The Genetic Variation Landscape of African Swine Fever Virus Reveals Frequent Positive Selection on Amino Acid Replacements

PaperPlayer biorxiv evolutionary biology

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.12.249045v1?rss=1 Authors: Bao, Y.-J., Qiu, J., Rodriguez, F., Qiu, H.-J. Abstract: African swine fever virus (ASFV) is a lethal disease agent that causes high mortality in swine population and devastating loss in swine industries. The development of efficacious vaccines has been hindered by the knowledge gap in genetic properties of ASFV and the interface of virus-host interactions. In this study, we performed a genetic study of ASFV aiming to profile the variation landscape and identify genetic factors with signatures of positive selection and relevance to virus-host interactions. To achieve this goal, we developed a new tool "SweepCluster" for systematic identification of selective sweep. Our data reveals a high level of genetic variability of ASFV shaped by both diversifying selection and selective sweep. The selection signatures are widely distributed across the genome with the diversifying selection falling within 29 genes and selection sweep within 25 genes. Further examination of the structure properties reveals the link of the selection signatures with virus-host interactions. Specifically, we discovered a site at 157th of the antigen protein EP402R under diversifying selection located in the cytotoxic T-cell epitope involved in the serotype-specific T-cell response. Moreover, we reported 24 novel candidate genes with relevance to virus-host interactions. By integrating the candidate genes with selection signatures into a unified framework of interactions between ASFV and hosts, we showed that those genes are involved in multiple processes of host immune evasion and virus life cycles, and may play crucial roles in circumventing host defense systems and enhancing adaptive fitness. Copy rights belong to original authors. Visit the link for more info