Natural Selection of H5N1 Avian Influenza A Viruses with Increased PA-X and NS1 Shutoff Activity

Abstract

Influenza A viruses (IAV) can infect a broad range of mammalian and avian species. However, the host innate immune system provides defenses that restrict IAV replication and infection. Likewise, IAV have evolved to develop efficient mechanisms to counteract host antiviral responses to efficiently replicate in their hosts. The IAV PA-X and NS1 non-structural proteins are key virulence factors that modulate innate immune responses and virus pathogenicity during infection. To study the determinants of IAV pathogenicity and their functional co-evolution, we evaluated amino acid differences in the PA-X and NS1 proteins of early (1996–1997) and more recent (since 2016) H5N1 IAV. H5N1 IAV have zoonotic and pandemic potential and represent an important challenge both in poultry farming and human health. The results indicate that amino acid changes occurred over time, affecting the ability of these two non-structural H5N1 IAV proteins to inhibit gene expression and affecting virus pathogenicity. These results highlight the importance to monitor the evolution of these two virulence factors of IAV, which could result in enhanced viral replication and virulence.

Characterization of the In Vitro and In Vivo Efficacy of Baloxavir Marboxil against H5 Highly Pathogenic Avian Influenza Virus Infection

“…In this study, a variant virus harboring I127V in the PA was detected in the mice after the dosing of BXM at 0.5 mg/kg twice daily for 5 days. According to a previous report, V127 in the PA was highly conserved in a recent isolate of H5N1 viruses [67]. In addition, some of the H5 HPAIVs tested in the study harbored V127 in the PA (Table S4), and they were susceptible to BXA such as the A/Hong Kong/483/1997 (H5N1) strain.…”

The cut site specificity of the influenza A virus endoribonuclease PA-X allows it to discriminate between host and viral mRNAs

“…While PA-X sequences are fairly conserved across strains because of the constraints on both PA-X and PA coding regions, the PA-X from the pH1N1 strain has an X-ORF of 41 amino acids, compared to 61 amino acids for the PR8 and Perth strains (Shi et al, 2012). Moreover, PA-Xs from different strains have been reported to have differences in host shutoff activity (Feng et al, 2016;Nogales et al, 2021;Oishi et al, 2019;Wang et al, 2020). It would thus be interesting to investigate whether the X-ORF has an effect on the cut site specificity, especially as we only tested our best PA-X targets and the differences in cleavage specificity may be subtle.…”

Live attenuated influenza A virus vaccines with modified NS1 proteins for veterinary use

“…This advantage has been broadly used to generate LAIV by introducing specific amino acid substitutions, or deletions, in the viral genome (Martinez-Sobrido et al, 2018;Rodriguez et al, 2018b;Blanco-Lobo et al, 2019;Hilimire et al, 2020). For instance, IAV encoding truncated versions of NS1 or where the NS1 sequence was completely removed (DNS1) have been generated and used as potential LAIV candidates in multiple animal species (Quinlivan et al, 2005;Solorzano et al, 2005;Richt et al, 2006;Vincent et al, 2007;Wang et al, 2008;Chambers et al, 2009;Steel et al, 2009;Kappes et al, 2012;Choi et al, 2015;Jang et al, 2016;Na et al, 2016;Chen et al, 2017;Nogales et al, 2017b;Jang et al, 2018;Nicolodi et al, 2019;Lee et al, 2021;Vandoorn et al, 2022a), or to study IAV infections (Nogales et al, 2021a), including the contribution of NS1, and its domains, in viral pathogenesis (Nogales et al, 2017a;Nogales et al, 2017c;Chauche et al, 2018;Nogales et al, 2018a;Nogales et al, 2018b;Nogales et al, 2021b). Because NS1 is the main countermeasure against cellular antiviral responses, the recovery of NS1 truncated or deficient viruses can be challenging, since these viruses have limited ability to inhibit the cellular innate immune responses induced during viral infection Kochs et al, 2007;Hale et al, 2008;Nogales et al, 2018b;Nogales et al, 2019b).…”

“…The ED is able to interact with multiple host factors, including cellular proteins involved in antiviral responses (Hale et al, 2008;Thulasi Raman and Zhou, 2016;Nogales et al, 2018b). However, many of these interactions can be strain-dependent, and host-adaptation processes could be important for this high variability (Kochs et al, 2007;Steidle et al, 2010;Marc, 2014;Clark et al, 2017;Nogales et al, 2017a;Nogales et al, 2017f;Chauche et al, 2018;Nogales et al, 2018a;Nogales et al, 2021b). The last domain is a C-terminal tail (CTT) of 11-33 amino acids, containing a PDZ-binding motif that is associated with IAV pathogenesis and is not present in all IAV NS1 proteins (Jackson et al, 2008;Hale, 2014).…”