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Data shows India's changing Covid-19 mix as share of omicron samples dips

Govt stopped updating weekly numbers on genetic sequencing in January

coronavirus
A health worker collects a swab sample for Covid-19 test at New Delhi railway station. The city recorded 331 fresh cases on Monday, the highest single-day spike since June 9. In Mumbai, 809 new cases were detected | Photo: PTI
Sachin P MampattaSohini Das Mumbai
4 min read Last Updated : Mar 31 2022 | 10:16 PM IST
Information submitted to GISAID, a global initiative for sharing genomic data accessed through numbers made available on their website and other trackers collating the numbers, shows a dropping share of Covid-19 samples which can be definitively identified as the Omicron variant.

Omicron accounted for around 97 per cent of samples tested on February 7. This has since dropped to around 88 per cent as of March 7. The share of 'others' or samples which cannot be classified under any one variant rose to 12 per cent from around 2 per cent earlier (see chart 1). The government’s initiative for monitoring genomic data Indian SARS-CoV-2 Genomics Consortium (INSACOG) last put out its weekly bulletin on January 10. The GISAID data was collected through numbers collated by online trackers Covariants.org, and Our World in Data.

Anurag Agrawal, director, Institute of Genomic and Integrative Biology clarified that the ‘others’ variants are not the hybrid version of the Delta and Omicron variants dubbed ‘Deltacron.’

“They are almost all sequences with small gaps that prevent exact classification. When the cases decline, the viral load is low, in most samples and the sequences are not as good. So, the share of ‘others’ rises because there are these sequencing gaps that prevent exact lineage matching. Whenever waves subside, viral load is low and such sequences rise. We saw this with the Delta wave as well….” Agarwal explained.

Agarwal also said that the term Deltacron is vague and best avoided.

As far as the Omicron variant goes, he said that the BA.2 sequence is extremely common in India. “Our Omicron wave was mostly BA.2. That is different from ‘Deltacron’ – a wrong term used to describe rare recombinants. Omicron is BA.1, BA.2 and BA.3. India Omicron wave has been mostly BA.2,” Agarwal explained.

Last month a senior member of the INSACOG had told Business Standard that so far there was no instance of the Deltacron variant in India. There are, however, cases of ‘mixed infections’

“There are instances of mixed infections – Omicron with Delta – which we have picked up initially….In the beginning of the third wave when Delta was in circulation, we saw some mixed cases. Now Omicron is the leading variant,” the official had said.

Explaining cases of mixed infections, he says — if someone meets two persons who are carrying two different strains, and that person can get both infections at the same time. This is called mixed or combination infection. This is caused by recombination of variants, not mutations in the virus.

The share of ‘others’ in the sample on 10th January was around 4 per cent.  Business Standard also looked at the latest available genomic data for the top five countries with the highest number of new cases over the last seven days. Vietnam has a 10 per cent share of the Delta variant in its analysed samples. Around 90 per cent of the rest is Omicron. The share of others is less than 1.5 per cent for each of the top five countries in terms of cases over the last seven days (see chart 2).

INSACOG has been scrutinizing samples closely. At present 51 institutions is part of the INSACOG network. It was trying to ramp up genomic sequencing from 10,000 samples a month to 8,000-10,000 samples every week.

An INSACOG source said that sampling has increased as a percentage of total cases, but an increase in absolute terms is not possible now with fewer samples and lower viral loads.

INSACOG started doing Covid-19 genome sequencing in December 2020.
 


Topics :CoronavirusOmicronDelta variant of coronavirusCoronavirus TestsCoronavirus VaccineVaccination

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