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High-throughput Detection Method for Influenza Virus
Published on: February 4, 2012
Full genome analysis and characterization of influenza C virus identified in Eastern India
Tapasi Roy Mukherjee1, Anupam Mukherjee, Satarupa Mullick
1National Institute of Cholera and Enteric Diseases, Beliaghata, Kolkata, India.
Insights
Influenza C virus, often overlooked, was detected in Indian children with acute respiratory illness (ARI). This study provides crucial genetic insights into influenza C strains circulating in India, contributing to understanding respiratory pathogen diversity.
Area of Science:
- Virology
- Public Health
- Genetics
Background:
- Acute respiratory illness (ARI) causes significant child mortality in tropical Asia, with influenza A and B viruses being common culprits.
- Information on influenza C virus, another respiratory pathogen, is limited, particularly in regions like India.
- Understanding the genetic diversity of influenza C is essential for public health surveillance and control strategies.
Purpose of the Study:
- To investigate the prevalence and genetic characteristics of influenza C virus in children with ARI in eastern India.
- To analyze the genetic relatedness of a detected influenza C strain to known influenza C strains globally.
- To contribute to the knowledge base of influenza C virus epidemiology and evolution in the Indian subcontinent.
Main Methods:
- Collection and analysis of 2737 nasal and/or throat swabs from children with ARI in eastern India between January 2011 and December 2012.
- Nucleotide sequencing of viral genes, followed by phylogenetic analysis and amino acid sequence comparison.
- Screening for influenza C virus in samples negative for influenza A and B viruses.
Main Results:
- Out of 2737 samples, 59.04% tested positive for respiratory viruses, with 23.72% positive for influenza A and B viruses.
- Influenza C virus was detected in 0.18% of samples, specifically from those negative for influenza A and B.
- Phylogenetic analysis revealed that the HE, matrix, NS, PB1, and PB2 genes of the Indian strain (C/Eastern-India/1202/2011) were closely related to C/Yamagata/26/81 like strains, while P3 and NP genes showed similarities to other global strains.
Conclusions:
- Influenza C virus circulates in India and is associated with acute respiratory illness in children.
- The genetic analysis of the Indian influenza C strain provides valuable data on its diversity and relationship to other global strains.
- Further research is needed to fully understand the public health impact and epidemiological significance of influenza C virus in India and similar regions.
Abstract:
In tropical countries of Asia, like India, approximately 0.5 million children of <5 years of age die annually due to acute respiratory illness (ARI). Of common respiratory pathogens, influenza viruses (A & B) are associated with annual worldwide epidemics; while the information on influenza C virus is inadequate. During January 2011 through December 2012, 2737 nasal and/or throat swabs were collected from patients reporting at outpatient department of hospitals in eastern India with ARI. Nucleotide sequencing was carried out using gene specific primers followed by pair-wise sequence alignments, multiple alignments, construction of phylogenetic tree and analysis of deduced amino acid sequences. Study reveals that, out of 2737 samples, 1616 (59.04%) were positive for one or more respiratory viruses; of which 23.72% were positive for influenza A and B viruses. From influenza A & B negative samples, influenza C virus was screened and detected with a frequency of 0.18%. Phylogenetic analysis showed that the HE, matrix, NS, PB1 and PB2 gene of the studied strain (C/Eastern-India/1202/2011) possessed a close relatedness to C/Yamagata/26/81 like strains. The P3 gene shows proximity with C/Mississipi/80 like strains whereas NP gene revealed similarity with C/Miyagi/1/93 like strains. The outcome of the whole genome analysis of the strain C/Eastern-India/1202/2011 provided useful information regarding genetic diversity of influenza C strains in India.
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