1
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Fay RL, Cruz-Loya M, Keyel AC, Price DC, Zink SD, Mordecai EA, Ciota AT. Population-specific thermal responses contribute to regional variability in arbovirus transmission with changing climates. iScience 2024; 27:109934. [PMID: 38799579 PMCID: PMC11126822 DOI: 10.1016/j.isci.2024.109934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 12/05/2023] [Accepted: 05/05/2024] [Indexed: 05/29/2024] Open
Abstract
Temperature is increasing globally, and vector-borne diseases are particularly responsive to such increases. While it is known that temperature influences mosquito life history traits, transmission models have not historically considered population-specific effects of temperature. We assessed the interaction between Culex pipiens population and temperature in New York State (NYS) and utilized novel empirical data to inform predictive models of West Nile virus (WNV) transmission. Genetically and regionally distinct populations from NYS were reared at various temperatures, and life history traits were monitored and used to inform trait-based models. Variation in Cx. pipiens life history traits and population-dependent thermal responses account for a predicted 2.9°C difference in peak transmission that is reflected in regional differences in WNV prevalence. We additionally identified genetic signatures that may contribute to distinct thermal responses. Together, these data demonstrate how population variation contributes to significant geographic variability in arbovirus transmission with changing climates.
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Affiliation(s)
- Rachel L. Fay
- Department of Biomedical Sciences, State University of New York at Albany School of Public Health, Rensselaer, NY, USA
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY, USA
| | | | - Alexander C. Keyel
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY, USA
| | - Dana C. Price
- Department of Entomology, Rutgers University, New Brunswick, NJ, USA
| | - Steve D. Zink
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY, USA
| | | | - Alexander T. Ciota
- Department of Biomedical Sciences, State University of New York at Albany School of Public Health, Rensselaer, NY, USA
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY, USA
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2
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Roy P, Walter Z, Berish L, Ramage H, McCullagh M. Motif-VI Loop Acts as a Nucleotide Valve in the West Nile Virus NS3 Helicase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.30.569434. [PMID: 38077049 PMCID: PMC10705498 DOI: 10.1101/2023.11.30.569434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
The flavivirus NS3 helicase (NS3h), a highly conserved protein, plays a pivotal role in virus replication and thus represents a potential drug target for flavivirus pathogenesis. NS3h utilizes nucleotide triphosphate, such as ATP, for hydrolysis energy (ATPase) to translocate on single-stranded nucleic acids, which is an important step in the unwinding of double-stranded nucleic acids. The intermediate states along the ATP binding and hydrolysis cycle, as well as the conformational changes between these states, represent important yet difficult-to-identify targets for potential inhibitors. We use extensive molecular dynamics simulations of apo, ATP, ADP+Pi, and ADP bound to WNV NS3h+ssRNA to model the conformational ensembles along this cycle. Energetic and structural clustering analyses on these trajectories depict a clear trend of differential enthalpic affinity of NS3h with ADP, demonstrating a probable mechanism of hydrolysis turnover regulated by the motif-VI loop (MVIL). These findings were experimentally corroborated using viral replicons encoding three mutations at the D471 position. Replication assays using these mutants demonstrated a substantial reduction in viral replication compared to the wild-type. Molecular simulations of the D471 mutants in the apo state indicate a shift in MVIL populations favoring either a closed or open 'valve' conformation, affecting ATP entry or stabilization, respectively. Combining our molecular modeling with experimental evidence highlights a conformation-dependent role for MVIL as a 'valve' for the ATP-pocket, presenting a promising target for antiviral development.
