title: Comparative genomic analysis of genogroup 1 (Wa-like) rotaviruses circulating in the USA, 2006-2009.
abstract: Group A rotaviruses (RVA) are double stranded RNA viruses that are a significant cause of acute pediatric gastroenteritis. Beginning in 2006 and 2008, respectively, two vaccines, Rotarix™ and RotaTeq®, have been approved for use in the USA for prevention of RVA disease. The effects of possible vaccine pressure on currently circulating strains in the USA and their genome constellations are still under investigation. In this study we report 33 complete RVA genomes (ORF regions) collected in multiple cities across USA during 2006-2009, including 8 collected from children with verified receipt of 3 doses of rotavirus vaccine. The strains included 16 G1P[8], 10 G3P[8], and 7 G9P[8]. All 33 strains had a Wa like backbone with the consensus genotype constellation of G(1/3/9)-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1. From maximum likelihood based phylogenetic analyses, we identified 3-7 allelic constellations grouped mostly by respective G types, suggesting a possible allelic segregation based on the VP7 gene of RVA, primarily for the G3 and G9 strains. The vaccine failure strains showed similar grouping for all genes in G9 strains and most genes of G3 strains suggesting that these constellations were necessary to evade vaccine-derived immune protection. Substitutions in the antigenic region of VP7 and VP4 genes were also observed for the vaccine failure strains which could possibly explain how these strains escape vaccine induced immune response. This study helps elucidate how RVA strains are currently evolving in the population post vaccine introduction and supports the need for continued RVA surveillance.
authors.affiliation: Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
authors.forename: Sunando
authors.initials: S
authors.lastname: Roy
authors.affiliation: Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
authors.forename: Mathew D
authors.initials: MD
authors.lastname: Esona
authors.affiliation: The J. Craig Venter Institute, Rockville, MD, USA.
authors.forename: Ewen F
authors.initials: EF
authors.lastname: Kirkness
authors.affiliation: The J. Craig Venter Institute, Rockville, MD, USA.
authors.forename: Asmik
authors.initials: A
authors.lastname: Akopov
authors.affiliation: The J. Craig Venter Institute, Rockville, MD, USA.
authors.forename: J Kyle
authors.initials: JK
authors.lastname: McAllen
authors.affiliation: Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
authors.forename: Mary E
authors.initials: ME
authors.lastname: Wikswo
authors.affiliation: Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
authors.forename: Margaret M
authors.initials: MM
authors.lastname: Cortese
authors.affiliation: Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
authors.forename: Daniel C
authors.initials: DC
authors.lastname: Payne
authors.affiliation: Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
authors.forename: Umesh D
authors.initials: UD
authors.lastname: Parashar
authors.affiliation: Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
authors.forename: Jon R
authors.initials: JR
authors.lastname: Gentsch
authors.affiliation: Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA. Electronic address: mkb6@cdc.gov.
authors.forename: Michael D
authors.initials: MD
authors.lastname: Bowen
mesh_terms: D036022:Capsid Proteins / Q000737:chemistry / Q000235:genetics; D002648:Child; D016000:Cluster Analysis; D005759:Gastroenteritis / Q000453:epidemiology / Q000266:history / Q000821:virology; D016679:Genome, Viral; D023281:Genomics; D005838:Genotype; D049674:History, 21st Century; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D010802:Phylogeny; D011159:Population Surveillance; D011487:Protein Conformation; D012401:Rotavirus / Q000145:classification* / Q000235:genetics*; D012400:Rotavirus Infections / Q000453:epidemiology* / Q000266:history / Q000821:virology*; D017422:Sequence Analysis, DNA; D014481:United States / Q000453:epidemiology
chemical_list: D036022:Capsid Proteins
keywords: Allele; Failure; Rotavirus; VP4; VP7; Vaccine