Sequencing and Analysis of Globally Obtained Human Respiratory Syncytial Virus A and B Genomes

Human respiratory syncytial virus (RSV) is the leading cause of respiratory tract infections in children globally, with nearly all children experiencing at least one infection by the age of two. Partial sequencing of the attachment glycoprotein gene is conducted routinely for genotyping, but relativ...

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Vydáno v:	PloS one Ročník 10; číslo 3; s. e0120098
Hlavní autoři:	Bose, Michael E., He, Jie, Shrivastava, Susmita, Nelson, Martha I., Bera, Jayati, Halpin, Rebecca A., Town, Christopher D., Lorenzi, Hernan A., Noyola, Daniel E., Falcone, Valeria, Gerna, Giuseppe, De Beenhouwer, Hans, Videla, Cristina, Kok, Tuckweng, Venter, Marietjie, Williams, John V., Henrickson, Kelly J.
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	United States Public Library of Science 20.03.2015 Public Library of Science (PLoS)
Témata:	Adenoviruses Analysis Base Sequence Bayesian analysis Children Cladistic analysis Committees Epidemiology Ethics Evolution, Molecular Gene sequencing Genes Genetic diversity Genome, Viral Genomes Genomics Genotyping Glycoproteins Health aspects Hospitals Humans Infection Infections Influenza Informed consent Laboratories Molecular Sequence Data Pediatrics Phylogeny Polymorphism, Genetic Proteins Respiratory syncytial virus Respiratory Syncytial Virus Infections - virology Respiratory Syncytial Virus, Human - classification Respiratory Syncytial Virus, Human - genetics Respiratory Syncytial Virus, Human - isolation & purification Respiratory tract Respiratory tract diseases Review boards Sampling methods Spatial distribution Strains (organisms) Venter, J Craig Virology Viruses Argentina Iran Belgium United States > US Adelaide South Australia Australia Italy Mexico South Africa Australia Wisconsin Germany
ISSN:	1932-6203, 1932-6203
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Shrnutí:	Human respiratory syncytial virus (RSV) is the leading cause of respiratory tract infections in children globally, with nearly all children experiencing at least one infection by the age of two. Partial sequencing of the attachment glycoprotein gene is conducted routinely for genotyping, but relatively few whole genome sequences are available for RSV. The goal of our study was to sequence the genomes of RSV strains collected from multiple countries to further understand the global diversity of RSV at a whole-genome level. We collected RSV samples and isolates from Mexico, Argentina, Belgium, Italy, Germany, Australia, South Africa, and the USA from the years 1998-2010. Both Sanger and next-generation sequencing with the Illumina and 454 platforms were used to sequence the whole genomes of RSV A and B. Phylogenetic analyses were performed using the Bayesian and maximum likelihood methods of phylogenetic inference. We sequenced the genomes of 34 RSVA and 23 RSVB viruses. Phylogenetic analysis showed that the RSVA genome evolves at an estimated rate of 6.72 × 10(-4) substitutions/site/year (95% HPD 5.61 × 10(-4) to 7.6 × 10(-4)) and for RSVB the evolutionary rate was 7.69 × 10(-4) substitutions/site/year (95% HPD 6.81 × 10(-4) to 8.62 × 10(-4)). We found multiple clades co-circulating globally for both RSV A and B. The predominant clades were GA2 and GA5 for RSVA and BA for RSVB. Our analyses showed that RSV circulates on a global scale with the same predominant clades of viruses being found in countries around the world. However, the distribution of clades can change rapidly as new strains emerge. We did not observe a strong spatial structure in our trees, with the same three main clades of RSV co-circulating globally, suggesting that the evolution of RSV is not strongly regionalized.
Bibliografie:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23 Conceived and designed the experiments: MEB JH RAH CDT HAL JVW KJH. Performed the experiments: MEB JH SS JB. Analyzed the data: MEB JH SS MIN JB RAH CDT HAL. Contributed reagents/materials/analysis tools: DEN VF GG HDB CV TK MV JVW KJH. Wrote the paper: MEB JH SS MIN HAL KJH. Current address: Global Disease Detection, US Centers for Disease Control and Prevention, Pretoria, South Africa. Competing Interests: DEN has participated as an advisory board member for Novartis and GlaxoSmithKline Biologicals and as a speaker for Abbvie and Roche. This does not alter the authors' adherence to PLOS ONE policies on sharing data and materials. Current address: U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States of America.
ISSN:	1932-6203 1932-6203
DOI:	10.1371/journal.pone.0120098