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Affiliation(s)
- Priti Roy
- Department of Chemistry, Oklahoma State University, Stillwater, OK, USA, 74078
| | - Zachary Walter
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA, USA, 19107
| | - Lauren Berish
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA, USA, 19107
| | - Holly Ramage
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA, USA, 19107
| | - Martin McCullagh
- Department of Chemistry, Oklahoma State University, Stillwater, OK, USA, 74078
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3
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Caldwell HS, Kuo L, Pata JD, Dupuis AP, Arnold JJ, Yeager C, Stout J, Koetzner CA, Payne AF, Bialosuknia SM, Banker EM, Nolen TA, Cameron CE, Ciota AT. Maintenance of a host-specific minority mutation in the West Nile virus NS3. iScience 2023; 26:107468. [PMID: 37593454 PMCID: PMC10428113 DOI: 10.1016/j.isci.2023.107468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 06/22/2023] [Accepted: 07/21/2023] [Indexed: 08/19/2023] Open
Abstract
West Nile virus (WNV), the most prevalent arthropod-borne virus (arbovirus) in the United States, is maintained in a cycle between Culex spp. mosquitoes and birds. Arboviruses exist within hosts and vectors as a diverse set of closely related genotypes. In theory, this genetic diversity can facilitate adaptation to distinct environments during host cycling, yet host-specific fitness of minority genotypes has not been assessed. Utilizing WNV deep-sequencing data, we previously identified a naturally occurring, mosquito-biased substitution, NS3 P319L. Using both cell culture and experimental infection in natural hosts, we demonstrated that this substitution confers attenuation in vertebrate hosts and increased transmissibility by mosquitoes. Biochemical assays demonstrated temperature-sensitive ATPase activity consistent with host-specific phenotypes. Together these data confirm the maintenance of host-specific minority variants in arbovirus mutant swarms, suggest a unique role for NS3 in viral fitness, and demonstrate that intrahost sequence data can inform mechanisms of host-specific adaptation.
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Affiliation(s)
- Haley S. Caldwell
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA
- Department of Biomedical Sciences, State University of New York at Albany, School of Public Health, Rensselaer, NY 12144, USA
| | - Lili Kuo
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA
| | - Janice D. Pata
- Department of Biomedical Sciences, State University of New York at Albany, School of Public Health, Rensselaer, NY 12144, USA
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Alan P. Dupuis
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA
| | - Jamie J. Arnold
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Calvin Yeager
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Jessica Stout
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA
| | - Cheri A. Koetzner
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA
| | - Anne F. Payne
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA
| | - Sean M. Bialosuknia
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA
| | - Elyse M. Banker
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA
| | - Taylor A. Nolen
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA
| | - Craig E. Cameron
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Alexander T. Ciota
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA
- Department of Biomedical Sciences, State University of New York at Albany, School of Public Health, Rensselaer, NY 12144, USA
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4
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Santos PD, Günther A, Keller M, Homeier-Bachmann T, Groschup MH, Beer M, Höper D, Ziegler U. An advanced sequence clustering and designation workflow reveals the enzootic maintenance of a dominant West Nile virus subclade in Germany. Virus Evol 2023; 9:vead013. [PMID: 37197362 PMCID: PMC10184446 DOI: 10.1093/ve/vead013] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 01/13/2023] [Accepted: 03/16/2023] [Indexed: 05/19/2023] Open
Abstract
West Nile virus (WNV) is the most widespread arthropod-borne (arbo) virus and the primary cause of arboviral encephalitis globally. Members of WNV species genetically diverged and are classified into different hierarchical groups below species rank. However, the demarcation criteria for allocating WNV sequences into these groups remain individual and inconsistent, and the use of names for different levels of the hierarchical levels is unstructured. In order to have an objective and comprehensible grouping of WNV sequences, we developed an advanced grouping workflow using the 'affinity propagation clustering' algorithm and newly included the 'agglomerative hierarchical clustering' algorithm for the allocation of WNV sequences into different groups below species rank. In addition, we propose to use a fixed set of terms for the hierarchical naming of WNV below species level and a clear decimal numbering system to label the determined groups. For validation, we applied the refined workflow to WNV sequences that have been previously grouped into various lineages, clades, and clusters in other studies. Although our workflow regrouped some WNV sequences, overall, it generally corresponds with previous groupings. We employed our novel approach to the sequences from the WNV circulation in Germany 2020, primarily from WNV-infected birds and horses. Besides two newly defined minor (sub)clusters comprising only three sequences each, Subcluster 2.5.3.4.3c was the predominant WNV sequence group detected in Germany from 2018 to 2020. This predominant subcluster was also associated with at least five human WNV infections in 2019-20. In summary, our analyses imply that the genetic diversity of the WNV population in Germany is shaped by enzootic maintenance of the dominant WNV subcluster accompanied by sporadic incursions of other rare clusters and subclusters. Moreover, we show that our refined approach for sequence grouping yields meaningful results. Although we primarily aimed at a more detailed WNV classification, the presented workflow can also be applied to the objective genotyping of other virus species.
