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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

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Agoti, Charles N., Mayieka, Lillian M., Otieno, James R., Ahmed, Jamal A., Fields, Barry S., Waiboci, Lilian W., Nyoka, Raymond, Eidex, Rachel B., Marano, Nina, Burton, Wagacha, Montgomery, Joel M., Breiman, Robert F. and Nokes, D. James (2014) 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. BMC Infectious Diseases, Volume 14 (Number 1). Article number 178. doi:10.1186/1471-2334-14-178

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Official URL: http://dx.doi.org/10.1186/1471-2334-14-178

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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.

Item Type: Journal Article
Subjects: Q Science > QR Microbiology > QR355 Virology
R Medicine > RA Public aspects of medicine
Divisions: Faculty of Science > Life Sciences (2010- )
Library of Congress Subject Headings (LCSH): Respiratory syncytial virus -- Kenya, Respiratory syncytial virus -- Genetics, Refugee camps -- Kenya, Refugees -- Health and hygiene
Journal or Publication Title: BMC Infectious Diseases
Publisher: BioMed Central Ltd.
ISSN: 1471-2334
Official Date: 1 April 2014
Dates:
DateEvent
1 April 2014Published
24 March 2014Accepted
5 January 2014Submitted
Date of first compliant deposit: 27 December 2015
Volume: Volume 14
Number: Number 1
Number of Pages: 14
Article Number: Article number 178
DOI: 10.1186/1471-2334-14-178
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Open Access
Funder: Wellcome Trust (London, England)
Grant number: 084633 (WT)

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