1
|
Carnegie L, Raghwani J, Fournié G, Hill SC. Phylodynamic approaches to studying avian influenza virus. Avian Pathol 2023; 52:289-308. [PMID: 37565466 DOI: 10.1080/03079457.2023.2236568] [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: 02/02/2023] [Revised: 06/23/2023] [Accepted: 07/07/2023] [Indexed: 08/12/2023]
Abstract
Avian influenza viruses can cause severe disease in domestic and wild birds and are a pandemic threat. Phylodynamics is the study of how epidemiological, evolutionary, and immunological processes can interact to shape viral phylogenies. This review summarizes how phylodynamic methods have and could contribute to the study of avian influenza viruses. Specifically, we assess how phylodynamics can be used to examine viral spread within and between wild or domestic bird populations at various geographical scales, identify factors associated with virus dispersal, and determine the order and timing of virus lineage movement between geographic regions or poultry production systems. We discuss factors that can complicate the interpretation of phylodynamic results and identify how future methodological developments could contribute to improved control of the virus.
Collapse
Affiliation(s)
- L Carnegie
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
| | - J Raghwani
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
| | - G Fournié
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
- Université de Lyon, INRAE, VetAgro Sup, UMR EPIA, Marcy l'Etoile, France
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, Saint Genes Champanelle, France
| | - S C Hill
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
| |
Collapse
|
2
|
Karo-karo D, Bodewes R, Restuadi R, Bossers A, Agustiningsih A, Stegeman JA, Koch G, Muljono DH. Phylodynamics of Highly Pathogenic Avian Influenza A(H5N1) Virus Circulating in Indonesian Poultry. Viruses 2022; 14:v14102216. [PMID: 36298771 PMCID: PMC9608721 DOI: 10.3390/v14102216] [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: 08/13/2022] [Revised: 09/27/2022] [Accepted: 10/05/2022] [Indexed: 11/07/2022] Open
Abstract
After its first detection in 1996, the highly pathogenic avian influenza A(H5Nx) virus has spread extensively worldwide. HPAIv A(H5N1) was first detected in Indonesia in 2003 and has been endemic in poultry in this country ever since. However, Indonesia has limited information related to the phylodynamics of HPAIv A(H5N1) in poultry. The present study aimed to increase the understanding of the evolution and temporal dynamics of HPAIv H5N1 in Indonesian poultry between 2003 and 2016. To this end, HPAIv A(H5N1) hemagglutinin sequences of viruses collected from 2003 to 2016 were analyzed using Bayesian evolutionary analysis sampling trees. Results indicated that the common ancestor of Indonesian poultry HPAIv H5N1 arose approximately five years after the common ancestor worldwide of HPAI A(H5Nx). In addition, this study indicated that only two introductions of HPAIv A(H5N1) occurred, after which these viruses continued to evolve due to extensive spread among poultry. Furthermore, this study revealed the divergence of H5N1 clade 2.3.2.1c from H5N1 clade 2.3.2.1b. Both clades 2.3.2.1c and 2.3.2.1b share a common ancestor, clade 1, suggesting that clade 2.3.2.1 originated and diverged from China and other Asian countries. Since there was limited sequence and surveillance data for the HPAIv A(H5N1) from wild birds in Indonesia, the exact role of wild birds in the spread of HPAIv in Indonesia is currently unknown. The evolutionary dynamics of the Indonesian HPAIv A(H5N1) highlight the importance of continuing and improved genomic surveillance and adequate control measures in the different regions of both the poultry and wild birds. Spatial genomic surveillance is useful to take adequate control measures. Therefore, it will help to prevent the future evolution of HPAI A(H5N1) and pandemic threats.
Collapse
Affiliation(s)
- Desniwaty Karo-karo
- Department Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands
- Centre of Diagnostic Standard Indonesian Agricultural Quarantine Agency, Ministry of Agriculture, Jakarta 13220, Indonesia
| | - Rogier Bodewes
- National Institute for Public Health and the Environment, 3720 BA Bilthoven, The Netherlands
| | - Restuadi Restuadi
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Alex Bossers
- Department Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands
- Institute for Risk Assessment Sciences (IRAS), Department Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands
| | | | - Jan Arend Stegeman
- Department Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands
| | - Guus Koch
- Wageningen Bioveterinary Research, 8221 RA Lelystad, The Netherlands
| | - David Handojo Muljono
- Faculty of Medicine, Universitas Hasanuddin, Makassar 90245, Indonesia
- Faculty of Medicine and Health, University of Sydney, Camperdown, NSW 2006, Australia
- Eijkman Institute for Molecular Biology, Jakarta 10430, Indonesia
- Correspondence: ; Tel.: +62-8161-923-563
| |
Collapse
|
3
|
Fagre AC, Cohen LE, Eskew EA, Farrell M, Glennon E, Joseph MB, Frank HK, Ryan SJ, Carlson CJ, Albery GF. Assessing the risk of human-to-wildlife pathogen transmission for conservation and public health. Ecol Lett 2022; 25:1534-1549. [PMID: 35318793 PMCID: PMC9313783 DOI: 10.1111/ele.14003] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 02/22/2022] [Accepted: 03/02/2022] [Indexed: 12/16/2022]
Abstract
The SARS‐CoV‐2 pandemic has led to increased concern over transmission of pathogens from humans to animals, and its potential to threaten conservation and public health. To assess this threat, we reviewed published evidence of human‐to‐wildlife transmission events, with a focus on how such events could threaten animal and human health. We identified 97 verified examples, involving a wide range of pathogens; however, reported hosts were mostly non‐human primates or large, long‐lived captive animals. Relatively few documented examples resulted in morbidity and mortality, and very few led to maintenance of a human pathogen in a new reservoir or subsequent “secondary spillover” back into humans. We discuss limitations in the literature surrounding these phenomena, including strong evidence of sampling bias towards non‐human primates and human‐proximate mammals and the possibility of systematic bias against reporting human parasites in wildlife, both of which limit our ability to assess the risk of human‐to‐wildlife pathogen transmission. We outline how researchers can collect experimental and observational evidence that will expand our capacity for risk assessment for human‐to‐wildlife pathogen transmission.
Collapse
Affiliation(s)
- Anna C Fagre
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA.,Bat Health Foundation, Fort Collins, Colorado, USA
| | - Lily E Cohen
- Icahn School of Medicine at Mount Sinai, New York, New York City, USA
| | - Evan A Eskew
- Department of Biology, Pacific Lutheran University, Tacoma, Washington, USA
| | - Max Farrell
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Emma Glennon
- Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Maxwell B Joseph
- Earth Lab, University of Colorado Boulder, Boulder, Colorado, USA
| | - Hannah K Frank
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, Louisina, USA
| | - Sadie J Ryan
- Quantitative Disease Ecology and Conservation (QDEC) Lab Group, Department of Geography, University of Florida, Gainesville, Florida, USA.,Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA.,School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Colin J Carlson
- Center for Global Health Science and Security, Georgetown University Medical Center, Washington, District of Columbia, USA.,Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, District of Columbia, USA
| | - Gregory F Albery
- Department of Biology, Georgetown University, Washington, District of Columbia, USA
| |
Collapse
|
4
|
Jara M, Crespo R, Roberts DL, Chapman A, Banda A, Machado G. Development of a Dissemination Platform for Spatiotemporal and Phylogenetic Analysis of Avian Infectious Bronchitis Virus. Front Vet Sci 2021; 8:624233. [PMID: 34017870 PMCID: PMC8129014 DOI: 10.3389/fvets.2021.624233] [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: 10/30/2020] [Accepted: 02/27/2021] [Indexed: 11/13/2022] Open
Abstract
Infecting large portions of the global poultry populations, the avian infectious bronchitis virus (IBV) remains a major economic burden in North America. With more than 30 serotypes globally distributed, Arkansas, Connecticut, Delaware, Georgia, and Massachusetts are among the most predominant serotypes in the United States. Even though vaccination is widely used, the high mutation rate exhibited by IBV is continuously triggering the emergence of new viral strains and hindering control and prevention measures. For that reason, targeted strategies based on constantly updated information on the IBV circulation are necessary. Here, we sampled IBV-infected farms from one US state and collected and analyzed 65 genetic sequences coming from three different lineages along with the immunization information of each sampled farm. Phylodynamic analyses showed that IBV dispersal velocity was 12.3 km/year. The majority of IBV infections appeared to have derived from the introduction of the Arkansas DPI serotype, and the Arkansas DPI and Georgia 13 were the predominant serotypes. When analyzed against IBV sequences collected across the United States and deposited in the GenBank database, the most likely viral origin of our sequences was from the states of Alabama, Georgia, and Delaware. Information about vaccination showed that the MILDVAC-MASS+ARK vaccine was applied on 26% of the farms. Using a publicly accessible open-source tool for real-time interactive tracking of pathogen spread and evolution, we analyzed the spatiotemporal spread of IBV and developed an online reporting dashboard. Overall, our work demonstrates how the combination of genetic and spatial information could be used to track the spread and evolution of poultry diseases, providing timely information to the industry. Our results could allow producers and veterinarians to monitor in near-real time the current IBV strain circulating, making it more informative, for example, in vaccination-related decisions.
