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Monkeypox A.2 Strain: ICMR Identifies 3 Sub-Groups, Analyzes Genome Cases In India

The Indian Council of Medical Research has analyzed the genome sequence of monkeypox cases detected in Kerala and Delhi from July to August 2022.

Written by Tavishi Dogra |Updated : September 17, 2022 9:24 PM IST

Monkeypox A.2 Strain: The ICMR has analyzed the whole genome sequence of monkeypox cases detected in Kerala and Delhi from July to August 2022. The analysis, led by ICMR-NIV Pune, said that it saw three subgroups among the A.2 lineage - the first cluster aligns with Delhi (N2) and Kerala (N5) USA-2022 ON674051.1, while The second (N3) of Delhi is aligned with USA-2022 ON675438.1 and the third cluster consists of the UK, US and Thailand.

ICMR-NIV Pune Study

According to the study, all THD sequences from India, covering 90 to 99 per cent of the genome, belong to the A.2 lineage of clade IIB. "All retrieved sequences encircling 90% to 99% of the genome belong to the A.2 line of clade IIB from India. The A.2 mpxv line is divided into three subgroups, the first cluster being Delhi N2, Kerala N5 of USA-2022. ON674051.1, the second part of Delhi N3 is aligned with VA-2022 ON675438.1, and the third is from the UK, USA and Thailand. Current updates in the MPXV lineage have put all five sequences from Kerala as A.2.1

Clinical Samples Of Monkeypox Cases

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Clinical samples of 96 suspected monkeypox cases, i.e. oropharyngeal swab (OPS), nasopharyngeal swab (NPS), lesion crust and wound fluid from 18 states and three union territories during the period July to August 2022, 18 states and three union territories were sent from ICMR-National Institute of Virology, Pune.


Clinical samples of all cases were tested using monkeypox-specific real-time PCR. Five patients each from Delhi and Kerala were discovered positive for MPXV.

  • All monkeypox-negative cases were screened for varicella zoster virus (VZV) and enterovirus (EV) specific real-time PCR. Of the 114 cases, MPXV infection was confirmed in ten cases from India using orthopox and monkeypox-specific real-time PCR.
  • Further screening of monkeypox-negative patients indicated the presence of VZV and EV by real-time PCR. 10 cases were confirmed in the country, in which three men and two women from Delhi were found infected.

They had no international travel history, while five men had reached Kerala, India, from the United Arab Emirates (UAE).

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