Sequence variability of the respiratory syncytial virus (RSV) fusion gene among contemporary and historical genotypes of RSV/A and RSV/B

Abstract

Background: The fusion (F) protein of RSV is the major vaccine target. This protein undergoes a conformational change from pre-fusion to post-fusion. Both conformations share antigenic sites II and IV. Pre-fusion F has unique antigenic sites p27, ø, α2α3β3β4, and MPE8; whereas, post-fusion F has unique antigenic site I. Our objective was to determine the antigenic variability for RSV/A and RSV/B isolates from contemporary and historical genotypes compared to a historical RSV/A strain.

Methods: The F sequences of isolates from GenBank, Houston, and Chile (N = 1,090) were used for this analysis. Sequences were compared pair-wise to a reference sequence, a historical RSV/A Long strain. Variability (calculated as %) was defined as changes at each amino acid (aa) position when compared to the reference sequence. Only aa at antigenic sites with variability ≥5% were reported.

Results: A total of 1,090 sequences (822 RSV/A and 268 RSV/B) were analyzed. When compared to the reference F, those domains with the greatest number of non-synonymous changes included the signal peptide, p27, heptad repeat domain 2, antigenic site ø, and the transmembrane domain. RSV/A subgroup had 7 aa changes in the antigenic sites: site I (N = 1), II (N = 1), p27 (N = 4), α2α3β3β4(AM14) (N = 1), ranging in frequency from 7-91%. In comparison, RSV/B had 19 aa changes in antigenic sites: I (N = 3), II (N = 1), p27 (N = 9), ø (N = 4), α2α3β3β4(AM14) (N = 1), and MPE8 (N = 1), ranging in frequency from 79-100%.

Discussion: Although antigenic sites of RSV F are generally well conserved, differences are observed when comparing the two subgroups to the reference RSV/A Long strain. Further, these discrepancies are accented in the antigenic sites in pre-fusion F of RSV/B isolates, often occurring with a frequency of 100%. This could be of importance if a monovalent F protein from the historical GA1 genotype of RSV/A is used for vaccine development.

Fig 1. Appearance of RSV/A and RSV/B genotypes and dominance over time (1961–2014).

Sequences assigned genotypes were assessed by their sample acquisition date. The included inset depicts those years (1961–2000) with a small number of available sequences.

Fig 2. The fusion genes of RSV/A isolates are more similar to the RSV/A Long strain than RSV/B isolates.

Non-synonymous/synonymous ratio graph of amino acids with non-synonymous or synonomous changes in the fusion gene for a) RSV/A isolates and b) RSV/B isolates (compared to the RSV/A Long strain). Fusion gene domains are depicted by assigned color blocks. Antigenic sites are highlighted in shades of gray respective to the protein conformation on which they are found.

Fig 3. The entropy values in amino acids within antigenic sites of the fusion gene of RSV/A and RSV/B have a similar distribution.

Entropy was defined as ∑_i−i log(i). Individual genotypes of each subgroup contributed equally to the proportion of amino acids found at a given residue.