What we know so far about the Delta Covid sub-variant AY.4.2

A new mutation detected in the Delta variant of the coronavirus is causing alarm in several countries as more cases are being detected.

AY.4.2 is an offshoot of the B.1.617.2 or Delta variant, known as a sub-lineage. Some fear that the “Delta plus” variant, as some are calling it, appears to be more transmissible than Delta, although there is currently no concrete evidence to confirm this.

AY.4.2 carries the Y145H and A222V mutations in its spike protein, which have emerged independently in other variants.

A222V was previously found in the B.1.177 lineage, which emerged in Spain and then spread across northern Europe. The Y145H mutation, though, has been seen much less frequently.

The UK’s Health Security Agency (HSA) moved up the AY.4.2 into the category of “variant under investigation” on 21 October, adding that it was “expanding” and “on an increasing trajectory”.

This variant has now been detected in 33 countries, including the UK, where it was reportedly first sequenced. Denmark, Germany and Ireland were among other countries where the Delta plus has been found, according to GISAID, a global, open-source database tracking the genomic signature of coronavirus variants.

Some isolated cases have been detected in the US, Israel, Russia and India as well.

The UK accounts for 96 per cent of all cases linked to AY.4.2 and is followed by Denmark and Germany, which have one per cent of their cases linked to the variant each, according to cov-lineages.org, a website that documents the lineages of the virus.

At least 75 AY lineages of the coronavirus have been identified till now, each with different, additional defining mutations in their genome, according to Matthew Bashton and Darren Smith, from Northumbria University in Newcastle, talking about the lineage in The Conversation.

The two said the AY forms of the virus were not vastly different from their genome as they were all sub lineages of Delta, which was first detected in India and which remains the dominant variant in many countries because of its high transmissibility.

It is yet to be determined if the AY.4.2 is more transmissible or dangerous than the original Delta variant.

The HSA said even as evidence is emerging, AY.4.2 does not appear to be causing more severe disease. It also does not render vaccines any less effective.

But the AY.4.2’s secondary attack rate – the probability of an infection occurring in a group of people – is around 12.4 per cent for a household in the UK, while it is 11.1 per cent for the Delta variant.

This means that there are greater chances of infection spreading within a household if they catch the virus with the AY.4.2 variant, reported Quartz.

The variant has also caused alarm in India. According to GISAID, at least 17 cases have been detected in India, with seven cases in Andhra Pradesh state, four in Kerala, two each in Telangana and Karnataka, and one each in Maharashtra and Jammu and Kashmir.

Meaghan Hill, an epidemiologist at the HSA, said in a tweet that it was likely “Delta plus” was no more transmissible than the original Delta variant, and that there was no need to panic.

“So how worried should we be? Don’t press the panic button yet. Remember Delta had 60-80 per cent transmission advantage, but that was in a partially vaxxed/unvaxxed population. Best case scenario it’s no more transmissible than Delta and growth is coincident w/case numbers rising,” she said.

Professor Francois Balloux, director of the University College London (UCL) Genetics Institute, said AY.4.2 has risen in frequency in the UK but remains rare outside the country.

“The AY.4.2 lineage has attracted attention because it has risen in frequency in the UK over recent weeks, now representing ~7 per cent of all sequenced strains. It remains exceptionally rare anywhere else (only two strains found in the US so far),” he said in a tweet.