ICMR performs genome characterisation of monkeypox cases, identifies 3 sub-clusters among A.2 lineage in India

New Delhi: The Indian Council of Medical Research (ICMR) has analysed the complete genome sequences of Monkeypox cases from Kerala and Delhi confirmed during July to August 2022.

It has found three sub clusters among A.2 lineage – first cluster Kerala (n5) and Delhi (n2) aligned with the USA-2022 ON674051.1; while second of Delhi (n3) aligned with USA-2022 ON675438.1 and third cluster consists of the UK, US and Thailand – in the study conducted by ICMR-NIV Pune.

According to the study, all the retrieved MPXV sequences from India covering 90 to 99 per cent of the genome belong to the A.2 lineage of clade IIb.

“All the retrieved MPXV sequences from India covering 90 to 99 per cent genome belong to A.2 lineage of clade IIb. The A.2 MPXV lineage divided in three sub clusters; first cluster Kerala n5, Delhi n2 aligned with the USA-2022 ON674051.1; while second of Delhi n3 aligned with USA-2022 ON675438.1 and third consists of the UK, USA and Thailand. Recent update in MPXV lineage designated all the five sequences from Kerala as A.2.1.”, the ICMR study has revealed, emphasizing the need of enhancing genomic surveillance to understand the mutation and its linkage.

During the period of July to August 2022, clinical specimens i.e., oropharyngeal swab (OPS), nasopharyngeal swab (NPS), lesion crust and lesion fluids of 96 suspected Monkeypox cases were referred from 18 states and 3 Union Territories to ICMR-National Institute of Virology, Pune, India for diagnosis of Monkeypox.

The clinical specimens of all the cases were tested using Monkeypox specific real time PCR. Of them, five cases each from Kerala and Delhi were found to be positive for MPXV. All the monkeypox negative cases were also screened for Varicella zoster virus (VZV) and enterovirus (EV) specific real time PCR.

Of 114 cases, the MPXV infection was confirmed in ten cases from India using both Orthopox and Monkeypox specific real time PCR. Further the screening of monkeypox negative cases indicated the presence of VZV and EV by real time PCR. The ten monkeypox confirmed cases were three male and two female from New Delhi with no international travel history; while five males were from Kerala with travel history from the United Arab Emirates (UAE) to India.

All the cases were immunocompetent with no comorbidities with their mean age 31 years and presented with short prodromal phase of fever, myalgia, vesiculo-pustular lesions primarily in genital area, face, trunk and extremities.

“Of all, nine cases had non tender firm lymphadenopathy in one or more sites (inguinal, cervical, submental, submandibular, retro-auricular), while one case didn’t show lymphadenopathy. All the cases have recovered without complications except a case from Kerala who succumbed to the infection following acute onset encephalitis”, the ICMR said.

“The MPXV sequences from India were grouped in two sub clusters; 7 sequences (Kerala n5, Delhi n2) aligned with the USA-2022 strain ON674051.1 and UK-2022 OP331335.1 formed the first cluster. In this sub cluster, five sequences from Kerala were designated as A.2.1 based on the lineage defining mutations in the position C 25072 T, A 140492 C, C 179537 T. Two sequences from Delhi are lacking all three mutations, hence still defined into A.2 lineage”, said the ICMR study.

The study further added, “While it was noted that A.2.1 lineage defining mutations are lacking in the 3 sequences from the second sub cluster of Delhi; aligned with USA-2022 strain ON675438.1. The third sub cluster consists of the MPXV sequences obtained from UK-2022 OP331336.1, USA-2021 ON676707.1 and three sequences of Thailand-2022”.