Go for dual RT-PCR testing to detect Omicron at low cost: Centre to states

Go for dual RT-PCR testing to detect Omicron at low cost: Centre to states

+ve Samples To Be Tested For S-Gene Drop

Umesh Isalkar & Sarfaraz Ahmed TNN

Pune/Nagpur:28.12.2021

The Union health ministry has advised states to adopt a dual RT-PCR testing strategy prior to genome sequencing of Covid samples for Omicron detection. Under the new plan, suspected patients’ throat/nasal swab samples will be tested using a standard RT-PCR kit and, if detected positive, the same sample will undergo a second test with an imported RT-PCR kit with an Sgene drop.

“Only those samples showing positive for S-gene drop-out or S-gene target failure (SGTF) will be genomically sequenced for Omicron. Besides cost-cutting, it will also help in picking up the highly probable Omicron cases and save resources,” a senior Union health ministry official told TOI on Monday.

The Maharashtra government is among the first to have already started implementing the dual test strategy. Quite a few districts with high floating populations have already received the imported kits.

“The cost of genome sequencing goes up to Rs5,000 per sample in India, including the transport, human resource, and other heads,” the official said, adding that whereas the cost of a standard RT-PCR kit and imported RT-PCR kit with SGTF is Rs19 and Rs240, respectively. The dual RT-PCR costs Rs260. Besides testing individuals with international travel history and their close contacts, these kits can also be used at government-run laboratories for routine Covid tests to rule out community spread from daily caseload having high viral load or below 25 cycle threshold CT) value.

Twenty-three of 60 Covidpositive samples have so far tested positive for S-gene dropout in Nagpur. Instead of sequencing all 60 samples, these 23 samples are being prioritised. The Virus Research Diagnostic Laboratory at Nagpur’s Indira Gandhi Government Medical College and Hospital — one of the key sentinel centres in Maharashtra — is carrying out the second RT-PCR test for SGTF prior to sending the samples for sequencing. The hospital’s head of microbiology department and principal investigator, Dr SS Raut said, “The civic and district administrations are forwarding positive samples from both public and private labs. We are testing these samples again using the specialized RT-PCR kits for SGTF.”Nagpur’s second confirmed Omicron patient, a 21-year-old who returned from Dubai, was the first whose throat/nasal swab sample when tested twice with RTPCR kit showed the SGTF. The sample was later genomically sequenced to confirm the presence of the Omicron variant.