Abstract
Even after three decades of antiretroviral therapy for HIV-1 (human immunodeficiency virus 1), therapy failure is a continual challenge. This is especially so if the viral variant is a recombinant of subtypes. Thus, improved diagnosis of recombined subtypes can help with the selection of therapy. We are using a new implementation of the previously published computational method recco to detect de novo recombination of known subtypes, independent of and in addition to known circulating recombinant forms (CRFs). We detect an optimal path in a multiple alignment of viral reference sequences based on mutation calls and probable breakpoints for recombination. A tuning parameter is used to favor either mutation calls or breakpoints. Besides novel recombinants, our tool g2p-recco integrated in the geno2pheno web service (https://geno2pheno.org) can successfully detect known recombinant events given only the full consensus references (without CRFs) of the involved subtypes with breakpoints. In addition, the tool can be applied to other viruses, i.e. hepatitis E virus (HEV). In this fashion, we could also detect several previously unknown recombinations in HEV.