Collapse
Affiliation(s)
- Manuel Jara
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
| | - Rocio Crespo
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
| | - David L Roberts
- Department of Computer Science North Carolina State University, Raleigh, NC, United States
| | - Ashlyn Chapman
- Department of Computer Science North Carolina State University, Raleigh, NC, United States
| | - Alejandro Banda
- Poultry Research and Diagnostic Laboratory, College of Veterinary Medicine, Mississippi State University, Pearl, MS, United States
| | - Gustavo Machado
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
| |
Collapse
|
5
|
Alkhamis MA, Li C, Torremorell M. Animal Disease Surveillance in the 21st Century: Applications and Robustness of Phylodynamic Methods in Recent U.S. Human-Like H3 Swine Influenza Outbreaks. Front Vet Sci 2020; 7:176. [PMID: 32373634 PMCID: PMC7186338 DOI: 10.3389/fvets.2020.00176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 03/16/2020] [Indexed: 11/22/2022] Open
Abstract
Emerging and endemic animal viral diseases continue to impose substantial impacts on animal and human health. Most current and past molecular surveillance studies of animal diseases investigated spatio-temporal and evolutionary dynamics of the viruses in a disjointed analytical framework, ignoring many uncertainties and made joint conclusions from both analytical approaches. Phylodynamic methods offer a uniquely integrated platform capable of inferring complex epidemiological and evolutionary processes from the phylogeny of viruses in populations using a single Bayesian statistical framework. In this study, we reviewed and outlined basic concepts and aspects of phylodynamic methods and attempted to summarize essential components of the methodology in one analytical pipeline to facilitate the proper use of the methods by animal health researchers. Also, we challenged the robustness of the posterior evolutionary parameters, inferred by the commonly used phylodynamic models, using hemagglutinin (HA) and polymerase basic 2 (PB2) segments of the currently circulating human-like H3 swine influenza (SI) viruses isolated in the United States and multiple priors. Subsequently, we compared similarities and differences between the posterior parameters inferred from sequence data using multiple phylodynamic models. Our suggested phylodynamic approach attempts to reduce the impact of its inherent limitations to offer less biased and biologically plausible inferences about the pathogen evolutionary characteristics to properly guide intervention activities. We also pinpointed requirements and challenges for integrating phylodynamic methods in routine animal disease surveillance activities.
Collapse
Affiliation(s)
- Moh A Alkhamis
- Department of Epidemiology and Biostatistics, Faculty of Public Health, Health Sciences Center, Kuwait University, Kuwait City, Kuwait.,Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, United States
| | - Chong Li
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, United States
| | - Montserrat Torremorell
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, United States
| |
Collapse
|
6
|
Scotch M, Tahsin T, Weissenbacher D, O'Connor K, Magge A, Vaiente M, Suchard MA, Gonzalez-Hernandez G. Incorporating sampling uncertainty in the geospatial assignment of taxa for virus phylogeography. Virus Evol 2019; 5:vey043. [PMID: 30838129 PMCID: PMC6395475 DOI: 10.1093/ve/vey043] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Discrete phylogeography using software such as BEAST considers the sampling location of each taxon as fixed; often to a single location without uncertainty. When studying viruses, this implies that there is no possibility that the location of the infected host for that taxa is somewhere else. Here, we relaxed this strong assumption and allowed for analytic integration of uncertainty for discrete virus phylogeography. We used automatic language processing methods to find and assign uncertainty to alternative potential locations. We considered two influenza case studies: H5N1 in Egypt; H1N1 pdm09 in North America. For each, we implemented scenarios in which 25 per cent of the taxa had different amounts of sampling uncertainty including 10, 30, and 50 per cent uncertainty and varied how it was distributed for each taxon. This includes scenarios that: (i) placed a specific amount of uncertainty on one location while uniformly distributing the remaining amount across all other candidate locations (correspondingly labeled 10, 30, and 50); (ii) assigned the remaining uncertainty to just one other location; thus ‘splitting’ the uncertainty among two locations (i.e. 10/90, 30/70, and 50/50); and (iii) eliminated uncertainty via two predefined heuristic approaches: assignment to a centroid location (CNTR) or the largest population in the country (POP). We compared all scenarios to a reference standard (RS) in which all taxa had known (absolutely certain) locations. From this, we implemented five random selections of 25 per cent of the taxa and used these for specifying uncertainty. We performed posterior analyses for each scenario, including: (a) virus persistence, (b) migration rates, (c) trunk rewards, and (d) the posterior probability of the root state. The scenarios with sampling uncertainty were closer to the RS than CNTR and POP. For H5N1, the absolute error of virus persistence had a median range of 0.005–0.047 for scenarios with sampling uncertainty—(i) and (ii) above—versus a range of 0.063–0.075 for CNTR and POP. Persistence for the pdm09 case study followed a similar trend as did our analyses of migration rates across scenarios (i) and (ii). When considering the posterior probability of the root state, we found all but one of the H5N1 scenarios with sampling uncertainty had agreement with the RS on the origin of the outbreak whereas both CNTR and POP disagreed. Our results suggest that assigning geospatial uncertainty to taxa benefits estimation of virus phylogeography as compared to ad-hoc heuristics. We also found that, in general, there was limited difference in results regardless of how the sampling uncertainty was assigned; uniform distribution or split between two locations did not greatly impact posterior results. This framework is available in BEAST v.1.10. In future work, we will explore viruses beyond influenza. We will also develop a web interface for researchers to use our language processing methods to find and assign uncertainty to alternative potential locations for virus phylogeography.
