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Penteado AB, de Oliveira Ribeiro G, Lima Araújo EL, Kato RB, de Melo Freire CC, de Araújo JMG, da Luz Wallau G, Salvato RS, de Jesus R, Bosco GG, Franz HF, da Silva PEA, de Souza Leal E, Goulart Trossini GH, de Lima Neto DF. Binding Evolution of the Dengue Virus Envelope Against DC-SIGN: A Combined Approach of Phylogenetics and Molecular Dynamics Analyses Over 30 Years of Dengue Virus in Brazil. J Mol Biol 2024; 436:168577. [PMID: 38642883 DOI: 10.1016/j.jmb.2024.168577] [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: 01/09/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 04/22/2024]
Abstract
The Red Queen Hypothesis (RQH), derived from Lewis Carroll's "Through the Looking-Glass", postulates that organisms must continually adapt in response to each other to maintain relative fitness. Within the context of host-pathogen interactions, the RQH implies an evolutionary arms race, wherein viruses evolve to exploit hosts and hosts evolve to resist viral invasion. This study delves into the dynamics of the RQH in the context of virus-cell interactions, specifically focusing on virus receptors and cell receptors. We observed multiple virus-host systems and noted patterns of co-evolution. As viruses evolved receptor-binding proteins to effectively engage with cell receptors, cells countered by altering their receptor genes. This ongoing mutual adaptation cycle has influenced the molecular intricacies of receptor-ligand interactions. Our data supports the RQH as a driving force behind the diversification and specialization of both viral and host cell receptors. Understanding this co-evolutionary dance offers insights into the unpredictability of emerging viral diseases and potential therapeutic interventions. Future research is crucial to dissect the nuanced molecular changes and the broader ecological consequences of this ever-evolving battle. Here, we combine phylogenetic inferences, structural modeling, and molecular dynamics analyses to describe the epidemiological characteristics of major Brazilian DENV strains that circulated from 1990 to 2022 from a combined perspective, thus providing us with a more detailed picture on the dynamics of such interactions over time.
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MESH Headings
- Dengue Virus/genetics
- Dengue Virus/metabolism
- Receptors, Cell Surface/metabolism
- Receptors, Cell Surface/genetics
- Receptors, Cell Surface/chemistry
- Phylogeny
- Molecular Dynamics Simulation
- Humans
- Cell Adhesion Molecules/metabolism
- Cell Adhesion Molecules/genetics
- Cell Adhesion Molecules/chemistry
- Brazil
- Lectins, C-Type/metabolism
- Lectins, C-Type/genetics
- Lectins, C-Type/chemistry
- Evolution, Molecular
- Dengue/virology
- Host-Pathogen Interactions/genetics
- Protein Binding
- Viral Envelope/metabolism
- Receptors, Virus/metabolism
- Receptors, Virus/chemistry
- Receptors, Virus/genetics
- Viral Envelope Proteins/genetics
- Viral Envelope Proteins/metabolism
- Viral Envelope Proteins/chemistry
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Affiliation(s)
- André Berndt Penteado
- School of Pharmaceutical Sciences, University of São Paulo, Department of Pharmacy, Av. Prof. Lineu Prestes, 580, Cidade Universitária, São Paulo, SP 05508-000, Brazil
| | - Geovani de Oliveira Ribeiro
- General-Coordination of Public Health Laboratories, Department of Strategic Coordination and Surveillance in Health and the Environment, Ministry of Health, Brasilia, Brazil; Department of Cellular Biology, University of Brasilia (UNB), Brasilia, Distrito Federal, Brazil
| | - Emerson Luiz Lima Araújo
- General Coordination of Attention to Communicable Diseases in Primary Care of the Department of Comprehensive Care Management of the Secretariat of Primary Health Care of the Ministry of Health (CDTAP/DGCI/SAPS-MS), Brazil
| | - Rodrigo Bentes Kato
- General-Coordination of Public Health Laboratories, Department of Strategic Coordination and Surveillance in Health and the Environment, Ministry of Health, Brasilia, Brazil
| | - Caio Cesar de Melo Freire
- Department of Genetics and Evolution, Centre of Biological and Health Sciences, Federal University of Sao Carlos, PO Box 676, Washington Luis Road, km 235, São Carlos, SP 13565-905, Brazil
| | - Joselio Maria Galvão de Araújo
- Federal University of Rio Grande do Norte, Biosciences Center, Department of Microbiology and Parasitology, Campus Universitário, S/N Lagoa Nova 59078900, Natal, RN, Brazil
| | - Gabriel da Luz Wallau
- Department of Entomology and Bioinformatics Center of the Aggeu Magalhães Institute - FIOCRUZ - IAM, Brazil
| | - Richard Steiner Salvato
- Center for Scientific and Technological Development, State Center for Health Surveillance of Rio Grande do Sul, State Department of Health of Rio Grande do Sul, Porto Alegre, Brazil
| | - Ronaldo de Jesus
- General-Coordination of Public Health Laboratories, Department of Strategic Coordination and Surveillance in Health and the Environment, Ministry of Health, Brasilia, Brazil
| | - Geraldine Goés Bosco
- University of São Paulo, Faculty of Philosophy Sciences and Letters of Ribeirão Preto. Av. Bandeirantes, 3900 Ribeirão Preto, SP, Brazil
| | - Helena Ferreira Franz
- General-Coordination of Public Health Laboratories, Department of Strategic Coordination and Surveillance in Health and the Environment, Ministry of Health, Brasilia, Brazil
| | - Pedro Eduardo Almeida da Silva
- General-Coordination of Public Health Laboratories, Department of Strategic Coordination and Surveillance in Health and the Environment, Ministry of Health, Brasilia, Brazil
| | - Elcio de Souza Leal
- Federal University of Pará, Faculty of Biotechnology, Institute of Biological Sciences, Rua Augusto Corrêa, Guamá, 04039-032 Belem, PA, Brazil
| | - Gustavo Henrique Goulart Trossini
- School of Pharmaceutical Sciences, University of São Paulo, Department of Pharmacy, Av. Prof. Lineu Prestes, 580, Cidade Universitária, São Paulo, SP 05508-000, Brazil
| | - Daniel Ferreira de Lima Neto
- School of Pharmaceutical Sciences, University of São Paulo, Department of Pharmacy, Av. Prof. Lineu Prestes, 580, Cidade Universitária, São Paulo, SP 05508-000, Brazil.
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2
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Chem YK, Yenamandra SP, Chong CK, Mudin RN, Wan MK, Tajudin N, Abu Bakar RS, Yamin MA, Yahya R, Chang CC, Koo C, Ng LC, Hapuarachchi HC. Molecular epidemiology of dengue in Malaysia: 2015-2021. Front Genet 2024; 15:1368843. [PMID: 38863443 PMCID: PMC11165242 DOI: 10.3389/fgene.2024.1368843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 04/16/2024] [Indexed: 06/13/2024] Open
Abstract
Dengue has been one of the major public health problems in Malaysia for decades. Over 600,000 dengue cases and 1,200 associated fatalities have been reported in Malaysia from 2015 to 2021, which was 100% increase from the cumulative total of dengue cases reported during the preceding 07-year period from 2008 to 2014. However, studies that describe the molecular epidemiology of dengue in Malaysia in recent years are limited. In the present study, we describe the genetic composition and dispersal patterns of Dengue virus (DENV) by using 4,004 complete envelope gene sequences of all four serotypes (DENV-1 = 1,567, DENV-2 = 1,417, DENV-3 = 762 and DENV-4 = 258) collected across Malaysia from 2015 to 2021. The findings revealed that DENV populations in Malaysia were highly diverse, and the overall heterogeneity was maintained through repetitive turnover of genotypes. Phylogeography analyses suggested that DENV dispersal occurred through an extensive network, mainly among countries in South and East Asia and Malaysian states, as well as among different states, especially within Peninsular Malaysia. The results further suggested Selangor and Johor as major hubs of DENV emergence and spread in Malaysia.
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Affiliation(s)
- Yu Kie Chem
- National Public Health Laboratory, Ministry of Health, Sungai Buloh, Malaysia
| | | | - Chee Keong Chong
- Disease Control Division, Ministry of Health, Putrajaya, Malaysia
| | - Rose Nani Mudin
- Disease Control Division, Ministry of Health, Putrajaya, Malaysia
| | - Ming Keong Wan
- Disease Control Division, Ministry of Health, Putrajaya, Malaysia
| | - Norazimah Tajudin
- National Public Health Laboratory, Ministry of Health, Sungai Buloh, Malaysia
| | | | - Mohd Asri Yamin
- National Public Health Laboratory, Ministry of Health, Sungai Buloh, Malaysia
| | - Rokiah Yahya
- National Public Health Laboratory, Ministry of Health, Sungai Buloh, Malaysia
| | - Chia-Chen Chang
- Environmental Health Institute, National Environment Agency, Singapore, Singapore
| | - Carmen Koo
- Environmental Health Institute, National Environment Agency, Singapore, Singapore
| | - Lee Ching Ng
- Environmental Health Institute, National Environment Agency, Singapore, Singapore
- School of Biological Sciences, Nangyang Technological University, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
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3
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da Costa Castilho M, de Filippis AMB, Machado LC, de Lima Calvanti TYV, Lima MC, Fonseca V, Giovanetti M, Docena C, Neto AM, Bôtto-Menezes CHA, Kara EO, de La Barrera R, Modjarrad K, Giozza SP, Pereira GF, Alcantara LCJ, Broutet NJN, Calvet GA, Wallau GL, Franca RFO. Evidence of Zika Virus Reinfection by Genome Diversity and Antibody Response Analysis, Brazil. Emerg Infect Dis 2024; 30:310-320. [PMID: 38270216 PMCID: PMC10826783 DOI: 10.3201/eid3002.230122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024] Open
Abstract
We generated 238 Zika virus (ZIKV) genomes from 135 persons in Brazil who had samples collected over 1 year to evaluate virus persistence. Phylogenetic inference clustered the genomes together with previously reported ZIKV strains from northern Brazil, showing that ZIKV has been remained relatively stable over time. Temporal phylogenetic analysis revealed limited within-host diversity among most ZIKV-persistent infected associated samples. However, we detected unusual virus temporal diversity from >5 persons, uncovering the existence of divergent genomes within the same patient. All those patients showed an increase in neutralizing antibody levels, followed by a decline at the convalescent phase of ZIKV infection. Of interest, in 3 of those patients, titers of neutralizing antibodies increased again after 6 months of ZIKV infection, concomitantly with real-time reverse transcription PCR re-positivity, supporting ZIKV reinfection events. Altogether, our findings provide evidence for the existence of ZIKV reinfection events.
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Sy AK, Koo C, Privaldos KJR, Quinones MAT, Igoy MAU, Villanueva SYAM, Hibberd ML, Ng LC, Hapuarachchi HC. Genetic Diversity and Dispersal of DENGUE Virus among Three Main Island Groups of the Philippines during 2015-2017. Viruses 2023; 15:v15051079. [PMID: 37243165 DOI: 10.3390/v15051079] [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: 03/29/2023] [Revised: 04/22/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
Dengue has been one of the major public health concerns in the Philippines for more than a century. The annual dengue case burden has been increasing in recent years, exceeding 200,000 in 2015 and 2019. However, there is limited information on the molecular epidemiology of dengue in the Philippines. We, therefore, conducted a study to understand the genetic composition and dispersal of DENV in the Philippines from 2015 to 2017 under UNITEDengue. Our analyses included 377 envelope (E) gene sequences of all 4 serotypes obtained from infections in 3 main island groups (Luzon, Visayas, and Mindanao) of the Philippines. The findings showed that the overall diversity of DENV was generally low. DENV-1 was relatively more diverse than the other serotypes. Virus dispersal was evident among the three main island groups, but each island group demonstrated a distinct genotype composition. These observations suggested that the intensity of virus dispersal was not substantive enough to maintain a uniform heterogeneity among island groups so that each island group behaved as an independent epidemiological unit. The analyses suggested Luzon as one of the major sources of DENV emergence and CAR, Calabarzon, and CARAGA as important hubs of virus dispersal in the Philippines. Our findings highlight the importance of virus surveillance and molecular epidemiological analyses to gain deep insights into virus diversity, lineage dominance, and dispersal patterns that could assist in understanding the epidemiology and transmission risk of dengue in endemic regions.
