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Epidemiology and Phylogenetic Analysis of Viral Respiratory Infections in Vietnam
Acute respiratory infections (ARIs) impose a major public health burden on fragile healthcare systems of developing Southeast Asian countries such as Vietnam. The epidemiology, genetic diversity and transmission patterns of respiratory viral pathogens that circulate in this region are not well chara...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Frontiers Media S.A.
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7242649/ https://www.ncbi.nlm.nih.gov/pubmed/32499763 http://dx.doi.org/10.3389/fmicb.2020.00833 |
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author | Lu, Lu Robertson, Gail Ashworth, Jordan Pham Hong, Anh Shi, Ting Ivens, Alasdair Thwaites, Guy Baker, Stephen Woolhouse, Mark |
author_facet | Lu, Lu Robertson, Gail Ashworth, Jordan Pham Hong, Anh Shi, Ting Ivens, Alasdair Thwaites, Guy Baker, Stephen Woolhouse, Mark |
author_sort | Lu, Lu |
collection | PubMed |
description | Acute respiratory infections (ARIs) impose a major public health burden on fragile healthcare systems of developing Southeast Asian countries such as Vietnam. The epidemiology, genetic diversity and transmission patterns of respiratory viral pathogens that circulate in this region are not well characterized. We used RT-PCR to screen for 14 common respiratory viruses in nasal/throat samples from 4326 ARI patients from 5 sites in Vietnam during 2012–2016. 64% of patients tested positive for viruses; 14% tested positive multiple co-infecting viruses. The most frequently detected viruses were Respiratory syncytial virus (RSV, 23%), Human Rhinovirus (HRV, 13%), Influenza A virus (IAV, 11%) and Human Bocavirus (HBoV, 7%). RSV infections peaked in July to October, were relatively more common in children <1 year and in the northernmost hospital. IAV infections peaked in December to February and were relatively more common in patients >5 years in the central region. Coinfection with IAV or RSV was associated with increased disease severity compared with patients only infected with HBoV or HRV. Over a hundred genomes belonging to 13 families and 24 genera were obtained via metagenomic sequencing, including novel viruses and viruses less commonly associated with ARIs. Phylogenetic and phylogeographic analyses further indicated that neighboring countries were the most likely source of many virus lineages causing ARIs in Vietnam and estimated the period that specific lineages have been circulating. Our study illustrates the value of applying the state-of-the-art virus diagnostic methods (multiplex RT-PCR and metagenomic sequencing) and phylodynamic analyses at a national level to generate an integrated picture of viral ARI epidemiology. |
format | Online Article Text |
id | pubmed-7242649 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-72426492020-06-03 Epidemiology and Phylogenetic Analysis of Viral Respiratory Infections in Vietnam Lu, Lu Robertson, Gail Ashworth, Jordan Pham Hong, Anh Shi, Ting Ivens, Alasdair Thwaites, Guy Baker, Stephen Woolhouse, Mark Front Microbiol Microbiology Acute respiratory infections (ARIs) impose a major public health burden on fragile healthcare systems of developing Southeast Asian countries such as Vietnam. The epidemiology, genetic diversity and transmission patterns of respiratory viral pathogens that circulate in this region are not well characterized. We used RT-PCR to screen for 14 common respiratory viruses in nasal/throat samples from 4326 ARI patients from 5 sites in Vietnam during 2012–2016. 64% of patients tested positive for viruses; 14% tested positive multiple co-infecting viruses. The most frequently detected viruses were Respiratory syncytial virus (RSV, 23%), Human Rhinovirus (HRV, 13%), Influenza A virus (IAV, 11%) and Human Bocavirus (HBoV, 7%). RSV infections peaked in July to October, were relatively more common in children <1 year and in the northernmost hospital. IAV infections peaked in December to February and were relatively more common in patients >5 years in the central region. Coinfection with IAV or RSV was associated with increased disease severity compared with patients only infected with HBoV or HRV. Over a hundred genomes belonging to 13 families and 24 genera were obtained via metagenomic sequencing, including novel viruses and viruses less commonly associated with ARIs. Phylogenetic and phylogeographic analyses further indicated that neighboring countries were the most likely source of many virus lineages causing ARIs in Vietnam and estimated the period that specific lineages have been circulating. Our study illustrates the value of applying the state-of-the-art virus diagnostic methods (multiplex RT-PCR and metagenomic sequencing) and phylodynamic analyses at a national level to generate an integrated picture of viral ARI epidemiology. Frontiers Media S.A. 2020-05-15 /pmc/articles/PMC7242649/ /pubmed/32499763 http://dx.doi.org/10.3389/fmicb.2020.00833 Text en Copyright © 2020 Lu, Robertson, Ashworth, Pham Hong, Shi, Ivens, Thwaites, Baker and Woolhouse. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Microbiology Lu, Lu Robertson, Gail Ashworth, Jordan Pham Hong, Anh Shi, Ting Ivens, Alasdair Thwaites, Guy Baker, Stephen Woolhouse, Mark Epidemiology and Phylogenetic Analysis of Viral Respiratory Infections in Vietnam |
title | Epidemiology and Phylogenetic Analysis of Viral Respiratory Infections in Vietnam |
title_full | Epidemiology and Phylogenetic Analysis of Viral Respiratory Infections in Vietnam |
title_fullStr | Epidemiology and Phylogenetic Analysis of Viral Respiratory Infections in Vietnam |
title_full_unstemmed | Epidemiology and Phylogenetic Analysis of Viral Respiratory Infections in Vietnam |
title_short | Epidemiology and Phylogenetic Analysis of Viral Respiratory Infections in Vietnam |
title_sort | epidemiology and phylogenetic analysis of viral respiratory infections in vietnam |
topic | Microbiology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7242649/ https://www.ncbi.nlm.nih.gov/pubmed/32499763 http://dx.doi.org/10.3389/fmicb.2020.00833 |
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