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Genomic Epidemiology Analysis of Circulating Virus Of Nepal.
  • Bimalesh Jha,
  • krishna Manandhar
Bimalesh Jha
National Public Health Laboratory kathmandu Nepal

Corresponding Author:[email protected]

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krishna Manandhar
Tribhuvan University
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Introduction Influenza viruses, due to rapid evolution, lead to great variability. There are 18 highly variable hemagglutinins (H1 to H18) and 11 distinct NAs (N1 to N11) for type A.Influenza type B has no subtypes due to fixed on small antigenic variabilities.Due to rapid evolution and diversification, it is essential to understand genomic epidemiology to detect emerging strains and track their transmission. Methods Samples of the strain were cultivated in the MDCK cell lines for the preparation of neat virus. viral genome after extraction from the neat virus was sent to the National Institute of Infectious Disease, Japan for whole genome sequencing in 2016. The sequences were submitted to GISAID. The H1N1 virus genomes(n=18), from this study, were investigated against the reference genome A/California/07/2009 (GenBank: CY121680). Similarly, the Influenza type B virus genomes(n=27) were investigated against reference genome B/Brisbane/60/2008 (GenBank: KX058884) and B/Wisconsin/01/2010 (GenBank: JN993010). The mutational analyses were performed using Nextclade. The mutations present in the sequences were,subsequently, investigated. Finally, the phylogenetic analysis was done using the Nextclade and CLUSTAL Omega. Out of the 18 HA genome segments, of H1N1, all (n=12) except 6 isolates were of clade 6B, while the rest were of clade 6B.1.For Influenza Type B, out of the 27 HA genome segments, all of the genomes were of clade V1A when compared to B/Brisbane/60/2008. Similarly, when compared to reference genome B/Wisconsin/01/2010 (GenBank: JN993010), all (n=22) except 5 isolates were of clade Y3, while the rest were of clade Y2