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Affiliation(s)
- Ava Kristy Sy
- National Reference Laboratory for Dengue and Other Arbovirus, Virology Department, Research Institute for Tropical Medicine, Filinvest Corporate City Compound, Alabang, Muntinlupa City 1781, Philippines
| | - Carmen Koo
- Environmental Health Institute, National Environment Agency, 11, Biopolis Way, #06-05-08, Singapore 138667, Singapore
| | - Kristine J R Privaldos
- National Reference Laboratory for Dengue and Other Arbovirus, Virology Department, Research Institute for Tropical Medicine, Filinvest Corporate City Compound, Alabang, Muntinlupa City 1781, Philippines
| | - Mary Ann T Quinones
- National Reference Laboratory for Dengue and Other Arbovirus, Virology Department, Research Institute for Tropical Medicine, Filinvest Corporate City Compound, Alabang, Muntinlupa City 1781, Philippines
| | - Mary A U Igoy
- National Reference Laboratory for Dengue and Other Arbovirus, Virology Department, Research Institute for Tropical Medicine, Filinvest Corporate City Compound, Alabang, Muntinlupa City 1781, Philippines
| | - Sharon Y A M Villanueva
- Department of Medical Microbiology, College of Public Health, University of the Philippines Manila, 625, Pedro Gil Street, Ermita, Manila 1000, Philippines
| | - Martin L Hibberd
- Department of Infection Biology, Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, UK
- Philippine Genome Centre, Dilliman Campus, University of the Philippines, Dilman, Ma. Regidor, U.P. Campus, Quezon City 1101, Philippines
- National Institutes of Health, University of the Philippines Manila, 623, Pedro Gil Street, Ermita, Manila 1000, Philippines
- Genome Institute of Singapore, 60, Biopolis Street, Genome, #02-01, Singapore 138672, Singapore
| | - Lee Ching Ng
- Environmental Health Institute, National Environment Agency, 11, Biopolis Way, #06-05-08, Singapore 138667, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore 639798, Singapore
| | - Hapuarachchige C Hapuarachchi
- Environmental Health Institute, National Environment Agency, 11, Biopolis Way, #06-05-08, Singapore 138667, Singapore
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5
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Nonyong P, Ekalaksananan T, Phanthanawiboon S, Overgaard HJ, Alexander N, Thaewnongiew K, Sawaswong V, Nimsamer P, Payungporn S, Phadungsombat J, Nakayama EE, Shioda T, Pientong C. Intrahost Genetic Diversity of Dengue Virus in Human Hosts and Mosquito Vectors under Natural Conditions Which Impact Replicative Fitness In Vitro. Viruses 2023; 15:982. [PMID: 37112962 PMCID: PMC10143933 DOI: 10.3390/v15040982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 04/08/2023] [Accepted: 04/16/2023] [Indexed: 04/29/2023] Open
Abstract
Dengue virus (DENV) is an arbovirus whose transmission cycle involves disparate hosts: humans and mosquitoes. The error-prone nature of viral RNA replication drives the high mutation rates, and the consequently high genetic diversity affects viral fitness over this transmission cycle. A few studies have been performed to investigate the intrahost genetic diversity between hosts, although their mosquito infections were performed artificially in the laboratory setting. Here, we performed whole-genome deep sequencing of DENV-1 (n = 11) and DENV-4 (n = 13) derived from clinical samples and field-caught mosquitoes from the houses of naturally infected patients, in order to analyze the intrahost genetic diversity of DENV between host types. Prominent differences in DENV intrahost diversity were observed in the viral population structure between DENV-1 and DENV-4, which appear to be associated with differing selection pressures. Interestingly, three single amino acid substitutions in the NS2A (K81R), NS3 (K107R), and NS5 (I563V) proteins in DENV-4 appear to be specifically acquired during infection in Ae. aegypti mosquitoes. Our in vitro study shows that the NS2A (K81R) mutant replicates similarly to the wild-type infectious clone-derived virus, while the NS3 (K107R), and NS5 (I563V) mutants have prolonged replication kinetics in the early phase in both Vero and C6/36 cells. These findings suggest that DENV is subjected to selection pressure in both mosquito and human hosts. The NS3 and NS5 genes may be specific targets of diversifying selection that play essential roles in early processing, RNA replication, and infectious particle production, and they are potentially adaptive at the population level during host switching.
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Affiliation(s)
- Patcharaporn Nonyong
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand; (P.N.); (T.E.); (S.P.)
| | - Tipaya Ekalaksananan
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand; (P.N.); (T.E.); (S.P.)
- HPV & EBV and Carcinogenesis Research Group, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Supranee Phanthanawiboon
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand; (P.N.); (T.E.); (S.P.)
| | - Hans J. Overgaard
- Faculty of Science and Technology, Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway;
| | - Neal Alexander
- MRC International Statistics and Epidemiology Group, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK;
| | - Kesorn Thaewnongiew
- Department of Disease Control, Office of Disease Prevention and Control, Region 7 Khon Kaen, Ministry of Public Health, Khon Kaen 40000, Thailand;
| | - Vorthon Sawaswong
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand;
- Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; (P.N.); (S.P.)
| | - Pattaraporn Nimsamer
- Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; (P.N.); (S.P.)
| | - Sunchai Payungporn
- Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; (P.N.); (S.P.)
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Juthamas Phadungsombat
- Mahidol-Osaka Center for Infectious Diseases (MOCID), Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (J.P.); (E.E.N.)
| | - Emi E. Nakayama
- Mahidol-Osaka Center for Infectious Diseases (MOCID), Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (J.P.); (E.E.N.)
- Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Tatsuo Shioda
- Mahidol-Osaka Center for Infectious Diseases (MOCID), Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (J.P.); (E.E.N.)
- Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Chamsai Pientong
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand; (P.N.); (T.E.); (S.P.)
- HPV & EBV and Carcinogenesis Research Group, Khon Kaen University, Khon Kaen 40002, Thailand
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6
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Jagtap S, Pattabiraman C, Sankaradoss A, Krishna S, Roy R. Evolutionary dynamics of dengue virus in India. PLoS Pathog 2023; 19:e1010862. [PMID: 37011104 PMCID: PMC10101646 DOI: 10.1371/journal.ppat.1010862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 04/13/2023] [Accepted: 03/17/2023] [Indexed: 04/05/2023] Open
Abstract
More than a hundred thousand dengue cases are diagnosed in India annually, and about half of the country's population carries dengue virus-specific antibodies. Dengue propagates and adapts to the selection pressures imposed by a multitude of factors that can lead to the emergence of new variants. Yet, there has been no systematic analysis of the evolution of the dengue virus in the country. Here, we present a comprehensive analysis of all DENV gene sequences collected between 1956 and 2018 from India. We examine the spatio-temporal dynamics of India-specific genotypes, their evolutionary relationship with global and local dengue virus strains, interserotype dynamics and their divergence from the vaccine strains. Our analysis highlights the co-circulation of all DENV serotypes in India with cyclical outbreaks every 3-4 years. Since 2000, genotype III of DENV-1, cosmopolitan genotype of DENV-2, genotype III of DENV-3 and genotype I of DENV-4 have been dominating across the country. Substitution rates are comparable across the serotypes, suggesting a lack of serotype-specific evolutionary divergence. Yet, the envelope (E) protein displays strong signatures of evolution under immune selection. Apart from drifting away from its ancestors and other contemporary serotypes in general, we find evidence for recurring interserotype drift towards each other, suggesting selection via cross-reactive antibody-dependent enhancement. We identify the emergence of the highly divergent DENV-4-Id lineage in South India, which has acquired half of all E gene mutations in the antigenic sites. Moreover, the DENV-4-Id is drifting towards DENV-1 and DENV-3 clades, suggesting the role of cross-reactive antibodies in its evolution. Due to the regional restriction of the Indian genotypes and immunity-driven virus evolution in the country, ~50% of all E gene differences with the current vaccines are focused on the antigenic sites. Our study shows how the dengue virus evolution in India is being shaped in complex ways.
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Affiliation(s)
- Suraj Jagtap
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, Karnataka, India
| | | | - Arun Sankaradoss
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, Karnataka, India
| | - Sudhir Krishna
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, Karnataka, India
- School of Interdisciplinary Life Sciences, Indian Institute of Technology Goa, Ponda, India
| | - Rahul Roy
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, Karnataka, India
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bengaluru, Karnataka, India
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7
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Terbot JW, Johri P, Liphardt SW, Soni V, Pfeifer SP, Cooper BS, Good JM, Jensen JD. Developing an appropriate evolutionary baseline model for the study of SARS-CoV-2 patient samples. PLoS Pathog 2023; 19:e1011265. [PMID: 37018331 PMCID: PMC10075409 DOI: 10.1371/journal.ppat.1011265] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023] Open
Abstract
Over the past 3 years, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has spread through human populations in several waves, resulting in a global health crisis. In response, genomic surveillance efforts have proliferated in the hopes of tracking and anticipating the evolution of this virus, resulting in millions of patient isolates now being available in public databases. Yet, while there is a tremendous focus on identifying newly emerging adaptive viral variants, this quantification is far from trivial. Specifically, multiple co-occurring and interacting evolutionary processes are constantly in operation and must be jointly considered and modeled in order to perform accurate inference. We here outline critical individual components of such an evolutionary baseline model-mutation rates, recombination rates, the distribution of fitness effects, infection dynamics, and compartmentalization-and describe the current state of knowledge pertaining to the related parameters of each in SARS-CoV-2. We close with a series of recommendations for future clinical sampling, model construction, and statistical analysis.
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Affiliation(s)
- John W Terbot
- University of Montana, Division of Biological Sciences, Missoula, Montana, United States of America
- Arizona State University, School of Life Sciences, Center for Evolution & Medicine, Tempe, Arizona, United States of America
| | - Parul Johri
- Arizona State University, School of Life Sciences, Center for Evolution & Medicine, Tempe, Arizona, United States of America
| | - Schuyler W Liphardt
- University of Montana, Division of Biological Sciences, Missoula, Montana, United States of America
| | - Vivak Soni
- Arizona State University, School of Life Sciences, Center for Evolution & Medicine, Tempe, Arizona, United States of America
| | - Susanne P Pfeifer
- Arizona State University, School of Life Sciences, Center for Evolution & Medicine, Tempe, Arizona, United States of America
| | - Brandon S Cooper
- University of Montana, Division of Biological Sciences, Missoula, Montana, United States of America
| | - Jeffrey M Good
- University of Montana, Division of Biological Sciences, Missoula, Montana, United States of America
| | - Jeffrey D Jensen
- Arizona State University, School of Life Sciences, Center for Evolution & Medicine, Tempe, Arizona, United States of America
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8
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Thi Hue Kien D, Edenborough K, da Silva Goncalves D, Thuy Vi T, Casagrande E, Thi Le Duyen H, Thi Long V, Thi Dui L, Thi Tuyet Nhu V, Thi Giang N, Thi Xuan Trang H, Lee E, Donovan-Banfield I, Thi Thuy Van H, Minh Nguyet N, Thanh Phong N, Van Vinh Chau N, Wills B, Yacoub S, Flores H, Simmons C. Genome evolution of dengue virus serotype 1 under selection by Wolbachia pipientis in Aedes aegypti mosquitoes. Virus Evol 2023; 9:vead016. [PMID: 37744653 PMCID: PMC10517695 DOI: 10.1093/ve/vead016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 01/26/2023] [Accepted: 03/03/2023] [Indexed: 09/26/2023] Open
Abstract
The introgression of antiviral strains of Wolbachia into Aedes aegypti mosquito populations is a public health intervention for the control of dengue. Plausibly, dengue virus (DENV) could evolve to bypass the antiviral effects of Wolbachia and undermine this approach. Here, we established a serial-passage system to investigate the evolution of DENV in Ae. aegypti mosquitoes infected with the wMel strain of Wolbachia. Using this system, we report on virus genetic outcomes after twenty passages of serotype 1 of DENV (DENV-1). An amino acid substitution, E203K, in the DENV-1 envelope protein was more frequently detected in the consensus sequence of virus populations passaged in wMel-infected Ae. aegypti than wild-type counterparts. Positive selection at residue 203 was reproducible; it occurred in passaged virus populations from independent DENV-1-infected patients and also in a second, independent experimental system. In wild-type mosquitoes and human cells, the 203K variant was rapidly replaced by the progenitor sequence. These findings provide proof of concept that wMel-associated selection of virus populations can occur in experimental conditions. Field-based studies are needed to explore whether wMel imparts selective pressure on DENV evolution in locations where wMel is established.
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Affiliation(s)
| | - Kathryn Edenborough
- World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, VIC 3800, Australia
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
- Oxford University Clinical Research Unit, Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
| | - Daniela da Silva Goncalves
- World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, VIC 3800, Australia
| | - Tran Thuy Vi
- Oxford University Clinical Research Unit, Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
| | - Etiene Casagrande
- World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, VIC 3800, Australia
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Huynh Thi Le Duyen
- Oxford University Clinical Research Unit, Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
| | - Vo Thi Long
- Oxford University Clinical Research Unit, Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
| | - Le Thi Dui
- Oxford University Clinical Research Unit, Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
| | - Vu Thi Tuyet Nhu
- Oxford University Clinical Research Unit, Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
| | - Nguyen Thi Giang
- Oxford University Clinical Research Unit, Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
| | - Huynh Thi Xuan Trang
- Oxford University Clinical Research Unit, Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
| | - Elvina Lee
- World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, VIC 3800, Australia
| | - I’ah Donovan-Banfield
- World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, VIC 3800, Australia
| | - Huynh Thi Thuy Van
- Oxford University Clinical Research Unit, Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
| | | | - Nguyen Thanh Phong
- Hospital for Tropical Diseases, 190 Ben Ham Tu, District 5, Ho Chi Minh City, Vietnam
| | - Nguyen Van Vinh Chau
- Hospital for Tropical Diseases, 190 Ben Ham Tu, District 5, Ho Chi Minh City, Vietnam
| | - Bridget Wills
- Oxford University Clinical Research Unit, Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sophie Yacoub
- Oxford University Clinical Research Unit, Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
| | - Heather Flores
- World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, VIC 3800, Australia
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Cameron Simmons
- World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, VIC 3800, Australia
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
- Oxford University Clinical Research Unit, Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
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9
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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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10
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Human pathogenic RNA viruses establish noncompeting lineages by occupying independent niches. Proc Natl Acad Sci U S A 2022; 119:e2121335119. [PMID: 35639694 PMCID: PMC9191635 DOI: 10.1073/pnas.2121335119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Numerous pathogenic viruses are endemic in humans and cause a broad variety of diseases, but what is their potential for causing new pandemics? We show that most human pathogenic RNA viruses form multiple, cocirculating lineages with low turnover rates. These lineages appear to be largely noncompeting and occupy distinct epidemiological niches that are not regionally or seasonally defined, and their persistence appears to stem from limited outbreaks in small communities so that only a small fraction of the global susceptible population is infected at any time. However, due to globalization, interaction and competition between lineages might increase, potentially leading to increased diversification and pathogenicity. Thus, endemic viruses appear to merit global attention with respect to the prevention of future pandemics. Many pathogenic viruses are endemic among human populations and can cause a broad variety of diseases, some potentially leading to devastating pandemics. How virus populations maintain diversity and what selective pressures drive population turnover is not thoroughly understood. We conducted a large-scale phylodynamic analysis of 27 human pathogenic RNA viruses spanning diverse life history traits, in search of unifying trends that shape virus evolution. For most virus species, we identify multiple, cocirculating lineages with low turnover rates. These lineages appear to be largely noncompeting and likely occupy semiindependent epidemiological niches that are not regionally or seasonally defined. Typically, intralineage mutational signatures are similar to interlineage signatures. The principal exception are members of the family Picornaviridae, for which mutations in capsid protein genes are primarily lineage defining. Interlineage turnover is slower than expected under a neutral model, whereas intralineage turnover is faster than the neutral expectation, further supporting the existence of independent niches. The persistence of virus lineages appears to stem from limited outbreaks within small communities, so that only a small fraction of the global susceptible population is infected at any time. As disparate communities become increasingly connected through globalization, interaction and competition between lineages might increase as well, which could result in changing selective pressures and increased diversification and/or pathogenicity. Thus, in addition to zoonotic events, ongoing surveillance of familiar, endemic viruses appears to merit global attention with respect to the prevention or mitigation of future pandemics.
