Omicron variant detected in Sri Lanka

By Shailendree Wickrama Adittiya

Health officials yesterday confirmed that the Omicron COVID-19 variant has been detected in the samples collected from an overseas arrival from Nigeria.

According to Deputy Director of Health Services Dr. Hemantha Herath, the overseas arrival returned from a country in Africa on 24 November and was undergoing treatment in an isolated room after testing positive for COVID-19. There was thus minimal risk of transmission to other people.

The individual was not vaccinated and was thus subjected to a PCR upon arrival in Sri Lanka. The patient was discharged on Thursday.

Dr. Herath stressed that the Health Ministry was taking all possible measures to prevent the spread of the variant, from carrying out genetic testing among high-risk groups to taking measures to contain the virus in areas that show rapid spread.

“A traveller from an African country has been identified with the Omicron variant. All measures have been taken and the overseas arrival is already undergoing quarantine,” Chief Epidemiologist Dr. Samitha Ginige said, adding that the person’s family, as well as fellow travellers, will also be tested.

He explained that restrictions were imposed preventing travellers from South Africa, Botswana, Lesotho, Namibia, Zimbabwe, and Eswatini from entering the country immediately after concerns were raised about the Omicron variant.

“In addition to this, information on all persons who arrived from these countries during the past month was collected.” “The health status of all these persons is being monitored and they are being subjected to additional PCR and RAT testing,” Dr. Ginige said, adding that none of the travellers has tested positive for COVID-19 yet.

Health officials have also sent all positive samples of recent overseas arrivals for genetic testing at the Sri Jayewardenepura University’s laboratory. It is as a result of this measure that the Omicron variant was detected in a sample.

The Sri Jayewardenepura University yesterday published the report on the whole genomic sequencing of COVID-19 variants in Sri Lanka by the Allergy, Immunology and Cell Biology Unit of the Department of Immunology Molecular and Molecular Medicine. The study was carried out by Sri Jayewardenepura University researchers, including Prof. Neelika Malavige and Dr. Chandima Jeewandara.

The researchers studied 94 samples of PCR-positive passengers who arrived in Sri Lanka during the last two weeks. Samples from Colombo, Gampaha, Ratnapura, Kalutara, Karapitiya, Trincomalee and Vavuniya districts were sequenced this week.

“Out of the 94 samples that were sequenced, Omicron was detected from a Nigerian passenger. All other samples were of the delta variant,” the report states.

Thirty-one samples were of the AY.28 Sri Lanka Delta sub-lineage and the samples were collected from Colombo, Gampaha, Nuwara Eliya, Balangoda, Bentota, Kuruwita, and Pottuvil. The AY.104 Sri Lanka Delta sub-lineage was detected in 43 samples from Colombo, Bandaragama, Getahena, Gampaha, Palindanuwara, Vavuniya, Waga, and Welgama.

The AY.122 sub-lineage was detected in a sample from Kosgama, the AY.33 sub-lineage from Kalutara, the AY.4 sub-lineage from Negombo, the AY.61 sub-lineage from Thalangama, and the AY.66 sub-lineage from Puwakpitiya.

The B.1.617.2 lineage was detected in samples from Colombo, Gampaha, Trincomalee, and Puwakpitiya.