The Indian Council of Medical Research (ICMR) examined the entire genome sequences of Monkeypox patients from Kerala and Delhi between July and August 2022 and discovered that the genome sequences from India, which included 90-99 percent of the genome, belonged to the A.2 Lineage of Clade IIb.
“Further A.2 lineage is mutating and sequences from affected countries holding the key for the evolution of Monkeypox. A slow and sharp alert for virologists and epidemiologists,” said Dr Pragya Yadav, Senior Scientist, ICMR-NIV, Pune. “We analyzed the complete genomes sequences of Monkeypox cases from Kerala (5 travellers from UAE) and Delhi (5 with no travel history), India confirmed during July to August 2022. All the retrieved MPXV sequences from India covering 90 to 99 per cent genome belong to A.2 lineage of clade IIb,” Yadav scientist added.
The study has further mentioned that the A.2 monkeypox lineage is divided into sublineages. The A.2 MPXV lineage is divided into three sub-clusters.
“First cluster Kerala with 5 numbers, Delhi with 2, aligned with the USA-2022 ON674051.1; while second of Delhi n=3 aligned with USA-2022 ON675438.1 and the third consists of the UK, USA and Thailand. The recent update in MPXV lineage designated all the five sequences from Kerala as A.2.1. In addition to known 16 single nucleotide polymorphisms (SNPs) along with 13 APOBEC3 cytosine deaminase activity determined specific lineage defining mutations in A.2 lineage, 25 additional APOBEC3 mutations were found in 10 reported sequences,” read the study.
The study emphasizes the need of enhancing genomic surveillance to understand the mutation and its linkage.
“All the cases have recovered without complications except a case from Kerala who succumbed to the infection following acute onset encephalitis,” it added.
“The MPXV sequences from India were grouped in two sub clusters; 7 sequences (Kerala n=5, Delhi n=2) aligned with the USA-2022 strain ON674051.1 and UK-2022 OP331335.1 formed 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,” the study noted.
“While it was noted that A.2.1 lineage defining mutations are lacking in the 3 sequences from 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,” the study further said.