Genetic analysis of Enterovirus D68 associated with pneumonia in children from South India

EV- D68 is an emerging enterovirus infection associated with severe acute respiratory illness (SARI), acute flaccid myelitis (AFM) and acute flaccid paralysis (AFP). While EV- D68 outbreaks and sporadic cases are reported globally, a single case has been reported from India. The present study aims to investigate the molecular epidemiology and clinical characteristics of EV- D68associated SARI cases from South India. We screened influenza- negative archived throat swab specimens from Influenza- Like Illness (ILI) and SARI cases (n=959; 2016 to 2018 period) for enteroviruses by pan- enterovirus real- time RT- PCR. Thirteen samples positive for enteroviruses were typed by PCR and sequencing based on VPI, VP2 and/or 5 ' NCR regions. One EV- D68 RNA sample was subjected to next- generation sequencing for whole genome characterisation. Among 13 enterovirus cases, four were ECHO-11, three EV- D68, two CV- A16 and one each EV-71, CV- B1, CV- B2 and CV- A9. All three cases of EV- D68 infection were reported in children below 2 years of age from Kerala state of South India during June and July 2017. The patients developed pneumonia without any neurological complications. Sequencing based on VPI and 5 ' NCR regions showed that EV- D68 strains belong to the novel subclade B3. The EV- D68 complete genome identified with two unique amino acid substitutions in VP1 (T-246- I) and 3D (K-344- R) regions. This study reiterates the EV- D68 novel subclade B3 circulation in India and indicates the urgent need for structured EV- D68 surveillance in the country to describe the epidemiology.