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Ashall J, Shah S, Biggs JR, Chang JNR, Jafari Y, Brady OJ, Mai HK, Lien LT, Do Thai H, Nguyen HAT, Anh DD, Iwasaki C, Kitamura N, Van Loock M, Herrera-Taracena G, Rasschaert F, Van Wesenbeeck L, Yoshida LM, Hafalla JCR, Hue S, Hibberd ML. A phylogenetic study of dengue virus in urban Vietnam shows long-term persistence of endemic strains. Virus Evol 2023; 9:vead012. [PMID: 36926448 PMCID: PMC10013730 DOI: 10.1093/ve/vead012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 10/31/2022] [Accepted: 02/15/2023] [Indexed: 02/17/2023] Open
Abstract
Dengue virus (DENV) causes repeated outbreaks of disease in endemic areas, with patterns of local transmission strongly influenced by seasonality, importation via human movement, immunity, and vector control efforts. An understanding of how each of these interacts to enable endemic transmission (continual circulation of local virus strains) is largely unknown. There are times of the year when no cases are reported, often for extended periods of time, perhaps wrongly implying the successful eradication of a local strain from that area. Individuals who presented at a clinic or hospital in four communes in Nha Trang, Vietnam, were initially tested for DENV antigen presence. Enrolled positive individuals then had their corresponding household members invited to participate, and those who enrolled were tested for DENV. The presence of viral nucleic acid in all samples was confirmed using quantitative polymerase chain reaction, and positive samples were then whole-genome sequenced using an amplicon and target enrichment library preparation techniques and Illumina MiSeq sequencing technology. Generated consensus genome sequences were then analysed using phylogenetic tree reconstruction to categorise sequences into clades with a common ancestor, enabling investigations of both viral clade persistence and introductions. Hypothetical introduction dates were additionally assessed using a molecular clock model that calculated the time to the most recent common ancestor (TMRCA). We obtained 511 DENV whole-genome sequences covering four serotypes and more than ten distinct viral clades. For five of these clades, we had sufficient data to show that the same viral lineage persisted for at least several months. We noted that some clades persisted longer than others during the sampling time, and by comparison with other published sequences from elsewhere in Vietnam and around the world, we saw that at least two different viral lineages were introduced into the population during the study period (April 2017-2019). Next, by inferring the TMRCA from the construction of molecular clock phylogenies, we predicted that two of the viral lineages had been present in the study population for over a decade. We observed five viral lineages co-circulating in Nha Trang from three DENV serotypes, with two likely to have remained as uninterrupted transmission chains for a decade. This suggests clade cryptic persistence in the area, even during periods of low reported incidence.
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Affiliation(s)
- James Ashall
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Sonal Shah
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Joseph R Biggs
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Jui-Ning R Chang
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Yalda Jafari
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Oliver J Brady
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Huynh Kim Mai
- Department of Microbiology and Immunology, Pasteur Institute of Nha Trang, Xương Huân, Nha Trang, 650000, Vietnam
| | - Le Thuy Lien
- Department of Microbiology and Immunology, Pasteur Institute of Nha Trang, Xương Huân, Nha Trang, 650000, Vietnam
| | - Hung Do Thai
- Department of Microbiology and Immunology, Pasteur Institute of Nha Trang, Xương Huân, Nha Trang, 650000, Vietnam
| | - Hien Anh Thi Nguyen
- National Institute of Hygiene and Epidemiology, 1 P. Yec Xanh, Phạm Đình Hổ, Hai Bà Trưng, Hà Nội, 100000, Vietnam
| | - Dang Duc Anh
- National Institute of Hygiene and Epidemiology, 1 P. Yec Xanh, Phạm Đình Hổ, Hai Bà Trưng, Hà Nội, 100000, Vietnam
| | - Chihiro Iwasaki
- Paediatric Infectious Diseases Department, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Noriko Kitamura
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
- Paediatric Infectious Diseases Department, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Marnix Van Loock
- Janssen R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, Beerse B-2340, Belgium
| | - Guillermo Herrera-Taracena
- Janssen Global Public Health, Janssen Research & Development, LLC, 800 Ridgeview Drive, Horsham, PA 19044, USA
| | - Freya Rasschaert
- Janssen R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, Beerse B-2340, Belgium
| | | | - Lay-Myint Yoshida
- Paediatric Infectious Diseases Department, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Julius Clemence R Hafalla
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Stephane Hue
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Martin L Hibberd
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
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Yu X, Cheng G. Contribution of phylogenetics to understanding the evolution and epidemiology of dengue virus. Animal Model Exp Med 2022; 5:410-417. [PMID: 36245335 PMCID: PMC9610151 DOI: 10.1002/ame2.12283] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 10/05/2022] [Indexed: 11/18/2022] Open
Abstract
Dengue virus (DENV) is one of the most important arboviral pathogens in the tropics and subtropics, and nearly one‐third of the world's population is at risk of infection. The transmission of DENV involves a sylvatic cycle between nonhuman primates (NHP) and Aedes genus mosquitoes, and an endemic cycle between human hosts and predominantly Aedes aegypti. DENV belongs to the genus Flavivirus of the family Flaviviridae and consists of four antigenically distinct serotypes (DENV‐1‐4). Phylogenetic analyses of DENV have revealed its origin, epidemiology, and the drivers that determine its molecular evolution in nature. This review discusses how phylogenetic research has improved our understanding of DENV evolution and how it affects viral ecology and improved our ability to analyze and predict future DENV emergence.
