Characterisation of RSV Fusion Proteins from South African Patients with RSV Disease, 2019 to 2020

Abstract

Respiratory syncytial virus (RSV) is classified into RSV-A and RSV-B, which are further classified into genotypes based on variability in the G gene. The fusion (F) protein is highly conserved; however, variability within antigenic sites has been reported. This study aimed to characterise F proteins from RSV strains detected in South Africa from 2019 to 2020. Patients of all ages, from whom respiratory samples were submitted to the National Health Laboratory Service at Charlotte Maxeke Johannesburg Academic Hospital, South Africa during 2019 to 2020, were included. Complete RSV F genes were amplified for next-generation sequencing. MEGA X software was used for phylogenetic analysis. The overall prevalence of RSV was 5.8% (101/1734). Among 101 RSV positive samples only 69.3% (70/101) were available for characterization of the RSV F protein gene. Among cases included for F gene characterisation, viral co-infections were observed in 50% (35/70) and 25.7% (18/70) were admitted to intensive care units (ICU). About 74.2% (23/31) of F gene sequences cluster with other African NA1/ON1 genotypes. At antigenic site I, the V384I mutation was replaced by V384T in South African strains. The S275F mutation was seen in a single South African strain. The N120 N-linked glycosylation site was present in 25.8% (8/31) of RSV-A F proteins described in this study. For the first time, we detected the rare S275F mutation that is associated with palivizumab resistance.

All Eyes on the Prefusion-Stabilized F Construct, but Are We Missing the Potential of Alternative Targets for Respiratory Syncytial Virus Vaccine Design?

“…Moreover, there has been insufficient evaluation of how viruses belonging to different genotypes and subtypes elicit varying levels of antibody responses [ 247 ]. This variability poses a risk, potentially reducing the efficacy of developed vaccines and therapeutics, particularly those targeting a limited number of epitopes [ 54 , 247 , 248 , 249 ]. Immunoprophylaxis strategies like nirsevimab and palivizumab, which target a single specific epitope [ 17 ], and vaccines that focus on only a few epitopes, such as prefusion-stabilized F protein vaccines like RSVpreF3 and RSVpreF, which primarily act on site Ø, may be particularly susceptible to this risk [ 54 ].…”

“…However, the spontaneous emergence of two mutations (L172Q and S173L) in the F protein of circulating RSV B strains led to an almost complete lack of neutralizing activity [ 247 , 250 , 251 , 252 ]. Through surveillance efforts, mutations in the F protein’s antigenic sites and in major domains like the mucin-like domain and the CCD of the G protein have been observed [ 247 , 248 , 249 , 253 , 254 ].…”

Respiratory syncytial virus infection in the modern era

“…Analysis of RSV fusion (F) sequences remains an important complement to WGS and can reveal variation in antigenic sites (, I-V), thus enabling identification of specific mutations, which might reduce the efficacy of vaccines and/or therapeutics [18,19]. RSV strains are now recommended to be named using this method: [virus name abbreviation]/ [HRSV subgroup]/[geographic identifier]/[unique sequence identifier]/[year of sampling], for example HRSV/A/USA/001/2011 [22 & ].…”

“…Analysis of RSV fusion (F) sequences remains an important complement to WGS and can reveal variation in antigenic sites (Ø, I-V), thus enabling identification of specific mutations, which might reduce the efficacy of vaccines and/or therapeutics [18,19]. Similarly, sequencing of G genes has shown the presence of mutations in the two large mucin like domains and surprisingly a single amino acid change (N178G) in the conserved central domain (CCD) of the G protein [20 ▪ ].…”