Genetic Characterization of the Influenza A Pandemic (H1N1) 2009 Virus Isolates from India

Abstract

BackgroundThe Influenza A pandemic H1N1 2009 (H1N1pdm) virus appeared in India in May 2009 and thereafter outbreaks with considerable morbidity and mortality have been reported from many parts of the country. Continuous monitoring of the genetic makeup of the virus is essential to understand its evolution within the country in relation to global diversification and to track the mutations that may affect the behavior of the virus.MethodsH1N1pdm viruses were isolated from both recovered and fatal cases representing major cities and sequenced. Phylogenetic analyses of six concatenated whole genomes and the hemagglutinin (HA) gene of seven more isolates from May-September 2009 was performed with reference to 685 whole genomes of global isolates available as of November 24, 2009. Molecular characterization of all the 8 segments was carried out for known pathogenic markers.ResultsThe first isolate of May 2009 belonged to clade 5. Although clade 7 was the dominant H1N1pdm lineage in India, both clades 6 and 7 were found to be co-circulating. The neuraminidase of all the Indian isolates possessed H275, the marker for sensitivity to the neuraminidase inhibitor Oseltamivir. Some of the mutations in HA are at or in the vicinity of antigenic sites and may therefore be of possible antigenic significance. Among these a D222G mutation in the HA receptor binding domain was found in two of the eight Indian isolates obtained from fatal cases.ConclusionsThe majority of the 13 Indian isolates grouped in the globally most widely circulating H1N1pdm clade 7. Further, correlations of the mutations specific to clade 7 Indian isolates to viral fitness and adaptability in the country remains to be understood. The D222G mutation in HA from isolates of fatal cases needs to be studied for pathogenicity.

A Subregional Analysis of Epidemiologic and Genetic Characteristics of Influenza A(H1N1)pdm09 in Africa: Senegal, Cape Verde, Mauritania, and Guinea, 2009–2010

“…25 The substitution D239G is clinically very interesting; this substitution was detected more frequently in viruses isolated from patients with fatal outcomes and isolates from lungs. 12,26 This strain was isolated from sample from a 20-year-old girl who came for consultation in a hospital in Dakar (Hô pital principal de Dakar). The symptoms were severe, with fever, intense coughing, myalgia, rhinitis, vomiting, and abdominal pain.…”

Evolution trends of the 2009 pandemic influenza A (H1N1) viruses in different continents from March 2009 to April 2012

“…Since then many researchers referred to the naming scheme as "global clades", e.g. in Potdar et al (2010). The graphic representation of the 7 clades (Nelson et al 2009;Potdar et al 2010) For HA gene, we first divided the analyzed sequences into 20 subsets according to 6 continents and 4 stages.…”

“…The analysis revealed that at least 7 phylogenetically distinct viral clades have spread globally and co-circulated in localities. Then according to the 7 clades suggested by Nelson et al (2009), subsequent study discussed the genetic characterization of the influenza A pandemic (H1N1) 2009 virus isolates from India (Potdar et al 2010). Recently, both phylogenetic and cluster analyses further confirm that the gene exchange of the influenza A pandemic (H1N1) 2009 virus takes place between viruses originated from different species (Arunachalam et al 2012).…”

Genetic and clinical assessment of 2009 pandemic influenza in southern China

“…Genetic analysis indicated the presence of several mutations in NA and HA genes including HA-E391K, P100S, T214A, 1338V, I208L, S220T and NA-N248D, V106I, which have already been observed in various strains globally [29,30]. Phylogenetic analysis of HA sequences reported by us and other Chinese labs showed that, during first pandemic wave, H1N1 virus was predominantly homogenous with prototypic strains with some minor mutations, unlike reports from the USA which showed distinct heterogeneities at that time [31].…”