Molecular detection and characterization of Influenza ‘C’ viruses from western India

• Published in: Infection, genetics and evolution genetics and evolution, 2017-10, Vol.54, p.466-477
• Main Authors: Potdar, V.A., Hinge, D.D., Dakhave, M.R., Manchanda, A., Jadhav, N., Kulkarni, P.B., Chadha, M.S.
• Format: Article
• Language: English
• Subjects: Adolescent; Bayes Theorem; Child; Evolution, Molecular; Gammainfluenzavirus - genetics; Gammainfluenzavirus - isolation & purification; Genome, Viral; Humans; India - epidemiology; Influenza C virus; Influenza, Human - epidemiology; Influenza, Human - virology; IPD/OPD; Phylogeny; Real time PCR; Real-Time Polymerase Chain Reaction; Reassortant Viruses - genetics; Retrospective Studies; Sequence Analysis, RNA - methods; Western India
• ISSN: 1567-1348; 1567-7257
• DOI: 10.1016/j.meegid.2017.08.005

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. •Study conducted in pediatric population of IPD and OPD setting at Pune, India from January 2009 to August 2015.•Three of 2530 samples, all ILI patients, had Influenza C infection and 105 & 31 samples were positive for Influenza A & B & Influenza C viruses were successfully isolated.•Phylogenetic analysis of HE gene showed that two lineage SP82 & KA76 however their internal gene composition was uniform.•Bayesian evolutionary analysis of HE showed Indian strains of KA76 lineage diverged from a common ancestor in 1965 and SA82 lineage viruses diverged from a common ancestor in 1977 and internal genes showed different evolutionary rate.