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.
Highlights
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]
The phylogenetic tree and the genetic map show that the Chilean H1 swine IAV sequences were grouped in 3 clusters, named: Chilean H1 A (ChH1A), and a Chilean H1 B (ChH1B), which cluster separately on the phylogenetic tree but both of them are classified as “Other-Human-1B.2” according to the new global clade designation[13]; and the A(H1N1) pdm09-like classified as global clade 1A.3.3.2 (Figs. 1 and 2, Supplementary Fig. S1)
Fourteen viruses from 10 farms were grouped within cluster ChH1A, 3 viruses from 1 farm were grouped within cluster ChH1B, and 21 viruses from 15 farms were grouped within the A(H1N1)pdm09-like cluster
Summary
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]. There are recent studies that identified novel reassortant H1N2 IAVs of swine origin in Chile with H1s of global clade “Other-Human-1B.2” that are genetically distinct from the clade 1B.2 strains of IAV in North American pigs. These novel H1N2 viruses have A(H1N1)pdm09-like virus internal genes associated with HA and NA genes that are genetically divergent from all other IAVs identified in swine and humans globally. We analyzed the genetic basis for the antigenic differences among circulating H1 IAVs, identifying glycosylations and amino acid substitutions in or near antigenic sites of HA that may lead to immune evasion
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