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11
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Grupstra CGB, Howe-Kerr LI, Veglia AJ, Bryant RL, Coy SR, Blackwelder PL, Correa AMS. Thermal stress triggers productive viral infection of a key coral reef symbiont. THE ISME JOURNAL 2022; 16:1430-1441. [PMID: 35046559 PMCID: PMC9038915 DOI: 10.1038/s41396-022-01194-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 01/03/2022] [Accepted: 01/07/2022] [Indexed: 04/27/2023]
Abstract
Climate change-driven ocean warming is increasing the frequency and severity of bleaching events, in which corals appear whitened after losing their dinoflagellate endosymbionts (family Symbiodiniaceae). Viral infections of Symbiodiniaceae may contribute to some bleaching signs, but little empirical evidence exists to support this hypothesis. We present the first temporal analysis of a lineage of Symbiodiniaceae-infecting positive-sense single-stranded RNA viruses ("dinoRNAVs") in coral colonies, which were exposed to a 5-day heat treatment (+2.1 °C). A total of 124 dinoRNAV major capsid protein gene "aminotypes" (unique amino acid sequences) were detected from five colonies of two closely related Pocillopora-Cladocopium (coral-symbiont) combinations in the experiment; most dinoRNAV aminotypes were shared between the two coral-symbiont combinations (64%) and among multiple colonies (82%). Throughout the experiment, seventeen dinoRNAV aminotypes were found only in heat-treated fragments, and 22 aminotypes were detected at higher relative abundances in heat-treated fragments. DinoRNAVs in fragments of some colonies exhibited higher alpha diversity and dispersion under heat stress. Together, these findings provide the first empirical evidence that exposure to high temperatures triggers some dinoRNAVs to switch from a persistent to a productive infection mode within heat-stressed corals. Over extended time frames, we hypothesize that cumulative dinoRNAV production in the Pocillopora-Cladocopium system could affect colony symbiotic status, for example, by decreasing Symbiodiniaceae densities within corals. This study sets the stage for reef-scale investigations of dinoRNAV dynamics during bleaching events.
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Affiliation(s)
| | | | - Alex J Veglia
- BioSciences at Rice, Rice University, Houston, TX, USA
| | - Reb L Bryant
- BioSciences at Rice, Rice University, Houston, TX, USA
- Department of Ecology and Evolutionary Biology, The University of Kansas, Lawrence, KS, USA
| | | | - Patricia L Blackwelder
- Department of Chemistry, University of Miami Center for Advanced Microscopy (UMCAM), 1301 Memorial Dr, Coral Gables, FL, 33146-0630, USA
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12
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Stica CJ, Barrero RA, Murray RZ, Devine GJ, Phillips MJ, Frentiu FD. Global Evolutionary History and Dynamics of Dengue Viruses Inferred from Whole Genome Sequences. Viruses 2022; 14:v14040703. [PMID: 35458433 PMCID: PMC9030598 DOI: 10.3390/v14040703] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 03/18/2022] [Accepted: 03/25/2022] [Indexed: 12/20/2022] Open
Abstract
Dengue is an arboviral disease caused by dengue virus (DENV), leading to approximately 25,000 deaths/year and with over 40% of the world’s population at risk. Increased international travel and trade, poorly regulated urban expansion, and warming global temperatures have expanded the geographic range and incidence of the virus in recent decades. This study used phylogenetic and selection pressure analyses to investigate trends in DENV evolution, using whole genome coding sequences from publicly available databases alongside newly sequenced isolates collected between 1963–1997 from Southeast Asia and the Pacific. Results revealed very similar phylogenetic relationships when using the envelope gene and the whole genome coding sequences. Although DENV evolution is predominantly driven by negative selection, a number of amino acid sites undergoing positive selection were found across the genome, with the majority located in the envelope and NS5 genes. Some genotypes appear to be diversifying faster than others within each serotype. The results from this research improve our understanding of DENV evolution, with implications for disease control efforts such as Wolbachia-based biocontrol and vaccine design.
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Affiliation(s)
- Caleb J. Stica
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland University of Technology, 300 Herston Road, Herston, QLD 4006, Australia;
| | - Roberto A. Barrero
- eResearch Office, Division of Research and Innovation, Queensland University of Technology, P Block, 2 George Street, Brisbane, QLD 4000, Australia;
| | - Rachael Z. Murray
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, KG-Q Block, 60 Musk Avenue, Kelvin Grove, Brisbane, QLD 4059, Australia;
| | - Gregor J. Devine
- Mosquito Control Lab, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD 4006, Australia;
| | - Matthew J. Phillips
- School of Biology and Environmental Science, Queensland University of Technology, R Block, 2 George Street, Brisbane, QLD 4000, Australia;
| | - Francesca D. Frentiu
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland University of Technology, 300 Herston Road, Herston, QLD 4006, Australia;
- Correspondence:
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13
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Ghafari M, du Plessis L, Raghwani J, Bhatt S, Xu B, Pybus OG, Katzourakis A. Purifying Selection Determines the Short-Term Time Dependency of Evolutionary Rates in SARS-CoV-2 and pH1N1 Influenza. Mol Biol Evol 2022; 39:6509523. [PMID: 35038728 PMCID: PMC8826518 DOI: 10.1093/molbev/msac009] [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] [Indexed: 12/03/2022] Open
Abstract
High-throughput sequencing enables rapid genome sequencing during infectious disease outbreaks and provides an opportunity to quantify the evolutionary dynamics of pathogens in near real-time. One difficulty of undertaking evolutionary analyses over short timescales is the dependency of the inferred evolutionary parameters on the timespan of observation. Crucially, there are an increasing number of molecular clock analyses using external evolutionary rate priors to infer evolutionary parameters. However, it is not clear which rate prior is appropriate for a given time window of observation due to the time-dependent nature of evolutionary rate estimates. Here, we characterize the molecular evolutionary dynamics of SARS-CoV-2 and 2009 pandemic H1N1 (pH1N1) influenza during the first 12 months of their respective pandemics. We use Bayesian phylogenetic methods to estimate the dates of emergence, evolutionary rates, and growth rates of SARS-CoV-2 and pH1N1 over time and investigate how varying sampling window and data set sizes affect the accuracy of parameter estimation. We further use a generalized McDonald-Kreitman test to estimate the number of segregating nonneutral sites over time. We find that the inferred evolutionary parameters for both pandemics are time dependent, and that the inferred rates of SARS-CoV-2 and pH1N1 decline by ∼50% and ∼100%, respectively, over the course of 1 year. After at least 4 months since the start of sequence sampling, inferred growth rates and emergence dates remain relatively stable and can be inferred reliably using a logistic growth coalescent model. We show that the time dependency of the mean substitution rate is due to elevated substitution rates at terminal branches which are 2-4 times higher than those of internal branches for both viruses. The elevated rate at terminal branches is strongly correlated with an increasing number of segregating nonneutral sites, demonstrating the role of purifying selection in generating the time dependency of evolutionary parameters during pandemics.
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Affiliation(s)
- Mahan Ghafari
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Louis du Plessis
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Jayna Raghwani
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Samir Bhatt
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, United Kingdom
| | - Bo Xu
- Department of Earth System Science, Tsinghua University, Beijing, China
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Aris Katzourakis
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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14
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Seabra SG, Libin PJK, Theys K, Zhukova A, Potter BI, Nebenzahl-Guimaraes H, Gorbalenya AE, Sidorov IA, Pimentel V, Pingarilho M, de Vasconcelos ATR, Dellicour S, Khouri R, Gascuel O, Vandamme AM, Baele G, Cuypers L, Abecasis AB. OUP accepted manuscript. Virus Evol 2022; 8:veac029. [PMID: 35478717 PMCID: PMC9035895 DOI: 10.1093/ve/veac029] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 01/24/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
The Zika virus (ZIKV) disease caused a public health emergency of international concern that started in February 2016. The overall number of ZIKV-related cases increased until November 2016, after which it declined sharply. While the evaluation of the potential risk and impact of future arbovirus epidemics remains challenging, intensified surveillance efforts along with a scale-up of ZIKV whole-genome sequencing provide an opportunity to understand the patterns of genetic diversity, evolution, and spread of ZIKV. However, a classification system that reflects the true extent of ZIKV genetic variation is lacking. Our objective was to characterize ZIKV genetic diversity and phylodynamics, identify genomic footprints of differentiation patterns, and propose a dynamic classification system that reflects its divergence levels. We analysed a curated dataset of 762 publicly available sequences spanning the full-length coding region of ZIKV from across its geographical span and collected between 1947 and 2021. The definition of genetic groups was based on comprehensive evolutionary dynamics analyses, which included recombination and phylogenetic analyses, within- and between-group pairwise genetic distances comparison, detection of selective pressure, and clustering analyses. Evidence for potential recombination events was detected in a few sequences. However, we argue that these events are likely due to sequencing errors as proposed in previous studies. There was evidence of strong purifying selection, widespread across the genome, as also detected for other arboviruses. A total of 50 sites showed evidence of positive selection, and for a few of these sites, there was amino acid (AA) differentiation between genetic clusters. Two main genetic clusters were defined, ZA and ZB, which correspond to the already characterized ‘African’ and ‘Asian’ genotypes, respectively. Within ZB, two subgroups, ZB.1 and ZB.2, represent the Asiatic and the American (and Oceania) lineages, respectively. ZB.1 is further subdivided into ZB.1.0 (a basal Malaysia sequence sampled in the 1960s and a recent Indian sequence), ZB.1.1 (South-Eastern Asia, Southern Asia, and Micronesia sequences), and ZB.1.2 (very similar sequences from the outbreak in Singapore). ZB.2 is subdivided into ZB.2.0 (basal American sequences and the sequences from French Polynesia, the putative origin of South America introduction), ZB.2.1 (Central America), and ZB.2.2 (Caribbean and North America). This classification system does not use geographical references and is flexible to accommodate potential future lineages. It will be a helpful tool for studies that involve analyses of ZIKV genomic variation and its association with pathogenicity and serve as a starting point for the public health surveillance and response to on-going and future epidemics and to outbreaks that lead to the emergence of new variants.
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Affiliation(s)
| | | | | | - Anna Zhukova
- Institut Pasteur, Université Paris Cité, Unité Bioinformatique Evolutive, 25-28 rue du Dr Roux, Paris F-75015, France
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, 25-28 rue du Dr Roux, Paris F-75015, France
| | | | - Hanna Nebenzahl-Guimaraes
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Rua da Junqueira 100, Lisboa 1349-008, Portugal
| | | | | | - Victor Pimentel
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Rua da Junqueira 100, Lisboa 1349-008, Portugal
| | - Marta Pingarilho
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Rua da Junqueira 100, Lisboa 1349-008, Portugal
| | | | - Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Clinical and Epidemiological Virology, KU Leuven, Herestraat 49 - box 1030, Leuven 3000, Belgium
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, CP 264/3, 50 av. F.D. Roosevelt, Bruxelles B-1050, Belgium
| | | | | | | | | | - Lize Cuypers
- Department of Laboratory Medicine, University Hospitals Leuven, Herestraat 49, Leuven 3000, Belgium
| | - Ana B Abecasis
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Rua da Junqueira 100, Lisboa 1349-008, Portugal
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15
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Zecchin B, Fusaro A, Milani A, Schivo A, Ravagnan S, Ormelli S, Mavian C, Michelutti A, Toniolo F, Barzon L, Monne I, Capelli G. The central role of Italy in the spatial spread of USUTU virus in Europe. Virus Evol 2021; 7:veab048. [PMID: 34513027 PMCID: PMC8427344 DOI: 10.1093/ve/veab048] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
USUTU virus (USUV) is an arbovirus maintained in the environment through a bird-mosquito enzootic cycle. Previous surveillance plans highlighted the endemicity of USUV in North-eastern Italy. In this work, we sequenced 138 new USUV full genomes from mosquito pools (Culex pipiens) and wild birds collected in North-eastern Italy and we investigated the evolutionary processes (phylogenetic analysis, selection pressure and evolutionary time-scale analysis) and spatial spread of USUV strains circulating in the European context and in Italy, with a particular focus on North-eastern Italy. Our results confirmed the circulation of viruses belonging to four different lineages in Italy (EU1, EU2, EU3 and EU4), with the newly sequenced viruses from the North-eastern regions, Veneto and Friuli Venezia Giulia, belonging to the EU2 lineage and clustering into two different sub-lineages, EU2-A and EU2-B. Specific mutations characterize each European lineage and geographic location seem to have shaped their phylogenetic structure. By investigating the spatial spread in Europe, we were able to show that Italy acted mainly as donor of USUV to neighbouring countries. At a national level, we identified two geographical clusters mainly circulating in Northern and North-western Italy, spreading both northward and southward. Our analyses provide important information on the spatial and evolutionary dynamics of USUTU virus that can help to improve surveillance plans and control strategies for this virus of increasing concern for human health.
