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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 ISSN 1471-2334.
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Official URL: http://dx.doi.org/10.1186/1471-2334-14-178
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 | ||||||||
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| Subjects: | Q Science > QR Microbiology > QR355 Virology R Medicine > RA Public aspects of medicine |
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| Divisions: | Faculty of Science, Engineering and Medicine > 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: |
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| 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 (Creative Commons) | ||||||||
| Date of first compliant deposit: | 27 December 2015 | ||||||||
| Date of first compliant Open Access: | 27 December 2015 | ||||||||
| Funder: | Wellcome Trust (London, England) | ||||||||
| Grant number: | 084633 (WT) |
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