Collapse
Affiliation(s)
- Matthew Scotch
- College of Health Solutions, Arizona State University, 550 N. 3rd St., Phoenix, AZ, USA.,Biodesign Center for Environmental Health Engineering, Arizona State University, 727 E. Tyler St, Tempe, AZ, USA
| | - Tasnia Tahsin
- College of Health Solutions, Arizona State University, 550 N. 3rd St., Phoenix, AZ, USA
| | - Davy Weissenbacher
- Department of Biostatistics, Epidemiology, and Informatics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 423 Guardian Drive, Philadelphia, PA, USA
| | - Karen O'Connor
- Department of Biostatistics, Epidemiology, and Informatics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 423 Guardian Drive, Philadelphia, PA, USA
| | - Arjun Magge
- College of Health Solutions, Arizona State University, 550 N. 3rd St., Phoenix, AZ, USA.,Biodesign Center for Environmental Health Engineering, Arizona State University, 727 E. Tyler St, Tempe, AZ, USA
| | - Matteo Vaiente
- College of Health Solutions, Arizona State University, 550 N. 3rd St., Phoenix, AZ, USA.,Biodesign Center for Environmental Health Engineering, Arizona State University, 727 E. Tyler St, Tempe, AZ, USA
| | - Marc A Suchard
- Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, 621 Charles E. Young Dr. South, Los Angeles, CA, USA.,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, 695 Charles E. Young Dr. South, Los Angeles, CA, USA.,Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, 650 Charles E Young Dr. South, Los Angeles, CA, USA
| | - Graciela Gonzalez-Hernandez
- Department of Biostatistics, Epidemiology, and Informatics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 423 Guardian Drive, Philadelphia, PA, USA
| |
Collapse
|
7
|
Bui CM, Adam DC, Njoto E, Scotch M, MacIntyre CR. Characterising routes of H5N1 and H7N9 spread in China using Bayesian phylogeographical analysis. Emerg Microbes Infect 2018; 7:184. [PMID: 30459301 PMCID: PMC6246557 DOI: 10.1038/s41426-018-0185-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 09/08/2018] [Accepted: 09/20/2018] [Indexed: 11/08/2022]
Abstract
Avian influenza H5N1 subtype has caused a global public health concern due to its high pathogenicity in poultry and high case fatality rates in humans. The recently emerged H7N9 is a growing pandemic risk due to its sustained high rates of human infections, and recently acquired high pathogenicity in poultry. Here, we used Bayesian phylogeography on 265 H5N1 and 371 H7N9 haemagglutinin sequences isolated from humans, animals and the environment, to identify and compare migration patterns and factors predictive of H5N1 and H7N9 diffusion rates in China. H7N9 diffusion dynamics and predictor contributions differ from H5N1. Key determinants of spatial diffusion included: proximity between locations (for H5N1 and H7N9), and lower rural population densities (H5N1 only). For H7N9, additional predictors included low avian influenza vaccination rates, low percentage of nature reserves and high humidity levels. For both H5N1 and H7N9, we found viral migration rates from Guangdong to Guangxi and Guangdong to Hunan were highly supported transmission routes (Bayes Factor > 30). We show fundamental differences in wide-scale transmission dynamics between H5N1 and H7N9. Importantly, this indicates that avian influenza initiatives designed to control H5N1 may not be sufficient for controlling the H7N9 epidemic. We suggest control and prevention activities to specifically target poultry transportation networks between Central, Pan-Pearl River Delta and South-West regions.
Collapse
Affiliation(s)
- Chau M Bui
- University of New South Wales (UNSW), Sydney, NSW, Australia.
| | - Dillon C Adam
- University of New South Wales (UNSW), Sydney, NSW, Australia
| | - Edwin Njoto
- University of New South Wales (UNSW), Sydney, NSW, Australia
| | - Matthew Scotch
- University of New South Wales (UNSW), Sydney, NSW, Australia
- Arizona State University (ASU), Tempe, AZ, USA
| | - C Raina MacIntyre
- University of New South Wales (UNSW), Sydney, NSW, Australia
- Arizona State University (ASU), Tempe, AZ, USA
| |
Collapse
|
8
|
Attenuation of highly pathogenic avian influenza A(H5N1) viruses in Indonesia following the reassortment and acquisition of genes from low pathogenicity avian influenza A virus progenitors. Emerg Microbes Infect 2018; 7:147. [PMID: 30131494 PMCID: PMC6104089 DOI: 10.1038/s41426-018-0147-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 06/06/2018] [Accepted: 06/23/2018] [Indexed: 12/13/2022]
Abstract
The highly pathogenic avian influenza (HPAI) A(H5N1) virus is endemic in Indonesian poultry and has caused sporadic human infection in Indonesia since 2005. Surveillance of H5N1 viruses in live bird markets (LBMs) during 2012 and 2013 was carried out to provide epidemiologic and virologic information regarding viral circulation and the risk of human exposure. Real-time RT-PCR of avian cloacal swabs and environmental samples revealed influenza A-positive specimens, which were then subjected to virus isolation and genomic sequencing. Genetic analysis of specimens collected at multiple LBMs in Indonesia identified both low pathogenicity avian influenza (LPAI) A(H3N8) and HPAI A(H5N1) viruses belonging to clade 2.1.3.2a. Comparison of internal gene segments among the LPAI and HPAI viruses revealed that the latter had acquired the PB2, PB1, and NS genes from LPAI progenitors and other viruses containing a wild type (wt) genomic constellation. Comparison of murine infectivity of the LPAI A(H3N8), wt HPAI A(H5N1) and reassortant HPAI A(H5N1) viruses showed that the acquisition of LPAI internal genes attenuated the reassortant HPAI virus, producing a mouse infectivity/virulence phenotype comparable to that of the LPAI virus. Comparison of molecular markers in each viral gene segment suggested that mutations in PB2 and NS1 may facilitate attenuation. The discovery of an attenuated HPAI A(H5N1) virus in mice that resulted from reassortment may have implications for the capability of these viruses to transmit and cause disease. In addition, surveillance suggests that LBMs in Indonesia may play a role in the generation of reassortant A(H5) viruses and should be monitored.
Collapse
|
9
|
Njoto EN, Scotch M, Bui CM, Adam DC, Chughtai AA, MacIntyre CR. Phylogeography of H5N1 avian influenza virus in Indonesia. Transbound Emerg Dis 2018; 65:1339-1347. [PMID: 29691995 DOI: 10.1111/tbed.12883] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Indexed: 11/27/2022]
Abstract
Highly pathogenic avian influenza (HPAI) viruses of the H5N1 subtype are a major concern to human and animal health in Indonesia. This study aimed to characterize transmission dynamics of H5N1 over time using novel Bayesian phylogeography methods to identify factors which have influenced the spread of H5N1 in Indonesia. We used publicly available hemagglutinin sequence data sampled between 2003 and 2016 to model ancestral state reconstruction of HPAI H5N1 evolution. We found strong support for H5N1 transmission routes between provinces in Java Island and inter-island transmissions, such as between Nusa Tenggara and Kalimantan Islands, not previously described. The spread is consistent with wild bird flyways and poultry trading routes. H5N1 migration was associated with the regions of high chicken densities and low human development indices. These results can be used to inform more targeted planning of H5N1 control and prevention activities in Indonesia.
Collapse
Affiliation(s)
- E N Njoto
- School of Public Health and Community Medicine, University of New South Wales Sydney, Sydney, NSW, Australia
| | - M Scotch
- School of Public Health and Community Medicine, University of New South Wales Sydney, Sydney, NSW, Australia.,Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, Arizona.,College of Health Solutions, Arizona State University, Phoenix, Arizona
| | - C M Bui
- School of Public Health and Community Medicine, University of New South Wales Sydney, Sydney, NSW, Australia
| | - D C Adam
- School of Public Health and Community Medicine, University of New South Wales Sydney, Sydney, NSW, Australia
| | - A A Chughtai
- School of Public Health and Community Medicine, University of New South Wales Sydney, Sydney, NSW, Australia
| | - C R MacIntyre
- School of Public Health and Community Medicine, University of New South Wales Sydney, Sydney, NSW, Australia.,College of Health Solutions, Arizona State University, Phoenix, Arizona.,College of Public Service and Community Solution, Arizona State University, Phoenix, Arizona
| |
Collapse
|
10
|
Alkhamis MA, Gallardo C, Jurado C, Soler A, Arias M, Sánchez-Vizcaíno JM. Phylodynamics and evolutionary epidemiology of African swine fever p72-CVR genes in Eurasia and Africa. PLoS One 2018; 13:e0192565. [PMID: 29489860 PMCID: PMC5831051 DOI: 10.1371/journal.pone.0192565] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 01/25/2018] [Indexed: 12/11/2022] Open
Abstract
African swine fever (ASF) is a complex infectious disease of swine that constitutes devastating impacts on animal health and the world economy. Here, we investigated the evolutionary epidemiology of ASF virus (ASFV) in Eurasia and Africa using the concatenated gene sequences of the viral protein 72 and the central variable region of isolates collected between 1960 and 2015. We used Bayesian phylodynamic models to reconstruct the evolutionary history of the virus, to identify virus population demographics and to quantify dispersal patterns between host species. Results suggest that ASFV exhibited a significantly high evolutionary rate and population growth through time since its divergence in the 18th century from East Africa, with no signs of decline till recent years. This increase corresponds to the growing pig trade activities between continents during the 19th century, and may be attributed to an evolutionary drift that resulted from either continuous circulation or maintenance of the virus within Africa and Eurasia. Furthermore, results implicate wild suids as the ancestral host species (root state posterior probability = 0.87) for ASFV in the early 1700s in Africa. Moreover, results indicate the transmission cycle between wild suids and pigs is an important cycle for ASFV spread and maintenance in pig populations, while ticks are an important natural reservoir that can facilitate ASFV spread and maintenance in wild swine populations. We illustrated the prospects of phylodynamic methods in improving risk-based surveillance, support of effective animal health policies, and epidemic preparedness in countries at high risk of ASFV incursion.
