The delta variant in Sri Lanka assigned a new sub-lineage (AY.28)

USJ researchers including Prof. Neelika Malavige and Dr. Chandima Jeewandara from Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine of University of Sri Jayewardenepura have been carrying out sequencing of the SARS-CoV-2 viruses since the onset of the pandemic. With the identification of the delta variant in Sri Lanka, they also detected a delta variant with several unique mutations in the spike protein (A701S, A222V, A1078S).

This delta variant with mutations has now been assigned a new lineage AY.28 and this delta variant is now names as B.1.617.2.28 Sri Lankan lineage. This AY.28 sub lineage that was initially detected during late May 2021, subsequently accounted for approximately 50-60% of the infections in the Western Province. Further investigations to characterize this sub-lineage is underway.


Figure 1: The cumulative prevalence of AY.28 delta sub lineage in different regions in Sri Lanka.


Figure 2: Locations where this particular delta variant is detected.


Figure 3: The relative frequency of detection of AY.28 delta sub lineage in comparison to other delta sub-lineages in Sri Lanka


Figure 4: Phylogenic tree of the delta variants and sub lineages detected in Sri Lanka


B.1.617.2 Lineage with S:A701S Report. Alaa Abdel Latif, Julia L. Mullen, Manar Alkuzweny, Ginger Tsueng, Marco Cano, Emily Haag, Jerry Zhou, Mark Zeller, Emory Hufbauer, Nate Matteson, Chunlei Wu, Kristian G. Andersen, Andrew I. Su, Karthik Gangavarapu, Laura D. Hughes, and the Center for Viral Systems Biology., (available at Accessed 26 September 2021.

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