India: Omicron BA.2 is now at 57% of genome samples, but is Delta rising again?

B.1.617.2, BA.1, BA.2, Coronavirus, Delta, India, Infection, Omicron, Transmission

India has seen quite considerable growth in the BA.2 sub-lineage of Omicron recently, lifting it to about 57% of all genome samples, with BA.1 now declining steadily.

What is surprising, however, is what looks like a recent increase in Delta variant cases, which now account for about 14% of samples according to CoVSpectrum. Delta was found in almost no genome samples at the turn of the year. This apparent increase could be an anomaly caused by the low number of samples submitted in 2022, but it’s something we’ll keep an eye on.


A plot using Cornelius Roemer’s lineage comparison app suggests Omicron BA.2 may be heading higher in India by outcompeting BA.1 completely:


It’s not clear which sub-lineage, if any, is responsible for a recent rise in Delta cases in India yet.


India has seen a large Omicron wave in January 2022, but it hasn’t yet reached the heights of its notoriously difficult Delta wave of Spring 2021.


Sri Lanka has also seen a few Delta cases since the New Year:


According to the latest SARS-CoV-2 variant report issued by the Sri Lanka Allergy Immunology and Cell Biology Unit of the Department of Immunology and Molecular Medicine of the University of Sri Jayewardenepura, 75 new cases of Omicron and 3 new cases of Delta were detected from 78 samples.

“These 78 samples were sequenced from the 1st 2nd and 3rd weeks of January from the community.” said Dr. Chandima Jeewandara, Director of the Allergy, Immunology and Cell Biology Unit of the Faculty of Medicine. The 78 Omicron cases include a mix of the two main Omicron lineages BA.1 and BA.2.

Different Delta sublineages were detected in the following locations.1 case of AY.98 (Sri Lanka delta sub-lineage) was detected in Thalangama. 1 case of AY.104 (Sri Lanka delta sub-lineage) was detected in Kaduwela. 1 case of B.1.617.2 was detected in Wellampitiya.

Currently, 8% of the sequences of Sri Lanka are BA.2, which was named as a variant of interest by the UK Health security agency. report



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Photo by Ravi N Jha on Unsplash


** This post was originally published on January 23, 2022 **