Data for Molecular evolutionary dynamics of respiratory syncytial virus group A in recurrent epidemics in coastal Kenya

Further, we identified 15 positively selected and 34 genotype-distinguishing codon sites, with six of these sites exhibiting both characteristics. The mean substitution rate of the G ectodomain for the Kilifi dataset was estimated at 3.58 x 10-3 [95% HPD: 3.04 – 4.16] nucleotide substitutions/site/year. Kilifi viruses were interspersed in the global phylogenetic tree, clustering mostly with Kenyan and European sequences.

Our findings highlight ongoing genetic evolution and high diversity of circulating strains, locally and globally, with potential antigenic differences. Taken together, these provide a possible explanation on the nature of recurrent local RSV epidemics.<br><br>Data record consists of 2 data files in plain text format. The data is from an on-going study aimed at understanding the epidemiology and disease burden of RSV-associated pneumonia cases in Kilifi.

This report details the evolutionary dynamics of RSV-A genotype in Kilifi. Respiratory swab samples (combined nasopharyngeal and oropharyngeal) were collected from January 2000 to December 2012 from: (i) LRTI cases for children <5 years admitted to Kilifi County Hospital (KCH) collected over the period from 2000 to 2012 (3, 24), (ii) KCH outpatient presentations for children <5 years with acute respiratory infection (ARI) from April to August 2002 (25, 26), and (iii) the Kilifi RSV birth cohort (KBC) ARI cases identified between January 2002 to August 2003.

The samples were screened for RSV and G-gene sequenced (RSV positives) using the Sanger method. Also included is a global RSV-A contemporenous comparison sequence dataset used in the analyses. The newly generated sequences analyzed here have been deposited in GenBank under accession numbers KT765213 to KT765836.

The previously sequenced and reported RSV-A sequences from Kilifi added to this analysis had been archived in GenBank under accession numbers AY524573 to AY524663 and AY660667 to AY660684.