Fig 1.
T cell immunogenic potential for RSV surface proteins based on MHC binding prediction.
(A) T cell immunogenic potential of RSV major surface proteins. T cell epitope density scores for RSV major surface proteins and other pathogen proteins are labeled on a scale bar. Low-scoring proteins are known to engender little to no immunogenicity while higher-scoring proteins are known immunogens. Proteins scoring above +20 on this scale are considered to have significant immunogenic potential. (B) Distribution of RSV T cell immunogenic potential across F and G protein in RSV reference strain A2 and RSV F protein main antigenic sites that are determined in previous studies [26]. Prefusion or post-fusion F protein surface was colored by the antigenic sites and relative immunogenetic potential at each location. Analyses are based on the RSV-A reference sequence.
Table 1.
Experimentally validated conserved MHC class I epitopes peptides in RSV major surface proteinsa.
Table 2.
Experimentally validated conserved MHC class II epitopes peptides in RSV major surface proteinsa.
Fig 2.
Predicted T cell epitope landscapes and genetic evolution of RSV surface proteins.
Filled circles indicate RSV F protein isolates or G protein isolates without duplication. Diamonds indicate G protein isolates with gene duplication. (A) Epitope landscapes of RSV major surface proteins are built with MHC class I and class II epitope content comparison across different strains. T cell immunity clusters are determined with k-means method and are used to color the sequenced isolates in the following panels. (B) The corresponding time-scaled phylogenies are reconstructed with the Maximum Likelihood (ML) approach. (C) T cell epitope immune distance and (D) genetic hamming distance from the estimated TMRCA are plotted against the isolated time of each sequence.
Fig 3.
Evaluation of previously used RSV vaccine candidate strains with T cell epitope content of circulating strains.
RSV-A and RSV-B major surface protein sequences are subsampled and then grouped by isolation year and 6 isolated WHO regions. African Region (AFRO), Region of the Americas (PAHO), South-East Asia Region (SEARO), European Region (EURO), Eastern Mediterranean Region (EMRO) and Western Pacific Region (WPRO). The proportion of cross-conserved T cell epitope content between live attenuated strains (CP248 or CP52) and wild circulating strains are displayed as radar plots.