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Tran-Kiem C, Paredes MI, Perofsky AC, Frisbie LA, Xie H, Kong K, Weixler A, Greninger AL, Roychoudhury P, Peterson JM, Delgado A, Halstead H, MacKellar D, Dykema P, Gamboa L, Frazar CD, Ryke E, Stone J, Reinhart D, Starita L, Thibodeau A, Yun C, Aragona F, Black A, Viboud C, Bedford T. Fine-scale spatial and social patterns of SARS-CoV-2 transmission from identical pathogen sequences. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.24.24307811. [PMID: 38826243 PMCID: PMC11142302 DOI: 10.1101/2024.05.24.24307811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Pathogen genomics can provide insights into disease transmission patterns, but new methods are needed to handle modern large-scale pathogen genome datasets. Genetically proximal viruses indicate epidemiological linkage and are informative about transmission events. Here, we leverage pairs of identical sequences using 114,298 SARS-CoV-2 genomes collected via sentinel surveillance from March 2021 to December 2022 in Washington State, USA, with linked age and residence information to characterize fine-scale transmission. The location of pairs of identical sequences is highly consistent with expectations from mobility and social contact data. Outliers in the relationship between genetic and mobility data can be explained by SARS-CoV-2 transmission between postal codes with male prisons, consistent with transmission between prison facilities. Transmission patterns between age groups vary across spatial scales. Finally, we use the timing of sequence collection to understand the age groups driving transmission. This work improves our ability to characterize transmission from large pathogen genome datasets.
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Affiliation(s)
- Cécile Tran-Kiem
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Miguel I. Paredes
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Amanda C. Perofsky
- Brotman Baty Institute, University of Washington, Seattle, WA, USA
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | | | - Hong Xie
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Kevin Kong
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Amelia Weixler
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Alexander L. Greninger
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Pavitra Roychoudhury
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | | | - Andrew Delgado
- Washington State Department of Health, Shoreline, WA, USA
| | - Holly Halstead
- Washington State Department of Health, Shoreline, WA, USA
| | - Drew MacKellar
- Washington State Department of Health, Shoreline, WA, USA
| | - Philip Dykema
- Washington State Department of Health, Shoreline, WA, USA
| | - Luis Gamboa
- Brotman Baty Institute, University of Washington, Seattle, WA, USA
| | - Chris D. Frazar
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Erica Ryke
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Jeremy Stone
- Brotman Baty Institute, University of Washington, Seattle, WA, USA
| | - David Reinhart
- Brotman Baty Institute, University of Washington, Seattle, WA, USA
| | - Lea Starita
- Brotman Baty Institute, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Cory Yun
- Washington State Department of Health, Shoreline, WA, USA
| | - Frank Aragona
- Washington State Department of Health, Shoreline, WA, USA
| | - Allison Black
- Washington State Department of Health, Shoreline, WA, USA
| | - Cécile Viboud
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Trevor Bedford
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
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Dellicour S, Bastide P, Rocu P, Fargette D, Hardy OJ, Suchard MA, Guindon S, Lemey P. How fast are viruses spreading in the wild? BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.10.588821. [PMID: 38645268 PMCID: PMC11030353 DOI: 10.1101/2024.04.10.588821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Genomic data collected from viral outbreaks can be exploited to reconstruct the dispersal history of viral lineages in a two-dimensional space using continuous phylogeographic inference. These spatially explicit reconstructions can subsequently be used to estimate dispersal metrics allowing to unveil the dispersal dynamics and evaluate the capacity to spread among hosts. Heterogeneous sampling intensity of genomic sequences can however impact the accuracy of dispersal insights gained through phylogeographic inference. In our study, we implement a simulation framework to evaluate the robustness of three dispersal metrics - a lineage dispersal velocity, a diffusion coefficient, and an isolation-by-distance signal metric - to the sampling effort. Our results reveal that both the diffusion coefficient and isolation-by-distance signal metrics appear to be robust to the number of samples considered for the phylogeographic reconstruction. We then use these two dispersal metrics to compare the dispersal pattern and capacity of various viruses spreading in animal populations. Our comparative analysis reveals a broad range of isolation-by-distance patterns and diffusion coefficients mostly reflecting the dispersal capacity of the main infected host species but also, in some cases, the likely signature of rapid and/or long-distance dispersal events driven by human-mediated movements through animal trade. Overall, our study provides key recommendations for the lineage dispersal metrics to consider in future studies and illustrates their application to compare the spread of viruses in various settings.
