogether our study suggests that mutations in the WNV genome may influence the range and dynamics of WNV circulation, and the ability of different strains to persist in new ecological niches.
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Affiliation(s)
- Chukwuemika Aroh
- UT Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, USA.
| | - Chaoying Liang
- UT Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, USA
| | - Prithvi Raj
- UT Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, USA
| | - Benjamin Wakeland
- UT Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, USA
| | - Nan Yan
- UT Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, USA
| | - Edward Wakeland
- UT Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, USA.
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17
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Increases in the competitive fitness of West Nile virus isolates after introduction into California. Virology 2017; 514:170-181. [PMID: 29195094 DOI: 10.1016/j.virol.2017.11.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 11/16/2017] [Accepted: 11/18/2017] [Indexed: 11/23/2022]
Abstract
To investigate the phenotypic evolution of West Nile virus (WNV) in California, we competed sixteen isolates made during 2007-08 against COAV997-5nt, a genetically marked clone from the founding 2003 California isolate COAV997-2003. Using in vivo fitness competitions in House Finches (HOFI) and Culex tarsalis mosquitoes, we found that the majority of WNV WN02 and SW03 genotype isolates exhibited elevated replicative fitness in both hosts compared to COAV997-5nt. Increased replicative capacity in HOFIs was not associated with increased mortality, indicating that these isolates had not gained avian virulence. One WN02 isolate from Coachella Valley, a region geographically close to the isolation of COAV997, showed neutral fitness in HOFIs and reduced fitness in Cx. tarsalis. Two isolates from Kern County and Sacramento/Yolo County out-competed COAV997-nt in HOFIs, but were transmitted less efficiently by Cx. tarsalis. Competition demonstrated neutral or increased fitness that appeared independent of both WN02 and SW03 genotypes.
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18
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Ballinger MJ, Medeiros AS, Qin J, Taylor DJ. Unexpected differences in the population genetics of phasmavirids ( Bunyavirales) from subarctic ponds. Virus Evol 2017; 3:vex015. [PMID: 28744370 PMCID: PMC5518175 DOI: 10.1093/ve/vex015] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Little is known of the evolution of RNA viruses in aquatic systems. Here, we assess the genetic connectivity of two bunyaviruses (Kigluaik phantom orthophasmavirus or KIGV and Nome phantom orthophasmavirus or NOMV) with zooplanktonic hosts from subarctic ponds. We expected weak genetic structure among populations as the hosts (phantom midges) have a terrestrial winged dispersal stage. To test whether their respective viruses mirror this structure, we collected and analyzed population datasets from 21 subarctic freshwater ponds and obtained sequences from all four genes in the viral genomes. Prevalence averaged 66 per cent for 514 host specimens and was not significantly different between recently formed thaw ponds and glacial ponds. Unexpectedly, KIGV from older ponds showed pronounced haplotype divergence with little evidence of genetic connectivity. However, KIGV populations from recent thaw ponds appeared to be represented by a closely related haplotype group, perhaps indicating a genotypic dispersal bias. Unlike KIGV, NOMV had modest structure and diversity in recently formed thaw ponds. For each virus, we found elevated genetic diversity relative to the host, but similar population structures to the host. Our results suggest that non-random processes such as virus-host interactions, genotypic bias, and habitat effects differ among polar aquatic RNA viruses.
