Examining strain diversity and phylogeography in relation to an unusual epidemic pattern of respiratory syncytial virus (RSV) in a long-term refugee camp in Kenya

Abstract

BackgroundA recent longitudinal study in the Dadaab refugee camp near the Kenya-Somalia border identified unusual biannual respiratory syncytial virus (RSV) epidemics. We characterized the genetic variability of the associated RSV strains to determine if viral diversity contributed to this unusual epidemic pattern.MethodsFor 336 RSV positive specimens identified from 2007 through 2011 through facility-based surveillance of respiratory illnesses in the camp, 324 (96.4%) were sub-typed by PCR methods, into 201 (62.0%) group A, 118 (36.4%) group B and 5 (1.5%) group A-B co-infections. Partial sequencing of the G gene (coding for the attachment protein) was completed for 290 (89.5%) specimens. These specimens were phylogenetically analyzed together with 1154 contemporaneous strains from 22 countries.ResultsOf the 6 epidemic peaks recorded in the camp over the period, the first and last were predominantly made up of group B strains, while the 4 in between were largely composed of group A strains in a consecutive series of minor followed by major epidemics. The Dadaab group A strains belonged to either genotype GA2 (180, 98.9%) or GA5 (2, < 1%) while all group B strains (108, 100%) belonged to BA genotype. In sequential epidemics, strains within these genotypes appeared to be of two types: those continuing from the preceding epidemics and those newly introduced. Genotype diversity was similar in minor and major epidemics.ConclusionRSV strain diversity in Dadaab was similar to contemporaneous diversity worldwide, suggested both between-epidemic persistence and new introductions, and was unrelated to the unusual epidemic pattern.

Description of respiratory syncytial virus genotypes circulating in Colombia

“…The GA2 and GA5 genotypes belonging to the A subtype were the predominant strains circulating in Colombia, as is the case in most countries [19][20][21]. Similarly, we detected only the BA genotype of the RSV-B subtype.…”

Molecular epidemiology of respiratory syncytial virus

“…Most molecular epidemiology studies to date have used these 2 classifications, and recently, RSV has been subclassified into 13 RSV A genotypes and 20 RSV B genotypes based on phylogenetic analysis of the high variable region 2 of the G protein gene . Several studies proposed new classification systems using different criteria, for example, by adopting influenza A(H5N1) classification systems and by using different bootstrap values . The re‐evaluation of RSV classification may improve the placement of emergent novel RSV strains, with several recent molecular epidemiology studies reporting sequences that could not be assigned to the currently circulating genotypes .…”

“…61,62 Several studies proposed new classification systems using different criteria, for example, by adopting influenza A(H5N1) classification systems and by using different bootstrap values. [63][64][65] The re-evaluation of RSV classification may improve the placement of emergent novel RSV strains, with several recent molecular epidemiology studies reporting sequences that could not be assigned to the currently circulating genotypes. 62,64 This global system of classification of RSV genotypes could be based upon agreed bootstrap values and pairwise distances of whole-genome sequences, which would also aid our understanding of transmission and global epidemiology.…”

Prevalence of human respiratory syncytial virus circulating in Iran

“…Monitoring circulating RSV strains in different geographical regions is essential, particularly in the western, eastern, northwestern, and southeastern parts of Iran, where available data is lacking. The continuous circulation of genotype GA2 emphasizes the stability of this subtype; it has become an epidemic in Europe, Asia and Africa [30,32,33]. Genotypes GA2 and BA are also the most common RSV genotypes worldwide [30,32,34].…”