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Affiliation(s)
| | | | - Markus Keller
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, 17493, Greifswald-Insel Riems, Germany
| | | | - Martin H Groschup
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, 17493, Greifswald-Insel Riems, Germany
- German Centre for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, 17493, Greifswald-Insel Riems, Germany
| | - Martin Beer
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Diagnostic Virology, 17493, Greifswald-Insel Riems, Germany
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5
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Bialosuknia SM, Dupuis II AP, Zink SD, Koetzner CA, Maffei JG, Owen JC, Landwerlen H, Kramer LD, Ciota AT. Adaptive evolution of West Nile virus facilitated increased transmissibility and prevalence in New York State. Emerg Microbes Infect 2022; 11:988-999. [PMID: 35317702 PMCID: PMC8982463 DOI: 10.1080/22221751.2022.2056521] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 03/17/2022] [Indexed: 11/12/2022]
Abstract
West Nile virus (WNV; Flavivirus, Flaviviridae) was introduced to New York State (NYS) in 1999 and rapidly expanded its range through the continental United States (US). Apart from the displacement of the introductory NY99 genotype with the WN02 genotype, there has been little evidence of adaptive evolution of WNV in the US. WNV NY10, characterized by shared amino acid substitutions R1331K and I2513M, emerged in 2010 coincident with increased WNV cases in humans and prevalence in mosquitoes. Previous studies demonstrated an increase in frequency of NY10 strains in NYS and evidence of positive selection. Here, we present updated surveillance and sequencing data for WNV in NYS and investigate if NY10 genotype strains are associated with phenotypic change consistent with an adaptive advantage. Results confirm a significant increase in prevalence in mosquitoes though 2018, and updated sequencing demonstrates a continued dominance of NY10. We evaluated NY10 strains in Culex pipiens mosquitoes to assess vector competence and found that the NY10 genotype is associated with both increased infectivity and transmissibility. Experimental infection of American robins (Turdus migratorius) was additionally completed to assess viremia kinetics of NY10 relative to WN02. Modelling the increased infectivity and transmissibility of the NY10 strains together with strain-specific viremia demonstrates a mechanistic basis for selection that has likely contributed to the increased prevalence of WNV in NYS.
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Affiliation(s)
- Sean M. Bialosuknia
- New York State Department of Health, The Arbovirus Laboratory, Wadsworth Center, Slingerlands, NY, USA
- Department of Biology, State University of New York at Albany, Albany, NY, USA
| | - Alan P. Dupuis II
- New York State Department of Health, The Arbovirus Laboratory, Wadsworth Center, Slingerlands, NY, USA
| | - Steven D. Zink
- New York State Department of Health, The Arbovirus Laboratory, Wadsworth Center, Slingerlands, NY, USA
| | - Cheri A. Koetzner
- New York State Department of Health, The Arbovirus Laboratory, Wadsworth Center, Slingerlands, NY, USA
| | - Joseph G. Maffei
- New York State Department of Health, The Arbovirus Laboratory, Wadsworth Center, Slingerlands, NY, USA
| | - Jennifer C. Owen
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, USA
| | - Hannah Landwerlen
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, USA
| | - Laura D. Kramer
- New York State Department of Health, The Arbovirus Laboratory, Wadsworth Center, Slingerlands, NY, USA
- Department of Biology, State University of New York at Albany, Albany, NY, USA
| | - Alexander T. Ciota
- New York State Department of Health, The Arbovirus Laboratory, Wadsworth Center, Slingerlands, NY, USA
- Department of Biology, State University of New York at Albany, Albany, NY, USA
- Department of Biomedical Sciences, State University of New York at Albany School of Public Health, Albany, NY, USA
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6
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Caldwell HS, Pata JD, Ciota AT. The Role of the Flavivirus Replicase in Viral Diversity and Adaptation. Viruses 2022; 14:1076. [PMID: 35632818 PMCID: PMC9143365 DOI: 10.3390/v14051076] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/03/2022] [Accepted: 05/06/2022] [Indexed: 02/04/2023] Open
Abstract
Flaviviruses include several emerging and re-emerging arboviruses which cause millions of infections each year. Although relatively well-studied, much remains unknown regarding the mechanisms and means by which these viruses readily alternate and adapt to different hosts and environments. Here, we review a subset of the different aspects of flaviviral biology which impact host switching and viral fitness. These include the mechanism of replication and structural biology of the NS3 and NS5 proteins, which reproduce the viral genome; rates of mutation resulting from this replication and the role of mutational frequency in viral fitness; and the theory of quasispecies evolution and how it contributes to our understanding of genetic and phenotypic plasticity.
