In silico analysis and molecular characterization of Influenza A (H1N1) pdm09 virus circulating and causing major outbreaks in central India, 2009-2019
Background and Objectives: Influenza A/H1N1pdm09 causes respiratory illness and remains a concern for public health. Since its first emergence in 2009, the virus has been continuously circulating in the form of its genetic variants. Influenza A/H1N1pdm09 surveillance is essential for uncovering eme...
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doaj-2f42cc11f82841c6a6f756f618a916e02020-12-02T06:37:07ZengTehran University of Medical SciencesIranian Journal of Microbiology2008-32892008-44472020-10-0112510.18502/ijm.v12i5.4611In silico analysis and molecular characterization of Influenza A (H1N1) pdm09 virus circulating and causing major outbreaks in central India, 2009-2019Arshi Siddiqui0Rashmi Chowdhary1Harjeet Singh Maan2Sudhir Kumar Goel3Nidhi Tripathi4Anil Prakash5Department of Biochemistry, All India Institute of Medical Sciences (AIIMS) Bhopal, Madhya Pradesh, India AND Department of Biotechnology, Barkatullah University, Bhopal, Madhya Pradesh, IndiaDepartment of Biochemistry, All India Institute of Medical Sciences (AIIMS) Bhopal, Madhya Pradesh, IndiaDepartment of Microbiology, State Virology Laboratory, Gandhi Medical College (GMC), Bhopal, Madhya Pradesh, IndiaDepartment of Biochemistry, All India Institute of Medical Sciences (AIIMS) Bhopal, Madhya Pradesh, IndiaDepartment of Biotechnology, Barkatullah University, Bhopal, Madhya Pradesh, IndiaDepartment of Biotechnology, Barkatullah University, Bhopal, Madhya Pradesh, India Background and Objectives: Influenza A/H1N1pdm09 causes respiratory illness and remains a concern for public health. Since its first emergence in 2009, the virus has been continuously circulating in the form of its genetic variants. Influenza A/H1N1pdm09 surveillance is essential for uncovering emerging variants of epidemiologic and vaccine efficacy. The present study attempts in silico analysis and molecular characterization of Influenza A (H1N1) pdm09 virus circulating and causing major outbreaks in central India during 2009-2019. Materials and Methods: We have investigated the antigenic drift analysis of 96 isolates’ hemagglutinin (HA) gene sequences (59 central Indian and 37 local Indian and 28 global reference HA gene sequences) of Influenza A/H1N1pdm09 viruses from 2009 to 2019. The study includes mutational (Multiple sequence Alignment), phylogenetic (Maximum Likelihood Method), and statistical analysis (Covariance and correlation) of HA sequences submitted in NCBI, IRD and GISAID from central India. Results: Phylogenetic analysis indicated maximum clustering of central Indian HA gene sequences in genogroup 6B. Analysis of amino acid sequence alignment revealed changes in receptor binding site (RBS). The frequency of S220T amino acid substitution was found to be high followed by S202T, K300E A273T, K180Q. The Karl Pearson correlation coefficient (r) and covariance between the number of mutations and the death toll was found +0.246 and +100.3 respectively. Conclusion: The study identifies the continuous genetic variations in the HA gene sequences of circulating Influenza A/H1N1pdm09 in central India from the year 2009 to 2019. Further suggesting importance of monitoring the gradual evolution of the virus with regards to an increase in virulence, pathogenicity and vaccine efficacy timely. https://ijm.tums.ac.ir/index.php/ijm/article/view/2620Influenza A virusH1N1 subtype;Haemagglutinin;Central India |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Arshi Siddiqui Rashmi Chowdhary Harjeet Singh Maan Sudhir Kumar Goel Nidhi Tripathi Anil Prakash |
spellingShingle |
Arshi Siddiqui Rashmi Chowdhary Harjeet Singh Maan Sudhir Kumar Goel Nidhi Tripathi Anil Prakash In silico analysis and molecular characterization of Influenza A (H1N1) pdm09 virus circulating and causing major outbreaks in central India, 2009-2019 Iranian Journal of Microbiology Influenza A virus H1N1 subtype; Haemagglutinin; Central India |
author_facet |
Arshi Siddiqui Rashmi Chowdhary Harjeet Singh Maan Sudhir Kumar Goel Nidhi Tripathi Anil Prakash |
author_sort |
Arshi Siddiqui |
title |
In silico analysis and molecular characterization of Influenza A (H1N1) pdm09 virus circulating and causing major outbreaks in central India, 2009-2019 |
title_short |
In silico analysis and molecular characterization of Influenza A (H1N1) pdm09 virus circulating and causing major outbreaks in central India, 2009-2019 |
title_full |
In silico analysis and molecular characterization of Influenza A (H1N1) pdm09 virus circulating and causing major outbreaks in central India, 2009-2019 |
title_fullStr |
In silico analysis and molecular characterization of Influenza A (H1N1) pdm09 virus circulating and causing major outbreaks in central India, 2009-2019 |
title_full_unstemmed |
In silico analysis and molecular characterization of Influenza A (H1N1) pdm09 virus circulating and causing major outbreaks in central India, 2009-2019 |
title_sort |
in silico analysis and molecular characterization of influenza a (h1n1) pdm09 virus circulating and causing major outbreaks in central india, 2009-2019 |
publisher |
Tehran University of Medical Sciences |
series |
Iranian Journal of Microbiology |
issn |
2008-3289 2008-4447 |
publishDate |
2020-10-01 |
description |
Background and Objectives: Influenza A/H1N1pdm09 causes respiratory illness and remains a concern for public health. Since its first emergence in 2009, the virus has been continuously circulating in the form of its genetic variants. Influenza A/H1N1pdm09 surveillance is essential for uncovering emerging variants of epidemiologic and vaccine efficacy. The present study attempts in silico analysis and molecular characterization of Influenza A (H1N1) pdm09 virus circulating and causing major outbreaks in central India during 2009-2019.
Materials and Methods: We have investigated the antigenic drift analysis of 96 isolates’ hemagglutinin (HA) gene sequences (59 central Indian and 37 local Indian and 28 global reference HA gene sequences) of Influenza A/H1N1pdm09 viruses from 2009 to 2019. The study includes mutational (Multiple sequence Alignment), phylogenetic (Maximum Likelihood Method), and statistical analysis (Covariance and correlation) of HA sequences submitted in NCBI, IRD and GISAID from central India.
Results: Phylogenetic analysis indicated maximum clustering of central Indian HA gene sequences in genogroup 6B. Analysis of amino acid sequence alignment revealed changes in receptor binding site (RBS). The frequency of S220T amino acid substitution was found to be high followed by S202T, K300E A273T, K180Q. The Karl Pearson correlation coefficient (r) and covariance between the number of mutations and the death toll was found +0.246 and +100.3 respectively.
Conclusion: The study identifies the continuous genetic variations in the HA gene sequences of circulating Influenza A/H1N1pdm09 in central India from the year 2009 to 2019. Further suggesting importance of monitoring the gradual evolution of the virus with regards to an increase in virulence, pathogenicity and vaccine efficacy timely.
|
topic |
Influenza A virus H1N1 subtype; Haemagglutinin; Central India |
url |
https://ijm.tums.ac.ir/index.php/ijm/article/view/2620 |
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