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Affiliation(s)
- Xi Yu
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, China.,Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, China.,Institute of Pathogenic Organisms, Shenzhen Center for Disease Control and Prevention, Shenzhen, China.,School of Life Sciences, Tsinghua University, Beijing, China
| | - Gong Cheng
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, China.,Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, China.,Institute of Pathogenic Organisms, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
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3
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Li C, Gong B, Sun Q, Xu H, Zhao J, Xiang L, Tang YD, Leng C, Li W, Guo Z, Fu J, Peng J, Wang Q, Zhou G, Yu Y, Meng F, An T, Cai X, Tian ZJ, Zhang H. First Detection of NADC34-like PRRSV as a Main Epidemic Strain on a Large Farm in China. Pathogens 2021; 11:pathogens11010032. [PMID: 35055980 PMCID: PMC8778757 DOI: 10.3390/pathogens11010032] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/27/2021] [Accepted: 12/27/2021] [Indexed: 11/16/2022] Open
Abstract
The newly emerged sublineage 1.5 (NADC34-like) porcine reproductive and respiratory syndrome virus (PRRSV) has posed a direct threat to the Chinese pig industry since 2018. However, the prevalence and impact of NADC34-like PRRSV on Chinese pig farms is unclear. In the present study, we continuously monitored pathogens—including PRRSV, African swine fever virus (ASFV), classical swine fever virus (CSFV), pseudorabies virus (PRV), and porcine circovirus 2 (PCV2)—on a fattening pig farm with strict biosecurity practices located in Heilongjiang Province, China, from 2020 to 2021. The results showed that multiple types of PRRSV coexisted on a single pig farm. NADC30-like and NADC34-like PRRSVs were the predominant strains on this pig farm. Importantly, NADC34-like PRRSV—detected during the period of peak mortality—was one of the predominant strains on this pig farm. Sequence alignment suggested that these strains shared the same 100 aa deletion in the NSP2 protein as IA/2014/NADC34 isolated from the United States (U.S.) in 2014. Phylogenetic analysis based on open reading frame 5 (ORF5) showed that the genetic diversity of NADC34-like PRRSV on this farm was relatively singular, but it had a relatively high rate of evolution. Restriction fragment length polymorphism (RFLP) pattern analysis showed that almost all ORF5 RFLPs were 1-7-4, with one 1-4-4. In addition, two complete genomes of NADC34-like PRRSVs were sequenced. Recombination analysis and sequence alignment demonstrated that both viruses, with 98.9% nucleotide similarity, were non-recombinant viruses. This study reports the prevalence and characteristics of NADC34-like PRRSVs on a large-scale breeding farm in northern China for the first time. These results will help to reveal the impact of NADC34-like PRRSVs on Chinese pig farms, and provide a reference for the detection and further prevention and control of NADC34-like PRRSVs.
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Affiliation(s)
- Chao Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Bangjun Gong
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Qi Sun
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Hu Xu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Jing Zhao
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Lirun Xiang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Yan-Dong Tang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Chaoliang Leng
- Henan Key Laboratory of Insect Biology in Funiu Mountain, Henan Provincial Engineering Laboratory of Insects Bio-Reactor, China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Nanyang Normal University, Nanyang 473061, China;
| | - Wansheng Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Zhenyang Guo
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Jun Fu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Jinmei Peng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Qian Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Guohui Zhou
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Ying Yu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China;
| | - Fandan Meng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Tongqing An
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Xuehui Cai
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Zhi-Jun Tian
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Hongliang Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
- Correspondence: ; Tel.: +86-13624503578
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Maljkovic Berry I, Melendrez MC, Bishop-Lilly KA, Rutvisuttinunt W, Pollett S, Talundzic E, Morton L, Jarman RG. Next Generation Sequencing and Bioinformatics Methodologies for Infectious Disease Research and Public Health: Approaches, Applications, and Considerations for Development of Laboratory Capacity. J Infect Dis 2021; 221:S292-S307. [PMID: 31612214 DOI: 10.1093/infdis/jiz286] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Next generation sequencing (NGS) combined with bioinformatics has successfully been used in a vast array of analyses for infectious disease research of public health relevance. For instance, NGS and bioinformatics approaches have been used to identify outbreak origins, track transmissions, investigate epidemic dynamics, determine etiological agents of a disease, and discover novel human pathogens. However, implementation of high-quality NGS and bioinformatics in research and public health laboratories can be challenging. These challenges mainly include the choice of the sequencing platform and the sequencing approach, the choice of bioinformatics methodologies, access to the appropriate computation and information technology infrastructure, and recruiting and retaining personnel with the specialized skills and experience in this field. In this review, we summarize the most common NGS and bioinformatics workflows in the context of infectious disease genomic surveillance and pathogen discovery, and highlight the main challenges and considerations for setting up an NGS and bioinformatics-focused infectious disease research public health laboratory. We describe the most commonly used sequencing platforms and review their strengths and weaknesses. We review sequencing approaches that have been used for various pathogens and study questions, as well as the most common difficulties associated with these approaches that should be considered when implementing in a public health or research setting. In addition, we provide a review of some common bioinformatics tools and procedures used for pathogen discovery and genome assembly, along with the most common challenges and solutions. Finally, we summarize the bioinformatics of advanced viral, bacterial, and parasite pathogen characterization, including types of study questions that can be answered when utilizing NGS and bioinformatics.
