Travel history alone should not be deciding factor for genome sequencing: Experts

The RT-PCR testing facility for COVID-19 at BIAL in Bengaluru  

In the wake of an anaesthetist from a government hospital in Bengaluru, who did not have any travel history, getting infected with the Omicron variant, COVID-19 experts here said that travel history alone should not be the deciding factor for genome sequencing of samples.

While the Indian SARS-CoV-2 Genomics Consortium (INSACOG), which monitors the genomic variations of the pandemic, has mandated random sequencing of samples (at least 10%) that test positive from among clusters, among the fully vaccinated and children, experts said health professionals at testing centres should be more vigilant and watch for parameters such as low cycle threshold (CT) values that indicate a high viral load.

“Although the fully vaccinated anaesthetist did not have a travel history, we sent his sample for genome sequencing as his viral load was high and the CT value was less than 15. CT value indicates the number of cycles needed in the RT-PCR test to amplify the viral RNA to a detectable level. The lower the CT value, the higher the viral load - because the virus has been spotted after fewer cycles,” said a senior doctor from the hospital.

In a tweet, TAC member Giridhar R. Babu, who also heads Lifecourse Epidemiology at Indian Institute of Public Health in Bengaluru, said: “Travel history can distract the detection of cases and clusters. Especially, when it is absent. Presumptive diagnosis by health professionals and proactive approach is critical.”

Sequence cluster samples

V. Ravi, nodal officer for genomic confirmation of SARS-CoV-2 in Karnataka, said it is important now to identify clusters of cases and do genomic sequencing.

Asserting on the importance of contact tracing now, Dr. Ravi said the principles of contact tracing principles should be followed in toto. “While it is difficult for a person to recall whom all he met in the last 10-15 days,we have to watch out for cluster outbreaks where even one of the contacts is involved.”

C.N. Manjunath, nodal officer for labs and testing in the State’s COVID-19 task force, said the focus is on genome sequencing now. “The variant may have been in circulation in many countries. However, the detection of the variant in South Africa has prompted other countries to sequence more and more samples,” he said.

“Better surveillance and genomic sequencing apart from reporting in a timely manner are the need of the hour now. The next three months are crucial, especially with Christmas and New Year celebrations ushering in,” the doctor asserted.

S-gene target failure

Quoting the World Health Organisation (WHO), U.S. Vishal Rao, member of the State’s Genomic Surveillance Committee, said the S-gene is not present in the Omicron variant. “This is the result of the multiple mutations that the variant has undergone and is a marker to identify the variant. The S-Gene dropout or as we say the S-gene target failure ( SGTF) is one of the proxy indicators to (ascertain) whether or not it is the Omicron variant,” he said.

“Thermo Fischer TaqPath assay can therefore be used as proxy test for this variant, pending sequencing confirmation,” he added.

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Printable version | Jan 20, 2022 1:32:38 PM | https://www.thehindu.com/news/national/karnataka/travel-history-alone-should-not-be-deciding-factor-for-genome-sequencing-experts/article37827877.ece

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