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Affiliation(s)
- Haley S. Caldwell
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA;
- Department of Biomedical Sciences, State University of New York at Albany, School of Public Health, Rensselaer, NY 12144, USA;
| | - Janice D. Pata
- Department of Biomedical Sciences, State University of New York at Albany, School of Public Health, Rensselaer, NY 12144, USA;
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Alexander T. Ciota
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA;
- Department of Biomedical Sciences, State University of New York at Albany, School of Public Health, Rensselaer, NY 12144, USA;
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7
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Dieme C, Maffei JG, Diarra M, Koetzner CA, Kuo L, Ngo KA, Dupuis AP, Zink SD, Bryon Backenson P, Kramer LD, Ciota AT. Aedes albopictus and Cache Valley virus: a new threat for virus transmission in New York State. Emerg Microbes Infect 2022; 11:741-748. [PMID: 35179429 PMCID: PMC8903793 DOI: 10.1080/22221751.2022.2044733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We report surveillance results of Cache Valley virus (CVV; Peribunyaviridae, Orthobunyavirus) from 2017 to 2020 in New York State (NYS). Infection rates were calculated using the maximum likelihood estimation (MLE) method by year, region, and mosquito species. The highest infection rates were identified among Anopheles spp. mosquitoes and we detected the virus in Aedes albopictus for the first time in NYS. Based on our previous Anopheles quadrimaculatus vector competence results for nine CVV strains, we selected among them three stains for further characterization. These include two CVV reassortants (PA and 15041084) and one CVV lineage 2 strain (Hu-2011). We analyzed full genomes, compared in vitro growth kinetics and assessed vector competence of Aedes albopictus. Sequence analysis of the two reassortant strains (PA and 15041084) revealed 0.3%, 0.4%, and 0.3% divergence; and 1, 10, and 6 amino acid differences for the S, M, and L segments, respectively. We additionally found that the PA strain was attenuated in vertebrate (Vero) and mosquito (C6/36) cell culture. Furthemore, Ae. albopictus mosquitoes are competent vectors for CVV Hu-2011 (16.7–62.1% transmission rates) and CVV 15041084 (27.3–48.0% transmission rates), but not for the human reassortant (PA) isolate, which did not disseminate from the mosquito midgut. Together, our results demonstrate significant phenotypic variability among strains and highlight the capacity for Ae. albopictus to act as a vector of CVV.
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Affiliation(s)
- Constentin Dieme
- Wadsworth Center, New York State Department of Health, Slingerlands, New York, USA (C. Dieme, J.G. Maffei, C.A Koetzner, L. Kuo, K.A. Ngo, A.P. Dupuis II, S.D. Zink, L.D. Kramer, and A.T. Ciota)
| | - Joseph G Maffei
- Wadsworth Center, New York State Department of Health, Slingerlands, New York, USA (C. Dieme, J.G. Maffei, C.A Koetzner, L. Kuo, K.A. Ngo, A.P. Dupuis II, S.D. Zink, L.D. Kramer, and A.T. Ciota)
| | - Maryam Diarra
- Institut Pasteur de Dakar, Dakar, Senegal (M. Diarra)
| | - Cheri A Koetzner
- Wadsworth Center, New York State Department of Health, Slingerlands, New York, USA (C. Dieme, J.G. Maffei, C.A Koetzner, L. Kuo, K.A. Ngo, A.P. Dupuis II, S.D. Zink, L.D. Kramer, and A.T. Ciota)
| | - Lili Kuo
- Wadsworth Center, New York State Department of Health, Slingerlands, New York, USA (C. Dieme, J.G. Maffei, C.A Koetzner, L. Kuo, K.A. Ngo, A.P. Dupuis II, S.D. Zink, L.D. Kramer, and A.T. Ciota)
| | - Kiet A Ngo
- Wadsworth Center, New York State Department of Health, Slingerlands, New York, USA (C. Dieme, J.G. Maffei, C.A Koetzner, L. Kuo, K.A. Ngo, A.P. Dupuis II, S.D. Zink, L.D. Kramer, and A.T. Ciota)
| | - Alan P Dupuis
- Wadsworth Center, New York State Department of Health, Slingerlands, New York, USA (C. Dieme, J.G. Maffei, C.A Koetzner, L. Kuo, K.A. Ngo, A.P. Dupuis II, S.D. Zink, L.D. Kramer, and A.T. Ciota)
| | - Steven D Zink
