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

Abstract

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.

Zooming in on the molecular characteristics of swine influenza virus circulating in Colombia before and after the H1N1pdm09 virus

“…These processes are most evident in the 2015 viruses, in which consistent phylogenetic grouping following geographic patterns is observed ( Figures 1 – 4 , Figures S1 – S3 ) and noticed as well in the relationship of M and NS genes from virus A/swine/Antioquia/0201/2009 with classic viruses encountered in the same region ( Figure S3 , Figures 4 , 5 ). Multiple studies with the H1N1 subtype reported variations among regions, where evidence of separate evolution could eventually generate new clades and subclades ( 16 , 60 ).…”

“…H1N1pdm09 viruses were introduced in the Colombian territory in 2009 (34), and since then, a clear dominance has been obeyed by being the only subtype detected. This indicates the displacement of the classic subtype due to a competitive dynamic (16,55) in which H1N1pdm09 virus was more efficient in terms of higher viral fitness and antigenic difference after its recent installment (17,56,57). Such sustained superiority is contrary to what has been seen in other countries, where H1N1pdm09 circulates but not as the dominant subtype (15,58,59).…”

“…Among the most predominant swine subtypes, a vast genetic and antigenic diversity is associated with interspecies jump events and geographic and temporal patterns ( 4 , 15 – 17 ). A recent analysis of the H1 subtype demonstrated how the principal swine lineages spread to new geographic regions and evolved to different clades after their establishment in pigs, albeit influenced by geographic barriers and animal movement patterns; viruses from a North American origin have disseminated to all continents while viruses from European source are mainly distributed across Asia ( 16 ).…”

Molecular Tracking of The Origin of Vesicular Stomatitis Outbreaks in 2004 and 2018, Ecuador

“…For Influenza A it has been shown that host and geographic barriers shape the competition, extinction, and coexistence patterns of H1N1 lineages and clades. [56] Also, like the Venezuelan equine encephalitis virus, a different and enzootic vector can be present in the Amazon or the interface between forest and agriculture [49,50]. It has been demonstrated that the genetic diversity of the West Nile virus depended on the mosquito species [57].…”

Influenza aviar de alta patogenicidad y sus saltos interfaces entre aves y mamíferos: situación actual

“…La influenza aviar, también conocida como gripe aviar es una de las enfermedades más comunes a nivel mundial; su importancia radica en las duras consecuencias que puede generar en la industria avícola por la muerta de los animales, que DOI: https://doi.org/10.22579/22484817.988 económicas (Kanaujia et al, 2022;Ravikumar et al, 2022); también al ser una enfermedad zoonótica (transmisión de animales a humanos), esta enfermedad puede cursar desde leves síntomas respiratorios hasta la muerte; lo anterior sumado a su alto potencial pandemiogeno, la convierte en una enfermedad de elevada importancia para la salud pública (Cheng et al, 2022;OMS, 2018;World Organisation for Animal Health, n.d.; Yago, 2016).…”