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Affiliation(s)
- Irina Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | | | - Kimberly A Bishop-Lilly
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Maryland
| | - Wiriya Rutvisuttinunt
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Simon Pollett
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland.,Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - Eldin Talundzic
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Lindsay Morton
- Global Emerging Infections Surveillance, Armed Forces Health Surveillance Branch, Silver Spring, Maryland
| | - Richard G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
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Lorenzo-Redondo R, Ozer EA, Achenbach CJ, D'Aquila RT, Hultquist JF. Molecular epidemiology in the HIV and SARS-CoV-2 pandemics. Curr Opin HIV AIDS 2021; 16:11-24. [PMID: 33186230 PMCID: PMC7723008 DOI: 10.1097/coh.0000000000000660] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
PURPOSE OF REVIEW The aim of this review was to compare and contrast the application of molecular epidemiology approaches for the improved management and understanding of the HIV versus SARS-CoV-2 epidemics. RECENT FINDINGS Molecular biology approaches, including PCR and whole genome sequencing (WGS), have become powerful tools for epidemiological investigation. PCR approaches form the basis for many high-sensitivity diagnostic tests and can supplement traditional contact tracing and surveillance strategies to define risk networks and transmission patterns. WGS approaches can further define the causative agents of disease, trace the origins of the pathogen, and clarify routes of transmission. When coupled with clinical datasets, such as electronic medical record data, these approaches can investigate co-correlates of disease and pathogenesis. In the ongoing HIV epidemic, these approaches have been effectively deployed to identify treatment gaps, transmission clusters and risk factors, though significant barriers to rapid or real-time implementation remain critical to overcome. Likewise, these approaches have been successful in addressing some questions of SARS-CoV-2 transmission and pathogenesis, but the nature and rapid spread of the virus have posed additional challenges. SUMMARY Overall, molecular epidemiology approaches offer unique advantages and challenges that complement traditional epidemiological tools for the improved understanding and management of epidemics.
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Affiliation(s)
- Ramon Lorenzo-Redondo
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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Pollett S, Fauver JR, Berry IM, Melendrez M, Morrison A, Gillis LD, Johansson MA, Jarman RG, Grubaugh ND. Genomic Epidemiology as a Public Health Tool to Combat Mosquito-Borne Virus Outbreaks. J Infect Dis 2020; 221:S308-S318. [PMID: 31711190 PMCID: PMC11095994 DOI: 10.1093/infdis/jiz302] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Next-generation sequencing technologies, exponential increases in the availability of virus genomic data, and ongoing advances in phylogenomic methods have made genomic epidemiology an increasingly powerful tool for public health response to a range of mosquito-borne virus outbreaks. In this review, we offer a brief primer on the scope and methods of phylogenomic analyses that can answer key epidemiological questions during mosquito-borne virus public health emergencies. We then focus on case examples of outbreaks, including those caused by dengue, Zika, yellow fever, West Nile, and chikungunya viruses, to demonstrate the utility of genomic epidemiology to support the prevention and control of mosquito-borne virus threats. We extend these case studies with operational perspectives on how to best incorporate genomic epidemiology into structured surveillance and response programs for mosquito-borne virus control. Many tools for genomic epidemiology already exist, but so do technical and nontechnical challenges to advancing their use. Frameworks to support the rapid sharing of multidimensional data and increased cross-sector partnerships, networks, and collaborations can support advancement on all scales, from research and development to implementation by public health agencies.
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Affiliation(s)
- S. Pollett
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Department of Preventive Medicine and Biostatistics, Uniformed Services University, Bethesda, Maryland
- Marie Bashir Institute, University of Sydney, Camperdown, New South Wales, Australia
| | - J. R. Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, Connecticut
- Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Irina Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | | | | | - L. D. Gillis
- Bureau of Public Health Laboratories–Miami, Florida Department of Health
| | - M. A. Johansson
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, San Juan, Puerto Rico
| | - R. G. Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - N. D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, Connecticut
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Hadfield J, Megill C, Bell SM, Huddleston J, Potter B, Callender C, Sagulenko P, Bedford T, Neher RA. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics 2019; 34:4121-4123. [PMID: 29790939 PMCID: PMC6247931 DOI: 10.1093/bioinformatics/bty407] [Citation(s) in RCA: 1968] [Impact Index Per Article: 393.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 05/16/2018] [Indexed: 01/19/2023] Open
Abstract
Summary Understanding the spread and evolution of pathogens is important for effective public health measures and surveillance. Nextstrain consists of a database of viral genomes, a bioinformatics pipeline for phylodynamics analysis, and an interactive visualization platform. Together these present a real-time view into the evolution and spread of a range of viral pathogens of high public health importance. The visualization integrates sequence data with other data types such as geographic information, serology, or host species. Nextstrain compiles our current understanding into a single accessible location, open to health professionals, epidemiologists, virologists and the public alike. Availability and implementation All code (predominantly JavaScript and Python) is freely available from github.com/nextstrain and the web-application is available at nextstrain.org.
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Affiliation(s)
- James Hadfield
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Colin Megill
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Sidney M Bell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - John Huddleston
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Barney Potter
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Charlton Callender
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Pavel Sagulenko
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Richard A Neher
- Max Planck Institute for Developmental Biology, Tübingen, Germany.,Biozentrum, University of Basel, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, Basel, Switzerland
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8
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Tsai MH, Liu YY, Chen CC. OutbreakFinder: a visualization tool for rapid detection of bacterial strain clusters based on optimized multidimensional scaling. PeerJ 2019; 7:e7600. [PMID: 31523522 PMCID: PMC6717506 DOI: 10.7717/peerj.7600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 08/01/2019] [Indexed: 11/30/2022] Open
Abstract
With the evolution of next generation sequencing (NGS) technologies, whole-genome sequencing of bacterial isolates is increasingly employed to investigate epidemiology. Phylogenetic analysis is the common method for using NGS data, usually for comparing closeness between bacterial isolates to detect probable outbreaks. However, interpreting a phylogenetic tree is not easy without training in evolutionary biology. Therefore, developing an easy-to-use tool that can assist people who wish to use a phylogenetic tree to investigate epidemiological relatedness is crucial. In this paper, we present a tool called OutbreakFinder that can accept a distance matrix in csv format; alignment files from Lyve-SET, Parsnp, and ClustalOmega; and a tree file in Newick format as inputs to compute a cluster-labeled two-dimensional plot based on multidimensional-scaling dimension reduction coupled with affinity propagation clustering. OutbreakFinder can be downloaded for free at https://github.com/skypes/Newton-method-MDS.
