Accounting for Defective Viral Genomes in Large-Scale Bioinformatics Viral Surveillance: Application to Influenza Virus Sequencing

In the context of viral epidemic surveillance, generating accurate consensus viral genomes from sequencing data is critical for tracking the emergence of mutations of concern, evaluating the genomic diversity of circulating viruses, and anticipating which viral strains could become most prevalent. However, this task is made difficult by the presence of Deletion-containing Viral Genomes (DelVGs), which contain truncated (or rearranged) and potentially mutated versions of the full length virus genome. Because these DelVGs can outnumber the full genome in terms of coverage, potential DelVG specific mutations may be erroneously incorporated into the final consensus, thereby compromising its accuracy. Automatic detection of these DelVGs and of the genomic positions that may harbor DelVG specific mutations is therefore crucial.