Molecular Epidemiology of Enteroviruses Associated with Hand, Foot and Mouth Disease in South India during 2015 to 2017

Abstract Hand, foot and mouth disease (HFMD) is a common childhood infection caused by human enteroviruses and clinically characterised by fever with vesicular rash on hand, foot or mouth. While Enterovirus A71 (EV-A71) and Coxsackievirus A16 (CVA16) were the major aetiologies of HFMD in India earlier, there were sparse data on recently circulating enteroviruses associated with HFMD. Here we describe the molecular epidemiology of enteroviruses associated with HFMD in South India from 2015 to 2017. We used archived enterovirus real-time reverse transcriptase (RT) PCR positive vesicle swab and or throat swab specimens from clinically suspected HFMD cases collected from four secondary care hospitals in South India between July 2015 to December 2017. PCR amplification and sequencing were done based on 5’VP1, 3’VP1, VP2 or 5´NCR regions to identify enterovirus types. Genetic diversity among enteroviruses was inferred by phylogenetic analysis. Of the 107 enterovirus RNA real-time RT-PCR positive HFMD cases, 69 (64%) were typed as CVA6, 16 (15%) were CVA16, and 1 (1%) was CVA10. Whereas 21 (20%) cases were not typable by any of the methods used in the study. The majority of HFMD cases (89, 83%) were children below five years, while 11 (10.3%) were adults. 5’VP1 yielded the maximum number of enteroviruses genotyped and the phylogenetic analysis showed the CVA6 strains belongs to the subclade D3 while the subclades of CVA16 and CVA10 were B1c and D, respectively. The predominant etiology of HFMD in South India during 2015-2017 period was CVA6 followed by CVA16 and CVA10.