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Doizy A, Prin A, Cornu G, Chiroleu F, Rieux A. Phylostems: a new graphical tool to investigate temporal signal of heterochronous sequences datasets. BIOINFORMATICS ADVANCES 2023; 3:vbad026. [PMID: 36936370 PMCID: PMC10017117 DOI: 10.1093/bioadv/vbad026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 02/16/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023]
Abstract
Motivation Molecular tip-dating of phylogenetic trees is a growing discipline that uses DNA sequences sampled at different points in time to co-estimate the timing of evolutionary events with rates of molecular evolution. Importantly, such inferences should only be performed on datasets displaying sufficient temporal signal, a feature important to test prior to any tip-dating inference. For this purpose, the most popular method considered to-date has been the 'root-to-tip regression' which consist in fitting a linear regression of the number of substitutions accumulated from the root to the tips of a phylogenetic tree as a function of sampling times. The main limitation of the regression method, in its current implementation, relies in the fact that the temporal signal can only be tested at the whole-tree scale (i.e. its root). Results To overcome this limitation we introduce Phylostems, a new graphical user-friendly tool developed to investigate temporal signal within every clade of a phylogenetic tree. We provide a 'how to' guide by running Phylostems on an empirical dataset and supply guidance for results interpretation. Availability and implementation Phylostems is freely available at https://pvbmt-apps.cirad.fr/apps/phylostems.
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Affiliation(s)
- Anna Doizy
- CIRAD, UMR PVBMT, La Réunion, St Pierre 97410, France
- DoAna—Statistiques Réunion, Reunion Island, Saint-Joseph F-97480, France
| | - Amaury Prin
- CIRAD, UMR PVBMT, La Réunion, St Pierre 97410, France
| | - Guillaume Cornu
- CIRAD, Univ Montpellier, UR Forests and Societies, 34398 Montpellier Cedex 5, France
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Noack D, Travar M, Mrdjen V, Voermans JJC, van de Vijver D, Molenkamp R, Koopmans MPG, Goeijenbier M, Rockx B. Serum Markers Associated with Disease Severity in a Bosnian Hemorrhagic Fever with Renal Syndrome Cohort. Viruses 2022; 14:v14071377. [PMID: 35891358 PMCID: PMC9316913 DOI: 10.3390/v14071377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 06/10/2022] [Accepted: 06/22/2022] [Indexed: 12/10/2022] Open
Abstract
Puumala orthohantavirus (PUUV) is endemic in Europe and can cause hemorrhagic fever with renal syndrome (nephropathia epidemica). Disease features include fever, thrombocytopenia, and acute kidney injury (AKI). This retrospective cohort study of forty PUUV patients aims to characterize associations of serum immunological, hemostatic or kidney injury markers to disease severity. While interleukin-18 (IL-18) was significantly increased in severely thrombocytopenic patients (<100 × 109 platelets/L) compared to patients with higher platelet counts, RANTES was significantly decreased in these patients. These data suggest that patients with significant thrombocytopenia might have experienced pronounced Th1 immune responses. When kidney dysfunction was used as the primary disease outcome, recently identified AKI biomarkers (Cystatin C, insulin-like growth factor-binding protein 7, Nephrin, and trefoil factor 3) were significantly upregulated in patients with severe PUUV infection, defined as the estimated glomerular filtration rate (eGFR) below 30 m/min/1.73 m2. The increased expression of these markers specifically indicates pathology in glomeruli and proximal tubuli. Furthermore, E-selectin was significantly higher while interferon gamma-induced protein 10 (IP-10) was significantly lower in PUUV patients with more severe kidney dysfunction compared to patients with higher eGFR-values. Increased E-selectin illustrates the central role of endothelial cell activation, whereas decreased IP-10 could indicate a less important role of this cytokine in the pathogenesis of kidney dysfunction.
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Affiliation(s)
- Danny Noack
- Department of Viroscience, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (D.N.); (J.J.C.V.); (D.v.d.V.); (R.M.); (M.P.G.K.); (M.G.)
| | - Maja Travar
- Department for Clinical Microbiology, University Clinical Center of Republika Srpska, 78000 Banja Luka, Bosnia and Herzegovina; (M.T.); (V.M.)
- Department for Microbiology and Immunology, Faculty of Medicine, University of Banja Luka, 78000 Banja Luka, Republika Srpska, Bosnia and Herzegovina
| | - Visnja Mrdjen
- Department for Clinical Microbiology, University Clinical Center of Republika Srpska, 78000 Banja Luka, Bosnia and Herzegovina; (M.T.); (V.M.)
