biostudies-literatureFaleye TOCNLM NIH HHS810https://www.ebi.ac.uk/biostudies/studies/S-EPMC8360813biostudies-literatureUnknown21(1)<h4>Background</h4>Local transmission of seasonal influenza viruses (IVs) can be difficult to resolve. Here, we study if coupling high-throughput sequencing (HTS) of hemagglutinin (HA) and neuraminidase (NA) genes with variant analysis can resolve strains from local transmission that have identical consensus genome. We analyzed 24 samples collected over four days in January 2020 at a large university in the US. We amplified complete hemagglutinin (HA) and neuraminidase (NA) genomic segments followed by Illumina sequencing. We identified consensus complete HA and NA segments using BLASTn and performed variant analysis on strains whose HA and NA segments were 100% similar.<h4>Results</h4>Twelve of the 24 samples were PCR positive, and we detected complete HA and/or NA segments by de novo assBMC infectious diseasesUse of hemagglutinin and neuraminidase amplicon-based high-throughput sequencing with variant analysis to detect co-infection and resolve identical consensus sequences of seasonal influenza in a university setting.PMC8360813U01 LM013129Halden RUScotch MFaleye TOCAdhikari SAdams DSandrolini HVarsani AfalseUse of hemagglutinin and neuraminidase amplicon-based high-throughput sequencing with variant analysis to detect co-infection and resolve identical consensus sequences of seasonal influenza in a university setting.<h4>Background</h4>Local transmission of seasonal influenza viruses (IVs) can be difficult to resolve. Here, we study if coupling high-throughput sequencing (HTS) of hemagglutinin (HA) and neuraminidase (NA) genes with variant analysis can resolve strains from local transmission that have identical consensus genome. We analyzed 24 samples collected over four days in January 2020 at a large university in the US. We amplified complete hemagglutinin (HA) and neuraminidase (NA) genomic segments followed by Illumina sequencing. We identified consensus complete HA and NA segments using BLASTn and performed variant analysis on strains whose HA and NA segments were 100% similar.<h4>Results</h4>Twelve of the 24 samples were PCR positive, and we detected complete HA and/or NA segments by de novo ass2021-01-01T00:00:00Z2021 Aug2026-05-09T03:25:39.399Z2022-02-11T08:09:59.413ZS-EPMC83608133438897910.1186/s12879-021-06526-5