Delta variant sub-lineage AY.12 found in India

India SARS-CoV-2 Genome consortium reports prevalence of the micro-lineage that has been linked to a surge in Israel.

August 25, 2021 10:08 pm | Updated August 26, 2021 11:15 am IST - NEW DELHI:

A medic seen collecting swab sample for conducting RT-PCR test for Covid-19 at Dilshad Garden - UP Border in New Delhi on Tuesday, August 24, 2021.

A medic seen collecting swab sample for conducting RT-PCR test for Covid-19 at Dilshad Garden - UP Border in New Delhi on Tuesday, August 24, 2021.

Some cases of the Delta variant , the most widely prevalent variant of concern in India, are being “reclassified” to another sub-lineage that has been associated with a large number of cases in Israel, the India SARS-CoV-2 Genome (INSACOG) consortium, which tracks emerging variants, said in a report on Monday.

The Delta variant (B.1.617.2) has birthed several sub-lineages called ‘Delta plus’ variants that bear most of its characteristic mutations but are different in other ways. One of these sub-lineages, called AY.12, has all the characteristic Delta mutations except one.

The spike in cases in Israel is of concern because it’s a country with nearly 60% of its adults fully vaccinated and reports that the Pfizer vaccine’s effectiveness in that country is significantly less than what emerged over clinical trials.


“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.”

The Delta variant, because of its preponderance in coronavirus cases globally, has several sub-lineages, making it necessary to reclassify them as not doing so would make naming them unwieldy, said Anurag Agrawal, Director, CSIR-Institute of Genomics and Integrative Biology. “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 Hindu .

A complete reclassification and estimating the prevalence of AY.12 in India is expected to take some time, according to the INSACOG. “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.

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So far, according to INSACOG, about 70,000 coronavirus samples have been sequenced for their genomic structure, of which 50,000 have been allotted to various lineages. About 60% of them 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. Within these VoC, the Delta variant comprises 70% of samples. The Delta plus cases, in which AY.12 is included, only number 67, though this is expected to swell after the reclassification.

Though the overall trajectory of daily cases in India is downwards, Kerala has reported nearly 31,000 cases on Wednesday, which accounts for nearly all of India’s caseload.

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