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Affiliation(s)
- B Zecchin
- Department of Research and Innovation, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - A Fusaro
- Department of Research and Innovation, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - A Milani
- Department of Research and Innovation, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - A Schivo
- Department of Research and Innovation, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - S Ravagnan
- National Reference Centre/OIE Collaborating Centre for Diseases at the Animal-Human Interface, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - S Ormelli
- Department of Research and Innovation, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - C Mavian
- Emerging Pathogens Institute, Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - A Michelutti
- National Reference Centre/OIE Collaborating Centre for Diseases at the Animal-Human Interface, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - F Toniolo
- National Reference Centre/OIE Collaborating Centre for Diseases at the Animal-Human Interface, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - L Barzon
- Department of Molecular Medicine, University of Padua, Padova, Italy
| | - I Monne
- Department of Research and Innovation, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - G Capelli
- National Reference Centre/OIE Collaborating Centre for Diseases at the Animal-Human Interface, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
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16
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Hayman DTS, Knox MA. Estimating the age of the subfamily Orthocoronavirinae using host divergence times as calibration ages at two internal nodes. Virology 2021; 563:20-27. [PMID: 34411808 PMCID: PMC8365511 DOI: 10.1016/j.virol.2021.08.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/11/2021] [Accepted: 08/11/2021] [Indexed: 12/04/2022]
Abstract
Viruses of the subfamily Orthocoronavirinae can cause mild to severe disease in people, including COVID-19, MERS and SARS. Their most common natural hosts are bat and bird species, which are mostly split across four virus genera. Molecular clock analyses of orthocoronaviruses suggested the most recent common ancestor of these viruses might have emerged either around 10,000 years ago or, using models accounting for selection, many millions of years. Here, we reassess the evolutionary history of these viruses. We present time-aware phylogenetic analyses of a RNA-dependent RNA polymerase locus from 123 orthocoronaviruses isolated from birds and bats, including those in New Zealand, which were geographically isolated from other bats around 35 million years ago. We used this age, as well as the age of the avian-mammals split, to calibrate the molecular clocks, under the assumption that these ages are applicable to the analyzed viruses. We found that the time to the most recent ancestor common for all orthocoronaviruses is likely 150 or more million years, supporting clock analyses that account for selection.
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Affiliation(s)
- David T S Hayman
- Molecular Epidemiology and Public Health Laboratory, School of Veterinary Science, Massey University, New Zealand.
| | - Matthew A Knox
- Molecular Epidemiology and Public Health Laboratory, School of Veterinary Science, Massey University, New Zealand
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17
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Rochman ND, Wolf YI, Faure G, Mutz P, Zhang F, Koonin EV. Ongoing global and regional adaptive evolution of SARS-CoV-2. Proc Natl Acad Sci U S A 2021; 118:e2104241118. [PMID: 34292871 PMCID: PMC8307621 DOI: 10.1073/pnas.2104241118] [Citation(s) in RCA: 143] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Understanding the trends in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolution is paramount to control the COVID-19 pandemic. We analyzed more than 300,000 high-quality genome sequences of SARS-CoV-2 variants available as of January 2021. The results show that the ongoing evolution of SARS-CoV-2 during the pandemic is characterized primarily by purifying selection, but a small set of sites appear to evolve under positive selection. The receptor-binding domain of the spike protein and the region of the nucleocapsid protein associated with nuclear localization signals (NLS) are enriched with positively selected amino acid replacements. These replacements form a strongly connected network of apparent epistatic interactions and are signatures of major partitions in the SARS-CoV-2 phylogeny. Virus diversity within each geographic region has been steadily growing for the entirety of the pandemic, but analysis of the phylogenetic distances between pairs of regions reveals four distinct periods based on global partitioning of the tree and the emergence of key mutations. The initial period of rapid diversification into region-specific phylogenies that ended in February 2020 was followed by a major extinction event and global homogenization concomitant with the spread of D614G in the spike protein, ending in March 2020. The NLS-associated variants across multiple partitions rose to global prominence in March to July, during a period of stasis in terms of interregional diversity. Finally, beginning in July 2020, multiple mutations, some of which have since been demonstrated to enable antibody evasion, began to emerge associated with ongoing regional diversification, which might be indicative of speciation.
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Affiliation(s)
- Nash D Rochman
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894;
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894
| | - Guilhem Faure
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Pascal Mutz
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142;
- HHMI, Massachusetts Institute of Technology, Cambridge, MA 02139
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894;
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18
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Yu Y, Li Y, Dong Y, Wang X, Li C, Jiang W. Natural selection on synonymous mutations in SARS-CoV-2 and the impact on estimating divergence time. Future Virol 2021. [PMCID: PMC8132620 DOI: 10.2217/fvl-2021-0078] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
To adapt to human host environment, synonymous mutations in SARS-CoV-2 are shaped by tRNA selection, energy cost and RNA structure.
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Affiliation(s)
- Yuanyuan Yu
- Department of Anesthesiology, Qingdao Haici Hospital, Qingdao, Shandong, China
| | - Yan Li
- Department of Cardiology, Qingdao Center Hospital, Qingdao, Shandong, China
| | - Yu Dong
- Department of Intervention, Qingdao Center Hospital, Qingdao, Shandong, China
| | - Xuekun Wang
- Department of Cardiology, Qingdao Center Hospital, Qingdao, Shandong, China
| | - Chunxiao Li
- Department of Cardiology, Qingdao Center Hospital, Qingdao, Shandong, China
| | - Wenqing Jiang
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, Shandong, China
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19
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Abstract
Recent field trials have demonstrated that dengue incidence can be substantially reduced by introgressing strains of the endosymbiotic bacterium Wolbachia into Aedes aegypti mosquito populations. This strategy relies on Wolbachia reducing the susceptibility of Ae. aegypti to disseminated infection by positive-sense RNA viruses like dengue. However, RNA viruses are well known to adapt to antiviral pressures. Here, we review the viral infection stages where selection for Wolbachia-resistant virus variants could occur. We also consider the genetic constraints imposed on viruses that alternate between vertebrate and invertebrate hosts, and the likely selection pressures to which dengue virus might adapt in order to be effectively transmitted by Ae. aegypti that carry Wolbachia. While there are hurdles to dengue viruses developing resistance to Wolbachia, we suggest that long-term surveillance for resistant viruses should be an integral component of Wolbachia-introgression biocontrol programs.
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Affiliation(s)
| | - Heather A. Flores
- Institute of Vector-Borne Disease, Monash University, Clayton, Victoria, Australia
| | - Cameron P. Simmons
- World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, Victoria, Australia
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Johanna E. Fraser
- Institute of Vector-Borne Disease, Monash University, Clayton, Victoria, Australia
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
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20
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Tiraki D, Singh K, Shrivastava S, Mishra AC, Arankalle V. Complete genome characterization and evolutionary analysis of dengue viruses isolated during 2016-2017 in Pune, India. INFECTION GENETICS AND EVOLUTION 2021; 93:104909. [PMID: 34082088 DOI: 10.1016/j.meegid.2021.104909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 04/14/2021] [Accepted: 05/06/2021] [Indexed: 11/15/2022]
Abstract
Dengue is the most common mosquito-borne viral infection in tropical and sub-tropical countries. In the recent years, frequent dengue outbreaks are being reported in many parts of India. DENV circulates as four independent serotypes posing a major public health threat around the globe. Phylogenetic and full genome sequence analyses of 19 complete DENV genome sequences presenting all the four serotypes in Pune, India (2016-2017) revealed no change in the circulating genotypes i.e., genotype V clade C (D1), genotype IVB (D2), genotype III lineage III (D3) and genotype I clade D (D4). Additionally, unique amino acid substitutions that may potentially influence viral fitness and virulence in host cells were identified. Mapping of the unique amino acid substitutions onto the T cell epitopes of the reference strains revealed that 8/10 (D1), 14/15 (D2), 3/4 (D3) and 21/74 (D4), amino acids were involved in T-cell epitope presentation for a maximum number of HLA alleles associated with disease outcome. Selection pressure analysis documented a positive selection pressure to be acting on few amino acid sites indicating continuous evolutionary changes in the viral RNA. Overall, the evolutionary and selection pressure data generated during this study may help in better understanding of DENV evolution and epidemiology.
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Affiliation(s)
- Divya Tiraki
- Department of Communicable Diseases, Interactive Research School for Health Affairs, Bharati Vidyapeeth Deemed University, Pune, Maharashtra, India
| | - Karuna Singh
- Department of Communicable Diseases, Interactive Research School for Health Affairs, Bharati Vidyapeeth Deemed University, Pune, Maharashtra, India
| | - Shubham Shrivastava
- Department of Communicable Diseases, Interactive Research School for Health Affairs, Bharati Vidyapeeth Deemed University, Pune, Maharashtra, India
| | - A C Mishra
- Department of Communicable Diseases, Interactive Research School for Health Affairs, Bharati Vidyapeeth Deemed University, Pune, Maharashtra, India
| | - Vidya Arankalle
- Department of Communicable Diseases, Interactive Research School for Health Affairs, Bharati Vidyapeeth Deemed University, Pune, Maharashtra, India.
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21
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White HN. B-Cell Memory Responses to Variant Viral Antigens. Viruses 2021; 13:565. [PMID: 33810456 PMCID: PMC8066974 DOI: 10.3390/v13040565] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/19/2021] [Accepted: 03/24/2021] [Indexed: 02/06/2023] Open
Abstract
A central feature of vertebrate immune systems is the ability to form antigen-specific immune memory in response to microbial challenge and so provide protection against future infection. In conflict with this process is the ability that many viruses have to mutate their antigens to escape infection- or vaccine-induced antibody memory responses. Mutable viruses such as dengue virus, influenza virus and of course coronavirus have a major global health impact, exacerbated by this ability to evade immune responses through mutation. There have been several outstanding recent studies on B-cell memory that also shed light on the potential and limitations of antibody memory to protect against viral antigen variation, and so promise to inform new strategies for vaccine design. For the purposes of this review, the current understanding of the different memory B-cell (MBC) populations, and their potential to recognize mutant antigens, will be described prior to some examples from antibody responses against the highly mutable RNA based flaviviruses, influenza virus and SARS-CoV-2.
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Affiliation(s)
- Harry N White
- Department of Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
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22
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Rochman ND, Wolf YI, Faure G, Mutz P, Zhang F, Koonin EV. Ongoing Global and Regional Adaptive Evolution of SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2020.10.12.336644. [PMID: 33083804 PMCID: PMC7574262 DOI: 10.1101/2020.10.12.336644] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Understanding the trends in SARS-CoV-2 evolution is paramount to control the COVID-19 pandemic. We analyzed more than 300,000 high quality genome sequences of SARS-CoV-2 variants available as of January 2021. The results show that the ongoing evolution of SARS-CoV-2 during the pandemic is characterized primarily by purifying selection, but a small set of sites appear to evolve under positive selection. The receptor-binding domain of the spike protein and the nuclear localization signal (NLS) associated region of the nucleocapsid protein are enriched with positively selected amino acid replacements. These replacements form a strongly connected network of apparent epistatic interactions and are signatures of major partitions in the SARS-CoV-2 phylogeny. Virus diversity within each geographic region has been steadily growing for the entirety of the pandemic, but analysis of the phylogenetic distances between pairs of regions reveals four distinct periods based on global partitioning of the tree and the emergence of key mutations. The initial period of rapid diversification into region-specific phylogenies that ended in February 2020 was followed by a major extinction event and global homogenization concomitant with the spread of D614G in the spike protein, ending in March 2020. The NLS associated variants across multiple partitions rose to global prominence in March-July, during a period of stasis in terms of inter-regional diversity. Finally, beginning July 2020, multiple mutations, some of which have since been demonstrated to enable antibody evasion, began to emerge associated with ongoing regional diversification, which might be indicative of speciation.
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Affiliation(s)
- Nash D Rochman
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894
| | - Guilhem Faure
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Pascal Mutz
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894
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23
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Nonsynonymous Polymorphism Counts in Bacterial Genomes: a Comparative Examination. Appl Environ Microbiol 2020; 87:AEM.02002-20. [PMID: 33097502 DOI: 10.1128/aem.02002-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 10/14/2020] [Indexed: 01/14/2023] Open
Abstract
Genomic data reveal single-nucleotide polymorphisms (SNPs) that may carry information about the evolutionary history of bacteria. However, it remains unclear what inferences about selection can be made from genomic SNP data. Bacterial species are often sampled during epidemic outbreaks or within hosts during the course of chronic infections. SNPs obtained from genomic analysis of these data are not necessarily fixed. Treating them as fixed during analysis by using measures such as the ratio of nonsynonymous to synonymous evolutionary changes (dN/dS) may lead to incorrect inferences about the strength and direction of selection. In this study, we consider data from a range of whole-genome sequencing studies of bacterial pathogens and explore patterns of nonsynonymous variation to assess whether evidence of selection can be identified by investigating SNP counts alone across multiple WGS studies. We visualize these SNP data in ways that highlight their relationship to neutral baseline expectations. These neutral expectations are based on a simple model of mutation, from which we simulate SNP accumulation to investigate how SNP counts are distributed under alternative assumptions about positive and negative selection. We compare these patterns with empirical SNP data and illustrate the general difficulty of detecting positive selection from SNP data. Finally, we consider whether SNP counts observed at the between-host population level differ from those observed at the within-host level and find some evidence that suggests that dynamics across these two scales are driven by different underlying processes.IMPORTANCE Identifying selection from SNP data obtained from whole-genome sequencing studies is challenging. Some current measures used to identify and quantify selection acting on genomes rely on fixed differences; thus, these are inappropriate for SNP data where variants are not fixed. With the increase in whole-genome sequencing studies, it is important to consider SNP data in the context of evolutionary processes. How SNPs are counted and analyzed can help in understanding mutation accumulation and trajectories of strains. We developed a tool for identifying possible evidence of selection and for comparative analysis with other SNP data. We propose a model that provides a rule-of-thumb guideline and two new visualization techniques that can be used to interpret and compare SNP data. We quantify the expected proportion of nonsynonymous SNPs in coding regions under neutrality and demonstrate its use in identifying evidence of positive and negative selection from simulations and empirical data.
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24
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Evolution and epidemiologic dynamics of dengue virus in Nicaragua during the emergence of chikungunya and Zika viruses. INFECTION GENETICS AND EVOLUTION 2020; 92:104680. [PMID: 33326875 DOI: 10.1016/j.meegid.2020.104680] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 11/19/2020] [Accepted: 12/10/2020] [Indexed: 11/23/2022]
Abstract
Arthropod-borne viruses (arboviruses) comprise a significant and ongoing threat to human health, infecting hundreds of millions annually. Three such arboviruses include circumtropical dengue, Zika, and chikungunya viruses, exhibiting continuous emergence primarily via Aedes mosquito vectors. Nicaragua has experienced endemic dengue virus (DENV) transmission involving multiple serotypes since 1985, with chikungunya virus (CHIKV) reported in 2014-2015, followed by Zika virus (ZIKV) first reported in 2016. In order to identify patterns of genetic variation and selection pressures shaping the evolution of co-circulating DENV serotypes in light of the arrival of CHIKV and ZIKV, we employed whole-genome sequencing on an Illumina MiSeq platform of random-amplified total RNA libraries to characterize 42 DENV low-passage isolates, derived from viremic patients in Nicaragua between 2013 and 2016. Our approach also revealed clinically undetected co-infections with CHIKV. Of the three DENV serotypes (1, 2, and 3) co-circulating during our study, we uncovered distinct patterns of evolution using comparative phylogenetic inference. DENV-1 genetic variation was structured into two distinct co-circulating lineages with no evidence of positive selection in the origins of either lineage, suggesting they are equally fit. In contrast, the evolutionary history of DENV-2 was marked by positive selection, and a unique, divergent lineage correlated with high epidemic potential emerged in 2015 to drive an outbreak in 2016. DENV-3 genetic variation remained unstructured into lineages throughout the period of study. Thus, this study reveals insights into evolutionary and epidemiologic trends exhibited during the circulation of multiple arboviruses in Nicaragua.