- Department for Microbiology and Immunology, Faculty of Medicine, University of Banja Luka, 78000 Banja Luka, Republika Srpska, Bosnia and Herzegovina
| | - Jolanda J. C. Voermans
- Department of Viroscience, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (D.N.); (J.J.C.V.); (D.v.d.V.); (R.M.); (M.P.G.K.); (M.G.)
| | - David van de Vijver
- Department of Viroscience, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (D.N.); (J.J.C.V.); (D.v.d.V.); (R.M.); (M.P.G.K.); (M.G.)
| | - Richard Molenkamp
- Department of Viroscience, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (D.N.); (J.J.C.V.); (D.v.d.V.); (R.M.); (M.P.G.K.); (M.G.)
| | - Marion P. G. Koopmans
- Department of Viroscience, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (D.N.); (J.J.C.V.); (D.v.d.V.); (R.M.); (M.P.G.K.); (M.G.)
| | - Marco Goeijenbier
- Department of Viroscience, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (D.N.); (J.J.C.V.); (D.v.d.V.); (R.M.); (M.P.G.K.); (M.G.)
- Department of Intensive Care, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Barry Rockx
- Department of Viroscience, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (D.N.); (J.J.C.V.); (D.v.d.V.); (R.M.); (M.P.G.K.); (M.G.)
- Correspondence:
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Castel G, Monchatre-Leroy E, López-Roig M, Murri S, Couteaudier M, Boué F, Augot D, Sauvage F, Pontier D, Hénaux V, Marianneau P, Serra-Cobo J, Tordo N. Puumala Virus Variants Circulating in Forests of Ardennes, France: Ten Years of Genetic Evolution. Pathogens 2021; 10:pathogens10091164. [PMID: 34578197 PMCID: PMC8472060 DOI: 10.3390/pathogens10091164] [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: 08/10/2021] [Revised: 09/03/2021] [Accepted: 09/06/2021] [Indexed: 11/29/2022] Open
Abstract
In Europe, Puumala virus (PUUV) transmitted by the bank vole (Myodes glareolus) is the causative agent of nephropathia epidemica (NE), a mild form of haemorrhagic fever with renal syndrome. In France, very little is known about the spatial and temporal variability of the virus circulating within bank vole populations. The present study involved monitoring of bank vole population dynamics and PUUV microdiversity over a ten-year period (2000–2009) in two forests of the Ardennes region: Elan and Croix-Scaille. Ardennes region is characterised by different environmental conditions associated with different NE epidemiology. Bank vole density and population parameters were estimated using the capture/marking/recapture method, and blood samples were collected to monitor the overall seroprevalence of PUUV in rodent populations. Phylogenetic analyses of fifty-five sequences were performed to illustrate the genetic diversity of PUUV variants between forests. The pattern of the two forests differed clearly. In the Elan forest, the rodent survival was higher, and this limited turn-over resulted in a lower seroprevalence and diversity of PUUV sequences than in the Croix-Scaille forest. Uncovering the links between host dynamics and virus microevolution is improving our understanding of PUUV distribution in rodents and the NE risk.
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Affiliation(s)
- Guillaume Castel
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Université Montpellier, 34000 Montpellier, France
- Correspondence: (G.C.); (E.M.-L.)
| | - Elodie Monchatre-Leroy
- Nancy Laboratory for Rabies and Wildlife, ANSES, 54220 Malzeville, France;
- Correspondence: (G.C.); (E.M.-L.)
| | - Marc López-Roig
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Spain; (M.L.-R.); (J.S.-C.)
- Institut de Recerca de la Biodiversitat (IRBio), Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
| | - Séverine Murri
- Lyon Laboratory, ANSES, Virology Unit, University of Lyon, 69007 Lyon, France; (S.M.); (P.M.)
