75 New Omicron Cases Recorded From Sri Lanka – Latest SARS-CoV-2 Variant Report by Department of Immunology and Molecular Medicine.

According to the latest SARS-CoV-2 variant report issued by the 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.

Omicron sublineages were detected in the following locations. 56 cases of BA.1 were detected in Colombo, Avissawella, Borelesgamuwa, Homagama, Katugoda, Kosgama, Madapatha, Padukka, Parakudawa and Wellampitiya. 12 cases of BA.2 were detected in Avissawella, Badulla, Colombo, Galle, Konnawala, Mt Lavinia, Nugegoda, and from one passenger from India. 7 cases of B.1.1.529 were detected in Angoda, Colombo, Ruwanwella, Mt Lavinia, Nugegoda and Padukka.

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.

Other variants identified within Sri Lanka are B.1.411: Sri Lankan variant, B.1.1.25, B.1.258, B.1.428, B.4, B.4.7, B.1.1.365, B.1.525, B.1, B.1.1.

The timeline of the emergence and displacement of different variants in Sri Lanka is as follows.

Figure 1: Change in the SARS-CoV-2 variants in Sri Lanka over time. The graph shows changes in the different variants.

Figure 2: Locations of samples sequenced during the past week (4th week of December and 1st week of January)

Phylogenetic tree of Omicron variants found in Sri Lanka

Locations where Omicron has been found in Sri Lanka so far

Figure 3: Prevalence of Omicron in different countries in the world based on sequencing data (The current round of SL data does not appear yet in this website)

Figure 4: Sequencing of viruses carried out in Sri Lanka so far.

Figure 5: Phylogenetic tree of all SARS-CoV-2 sequences identified in Sri Lanka so far.

 Sequencing report 22.01.2022


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