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25
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Thomazella MV, Lima Neto QA, Duarte Junior FF, Jorge FA, de Castro Moreira D, Leal Junior AD, Presibella MM, Riediger IN, da Silva RA, de Carvalho IMVG, Bertolini DA. Insights on Zika virus envelope gene conservation in American outbreaks. Braz J Microbiol 2020; 51:1601-1605. [PMID: 32749573 PMCID: PMC7688768 DOI: 10.1007/s42770-020-00349-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 07/25/2020] [Indexed: 10/23/2022] Open
Abstract
Phylogenetic studies with Zika virus (ZIKV) have been conducted in Brazil. In this study, we sequenced 8 new sequences of the ZIKV envelope (E) gene from strains of cases from the Paraná and Mato Grosso do Sul states in 2016. A low phylogenetic signal was observed, with more than 40% of unresolved quartets, and the Maximum Likelihood Tree grouped all sequences in the Brazilian branches within the Asian genotype. In addition, a Shannon entropy analysis was conducted, showing a high stability in the E protein through the ZIKV polyprotein. Taken together, these results suggest a high degree of conservation in the ZIKV E gene from the recent American outbreaks.
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Affiliation(s)
- Mateus V Thomazella
- Laboratório de Virologia Clínica, Universidade Estadual de Maringá - UEM, Avenida Colombo, 5790, Maringá, Paraná, 87020-900, Brazil.
| | - Quirino A Lima Neto
- Laboratório de Virologia Clínica, Universidade Estadual de Maringá - UEM, Avenida Colombo, 5790, Maringá, Paraná, 87020-900, Brazil
| | - Francisco F Duarte Junior
- Laboratório de Virologia Clínica, Universidade Estadual de Maringá - UEM, Avenida Colombo, 5790, Maringá, Paraná, 87020-900, Brazil
| | - Fernando A Jorge
- Laboratório de Virologia Clínica, Universidade Estadual de Maringá - UEM, Avenida Colombo, 5790, Maringá, Paraná, 87020-900, Brazil
| | - Déborah de Castro Moreira
- Laboratório de Virologia Clínica, Universidade Estadual de Maringá - UEM, Avenida Colombo, 5790, Maringá, Paraná, 87020-900, Brazil
| | - Amauri D Leal Junior
- Laboratório de Virologia Clínica, Universidade Estadual de Maringá - UEM, Avenida Colombo, 5790, Maringá, Paraná, 87020-900, Brazil
| | - Mayra M Presibella
- Laboratório Central do Estado do Paraná - LACEN-PR, Curitiba, Paraná, Brazil
| | - Irina N Riediger
- Laboratório Central do Estado do Paraná - LACEN-PR, Curitiba, Paraná, Brazil
| | - Rafael A da Silva
- Instituto Butantan, São Paulo, São Paulo, Brazil
- Universidade Federal de São Paulo - UNIFESP/EPM, São Paulo, São Paulo, Brazil
| | - Isabel Maria V G de Carvalho
- Instituto Butantan, São Paulo, São Paulo, Brazil
- Universidade Federal de São Paulo - UNIFESP/EPM, São Paulo, São Paulo, Brazil
| | - Dennis A Bertolini
- Laboratório de Virologia Clínica, Universidade Estadual de Maringá - UEM, Avenida Colombo, 5790, Maringá, Paraná, 87020-900, Brazil
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26
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Biological Characteristics and Patterns of Codon Usage Evolution for the African Genotype Zika Virus. Viruses 2020; 12:v12111306. [PMID: 33202554 PMCID: PMC7696518 DOI: 10.3390/v12111306] [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: 09/08/2020] [Revised: 10/11/2020] [Accepted: 10/12/2020] [Indexed: 11/17/2022] Open
Abstract
We investigated temporal trends of codon usage changes for different host species to determine their importance in Zika virus (ZIKV) evolution. Viral spillover resulting from the potential of codon adaptation to host genome was also assessed for the African genotype ZIKV in comparison to the Asian genotype. To improve our understanding on its zoonotic maintenance, we evaluated in vitro the biological properties of the African genotype ZIKV in vertebrate and mosquito cell lines. Analyses were performed in comparison to Yellow fever virus (YFV). Despite significantly lower codon adaptation index trends than YFV, ZIKV showed evident codon adaptation to vertebrate hosts, particularly for the green African monkey Chlorocebus aethiops. PCA and CAI analyses at the individual ZIKV gene level for both human and Aedes aegypti indicated a clear distinction between the two genotypes. African ZIKV isolates showed higher virulence in mosquito cells than in vertebrate cells. Their higher replication in mosquito cells than African YFV confirmed the role of mosquitoes in the natural maintenance of the African genotype ZIKV. An analysis of individual strain growth characteristics indicated that the widely used reference strain MR766 replicates poorly in comparison to African ZIKV isolates. The recombinant African Zika virus strain ArD128000*E/NS5 may be a good model to include in studies on the mechanism of host tropism, as it cannot replicate in the tested vertebrate cell line.
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27
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King CA, Wegman AD, Endy TP. Mobilization and Activation of the Innate Immune Response to Dengue Virus. Front Cell Infect Microbiol 2020; 10:574417. [PMID: 33224897 PMCID: PMC7670994 DOI: 10.3389/fcimb.2020.574417] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 09/28/2020] [Indexed: 12/17/2022] Open
Abstract
Dengue virus is an important human pathogen, infecting an estimated 400 million individuals per year and causing symptomatic disease in a subset of approximately 100 million. Much of the effort to date describing the host response to dengue has focused on the adaptive immune response, in part because of the well-established roles of antibody-dependent enhancement and T cell original sin as drivers of severe dengue upon heterotypic secondary infection. However, the innate immune system is a crucial factor in the host response to dengue, as it both governs the fate and vigor of the adaptive immune response, and mediates the acute inflammatory response in tissues. In this review, we discuss the innate inflammatory response to dengue infection, focusing on the role of evolutionarily conserved innate immune cells, their effector functions, and clinical course.
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Affiliation(s)
- Christine A. King
- Department of Microbiology and Immunology, State University of New York (SUNY) Upstate Medical University, Syracuse, NY, United States
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28
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The Genetic Diversification of a Single Bluetongue Virus Strain Using an In Vitro Model of Alternating-Host Transmission. Viruses 2020; 12:v12091038. [PMID: 32961886 PMCID: PMC7551957 DOI: 10.3390/v12091038] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 08/31/2020] [Accepted: 09/15/2020] [Indexed: 12/16/2022] Open
Abstract
Bluetongue virus (BTV) is an arbovirus that has been associated with dramatic epizootics in both wild and domestic ruminants in recent decades. As a segmented, double-stranded RNA virus, BTV can evolve via several mechanisms due to its genomic structure. However, the effect of BTV’s alternating-host transmission cycle on the virus’s genetic diversification remains poorly understood. Whole genome sequencing approaches offer a platform for investigating the effect of host-alternation across all ten segments of BTV’s genome. To understand the role of alternating hosts in BTV’s genetic diversification, a field isolate was passaged under three different conditions: (i) serial passages in Culicoides sonorensis cells, (ii) serial passages in bovine pulmonary artery endothelial cells, or (iii) alternating passages between insect and bovine cells. Aliquots of virus were sequenced, and single nucleotide variants were identified. Measures of viral population genetics were used to quantify the genetic diversification that occurred. Two consensus variants in segments 5 and 10 occurred in virus from all three conditions. While variants arose across all passages, measures of genetic diversity remained largely similar across cell culture conditions. Despite passage in a relaxed in vitro system, we found that this BTV isolate exhibited genetic stability across passages and conditions. Our findings underscore the valuable role that whole genome sequencing may play in improving understanding of viral evolution and highlight the genetic stability of BTV.
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29
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Clark JJ, Gilray J, Orton RJ, Baird M, Wilkie G, Filipe ADS, Johnson N, McInnes CJ, Kohl A, Biek R. Population genomics of louping ill virus provide new insights into the evolution of tick-borne flaviviruses. PLoS Negl Trop Dis 2020; 14:e0008133. [PMID: 32925939 PMCID: PMC7515184 DOI: 10.1371/journal.pntd.0008133] [Citation(s) in RCA: 9] [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: 02/11/2020] [Revised: 09/24/2020] [Accepted: 08/07/2020] [Indexed: 12/30/2022] Open
Abstract
The emergence and spread of tick-borne arboviruses pose an increased challenge to human and animal health. In Europe this is demonstrated by the increasingly wide distribution of tick-borne encephalitis virus (TBEV, Flavivirus, Flaviviridae), which has recently been found in the United Kingdom (UK). However, much less is known about other tick-borne flaviviruses (TBFV), such as the closely related louping ill virus (LIV), an animal pathogen which is endemic to the UK and Ireland, but which has been detected in other parts of Europe including Scandinavia and Russia. The emergence and potential spatial overlap of these viruses necessitates improved understanding of LIV genomic diversity, geographic spread and evolutionary history. We sequenced a virus archive composed of 22 LIV isolates which had been sampled throughout the UK over a period of over 80 years. Combining this dataset with published virus sequences, we detected no sign of recombination and found low diversity and limited evidence for positive selection in the LIV genome. Phylogenetic analysis provided evidence of geographic clustering as well as long-distance movement, including movement events that appear recent. However, despite genomic data and an 80-year time span, we found that the data contained insufficient temporal signal to reliably estimate a molecular clock rate for LIV. Additional analyses revealed that this also applied to TBEV, albeit to a lesser extent, pointing to a general problem with phylogenetic dating for TBFV. The 22 LIV genomes generated during this study provide a more reliable LIV phylogeny, improving our knowledge of the evolution of tick-borne flaviviruses. Our inability to estimate a molecular clock rate for both LIV and TBEV suggests that temporal calibration of tick-borne flavivirus evolution should be interpreted with caution and highlight a unique aspect of these viruses which may be explained by their reliance on tick vectors. Tick-borne pathogens represent a major emerging threat to public health and in recent years have been expanding into new areas. LIV is a neglected virus endemic to the UK and Ireland (though it has been detected in Scandinavia and Russia) which is closely related to the major human pathogen TBEV, but predominantly causes disease in sheep and grouse. The recent detection of TBEV in the UK, which has also emerged elsewhere in Europe, requires more detailed understanding of the spread and sequence diversity of LIV. This could be important for diagnosis and vaccination, but also to improve our understanding of the evolution and emergence of these tick-borne viruses. Here we describe the sequencing of 22 LIV isolates which have been sampled from several host species across the past century. We have utilised this dataset to investigate the evolutionary pressures that LIV is subjected to and have explored the evolution of LIV using phylogenetic analysis. Crucially we were unable to estimate a reliable molecular clock rate for LIV and found that this problem also extends to a larger phylogeny of TBEV sequences. This work highlights a previously unknown caveat of tick-borne flavivirus evolutionary analysis which may be important for understanding the evolution of these important pathogens.
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Affiliation(s)
- Jordan J. Clark
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
- Moredun Research Institute, Edinburgh, United Kingdom
- * E-mail: (JC); (RB)
| | - Janice Gilray
- Moredun Research Institute, Edinburgh, United Kingdom
| | - Richard J. Orton
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Margaret Baird
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Gavin Wilkie
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Ana da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Nicholas Johnson
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
- Faculty of Health and Medical Science, University of Surrey, Guildford, Surrey, United Kingdom
| | | | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Roman Biek
- Institute of Biodiversity, Animal Health and Comparative Medicine - University of Glasgow, Glasgow, United Kingdom
- * E-mail: (JC); (RB)
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30
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Ko HY, Salem GM, Chang GJJ, Chao DY. Application of Next-Generation Sequencing to Reveal How Evolutionary Dynamics of Viral Population Shape Dengue Epidemiology. Front Microbiol 2020; 11:1371. [PMID: 32636827 PMCID: PMC7318875 DOI: 10.3389/fmicb.2020.01371] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 05/27/2020] [Indexed: 12/13/2022] Open
Abstract
Dengue viral (DENV) infection results in a wide spectrum of clinical manifestations from asymptomatic, mild fever to severe hemorrhage diseases upon infection. Severe dengue is the leading cause of pediatric deaths and/or hospitalizations, which are a major public health burden in dengue-endemic or hyperendemic countries. Like other RNA viruses, DENV continues to evolve. Adaptive mutations are obscured by the major consensus sequence (so-called wild-type sequences) and can only be identified once they become the dominant viruses in the virus population, a process that can take months or years. Traditional surveillance systems still rely on Sanger consensus sequencing. However, with the recent advancement of high-throughput next-generation sequencing (NGS) technologies, the genome-wide investigation of virus population within-host and between-hosts becomes achievable. Thus, viral population sequencing by NGS can increase our understanding of the changing epidemiology and evolution of viral genomics at the molecular level. This review focuses on the studies within the recent decade utilizing NGS in different experimental and epidemiological settings to understand how the adaptive evolution of dengue variants shapes the dengue epidemic and disease severity through its transmission. We propose three types of studies that can be pursued in the future to enhance our surveillance for epidemic prediction and better medical management.