| | - Mathilde Couteaudier
- INSERM U1259 MAVIVH, Université de Tours and CHRU de Tours, 37032 Tours, France;
| | - Franck Boué
- Nancy Laboratory for Rabies and Wildlife, ANSES, SEEpiAS Unit, 54220 Malzéville, France;
| | - Denis Augot
- Nancy Laboratory for Rabies and Wildlife, ANSES, 54220 Malzeville, France;
- USC Vecpar, ANSES-LSA, EA 7510, Université de Reims Champagne-Ardenne, SFR Cap Santé, Faculté de Pharmacie, 51096 Reims, France
| | - Frank Sauvage
- SEENOVATE, 69002 Lyon, France;
- UMR–CNRS 5558 Biométrie et Biologie Evolutive, Université C. Bernard Lyon-1, 69622 Villeurbanne, France;
| | - Dominique Pontier
- UMR–CNRS 5558 Biométrie et Biologie Evolutive, Université C. Bernard Lyon-1, 69622 Villeurbanne, France;
- LabEx Ecofect, Eco-Evolutionary Dynamics of Infectious Diseases, University of Lyon, 69622 Lyon, France
| | - Viviane Hénaux
- Lyon Laboratory, ANSES, Epidemiology and support to Surveillance Unit, University of Lyon, 69007 Lyon, France;
| | - Philippe Marianneau
- Lyon Laboratory, ANSES, Virology Unit, University of Lyon, 69007 Lyon, France; (S.M.); (P.M.)
| | - Jordi Serra-Cobo
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Spain; (M.L.-R.); (J.S.-C.)
- Institut de Recerca de la Biodiversitat (IRBio), Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
| | - Noël Tordo
- Institut Pasteur, Antiviral Strategies Unit, Department of Virology, 75015 Paris, France;
- Institut Pasteur de Guinée, Conakry BP 4416, Guinea
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Razzauti M, Castel G, Cosson JF. Impact of Landscape on Host-Parasite Genetic Diversity and Distribution Using the Puumala orthohantavirus-Bank Vole System. Microorganisms 2021; 9:microorganisms9071516. [PMID: 34361952 PMCID: PMC8306195 DOI: 10.3390/microorganisms9071516] [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: 06/04/2021] [Revised: 07/09/2021] [Accepted: 07/12/2021] [Indexed: 11/16/2022] Open
Abstract
In nature, host specificity has a strong impact on the parasite's distribution, prevalence, and genetic diversity. The host's population dynamics is expected to shape the distribution of host-specific parasites. In turn, the parasite's genetic structure is predicted to mirror that of the host. Here, we study the tandem Puumala orthohantavirus (PUUV)-bank vole system. The genetic diversity of 310 bank voles and 33 PUUV isolates from 10 characterized localities of Northeast France was assessed. Our findings show that the genetic diversity of both PUUV and voles, was positively correlated with forest coverage and contiguity of habitats. While the genetic diversity of voles was weakly structured in space, that of PUUV was found to be strongly structured, suggesting that the dispersion of voles was not sufficient to ensure a broad PUUV dissemination. Genetic diversity of PUUV was mainly shaped by purifying selection. Genetic drift and extinction events were better reflected than local adaptation of PUUV. These contrasting patterns of microevolution have important consequences for the understanding of PUUV distribution and epidemiology.
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Affiliation(s)
- Maria Razzauti
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Université Montpellier, 34000 Montpellier, France;
- Correspondence:
| | - Guillaume Castel
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Université Montpellier, 34000 Montpellier, France;
| | - Jean-François Cosson
- UMR BIPAR, Animal Health Laboratory, ANSES, INRAE, Ecole Nationale Vétérinaire d’Alfort, Université Paris-Est, 94700 Maisons-Alfort, France;
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Camp JV, Schmon E, Krause R, Sixl W, Schmid D, Aberle SW. Genetic Diversity of Puumala orthohantavirus in Rodents and Human Patients in Austria, 2012-2019. Viruses 2021; 13:v13040640. [PMID: 33918083 PMCID: PMC8069475 DOI: 10.3390/v13040640] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/06/2021] [Accepted: 04/07/2021] [Indexed: 12/14/2022] Open
Abstract
Puumala orthohantavirus (PUUV) has a wide distribution throughout Europe. Distinctive temporal patterns of spillover into the human population are related to population dynamics of the reservoir host, the bank vole (Clethrionomys glareolus). As the rodent host is tied to specific habitats with small individual ranges, PUUV genetic diversity is also highly correlated with geographic distance. Using sequenced portions of viral S and M segments, we determined whether geographic clusters were supported. Human cases of PUUV infections are concentrated in southeastern Austria. We detected four distinct genotypes: two genotypes of the Alpe-Adria (ALAD) lineage typically associated with southeast Europe, and two sublineages of the Central Europe (CE) lineage. One cluster of CE genotypes represents a phylogenetically distinct sublineage compared to previously reported CE clades, and extends the boundary of the CE lineage further south than previously reported.
