With the number of cases constantly declining in India but with signs that a third wave may be round the corner, India’s efforts to sequence genomes to track for emerging variants have nose-dived after April.
According to an exclusive report by The Hindu, data from the National SARS-CoV-2 Genome Consortium (INSACOG), a network of 28 labs across the country equipped to sequence genomes of the coronavirus for emerging variants, shows that in July, only 184 genomes were sequenced. In June, 4,381 samples were sequenced, which is itself a stark decline from May (13,142 samples) and April (15,546 samples). The latter two months were when India bore the brunt of the second wave that saw daily cases grow to as many as 400,000.
The Delta variant of SARS-CoV2 continues to be the dominant lineage for new cases across the country, while the other Variants of Concern (VoC) are at a lower rate and declining, INSACOG has said.
There is currently no evidence of any new Delta sub-lineage that is of greater concern than Delta, it has said.
“Delta continues to be the dominant lineage for new cases across all parts of India in recent samples and remains the most rapidly rising lineage globally that is responsible for multiple outbreaks, including across Southeast Asia, which shows the fastest growth in new cases globally,” the INSACOG said.
Regions with high vaccination and strong public health measures, such as Singapore, continue to do well, it noted.
The Delta variant was behind the deadly second wave of the coronavirus in India that killed thousands and infected lakhs during March to May.
The INSACOG said a study by the Indian Council of Medical Research (ICMR) has confirmed that most of the clinical cases in vaccine breakthrough were infected with the Delta variant but only 9.8% cases required hospitalisation, while fatality was found to be restricted to 0.4%.
It added that the data for higher infectivity of Delta continues to grow with the secondary attack rate in household contacts being almost double for Delta compared to Alpha (Public Health England, July 9 update). The other VoC continue to be very low in India and are declining relative to Delta globally.
“Public health measures to reduce transmission and vaccination remain critical,” the INSACOG stressed.
No cases of the Lambda variant have so far been reported in the country, it added.
In data from the U.K., Lambda is still seen primarily in travellers or their contacts and is not growing relative to Delta.
A growing spectrum of mutations is seen in the Delta background in the U.K., the U.S. and India.
The most frequent spike protein mutations, other than K417N (AY.1/AY.2), seen in the U.K. are G446V and P251L. In India, A222V and K77T have been reported as possible markers of sub-lineages.
Previous research into the A222V mutation for either transmissibility or immune escape was negative. In case of the K77T mutation, it has previously been reported in a cluster of Delta that spread to Asiatic lions in a zoo, and seen in sequences from Tamil Nadu, but has no known impact on transmission or immune escape in humans, the INSACOG said.
The INSACOG jointly initiated by the Union Ministry of Health and the Department of Biotechnology (DBT) with the Council for Scientific and Industrial Research (CSIR) and the ICMR, is a consortium of 28 national laboratories to monitor the genomic variations in SARS-CoV-2.