RSV sequence variation and within-host minority variant dynamics

Abstract

Respiratory syncytial virus (RSV) infection is a common disease that causes the most severe disease in the extremes of age. Parts of the RSV genome are extremely variable, however, origination of genomic variation of RSV is not studied very well. Epidemiology studies have shown rapidly changing RSV strains and grouped these in genotypes based on a part of the RSV genome that consists of the (partial) G gene. In this thesis, the genotyping system was inspected and it showed that the part of the G gene previously used for genotyping did not contain enough information to reliably determine which genotype a strain belonged to. Phylogenetic analysis was performed to determine the necessary and sufficient part of the genome to determine the genotype reliably, which was full G. Other proteins were investigated for variability as well and both F and L carried plenty of variation as well. The amount of variation within a patient has been understudied. Therefore, a new method was optimised to detect the prevalence of minority variations in clinical samples. The prevalence of minority variants was examined in a community cohort and hospital cohort from season 2015-2016 of which all samples were spatiotemporally and age-matched. The detected genotypes were GA2 and ON1. Most clinical samples in this study did carry minority variants, however, there was no difference in the amount of variation between community and hospital samples. The gene that displayed the most variations per nucleotide, and most non-synonymous variations was G. This research also demonstrates that these variations can be transmitted or develop during acute infection. Consecutive samples from volunteers inoculated with a known RSV strain showed that both synonymous and non-synonymous variations can occur and their frequency can increase, decrease or remain stable over time. The F gene rarely developed non-synonymous variations in this study.Open Acces