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Affiliation(s)
- Jeremy V. Camp
- Center for Virology, Medical University of Vienna, 1090 Vienna, Austria;
| | - Eva Schmon
- Institute of Hospital Hygiene and Microbiology, Styrian Hospital Corporation, 8010 Graz, Austria;
| | - Robert Krause
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, 8036 Graz, Austria;
| | - Wolfdieter Sixl
- Institute of Hygiene, University of Graz, 8010 Graz, Austria;
| | - Daniela Schmid
- Austrian Agency for Health and Food Safety (AGES), 1090 Vienna, Austria;
| | - Stephan W. Aberle
- Center for Virology, Medical University of Vienna, 1090 Vienna, Austria;
- Correspondence: ; Tel.: +43-1-40160-65555
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Abstract
The conservation field is experiencing a rapid increase in the amount, variety, and quality of spatial data that can help us understand species movement and landscape connectivity patterns. As interest grows in more dynamic representations of movement potential, modelers are often limited by the capacity of their analytic tools to handle these datasets. Technology developments in software and high-performance computing are rapidly emerging in many fields, but uptake within conservation may lag, as our tools or our choice of computing language can constrain our ability to keep pace. We recently updated Circuitscape, a widely used connectivity analysis tool developed by Brad McRae and Viral Shah, by implementing it in Julia, a high-performance computing language. In this initial re-code (Circuitscape 5.0) and later updates, we improved computational efficiency and parallelism, achieving major speed improvements, and enabling assessments across larger extents or with higher resolution data. Here, we reflect on the benefits to conservation of strengthening collaborations with computer scientists, and extract examples from a collection of 572 Circuitscape applications to illustrate how through a decade of repeated investment in the software, applications have been many, varied, and increasingly dynamic. Beyond empowering continued innovations in dynamic connectivity, we expect that faster run times will play an important role in facilitating co-production of connectivity assessments with stakeholders, increasing the likelihood that connectivity science will be incorporated in land use decisions.
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Genomic and phylodynamic analysis of sapoviruses isolated in Henan Province, China. Arch Virol 2020; 166:265-270. [PMID: 33164116 DOI: 10.1007/s00705-020-04876-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/28/2020] [Indexed: 10/23/2022]
Abstract
In this study, we determined the near-complete and partial genome sequences of ten SaV isolates. Phylogenetic analysis based on full-length VP1 and RdRp nucleotide sequences indicated that nine isolates were of GI.1 and one was GII.3. Evolutionary dynamics analysis indicated that GI.1 and GII.3 SaVs evolved at different rates, the latter evolving more rapidly. Cluster analysis indicated that distantly related GI.1 SaVs were more similar in their amino acid compositions than were GII.3 SaVs. The data provided in this study may facilitate studies on SaV genomic diversity and epidemiological patterns in China and worldwide.
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10
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Murri S, Madrières S, Tatard C, Piry S, Benoit L, Loiseau A, Pradel J, Artige E, Audiot P, Leménager N, Lacôte S, Vulin J, Charbonnel N, Marianneau P, Castel G. Detection and Genetic Characterization of Puumala Orthohantavirus S-Segment in Areas of France Non-Endemic for Nephropathia Epidemica. Pathogens 2020; 9:pathogens9090721. [PMID: 32882953 PMCID: PMC7559001 DOI: 10.3390/pathogens9090721] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 08/15/2020] [Accepted: 08/22/2020] [Indexed: 12/30/2022] Open
Abstract
Puumala virus (PUUV) in Europe causes nephropathia epidemica (NE), a mild form of hemorrhagic fever with renal syndrome (HFRS). The incidence of NE is highly heterogeneous spatially, whereas the geographic distribution of the wild reservoir of PUUV, the bank vole, is essentially homogeneous. Our understanding of the processes driving this heterogeneity remains incomplete due to gaps in knowledge. Little is known about the current distribution and genetic variation of PUUV in the areas outside the well-identified zones of NE endemicity. We trapped bank voles in four forests in French regions in which NE is considered non-endemic, but sporadic NE cases have been reported recently. We tested bank voles for anti-PUUV IgG and characterized the S segment sequences of PUUV from seropositive animals. Phylogenetic analyses revealed specific amino-acid signatures and genetic differences between PUUV circulating in non-endemic and nearby NE-endemic areas. We also showed, in temporal surveys, that the amino-acid sequences of PUUV had undergone fewer recent changes in areas non-endemic for NE than in endemic areas. The evolutionary history of the current French PUUV clusters was investigated by phylogeographic approaches, and the results were considered in the context of the history of French forests. Our findings highlight the need to monitor the circulation and genetics of PUUV in a larger array of bank vole populations, to improve our understanding of the risk of NE.