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Affiliation(s)
- Matthew J. Ballinger
- The Department of Biological Sciences, State University of New York, Buffalo, NY, USA
| | | | - Jie Qin
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Derek J. Taylor
- The Department of Biological Sciences, State University of New York, Buffalo, NY, USA
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19
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Rimoldi G, Mete A, Adaska JM, Anderson ML, Symmes KP, Diab S. West Nile Virus Infection in Sheep. Vet Pathol 2016; 54:155-158. [PMID: 27312367 DOI: 10.1177/0300985816653796] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
West Nile virus (WNV) infection has been detected in many species of birds and mammals, but scant information is available about the disease in small ruminants. West Nile virus was diagnosed in 6 sheep with neurological signs and encephalitis, in California between 2002 and 2014. All sheep had severe lymphoplasmacytic meningoencephalitis. Lymphoplasmacytic myelitis was also detected in 2 sheep where the spinal cord was examined. Brain tissue was positive for WNV detected by polymerase chain reaction in 6 of 6 sheep and by immunohistochemistry (IHC) in 5 of 6 sheep. Viral antigen was not detected by IHC in extraneural tissues in the 3 sheep examined. West Nile virus RNA was sequenced from 2 of 6 sheep, and each one clusters closely with WNV isolated from mosquito pools from nearby locations at similar times. West Nile virus was the most common cause of viral encephalitis in sheep diagnosed at this laboratory between 2002 and 2014, accounting for 6 of 9 sheep.
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Affiliation(s)
- G Rimoldi
- 1 California Animal Health and Food Safety Laboratory System, University of California-Davis, Tulare, CA, USA
| | - A Mete
- 2 California Animal Health and Food Safety Laboratory System, University of California-Davis, USA
| | - J M Adaska
- 1 California Animal Health and Food Safety Laboratory System, University of California-Davis, Tulare, CA, USA
| | - M L Anderson
- 2 California Animal Health and Food Safety Laboratory System, University of California-Davis, USA
| | - K P Symmes
- 3 Davis Arbovirus Research and Training, Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California-Davis, USA
| | - S Diab
- 2 California Animal Health and Food Safety Laboratory System, University of California-Davis, USA
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Genetic Variability of West Nile Virus in U.S. Blood Donors from the 2012 Epidemic Season. PLoS Negl Trop Dis 2016; 10:e0004717. [PMID: 27182734 PMCID: PMC4868353 DOI: 10.1371/journal.pntd.0004717] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 04/27/2016] [Indexed: 12/26/2022] Open
Abstract
West Nile virus (WNV) is an arbovirus maintained in nature in a bird-mosquito enzootic cycle which can also infect other vertebrates including humans. WNV is now endemic in the United States (U.S.), causing yearly outbreaks that have resulted in an estimated total of 4-5 million human infections. Over 41,700 cases of West Nile disease, including 18,810 neuroinvasive cases and 1,765 deaths, were reported to the CDC between 1999 and 2014. In 2012, the second largest West Nile outbreak in the U.S. was reported, which caused 5,674 cases and 286 deaths. WNV continues to evolve, and three major WNV lineage I genotypes (NY99, WN02, and SW/WN03) have been described in the U.S. since introduction of the virus in 1999. We report here the WNV sequences obtained from 19 human samples acquired during the 2012 U.S. outbreak and our examination of the evolutionary dynamics in WNV isolates sequenced from 1999-2012. Maximum-likelihood and Bayesian methods were used to perform the phylogenetic analyses. Selection pressure analyses were performed with the HyPhy package using the Datamonkey web-server. Using different codon-based and branch-site selection models, we detected a number of codons subjected to positive pressure in WNV genes. Thirteen of the 19 completely sequenced isolates from 10 U.S. states were genetically similar, sharing up to 55 nucleotide mutations and 4 amino acid substitutions when compared with the prototype isolate WN-NY99. Overall, these analyses showed that following a brief contraction in 2008-2009, WNV genetic divergence in the U.S. continued to increase in 2012, and that closely related variants were found across a broad geographic range of the U.S., coincident with the second-largest WNV outbreak in U.S.