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Affiliation(s)
- Hui-Ying Ko
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung-Hsing University, Taichung, Taiwan
| | - Gielenny M Salem
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung-Hsing University, Taichung, Taiwan
| | - Gwong-Jen J Chang
- Arboviral Diseases Branch, Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, United States
| | - Day-Yu Chao
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung-Hsing University, Taichung, Taiwan
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31
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Abstract
The evolutionary dynamics of a virus can differ within hosts and across populations. Studies of within-host evolution provide an important link between experimental studies of virus evolution and large-scale phylodynamic analyses. They can determine the extent to which global processes are recapitulated on local scales and how accurately experimental infections model natural ones. They may also inform epidemiologic models of disease spread and reveal how host-level dynamics contribute to a virus's evolution at a larger scale. Over the last decade, advances in viral sequencing have enabled detailed studies of viral genetic diversity within hosts. I review how within-host diversity is sampled, measured, and expressed, and how comparative studies of viral diversity can be leveraged to elucidate a virus's evolutionary dynamics. These concepts are illustrated with detailed reviews of recent research on the within-host evolution of influenza virus, dengue virus, and cytomegalovirus.
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Affiliation(s)
- Adam S Lauring
- Division of Infectious Diseases, Department of Internal Medicine, and Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109, USA;
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32
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West Nile Virus Epidemic in Germany Triggered by Epizootic Emergence, 2019. Viruses 2020; 12:v12040448. [PMID: 32326472 PMCID: PMC7232143 DOI: 10.3390/v12040448] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 04/09/2020] [Accepted: 04/13/2020] [Indexed: 01/10/2023] Open
Abstract
One year after the first autochthonous transmission of West Nile virus (WNV) to birds and horses in Germany, an epizootic emergence of WNV was again observed in 2019. The number of infected birds and horses was considerably higher compared to 2018 (12 birds, two horses), resulting in the observation of the first WNV epidemy in Germany: 76 cases in birds, 36 in horses and five confirmed mosquito-borne, autochthonous human cases. We demonstrated that Germany experienced several WNV introduction events and that strains of a distinct group (Eastern German WNV clade), which was introduced to Germany as a single introduction event, dominated mosquito, birds, horse and human-related virus variants in 2018 and 2019. Virus strains in this clade are characterized by a specific-Lys2114Arg mutation, which might lead to an increase in viral fitness. Extraordinary high temperatures in 2018/2019 allowed a low extrinsic incubation period (EIP), which drove the epizootic emergence and, in the end, most likely triggered the 2019 epidemic. Spatiotemporal EIP values correlated with the geographical WNV incidence. This study highlights the risk of a further spread in Germany in the next years with additional human WNV infections. Thus, surveillance of birds is essential to provide an early epidemic warning and thus, initiate targeted control measures.
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33
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Abstract
Influenza viruses rapidly diversify within individual human infections. Several recent studies have deep-sequenced clinical influenza infections to identify viral variation within hosts, but it remains unclear how within-host mutations fare at the between-host scale. Here, we compare the genetic variation of H3N2 influenza within and between hosts to link viral evolutionary dynamics across scales. Synonymous sites evolve at similar rates at both scales, indicating that global evolution at these putatively neutral sites results from the accumulation of within-host variation. However, nonsynonymous mutations are depleted between hosts compared to within hosts, suggesting that selection purges many of the protein-altering changes that arise within hosts. The exception is at antigenic sites, where selection detectably favors nonsynonymous mutations at the global scale, but not within hosts. These results suggest that selection against deleterious mutations and selection for antigenic change are the main forces that act on within-host variants of influenza virus as they transmit and circulate between hosts.
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Affiliation(s)
- Katherine S Xue
- Department of Genome Sciences, University of Washington, Foege Building S-250, Box 3550653720 15th Ave NE, Seattle WA 98195-5065, USA.,Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109-1024, USA.,Department of Biology, Stanford University, Stanford, CA, USA
| | - Jesse D Bloom
- Department of Genome Sciences, University of Washington, Foege Building S-250, Box 3550653720 15th Ave NE, Seattle WA 98195-5065, USA.,Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109-1024, USA.,Howard Hughes Medical Institute, 1100 Fairview Ave N, Seattle, WA 98109-1024, USA
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Bergren NA, Haller S, Rossi SL, Seymour RL, Huang J, Miller AL, Bowen RA, Hartman DA, Brault AC, Weaver SC. "Submergence" of Western equine encephalitis virus: Evidence of positive selection argues against genetic drift and fitness reductions. PLoS Pathog 2020; 16:e1008102. [PMID: 32027727 PMCID: PMC7029877 DOI: 10.1371/journal.ppat.1008102] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 02/19/2020] [Accepted: 09/22/2019] [Indexed: 11/18/2022] Open
Abstract
Understanding the circumstances under which arboviruses emerge is critical for the development of targeted control and prevention strategies. This is highlighted by the emergence of chikungunya and Zika viruses in the New World. However, to comprehensively understand the ways in which viruses emerge and persist, factors influencing reductions in virus activity must also be understood. Western equine encephalitis virus (WEEV), which declined during the late 20th century in apparent enzootic circulation as well as equine and human disease incidence, provides a unique case study on how reductions in virus activity can be understood by studying evolutionary trends and mechanisms. Previously, we showed using phylogenetics that during this period of decline, six amino acid residues appeared to be positively selected. To assess more directly the effect of these mutations, we utilized reverse genetics and competition fitness assays in the enzootic host and vector (house sparrows and Culex tarsalis mosquitoes). We observed that the mutations contemporary with reductions in WEEV circulation and disease that were non-conserved with respect to amino acid properties had a positive effect on enzootic fitness. We also assessed the effects of these mutations on virulence in the Syrian-Golden hamster model in relation to a general trend of increased virulence in older isolates. However, no change effect on virulence was observed based on these mutations. Thus, while WEEV apparently underwent positive selection for infection of enzootic hosts, residues associated with mammalian virulence were likely eliminated from the population by genetic drift or negative selection. These findings suggest that ecologic factors rather than fitness for natural transmission likely caused decreased levels of enzootic WEEV circulation during the late 20th century.
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Affiliation(s)
- Nicholas A. Bergren
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Sherry Haller
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
- Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Shannan L. Rossi
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
- Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Robert L. Seymour
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Jing Huang
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Aaron L. Miller
- Department of Pediatrics, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Richard A. Bowen
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
- Department of Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Daniel A. Hartman
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Aaron C. Brault
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
| | - Scott C. Weaver
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
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Blight J, Alves E, Reyes-Sandoval A. Considering Genomic and Immunological Correlates of Protection for a Dengue Intervention. Vaccines (Basel) 2019; 7:E203. [PMID: 31816907 PMCID: PMC6963661 DOI: 10.3390/vaccines7040203] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/25/2019] [Accepted: 11/27/2019] [Indexed: 01/18/2023] Open
Abstract
Over three billion are at risk of dengue infection with more than 100 million a year presenting with symptoms that can lead to deadly haemorrhagic disease. There are however no treatments available and the only licensed vaccine shows limited efficacy and is able to enhance the disease in some cases. These failures have mainly been due to the complex pathology and lack of understanding of the correlates of protection for dengue virus (DENV) infection. With increasing data suggesting both a protective and detrimental effect for antibodies and CD8 T-cells whilst having complex environmental dynamics. This review discusses the roles of genomic and immunological aspects of DENV infection, providing both a historical interpretation and fresh discussion on how this information can be used for the next generation of dengue interventions.
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Affiliation(s)
- Joshua Blight
- Department of Life Sciences, Imperial College London, Sir Alexander Fleming Building, Exhibition Road, South Kensington, London SW7 2AZ, UK; (J.B.); (E.A.)
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, The Henry Wellcome Building for Molecular Physiology, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Eduardo Alves
- Department of Life Sciences, Imperial College London, Sir Alexander Fleming Building, Exhibition Road, South Kensington, London SW7 2AZ, UK; (J.B.); (E.A.)
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, The Henry Wellcome Building for Molecular Physiology, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Arturo Reyes-Sandoval
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, The Henry Wellcome Building for Molecular Physiology, Roosevelt Drive, Oxford OX3 7BN, UK
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Lewitus E, Rolland M. A non-parametric analytic framework for within-host viral phylogenies and a test for HIV-1 founder multiplicity. Virus Evol 2019; 5:vez044. [PMID: 31700680 PMCID: PMC6826062 DOI: 10.1093/ve/vez044] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Phylogenetics is a powerful tool for understanding the diversification dynamics of viral pathogens. Here we present an extension of the spectral density profile of the modified graph Laplacian, which facilitates the characterization of within-host molecular evolution of viruses and the direct comparison of diversification dynamics between hosts. This approach is non-parametric and therefore fast and model-free. We used simulations of within-host evolutionary scenarios to evaluate the efficiency of our approach and to demonstrate the significance of interpreting a viral phylogeny by its spectral density profile in terms of diversification dynamics. The key features that are captured by the profile are positive selection on the viral gene (or genome), temporal changes in substitution rates, mutational fitness, and time between sampling. Using sequences from individuals infected with HIV-1, we showed the utility of this approach for characterizing within-host diversification dynamics, for comparing dynamics between hosts, and for charting disease progression in infected individuals sampled over multiple years. We furthermore propose a heuristic test for assessing founder heterogeneity, which allows us to classify infections with single and multiple HIV-1 founder viruses. This non-parametric approach can be a valuable complement to existing parametric approaches.
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Affiliation(s)
- Eric Lewitus
- U.S. Military HIV Research Program (MHRP), WRAIR, 503 Robert Grant Avenue, Silver Spring, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Dr, Bethesda, MD, USA
| | - Morgane Rolland
- U.S. Military HIV Research Program (MHRP), WRAIR, 503 Robert Grant Avenue, Silver Spring, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Dr, Bethesda, MD, USA
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Evolutionary timescale and geographical movement of cucumber mosaic virus, with focus on Iranian strains. Arch Virol 2019; 165:185-192. [PMID: 31637514 DOI: 10.1007/s00705-019-04439-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 09/16/2019] [Indexed: 10/25/2022]
Abstract
Cucumber mosaic virus (CMV) is a geographically widespread plant virus with a very broad host range. The virus has been detected in diverse crops all over Iran. In this study, we estimated the timescale of the evolution of CMV subgroup I and the geographical movement of the virus with a focus on Iranian strains. Analyses using the MP and CP genes and their concatenation revealed that the CMV population within subgroup I had a single ancestor dating back to about 450-550 years ago. The Iranian strains formed three clusters in a maximum-clade-credibility phylogenetic tree. It was found that the most recent common ancestor of the Iranian strains within each cluster dates back to less than 100 years ago. Our results also suggest that both short- and long-distance migration of Iranian CMV strains has occurred in the last 100 years.
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38
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Many human RNA viruses show extraordinarily stringent selective constraints on protein evolution. Proc Natl Acad Sci U S A 2019; 116:19009-19018. [PMID: 31484772 DOI: 10.1073/pnas.1907626116] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
How negative selection, positive selection, and population size contribute to the large variation in nucleotide substitution rates among RNA viruses remains unclear. Here, we studied the ratios of nonsynonymous-to-synonymous substitution rates (d N/d S) in protein-coding genes of human RNA and DNA viruses and mammals. Among the 21 RNA viruses studied, 18 showed a genome-average d N/d S from 0.01 to 0.10, indicating that over 90% of nonsynonymous mutations are eliminated by negative selection. Only HIV-1 showed a d N/d S (0.31) higher than that (0.22) in mammalian genes. By comparing the d N/d S values among genes in the same genome and among species or strains, we found that both positive selection and population size play significant roles in the d N/d S variation among genes and species. Indeed, even in flaviviruses and picornaviruses, which showed the lowest ratios among the 21 species studied, positive selection appears to have contributed significantly to d N/d S We found the view that positive selection occurs much more frequently in influenza A subtype H3N2 than subtype H1N1 holds only for the hemagglutinin and neuraminidase genes, but not for other genes. Moreover, we found no support for the view that vector-borne RNA viruses have lower d N/d S ratios than non-vector-borne viruses. In addition, we found a correlation between d N and d S, implying a correlation between d N and the mutation rate. Interestingly, only 2 of the 8 DNA viruses studied showed a d N/d S < 0.10, while 4 showed a d N/d S > 0.22. These observations increase our understanding of the mechanisms of RNA virus evolution.
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Chikungunya Virus Vaccine Candidates with Decreased Mutational Robustness Are Attenuated In Vivo and Have Compromised Transmissibility. J Virol 2019; 93:JVI.00775-19. [PMID: 31270226 PMCID: PMC6714818 DOI: 10.1128/jvi.00775-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 06/11/2019] [Indexed: 11/20/2022] Open
Abstract
Chikungunya virus (CHIKV) is a reemerged arbovirus, a member of the Togaviridae family. It circulates through mosquito vectors mainly of the Aedes family and a mammalian host. CHIKV causes chikungunya fever, a mild to severe disease characterized by arthralgia, with some fatal outcomes described. In the past years, several outbreaks mainly caused by enhanced adaptation of the virus to the vector and ineffective control of the contacts between infected mosquito populations and the human host have been reported. Vaccines represent the best solution for the control of insect-borne viruses, including CHIKV, but are often unavailable. We designed live attenuated CHIKVs by applying a rational genomic design based on multiple replacements of synonymous codons. In doing so, the virus mutational robustness (capacity to maintain phenotype despite introduction of mutations to genotype) is decreased, driving the viral population toward deleterious evolutionary trajectories. When the candidate viruses were tested in the insect and mammalian hosts, we observed overall strong attenuation in both and greatly diminished signs of disease. Moreover, we found that the vaccine candidates elicited protective immunity related to the production of neutralizing antibodies after a single dose. During an experimental transmission cycle between mosquitoes and naive mice, vaccine candidates could be transmitted by mosquito bite, leading to asymptomatic infection in mice with compromised dissemination. Using deep-sequencing technology, we observed an increase in detrimental (stop) codons, which confirmed the effectiveness of this genomic design. Because the approach involves hundreds of synonymous modifications to the genome, the reversion risk is significantly reduced, rendering the viruses promising vaccine candidates.IMPORTANCE Chikungunya fever is a debilitating disease that causes severe pain to the joints, which can compromise the patient's lifestyle for several months and even in some grave cases lead to death. The etiological agent is chikungunya virus, an alphavirus transmitted by mosquito bite. Currently, there are no approved vaccines or treatments against the disease. In our research, we developed novel live attenuated vaccine candidates against chikungunya virus by applying an innovative genomic design. When tested in the insect and mammalian host, the vaccine candidates did not cause disease, elicited strong protection against further infection, and had low risk of reversion to pathogenic phenotypes.