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Affiliation(s)
- Séverine Murri
- ANSES—Laboratoire de Lyon, Unité Virologie, 69007 Lyon, France; (S.M.); (S.M.); (S.L.); (J.V.); (P.M.)
| | - Sarah Madrières
- ANSES—Laboratoire de Lyon, Unité Virologie, 69007 Lyon, France; (S.M.); (S.M.); (S.L.); (J.V.); (P.M.)
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, 34000 Montpellier, France; (C.T.); (S.P.); (L.B.); (A.L.); (J.P.); (E.A.); (P.A.); (N.L.); (N.C.)
| | - Caroline Tatard
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, 34000 Montpellier, France; (C.T.); (S.P.); (L.B.); (A.L.); (J.P.); (E.A.); (P.A.); (N.L.); (N.C.)
| | - Sylvain Piry
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, 34000 Montpellier, France; (C.T.); (S.P.); (L.B.); (A.L.); (J.P.); (E.A.); (P.A.); (N.L.); (N.C.)
| | - Laure Benoit
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, 34000 Montpellier, France; (C.T.); (S.P.); (L.B.); (A.L.); (J.P.); (E.A.); (P.A.); (N.L.); (N.C.)
| | - Anne Loiseau
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, 34000 Montpellier, France; (C.T.); (S.P.); (L.B.); (A.L.); (J.P.); (E.A.); (P.A.); (N.L.); (N.C.)
| | - Julien Pradel
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, 34000 Montpellier, France; (C.T.); (S.P.); (L.B.); (A.L.); (J.P.); (E.A.); (P.A.); (N.L.); (N.C.)
| | - Emmanuelle Artige
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, 34000 Montpellier, France; (C.T.); (S.P.); (L.B.); (A.L.); (J.P.); (E.A.); (P.A.); (N.L.); (N.C.)
| | - Philippe Audiot
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, 34000 Montpellier, France; (C.T.); (S.P.); (L.B.); (A.L.); (J.P.); (E.A.); (P.A.); (N.L.); (N.C.)
| | - Nicolas Leménager
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, 34000 Montpellier, France; (C.T.); (S.P.); (L.B.); (A.L.); (J.P.); (E.A.); (P.A.); (N.L.); (N.C.)
| | - Sandra Lacôte
- ANSES—Laboratoire de Lyon, Unité Virologie, 69007 Lyon, France; (S.M.); (S.M.); (S.L.); (J.V.); (P.M.)
| | - Johann Vulin
- ANSES—Laboratoire de Lyon, Unité Virologie, 69007 Lyon, France; (S.M.); (S.M.); (S.L.); (J.V.); (P.M.)
| | - Nathalie Charbonnel
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, 34000 Montpellier, France; (C.T.); (S.P.); (L.B.); (A.L.); (J.P.); (E.A.); (P.A.); (N.L.); (N.C.)
| | - Philippe Marianneau
- ANSES—Laboratoire de Lyon, Unité Virologie, 69007 Lyon, France; (S.M.); (S.M.); (S.L.); (J.V.); (P.M.)
| | - Guillaume Castel
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, 34000 Montpellier, France; (C.T.); (S.P.); (L.B.); (A.L.); (J.P.); (E.A.); (P.A.); (N.L.); (N.C.)
- Correspondence:
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11
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Kamau E, Otieno JR, Murunga N, Oketch JW, Ngoi JM, de Laurent ZR, Mwema A, Nyiro JU, Agoti CN, Nokes DJ. Genomic epidemiology and evolutionary dynamics of respiratory syncytial virus group B in Kilifi, Kenya, 2015-17. Virus Evol 2020; 6:veaa050. [PMID: 32913665 PMCID: PMC7474930 DOI: 10.1093/ve/veaa050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Respiratory syncytial virus (RSV) circulates worldwide, occurring seasonally in communities, and is a leading cause of acute respiratory illness in young children. There is paucity of genomic data from purposively sampled populations by which to investigate evolutionary dynamics and transmission patterns of RSV. Here we present an analysis of 295 RSV group B (RSVB) genomes from Kilifi, coastal Kenya, sampled from individuals seeking outpatient care in nine health facilities across a defined geographical area (∼890 km2), over two RSV epidemics between 2015 and 2017. RSVB diversity was characterized by multiple virus introductions into the area and co-circulation of distinct genetic clusters, which transmitted and diversified locally with varying frequency. Increase in relative genetic diversity paralleled seasonal virus incidence. Importantly, we identified a cluster of viruses that emerged in the 2016/17 epidemic, carrying distinct amino-acid signatures including a novel nonsynonymous change (K68Q) in antigenic site ∅ in the Fusion protein. RSVB diversity was additionally marked by signature nonsynonymous substitutions that were unique to particular genomic clusters, some under diversifying selection. Our findings provide insights into recent evolutionary and epidemiological behaviors of RSVB, and highlight possible emergence of a novel antigenic variant, which has implications on current prophylactic strategies in development.
