Delta sub-lineage spotted in 10% of Covid-19 samples

The Delta variant of the Sars-CoV-2 virus is the most common in Delhi, although one the variant’s sub-lineages, the so-called AY.12 variant, is being seen in around 10% of the samples, according to a doctor at one of the four centres sequencing viral genomes in the Capital.

The numbers present a stark difference from national data (excluding Delhi’s) which show that another Delta lineage, AY.4, was seen in 53% of the samples sequenced by India’s genomic sequencing consortium, INSACOG. The increase was driven by AY.4’s presence in Maharashtra and Kerala, states that together account for nearly 34% of all the samples sequenced in the country till August.

Delhi’s data for August hasn’t been uploaded on the INSACOG dashboard. Data for September hasn’t been uploaded for any of the states.

“In Delhi, we find Delta and its sub-lineages in almost 99% of the samples, with the other 1% being the Alpha variant. The Delta variant (B1.617.2) which caused the fourth wave in the city, is the most common, followed by the AY.12 variant, which accounts for about 10% of delta variant in August and early September,” said Dr Ekta Gupta, professor of virology at the Institute of Liver and Biliary Sciences, which is one of the four labs sequencing viral genomes in the city.

Samples from Delhi are sequenced at ILBS, Lok Nayak Hospital, National Centre for Disease Control, and Institute of Genomics and Integrative Biology.

“Samples are collected from the district and hospitals and sent to the lab for genomic analysis. Maybe all of the labs are not receiving samples right now because the number of cases is very low in Delhi at the moment. However, from the report that we have received so far, there is no need to worry (about AY.12),” said a senior official from Delhi’s health department.

Dr Gupta said Delhi is unlikely to see a surge of AY.12. “The antigen is more or less the same as the Delta variant that led to the huge surge in cases in April. A huge proportion of the population has already been exposed to delta, hence the similar AY.12 is unlikely to cause a surge in cases again in the city.”

According to a September 20 bulletin from INSACOG: “AY.12 has lost some of the mutations seen in Delta parent lineage. No new mutations of concern are noted in the spike protein.”

Mutations in the spike protein are of significance as the Sars-CoV-2 virus uses the protein to enter human cells. There were several mutations on the spike protein of the Delta variant that made it highly transmissible and increased its ability to evade immunity from a previous infection or the current vaccines.

Despite no significant mutations on the spike protein, AY.12 is the second most commonly sequenced variant in Israel that is seeing a surge in cases despite over 60% of the population being vaccinated.

The most common variant is AY.4 (48%); AY.12 was found in 17% samples, and the original Delta variant in 9%, according to data from outbreak.com that aggregates data from the global database GISAID. To be sure, Israel did not see a previous outbreak on account of Delta like India did.