160 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, 160 new cases of Omicron and 22 new cases of Delta were detected from 182 samples.

“These 182 samples were sequenced from the last week of December and the first week of January from the community and arrival and departure samples from the airport.” said Dr. Chandima Jeewandara, Director of the Allergy, Immunology and Cell Biology Unit of the Faculty of Medicine.

The 160 Omicron cases include a mix of the two main Omicron lineages BA.1 and BA.2. BA.1 is detected in at least 113 countries and whereas BA.2 is directed in at least 3o countries. BA.1 /B.1.1.529.1. is the standard variety. BA.2 /B.1.1.529.2 is stealth omicron that differs from the standard variety. BA.3 /B.1.1.529.3 is the third sublinaege. BA.1 and BA. 3 has the characteristic S gene target failure whereas BA. 2 sub-lineage does not have it.

In Sri Lanka, Omicron sublineages were detected in the following locations. 139 cases of BA.1 were detected in Angoda, Colombo, Dehiwala, Galle, Kaduwela, Kandy, Matara, Minuwangoda, Negombo and Trincomalee. 17 cases of BA.2 and 4 cases of B.1.1.529 were detected in Colombo. 98 samples from Bandaranaike International Airport that were positive and were found to be infected with Omicron are from departure passengers and not arrival passengers while some of them were Sri Lankans and some were foreign nationals.

Different Delta sublineages were detected in the following locations. 4 cases of AY.28 (Sri Lanka delta sub-lineage) were detected in Nugegoda. 10 cases of AY.104 (Sri Lanka delta sub-lineage) were detected in ColomboFurther, AY.25 and AY.114 were detected in Colombo. AY.5.3 was detected in Angoda whilst B.1.617.2 was detected in Angoda, Colombo, and Ratnapura.

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 and 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)

Figure 3: Differences in Omicron BA.1 vs BA.2

Figure 4: Countries reporting BA.1

Figure 5: Countries reporting BA.2

Table 1: Number of sequences shared by each country in the South East Asia Region. (excluding samples sequenced in this round)

Figure 6: 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 7: Share of confirmed covid-19 cases sequenced.

Figure 8: Sequencing of viruses carried out in Sri Lanka so far.

Figure 9: Phylogenetic tree of all SARS-CoV-2 sequences identified in Sri Lanka so far.


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