A27 Using whole genome sequence data and minority variant profiles to elucidate transmission patterns during RSV household outbreaks

Abstract

Reconstructing transmission chains for outbreaks is importantin understanding how viruses spread. Furthermore, definingthe main underlying determinants of transmission chains isimportant for developing effective interventions. Whole genome consensus sequence data provides information thatrepresents the dominant virus subtype. It does not provide sufficient information to resolve transmission events particularlyfor rapidly spreading viruses. However, changes in the composition of minor variants between hosts and the pattern of minorvariants fixation during outbreaks, could provide additionalhigh-resolution data on who is infecting whom. The same datacould also potentially inform the extent of within-host virusdiversity as well as the proportion of diversity that is transmitted between individuals. We have developed a reproduciblesemi-automated whole genome variant calling pipeline toexplore the role of minority variants in resolving transmissionpatterns and within host viral evolution. The pipeline is available as modular Bash scripts that run on a Linux clusterenvironment.