Antigenic characterization of novel H1 influenza A viruses in swine

Abstract

Novel H1N2 influenza A viruses (IAVs) in swine have been identified in Chile co-circulating with pandemic H1N1 2009-like (A(H1N1)pdm09-like) viruses. The objective of this study was to characterize antigenically the swine H1 IAVs circulating in Chile. Genetic analysis based on the HA1 domain and antigenic analysis by hemagglutination inhibition assay were carried out. Three antigenic clusters were identified, named Chilean H1 A (ChH1A), Chilean H1 B (ChH1B), and A(H1N1)pdm09-like. The antigenic sites of ChH1A and ChH1B strains were 10-60% distant from those of commercial vaccine strains at the amino acid sequence level. Antigenic variants were identified within the clusters ChH1A and A(H1N1)pdm09-like. Substitutions in the main antigenic sites (E153G in Sa, Q193H in Sb, D168N in Ca1, P137S in Ca2, and F71L in Cb) were detected in variants from the ChH1A cluster, whereas only a single substitution in antigenic site Sa (G155E) was detected in variants from A(H1N1)pdm09-like cluster, which confirms the importance to carrying out antigenic analyses in addition to genetic analyses to evaluate control measures such as vaccination. These results highlight the need to update vaccines for swine in Chile and the importance of continued surveillance to determine the onward transmission of antigenic variants in Chilean pig populations. Influenza A virus (IAV) is a member of the family Orthomyxoviridae possessing 8 negative sense single-stranded RNA segments 1 and classified in subtypes based on the antigenicity of their surface glycoproteins: 18 subtypes for hemagglutinin (HA) and 11 subtypes for neuraminidase (NA) 2. IAV can infect birds and several mammalian species, including human and swine. Pigs have an important role in the ecology of IAV, since they can become infected with both human and avian strains 3,4. Co-infection with IAVs from different lineages can generate reassortant strains with potential epidemic and zoonotic risks 5-7. IAVs are ubiquitous in swine worldwide, generating significant economic losses and representing a public health concern 8,9. The main control measure in many swine farms is the use of vaccines, but the commercial vaccines currently available are based on North American or European IAV strains 10,11. H1N1, H1N2 and H3N2 are the main subtypes circulating in swine globally; however, IAVs in swine are genetically and antigenically diverse even within each subtype, and several lineages have been reported 12,13. This IAV diversity is the result of genetic evolution and antigenic changes that occur primarily through 2 mechanisms: 'antigenic shift' , by reassortment of gene segments encoding surface glycoproteins, HA and NA; and 'antigenic drift' , by non-synonymous substitutions in these glycoproteins, mainly in the antigenic sites of the HA, against which neutralizing antibodies against IAV are predominantly generated 14,15. The HA is organized as a non-covalent homo-trimer on the viral surface where each monomer consists of two polypeptides, HA1 and HA2 16. HA1 is the major immunogenic polypept...

Antigenic and Genetic Characterization of Swine Influenza Viruses Identified in the European Region of Russia, 2014–2020

“…The S183P amino acid change located near the receptorbinding site was a key marker of change for many human influenza A(H1N1)pdm09 viruses that was noticed early in the development of the 2009-2010 pandemic before spreading globally (WHO Influenza Centre London, 2011). D168N amino acid substitution, located at the Ca antigenic site, has also been observed in human and swine influenza A viruses multiple times (Tapia et al, 2020).…”

“…Detailed HA sequence analysis of these strains showed that all of them feature D168N amino acid substitutions located at the Ca antigenic site, along with S183P. This explains their poor recognition by antisera raised against the A/California/07/2009 strain and other antigenically related strains (Tapia et al, 2020).…”

Identification of novel human derived influenza viruses in pigs with zoonotic potential

“…We had previously reported the identification of the H1N2 strains from Chile, however; the in depth characterization of the ChH1N2B and ChH1N2A clusters presented here (also classified as humans seasonal lineage 1B.2 according to the new proposed designation (Anderson et al, 2016)) had not been done (Nelson et al, 2015a;Tapia et al, 2018;Tapia et al, 2020). The ChH1A virus appears to have spread more efficiently in pigs, since it was found in 12 farms that were geographically unrelated, while ChH1B was only found in two farms (Fig.…”

Circulation Patterns of Human Seasonal Influenza a Virus in Chile Before H1N1pdm09 Pandemic

“…However, we did not differentiate between some previously described antigenic clusters 24 , because there are only a few amino acid substitutions in HA1 domain between strains from these clusters. Only amino acid substitution in HA1 domain can cause a high antigenic impact 25 .…”