Our first publication of the year features the work of Frances Shepherd, a PhD student (who recently received an award at the CRWAD meeting) with Drs. Michael Murtaugh and Douglas Marthaler. The paper is in open access in the journal Pathogens and you can read it here.
In this experiment, 174 clinical samples from US and Canadian swine herds and positive for rotavirus B by PCR were used to sequence the gene for the protein VP7.
VP7 is a protein of interest in rotaviruses B because it is structural and can be found on the outer layer of the virus capsid. Along with VP4, they stimulate the creation of neutralizing antibodies in pigs.
Based on those sequences, 169 of the viruses were allocated to 8 defined genotypes: G8, G11, G12, G14, G16, G17, G18, and G20. However, five strains had less than 80% similarity with those genotypes and were assigned to the new genotypes G22, G23 (2 strains), G24, and G25. The G16 genotype was the most prevalent genotype each year. The predominant genotypes clustered geographically, with G12 being predominant on the east coast, G16 in the Midwest, and G20 within the Great Plains states.
Investigation of the variability within the VP7 proteins identified 8 variable regions. However, those regions did not align with the sites of high antigenicity detected in the predominant groups. Indeed, surface-exposed antigenic residues underwent negative selection more often than positive selection.
Rotavirus B (RVB) is an important swine pathogen, but control and prevention strategies are limited without an available vaccine. To develop a subunit RVB vaccine with maximal effect, we characterized the amino acid sequence variability and predicted antigenicity of RVB viral protein 7 (VP7), a major neutralizing antibody target, from clinically infected pigs in the United States and Canada. We identified genotype-specific antigenic sites that may be antibody neutralization targets. While some antigenic sites had high amino acid functional group diversity, nine antigenic sites were completely conserved. Analysis of nucleotide substitution rates at amino acid sites (dN/dS) suggested that negative selection appeared to be playing a larger role in the evolution of the identified antigenic sites when compared to positive selection, and was identified in six of the nine conserved antigenic sites. These results identified important characteristics of RVB VP7 variability and evolution and suggest antigenic residues on RVB VP7 that are negatively selected and highly conserved may be good candidate regions to include in a subunit vaccine design due to their tendency to remain stable.