Phylodynamics of the Emergence of Influenza Viruses after Cross-Species Transmission

Abstract

Human populations are constantly exposed to emerging pathogens such as influenza A viruses that result from cross-species transmissions. Generally these sporadic events are evolutionary dead-ends, but occasionally, viruses establish themselves in a new host that offers a novel genomic context to which the virus must adjust to avoid attenuation. However, the dynamics of this process are unknown. Here we present a novel method to characterize the time it takes to G+C composition at third codon positions (GC3 content) of influenza viruses to adjust to that of a new host. We compare the inferred dynamics in two subtypes, H1N1 and H3N2, based on complete genomes of viruses circulating in humans, swine and birds between 1900–2009. Our results suggest that both subtypes have the same fast-adjusting genes, which are not necessarily those with the highest absolute rates of evolution, but those with the most relaxed selective pressures. Our analyses reveal that NA and NS2 genes adjust the fastest to a new host and that selective pressures of H3N2 viruses are relaxed faster than for H1N1. The asymmetric nature of these processes suggests that viruses with the greatest adjustment potential to humans are coming from both birds and swine for H3N2, but only from birds for H1N1.

Animal Disease Surveillance in the 21st Century: Applications and Robustness of Phylodynamic Methods in Recent U.S. Human-Like H3 Swine Influenza Outbreaks

“…This raises the question of whether using longer gene segments or whole genomes provides deeper resolution into the evolutionary history of rapidly evolving pathogens. Past influenza A studies (41,123,124), including the present study, showed that HA and NA segments typically exhibit higher evolutionary rates than more conserved segments like PB1 and PB2. Subsequently, segments with higher evolutionary rate will also display stronger evolutionary signals, as described above.…”

Host-range shift of H3N8 canine influenza virus: a phylodynamic analysis of its origin and adaptation from equine to canine host

“…In addition, the U content of each gene segment was analysed for both H3N8 CIV and H3N8 EIV. An increasing U content in viral gene segments is an indicator of viral adaptation to a new host species [64]. There was an increasing trend in the U content of each gene segment over time for both H3N8 CIV and H3N8 EIV (Figure 8), indicating that both viruses were adapting to their respective hosts.…”

Influenza A virus vaccine research conducted in swine from 1990 to May 2018: A scoping review

“…In both vaccinated and non-vaccinated pigs, influenza A viruses can be diverse at the level of the population, within an individual pig, and even within a cell [72][73][74][75]. Investigation of virus characterization and of transmissibility is necessary to understand, at the individual animal level, vaccine induced cross-protection and duration of immunity, and at the population level, the impact of vaccination on the viral ecology of influenza in swine [1,21,56,[76][77][78][79][80][81][82]. In poultry, vaccination has been associated with selective transmission of more virulent strains of IAV [83].…”