SARS CoV-2 variant surveillance based on gene sequencing

Department of Molecular Biology, Medical Research Institute, Colombo and Department of Zoology and Environmental Sciences, University of Colombo have conducted SARS CoV-2 variant analysis based on gene sequencing data generated by Oxford Nanopore gene sequencing method since July 2021. Prof. Inoka C Perera has been coordinating the team at University of Colombo and Ministry of Health has supported this surveillance work.

It could be observed the gradual transition of the dominant SARS CoV-2 variant type over the time from July to October 2021. Alpha variant (B.1.1.7) was the dominant circulating virus type initially, but it gradually changed to Delta variant (B.1.617.2) from August to September. Delta variant (B.1.617.2) was associated with significant disease severity and transmissibility compared to initial Alpha variant (B.1.1.7).

From September to October, circulating Delta variant (B.1.617.2) has acquired few more changes in its genetic composition giving rise to Delta sublineages as described in the following table. A significant difference in immune escape, clinical severity or transmissibility hasn’t been noted in the identified Delta sublineages in Sri Lanka compared to the original Delta variant (B.1.617.2) so far.

It is essential to closely monitor the ongoing emergence of new virus variants and detect any impact on their ability for immune escape, clinical severity, transmissibility and treatment resistance on both vaccinated and unvaccinated population. Therefore, it is necessary to regularly refer some SARS CoV-2 positive samples to the Department of Molecular Biology, Medical Research Institute (for gene sequencing) from different locations in the country. It is also useful to do the SARS CoV-2 gene analysis on the samples from individuals presented with moderate to severe disease after breakthrough infections despite vaccination or as community/family clusters. The samples should be always referred with properly filled designated request form including the relevant clinical and vaccination information to support the ongoing analysis of potential immune escape, clinical severity, transmissibility and treatment failure in emerging new variants.