- Wadsworth Center, New York State Department of Health, Slingerlands, New York, USA (C. Dieme, J.G. Maffei, C.A Koetzner, L. Kuo, K.A. Ngo, A.P. Dupuis II, S.D. Zink, L.D. Kramer, and A.T. Ciota)
| | - P Bryon Backenson
- New York State Department of Health, Bureau of Communicable Disease Control, Albany, New York (P.B. Backenson)
| | - Laura D Kramer
- Wadsworth Center, New York State Department of Health, Slingerlands, New York, USA (C. Dieme, J.G. Maffei, C.A Koetzner, L. Kuo, K.A. Ngo, A.P. Dupuis II, S.D. Zink, L.D. Kramer, and A.T. Ciota).,Department of Biomedical Sciences, School of Public Health, State University of New York at Albany, Albany, New York, USA (L.D. Kramer, and A.T. Ciota)
| | - Alexander T Ciota
- Wadsworth Center, New York State Department of Health, Slingerlands, New York, USA (C. Dieme, J.G. Maffei, C.A Koetzner, L. Kuo, K.A. Ngo, A.P. Dupuis II, S.D. Zink, L.D. Kramer, and A.T. Ciota).,Department of Biomedical Sciences, School of Public Health, State University of New York at Albany, Albany, New York, USA (L.D. Kramer, and A.T. Ciota)
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8
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Dupuis AP, Prusinski MA, O'Connor C, Maffei JG, Ngo KA, Koetzner CA, Santoriello MP, Romano CL, Xu G, Ribbe F, Campbell SR, Rich SM, Backenson PB, Kramer LD, Ciota AT. Heartland Virus Transmission, Suffolk County, New York, USA. Emerg Infect Dis 2021; 27:3128-3132. [PMID: 34648421 PMCID: PMC8632170 DOI: 10.3201/eid2712.211426] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
During 2018, Heartland virus RNA was detected in an Amblyomma americanum tick removed from a resident of Suffolk County, New York, USA. The person showed seroconversion. Tick surveillance and white-tailed deer (Odocoileus virginianus) serosurveys showed widespread distribution in Suffolk County, emphasizing a need for disease surveillance anywhere A. americanum ticks are established or emerging.
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9
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Fay RL, Ngo KA, Kuo L, Willsey GG, Kramer LD, Ciota AT. Experimental Evolution of West Nile Virus at Higher Temperatures Facilitates Broad Adaptation and Increased Genetic Diversity. Viruses 2021; 13:1889. [PMID: 34696323 PMCID: PMC8540194 DOI: 10.3390/v13101889] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/14/2021] [Accepted: 09/16/2021] [Indexed: 11/18/2022] Open
Abstract
West Nile virus (WNV, Flaviviridae, Flavivirus) is a mosquito-borne flavivirus introduced to North America in 1999. Since 1999, the Earth's average temperature has increased by 0.6 °C. Mosquitoes are ectothermic organisms, reliant on environmental heat sources. Temperature impacts vector-virus interactions which directly influence arbovirus transmission. RNA viral replication is highly error-prone and increasing temperature could further increase replication rates, mutation frequencies, and evolutionary rates. The impact of temperature on arbovirus evolutionary trajectories and fitness landscapes has yet to be sufficiently studied. To investigate how temperature impacts the rate and extent of WNV evolution in mosquito cells, WNV was experimentally passaged 12 times in Culex tarsalis cells, at 25 °C and 30 °C. Full-genome deep sequencing was used to compare genetic signatures during passage, and replicative fitness was evaluated before and after passage at each temperature. Our results suggest adaptive potential at both temperatures, with unique temperature-dependent and lineage-specific genetic signatures. Further, higher temperature passage was associated with significantly increased replicative fitness at both temperatures and increases in nonsynonymous mutations. Together, these data indicate that if similar selective pressures exist in natural systems, increases in temperature could accelerate emergence of high-fitness strains with greater phenotypic plasticity.
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Affiliation(s)
- Rachel L. Fay
- Department of Biomedical Sciences, State University of New York at Albany School of Public Health, Rensselaer, NY 12144, USA; (R.L.F.); (L.D.K.)