Collapse
Affiliation(s)
- Moh A Alkhamis
- Faculty of Public Heath, Health Sciences Centre, Kuwait University, Kuwait City, Kuwait
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Carmina Gallardo
- European Union Reference Laboratory for African swine fever. Centro de Investigación en Sanidad Animal (INIA-CISA), Madrid, Spain
| | - Cristina Jurado
- VISAVET Health Surveillance Centre and Animal Health Department, Veterinary School, Complutense University of Madrid, Madrid, Spain
| | - Alejandro Soler
- European Union Reference Laboratory for African swine fever. Centro de Investigación en Sanidad Animal (INIA-CISA), Madrid, Spain
| | - Marisa Arias
- European Union Reference Laboratory for African swine fever. Centro de Investigación en Sanidad Animal (INIA-CISA), Madrid, Spain
| | - José M Sánchez-Vizcaíno
- VISAVET Health Surveillance Centre and Animal Health Department, Veterinary School, Complutense University of Madrid, Madrid, Spain
| |
Collapse
|
11
|
Saxenhofer M, Weber de Melo V, Ulrich RG, Heckel G. Revised time scales of RNA virus evolution based on spatial information. Proc Biol Sci 2018; 284:rspb.2017.0857. [PMID: 28794221 DOI: 10.1098/rspb.2017.0857] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 07/06/2017] [Indexed: 12/18/2022] Open
Abstract
The time scales of pathogen evolution are of major concern in the context of public and veterinary health, epidemiology and evolutionary biology. Dating the emergence of a pathogen often relies on estimates of evolutionary rates derived from nucleotide sequence data. For many viruses, this has yielded estimates of evolutionary origins only a few hundred years in the past. Here we demonstrate through the incorporation of geographical information from virus sampling that evolutionary age estimates of two European hantaviruses are severely underestimated because of pervasive mutational saturation of nucleotide sequences. We detected very strong relationships between spatial distance and genetic divergence for both Puumala and Tula hantavirus-irrespective of whether nucleotide or derived amino acid sequences were analysed. Extrapolations from these relationships dated the emergence of these viruses most conservatively to at least 3700 and 2500 years ago, respectively. Our minimum estimates for the age of these hantaviruses are ten to a hundred times older than results from current non-spatial methods, and in much better accordance with the biogeography of these viruses and their respective hosts. Spatial information can thus provide valuable insights on the deeper time scales of pathogen evolution and improve our understanding of disease emergence.
Collapse
Affiliation(s)
- Moritz Saxenhofer
- Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge-Bâtiment Génopode, Lausanne, Switzerland
| | - Vanessa Weber de Melo
- Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Rainer G Ulrich
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, Greifswald-Insel Riems, Germany.,German Center for Infection Research (DZIF), partner site Hamburg-Luebeck-Borstel-Insel Riems, Germany
| | - Gerald Heckel
- Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland .,Swiss Institute of Bioinformatics, Quartier Sorge-Bâtiment Génopode, Lausanne, Switzerland
| |
Collapse
|
12
|
Tarigan S, Wibowo MH, Indriani R, Sumarningsih S, Artanto S, Idris S, Durr PA, Asmara W, Ebrahimie E, Stevenson MA, Ignjatovic J. Field effectiveness of highly pathogenic avian influenza H5N1 vaccination in commercial layers in Indonesia. PLoS One 2018; 13:e0190947. [PMID: 29320563 PMCID: PMC5761929 DOI: 10.1371/journal.pone.0190947] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 12/24/2017] [Indexed: 12/30/2022] Open
Abstract
Although vaccination of poultry for control of highly pathogenic avian influenza virus (HPAIV) H5N1 has been practiced during the last decade in several countries, its effectiveness under field conditions remains largely unquantified. Effective HPAI vaccination is however essential in preventing incursions, silent infections and generation of new H5N1 antigenic variants. The objective of this study was to asses the level and duration of vaccine induced immunity in commercial layers in Indonesia. Titres of H5N1 haemagglutination inhibition (HI) antibodies were followed in individual birds from sixteen flocks, age 18-68 week old (wo). The study revealed that H5N1 vaccination had highly variable outcome, including vaccination failures, and was largely ineffective in providing long lasting protective immunity. Flocks were vaccinated with seven different vaccines, administer at various times that could be grouped into three regimes: In regime A, flocks (n = 8) were vaccinated two or three times before 19 wo; in regime B (n = 2), two times before and once after 19 wo; and in regime C (n = 6) three to four times before and two to three times after 19 wo. HI titres in regime C birds were significantly higher during the entire observation period in comparison to titres of regime A or B birds, which also differed significantly from each other. The HI titres of individual birds in each flock differed significantly from birds in other flocks, indicating that the effectiveness of field vaccination was highly variable and farm related. Protective HI titres of >4log2, were present in the majority of flocks at 18 wo, declined thereafter at variable rate and only two regime C flocks had protective HI titres at 68 wo. Laboratory challenge with HPAIV H5N1 of birds from regime A and C flocks confirmed that protective immunity differed significantly between flocks vaccinated by these two regimes. The study revealed that effectiveness of the currently applied H5N1 vaccination could be improved and measures to achieve this are discussed.
Collapse
Affiliation(s)
- Simson Tarigan
- Indonesian Research Centre for Veterinary Science, Bogor, Indonesia
| | | | - Risa Indriani
- Indonesian Research Centre for Veterinary Science, Bogor, Indonesia
| | | | - Sidna Artanto
- Faculty of Veterinary Science, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Syafrison Idris
- Directorate General of Livestock and Animal Health Services, Jakarta, Indonesia
| | - Peter A. Durr
- CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Widya Asmara
- Faculty of Veterinary Science, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Esmaeil Ebrahimie
- School of Information Technology and Mathematical Sciences, Division of Information Technology, Engineering and the Environment, University of South Australia, Adelaide, South Australia, Australia
| | - Mark A. Stevenson
- School of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Jagoda Ignjatovic
- School of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, Victoria, Australia
| |
Collapse
|
13
|
Sumo Frien U. Changes in Germs: A Potential Preemptive Strike Against the Next Pandemic. JOURNAL OF MEDICAL SCIENCES 2017. [DOI: 10.3923/jms.2018.48.55] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
|
14
|
Creanga A, Hang NLK, Cuong VD, Nguyen HT, Phuong HVM, Thanh LT, Thach NC, Hien PT, Tung N, Jang Y, Balish A, Dang NH, Duong MT, Huong NT, Hoa DN, Tho ND, Klimov A, Kapella BK, Gubareva L, Kile JC, Hien NT, Mai LQ, Davis CT. Highly Pathogenic Avian Influenza A(H5N1) Viruses at the Animal-Human Interface in Vietnam, 2003-2010. J Infect Dis 2017; 216:S529-S538. [PMID: 28934457 DOI: 10.1093/infdis/jix003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Mutation and reassortment of highly pathogenic avian influenza A(H5N1) viruses at the animal-human interface remain a major concern for emergence of viruses with pandemic potential. To understand the relationship of H5N1 viruses circulating in poultry and those isolated from humans, comprehensive phylogenetic and molecular analyses of viruses collected from both hosts in Vietnam between 2003 and 2010 were performed. We examined the temporal and spatial distribution of human cases relative to H5N1 poultry outbreaks and characterized the genetic lineages and amino acid substitutions in each gene segment identified in humans relative to closely related viruses from avian hosts. Six hemagglutinin clades and 8 genotypes were identified in humans, all of which were initially identified in poultry. Several amino acid mutations throughout the genomes of viruses isolated from humans were identified, indicating the potential for poultry viruses infecting humans to rapidly acquire molecular markers associated with mammalian adaptation and antiviral resistance.
