Molecular epidemiology and evolution of human respiratory syncytial virus and human metapneumovirus

Abstract

Human respiratory syncytial virus (HRSV) and human metapneumovirus (HMPV) are ubiquitous respiratory pathogens of the Pneumovirinae subfamily of the Paramyxoviridae. Two major surface antigens are expressed by both viruses; the highly conserved fusion (F) protein, and the extremely diverse attachment (G) glycoprotein. Both viruses comprise two genetic groups, A and B. Circulation frequencies of the two genetic groups fluctuate for both viruses, giving rise to frequently observed switching of the predominantly circulating group. Nucleotide sequence data for the F and G gene regions of HRSV and HMPV variants from the UK, The Netherlands, Bangkok and data available from Genbank were used to identify clades of both viruses. Several contemporary circulating clades of HRSV and HMPV were identified by phylogenetic reconstructions. The molecular epidemiology and evolutionary dynamics of clades were modelled in parallel. Times of origin were determined and positively selected sites were identified. Sustained circulation of contemporary clades of both viruses for decades and their global dissemination demonstrated that switching of the predominant genetic group did not arise through the emergence of novel lineages each respiratory season, but through the fluctuating circulation frequencies of pre-existing lineages which undergo proliferative and eclipse phases. An abundance of sites were identified as positively selected within the G protein but not the F protein of both viruses. For HRSV, these were discordant with previously identified residues under selection, suggesting the virus can evade immune responses by generating diversity at multiple sites within linear epitopes. For both viruses, different sites were identified as positively selected between genetic groups.

Figure 1. Phylogenetic analysis of HRSV (A) and HMPV (B) partial F gene sequences.

Phyogenetic reconstruction was by neighbour joining of MCL-corrected pair-wise distances. Clades identified as described in the methods are indicated by grey shaded boxes. Sequence symbols are colour coded by year of isolation. Symbol shape denotes geographic origins sequences. Bootstrap values >70% are indicated. (A) Phylogenies rooted with bovine RSV (not shown). Subgroups A and B are indicated by the blue and yellow boxes respectively. (B) rooted with avian metapneumovirus species C (not shown). Genotypes A and B are indicated by the blue and yellow boxes respectively. NA, None analysed.

Figure 2. Phylogenetic analysis of 58 HRSV sequences in the F and G genes.

Phylogenetic reconstruction was by neighbour joining of MCL-corrected pair-wise distances. F gene sequences rooted with bovine RSV; G gene sequences unrooted. Sequence symbols are colour coded by geography to emphasize the congruence between the phylogenies of the two genome regions. Monophyletic groupings which contain sequences from the 07/08 respiratory season for which sequence data was available from all four referral centres are indicated in shaded boxes. Bootstrap values >70% are indicated.

Figure 3. Phylogenetic analysis of HMPV partial G gene sequences (unrooted).

Phylogenetic reconstruction was by neighbour joining of MCL-corrected pair-wise distances. Genotypes (A and B) and sub-genotypes (A1, A2, B1 and B2) are indicated. Sequence symbols are colour coded by year of isolation and symbol shape is designated depending on geographic origin of sequence. Bootstrap values >70% are indicated.