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40
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Sang S, Liu-Helmersson J, Quam MBM, Zhou H, Guo X, Wu H, Liu Q. The evolutionary dynamics of DENV 4 genotype I over a 60-year period. PLoS Negl Trop Dis 2019; 13:e0007592. [PMID: 31356608 PMCID: PMC6663010 DOI: 10.1371/journal.pntd.0007592] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 07/01/2019] [Indexed: 01/26/2023] Open
Abstract
Dengue virus serotype 4 (DENV 4) has had a relatively low prevalence worldwide for decades; however, likely due to data paucity, no study has investigated the epidemiology and evolutionary dynamics of DENV 4 genotype I (DENV 4-I). This study aims to understand the diversity, epidemiology and dynamics of DENV 4-I. We collected 404 full length DENV4-1 envelope (E) gene sequences from 14 countries using two sources: Yunnan Province in China (15 strains during 2013–2016) and GenBank (489 strains up to 2018-01-11). Conducting phylogenetic and phylogeographical analyses, we estimated the virus spread, population dynamics, and selection pressures using different statistical analysis methods (substitution saturation, likelihood mapping, Bayesian coalescent inference, and maximum likelihood estimation). Our results show that during the last 60 years (1956–2016), DENV 4-I was present in mainland and maritime Southeast Asia, the Indian subcontinent, the southern provinces of China, parts of Brazil and Australia. The recent spread of DENV 4-I likely originated in the Philippines and later spread to Thailand. From Thailand, it spread to adjacent countries and eventually the Indian subcontinent. Apparently diverging around years 1957, 1963, 1976 and 1990, the different Clades (Clade I-V) were defined. The mean overall evolution rate of DENV 4-I was 9.74 (95% HPD: 8.68–10.82) × 10−4 nucleotide substitutions/site/year. The most recent common ancestor for DENV 4-I traces back to 1956. While the demographic history of DENV 4-I fluctuated, peaks appeared around 1982 and 2006. While purifying selection dominated the majority of E-gene evolution of DENV 4-I, positive selection characterized Clade III (Vietnam). DENV 4-I evolved in situ in Southeast Asia and the Indian subcontinent. Thailand and Indian acted as the main and secondary virus distribution hubs globally and regionally. Our phylogenetic analysis highlights the need for strengthened regional cooperation on surveillance and sharing of sample sequences to improve global dengue control and cross-border transmission prevention efforts. Dengue virus (DENV) can be classified into four serotypes, DENV 1, 2, 3 and 4. Although DENV 4 is the first dengue serotype to diverge in phylogenetic analyses of the genus Flavivirus, this serotype occurs at a low prevalence worldwide and spreads the least rapidly. Similar to other serotypes, DENV 4 can also cause severe dengue (SD) disease manifestations, such as dengue haemorrhagic fever (DHF) and dengue shock syndrome (DSS). To date, no study has investigated the epidemiology and dynamics of DENV 4 genotype I comprehensively. In this study, we seek to address this gap. Our study shows that the distribution of DENV 4-I is mainly restricted to Southeast Asia and the Indian subcontinent. The most recent spread of DENV 4-I likely originated from Southeast Asia–initially circulating in the Philippines, then Thailand and later on the Indian subcontinent. Viruses evolved in situ in Southeast Asia and the Indian subcontinent, respectively. Although DENV 4-I occasionally spread elsewhere, this genotype did not become widely established. The overall evolution rate of DENV 4-I was comparable with that of DENV 2–4. The nucleotide sequences indicates that the demographic history of DENV 4-I fluctuated with peaks apparent during parts of the 1980s and 2000s. Although a weak positive selection existed in Clade III -predominately in Vietnam, purifying selection dominated the E-gene evolution of DENV 4-I.
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Affiliation(s)
- Shaowei Sang
- Clinical Epidemiology Unit, Qilu Hospital of Shandong University, Jinan, Shandong, People's Republic of China
- Department of Epidemiology and Health Statistics, School of Public Health, Shandong University, Jinan, Shandong, People's Republic of China
- * E-mail: (SS); (QL)
| | | | - Mikkel B. M. Quam
- Department of Epidemiology and Global Health, Umea University, Umea, Sweden
| | - Hongning Zhou
- Yunnan Provincial Center of Arborvirus Research, Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Yunnan Institute of Parasitic Diseases, Pu'er, Yunnan, People's Republic of China
| | - Xiaofang Guo
- Yunnan Provincial Center of Arborvirus Research, Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Yunnan Institute of Parasitic Diseases, Pu'er, Yunnan, People's Republic of China
| | - Haixia Wu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, People's Republic of China
| | - Qiyong Liu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, People's Republic of China
- * E-mail: (SS); (QL)
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Endless Forms: Within-Host Variation in the Structure of the West Nile Virus RNA Genome during Serial Passage in Bird Hosts. mSphere 2019; 4:4/3/e00291-19. [PMID: 31243074 PMCID: PMC6595145 DOI: 10.1128/msphere.00291-19] [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] [Indexed: 02/05/2023] Open
Abstract
The enzymes that copy RNA genomes lack proofreading, and viruses that possess RNA genomes, such as West Nile virus, rapidly diversify into swarms of mutant lineages within a host. Intrahost variation of the primary genomic sequence of RNA viruses has been studied extensively because the extent of this variation shapes key virus phenotypes. However, RNA genomes also form complex secondary structures based on within-genome nucleotide complementarity, which are critical regulators of the cyclization of the virus genome that is necessary for efficient replication and translation. We sought to characterize variation in these secondary structures within populations of West Nile virus during serial passage in three bird species. Our study indicates that the intrahost population of West Nile virus is a diverse assortment of RNA secondary structures that should be considered in future analyses of intrahost viral diversity, but some regions that are critical for genome cyclization are conserved within hosts. Besides potential impacts on viral replication, structural diversity can influence the efficacy of small RNA antiviral therapies. RNA viruses are infamous for their high rates of mutation, which produce swarms of genetic variants within individual hosts. To date, analyses of intrahost genetic diversity have focused on the primary genome sequence. However, virus phenotypes are shaped not only by primary sequence but also by the secondary structures into which this sequence folds. Such structures enable viral replication, translation, and binding of small RNAs, yet within-host variation at the structural level has not been adequately explored. We characterized the structural diversity of the 5′ untranslated region (UTR) of populations of West Nile virus (WNV) that had been subject to five serial passages in triplicate in each of three bird species. Viral genomes were sampled from host serum samples at each passage (n = 45 populations) and subjected to next-generation sequencing. For populations derived from passages 1, 3, and 5 (n = 9 populations), we predicted the impact of each mutation occurring at a frequency of ≥1% on the secondary structure of the 5′ UTR. As expected, mutations in double-stranded (DS) regions of the 5′ UTR stem structures caused structural changes of significantly greater magnitude than did mutations in single-stranded (SS) regions. Despite the greater impact of mutations in DS regions, mutations in DS and SS regions occurred at similar frequencies, with no evidence of enhanced selection against mutation in DS regions. In contrast, mutations in two regions that mediate genome cyclization and thereby regulate replication and translation, the 5′ cyclization sequence and the UAR flanking stem (UFS), were suppressed in all three hosts. IMPORTANCE The enzymes that copy RNA genomes lack proofreading, and viruses that possess RNA genomes, such as West Nile virus, rapidly diversify into swarms of mutant lineages within a host. Intrahost variation of the primary genomic sequence of RNA viruses has been studied extensively because the extent of this variation shapes key virus phenotypes. However, RNA genomes also form complex secondary structures based on within-genome nucleotide complementarity, which are critical regulators of the cyclization of the virus genome that is necessary for efficient replication and translation. We sought to characterize variation in these secondary structures within populations of West Nile virus during serial passage in three bird species. Our study indicates that the intrahost population of West Nile virus is a diverse assortment of RNA secondary structures that should be considered in future analyses of intrahost viral diversity, but some regions that are critical for genome cyclization are conserved within hosts. Besides potential impacts on viral replication, structural diversity can influence the efficacy of small RNA antiviral therapies.
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Abstract
Very little is known about aquatic RNA virus populations and genome evolution. This is the first study that analyzes marine environmental RNA viral assemblages in an evolutionary and broad geographical context. This study contributes the largest marine RNA virus metagenomic data set to date, substantially increasing the sequencing space for RNA viruses and also providing a baseline for comparisons of marine RNA virus diversity. The new viruses discovered in this study are representative of the most abundant family of marine RNA viruses, the Marnaviridae, and expand our view of the diversity of this important group. Overall, our data and analyses provide a foundation for interpreting marine RNA virus diversity and evolution. RNA viruses, particularly genetically diverse members of the Picornavirales, are widespread and abundant in the ocean. Gene surveys suggest that there are spatial and temporal patterns in the composition of RNA virus assemblages, but data on their diversity and genetic variability in different oceanographic settings are limited. Here, we show that specific RNA virus genomes have widespread geographic distributions and that the dominant genotypes are under purifying selection. Genomes from three previously unknown picorna-like viruses (BC-1, -2, and -3) assembled from a coastal site in British Columbia, Canada, as well as marine RNA viruses JP-A, JP-B, and Heterosigma akashiwo RNA virus exhibited different biogeographical patterns. Thus, biotic factors such as host specificity and viral life cycle, and not just abiotic processes such as dispersal, affect marine RNA virus distribution. Sequence differences relative to reference genomes imply that virus quasispecies are under purifying selection, with synonymous single-nucleotide variations dominating in genomes from geographically distinct regions resulting in conservation of amino acid sequences. Conversely, sequences from coastal South Africa that mapped to marine RNA virus JP-A exhibited more nonsynonymous mutations, probably representing amino acid changes that accumulated over a longer separation. This biogeographical analysis of marine RNA viruses demonstrates that purifying selection is occurring across oceanographic provinces. These data add to the spectrum of known marine RNA virus genomes, show the importance of dispersal and purifying selection for these viruses, and indicate that closely related RNA viruses are pathogens of eukaryotic microbes across oceans. IMPORTANCE Very little is known about aquatic RNA virus populations and genome evolution. This is the first study that analyzes marine environmental RNA viral assemblages in an evolutionary and broad geographical context. This study contributes the largest marine RNA virus metagenomic data set to date, substantially increasing the sequencing space for RNA viruses and also providing a baseline for comparisons of marine RNA virus diversity. The new viruses discovered in this study are representative of the most abundant family of marine RNA viruses, the Marnaviridae, and expand our view of the diversity of this important group. Overall, our data and analyses provide a foundation for interpreting marine RNA virus diversity and evolution.
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Salvo MA, Aliota MT, Moncla LH, Velez ID, Trujillo AI, Friedrich TC, Osorio JE. Tracking dengue virus type 1 genetic diversity during lineage replacement in an hyperendemic area in Colombia. PLoS One 2019; 14:e0212947. [PMID: 30845200 PMCID: PMC6405123 DOI: 10.1371/journal.pone.0212947] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 02/12/2019] [Indexed: 12/16/2022] Open
Abstract
Dengue virus (DENV) is a flavivirus responsible for the most common and burdensome arthropod-borne viral disease of humans[1]. DENV evolution has been extensively studied on broad geographic and time scales, using sequences from a single gene[2,3]. It is believed that DENV evolution in humans is dominated primarily by purifying selection due to the constraint of maintaining fitness in both humans and mosquitoes[4,5]. Few studies have explored DENV evolutionary dynamics using whole genome sequences, nor have they explored changes in viral diversity that occur during intra-epidemic periods. We used deep sequencing of the viral coding region to characterize DENV-1 evolution in a Colombian population sampled during two high-prevalence dengue seasons in which serotype dominance shifted. Our data demonstrate patterns of strain extinction and replacement within DENV-1 as its prevalence waned and DENV-3 became established. A comparison of whole-genome versus single-gene-based phylogenetic analyses highlights an important difference in evolutionary patterns. We report a trend of higher nonsynonymous to synonymous diversity ratios among non-structural (NS) genes, and statistically significantly higher values among these ratios in the NS1 gene after DENV-1 strain replacement. These results suggest that positive selection could be driving DENV evolution within individual communities. Signals of positive selection coming from distinct samples may be drowned out when combining multiple regions with differing patterns of endemic transmission as commonly done by large-scale geo-temporal assessments. Here, we frame our findings within a small, local transmission history which aids significance. Moreover, these data suggest that the NS1 gene, rather than the E gene, may be a target of positive selection, although not mutually exclusive, and potentially useful sentinel of adaptive changes at the population level.
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Affiliation(s)
- Mauricio A. Salvo
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Matthew T. Aliota
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Louise H. Moncla
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Ivan D. Velez
- Programa de Estudio y Control de Enfermedades Tropicales (PECET), Universidad de Antioquia, Medellin, Colombia
| | - Andrea I. Trujillo
- Programa de Estudio y Control de Enfermedades Tropicales (PECET), Universidad de Antioquia, Medellin, Colombia
| | - Thomas C. Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Jorge E. Osorio
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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Chisholm PJ, Busch JW, Crowder DW. Effects of life history and ecology on virus evolutionary potential. Virus Res 2019; 265:1-9. [PMID: 30831177 DOI: 10.1016/j.virusres.2019.02.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 02/27/2019] [Accepted: 02/28/2019] [Indexed: 11/28/2022]
Abstract
The life history traits of viruses pose many consequences for viral population structure. In turn, population structure may influence the evolutionary trajectory of a virus. Here we review factors that affect the evolutionary potential of viruses, including rates of mutation and recombination, bottlenecks, selection pressure, and ecological factors such as the requirement for hosts and vectors. Mutation, while supplying a pool of raw genetic material, also results in the generation of numerous unfit mutants. The infection of multiple host species may expand a virus' ecological niche, although it may come at a cost to genetic diversity. Vector-borne viruses often experience a diminished frequency of positive selection and exhibit little diversity, and resistance against vector-borne viruses may thus be more durable than against non-vectored viruses. Evidence indicates that adaptation to a vector is more evolutionarily difficult than adaptation to a host. Overall, a better understanding of how various factors influence viral dynamics in both plant and animal pathosystems will lead to more effective anti-viral treatments and countermeasures.
