New test to replace RT-PCR to detect influenza virus along with Covid-19

Passengers being tested at Dadar station. RT-PCR test is advised as the standard for Covid detection currently. Pic/Suresh Karkera

Covid-19 RT-PCR test is likely to be replaced by the Multiplex Assay - a single test which will diagnose SARS-CoV-2, Influenza A and Influenza B at same time, as per the new Center for Disease Control (CDC) USA directives. Health experts here say this will help us in diagnosing superadded infection of influenza along with Covid and also will save material used to perform three different tests. Experts have urged authorities to make this test available in India, especially at a time when our country is witnessing a massive surge in Covid cases.

Dr Subhash Hira, professor of Global Health at University of Washington-Seattle and invited member to WHO-Geneva Covid-19 review panels, said, "US-CDC/US-FDA have just discontinued the Novel Coronavirus (2019-nCoV) RT-PCR Diagnostic Panel that was launched in February 2020 and replaced it with the CDC Influenza SARS-CoV-2 (named Flu SC2) Multiplex Assay, which allows laboratories to run three tests in a single reaction well. The Flu SC2 multiplex is more efficient in its use of test reagents, is faster, and simultaneously gives accurate results."

"The new test probe is claimed to have included many of Covid variants spike epitopes to improve the diagnosis of Covid infection. Since symptoms of Covid and the flu are generally similar, testing for all three viruses at the same time will provide information that doctors need to treat appropriately, help reduce the spread of these viruses, reduce testing cost and conserve resources that are in short supply," he said. Dr Hira added, "This improved version of reagents and test software do not affect the RT-PCR machines. The Indian diagnostic industry is up to upgrade and is rapidly improving its RT-PCR version.

History of RT-PCR

Dr Wiqar Shaikh, professor of Medicine at Grant Medical College and Sir J J Group of Hospitals, said RT-PCR test, discovered by Kary Mullis, an American Biochemist, who won the Nobel Prize for Chemistry in 1993 for his discovery, has been the workhorse in detecting Covid. Several changes and enhancements have been made to the original discovery and today RT-PCR is accepted as a standard diagnostic technique, not only for SARS-CoV-2 but for several other ailments.

He added that after the pandemic began, it was found that Covid-19 was often associated with other respiratory pathogens, which led the US-CDC to develop the RT-PCR Diagnostic Panel. This test was approved by the US FDA. However, the development of the next test, Multiplex Assay by CDC led to the decline of the Diagnostic Panel and it was finally discontinued as of December 31, 2021.

What is Multiplex Assay

Dr Shaikh explained that the CDC Influenza SARS-CoV-2 Multiplex Assay or FLU SC2 Multiplex Assay also uses the RT-PCR technique. He said the Multiplex Assay is designed to use information on SARS-CoV-2 genomes that were not available when the first test for Covid-19 was developed. This, he said, will improve detection of the viruses, especially SARS-CoV-2 when compared to the original RT-PCR Diagnostic Panel.

Dr Ketan Vagholkar, professor of Surgery at D Y Patil Medical College, said, "With the passage of time, more mutant strains are evolving, making testing more difficult. The sensitivity and specificity of existing tests have significantly changed. The initial tests are falling short and giving false positive results even for flu viruses. CDC is working on this issue and has developed a newer testing method. This will not only allow laboratories to conserve testing materials which are in short supply but also test more samples. Currently, these tests are available in the US. However, other countries including ours will need to look into these challenging issues which will render testing more comprehensive."

Dr Santosh Bansode, Head of the Department, Emergency Medicine at Wockhardt Hospitals, Mumbai Central, said, "RT-PCR for Covid is advised to most of the patients now and we generally don't do tests to diagnose Influenza A and B, so we don't know how many Covid-negative patients with complaints of flu are infected with these viruses. With the help of Multiplex Assay, we will now know exactly which flu virus is causing problems. I feel replacing RT-PCR with Multiplex Assay, as initiated by CDC, will be a good move."

31 Dec
Day when US discontinued Covid RT-PCR last year