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

Michael E. Bose, Jie He, Susmita Shrivastava, Martha I. Nelson, Jayati Bera, Rebecca A. Halpin, Christopher D. Town, Hernan A. Lorenzi, Daniel E. Noyola, Valeria Falcone, Giuseppe Gerna, Hans De Beenhouwer, Cristina Videla, Tuckweng Kok, Marietjie Venter, John V. Williams, Kelly J. Henrickson

Research output: Contribution to journalArticle

28 Citations (Scopus)

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.

Original languageEnglish
Article numbere0120098
JournalPLoS One
Volume10
Issue number3
DOIs
Publication statusPublished - Mar 20 2015

Fingerprint

Human respiratory syncytial virus
Respiratory Syncytial Viruses
Viruses
Genes
Genome
viruses
genome
phylogeny
Substitution reactions
Belgium
Argentina
South Africa
Mexico
Respiratory Tract Infections
Italy
Germany
Glycoproteins
respiratory tract diseases
genotyping
glycoproteins

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Bose, M. E., He, J., Shrivastava, S., Nelson, M. I., Bera, J., Halpin, R. A., ... Henrickson, K. J. (2015). Sequencing and analysis of globally obtained human respiratory syncytial virus a and B genomes. PLoS One, 10(3), [e0120098]. https://doi.org/10.1371/journal.pone.0120098

Sequencing and analysis of globally obtained human respiratory syncytial virus a and B genomes. / 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.

In: PLoS One, Vol. 10, No. 3, e0120098, 20.03.2015.

Research output: Contribution to journalArticle

Bose, ME, He, J, Shrivastava, S, Nelson, MI, Bera, J, Halpin, RA, Town, CD, Lorenzi, HA, Noyola, DE, Falcone, V, Gerna, G, De Beenhouwer, H, Videla, C, Kok, T, Venter, M, Williams, JV & Henrickson, KJ 2015, 'Sequencing and analysis of globally obtained human respiratory syncytial virus a and B genomes', PLoS One, vol. 10, no. 3, e0120098. https://doi.org/10.1371/journal.pone.0120098
Bose ME, He J, Shrivastava S, Nelson MI, Bera J, Halpin RA et al. Sequencing and analysis of globally obtained human respiratory syncytial virus a and B genomes. PLoS One. 2015 Mar 20;10(3). e0120098. https://doi.org/10.1371/journal.pone.0120098
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. / Sequencing and analysis of globally obtained human respiratory syncytial virus a and B genomes. In: PLoS One. 2015 ; Vol. 10, No. 3.
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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.",
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AU - He, Jie

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AU - Bera, Jayati

AU - Halpin, Rebecca A.

AU - Town, Christopher D.

AU - Lorenzi, Hernan A.

AU - Noyola, Daniel E.

AU - Falcone, Valeria

AU - Gerna, Giuseppe

AU - De Beenhouwer, Hans

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N2 - 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.

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