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Four-times mutated Delta variant: Fourth mutation hampers diagnostics?

28 Aug 2021

  • Too early to predict ‘super variant’ emergence in SL: J’pura Uni 
  • 'Scientific prediction-wise, such emergence is worst-case scenario'
  • Delta variant's R-24C mutation is the latest to be identified 
 BY Aazam Ameen With the increase in detections of mutations of the virulent Covid-19 Delta (B.1.617.2) variant in the country, the latest sequencing data has noted a rapid spread of the variant in Colombo, while experts are now concerned that its latest mutation may even hamper diagnostic assessments of PCR tests. So far, the SA 222V, SA 701S, SA 1078S, and R-24C mutations of the Delta variant have been observed in Sri Lanka. It was reported yesterday (28) that the latest sequencing data from the University of Sri Jayewardenepura had indicated an increase in the number of Covid-19-positive cases infected with the Delta variant, to 292. The data has also revealed a rapid spread of the Delta variant in Colombo. When queried about the most recent detection of the R-24C mutation, Sri Jayewardenepura University Allergy, Immunology, and Cell Biology Unit Director Dr. Chandima Jeewandara explained that concerns have arisen on how it may affect certain diagnostics such as PCR tests.   “The fourth mutation (R-24C) is of the ORF1a region, which is a non-structural protein. This region is one of the targets used in the diagnostic assessment of PCR tests. At present, we don’t know about the effect it will have on the relevant diagnostics,” he noted.  Despite this, Dr. Jeewandara highlighted that the main concern at the moment is the mutations in the S gene of the virus, as most vaccines are developed targeting the S gene. In terms of sequencing runs to detect such mutations, even after nearly two years, the laboratory at the Sri Jayewardenepura University continues to be the only facility which carries out this essential process.   When queried as to why other laboratories have not begun this process, Dr. Jeewandara observed that while he cannot comment on a specific reason, he noted that to do so is not a difficult task. “Several universities were invited to start this process as well. It is not a difficult thing to do, as the latest technology is available. For example, the Oxford Nanopore advanced Covid-19 sequencing platform comes with the relevant reagents needed as a package. It can be implemented in Sri Lanka without any issue. Meanwhile, in our lab, we use the Illumina technology which is used to detect normal pathogens,” he elaborated. Dr. Jeewandara also added that his lab conducted sequencing runs on Wednesday (25) and Thursday (26). The relevant reports were handed over to the Director General of Health Services (DGHS) on Friday (27). He said that the Sri Jayewardenepura University’s Allergy, Immunology, and Cell Biology Unit will continue to carry out weekly gene sequencing runs.  Meanwhile, even though fear mounts over a possible emergence of a “super variant” of Covid-19, which may be even more transmissible and vaccine-resistant when compared to variants of concern (VOCs) identified by the World Health Organisation (WHO), an expert immunologist of international repute informed The Sunday Morning that it is still too early to predict if such a situation may develop in Sri Lanka. Dr. Jeewandara explained that in terms of scientific predictions, the emergence of a “super variant” is viewed as a worst-case scenario. “Covid-19 is spreading all over the country. When a virus spreads in a given population, it tends to mutate. That is when this discussion of a ‘super variant’ emerges. It is a worst-case scenario in terms of scientific predictions,” he pointed out.


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