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Updated: Feb 24, 2026
High-throughput Detection Method for Influenza Virus
Published on: February 4, 2012
Molecular detection and characterization of Influenza 'C' viruses from western India
V A Potdar1, D D Hinge1, M R Dakhave1
1National Institute of Virology, Pune, India.
Abstract:
Since 2003, India has had a well-established influenza surveillance network, though Influenza C virus was not the focus of study. We therefore retrospectively analyzed clinical samples from Pune, western India collected during January 2009 to August 2015, by real-time RT-PCR. Three of 2530 samples of patients with influenza-like illness (ILI) or severe acute respiratory illness (SARI) showed positivity for Influenza C virus infection, while 105 and 31 samples were positive for Influenza A and B viruses respectively. Influenza C viruses were successfully isolated using the embryonated egg system and whole genomes were sequenced and analyzed phylogenetically. HE gene-based phylogeny showed that two viruses C/India/P119564/2011 and C/India P121719/2012 clustered with the C/Sao Paulo/378/82 (SP82) lineage, whereas C/India/P135047/2013 clustered with the C/Kanagawa/1/76 (KA76) lineage. The internal gene of these viruses grouped in two lineages. The PB1, PB2, M and NS genes of the study viruses grouped with C/Yamagata/26/81 (YA81), while the P3 (PA) and NP genes grouped with C/Mississippi/80 (MS80). Bayesian clock studies conclude that the Indian strains may have emerged through multiple reassortment events.
Insights
Influenza C virus, previously understudied in India, was detected in clinical samples. Phylogenetic analysis revealed Indian strains emerged through multiple reassortment events, highlighting the need for broader surveillance.
Area of Science:
- Virology
- Genomics
- Epidemiology
Background:
- India has a surveillance network for influenza since 2003, but Influenza C virus (ICV) has not been a primary focus.
- Retrospective analysis of clinical samples from Pune, India, spanning January 2009 to August 2015 was conducted.
Purpose of the Study:
- To investigate the presence and genetic characteristics of Influenza C virus in India.
- To understand the evolutionary history and potential reassortment events of Indian ICV strains.
Main Methods:
- Real-time RT-PCR was used to screen 2530 clinical samples for influenza viruses.
- Positive ICV samples were isolated using embryonated eggs, followed by whole-genome sequencing and phylogenetic analysis.
- HE gene-based phylogeny and internal gene analysis were performed.
Main Results:
- Three out of 2530 samples tested positive for ICV, alongside 105 for Influenza A and 31 for Influenza B.
- Phylogenetic analysis showed two Indian ICV strains clustering with the C/Sao Paulo/378/82 lineage and one with the C/Kanagawa/1/76 lineage.
- Internal genes grouped into two lineages, with PB1, PB2, M, and NS genes aligning with C/Yamagata/26/81, and PA and NP genes with C/Mississippi/80.
Conclusions:
- This study confirms the circulation of Influenza C virus in India.
- The genetic analysis suggests that Indian ICV strains may have arisen from multiple reassortment events.
- Findings underscore the importance of including ICV in routine influenza surveillance programs.
