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Explained: What is the new AY.12 sub-lineage of Delta variant, and should you be concerned?

The Delta variant (B.1.617.2) has given birth to 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, AY.12, has all the characteristic Delta mutations except one.

People stand in queue to receive a dose of Covid-19 vaccine at a temporary vaccination centre set up inside a school in Mumbai, Tuesday, Aug. 17, 2021. (PTI Photo/Kunal Patil)

As the world nervously keeps a track of all the new Covid-19 variants and its sub-lineages, every virus sample is technically a new ‘variant’, as its sequence does not match with that of any other virus’ sequence.

Now, the scientists have expanded the Delta family from four to 13 variants. Some cases of the Delta variant, the most widely prevalent variant of concern in India, are being “reclassified” to another sub-lineage — AY.12 — 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.

“However, since the AY.12 definition is inconsistent, final numbers will take some time,” a statement by the consortium read.

So, what is this AY.12 mutation?

Fundamentally, viral evolution works like any other kind. As the virus spreads through the body, it makes copies of itself, which often have small mistakes and changes.

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As such, the Delta variant (B.1.617.2) has given birth to 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, 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.”

Is there any difference between AY.12 and the other strains?


According to INSACOG, it is not known yet whether AY.12 is clinically different from Delta or B.1.617.2.

However, AY.12 has lost some of the mutations seen in the Delta lineage, such as G142D in spike protein. No new mutations of concern are noted in the spike protein of this variant.

AY.12 is, at present, the most dominant strain in Israel — 51 per cent of samples studied have shown the prevalence of this variant. Based on the number of sequences that have so far been uploaded on the GISAID by Indian research groups, the prevalence of this variant over the last week has increased to over 20 per cent.


While asking states to maintain caution and look out for this variant, INSACOG said: “AY.12, a reassigned sub-lineage of Delta is being seen in many states, but the numbers need closer examination. The functional impact of the changes between Delta and AY.12 is not known but the two appear to be very similar at a molecular level.”

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.

Tracking the evolution, which tracks new variants and their prevalence, states that the first case of the AY.12 lineage was recorded on September 7, 2020. Since then, 44,083 sequences in the AY.12 lineage have been detected across the world till August 26.

However, the variant came to the fore after becoming the dominant strain in Israel. A fourth wave of infections is rapidly approaching the levels of Israel’s worst days of the pandemic last winter. The daily rate of confirmed new virus cases has more than doubled in the past two weeks, making Israel a rising hot spot on the international charts. Restrictions on gatherings and commercial and entertainment venues were reinstated this week, and the government is considering a new lockdown.


However, the matter that most experts are concerned about is that Israel’s high rate of infections among early vaccine recipients may indicate a waning of the vaccine’s protections over time, a finding that contributed to a US decision to begin offering booster shots to Americans widely starting next month. The vaccine may be less effective at preventing infection with the highly contagious A.12 Delta variant, now the primary version of the virus in Israel.

Data published by Israel’s Ministry of Health in late July suggested that the Pfizer shot was just 39% effective against preventing infection in the country in late June and early July, compared with 95% from January to early April. In both periods, however, the shot was more than 90% effective in preventing severe disease. As such, Israel is now pinning its hopes on booster shots.


According to, the first sample of AY.12 in India dates back to September 7, 2020.

INSACOG has so far sequenced 67,699 samples of the virus from India, of which 50,869 have been analysed in detail. An additional 11,016 sequences of samples have been shared by state governments — taking the total number of samples sequenced to 78,865.


However, the worrying trend is that as more than 3.2 crore people have been infected in India so far, only about 0.002% of the samples have been sequenced to date.

What matters to the general people?

Not all variants that the World Health Organisation has recognized are equally bad. When the organization gives a new family a name, it also adds a label telling us how worried we should be.

The lowest level is a variant of interest, which means it is worth keeping an eye on. In the middle is a variant of concern, like Delta, which has evolved to be more dangerous. Often, variants of interest are given that label because they share a mutation with variants of concern—they’re under surveillance. The CDC has an additional, more severe category, a variant of high consequence, which has never been given to a family of Covid. It’s reserved for potential future strains that might cause serious illness in vaccinated people, fail to show up on commonly used diagnostic tests, or perhaps resist multiple treatments for covid symptoms.

Mutations happen randomly across the genomes of viruses in all the millions of people who are infected. Some of those mutations die out, and a few spread to other people. As such, scientists are keeping a close eye on patterns in Delta, especially, since it’s spreading so rapidly.

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First published on: 27-08-2021 at 10:38 IST
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