MrHAMER yields highly accurate single molecule viral sequences enabling analysis of intra-host evolution.

ABSTRACT: Technical challenges remain in the sequencing of RNA viruses due to their high intra-host diversity. This bottleneck is particularly pronounced when interrogating long-range co-evolved genetic interactions given the read-length limitations of next-generation sequencing platforms. This has hampered the direct observation of these genetic interactions that code for protein-protein interfaces with relevance in both drug and vaccine development. Here we overcome these technical limitations by developing a nanopore-based long-range viral sequencing pipeline that yields accurate single molecule sequences of circulating virions from clinical samples. We demonstrate its utility in observing the evolution of individual HIV Gag-Pol genomes in response to antiviral pressure. Our pipeline, called Mult

SUBMITTER: Gallardo CM 

PROVIDER: S-EPMC8266615 | biostudies-literature | 2021 Jul

REPOSITORIES: biostudies-literature