Collapse
Affiliation(s)
- Adrian Creanga
- Influenza Division, Centers for Disease Control and Prevention.,Battelle Memorial Institute, Atlanta, Georgia
| | | | | | - Ha T Nguyen
- Influenza Division, Centers for Disease Control and Prevention
| | | | | | | | | | | | - Yunho Jang
- Influenza Division, Centers for Disease Control and Prevention
| | - Amanda Balish
- Influenza Division, Centers for Disease Control and Prevention
| | | | | | | | | | | | | | - Bryan K Kapella
- Influenza Division, Centers for Disease Control and Prevention.,Influenza and Animal-Human Interface Program, Centers for Disease Control and Prevention, Hanoi, Vietnam
| | - Larisa Gubareva
- Influenza Division, Centers for Disease Control and Prevention
| | - James C Kile
- Influenza Division, Centers for Disease Control and Prevention.,Influenza and Animal-Human Interface Program, Centers for Disease Control and Prevention, Hanoi, Vietnam
| | | | | | - C Todd Davis
- Influenza Division, Centers for Disease Control and Prevention
| |
Collapse
|
15
|
Ekong PS, Fountain-Jones NM, Alkhamis MA. Spatiotemporal evolutionary epidemiology of H5N1 highly pathogenic avian influenza in West Africa and Nigeria, 2006-2015. Transbound Emerg Dis 2017; 65:e70-e82. [PMID: 28710829 DOI: 10.1111/tbed.12680] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Indexed: 11/28/2022]
Abstract
H5N1 highly pathogenic avian influenza virus (HPAIV) was first observed in Nigeria in early 2006 and has now spread to more than 17 African countries having severe economic and public health implications. Here, we explore the spatiotemporal patterns of viral dispersal both among West African countries and within Nigeria using sequence data from hemagglutinin (HA) gene region of the virus. Analyses were performed within a statistical Bayesian framework using phylodynamic models on data sets comprising of all publically available HA sequence data collected from seven West African countries and Egypt between 2006 and 2015. Our regional-level analyses indicated that H5N1 in West Africa originated in Nigeria in three geopolitical regions, specifically north central and north-east, where backyard poultry and wild birds are in frequent contact, as well as south-west, a major commercial poultry area, then dispersed to West African countries. We inferred significant virus dispersal routes between Niger and Nigeria on one side and Burkina Faso, Ivory Coast, Ghana and Egypt on the other. Furthermore, south-west Nigeria identified as a primary source for virus dispersal within Nigeria as well as to Niger in 2006 and 2008. Niger was an important epicentre for the virus spread into other West African countries in 2015. Egyptian introductions from West Africa were sporadic and resulted most likely from poultry trade with Nigeria rather than contact with infected wild birds. Our inferred viral dispersal routes reflected the large-scale unrestricted movements of infected poultry in the region. Our study illustrates the ability of phylodynamic models to trace important HPAIV dispersal routes at a regional and national level. Our results have clear implications for the control and prevention of this pathogen across scales and will help improve molecular surveillance of transboundary HPAIVs.
Collapse
Affiliation(s)
- P S Ekong
- Central Diagnostic Laboratory, Epidemiology Unit, National Veterinary Research Institute, Vom, Nigeria.,Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - N M Fountain-Jones
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN, USA
| | - M A Alkhamis
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN, USA.,Faculty of Public Heath, Health Sciences Center, Kuwait University, Kuwait city, Kuwait
| |
Collapse
|
16
|
Abstract
The frequency and global impact of infectious disease outbreaks, particularly those caused by emerging viruses, demonstrate the need for a better understanding of how spatial ecology and pathogen evolution jointly shape epidemic dynamics. Advances in computational techniques and the increasing availability of genetic and geospatial data are helping to address this problem, particularly when both information sources are combined. Here, we review research at the intersection of evolutionary biology, human geography and epidemiology that is working towards an integrated view of spatial incidence, host mobility and viral genetic diversity. We first discuss how empirical studies have combined viral spatial and genetic data, focusing particularly on the contribution of evolutionary analyses to epidemiology and disease control. Second, we explore the interplay between virus evolution and global dispersal in more depth for two pathogens: human influenza A virus and chikungunya virus. We discuss the opportunities for future research arising from new analyses of human transportation and trade networks, as well as the associated challenges in accessing and sharing relevant spatial and genetic data.
Collapse
Affiliation(s)
- Oliver G Pybus
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Andrew J Tatem
- Department of Geography and Environment, University of Southampton, Highfield, Southampton SO17 1BJ, UK Fogarty International Center, National Institutes of Health, Bethesda, MA, USA Flowminder Foundation, Stockholm, Sweden
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute, KU Leuven-University of Leuven, Leuven, Belgium
| |
Collapse
|
17
|
Yu G, Smith DK, Zhu H, Guan Y, Lam TT. ggtree
: an
r
package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods Ecol Evol 2016. [DOI: 10.1111/2041-210x.12628] [Citation(s) in RCA: 1855] [Impact Index Per Article: 231.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Guangchuang Yu
- State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research School of Public Health The University of Hong Kong 21 Sassoon Road Pokfulam Hong Kong SAR China
| | - David K. Smith
- State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research School of Public Health The University of Hong Kong 21 Sassoon Road Pokfulam Hong Kong SAR China
| | - Huachen Zhu
- State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research School of Public Health The University of Hong Kong 21 Sassoon Road Pokfulam Hong Kong SAR China
| | - Yi Guan
- State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research School of Public Health The University of Hong Kong 21 Sassoon Road Pokfulam Hong Kong SAR China
| | - Tommy Tsan‐Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research School of Public Health The University of Hong Kong 21 Sassoon Road Pokfulam Hong Kong SAR China
| |
Collapse
|
18
|
Lam TTY, Zhu H, Guan Y, Holmes EC. Genomic Analysis of the Emergence, Evolution, and Spread of Human Respiratory RNA Viruses. Annu Rev Genomics Hum Genet 2016; 17:193-218. [PMID: 27216777 DOI: 10.1146/annurev-genom-083115-022628] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The emergence and reemergence of rapidly evolving RNA viruses-particularly those responsible for respiratory diseases, such as influenza viruses and coronaviruses-pose a significant threat to global health, including the potential of major pandemics. Importantly, recent advances in high-throughput genome sequencing enable researchers to reveal the genomic diversity of these viral pathogens at much lower cost and with much greater precision than they could before. In particular, the genome sequence data generated allow inferences to be made on the molecular basis of viral emergence, evolution, and spread in human populations in real time. In this review, we introduce recent computational methods that analyze viral genomic data, particularly in combination with metadata such as sampling time, geographic location, and virulence. We then outline the insights these analyses have provided into the fundamental patterns and processes of evolution and emergence in human respiratory RNA viruses, as well as the major challenges in such genomic analyses.
