Genetic drift and purifying selection shape within-host influenza A virus populations during natural swine infections
Fig 3
Classification of gene segments and samples into lineages.
(A) Mapping of sample reads on to reference H1, N1, H3, and N2 gene segments for four selected samples. Based on this mapping, a sample’s HA gene segment was classified as belonging to either lineage I (with reads mapped to H1; vial#14SW6024), lineage II (with reads mapped to H3; vial#14SW6331 and vial#14SW5957), or coinfected (with reads mapped to both H1 and H3; vial#14SW6164). Similarly, a sample’s NA gene segment was classified as belonging to either lineage I (with reads mapped to N1; vial#14SW6024), lineage II (with reads mapped to N2; vial#14SW6331 and vial#14SW5957), or coinfected (with reads mapped to both N1 and N2; vial#14SW6164). (B) Detection of dSNPs characteristic of lineages I and II for each of the six internal gene segments of the four selected samples. (C) The proportion of samples classified as lineage I, II, or coinfected, by gene segment. Segments were labeled as unknown when there was insufficient coverage across the focal gene segment to determine nucleotide identities at the dSNP sites or to robustly map to the HA and NA gene segments. Samples (‘All’) were classified as belonging to lineage I, lineage II, coinfected, or reassortant based on their constituent segments. A sample was defined as a lineage I or II sample if at least five of its gene segments were successfully classified and found to be either singly infected lineage I or singly infected lineage II, with no evidence of coinfection. A sample was considered a reassortant if at least five segments were successfully classified and a combination of lineage I singly infected and lineage II singly infected segments were present in the same sample. A sample was considered coinfected if at least one of its gene segments was classified as coinfected. In panels (A) and (B), each row corresponds to a different sample classification. Vial#14SW6024 corresponds to a sample with a lineage I virus, vial#14SW6331 corresponds to a sample with a lineage II virus, vial#14SW6164 corresponds to a coinfected sample, and vial#14SW5957 corresponds to a reassortant virus.