Alternative conformations of a major antigenic site on RSV F

Jones, Harrison G.; Battles, Michael B.; Lin, Chun-Chi; Bianchi, Siro; Corti, Davide; McLellan, Jason S.

The amino acid sequence for the human respiratory syncytial virus subtype A (strain A2) fusion protein was used as the original sequence for comparison with all known pneumovirus and paramyxovirus fusion proteins. NCBI basic local alignment search tool (BLAST) was used to identify homologous regions between the hRSV fusion protein sequence (strain A2) and other pneumovirus and paramyxovirus fusion proteins. Specifically, we identified sequences that were indicated to be partially homologous with the residues 195-214 of the hRSV fusion protein sequence derived from strain A2. These residues correspond to the α4-helix and α4-α5 loop within the prefusion RSV F structure. For all known structures of prefusion pneumovirus or paramyxovirus fusion proteins, the homologous sequence also corresponds to the equivalent α4-helix and α4-α5 loop, even if the residue numbering differs. To prevent overrepresentation from viral species which have multiple subtypes sequenced, we only included a single amino acid sequence from each species when the multiple subtypes were >90% identical throughout the residue range corresponding to 195-214 in hRSV F. However, if two subtypes within a single viral species differed by >10% in the residue range corresponding to 195-214 in hRSV F, then they were both included when performing sequence analysis and generating the sequence WebLogo. For example, there are four sequenced strains of human metapneumovirus F, but they are all mostly identical and hence only two representative sequences were included in the final WebLogo (strain A1 and B1). However, there are multiple distinct sequences for the different types of parainfluenza virus (PIV), and therefore all the distinct sequences are included separately when generating the WebLogo. See S1 Table for a full list of sequences used in the WebLogo. The WebLogo was generated using publicly available software at weblogo.berkley.edu.