Collapse
Affiliation(s)
- Tommy T-Y Lam
- State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong, China; , ,
- Joint Influenza Research Center and Joint Institute of Virology, Shantou University Medical College, Shantou 515041, China
- State Key Laboratory of Emerging Infectious Diseases (HKU-Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen 518112, China
| | - Huachen Zhu
- State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong, China; , ,
- Joint Influenza Research Center and Joint Institute of Virology, Shantou University Medical College, Shantou 515041, China
- State Key Laboratory of Emerging Infectious Diseases (HKU-Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen 518112, China
| | - Yi Guan
- State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong, China; , ,
- Joint Influenza Research Center and Joint Institute of Virology, Shantou University Medical College, Shantou 515041, China
- State Key Laboratory of Emerging Infectious Diseases (HKU-Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen 518112, China
- Department of Microbiology, Guangxi Medical University, Nanning 530021, China
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales 2006, Australia;
| |
Collapse
|
19
|
Alkhamis MA, Perez AM, Murtaugh MP, Wang X, Morrison RB. Applications of Bayesian Phylodynamic Methods in a Recent U.S. Porcine Reproductive and Respiratory Syndrome Virus Outbreak. Front Microbiol 2016; 7:67. [PMID: 26870024 PMCID: PMC4735353 DOI: 10.3389/fmicb.2016.00067] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 01/14/2016] [Indexed: 12/14/2022] Open
Abstract
Classical phylogenetic methods such as neighbor-joining or maximum likelihood trees, provide limited inferences about the evolution of important pathogens and ignore important evolutionary parameters and uncertainties, which in turn limits decision making related to surveillance, control, and prevention resources. Bayesian phylodynamic models have recently been used to test research hypotheses related to evolution of infectious agents. However, few studies have attempted to model the evolutionary dynamics of porcine reproductive and respiratory syndrome virus (PRRSV) and, to the authors' knowledge, no attempt has been made to use large volumes of routinely collected data, sometimes referred to as big data, in the context of animal disease surveillance. The objective of this study was to explore and discuss the applications of Bayesian phylodynamic methods for modeling the evolution and spread of a notable 1-7-4 RFLP-type PRRSV between 2014 and 2015. A convenience sample of 288 ORF5 sequences was collected from 5 swine production systems in the United States between September 2003 and March 2015. Using coalescence and discrete trait phylodynamic models, we were able to infer population growth and demographic history of the virus, identified the most likely ancestral system (root state posterior probability = 0.95) and revealed significant dispersal routes (Bayes factor > 6) of viral exchange among systems. Results indicate that currently circulating viruses are evolving rapidly, and show a higher level of relative genetic diversity over time, when compared to earlier relatives. Biological soundness of model results is supported by the finding that sow farms were responsible for PRRSV spread within the systems. Such results cannot be obtained by traditional phylogenetic methods, and therefore, our results provide a methodological framework for molecular epidemiological modeling of new PRRSV outbreaks and demonstrate the prospects of phylodynamic models to inform decision-making processes for routine surveillance and, ultimately, to support prevention and control of food animal disease at local and regional scales.
Collapse
Affiliation(s)
- Mohammad A Alkhamis
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of MinnesotaSt. Paul, MN, USA; Environmental and Life Sciences Research Center, Kuwait Institute for Scientific ResearchKuwait City, Kuwait
| | - Andres M Perez
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota St. Paul, MN, USA
| | - Michael P Murtaugh
- Department of Veterinary and Biomedical Sciences, University of Minnesota St. Paul, MN, USA
| | - Xiong Wang
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of MinnesotaSt. Paul, MN, USA; Department of Veterinary and Biomedical Sciences, University of MinnesotaSt. Paul, MN, USA
| | - Robert B Morrison
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota St. Paul, MN, USA
| |
Collapse
|
20
|
Magee D, Beard R, Suchard MA, Lemey P, Scotch M. Combining phylogeography and spatial epidemiology to uncover predictors of H5N1 influenza A virus diffusion. Arch Virol 2014; 160:215-24. [PMID: 25355432 DOI: 10.1007/s00705-014-2262-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 10/19/2014] [Indexed: 11/28/2022]
Abstract
Emerging and re-emerging infectious diseases of zoonotic origin like highly pathogenic avian influenza pose a significant threat to human and animal health due to their elevated transmissibility. Identifying the drivers of such viruses is challenging, and estimation of spatial diffusion is complicated by the fact that the variability of viral spread from locations could be caused by a complex array of unknown factors. Several techniques exist to help identify these drivers, including bioinformatics, phylogeography, and spatial epidemiology, but these methods are generally evaluated separately and do not consider the complementary nature of each other. Here, we studied an approach that integrates these techniques and identifies the most important drivers of viral spread by focusing on H5N1 influenza A virus in Egypt because of its recent emergence as an epicenter for the disease. We used a Bayesian phylogeographic generalized linear model (GLM) to reconstruct spatiotemporal patterns of viral diffusion while simultaneously assessing the impact of factors contributing to transmission. We also calculated the cross-species transmission rates among hosts in order to identify the species driving transmission. The densities of both human and avian species were supported contributors, along with latitude, longitude, elevation, and several meteorological variables. Also supported was the presence of a genetic motif found near the hemagglutinin cleavage site. Various genetic, geographic, demographic, and environmental predictors each play a role in H1N1 diffusion. Further development and expansion of phylogeographic GLMs such as this will enable health agencies to identify variables that can curb virus diffusion and reduce morbidity and mortality.
Collapse
Affiliation(s)
- Daniel Magee
- Department of Biomedical Informatics, Arizona State University, 13212 E. Shea Blvd., Scottsdale, 85259, AZ, USA
| | | | | | | | | |
Collapse
|
21
|
Dalby AR, Iqbal M. A global phylogenetic analysis in order to determine the host species and geography dependent features present in the evolution of avian H9N2 influenza hemagglutinin. PeerJ 2014; 2:e655. [PMID: 25374791 PMCID: PMC4217197 DOI: 10.7717/peerj.655] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Accepted: 10/15/2014] [Indexed: 01/18/2023] Open
Abstract
A complete phylogenetic analysis of all of the H9N2 hemagglutinin sequences that were collected between 1966 and 2012 was carried out in order to build a picture of the geographical and host specific evolution of the hemagglutinin protein. To improve the quality and applicability of the output data the sequences were divided into subsets based upon location and host species. The phylogenetic analysis of hemagglutinin reveals that the protein has distinct lineages between China and the Middle East, and that wild birds in both regions retain a distinct form of the H9 molecule, from the same lineage as the ancestral hemagglutinin. The results add further evidence to the hypothesis that the current predominant H9N2 hemagglutinin lineage might have originated in Southern China. The study also shows that there are sampling problems that affect the reliability of this and any similar analysis. This raises questions about the surveillance of H9N2 and the need for wider sampling of the virus in the environment. The results of this analysis are also consistent with a model where hemagglutinin has predominantly evolved by neutral drift punctuated by occasional selection events. These selective events have produced the current pattern of distinct lineages in the Middle East, Korea and China. This interpretation is in agreement with existing studies that have shown that there is widespread intra-country sequence evolution.
Collapse
Affiliation(s)
- Andrew R Dalby
- Faculty of Science and Technology, University of Westminster , Westminster , UK
| | - Munir Iqbal
- Avian Viral Diseases Programme, The Pirbright Institute, Compton Laboratory , Newbury, Berkshire , UK
| |
Collapse
|
22
|
Antigenic variation of clade 2.1 H5N1 virus is determined by a few amino acid substitutions immediately adjacent to the receptor binding site. mBio 2014; 5:e01070-14. [PMID: 24917596 PMCID: PMC4056550 DOI: 10.1128/mbio.01070-14] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Highly pathogenic avian influenza (HPAI) viruses of the H5N1 subtype are genetically highly variable and have diversified into multiple phylogenetic clades over the past decade. Antigenic drift is a well-studied phenomenon for seasonal human influenza viruses, but much less is known about the antigenic evolution of HPAI H5N1 viruses that circulate in poultry. In this study, we focused on HPAI H5N1 viruses that are enzootic to Indonesia. We selected representative viruses from genetically distinct lineages that are currently circulating and determined their antigenic properties by hemagglutination inhibition assays. At least six antigenic variants have circulated between 2003, when H5N1 clade 2.1 viruses were first detected in Indonesia, and 2011. During this period, multiple antigenic variants cocirculated in the same geographic regions. Mutant viruses were constructed by site-directed mutagenesis to represent each of the circulating antigenic variants, revealing that antigenic differences between clade 2.1 viruses were due to only one or very few amino acid substitutions immediately adjacent to the receptor binding site. Antigenic variants of H5N1 virus evaded recognition by both ferret and chicken antibodies. The molecular basis for antigenic change in clade 2.1 viruses closely resembled that of seasonal human influenza viruses, indicating that the hemagglutinin of influenza viruses from different hosts and subtypes may be similarly restricted to evade antibody recognition. Highly pathogenic avian influenza (HPAI) H5N1 viruses are responsible for severe outbreaks in both commercial and backyard poultry, causing considerable economic losses and regular zoonotic transmissions to humans. Vaccination is used increasingly to reduce the burden of HPAI H5N1 virus in poultry. Influenza viruses can escape from recognition by antibodies induced upon vaccination or infection through genetic changes in the hemagglutinin protein. The evolutionary patterns and molecular basis of antigenic change in HPAI H5N1 viruses are poorly understood, hampering formulation of optimal vaccination strategies. We have shown here that HPAI H5N1 viruses in Indonesia diversified into multiple antigenic variants, that antigenic differences were due to one or a very few substitutions near the receptor binding site, and that the molecular basis for antigenic change was remarkably similar to that for seasonal human influenza viruses. These findings have consequences for future vaccination and surveillance considerations and contribute to the understanding of the antigenic evolution of influenza viruses.