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Affiliation(s)
- Ming-Hsin Tsai
- Institute of Population Health Sciences, National Health Research Institutes, Miaoli, Taiwan
| | - Yen-Yi Liu
- Center for Research, Diagnostics and Vaccine Development, Centers for Disease Control, Ministry of Health and Welfare, Taichung, Taiwan
| | - Chih-Chieh Chen
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung, Taiwan
- Rapid Screening Research Center for Toxicology and Biomedicine, National Sun Yat-sen University, Kaohsiung, Taiwan
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9
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Microbial evolutionary medicine: from theory to clinical practice. THE LANCET. INFECTIOUS DISEASES 2019; 19:e273-e283. [PMID: 31053492 DOI: 10.1016/s1473-3099(19)30045-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 11/21/2018] [Accepted: 02/04/2019] [Indexed: 12/15/2022]
Abstract
Medicine and clinical microbiology have traditionally attempted to identify and eliminate the agents that cause disease. However, this traditional approach is becoming inadequate for dealing with a changing disease landscape. Major challenges to human health are non-communicable chronic diseases, often driven by altered immunity and inflammation, and communicable infections from agents which harbour antibiotic resistance. This Review focuses on the so-called evolutionary medicine framework, to study how microbial communities influence human health. The evolutionary medicine framework aims to predict and manipulate microbial effects on human health by integrating ecology, evolutionary biology, microbiology, bioinformatics, and clinical expertise. We focus on the potential of evolutionary medicine to address three key challenges: detecting microbial transmission, predicting antimicrobial resistance, and understanding microbe-microbe and human-microbe interactions in health and disease, in the context of the microbiome.
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10
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Lau MSY, Grenfell BT, Worby CJ, Gibson GJ. Model diagnostics and refinement for phylodynamic models. PLoS Comput Biol 2019; 15:e1006955. [PMID: 30951528 PMCID: PMC6469796 DOI: 10.1371/journal.pcbi.1006955] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 04/17/2019] [Accepted: 03/18/2019] [Indexed: 11/29/2022] Open
Abstract
Phylodynamic modelling, which studies the joint dynamics of epidemiological and evolutionary processes, has made significant progress in recent years due to increasingly available genomic data and advances in statistical modelling. These advances have greatly improved our understanding of transmission dynamics of many important pathogens. Nevertheless, there remains a lack of effective, targetted diagnostic tools for systematically detecting model mis-specification. Development of such tools is essential for model criticism, refinement, and calibration. The idea of utilising latent residuals for model assessment has already been exploited in general spatio-temporal epidemiological settings. Specifically, by proposing appropriately designed non-centered, re-parameterizations of a given epidemiological process, one can construct latent residuals with known sampling distributions which can be used to quantify evidence of model mis-specification. In this paper, we extend this idea to formulate a novel model-diagnostic framework for phylodynamic models. Using simulated examples, we show that our framework may effectively detect a particular form of mis-specification in a phylodynamic model, particularly in the event of superspreading. We also exemplify our approach by applying the framework to a dataset describing a local foot-and-mouth (FMD) outbreak in the UK, eliciting strong evidence against the assumption of no within-host-diversity in the outbreak. We further demonstrate that our framework can facilitate model calibration in real-life scenarios, by proposing a within-host-diversity model which appears to offer a better fit to data than one that assumes no within-host-diversity of FMD virus. Integrated modelling of conventional epidemiological data and modern genomic data (i.e. phylodynamics) has made significant progress in recent years, due to the ever-increasing availability of genomic data and development of statistical methods. However, there is a lack of tools for carrying out effective diagnostics for phylodynamic models. We propose a novel model diagnostic framework that involves a latent residual process which is a priori independent of model assumptions and which can be used to quantify, and reveal the nature of, model inadequacy. Our results suggest that our framework may systematically detect deviation from a particular model assumption and greatly facilitate subsequent model calibration.
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Affiliation(s)
- Max S. Y. Lau
- Department of Ecology and Evolutionary Biology, Princeton University, New Jersey, USA
- * E-mail:
| | - Bryan T. Grenfell
- Department of Ecology and Evolutionary Biology, Princeton University, New Jersey, USA
- Fogarty International Center, National Institute of Health, Bethesda, MD, USA
| | | | - Gavin J. Gibson
- Maxwell Institute for Mathematical Sciences, School of Mathematical and Computer Sciences, Heriot-Watt University, Edinburgh, EH14 4AS, UK
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11
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Correa-Fiz F, Franzo G, Llorens A, Segalés J, Kekarainen T. Porcine circovirus 2 (PCV-2) genetic variability under natural infection scenario reveals a complex network of viral quasispecies. Sci Rep 2018; 8:15469. [PMID: 30341330 PMCID: PMC6195574 DOI: 10.1038/s41598-018-33849-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 10/04/2018] [Indexed: 11/09/2022] Open
Abstract
Porcine circovirus 2 (PCV-2) is a virus characterized by a high evolutionary rate, promoting the potential emergence of different genotypes and strains. Despite the likely relevance in the emergence of new PCV-2 variants, the subtle evolutionary patterns of PCV-2 at the individual-host level or over short transmission chains are still largely unknown. This study aimed to analyze the within-host genetic variability of PCV-2 subpopulations to unravel the forces driving PCV-2 evolution. A longitudinal weekly sampling was conducted on individual animals located in three farms after the first PCV-2 detection. The analysis of polymorphisms evaluated throughout the full PCV-2 genome demonstrated the presence of several single nucleotide polymorphisms (SNPs) especially in the genome region encoding for the capsid gene. The global haplotype reconstruction allowed inferring the virus transmission network over time, suggesting a relevant within-farm circulation. Evidences of co-infection and recombination involving multiple PCV-2 genotypes were found after mixing with pigs originating from other sources. The present study demonstrates the remarkable within-host genetic variability of PCV-2 quasispecies, suggesting the role of the natural selection induced by the host immune response in driving PCV-2 evolution. Moreover, the effect of pig management in multiple genotype coinfections occurrence and recombination likelihood was demonstrated.
