Respiratory Syncytial Virus G Protein Sequence Variability among Isolates from St. Petersburg, Russia, during the 2013-2014 Epidemic Season

Abstract

Human respiratory syncytial virus (RSV) is the most common cause of upper and lower respiratory tract infections in infants and young children. It is actively evolving under environmental and herd immunity influences. This work presents, for the first time, sequence variability analysis of RSV G gene and G protein using St. Petersburg (Russia) isolates. Viruses were isolated in a cell culture from the clinical samples of 61 children hospitalized (January-April 2014) with laboratory-confirmed RSV infection. Real-time RT-PCR data showed that 56 isolates (91.8%) belonged to RSV-A and 5 isolates (8.2%) belonged to RSV-B. The G genes were sequenced for 27 RSV-A isolates and all of them belonged to genotype ON1/GA2. Of these RSV-A, 77.8% belonged to the ON1(1.1) genetic sub-cluster, and 14.8% belonged to the ON1(1.2) sub-cluster. The ON1(1.3) sub-cluster constituted a minor group (3.7%). Many single-amino acid substitutions were identified in the G proteins of St. Petersburg isolates, compared with the Canadian ON1/GA2 reference virus (ON67-1210A). Most of the amino acid replacements were found in immunodominant B- and T-cell antigenic determinants of G protein. These may affect the antigenic characteristics of RSV and influence the host antiviral immune response to currently circulating viruses.

Keywords: G protein variability; ON1/GA2 genotype; human respiratory syncytial virus; phylogenetic analysis.

Figure 1

Phylogenetic trees by G gene sequence, St. Petersburg RSV-A isolates, 2013–2014 epidemic season. Radial tree (1491 sequences from GenBank) with a focus on geographic distribution. Rectangular tree with reference strains for each genotype colored in blue; original Canadian reference virus (ON67-1210A)—green; progenitors of RSV-A (Long and A2 strains) colored in red.

Figure 2

Variability of G protein structural regions compared with the reference strain. Comparison uses St. Petersburg RSV-A isolates (n = 27) from the 2013–2014 epidemic season. The rate of strains (A) and position frequencies (B) with aa substitutions identified in specific G protein structural domains. In brackets, in the signature to the X-axis, the numbering and quantity (n) of the amino acid residues of the regions are indicated. Above the diagrams, the number of divergent strains (A) or amino acid positions (B) is indicated. The positions of the amino acid substitutions are shown with red triangles (filled and empty for non-unique and unique mutations, respectively) at the Shannon entropy plot (C) (based on 1491 sequences available in the GenBank database). CD—central domain, TMD—transmembrane domain, I HVR—I hypervariable region, II HVR—II hypervariable region.

Figure 2

Variability of G protein structural regions compared with the reference strain. Comparison uses St. Petersburg RSV-A isolates (n = 27) from the 2013–2014 epidemic season. The rate of strains (A) and position frequencies (B) with aa substitutions identified in specific G protein structural domains. In brackets, in the signature to the X-axis, the numbering and quantity (n) of the amino acid residues of the regions are indicated. Above the diagrams, the number of divergent strains (A) or amino acid positions (B) is indicated. The positions of the amino acid substitutions are shown with red triangles (filled and empty for non-unique and unique mutations, respectively) at the Shannon entropy plot (C) (based on 1491 sequences available in the GenBank database). CD—central domain, TMD—transmembrane domain, I HVR—I hypervariable region, II HVR—II hypervariable region.