Sequencing and analysis of globally obtained human respiratory syncytial virus A and B genomes

Show simple item record 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. 2015-08-03T09:57:02Z 2015-08-03T09:57:02Z 2015-03-20
dc.description All genome sequence files are available from the GenBank database (bioproject id PRJNA73049 and accession numbers KF530258 - KF530269 and KF826816 - KF826860). All other relevant data are within the paper and its Supporting Information files. en_ZA
dc.description.abstract BACKGROUND 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. METHODS 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 nextgeneration 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. RESULTS 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. CONCLUSIONS 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. en_ZA
dc.description.librarian am2015 en_ZA
dc.description.sponsorship This project has been funded in whole or part with federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services ( under contract number HHSN272200900007C and grant numbers 5U01AI070428 and 5U01AI077988. This work was supported in part by the Multinational Influenza Seasonal Mortality Study (MISMS), led by the Fogarty International Center, National Institutes of Health, with funding from the Department of Health and Human Services ( en_ZA
dc.description.uri en_ZA
dc.identifier.citation Bose ME, He J, Shrivastava S, Nelson MI, Bera J, Halpin RA, et al. (2015) Sequencing and Analysis of Globally Obtained Human Respiratory Syncytial Virus A and B Genomes. PLoS ONE 10(3): e0120098. DOI: 10.1371/journal.pone.0120098. en_ZA
dc.identifier.issn 1932-6203
dc.identifier.other 10.1371/journal.pone.0120098
dc.language.iso en en_ZA
dc.publisher Public Library of Science en_ZA
dc.rights The work is made available under the Creative Commons CC0. en_ZA
dc.subject Human respiratory syncytial virus en_ZA
dc.subject Infections en_ZA
dc.subject Children en_ZA
dc.subject Genomes en_ZA
dc.title Sequencing and analysis of globally obtained human respiratory syncytial virus A and B genomes en_ZA
dc.type Article en_ZA

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