Molecular characterization of circulating pandemic strains of influenza A virus during 2012 to 2013 in Lucknow (India)

Abstract

The pandemic H1N1 strain of Influenza A virus [A(H1N1)pdm09] is now well adapted in human populations. However, it is still causing sporadic outbreaks worldwide with different severity. The present study was planned to understand the genetic diversity (based on the HA1 gene) of influenza A(H1N1)pdm09 strains circulating during the post pandemic period. The HA1 gene was selected because the HA1 protein is immunogenic, functions as a receptor binding site and indirectly affects transmission and pathogenicity of virus. A total of 2,818 cases were enrolled. Nasal/throat swabs from all cases were tested by one-step real time PCR for detection of influenza virus types and subtypes according to the CDC protocol. Of these, 134 cases were A(H1N1)pdm09 positive, 34 of which were screened for HA1 gene (position 434-905) sequencing (Big-Dye terminator using 3130 ABI, Genetic analyzer). Molecular and phylogenetic analysis was performed using PhyML approach (v. 3.0). All A(H1N1)pdm09 positive and negative cases were clinically characterized. Phylogentically, all Lucknow strains (n = 33) except one fall with the clade seven reference strain. One strain showed 99.9% similarities with clade one reference strain A/California/07/2009. In mutational analysis, 33 strains had the S220T mutation, which is at an antigenic site and characteristic of clade seven along with few minor mutations; K180I/T/Q, V190I, S200P, S202T, A203T, A214T, S220T, V251I, and A273T. These results suggest that clade seven was the most widely circulating clade in Lucknow and A(H1N1)pdm09 cases showed mild clinical symptoms as compared to A(H3N2) or influenza B cases.

Changes in Hemagglutinin and Neuraminidase Genes of pH1N1 Influenza Virus Strains Collected from a North Indian Tertiary Care Hospital during 2015

“…Molecular analysis at gene level (especially HA1 and NA genes) identified few mutational changes which were different from the previously circulating strains of pH1N1 virus as described earlier [6,10]. Mutational changes in the active site of HA1 protein showed 5 mutations, similar to previously circulating pH1N1 strains of Indian region along with 3 new mutations in 2015 strains at different positions (D185N, D213N, and H290Q) [11].…”

“…According to Indian health officials, the pH1N1 strain has not changed much from the first strain that emerged in 2009 [20]. The phylogenetic analysis based on partial HA1 gene sequences of study strains revealed the presence of 2 mutations (S220T and S202T) in HA1 gene of all study strains which are specific to clade 7 genotype of pH1N1 [6,10,[21][22][23].…”

“…The 447 bp segment of HA1 gene (nucleotide position 434-905) and 1,159 bp segment of NA gene (nucleotide position 10-1,159) were amplified by one-step RT PCR assay as described earlier [6,7]. Amplified products were confirmed by running on 2% agarose gel-electrophoresis and visualized on a UV trans-illuminator after staining with ethidium bromide solution.…”

Molecular epidemiology and evolution of influenza A and B viruses during winter 2013-2014 in Beijing, China

“…This transient mutation, also called an ''adaptive mutation'', may be the consequence of individual mutations that relieve the selective pressure caused by survival [11]. The K180Q mutation was (at least, in the Beijing area) a novel substitution within the Sa antigenic site of the H1 segment; this mutation has also been observed in Peru and India since 2013 [9,26]. In H3, three amino acid mutations were detected at two antigenic sites (A and B); these substitutions were observed in 2012-2013, but at a lower frequency [10].…”

Genetic changes in influenza A(H3N2) viruses circulating during 2011 to 2013 in northern India (Lucknow)

“…One strand complementary DNA (c‐DNA) was synthesized in two separate eppendorfs using the HA and the NA gene‐specific primers by the method as described previously [Dangi et al, ]. Two step conventional reverse transcription PCR (RT‐PCR) was done to amplify viral c‐DNA specific for 824 bp fragment (nucleotide position 360–1184) in the HA1 domain and 931 bp fragments (nucleotide position 367–1298) in the NA gene [Hoffmann et al, ; Chutinimitkul et al, ].…”