Positive selection results in frequent reversible amino acid replacements in the G protein gene of human respiratory syncytial virus

Abstract

Human respiratory syncytial virus (HRSV) is the major cause of lower respiratory tract infections in children under 5 years of age and the elderly, causing annual disease outbreaks during the fall and winter. Multiple lineages of the HRSVA and HRSVB serotypes co-circulate within a single outbreak and display a strongly temporal pattern of genetic variation, with a replacement of dominant genotypes occurring during consecutive years. In the present study we utilized phylogenetic methods to detect and map sites subject to adaptive evolution in the G protein of HRSVA and HRSVB. A total of 29 and 23 amino acid sites were found to be putatively positively selected in HRSVA and HRSVB, respectively. Several of these sites defined genotypes and lineages within genotypes in both groups, and correlated well with epitopes previously described in group A. Remarkably, 18 of these positively selected tended to revert in time to a previous codon state, producing a "flip-flop" phylogenetic pattern. Such frequent evolutionary reversals in HRSV are indicative of a combination of frequent positive selection, reflecting the changing immune status of the human population, and a limited repertoire of functionally viable amino acids at specific amino acid sites.

Figure 1. The most parsimonious reconstructions of positively selected sites on the HRSVA phylogeny rooted with the Long and A2 and GA1 strains (not shown for clarity) are depicted.

Basal positively selected sites of HRSVA are indicated near the root of the tree. MPRs along the tree supporting the main splits are also indicated near the nodes at the base of each genotype. Lineages that did not experience evolutionary reversals were collapsed for the sake of clarity. For both A) and B) sites experiencing evolutionary mutations (Table 1) are indicated by the symbols: > for the ‘forward’ (Fr) mutation and < for the ‘backward’ mutation (Br). The Fr I is indicated by blue quadrilateral >, and the Br I by blue quadrilateral <. The Fr II is indicated by pink quadrilateral > and the Br II by pink quadrilateral <. The Fr III is indicated by blue circle > and the Br III by blue circle <. The Fr IV is indicated by green circle > and the Br IV by green circle <. The Fr V is indicated by violet triangle > and the Br V by violet triangle <. The Fr VI is indicated by violet circle > and the Br VI by violet circle <. The Fr VII is indicated by orange quadrilateral > and the Br VII by orange quadrilateral <. The Fr VII is indicated by green triangle > and the Br VIII by green triangle <. The Fr IX is indicated by black triangle > and the Br by black triangle <.

Figure 2. The most parsimonious reconstructions of positively selected sites on the HRSVA phylogeny rooted with the CH18537 and SW860 (not shown for clarity) are shown.

Basal positively selected sites of HRSVB are indicated near the root of the tree. MPRs along the tree supporting the main splits are also indicated near the nodes at the base of each genotype. Lineages did not experience evolutionary reversals were collapsed for the sake of clarity. For both A) and B) sites experiencing evolutionary mutations (Table 1) are indicated by the symbols: pink quadrilateral > and the Br I by pink quadrilateral <. The Fr II is indicated by blue circle > and the Br by blue circle <. The Fr III is indicated by green circle > and the Br by green circle <. The Fr IV is indicated by violet triangle > and the Br by violet triangle<. The Fr V is indicated by orange quadrilateral > and the Br by orange quadrilateral <. The Fr VI is indicated by red triangle > and the Br by red triangle and the Br VII by green triangle <. The Fr VIII is indicated by gray circle > and the Br VIII by gray circle <. The Fr IX is indicate by dark green quadrilateral > and the Br IX by dark green quadrilateral <.

Figure 3. Graphical representation of the third C-terminal hypervariable region of HRSVA G [Long strain], showing a partial antigenic map.

The amino acid changes associated with epitope loss in natural isolates and in escape mutants selected with specific Mabs are indicated by arrows ,,,. The positions, relative to the Long strain, of codons with evidence of positive selection that also experienced evolutionary reversals are shown by Roman numbers and coloured arrows.

Figure 4. Graphical representation of the third C-terminal hypervariable region of HRSVB G (CH18537).

The positions of the first amino acid in the amplicon and that for the insertion are shown in relation to the CH18537 isolate. The codon positions of sites with evidence of positive selective pressure that also experienced evolutionary reversals are indicated by Roman numbers and by coloured arrows.