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Affiliation(s)
| | - Giovanni Franzo
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Legnaro, PD, Italy
| | - Anna Llorens
- Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), IRTA, Bellaterra, Spain
| | - Joaquim Segalés
- Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), IRTA, Bellaterra, Spain.,Departament de Sanitat i Anatomia Animals, Facultat de Veterinària, UAB, Bellaterra, Spain
| | - Tuija Kekarainen
- Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), IRTA, Bellaterra, Spain.,Kuopio Center for Gene and Cell Therapy, Microkatu 1, Kuopio, Finland
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12
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Pollett S, Melendrez MC, Maljkovic Berry I, Duchêne S, Salje H, Cummings DAT, Jarman RG. Understanding dengue virus evolution to support epidemic surveillance and counter-measure development. INFECTION GENETICS AND EVOLUTION 2018; 62:279-295. [PMID: 29704626 DOI: 10.1016/j.meegid.2018.04.032] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 04/20/2018] [Accepted: 04/24/2018] [Indexed: 11/30/2022]
Abstract
Dengue virus (DENV) causes a profound burden of morbidity and mortality, and its global burden is rising due to the co-circulation of four divergent DENV serotypes in the ecological context of globalization, travel, climate change, urbanization, and expansion of the geographic range of the Ae.aegypti and Ae.albopictus vectors. Understanding DENV evolution offers valuable opportunities to enhance surveillance and response to DENV epidemics via advances in RNA virus sequencing, bioinformatics, phylogenetic and other computational biology methods. Here we provide a scoping overview of the evolution and molecular epidemiology of DENV and the range of ways that evolutionary analyses can be applied as a public health tool against this arboviral pathogen.
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Affiliation(s)
- S Pollett
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Marie Bashir Institute, University of Sydney, NSW, Australia; Institute for Global Health Sciences, University of California at San Francisco, CA, USA.
| | - M C Melendrez
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - I Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - S Duchêne
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Australia
| | - H Salje
- Institut Pasteur, Paris, France; Johns Hopkins School of Public Health, Baltimore, MD, USA
| | - D A T Cummings
- Johns Hopkins School of Public Health, Baltimore, MD, USA; University of Florida, FL, USA
| | - R G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
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13
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Grear DA, Hall JS, Dusek RJ, Ip HS. Inferring epidemiologic dynamics from viral evolution: 2014-2015 Eurasian/North American highly pathogenic avian influenza viruses exceed transmission threshold, R0 = 1, in wild birds and poultry in North America. Evol Appl 2017; 11:547-557. [PMID: 29636805 PMCID: PMC5891053 DOI: 10.1111/eva.12576] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 11/02/2017] [Indexed: 12/18/2022] Open
Abstract
Highly pathogenic avian influenza virus (HPAIV) is a multihost pathogen with lineages that pose health risks for domestic birds, wild birds, and humans. One mechanism of intercontinental HPAIV spread is through wild bird reservoirs, and wild birds were the likely sources of a Eurasian (EA) lineage HPAIV into North America in 2014. The introduction resulted in several reassortment events with North American (NA) lineage low‐pathogenic avian influenza viruses and the reassortant EA/NA H5N2 went on to cause one of the largest HPAIV poultry outbreaks in North America. We evaluated three hypotheses about novel HPAIV introduced into wild and domestic bird hosts: (i) transmission of novel HPAIVs in wild birds was restricted by mechanisms associated with highly pathogenic phenotypes; (ii) the HPAIV poultry outbreak was not self‐sustaining and required viral input from wild birds; and (iii) reassortment of the EA H5N8 generated reassortant EA/NA AIVs with a fitness advantage over fully Eurasian lineages in North American wild birds. We used a time‐rooted phylodynamic model that explicitly incorporated viral population dynamics with evolutionary dynamics to estimate the basic reproductive number (R0) and viral migration among host types in domestic and wild birds, as well as between the EA H5N8 and EA/NA H5N2 in wild birds. We did not find evidence to support hypothesis (i) or (ii) as our estimates of the transmission parameters suggested that the HPAIV outbreak met or exceeded the threshold for persistence in wild birds (R0 > 1) and poultry (R0 ≈ 1) with minimal estimated transmission among host types. There was also no evidence to support hypothesis (iii) because R0 values were similar among EA H5N8 and EA/NA H5N2 in wild birds. Our results suggest that this novel HPAIV and reassortments did not encounter any transmission barriers sufficient to prevent persistence when introduced to wild or domestic birds.
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Affiliation(s)
- Daniel A Grear
- United States Geological Survey National Wildlife Health Center Madison WI USA
| | - Jeffrey S Hall
- United States Geological Survey National Wildlife Health Center Madison WI USA
| | - Robert J Dusek
- United States Geological Survey National Wildlife Health Center Madison WI USA
| | - Hon S Ip
- United States Geological Survey National Wildlife Health Center Madison WI USA
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14
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Novel approaches for Spatial and Molecular Surveillance of Porcine Reproductive and Respiratory Syndrome Virus (PRRSv) in the United States. Sci Rep 2017; 7:4343. [PMID: 28659596 PMCID: PMC5489505 DOI: 10.1038/s41598-017-04628-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 05/17/2017] [Indexed: 01/29/2023] Open
Abstract
The US swine industry has been impaired over the last 25 years by the far-reaching financial losses caused by the porcine reproductive and respiratory syndrome (PRRS). Here, we explored the relations between the spatial risk of PRRS outbreaks and its phylodynamic history in the U.S during 1998–2016 using ORF5 sequences collected from swine farms in the Midwest region. We used maximum entropy and Bayesian phylodynamic models to generate risk maps for PRRS outbreaks and reconstructed the evolutionary history of three selected phylogenetic clades (A, B and C). High-risk areas for PRRS were best-predicted by pig density and climate seasonality and included Minnesota, Iowa and South Dakota. Phylodynamic models demonstrated that the geographical spread of the three clades followed a heterogeneous spatial diffusion process. Furthermore, PRRS viruses were characterized by typical seasonality in their population size. However, endemic strains were characterized by a substantially slower population growth and evolutionary rates, as well as smaller spatial dispersal rates when compared to emerging strains. We demonstrated the prospects of combining inferences derived from two unique analytical methods to inform decisions related to risk-based interventions of an important pathogen affecting one of the largest food animal industries in the world.
