Experts to examine samples afresh as AY.4.2 worry grows

Experts spearheading the genome surveillance of the Sars-Cov-2 virus in India are analysing a set of 15-17 sequences for a second time to see if they fall under the classification of the AY.4.2 variant, days after authorities in the UK said they suspect it could be somewhat fitter (stronger) than its parent Delta variant, which in itself is one of the most dangerous versions of the coronavirus that causes Covid-19.

Union health minister Mansukh Mandaviya confirmed on Tuesday that experts are investigating the new variant, although he did not give more details.

Variants of the coronavirus typically have several mutations. When scientists analyse their genome sequence, they add a classification based on whether the mutations are common with other samples. If too many samples begin returning the same mutations, it becomes a distinct variant.

The AY.4.2 is an evolution of the Delta variant and largely has the same mutations as Delta, but with three additional ones that scientists say should be treated as a characteristic: A222V and Y145H in the Spike protein of the virus, and A2529V in a portion known as the ORF1ab.

Researchers from the Indian SARS-CoV-2 Consortium on Genomics (INSACOG) told HT that 15-17 sequences contain one of these three mutations, and they will now be further analysed to check if they contain the others as well – this could determine if they are AY.4.2 or something like it.

“AY4.2 is a new classification and the PANGO software used to assign lineages to sequenced samples is still being updated. There are two mutations on the spike protein of AY.4.2 and one on ORF region; a sequence is designated as AY4.2 if it has two of the three mutations. We have detected fifteen to seventeen samples across India that have at least one of the mutations. Now, we will go back and check whether they have one of the other two,” said Dr Saumitra Das, director of National Institute of Biomedical Genomics (NIBMG-Kalyani), which is one of the 28 central laboratories under INSACOG.

INSACOG reports genomic surveillance of SARS CoV-2 across the country through sequencing of samples from sentinel sites and also detailed state-wise district analysis for some states under State memoranda of understanding (MoUs) including Maharashtra and Kerala.

Dr Anurag Agarwal, director of the Institute of Genomics and Integrative Biology (IGIB)-Delhi, which is also one of the INSACOG laboratories, said, “We have seen very few AY.4.2, but again there are classification problems.”

The parent sub-lineage AY.4 has become one of the main variants being isolated by the INSACOG network after the Delta variant (which is also known as B.1.617.2.

According to outbreak.info’s analysis of sequences submitted from India to a global repository known as GISAID in the last 60 days, AY.4 lineage made up for 29% of the samples. The largest proportion, 52%, were of the Delta variant.

According to INSACOG’s dashboard that has data up to September, AY.33 is the most sequenced variant constituting 71%. Explaining the discrepancy, Dr Agarwal said, “AY.33 is a PANGO misclassification and will break up.”

Dr Das, explained, “AY.33 is the new name that PANGO has assigned to what was previously reported as AY.4; the classifications and re-classifications keep on happening. In India, Delta still continues to be the dominant variant, followed by AY 4.”

The scrutiny around AY.4.2 arose after the latest technical briefing by Public Health England (PHE) upgraded the variant as being under investigation. The PHE document, dated October 22, said the key decision is based on AY.4.2 having a modestly increased growth rate and a higher secondary rate of attack – the ability to pass the infection on to someone – was higher than Delta’s (12.4% versus 11.1%).

If a variant spreads faster, leads to more severe disease or causes a repeat infection after a past episode of Covid-19 or vaccination, it is classified as a variant of concern (VOC). Delta was the latest VOC of the Sars-Cov-2 – the label is added only after detailed analysis involving lab findings, clinical evaluation and epidemiological studies.

In India, of the 104,441 samples sequenced so far, 40,682 are either VOCs or VUIs. Of these, 26,043 are of the Delta variant, which was first found in India and is believed to have led to the devastating wave of infections in April-May..

Dr Ekta Gupta, who heads the regional INSACOG laboratory at the Institute of Liver and Biliary Sciences in Delhi said, “We have not seen any AY.4.2 cases in Delhi as of now, but AY.4 has been reported for months now. These keep changing as per the re-classification, the important thing is that so far we have not seen any clinical significance of any of these variants. And, being close to Delta, they are unlikely to affect a high number of people who might already have been exposed to the Delta variant during the second wave.”

Experts agreed that this might be the most crucial aspect to remember – and that none of the Delta sub-lineages have so far raised any concern.

“There are no clinical implications that we have seen from any of the sub-lineages at present. The viruses will continue mutating slowly, but some increases in cases that have been reported are largely due to the human behaviour,” said Dr Rakesh Mishra, former director of Centre for Cellular & Molecular Biology (CCMB-Hyderabad).

Dr Das said, “So far no clinicians have reported any change in symptoms or such. We have to keep an eye out for change in symptoms, more hospitalisations, infections in the vaccinated, and cluster formation and link it to the variant. Right now there is no such concern, but we have to keep an eye on things.”