Open Access Research article

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

Charles N Agoti1*, Lillian M Mayieka2, James R Otieno1, Jamal A Ahmed2, Barry S Fields2, Lilian W Waiboci2, Raymond Nyoka2, Rachel B Eidex2, Nina Marano2, Wagacha Burton24, Joel M Montgomery24, Robert F Breiman34 and D James Nokes15

Author Affiliations

1 Kenya Medical Research Institute (KEMRI)–Wellcome Trust Research Programme, Kilifi, Kenya

2 United States Centers for Disease Control and Prevention, Nairobi, Kenya

3 Emory University, Atlanta, USA

4 Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, USA

5 School of Life Sciences and WIDER, Warwick University, Coventry, UK

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BMC Infectious Diseases 2014, 14:178  doi:10.1186/1471-2334-14-178

Published: 1 April 2014



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.


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.


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.


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.

Attachment (G) protein; Displaced population; Epidemics; Genetic diversity; Genotype; Refugee; RSV