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

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.

Figure 1

Summary of results of sub-typing and sequencing of 336 RSV positive Dadaab samples that were selected from 2007–11 during the surveillance. Note that of 5 co-infections of RSV group A and B, only group A sequences were obtained.

Figure 2

Monthly cases of RSV group A and group B in Dadaab from September 2007 through November 2011. RSV group A data points are joined by a black continuous line while group B data points are joined by a grey dashed line. The horizontal dot-dashed line marks 15 cases per month which was used to distinguish major from minor epidemics.

Figure 3

A Maximum Likelihood tree showing the relatedness of the unique 52 RSV A Dadaab sequences. Eight reference sequences within the previously identified RSV A genotypes (GA1-GA7 and SAA1) are included on the tree to allow determination of the genotypes of the Dadaab strain. Dadaab sequence taxon names are preceded by unfilled triangles. The tree was bootstrapped with 1000 iterations and only bootstrap support values ≥60 are shown. The clades identified within the GA2 genotype have been indicated on the tree as GA2 (2.1) and GA2 (2.2). The red branches identify those supported by a >60% bootstrap but did not meet the minimum genetic distance to be assigned into independent clades. Taxon names include country name/unique strain identifier/date of sampling.

Figure 4

A Maximum Likelihood tree showing the relatedness of the unique 41 RSV B Dadaab sequences. Eight reference sequences representative of the 8 previously recognized RSV B genotypes (GB1-GB4, SAB1-3, and BA) are included on the tree to allow classification of the Dadaab strains into these genotypes. The Dadaab sequence taxon names are preceded by unfilled triangles. The tree was bootstrapped with 1000 iterations and only bootstrap support values ≥60 are shown. The clades identified within the BA genotype have been indicated on the tree (BA (2.1)-BA (2.4). The red branches identify those supported by a >60% bootstrap but did not meet the minimum genetic distance to be assigned into independent clades. Taxon name includes country name/unique strain identifier/date of sampling.

Figure 5

A Neighbor-joining phylogenetic tree showing the relationships of all RSV A GenBank sequences (649) that we processed for the period 2006–11 combined with the Dadaab sequence data (182). Sequences are compared in the second hyper-variable region of the G gene. The Dadaab sequences are indicated by the coloured triangles; their respective colours indicate the year of detection: maroon: 2007, pink: 2008, green: 2009, blue: 2010, red: 2011. The red arrows point to the nodes (or branches) that bring together sequences of the same genotype or clade identified at Dadaab and the number (n) indicates the number of sequences that fall within that branch. Tips without a triangle imply that the sequence was observed somewhere other than Dadaab. The tree is bootstrapped with 1000 iterations and whenever the percentage was greater than 60, the value is indicated next to the branch.

Figure 6

A Neighbor-joining global phylogenetic tree showing the relationships of all the RSV B GenBank sequences (505) that we processed for the period 2006–11 and the Dadaab sequence data (108), i.e., a total of 613. Sequences are compared in the second hyper-variable region of the G gene. The Dadaab sequences are indicated by the coloured triangles; their respective colours indicate the year of detection: maroon: 2007, pink: 2008, green: 2009, blue: 2010, red: 2011. The red arrows point to the nodes (or branches) that bring together sequences of the same genotype or clade identified at Dadaab and the number (n) indicates the number of sequences that fall within that branch. Tips without a triangle imply that the sequence was observed somewhere other than Dadaab. The tree was bootstrapped with 1000 iterations and whenever the percentage was greater than 60 the value is indicated next to the branch.