Information and sequences of the six lineages identified in the H1N1 influenza A virus

The influenza virus mutates and spreads rapidly, making it an ideal model
for studying evolutionary and ecological processes. The ecological factors
and processes by which different lineages compete or coexist within hosts,
through time and across geographical space are poorly known. We
hypothesize that competition would be higher for influenza viruses sharing
the same host than those sharing different hosts (Host Barrier
Hypothesis), or for influenza viruses with a higher cross-region
transmission intensity than those with a lower cross-region transmission
intensity (Geographic Barrier Hypothesis). Using available sequences of
influenza A (H1N1) virus in GenBank we identified six lineages of H1N1 and
twelve clades with several replacement events. We found the human-hosted
lineages had a higher cross-region transmission intensity than
swine-hosted lineages. The estimated co-occurrence probability of lineages
sharing the same host is much lower than those sharing different hosts,
and human-hosted lineages had lower co-occurrence probability and genetic
diversity than swine-hosted lineages. Our results indicate that H1N1
lineages sharing the same host or having a higher cross-region
transmission intensity experienced a higher competition and extinction
pressure. Our study highlights the significant roles of the host and
geographic barriers in shaping the competition, extinction and coexistence
patterns of H1N1 lineages or clades.