Inferring epidemic characteristics with networks

National Institute Of Diabetes And Digestive And Kidney Diseases

Investigators

Abstract

We are updating previous analysis which computed genome-wide covariation of the SARS-CoV-2 genome to an alignment of 7000000 SARS-CoV-2 complete genome sequences obtained from GISAID. We are delineating functional genome interactions from the effects of random evolution by characterizing a substitution matrix for the full alignment and artificially mutating the SARS-CoV-2 reference genome to acquire a baseline genome covariation which is compared directly against the actual genome covariation. We will then extend previous work characterizing clade-specific covariation to consider phylogenetic distance versus differences in genome covariation. Taking time and space annotations into account, we hope to detect changes in genome coevolution upon the introduction of vaccines, detecting escape routes that may be relevant for vaccine design.