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Lustig Y, Hindiyeh M, Orshan L, Weiss L, Koren R, Katz-Likvornik S, Zadka H, Glatman-Freedman A, Mendelson E, Shulman LM. Mosquito Surveillance for 15 Years Reveals High Genetic Diversity Among West Nile Viruses in Israel. J Infect Dis 2015; 213:1107-14. [PMID: 26597260 DOI: 10.1093/infdis/jiv556] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 11/12/2015] [Indexed: 12/16/2022] Open
Abstract
West Nile Virus (WNV) is endemic in Israel and has been the cause of several outbreaks in recent years. In 2000, a countrywide mosquito survey was established to monitor WNV activity and characterize viral genotypes in Israel. We analyzed data from 7135 pools containing 277 186 mosquitoes collected over the past 15 years and, here, report partial sequences of WNV genomes obtained from 102 of the 336 positive mosquito pools. Phylogenetic analysis demonstrated that cluster 4 and the Mediterranean and Eastern European subtypes of cluster 2 within WNV lineage 1 circulated in Israel, as did WNV lineage 2, highlighting a high genetic diversity of WNV genotypes in our region. As a major crossroads for bird migration between Africa and Eurasia and with a long history of human infection, Israel serves as a resource hub for WNV in Africa and Eurasia and provides valuable information on WNV circulation in these regions.
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Affiliation(s)
- Yaniv Lustig
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical center, Tel-Hashomer
| | - Musa Hindiyeh
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical center, Tel-Hashomer Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Israel
| | - Laor Orshan
- Laboratory of Entomology, Ministry of Health, Jerusalem
| | - Leah Weiss
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical center, Tel-Hashomer
| | - Ravit Koren
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical center, Tel-Hashomer
| | - Shiri Katz-Likvornik
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical center, Tel-Hashomer
| | - Hila Zadka
- Israel Center for Disease Control, Ministry of Health, Chaim Sheba Medical center, Tel-Hashomer
| | - Aharona Glatman-Freedman
- Israel Center for Disease Control, Ministry of Health, Chaim Sheba Medical center, Tel-Hashomer New York Medical College, Valhalla, New York
| | - Ella Mendelson
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical center, Tel-Hashomer Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Israel
| | - Lester M Shulman
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical center, Tel-Hashomer Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Israel
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Fluid Spatial Dynamics of West Nile Virus in the United States: Rapid Spread in a Permissive Host Environment. J Virol 2015; 90:862-72. [PMID: 26512086 DOI: 10.1128/jvi.02305-15] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 10/24/2015] [Indexed: 12/29/2022] Open
Abstract
UNLABELLED The introduction of West Nile virus (WNV) into North America in 1999 is a classic example of viral emergence in a new environment, with its subsequent dispersion across the continent having a major impact on local bird populations. Despite the importance of this epizootic, the pattern, dynamics, and determinants of WNV spread in its natural hosts remain uncertain. In particular, it is unclear whether the virus encountered major barriers to transmission, or spread in an unconstrained manner, and if specific viral lineages were favored over others indicative of intrinsic differences in fitness. To address these key questions in WNV evolution and ecology, we sequenced the complete genomes of approximately 300 avian isolates sampled across the United States between 2001 and 2012. Phylogenetic analysis revealed a relatively star-like tree structure, indicative of explosive viral spread in the United States, although with some replacement of viral genotypes through time. These data are striking in that viral sequences exhibit relatively limited clustering according to geographic region, particularly for those viruses sampled from birds, and no strong phylogenetic association with well-sampled avian species. The genome sequence data analyzed here also contain relatively little evidence for adaptive evolution, particularly of structural proteins, suggesting that most viral lineages are of similar fitness and that WNV is well adapted to the ecology of mosquito vectors and diverse avian hosts in the United States. In sum, the molecular evolution of WNV in North America depicts a largely unfettered expansion within a permissive host and geographic population with little evidence of major adaptive barriers. IMPORTANCE How viruses spread in new host and geographic environments is central to understanding the emergence and evolution of novel infectious diseases and for predicting their likely impact. The emergence of the vector-borne West Nile virus (WNV) in North America in 1999 represents a classic example of this process. Using approximately 300 new viral genomes sampled from wild birds, we show that WNV experienced an explosive spread with little geographical or host constraints within birds and relatively low levels of adaptive evolution. From its introduction into the state of New York, WNV spread across the United States, reaching California and Florida within 4 years, a migration that is clearly reflected in our genomic sequence data, and with a general absence of distinct geographical clusters of bird viruses. However, some geographically distinct viral lineages were found to circulate in mosquitoes, likely reflecting their limited long-distance movement compared to avian species.
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