Investigation of secretor status, rotavirus VP4 genotypes, and gastrointestinal microbiomes in cases of diarrhoea in South Africa

Abstract

Rotavirus gastroenteritis is a preventable public health concern, and diarrhoeal deaths persist in low-income settings. Rotavirus is prevalent in children under five years, despite widespread vaccination. Rotavirus P[8] vaccines display lowered efficacy (30-50%) in low-income settings compared to high-income (~80%). Disparities in vaccine efficacy are multifactorial but may be influenced by host factors. Understanding the interplay between the host, pathogen infection, and gut microbes may allow for targeted interventions against diarrhoeal disease. The FUT2 secretor gene encodes the availability of human histo-blood group antigens (HBGAs) in the gut, and the VP4 spike of rotavirus displayed binding affinity in a strain-specific manner to HBGAs. Secretor status may, therefore, influence rotavirus susceptibility, strain distribution, and partially contribute to varied vaccine efficacy. Furthermore, gut microbiomes may be shaped by HBGAs, influencing gut health and the subsequent risk of diarrhoeal disease. The aim of this study was to investigate secretor status, rotavirus VP4 genotypes, and gut microbiomes in South African children to elucidate the interplay between these factors. Methods for determining secretor status were evaluated since unique strengths and limitations exist that should be tailored to study design and population. Genotyping of the FUT2 gene targeting a known non-secretor mutation proved to be limited in genetically diverse participants. Phenotyping methods inaccurately classified children potentially due to an underdeveloped secretor phenotype that is masked by maternal antibodies introduced via breastmilk. Both methods yielded comparable yet distinct information about the cohort, and the study aim is essential to consider prior to method choice. In this study, South African secretors were significantly more susceptible to rotavirus infection, while non-secretors displayed a natural resistance. Rotavirus susceptibility was also strain-specific, where secretors were susceptible to predominantly circulating P[8] and P[4] strains, while less prevalent rotavirus P[6] strains were more common in non-secretors. Our findings indicate that secretor status is an important mediator of VP4 strain-specific rotavirus susceptibility in the South African population. Non-secretors in a population could modulate the circulation of wild-type rotavirus and contribute to lowered vaccine efficacy. In our study, non-secretors made up ~30% of the population. Higher frequencies of non-secretors in a population could reduce P[8] and P[4] rotavirus circulation, causing increased prevalence of P[6] strains with phylogenetically different VP4 genes. P[6] rotavirus strains are relatively common in South Africa, which contrasts to regions where non-secretors and P[6] strains are uncommon. Non-secretors may also respond poorly to rotavirus P[8] vaccines, and although their resistance to wild-type P[8] strains negates the need for a strong P[8] response, it may be important in areas where rare rotavirus strains are prevalent. Investigating the gut microbiome of healthy children did not show that microbial composition was influenced by secretor status. However, this pilot study provided valuable insights into microbiome methods and analysis pipelines. The gut microbiome is an emerging field of study, with advancements in sequencing technologies making the field more accessible to young scientists. The fight against diarrhoeal disease will require comprehensive insight into the gut environment.