Nucleoprotein reassortment enhanced transmissibility of H3 1990.4.a clade influenza A virus in swine

Authors: THOMAS, MEGAN - Iowa State University; CIACCI ZANELLA, GIOVANA - Iowa State University; COWAN, BRIANNA - University Of Georgia; CACERES, JOAQUIN - University Of Georgia; RAJAO, DANIELA - University Of Georgia; PEREZ, DANIEL - University Of Georgia; GAUGER, PHILLIP - Iowa State University; Baker, Amy; Anderson, Tavis

Submitted to: Journal of Virology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/22/2024
Publication Date: 2/14/2024
Citation: Thomas, M.N., Ciacci Zanella, G., Cowan, B., Caceres, J.C., Rajao, D.S., Perez, D.R., Gauger, P.C., Baker, A.L., Anderson, T.K. 2024. Nucleoprotein reassortment enhanced transmissibility of H3 1990.4.a clade influenza A virus in swine. Journal of Virology. https://doi.org/10.1128/jvi.01703-23.
DOI: https://doi.org/10.1128/jvi.01703-23

Interpretive Summary: Influenza A viruses (IAV) are composed of eight non-continuous gene segments that can reassort during coinfection of an animal host to create new combinations. Some gene combinations may convey a selective advantage and be paired together preferentially. A reassortment event was detected in swine in the United States that involved the exchange of two lineages of nucleoprotein (NP) genes (trigNP to pdmNP) that then became a predominant genotype detected in genomic surveillance. Using a transmission study, we demonstrated that exchanging the trigNP to a pdmNP caused the virus to shed from the nose at higher levels and transmit more rapidly to other pigs. Replacing a pdmNP with a trigNP did not decrease transmission, suggesting that transmission efficiency depends on interactions between multiple genes. This demonstrates how reassortment alters IAV transmission and that reassortments events can provide an explanation for why genetically related viruses with different internal gene combinations experience rapid fluxes in detection frequency.

Technical Abstract: The increased detection of H3 C-IVA (1990.4.a) clade influenza A viruses (IAV) in U.S. swine in 2019 was associated with a reassortment event to acquire an H1N1pdm09 lineage nucleoprotein (pdmNP) gene, replacing a TRIG lineage NP (trigNP). We hypothesized that acquiring the pdmNP conferred a selective advantage over prior circulating H3 viruses with a trigNP. To investigate the role of the NP reassortment in transmission, we identified two contemporary 1990.4.a representative strains (NC/19 and MN/18) with different evolutionary origins of the NP gene. A reverse genetics system was used to generate wild-type (wt) strains and to swap the pdm and TRIG lineage NP genes, generating four viruses: wtNC/19-pdmNP, NC/19-trigNP, wtMN/18-trigNP, MN/18-pdmNP. Pathogenicity and transmission of the four viruses were compared in pigs. All four viruses infected 10 primary pigs and transmitted to 5 indirect contact pigs per group. Pigs infected via contact with MN/18-pdmNP shed virus two days earlier than pigs infected with wtMN/18-trigNP. In contrast, the inverse did not occur for wtNC/19-pdmNP and NC/19-trigNP. These data suggest that reassortment to acquire a pdmNP gene improved transmission efficiency in the 1990.4.a, but this is likely a multigenic trait. Replacing a trigNP gene alone may not completely diminish the transmission of a wild-type virus detected in surveillance of swine populations. This study demonstrates how reassortment and subsequent evolutionary change of internal genes can result in more transmissible viruses that impacts the detection frequency of specific HA clades. Thus, rapidly identifying novel reassortants paired with dominant HA/NA may improve prediction of strains to include in vaccines.