Delta variant sub-lineage AY.12, driving surge in Israel, found in India: Report

A new sub-lineage of the Delta variant of SARS-CoV-2, AY.12, has been found in many states in the country, according to a report by The Hindu.

The sub-lineage has been attributed for a surge in Covid-19 cases in Israel, according to the latest report of Indian SARS-CoV-2 Genomics Consortium INSACOG. In Israel, the sub-lineage has caused a spike in Covid-19 cases giving rise to concerns as the country has fully vaccinated 60 per cent of its citizens. The surge has also raised doubts about the Pfizer vaccine’s effectiveness, which is significantly less in the country than what emerged over clinical trials.

The consortium said that many cases that were earlier recorded as having been caused by the Delta variant are now being reclassified as AY.12 infections, which has all the characteristic Delta mutations except one.

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“The reclassification is primarily to assist micro-epidemiology and is not based on acquisition of significant mutations. Thus, it is not currently known whether AY.12 is clinically different from Delta,” the INSACOG report noted.

“No new mutations of concern are noted in the spike protein (S). However, its rapid growth in Israel means that it should be examined further.”

Recently, the consortium had attribued the continuing Covid-19 outbreaks across India to the Delta variant. As of now sequencing of vaccination breakthroughs in India is also showing a very high proportion of Delta variant, the INSACOG said. Of the 30,230 samples of Variants of Concern and Variants of Interest sequenced by the INSACOG, 20,324 were of Delta.

Anurag Agrawal, Director, CSIR-Institute of Genomics and Integrative Biology said that since the Delta variant has several sub-lineages it is necessary to reclassify them as not doing so would make naming them unwieldy. “A large number of cases in Israel have been linked to AY.12. In India, there are several micro-lineages and some of them are AY.12. We need to wait and watch to see how significant this micro-lineage is in driving infections in India. But as of now, it has exactly the same risk classification, no more and no less, than Delta,” he told the publication.

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A complete reclassification and estimating the prevalence of AY.12 in India may take some time. “Since the AY.12 definition is inconsistent, final numbers will take some time. AY.12 analysis will be added to the portal (a public website), along with other new lineages, once there is greater consensus,” their report noted.

About 70,000 coronavirus samples have been sequenced for their genomic structure, of which 50,000 have been allotted to various lineages, according to INSACOG. About 60 per cent of these lineages consist of international variants of concern or interest (VoC or VoI) that are globally tracked and linked to outbreaks as well as instances of vaccine breakthrough and reinfections.