Identification of group B respiratory syncytial viruses that lack the 60-nucleotide duplication after six consecutive epidemics of total BA dominance at coastal Kenya

Abstract

Respiratory syncytial virus BA genotype has reportedly replaced other group B genotypes worldwide. We report the observation of three group B viruses, all identical in G sequence but lacking the BA duplication, at a coastal district hospital in Kenya in early 2012. This follows a period of six consecutive respiratory syncytial virus (RSV) epidemics with 100% BA dominance among group B isolates. The new strains appear only distantly related to BA variants and to previously circulating SAB1 viruses last seen in the district in 2005, suggesting that they were circulating elsewhere undetected. These results are of relevance to an understanding of RSV persistence.

Keywords: Attachment (G gene); BA genotype; genetic diversity; respiratory syncytial virus.

Figure 1

A maximum‐likelihood tree of 53 sequences including the top 25 blast hits, the 3 new non‐BA Kilifi sequences, 10 sequences representative strains previously collected at Kilifi (both BA and non‐BA), and 15 representative sequences of all the previously described group B genotypes. The tree is derived from an alignment of the carboxy terminus region nucleotide sequences of the RSV G protein gene [264‐nt‐long region (324 for BA)]. The nodes of branches with exclusively Kilifi sequences are indicated with a red‐filled square box, and the associated branches of these Kilifi sequences are also colored in red. The nomenclature of the taxa is a three‐letter code for the country of sequence origin/GenBank accession number/strain name.

Figure 2

The figure shows an alignment of partial G‐protein‐predicted amino acid sequences for the Brazilian, Chinese, and Cambodian non‐BA sequences that were identified in the second half of the last decade and the Kilifi non‐BA sequences [both the new 2012 and the old (SAB1 strains)]. The sequences are compared with GB1 strain (USA/CH10b) given at the top of the alignment as a reference strain. Where the amino acid sequence is similar to the GB1 strain sequence, the position is shown with dot along the column otherwise implies a mutation. The asterisks denote stop codons. At the bottom of the columns, positions previously identified as positively selected in group B RSV are indicated with a plus (+) symbol.13, 14 Gray‐highlighted columns show amino acid sequence positions that changed and were also identified to be positively selected. The taxa nomenclature is a three‐letter code for the country of sequence origin/GenBank accession number/strain name.

Figure 3

Panel (A) shows a maximum‐likelihood tree from 232 sequences comparing 599 nucleotide positions of the RSV G protein gene. This includes all unique BA sequences observed at Kilifi between 2003 and 2012 (224 sequences), the 3 Kilifi 2012 non‐BA strains (marked red), and 5 of the close Brazilian non‐BA sequences collected in 2007 that span this length (marked green). In the alignment used to generate this tree, the 60‐nucleotide insertion of the BA strains was removed to investigate whether the remaining nucleotide positions were highly similar to BA, which could then suggest that the new non‐BA strains emerged by spontaneous deletion of this region from BA genotype. However, we observe that these new Kilifi non‐BA strains cluster far away on the tree from the current BA strains and are close to the Brazilian non‐BA strains – boxed in (a) with a dashed rectangle and expanded as panel (B). Panel (C) shows the seven amino acid changes in the Kilifi 2012 non‐BA strains from the Brazilian 2007 strains and their respective positions that they were observed (six of the seven changes occur in the second hypervariable region).