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15
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Rife BD, Mavian C, Chen X, Ciccozzi M, Salemi M, Min J, Prosperi MCF. Phylodynamic applications in 21 st century global infectious disease research. Glob Health Res Policy 2017; 2:13. [PMID: 29202081 PMCID: PMC5683535 DOI: 10.1186/s41256-017-0034-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 03/31/2017] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Phylodynamics, the study of the interaction between epidemiological and pathogen evolutionary processes within and among populations, was originally defined in the context of rapidly evolving viruses and used to characterize transmission dynamics. The concept of phylodynamics has evolved since the early 21st century, extending its reach to slower-evolving pathogens, including bacteria and fungi, and to the identification of influential factors in disease spread and pathogen population dynamics. RESULTS The phylodynamic approach has now become a fundamental building block for the development of comparative phylogenetic tools capable of incorporating epidemiological surveillance data with molecular sequences into a single statistical framework. These innovative tools have greatly enhanced scientific investigations of the temporal and geographical origins, evolutionary history, and ecological risk factors associated with the growth and spread of viruses such as human immunodeficiency virus (HIV), Zika, and dengue and bacteria such as Methicillin-resistant Staphylococcus aureus. CONCLUSIONS Capitalizing on an extensive review of the literature, we discuss the evolution of the field of infectious disease epidemiology and recent accomplishments, highlighting the advancements in phylodynamics, as well as the challenges and limitations currently facing researchers studying emerging pathogen epidemics across the globe.
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Affiliation(s)
- Brittany D Rife
- Emerging Pathogens Institute and Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL USA
| | - Carla Mavian
- Emerging Pathogens Institute and Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL USA
| | - Xinguang Chen
- Department of Epidemiology, University of Florida, Gainesville, FL USA
| | - Massimo Ciccozzi
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di Sanità, Rome, Italy
- Unit of Clinical Pathology and Microbiology, University Campus Biomedico of Rome, Rome, Italy
| | - Marco Salemi
- Emerging Pathogens Institute and Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL USA
| | - Jae Min
- Department of Epidemiology, University of Florida, Gainesville, FL USA
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16
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Gandon S, Day T, Metcalf CJE, Grenfell BT. Forecasting Epidemiological and Evolutionary Dynamics of Infectious Diseases. Trends Ecol Evol 2016; 31:776-788. [PMID: 27567404 DOI: 10.1016/j.tree.2016.07.010] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 07/20/2016] [Accepted: 07/21/2016] [Indexed: 10/21/2022]
Abstract
Mathematical models have been powerful tools in developing mechanistic understanding of infectious diseases. Furthermore, they have allowed detailed forecasting of epidemiological phenomena such as outbreak size, which is of considerable public-health relevance. The short generation time of pathogens and the strong selection they are subjected to (by host immunity, vaccines, chemotherapy, etc.) mean that evolution is also a key driver of infectious disease dynamics. Accurate forecasting of pathogen dynamics therefore calls for the integration of epidemiological and evolutionary processes, yet this integration remains relatively rare. We review previous attempts to model and predict infectious disease dynamics with or without evolution and discuss major challenges facing the development of the emerging science of epidemic forecasting.
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Affiliation(s)
- Sylvain Gandon
- CEFE UMR 5175, CNRS-Université de Montpellier-Université Paul-Valéry Montpellier-EPHE, 1919 route de Mende, 34293 Montpellier cedex 5, France.
| | - Troy Day
- Department of Biology, Queen's University, Kingston, Canada
| | - C Jessica E Metcalf
- Department of Ecology and Evolutionary Biology and Woodrow Wilson School of Public and International Affairs, Princeton University, Princeton, NJ, USA
| | - Bryan T Grenfell
- Department of Ecology and Evolutionary Biology and Woodrow Wilson School of Public and International Affairs, Princeton University, Princeton, NJ, USA
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17
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Restif O, Graham AL. Within-host dynamics of infection: from ecological insights to evolutionary predictions. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2014.0304. [PMID: 26150670 PMCID: PMC4528502 DOI: 10.1098/rstb.2014.0304] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Affiliation(s)
- Olivier Restif
- Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Andrea L Graham
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
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18
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Abstract
In many host populations, one of the most striking differences among hosts is their age. While parasite prevalence differences in relation to host age are well known, little is known on how host age impacts ecological and evolutionary dynamics of diseases. Using two clones of the water flea Daphnia magna and two clones of its bacterial parasite Pasteuria ramosa, we examined how host age at exposure influences within-host parasite competition and virulence. We found that multiply-exposed hosts were more susceptible to infection and suffered higher mortality than singly-exposed hosts. Hosts oldest at exposure were least often infected and vice versa. Furthermore, we found that in young multiply-exposed hosts competition was weak, allowing coexistence and transmission of both parasite clones, whereas in older multiply-exposed hosts competitive exclusion was observed. Thus, age-dependent parasite exposure and host demography (age structure) could together play an important role in mediating parasite evolution. At the individual level, our results demonstrate a previously unnoticed interaction of the host's immune system with host age, suggesting that the specificity of immune function changes as hosts mature. Therefore, evolutionary models of parasite virulence might benefit from incorporating age-dependent epidemiological parameters.
