Tamil Nadu on Monday decided to use Thermo Fischer TaqPath Assay, a test recommended by the World Health Organization, to detect the Omicron variant of the Covid-19 virus at the 12 RT-PCR government labs in the state. The routine RT-PCRtests are not technically complete as they often do not test for the S gene, which is absent in the Omicron variant of the virus.
The World Health Organisation has said that in the RT-PCR tests targeting three genes (N, S and E), the S gene is not present in the case of Omicron mutations, therefore, the absence of ‘S gene dropout’ or ‘S gene target failure’ (SGTF) can be used as the marker for this variant, pending genome sequencing confirmation.
A circular issued on Monday by the director of public health (DPH) Dr T S Selvavinayagam directed the government labs to use TaqPath kits to test for the three target genes. Five of these 12 labs are in Chennai, two in Coimbatore and one each in Trichy, Salem, Madurai, Thoothukudi and Kanyakumari.
The Tamil Nadu government will supply Thermo Fisher TaqPath RT-PCR kits with higher specificity and better detection rate to the labs that have superior access to airports in the state. “All inbound international travellers found with the symptoms of influenza like Illness (ILI) will be screened for S gene drop out using the Thermo Taqpath by the government RT-PCR labs,” the circular said.
In addition to international travellers, the TaqPath tests will be used for testing samples of reinfection, vaccine breakthrough infections, unusual transmission events, positive children, severity of illness in patients without comorbidities. Any sample with S gene target failure, found since October 15, will have to be referred to the State Public Health Laboratory for sequencing confirmation of the Omicron variant, the circular said, and added that samples of all Covid-19 positive travellers have to be sent for genome sequencing.
{{/usCountry}}In addition to international travellers, the TaqPath tests will be used for testing samples of reinfection, vaccine breakthrough infections, unusual transmission events, positive children, severity of illness in patients without comorbidities. Any sample with S gene target failure, found since October 15, will have to be referred to the State Public Health Laboratory for sequencing confirmation of the Omicron variant, the circular said, and added that samples of all Covid-19 positive travellers have to be sent for genome sequencing.
{{/usCountry}}On November 27, WHO designated the variant, B.1.1.529, as a variant of concern with the potential of being more dangerous than its predecessors, and gave it a name, Omicron. According to the international organisation, similar to the alpha variant, the S gene target failure (SGTF) or dropout due to deletion at Spike position 69-70 has been reported in the new variant.
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“Thermo Fischer TaqPath Assay can therefore be used as proxy test for this variant pending sequencing confirmation. Use of the SGTF approach may lead to faster detection rates,” the circular said, noting WHO’s guidelines for labs. It however acknowledged that most diagnostic tests can detect Omicron.
Tamil Nadu has been using only the RT-PCR test to detect the virus since it entered the state in March 2020. As fresh travel bans are being imposed across the globe due to the spread of the Omicron variant to Europe and Australia, Tamil Nadu’s health department has appointed assistant program managers at the state’s four international airports in Chennai, Coimbatore, Madurai and Trichy.
The ,managers will coordinate with the staff screening and testing passengers on arrival. RT-PCR tests are being done for all international arrivals at the Chennai airport. Since October 21, as many as 55,090 RT-PCR tests were conducted at Chennai airport, of which, three tested positive for Covid-19. The health minister M Subramanian had earlier said that most of the positive samples were of the Delta variant.