Molecular characterization and comparative analysis of pandemic H1N1/2009 strains with co-circulating seasonal H1N1/2009 strains from eastern India

Abstract

During the peak outbreak (July-September 2009), a total 1886 patients were screened in eastern India, of which 139 (7.37%) and 52 (2.76%) were positive for pH1N1 and seasonal H1N1, respectively. Full-length HA1, NA, NS1 and PB1-F2 genes of representative strains were sequenced. Phylogenetic analysis of deduced amino acid sequences of pH1N1 strains revealed HA1 and NS1 to be of North American swine lineage, and the NA gene of Eurasian swine lineage. Consistent with previous reports, the PB1-F2 gene of pH1N1 strains was unique due to a mutation resulting in a truncated protein of 11 aa. The HA, NA and NS1 genes of H1N1/2009 strains clustered with H1N1 strains of 2000-2009, whereas a subset of strains contained a pH1N1-like truncated PB1-F2. The truncated PB1-F2 may confer the advantage of lower pathogenicity but higher replication and infectivity to the human H1N1 strains. This is the first report of seasonal H1N1/2009 strains with a pH1N1/2009-like gene segment.

Comparative analysis of hemagglutinin of 2009 H1N1 influenza A pandemic indicates its evolution to 1918 H1N1 pandemic

“…1) (Fig. 1) which corroborates with the previous study (Sarkar et al, 2011). Thus it is evident from these results and phylogenetic tree that 2009 and 1918 pandemics are closely related.…”

Surveillance in eastern India (2007-2009) revealed reassortment event involving ns and PB1-F2 gene segments among co-circulating influenza a subtypes

“…The significance of selectively lateral transmission of PB1-F2 gene among co-circulating strains is not clear, but since PB1-F2 protein is associated with pathogenesis, it may confer improved infectivity or replication efficiency. As reported earlier by our group [25], six A/H1N1 strains had truncated 11 aa PB1-F2 similar to 2009 pH1N1 viruses. Rest twenty A/H1N1 strains with 57 aa PB1-F2 peptide were similar to the concurrent A/H1N1 vaccine strains (Figure 6).…”

“…Group I was represented by the globally reported H3N2 strains including all (n = 24) eastern India strains and representative 2009 pH1N1 strains, whereas, 20/31 A/H1N1 strains of eastern India and other reference A/H1N1 strains clustered in group II. Among rest 11 A/H1N1 strains, 5 strains [A/KOL/507/2007(H1N1), A/KOL/536/2007(H1N1), A/KOL/596/2007(H1N1), A/KOL/611/2007(H1N1) and A/KOL/968/2007(H1N1)] clustered with H3N2 strains in group I, whereas, 6 strains clustered with pH1N1/2009 strains in sub-group 2 within group I as reported earlier [25]. Nucleotide sequence alignment for PB1-F2 gene of the group I H1N1 strains (n = 5) showed only 83%-86% identity with A/Puerto Rico/8/34(H1N1) and the concurrent vaccine strain A/Brisbane/59/2007 (H1N1), compared to 91-94% sequence similarity with co-circulating seasonal A/H3N2 strains, suggesting possible H3N2 origin of PB1-F2 gene segment of these strains.…”

“…All 31 A/KOL/H1N1 showed an alternative start codon (AUG) at positions 119 to 121 in the PB1 gene, which translated into Met (M) and marked the beginning 6 of PB1-F2 ORF. Consistent with the concurrent vaccine H1N1 strain (A/Brisbane/59/2007(H1N1)), 20/31 H1N1 strains encountered a stop codon (UAG) at positions 290 to 292 resulting in the production of a 57 residue truncated PB1-F2 protein and six A/H1N1 strains from 2009 revealed 11 aa truncated PB1-F2 protein similar to 2009 pandemic H1N1 [25]. Rest five strains [A/KOL/507/2007(H1N1), A/KOL/536/2007(H1N1), A/KOL/596/2007(H1N1), A/KOL/611/2007(H1N1) and A/KOL/968/2007(H1N1)] covered the entire ORF as in these strains, stop codon was observed at aa 391, indicating putative 90 aa PB1-F2 protein, which is three residues longer than PB1-F2 of PR8, but similar to A/Wisconsin/67/2005(H3N2) strain (Figure 6).…”

Full genomic analysis of an influenza A (H1N2) virus identified during 2009 pandemic in Eastern India: evidence of reassortment event between co-circulating A(H1N1)pdm09 and A/Brisbane/10/2007-like H3N2 strains

“…Interestingly, inspite of oseltamivir treatment during pandemic H1N1, the co-circulating influenza A(H1N1)pdm09 strains as well as the H3N2 strains did not show any mutation containing oseltamivir resistance. Again the influenza A(H1N1)pdm09 virus, with gene segments from avian, swine and human origin had spread globally within 3 months resulting in declaration of pandemic level 6 by W.H.O [9] was unique compared to previous pandemics since it had high transmission ability but low virulence compared to previous pandemic viruses of this century [10]. In Eastern India, we have observed circulation of H1N1 and H3N2 subtypes during 2005-2009 [5].…”