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Affiliation(s)
- Rony Izhar
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Jarkko Routtu
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Frida Ben-Ami
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
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19
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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.
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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
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20
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Alvarez J, Valdes-Donoso P, Tousignant S, Alkhamis M, Morrison R, Perez A. Novel analytic tools for the study of porcine reproductive and respiratory syndrome virus (PRRSv) in endemic settings: lessons learned in the U.S. Porcine Health Manag 2016; 2:3. [PMID: 28405429 PMCID: PMC5382381 DOI: 10.1186/s40813-016-0019-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 12/15/2015] [Indexed: 12/11/2022] Open
Abstract
Since its emergence in the late 1980's, the porcine reproductive and respiratory syndrome virus (PRRSv) has posed a significant challenge to the pig industry worldwide. Since then, a number of epidemiological tools have been created to support control and eventual elimination of the disease at the farm and regional levels. Still, many aspects of the disease dynamics are yet-to-be elucidated, such as what are the economically optimal control strategies at the farm and regional level, what is the role that the voluntary regional control programs may play, how to optimize the use of molecular tools for surveillance and monitoring in infected settings, what is the full impact of the disease in a farm, or what is the relative contribution of alternative transmission routes on the occurrence of PRRSv outbreaks. Here, we summarize a number of projects demonstrating the use of novel analytical tools in the assessment of PRRSv epidemiology in the United States. Results presented demonstrate how quantitative analysis of routinely collected data may help in understanding regional epidemiology of PRRSv and to quantify its full impact, and how the integration of phylodynamic methods as a standard tool for molecular surveillance of PRRSv might help to inform control and prevention strategies in high-risk epidemiological situations. Ultimately, these tools will help to support PRRSv control at farm and regional levels in endemically infected settings.
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Affiliation(s)
- Julio Alvarez
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN USA
| | - Pablo Valdes-Donoso
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN USA
- Department of Agriculture and Resource Economics, University of California Davis, Davis, CA USA
| | - Steven Tousignant
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN USA
| | - Mohammad Alkhamis
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN USA
- Environmental and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait City, Kuwait
| | - Robert Morrison
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN USA
| | - Andres Perez
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN USA
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21
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Hayman DTS. Biannual birth pulses allow filoviruses to persist in bat populations. Proc Biol Sci 2015; 282:20142591. [PMID: 25673678 DOI: 10.1098/rspb.2014.2591] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Filoviruses Ebolavirus (EBOV) and Marburgvirus (MARV) cause haemorrhagic fevers with high mortality rates, posing significant threats to public health. To understand transmission into human populations, filovirus dynamics within reservoir host populations must be understood. Studies have directly linked filoviruses to bats, but the mechanisms allowing viral persistence within bat populations are poorly understood. Theory suggests seasonal birthing may decrease the probability of pathogen persistence within populations, but data suggest MARV may persist within colonies of seasonally breeding Egyptian fruit bats, Rousettus aegyptiacus. I synthesize available filovirus and bat data in a stochastic compartmental model to explore fundamental questions relating to filovirus ecology: can filoviruses persist within isolated bat colonies; do critical community sizes exist; and how do host-pathogen relationships affect spillover transmission potential? Synchronous annual breeding and shorter incubation periods did not allow filovirus persistence, whereas bi-annual breeding and longer incubation periods, such as reported for Egyptian fruit bats and EBOV in experimental studies, allowed persistence in colony sizes often found in nature. Serological data support the findings, with bats from species with two annual birth pulses more likely to be seropositive (odds ratio (OR) 4.4, 95% confidence interval (CI) 2.5-8.7) than those with one, suggesting that biannual birthing is necessary for filovirus persistence.
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Affiliation(s)
- David T S Hayman
- Molecular Epidemiology and Public Health Laboratory, Hopkirk Research Institute, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
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22
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Muellner P, Stärk KDC, Dufour S, Zadoks RN. ‘Next-Generation’ Surveillance: An Epidemiologists’ Perspective on the Use of Molecular Information in Food Safety and Animal Health Decision-Making. Zoonoses Public Health 2015; 63:351-7. [DOI: 10.1111/zph.12230] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Indexed: 01/01/2023]
Affiliation(s)
- P. Muellner
- Epi-interactive; Miramar Wellington New Zealand
- Epi-interactive; Eppingen Germany
| | - K. D. C. Stärk
- Royal Veterinary College; North Mymms UK
- SAFOSO AG; Bern Switzerland
| | - S. Dufour
- Faculté de médecine vétérinaire; Université de Montréal; St-Hyacinthe QC Canada
- Canadian Bovine Mastitis Research Network; St-Hyacinthe QC Canada
| | - R. N. Zadoks
- Institute for Biodiversity, Animal Health and Comparative Medicine; College of Medical, Veterinary and Life Sciences; University of Glasgow; Glasgow UK
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Alkhamis MA, Moore BR, Perez AM. Phylodynamics of H5N1 Highly Pathogenic Avian Influenza in Europe, 2005-2010: Potential for Molecular Surveillance of New Outbreaks. Viruses 2015; 7:3310-28. [PMID: 26110587 PMCID: PMC4488740 DOI: 10.3390/v7062773] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 06/02/2015] [Accepted: 06/16/2015] [Indexed: 11/16/2022] Open
Abstract
Previous Bayesian phylogeographic studies of H5N1 highly pathogenic avian influenza viruses (HPAIVs) explored the origin and spread of the epidemic from China into Russia, indicating that HPAIV circulated in Russia prior to its detection there in 2005. In this study, we extend this research to explore the evolution and spread of HPAIV within Europe during the 2005-2010 epidemic, using all available sequences of the hemagglutinin (HA) and neuraminidase (NA) gene regions that were collected in Europe and Russia during the outbreak. We use discrete-trait phylodynamic models within a Bayesian statistical framework to explore the evolution of HPAIV. Our results indicate that the genetic diversity and effective population size of HPAIV peaked between mid-2005 and early 2006, followed by drastic decline in 2007, which coincides with the end of the epidemic in Europe. Our results also suggest that domestic birds were the most likely source of the spread of the virus from Russia into Europe. Additionally, estimates of viral dispersal routes indicate that Russia, Romania, and Germany were key epicenters of these outbreaks. Our study quantifies the dynamics of a major European HPAIV pandemic and substantiates the ability of phylodynamic models to improve molecular surveillance of novel AIVs.
