Reassortment Complements Spontaneous Mutation in Influenza A Virus NP and M1 Genes To Accelerate Adaptation to a New Host

Abstract

Influenza A virus (IAV) infects a remarkably wide variety of avian and mammalian hosts. Evolution finely hones IAV genes to optimally infect and be transmitted in a particular host species. Sporadically, IAV manages to jump between species, introducing novel antigenic strains into the new host population that wreak havoc until herd immunity develops. IAV adaptation to new hosts typically involves reassortment of IAV gene segments from coinfecting virus strains adapted to different hosts in conjunction with multiple adaptive mutations in the various IAV genes. To better understand host adaptation between mammalian species in real time, we passaged mouse-adapted A/PR8/34 (PR8) in guinea pigs. Guinea pigs, unlike mice, support spontaneous and robust IAV transmission. For some IAV strains, including PR8, adaptation is required for a virus to attain transmissibility, providing an opportunity to understand the evolution of transmissibility in guinea pigs. Multiple guinea pig-adapted PR8 mutants generated by serial nasal wash passaging in independent lines replicated more efficiently and were transmitted by cocaging. All transmissible variants possessed one of two nonsynonymous mutations in M1, either alone or in combination with mutations in PB2, HA, NP, or NA. Rapid reassortment between independently selected variants combined beneficial mutations in NP and M1 to form the fittest virus capable of being transmitted. These findings provide further insight into genetic determinants in NP and M1 involved in PR8 IAV adaptation to be transmitted in a new host and clearly show the benefit of a segmented genome in rapidly generating optimal combinations of mutations in IAV evolution.

Influenza A virus nucleoprotein selectively decreases neuraminidase gene-segment packaging while enhancing viral fitness and transmissibility

“…Importantly, decreased gene-packaging frequency can be associated with enhanced in vivo fitness, likely because frequent coinfection and complementation allow particles with incomplete genome sets to contribute to the propagation of the population. Under these conditions, the costs of producing SI particles may be outweighed by the potential benefits, the most important of which might be promoting reassortment and thus the adaptive potential of the population (4,7).…”

“…The importance of multiplicity reactivation during natural infection depends entirely on the prevalence of coinfection in vivo. Although the high frequency of reassortants generated during guinea pig infection demonstrates that coinfection occurs in vivo (4,26,27), its actual incidence is unknown.…”

“…Genome segmentation complements the high mutation rate of IAV by facilitating reassortment, which can maximize positive intergenic epistasis (2)(3)(4)(5) and allow selective elimination of segments with deleterious mutations (6,7). Although reassortment is the most obvious and best-characterized benefit of segmentation, there are likely additional evolutionary advantages.…”

“…We previously described a single amino acid substitution (F346S) in the nucleoprotein (NP) of mouse-adapted A/Puerto Rico/8/34 (PR8), selected during serial passage in guinea pigs, which enhances replication in the guinea pig respiratory tract and enables contact transmission (4). Here, we report that this adaptive mutation selectively decreases both the expression and packaging of the NA gene segment, thus revealing a surprising role for NP in the regulation of glycoprotein function and demonstrating that decreased gene packaging can be associated with increased in vivo fitness and transmissibility.…”

Novel H7N9 Influenza Virus Shows Low Infectious Dose, High Growth Rate, and Efficient Contact Transmission in the Guinea Pig Model

“…Nevertheless, rhinitis and bronchointerstitial pneumonia have been described (22,32). The utility of the guinea pig model is underlined by the fact that, since 2006, many additional labs have adopted it for the study of influenza virus transmission (33)(34)(35)(36)(37)(38). Since no animal model is perfect, efforts to accurately model human disease are strengthened by the use of multiple animal species, and ideally by the development of practical models in which specific animals are used to model specific aspects of disease.…”