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Affiliation(s)
- Paul J Chisholm
- Department of Entomology, Washington State University, 166 FSHN Building, Pullman, WA, 99164, USA.
| | - Jeremiah W Busch
- School of Biological Sciences, Washington State University, PO Box 644236, Pullman, WA, 99164, USA.
| | - David W Crowder
- Department of Entomology, Washington State University, 166 FSHN Building, Pullman, WA, 99164, USA.
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Infectivity of Dengue Virus Serotypes 1 and 2 Is Correlated with E-Protein Intrinsic Dynamics but Not to Envelope Conformations. Structure 2019; 27:618-630.e4. [PMID: 30686666 DOI: 10.1016/j.str.2018.12.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 10/02/2018] [Accepted: 12/09/2018] [Indexed: 11/20/2022]
Abstract
Dengue is a mosquito-borne virus with dire health and economic impacts. Dengue is responsible for an estimated 390 million infections per year, with dengue 2 (DENV2) being the most virulent strain among the four serotypes. Interestingly, it is also in strains of this serotype that temperature-dependent large-scale morphological changes, termed "breathing," have been observed. Although the structure of these morphologies has been solved to 3.5-Å resolution, the dynamics of the viral envelope are unknown. Here, we combine fluorescence and mass spectrometry with molecular dynamics simulations to provide insights into DENV2 (NGC strain) structural dynamics in comparison with DENV1 (PVP 159). We observe hitherto unseen conformational changes and structural dynamics of the DENV2 envelope that are influenced by both temperature and divalent cations. Our results show that for DENV2 and DENV1 the intrinsic dynamics, but not the specific morphologies, are correlated with viral infectivity.
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Morsky B, Bauch CT. The impact of truncation selection and diffusion on cooperation in spatial games. J Theor Biol 2019; 466:64-83. [PMID: 30684498 DOI: 10.1016/j.jtbi.2019.01.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 01/16/2019] [Accepted: 01/22/2019] [Indexed: 11/30/2022]
Abstract
Natural Selection is frequently modelled via proportional selection where survival is proportional to the average payoff differential. There has been little attention devoted to modelling truncation selection where replicators below a threshold are culled and survivors reproduce. Here, we systematically explore truncation selection for two strategy games in a spatial setting. We employ two variations of truncation selection: independent, where the threshold is fixed; and dependent, where the proportion culled is fixed. Further, we explore the effects of diffusion with the algorithms: contest-diffusion-offspring (CDO), and diffusion-contest-offspring (DCO). CDO and DCO frequently facilitate and diminish cooperation, respectively. For independent truncation, there are three qualitative regimes determined by the payoff threshold: cooperation decreases as the threshold rises; polymorphisms are stable; and extinction is frequent. Further, an intermediate payoff to cooperators playing defectors can maximize cooperation for the DCO algorithm with a high payoff threshold. Dependent truncation affects games differently; lower levels reduce cooperation for the Hawk Dove game and increase it for the Stag Hunt, and higher levels produce the opposite effects. Comparing these truncation methods to proportional selection, we show how they impact the prevalence of cooperation.
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Affiliation(s)
- Bryce Morsky
- Department of Mathematics and Statistics, University of Guelph, 50 Stone Road East, Room 437 MacNaughton Building, Guelph, Ontario N1G 2W1, Canada; Department of Physics, University of Notre Dame, Nieuwland Science Hall, Notre Dame, IN 46556, USA; Department of Biology, University of Pennsylvania, Carolyn Lynch Laboratory, Philadelphia, PA 19104, USA.
| | - Chris T Bauch
- Department of Applied Mathematics, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
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Oliveira DBL, Durigon GS, Mendes ÉA, Ladner JT, Andreata-Santos R, Araujo DB, Botosso VF, Paola ND, Neto DFL, Cunha MP, Braconi CT, Alves RPS, Jesus MR, Pereira LR, Melo SR, Mesquita FS, Silveira VB, Thomazelli LM, Favoretto SR, Almonfrey FB, Abdulkader RCRM, Gabrili JM, Tambourgi DV, Oliveira SF, Prieto K, Wiley MR, Ferreira LCS, Silva MV, Palacios GF, Zanotto PMA, Durigon EL. Persistence and Intra-Host Genetic Evolution of Zika Virus Infection in Symptomatic Adults: A Special View in the Male Reproductive System. Viruses 2018; 10:v10110615. [PMID: 30405055 PMCID: PMC6267439 DOI: 10.3390/v10110615] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 10/04/2018] [Accepted: 10/20/2018] [Indexed: 01/27/2023] Open
Abstract
We followed the presence of Zika virus (ZIKV) in four healthy adults (two men and two women), for periods ranging from 78 to 298 days post symptom onset. The patients were evaluated regarding the presence of the virus in different body fluids (blood, saliva, urine and semen), development of immune responses (including antibodies, cytokines and chemokines), and virus genetic variation within samples collected from semen and urine during the infection course. The analysis was focused primarily on the two male patients who shed the virus for up to 158 days after the initial symptoms. ZIKV particles were detected in the spermatozoa cytoplasm and flagella, in immature sperm cells and could also be isolated from semen in cell culture, confirming that the virus is able to preserve integrity and infectivity during replication in the male reproductive system (MRS). Despite the damage caused by ZIKV infection within the MRS, our data showed that ZIKV infection did not result in infertility at least in one of the male patients. This patient was able to conceive a child after the infection. We also detected alterations in the male genital cytokine milieu, which could play an important role in the replication and transmission of the virus which could considerably increase the risk of ZIKV sexual spread. In addition, full genome ZIKV sequences were obtained from several samples (mainly semen), which allowed us to monitor the evolution of the virus within a patient during the infection course. We observed genetic changes over time in consensus sequences and lower frequency intra-host single nucleotide variants (iSNV), that suggested independent compartmentalization of ZIKV populations in the reproductive and urinary systems. Altogether, the present observations confirm the risks associated with the long-term replication and shedding of ZIKV in the MRS and help to elucidate patterns of intra-host genetic evolution during long term replication of the virus.
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Affiliation(s)
- Danielle B L Oliveira
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Giuliana S Durigon
- Medical School Clinic Hospital, University of São Paulo, São Paulo, SP 05403-000, Brazil.
| | - Érica A Mendes
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Jason T Ladner
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA.
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011-4073, USA.
| | - Robert Andreata-Santos
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Danielle B Araujo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Viviane F Botosso
- Virology Laboratory, Butantan Institute, São Paulo, SP 05503-900, Brazil.
| | - Nicholas D Paola
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Daniel F L Neto
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Marielton P Cunha
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Carla T Braconi
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Rúbens P S Alves
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Monica R Jesus
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Lennon R Pereira
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Stella R Melo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Flávio S Mesquita
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Vanessa B Silveira
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Luciano M Thomazelli
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | | | - Franciane B Almonfrey
- Medical School Clinic Hospital, University of São Paulo, São Paulo, SP 05403-000, Brazil.
| | | | - Joel M Gabrili
- Virology Laboratory, Butantan Institute, São Paulo, SP 05503-900, Brazil.
- Immunochemistry Laboratory, Butantan Institute, São Paulo, SP 05503-900, Brazil.
| | - Denise V Tambourgi
- Virology Laboratory, Butantan Institute, São Paulo, SP 05503-900, Brazil.
| | - Sérgio F Oliveira
- Department of Cellular and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Karla Prieto
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA.
- Department of Environmental, Agricultural and Occupational Health, University of Nebraska Medical Center, Omaha, NE 68198-4388, USA.
| | - Michael R Wiley
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA.
- Department of Environmental, Agricultural and Occupational Health, University of Nebraska Medical Center, Omaha, NE 68198-4388, USA.
| | - Luís C S Ferreira
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Marcos V Silva
- Institute of Infectology Emílio Ribas e Pontifícia Universidade Católica (PUC-SP), São Paulo, SP 01246-900, Brazil.
| | - Gustavo F Palacios
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA.
| | - Paolo M A Zanotto
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Edison L Durigon
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
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Shrivastava S, Puri V, Dilley KA, Ngouajio E, Shifflett J, Oldfield LM, Fedorova NB, Hu L, Williams T, Durbin A, Amedeo P, Rashid S, Shabman RS, Pickett BE. Whole genome sequencing, variant analysis, phylogenetics, and deep sequencing of Zika virus strains. Sci Rep 2018; 8:15843. [PMID: 30367096 PMCID: PMC6203802 DOI: 10.1038/s41598-018-34147-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 10/08/2018] [Indexed: 12/25/2022] Open
Abstract
The recent emergence of Zika virus (ZIKV) has been concentrated in the Caribbean, Southeastern United States, and South- and Central America; resulting in travel-based cases being reported around the globe. As multi-disciplinary collaborations are combatting the ZIKV outbreak, the need to validate the sequence of existing strains has become apparent. Here, we report high-quality sequence data for multiple ZIKV strains made publicly available through the National Institutes of Health- (NIH) funded biorepository, BEI Resources (www.beiresources.org). Next-generation sequencing, 3' rapid amplification of cDNA ends (RACE), and viral genome annotation pipelines generated GenBank sequence records for 16 BEI Resources strains. Minor variants, consensus mutations, and consensus insertions/deletions were identified within the viral stocks using next-generation sequencing (NGS) and consensus changes were confirmed with Sanger sequencing. Bioinformatics analyses of the sequencing results confirm that the virus stocks available to the scientific research community through BEI Resources adequately represent the viral population diversity of ZIKV.
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Affiliation(s)
| | - Vinita Puri
- J. Craig Venter Institute, Rockville, MD, USA
| | - Kari A Dilley
- J. Craig Venter Institute, Rockville, MD, USA
- Sharp Edge Labs, Pittsburgh, PA, USA
| | - Erica Ngouajio
- J. Craig Venter Institute, Rockville, MD, USA
- University of Maryland, College Park, MD, USA
| | | | | | | | - Lihui Hu
- J. Craig Venter Institute, Rockville, MD, USA
| | | | - Alan Durbin
- J. Craig Venter Institute, La Jolla, CA, USA
| | | | | | - Reed S Shabman
- J. Craig Venter Institute, Rockville, MD, USA
- American Type Culture Collection, Manassas, VA, USA
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49
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Ko HY, Li YT, Chao DY, Chang YC, Li ZRT, Wang M, Kao CL, Wen TH, Shu PY, Chang GJJ, King CC. Inter- and intra-host sequence diversity reveal the emergence of viral variants during an overwintering epidemic caused by dengue virus serotype 2 in southern Taiwan. PLoS Negl Trop Dis 2018; 12:e0006827. [PMID: 30286095 PMCID: PMC6191158 DOI: 10.1371/journal.pntd.0006827] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 10/16/2018] [Accepted: 09/10/2018] [Indexed: 12/23/2022] Open
Abstract
Purifying selection during dengue viral infection has been suggested as the driving force of viral evolution and the higher complexity of the intra-host quasi-species is thought to offer an adaptive advantage for arboviruses as they cycle between arthropod and vertebrate hosts. However, very few studies have been performed to investigate the viral genetic changes within (intra-host) and between (inter-host) humans in a spatio-temporal scale. Viruses of different serotypes from various countries imported to Taiwan cause annual outbreaks. During 2001-2003, two consecutive outbreaks were caused by dengue virus serotype 2 (DENV-2) and resulted in a larger-scale epidemic with more severe dengue cases in the following year. Phylogenetic analyses showed that the viruses from both events were similar and related to the 2001 DENV-2 isolate from the Philippines. We comprehensively analyzed viral sequences from representative dengue patients and identified three consensus genetic variants, group Ia, Ib and II, with different spatio-temporal population dynamics. The phylodynamic analysis suggested group Ib variants, characterized by lower genetic diversity, transmission rate, and intra-host variant numbers, might play the role of maintenance variants. The residential locations among the patients infected by group Ib variants were in the outer rim of case clusters throughout the 2001-2003 period whereas group Ia and II variants were located in the centers of case clusters, suggesting that group Ib viruses might serve as "sheltered overwintering" variants in an undefined ecological niche. Further deep sequencing of the viral envelope (E) gene directly from individual patient serum samples confirmed the emergence of variants belonging to three quasi-species (group Ia, Ib, and II) and the ancestral role of the viral variants in the latter phase of the 2001 outbreak contributed to the later, larger-scale epidemic beginning in 2002. These findings enhanced our understanding of increasing epidemic severity over time in the same epidemic area. It also highlights the importance of combining phylodynamic and deep sequencing analysis as surveillance tools for detecting dynamic changes in viral variants, particularly searching for and monitoring any specific viral subpopulation. Such subpopulations might have selection advantages in both fitness and transmissibility leading to increased epidemic severity.
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Affiliation(s)
- Hui-Ying Ko
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan, Republic of China
| | - Yao-Tsun Li
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan, Republic of China
| | - Day-Yu Chao
- School of Veterinary Medicine, Institute of Microbiology and Public Health, National Chung-Hsing University, Taichung, Taiwan, Republic of China
- * E-mail: (DYC); (GJC); (CCK)
| | - Yun-Cheng Chang
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan, Republic of China
| | - Zheng-Rong T. Li
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan, Republic of China
| | - Melody Wang
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan, Republic of China
| | - Chuan-Liang Kao
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan, Republic of China
| | - Tzai-Hung Wen
- Department of Geography, College of Science, National Taiwan University, Taipei, Taiwan, Republic of China
| | - Pei-Yun Shu
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Ministry of Health and Welfare, Taiwan, Republic of China
| | - Gwong-Jen J. Chang
- Arboviral Diseases Branch, Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
- * E-mail: (DYC); (GJC); (CCK)
| | - Chwan-Chuen King
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan, Republic of China
- * E-mail: (DYC); (GJC); (CCK)
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50
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Pontremoli C, Forni D, Cagliani R, Sironi M. Analysis of Reptarenavirus genomes indicates different selective forces acting on the S and L segments and recent expansion of common genotypes. INFECTION GENETICS AND EVOLUTION 2018; 64:212-218. [DOI: 10.1016/j.meegid.2018.06.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 06/28/2018] [Accepted: 06/28/2018] [Indexed: 01/20/2023]
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