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA; (K.A.N.); (L.K.)
| | - Kiet A. Ngo
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA; (K.A.N.); (L.K.)
| | - Lili Kuo
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA; (K.A.N.); (L.K.)
| | - Graham G. Willsey
- Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA;
| | - Laura D. Kramer
- Department of Biomedical Sciences, State University of New York at Albany School of Public Health, Rensselaer, NY 12144, USA; (R.L.F.); (L.D.K.)
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA; (K.A.N.); (L.K.)
| | - Alexander T. Ciota
- Department of Biomedical Sciences, State University of New York at Albany School of Public Health, Rensselaer, NY 12144, USA; (R.L.F.); (L.D.K.)
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA; (K.A.N.); (L.K.)
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10
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Divergent Mutational Landscapes of Consensus and Minority Genotypes of West Nile Virus Demonstrate Host and Gene-Specific Evolutionary Pressures. Genes (Basel) 2020; 11:genes11111299. [PMID: 33143358 PMCID: PMC7692055 DOI: 10.3390/genes11111299] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/19/2020] [Accepted: 10/29/2020] [Indexed: 01/12/2023] Open
Abstract
Our current understanding of the natural evolution of RNA viruses comes largely from consensus level genetic analyses which ignore the diverse mutant swarms that comprise within-host viral populations. The breadth and composition of viral mutant swarms impact viral fitness and adaptation, and the capacity for swarm plasticity is likely to be particularly important for arthropod-borne viruses (arboviruses) that cycle between taxonomically divergent hosts. Despite this, characterization of the relationship between the selective pressures and genetic signatures of the mutant swarm and consensus sequences is lacking. To clarify this, we analyzed previously generated whole genome, deep-sequencing data from 548 West Nile virus samples isolated from avian tissues or mosquitoes in New York State from 1999-2018. Both consensus level (interhost) and minority level (intrahost) nucleotide and amino acid sequences were analyzed, and diversity at each position was calculated across the genome in order to assess the relationship between minority and consensus sequences for individual genes and hosts. Our results indicate that consensus sequences are an inept representation of the overall genetic diversity. Unique host and gene-specific signatures and selective pressures were identified. These data demonstrate that an accurate and comprehensive understanding of arbovirus evolution and adaptation within and between hosts requires consideration of minority genotypes.
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Kramer LD, Ciota AT, Kilpatrick AM. Introduction, Spread, and Establishment of West Nile Virus in the Americas. JOURNAL OF MEDICAL ENTOMOLOGY 2019; 56:1448-1455. [PMID: 31549719 PMCID: PMC7182919 DOI: 10.1093/jme/tjz151] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Indexed: 05/04/2023]
Abstract
The introduction of West Nile virus (WNV) to North America in 1999 and its subsequent rapid spread across the Americas demonstrated the potential impact of arboviral introductions to new regions, and this was reinforced by the subsequent introductions of chikungunya and Zika viruses. Extensive studies of host-pathogen-vector-environment interactions over the past two decades have illuminated many aspects of the ecology and evolution of WNV and other arboviruses, including the potential for pathogen adaptation to hosts and vectors, the influence of climate, land use and host immunity on transmission ecology, and the difficulty in preventing the establishment of a zoonotic pathogen with abundant wildlife reservoirs. Here, we focus on outstanding questions concerning the introduction, spread, and establishment of WNV in the Americas, and what it can teach us about the future of arboviral introductions. Key gaps in our knowledge include the following: viral adaptation and coevolution of hosts, vectors and the virus; the mechanisms and species involved in the large-scale spatial spread of WNV; how weather modulates WNV transmission; the drivers of large-scale variation in enzootic transmission; the ecology of WNV transmission in Latin America; and the relative roles of each component of host-virus-vector interactions in spatial and temporal variation in WNV transmission. Integrative studies that examine multiple factors and mechanisms simultaneously are needed to advance our knowledge of mechanisms driving transmission.
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Affiliation(s)
- Laura D Kramer
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY
- Department of Biomedical Sciences, State University of New York at Albany School of Public Health, Albany, NY
- Corresponding author, e-mail:
| | - Alexander T Ciota
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY
- Department of Biomedical Sciences, State University of New York at Albany School of Public Health, Albany, NY
| | - A Marm Kilpatrick
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA
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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: 64] [Impact Index Per Article: 12.8] [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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