Collapse
|
23
|
Abstract
UNLABELLED Sporadic activity by H5N2 influenza viruses has been observed in chickens in Taiwan from 2003 to 2012. The available information suggests that these viruses were generated by reassortment between a Mexican-like H5N2 virus and a local enzootic H6N1 virus. Yet the origin, prevalence, and pathogenicity of these H5N2 viruses have not been fully defined. Following the 2012 highly pathogenic avian influenza (HPAI) outbreaks, surveillance was conducted from December 2012 to July 2013 at a live-poultry wholesale market in Taipei. Our findings showed that H5N2 and H6N1 viruses cocirculated at low levels in chickens in Taiwan. Phylogenetic analyses revealed that all H5N2 viruses had hemagglutinin (HA) and neuraminidase (NA) genes derived from a 1994 Mexican-like virus, while their internal gene complexes were incorporated from the enzootic H6N1 virus lineage by multiple reassortment events. Pathogenicity studies demonstrated heterogeneous results even though all tested viruses had motifs (R-X-K/R-R) supportive of high pathogenicity. Serological surveys for common subtypes of avian viruses confirmed the prevalence of the H5N2 and H6N1 viruses in chickens and revealed an extraordinarily high seroconversion rate to an H9N2 virus, a subtype that is not found in Taiwan but is prevalent in mainland China. These findings suggest that reassortant H5N2 viruses, together with H6N1 viruses, have become established and enzootic in chickens throughout Taiwan and that a large-scale vaccination program might have been conducted locally that likely led to the introduction of the 1994 Mexican-like virus to Taiwan in 2003. IMPORTANCE H5N2 avian influenza viruses first appeared in chickens in Taiwan in 2003 and caused a series of outbreaks afterwards. Phylogenetic analyses show that the chicken H5N2 viruses have H5 and N2 genes that are closely related to those of a vaccine strain originating from Mexico in 1994, while the contemporary duck H5N2 viruses in Taiwan belong to the Eurasian gene pool. The unusually high similarity of the chicken H5N2 viruses to the Mexican vaccine strain suggests that these viruses might have been introduced to Taiwan by using inadequately inactivated or attenuated vaccines. These chicken H5N2 viruses are developing varying levels of pathogenicity that could lead to significant consequences for the local poultry industry. These findings emphasize the need for strict quality control and competent oversight in the manufacture and usage of avian influenza virus vaccines and indicate that alternatives to widespread vaccination may be desirable.
Collapse
|
24
|
Sonnberg S, Webby RJ, Webster RG. Natural history of highly pathogenic avian influenza H5N1. Virus Res 2013; 178:63-77. [PMID: 23735535 PMCID: PMC3787969 DOI: 10.1016/j.virusres.2013.05.009] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 05/03/2013] [Accepted: 05/20/2013] [Indexed: 12/27/2022]
Abstract
The ecology of highly pathogenic avian influenza (HPAI) H5N1 has significantly changed from sporadic outbreaks in terrestrial poultry to persistent circulation in terrestrial and aquatic poultry and potentially in wild waterfowl. A novel genotype of HPAI H5N1 arose in 1996 in Southern China and through ongoing mutation, reassortment, and natural selection, has diverged into distinct lineages and expanded into multiple reservoir hosts. The evolution of Goose/Guangdong-lineage highly pathogenic H5N1 viruses is ongoing: while stable interactions exist with some reservoir hosts, these viruses are continuing to evolve and adapt to others, and pose an un-calculable risk to sporadic hosts, including humans.
Collapse
Affiliation(s)
- Stephanie Sonnberg
- Department of Infectious Diseases St. Jude Children's Research Hospital 262 Danny Thomas Drive MS 330, Memphis, TN, 38103 USA
| | - Richard J. Webby
- Department of Infectious Diseases St. Jude Children's Research Hospital 262 Danny Thomas Drive MS 330, Memphis, TN, 38103 USA
| | - Robert G. Webster
- corresponding author, Department of Infectious Diseases St. Jude Children's Research Hospital 262 Danny Thomas Drive MS 330, Memphis, TN, 38103 USA Tel +1 901 595 3400 Fax +1 901 595 8559
| |
Collapse
|
25
|
Wiwanitkit V, Shi B, Xia S, Yang GJ, Zhou XN, Liu J. Research priorities in modeling the transmission risks of H7N9 bird flu. Infect Dis Poverty 2013; 2:17. [PMID: 23927386 PMCID: PMC3751567 DOI: 10.1186/2049-9957-2-17] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 08/06/2013] [Indexed: 11/10/2022] Open
Abstract
The epidemic of H7N9 bird flu in eastern China in early 2013 has caused much attention from researchers as well as public health workers. The issue on modeling the transmission risks is very interesting topic. In this article, this issue is debated and discussed in order to promote further researches on prediction and prevention of avian influenza viruses supported by better interdisciplinary datasets from the surveillance and response system.
Collapse
|
26
|
Chong YL, Lam TTY, Kim O, Lu H, Dunn P, Poss M. Successful establishment and global dispersal of genotype VI avian paramyxovirus serotype 1 after cross species transmission. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2013; 17:260-8. [PMID: 23628639 PMCID: PMC7106292 DOI: 10.1016/j.meegid.2013.04.025] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2013] [Revised: 04/08/2013] [Accepted: 04/22/2013] [Indexed: 02/02/2023]
Abstract
The evolutionary history of avian paramyxovirus serotype 1 (PMV1), which includes the agents of Newcastle disease (ND), is characterized by a series of strain emergence events since viruses in this family were first recognized in the 1920s. Despite the importance of ND to the poultry industry, little is known about PMV1 strain emergence events and the subsequent dispersal and evolution of new strains. The genotype VI-PMV1 was first identified in the 1980s and has been named pigeon paramyxovirus-1 (PPMV1) because of unusual host specificity with Columbiformes (Collins et al., 1996); it has been responsible for panzootics in both chickens and pigeons during that time. Here, we used evolutionary analyses to characterize the emergence of this contemporary PMV1 lineage. We demonstrate that GVI-PMV1 arose through cross-species transmission events from Galliformes (i.e. chicken) to Columbiformes, and quickly established in pigeon populations. Our studies revealed a close association between the time of viral emergence and panzootic events of this virus. The virus appeared first in Southeastern Europe and quickly spread across the European continent, which became the epicenter for global virus dissemination. With new viral gene sequences, we show that GVI-PMV1 viruses currently circulating in North America resulted from multiple invasion events from Europe, one associated with an exotic European Columbiformes species, and that extant lineages have diversified locally. This study extends our understanding of successful viral emergence subsequent to cross-species transmission and dispersal patterns of newly emerged avian viruses, which may improve surveillance awareness and disease control of this and other important avian pathogens.
