Host and geographic barriers shape the competition, coexistence, and extinction patterns of influenza A (H1N1) viruses

The influenza virus mutates and spreads rapidly, making it suitable for studying evolutionary and ecological processes. The ecological factors and processes by which different lineages of influenza compete or coexist within hosts through time and across geographical space are poorly known. We hypothesized that competition would be stronger for influenza viruses infecting the same host compared to different hosts (the Host Barrier Hypothesis), and for those with a higher cross‐region transmission intensity (the Geographic Barrier Hypothesis). Using available sequences of the influenza A (H1N1) virus in GenBank, we identified six lineages, twelve clades, and several replacement events. We found that human‐hosted lineages had a higher cross‐region transmission intensity than swine‐hosted lineages. Co‐occurrence probabilities of lineages infecting the same host were lower than those infecting different hosts, and human‐hosted lineages had lower co‐occurrence probabilities and genetic diversity than swine‐hosted lineages. These results show that H1N1 lineages infecting the same host or with high cross‐region transmission rates experienced stronger competition and extinction pressures than those infecting different hosts or with low cross‐region transmission. Our study highlights how host and geographic barriers shape the competition, extinction, and coexistence patterns of H1N1 lineages and clades. Using available sequences of influenza A (H1N1) virus in public database we identified six lineages of H1N1 and twelve clades with several replacement events for human‐hosted lineages. We found 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.