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

D James Nokes²  Robert F Breiman³  Joel M Montgomery³  Wagacha Burton³  Nina Marano¹  Rachel B Eidex¹  Raymond Nyoka¹  Lilian W Waiboci¹  Barry S Fields¹  Jamal A Ahmed¹  James R Otieno⁴  Lillian M Mayieka¹  Charles N Agoti⁴ 

[1] United States Centers for Disease Control and Prevention, Nairobi, Kenya;School of Life Sciences and WIDER, Warwick University, Coventry, UK;Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, USA;Kenya Medical Research Institute (KEMRI)–Wellcome Trust Research Programme, Kilifi, Kenya

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

Others  :  1134217
DOI  :  10.1186/1471-2334-14-178

 received in 2014-01-05, accepted in 2014-03-24,  发布年份 2014

【 摘 要 】

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.

【 授权许可】

   
2014 Agoti et al.; licensee BioMed Central Ltd.

【 图 表 】

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