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Affiliation(s)
- Mohammad A Alkhamis
- Environmental and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait City, Safat 13109, Kuwait.
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MA 55108, USA.
| | - Brian R Moore
- Department of Evolution and Ecology, Center for Population Biology, University of California Davis, Davis, CA 95616, USA.
| | - Andres M Perez
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MA 55108, USA.
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Deciphering the origins and tracking the evolution of cholera epidemics with whole-genome-based molecular epidemiology. mBio 2013; 4:e00670-13. [PMID: 24023387 PMCID: PMC3774194 DOI: 10.1128/mbio.00670-13] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The devastating Haitian cholera outbreak that began in October 2010 is the first known cholera epidemic in this island nation. Epidemiological and genomic data have provided strong evidence that United Nations security forces from Nepal introduced toxigenic Vibrio cholerae O1, the cause of epidemic cholera, to Haiti shortly before the outbreak arose. However, some have contended that indigenous V. cholerae contributed to the outbreak. In a recent paper (mBio4:e00398-13, 2013), L. S. Katz et al. explored the nature and rate of changes in this ancient pathogen’s genome during an outbreak, based on whole-genome sequencing of 23 Haitian V. cholerae clinical isolates obtained over a 20-month period. Notably, they detected point mutations, deletions, and inversions but found no insertion of horizontally transmitted DNA, arguing strongly against the idea that autochthonous V. cholerae donated DNA to the outbreak strain. Furthermore, they found that Haitian epidemic V. cholerae isolates were virtually untransformable. Comparative genomic analyses revealed that the Haitian isolates were nearly identical to isolates from Nepal and that the Nepalese-Haitian isolates were distinguishable from isolates circulating elsewhere in the world. Reconstruction of the phylogeny of the Haitian isolates was consistent with a single introduction of V. cholerae to Haiti sometime between late July and late October 2010, dates remarkably concordant with epidemiological observations. In aggregate, this paper provides additional compelling evidence that the V. cholerae strain responsible for the Haitian cholera epidemic came from Nepal and illustrates the power of whole-genome-based analyses for epidemiology, pathogen evolution, and forensics.
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González-Candelas F, Bracho MA, Wróbel B, Moya A. Molecular evolution in court: analysis of a large hepatitis C virus outbreak from an evolving source. BMC Biol 2013; 11:76. [PMID: 23870105 PMCID: PMC3717074 DOI: 10.1186/1741-7007-11-76] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 05/24/2013] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Molecular phylogenetic analyses are used increasingly in the epidemiological investigation of outbreaks and transmission cases involving rapidly evolving RNA viruses. Here, we present the results of such an analysis that contributed to the conviction of an anesthetist as being responsible for the infection of 275 of his patients with hepatitis C virus. RESULTS We obtained sequences of the NS5B and E1-E2 regions in the viral genome for 322 patients suspected to have been infected by the doctor, and for 44 local, unrelated controls. The analysis of 4,184 cloned sequences of the E1-E2 region allowed us to exclude 47 patients from the outbreak. A subset of patients had known dates of infection. We used these data to calibrate a relaxed molecular clock and to determine a rough estimate of the time of infection for each patient. A similar analysis led to an estimate for the time of infection of the source. The date turned out to be 10 years before the detection of the outbreak. The number of patients infected was small at first, but it increased substantially in the months before the detection of the outbreak. CONCLUSIONS We have developed a procedure to integrate molecular phylogenetic reconstructions of rapidly evolving viral populations into a forensic setting adequate for molecular epidemiological analysis of outbreaks and transmission events. We applied this procedure to a large outbreak of hepatitis C virus caused by a single source and the results obtained played a key role in the trial that led to the conviction of the suspected source.
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Affiliation(s)
- Fernando González-Candelas
- Joint Research Unit ‘Genómica y Salud’ CSISP (FISABIO), Instituto Cavanilles/Universidad de Valencia, c/ Catedrático José Beltrán, 2 46980-Paterna, Valencia, Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Valencia, Spain
| | - María Alma Bracho
- Joint Research Unit ‘Genómica y Salud’ CSISP (FISABIO), Instituto Cavanilles/Universidad de Valencia, c/ Catedrático José Beltrán, 2 46980-Paterna, Valencia, Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Valencia, Spain
| | - Borys Wróbel
- Joint Research Unit ‘Genómica y Salud’ CSISP (FISABIO), Instituto Cavanilles/Universidad de Valencia, c/ Catedrático José Beltrán, 2 46980-Paterna, Valencia, Spain
- Department of Genetics and Marine Biotechnology, Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland
- Laboratory of Bioinformatics, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614 Poznań, Poland
| | - Andrés Moya
- Joint Research Unit ‘Genómica y Salud’ CSISP (FISABIO), Instituto Cavanilles/Universidad de Valencia, c/ Catedrático José Beltrán, 2 46980-Paterna, Valencia, Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Valencia, Spain
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