Collapse
Affiliation(s)
- Yee Ling Chong
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | | | | | | | | | | |
Collapse
|
27
|
Davino S, Willemsen A, Panno S, Davino M, Catara A, Elena SF, Rubio L. Emergence and phylodynamics of Citrus tristeza virus in Sicily, Italy. PLoS One 2013; 8:e66700. [PMID: 23818960 PMCID: PMC3688570 DOI: 10.1371/journal.pone.0066700] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 05/09/2013] [Indexed: 11/19/2022] Open
Abstract
Citrus tristeza virus (CTV) outbreaks were detected in Sicily island, Italy for the first time in 2002. To gain insight into the evolutionary forces driving the emergence and phylogeography of these CTV populations, we determined and analyzed the nucleotide sequences of the p20 gene from 108 CTV isolates collected from 2002 to 2009. Bayesian phylogenetic analysis revealed that mild and severe CTV isolates belonging to five different clades (lineages) were introduced in Sicily in 2002. Phylogeographic analysis showed that four lineages co-circulated in the main citrus growing area located in Eastern Sicily. However, only one lineage (composed of mild isolates) spread to distant areas of Sicily and was detected after 2007. No correlation was found between genetic variation and citrus host, indicating that citrus cultivars did not exert differential selective pressures on the virus. The genetic variation of CTV was not structured according to geographical location or sampling time, likely due to the multiple introduction events and a complex migration pattern with intense co- and re-circulation of different lineages in the same area. The phylogenetic structure, statistical tests of neutrality and comparison of synonymous and nonsynonymous substitution rates suggest that weak negative selection and genetic drift following a rapid expansion may be the main causes of the CTV variability observed today in Sicily. Nonetheless, three adjacent amino acids at the p20 N-terminal region were found to be under positive selection, likely resulting from adaptation events.
Collapse
Affiliation(s)
| | | | | | | | - Antonino Catara
- Parco Scientifico e Tecnologico della Sicilia, Cataia, Italy
| | - Santiago F. Elena
- IBMCP, CSIC-UPV, Valencia, Spain
- The Santa Fe Institute, Santa Fe, New Mexico, United States of America
| | | |
Collapse
|
28
|
Camargo A, Werneck FP, Morando M, Sites JW, Avila LJ. Quaternary range and demographic expansion of Liolaemus darwinii (Squamata: Liolaemidae) in the Monte Desert of Central Argentina using Bayesian phylogeography and ecological niche modelling. Mol Ecol 2013; 22:4038-54. [PMID: 23786355 DOI: 10.1111/mec.12369] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 04/25/2013] [Accepted: 04/25/2013] [Indexed: 12/29/2022]
Abstract
Until recently, most phylogeographic approaches have been unable to distinguish between demographic and range expansion processes, making it difficult to test for the possibility of range expansion without population growth and vice versa. In this study, we applied a Bayesian phylogeographic approach to reconstruct both demographic and range expansion in the lizard Liolaemus darwinii of the Monte Desert in Central Argentina, during the Late Quaternary. Based on analysis of 14 anonymous nuclear loci and the cytochrome b mitochondrial DNA gene, we detected signals of demographic expansion starting at ~55 ka based on Bayesian Skyline and Skyride Plots. In contrast, Bayesian relaxed models of spatial diffusion suggested that range expansion occurred only between ~95 and 55 ka, and more recently, diffusion rates were very low during demographic expansion. The possibility of population growth without substantial range expansion could account for the shared patterns of demographic expansion during the Last Glacial Maxima (OIS 2 and 4) in fish, small mammals and other lizards of the Monte Desert. We found substantial variation in diffusion rates over time, and very high rates during the range expansion phase, consistent with a rapidly advancing expansion front towards the southeast shown by palaeo-distribution models. Furthermore, the estimated diffusion rates are congruent with observed dispersal rates of lizards in field conditions and therefore provide additional confidence to the temporal scale of inferred phylogeographic patterns. Our study highlights how the integration of phylogeography with palaeo-distribution models can shed light on both demographic and range expansion processes and their potential causes.
Collapse
Affiliation(s)
- Arley Camargo
- Unidad de Diversidad, Sistemática y Evolución, Centro Nacional Patagónico, Consejo Nacional de Investigaciones Científicas y Técnicas, Boulevard Almirante Brown 2915, U9120ACD, Puerto Madryn, Chubut, Argentina.
| | | | | | | | | |
Collapse
|
29
|
Kitikoon P, Nelson MI, Killian ML, Anderson TK, Koster L, Culhane MR, Vincent AL. Genotype patterns of contemporary reassorted H3N2 virus in US swine. J Gen Virol 2013. [DOI: 10.1099/vir.0.051839-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
To understand the evolution of swine-origin H3N2v influenza viruses that have infected 320 humans in the USA since August 2011, we performed a phylogenetic analysis at a whole genome scale of North American swine influenza viruses (n = 200). All viral isolates evolved from the prototypical North American H3 cluster 4 (c4), with evidence for further diversification into subclusters. At least ten distinct reassorted H3N2/pandemic H1N1 (rH3N2p) genotypes were identified in swine. Genotype 1 (G1) was most frequently detected in swine and all human H3N2v viruses clustered within a single G1 clade. These data suggest that the genetic requirements for transmission to humans may be restricted to a specific subset of swine viruses. Mutations at putative antigenic sites as well as reduced serological cross-reactivity among the H3 subclusters suggest antigenic drift of these contemporary viruses.
Collapse
Affiliation(s)
- Pravina Kitikoon
- Virus and Prion Disease Research Unit, National Animal Disease Center, USDA-ARS, Ames, IA 50010, USA
| | - Martha I. Nelson
- Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mary Lea Killian
- National Veterinary Services Laboratories, USDA-APHIS, Ames, IA 50010, USA
| | - Tavis K. Anderson
- Virus and Prion Disease Research Unit, National Animal Disease Center, USDA-ARS, Ames, IA 50010, USA
| | - Leo Koster
- National Veterinary Services Laboratories, USDA-APHIS, Ames, IA 50010, USA
| | - Marie R. Culhane
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, USA
| | - Amy L. Vincent
- Virus and Prion Disease Research Unit, National Animal Disease Center, USDA-ARS, Ames, IA 50010, USA
| |
Collapse
|
30
|
Lam TTY, Liu W, Bowden TA, Cui N, Zhuang L, Liu K, Zhang YY, Cao WC, Pybus OG. Evolutionary and molecular analysis of the emergent severe fever with thrombocytopenia syndrome virus. Epidemics 2012; 5:1-10. [PMID: 23438426 PMCID: PMC4330987 DOI: 10.1016/j.epidem.2012.09.002] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 09/13/2012] [Indexed: 01/08/2023] Open
Abstract
In 2009, a novel Bunyavirus, called severe fever with thrombocytopenia syndrome virus (SFTSV) was identified in the vicinity of Huaiyangshan, China. Clinical symptoms of this zoonotic virus included severe fever, thrombocytopenia, and leukocytopenia, with a mortality rate of ∼10%. By the end of 2011 the disease associated with this pathogen had been reported from eleven Chinese provinces and human-to-human transmission suspected. However, current understanding of the evolution and molecular epidemiology of SFTSV before and after its identification is limited. To address this we undertake phylogenetic, evolutionary and structural analyses of all available SFTSV genetic sequences, including a new SFTSV complete genome isolated from a patient from Henan in 2011. Our discovery of a mosaic L segment sequence, which is descended from two major circulating lineages of SFTSV in China, represents the first evidence that homologous recombination plays a role in SFTSV evolution. Selection analyses indicate that negative selection is predominant in SFTSV genes, yet differences in selective forces among genes are consistent between Phlebovirus species. Further analysis reveals structural conservation between SFTSV and Rift Valley fever virus in the residues of their nucleocapsids that are responsible for oligomerisation and RNA-binding, suggesting the viruses share similar modes of higher-order assembly. We reconstruct the epidemic history of SFTSV using molecular clock and coalescent-based methods, revealing that the extant SFTSV lineages originated 50–150 years ago, and that the viral population experienced a recent growth phase that concurs with and extends the earliest serological reports of SFTSV infection. Taken together, our combined structural and phylogenetic analyses shed light into the evolutionary behaviour of SFTSV in the context of other, better-known, pathogenic Phleboviruses.
Collapse
|