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Affiliation(s)
- Everlyn Kamau
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - James R Otieno
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Nickson Murunga
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - John W Oketch
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Joyce M Ngoi
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Zaydah R de Laurent
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Anthony Mwema
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Joyce U Nyiro
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Charles N Agoti
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.,School of Health and Human Sciences, Pwani University, Kilifi, Kenya
| | - D James Nokes
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.,School of Life Sciences and Zeeman Institute (SBIDER), University of Warwick, Coventry, UK
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12
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Hiltbrunner M, Heckel G. Assessing Genome-Wide Diversity in European Hantaviruses through Sequence Capture from Natural Host Samples. Viruses 2020; 12:v12070749. [PMID: 32664593 PMCID: PMC7412162 DOI: 10.3390/v12070749] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/08/2020] [Accepted: 07/09/2020] [Indexed: 12/19/2022] Open
Abstract
Research on the ecology and evolution of viruses is often hampered by the limitation of sequence information to short parts of the genomes or single genomes derived from cultures. In this study, we use hybrid sequence capture enrichment in combination with high-throughput sequencing to provide efficient access to full genomes of European hantaviruses from rodent samples obtained in the field. We applied this methodology to Tula (TULV) and Puumala (PUUV) orthohantaviruses for which analyses from natural host samples are typically restricted to partial sequences of their tri-segmented RNA genome. We assembled a total of ten novel hantavirus genomes de novo with very high coverage (on average >99%) and sequencing depth (average >247×). A comparison with partial Sanger sequences indicated an accuracy of >99.9% for the assemblies. An analysis of two common vole (Microtus arvalis) samples infected with two TULV strains each allowed for the de novo assembly of all four TULV genomes. Combining the novel sequences with all available TULV and PUUV genomes revealed very similar patterns of sequence diversity along the genomes, except for remarkably higher diversity in the non-coding region of the S-segment in PUUV. The genomic distribution of polymorphisms in the coding sequence was similar between the species, but differed between the segments with the highest sequence divergence of 0.274 for the M-segment, 0.265 for the S-segment, and 0.248 for the L-segment (overall 0.258). Phylogenetic analyses showed the clustering of genome sequences consistent with their geographic distribution within each species. Genome-wide data yielded extremely high node support values, despite the impact of strong mutational saturation that is expected for hantavirus sequences obtained over large spatial distances. We conclude that genome sequencing based on capture enrichment protocols provides an efficient means for ecological and evolutionary investigations of hantaviruses at an unprecedented completeness and depth.
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Affiliation(s)
- Melanie Hiltbrunner
- Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland;
| | - Gerald Heckel
- Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland;
- Swiss Institute of Bioinformatics, Quartier Sorge, 1011 Lausanne, Switzerland
- Correspondence:
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13
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Spatial and Temporal Evolutionary Patterns in Puumala Orthohantavirus (PUUV) S Segment. Pathogens 2020; 9:pathogens9070548. [PMID: 32650456 PMCID: PMC7400055 DOI: 10.3390/pathogens9070548] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/24/2020] [Accepted: 06/28/2020] [Indexed: 12/12/2022] Open
Abstract
The S segment of bank vole (Clethrionomys glareolus)-associated Puumala orthohantavirus (PUUV) contains two overlapping open reading frames coding for the nucleocapsid (N) and a non-structural (NSs) protein. To identify the influence of bank vole population dynamics on PUUV S segment sequence evolution and test for spillover infections in sympatric rodent species, during 2010–2014, 883 bank voles, 357 yellow-necked mice (Apodemus flavicollis), 62 wood mice (A. sylvaticus), 149 common voles (Microtus arvalis) and 8 field voles (M. agrestis) were collected in Baden-Wuerttemberg and North Rhine-Westphalia, Germany. In total, 27.9% and 22.3% of bank voles were positive for PUUV-reactive antibodies and PUUV-specific RNA, respectively. One of eight field voles was PUUV RNA-positive, indicating a spillover infection, but none of the other species showed evidence of PUUV infection. Phylogenetic and isolation-by-distance analyses demonstrated a spatial clustering of PUUV S segment sequences. In the hantavirus outbreak years 2010 and 2012, PUUV RNA prevalence was higher in our study regions compared to non-outbreak years 2011, 2013 and 2014. NSs amino acid and nucleotide sequence types showed temporal and/or local variation, whereas the N protein was highly conserved in the NSs overlapping region and, to a lower rate, in the N alone coding part.
