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)

• Type of Material: Article
• Authors: Charles N Agoti, Kenya Medical Research Institute; Lillian M Mayieka, Centers for Disease Control and Prevention, Kenya; James R Otieno, Kenya Medical Research Institute; Jamal A Ahmed, Centers for Disease Control and Prevention, Kenya; Barry S Fields, Centers for Disease Control and Prevention, Kenya; Lilian W Waiboci, Centers for Disease Control and Prevention, Kenya; Raymond Nyoka, Centers for Disease Control and Prevention, Kenya; Rachel B Eidex, Centers for Disease Control and Prevention, Kenya; Nina Marano, Centers for Disease Control and Prevention, Kenya; Wagacha Burton, Centers for Disease Control and Prevention, Kenya; Joel M Montgomery, Centers for Disease Control and Prevention, Kenya; Robert F Breiman, Emory University; D James Nokes, Kenya Medical Research Institute
• Language: English
• Date: 2014
• Publisher: BioMed Central
• Publication Version: Final Published Version
• Copyright Statement: © 2014 Agoti et al.; licensee BioMed Central Ltd.
• License: Creative Commons Attribution 2.0 Generic
• Final Published Version (URL): http://www.biomedcentral.com/1471-2334/14/178
• Title of Journal or Parent Work: BMC Infectious Diseases
• ISSN: 1471-2334
• Volume: 14
• Issue: 178
• Grant/Funding Information: The primary surveillance project is supported by a cooperative agreement between KEMRI, CDC, and the International Rescue Committee.; The work presented here was supported by a Wellcome Trust, UK, Programme Grant to DJN (Ref no.084633) and CDC.
• Keywords: Genotype; Refugee; Attachment (G) protein; Displaced population; RSV; Epidemics; Genetic diversity
• Research Categories: Health Sciences, Epidemiology; Health Sciences, Public Health

Abstract

Background A 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. Methods For 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. Results Of 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. Conclusion RSV 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.