vsgseq2: an updated pipeline for analysis of the diversity and abundance of population-wide Trypanosoma brucei VSG expression

Abstract

Trypanosoma brucei is an extracellular eukaryotic parasite that causes sleeping sickness in humans and Nagana, Surra and Dourine in livestock, game animals and horses. The parasite displays an extensive immune evasion mechanism, utilising the expression and ability to switch antigenically distinct variant surface glycoprotein (VSG) coats. VSG encoding genes account for ~10% of the T. brucei genome, and mosaic VSGs, assembled from distinct incomplete VSG gene copies, can be produced from this VSG library, generating an almost infinite VSG repertoire, which enables chronic infections. Each parasite expresses just one VSG at a time, but within a host, many VSGs can be expressed simultaneously. VSGSeq is an amplicon sequencing approach that enables surveillance of the population-wide diversity and abundance of expressed VSGs. vsgseq2 is an updated bioinformatics pipeline that enhances the reproducibility, accuracy, and efficiency of VSGseq analysis, utilising publicly available analytical tools. Plain Language SummaryAfrican trypanosomes, such as Trypanosoma brucei, are parasites that cause deadly diseases in humans and livestock. They survive in their hosts blood by constantly changing a protective coat of proteins, known as variant surface glycoproteins (VSGs). Switching VSG makes it very hard for the immune system to keep up, allowing infections to last for months or even years. At any one time, each parasite uses only one VSG, but across the whole population inside a host, many different VSGs are used simultaneously. To study how parasites change their coats, a method called VSGSeq was developed, which shows the genetic basis that makes the VSG coat. This research introduces vsgseq2, which provides an enhanced workflow for population-scale analysis of VSG expression, helping future research to understand how trypanosomes evade their hosts immune attack.