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14
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Meeting report: Eleventh International Conference on Hantaviruses. Antiviral Res 2020; 176:104733. [PMID: 32068071 DOI: 10.1016/j.antiviral.2020.104733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 02/01/2020] [Indexed: 12/24/2022]
Abstract
The 2019 11th International Conference on Hantaviruses (ICH 2019) was organized by the International Society for Hantaviruses (ISH), and held on September 1-4, 2019, at the Irish College, in Leuven, Belgium. These ICHs have been held every three years since 1989. ICH 2019 was attended by 158 participants from 33 countries. The current report summarizes research presented on all aspects of hantavirology: ecology; pathogenesis and immune responses; virus phylogeny, replication and morphogenesis; epidemiology; vaccines, therapeutics and prevention; and clinical aspects and diagnosis.
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15
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Gravinatti ML, Barbosa CM, Soares RM, Gregori F. Synanthropic rodents as virus reservoirs and transmitters. Rev Soc Bras Med Trop 2020; 53:e20190486. [PMID: 32049206 PMCID: PMC7083353 DOI: 10.1590/0037-8682-0486-2019] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 01/09/2020] [Indexed: 12/27/2022] Open
Abstract
This review focuses on reports of hepatitis E virus, hantavirus, rotavirus,
coronavirus, and arenavirus in synanthropic rodents (Rattus
rattus, Rattus norvegicus, and Mus
musculus) within urban environments. Despite their potential impact
on human health, relatively few studies have addressed the monitoring of these
viruses in rodents. Comprehensive control and preventive activities should
include actions such as the elimination or reduction of rat and mouse
populations, sanitary education, reduction of shelters for the animals, and
restriction of the access of rodents to residences, water, and food
supplies.
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Affiliation(s)
- Mara Lucia Gravinatti
- Departamento de Medicina Veterinária Preventiva e Saúde Animal, Faculdade de Medicina Veterinária, Universidade de São Paulo, São Paulo, SP, Brazil
| | | | - Rodrigo Martins Soares
- Departamento de Medicina Veterinária Preventiva e Saúde Animal, Faculdade de Medicina Veterinária, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Fábio Gregori
- Departamento de Medicina Veterinária Preventiva e Saúde Animal, Faculdade de Medicina Veterinária, Universidade de São Paulo, São Paulo, SP, Brazil
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16
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Phylogeography of Puumala orthohantavirus in Europe. Viruses 2019; 11:v11080679. [PMID: 31344894 PMCID: PMC6723369 DOI: 10.3390/v11080679] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/12/2019] [Accepted: 07/22/2019] [Indexed: 12/21/2022] Open
Abstract
Puumala virus is an RNA virus hosted by the bank vole (Myodes glareolus) and is today present in most European countries. Whilst it is generally accepted that hantaviruses have been tightly co-evolving with their hosts, Puumala virus (PUUV) evolutionary history is still controversial and so far has not been studied at the whole European level. This study attempts to reconstruct the phylogeographical spread of modern PUUV throughout Europe during the last postglacial period in the light of an upgraded dataset of complete PUUV small (S) segment sequences and by using most recent computational approaches. Taking advantage of the knowledge on the past migrations of its host, we identified at least three potential independent dispersal routes of PUUV during postglacial recolonization of Europe by the bank vole. From the Alpe-Adrian region (Balkan, Austria, and Hungary) to Western European countries (Germany, France, Belgium, and Netherland), and South Scandinavia. From the vicinity of Carpathian Mountains to the Baltic countries and to Poland, Russia, and Finland. The dissemination towards Denmark and North Scandinavia is more hypothetical and probably involved several independent streams from south and north Fennoscandia.
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