Three stages of tests confirm virus cases
NEWDELHI:Since January 17, 2020, India has tested 5,255 samples for coronavirus disease (Covid-19), of which 44 positive samples have been confirmed positive by the country’s apex virology laboratory, the Indian Council of Medical Research (ICMR)-run National Institute of Virology (NIV) in Pune.
The ICMR-NIV lab is a part of the World Health Organisation’s (WHO) global network of 15 Covid-19 reference laboratories with demonstrated expertise in the molecular detection of the disease.
The virus responsible for causing Covid-19 (or 2019 novel coronavirus) has been named severe acute respiratory syndrome coronavirus 2 (Sars-CoV-2).
ICMR has certified 52 laboratories across India, including NIV, to collect and test the nose and throat swab samples of suspected Covid-19 cases. New Delhi’s National Centre for Disease Control (NCDC), which is not part of ICMR’s network, is also performing the Covid-19 test.
Scientists have identified seven strains of coronavirus that infect humans. These cause illness, ranging from common cold to more severe diseases such as Middle East Respiratory Syndrome, or Mers.
The harmless strains of coronavirus are Serotype 229E, Serotype OC43, Serotype NL63 and Serotype HUK1. These cause symptoms of common cold and rarely cause severe pneumonia. But the more dangerous strains are Sars-CoV, which causes severe acute respiratory syndrome or Sars; Mers-CoV, which leads to Mers; and Sars-CoV-2, which causes the novel coronavirus disease Covid-19.
The preliminary test for the new disease, called conventional polymerase chain reaction (PCR), is being conducted at state laboratories and is meant to find out the presence of a virus belonging to the coronavirus family.
“There are seven types of coronaviruses, and the local laboratories use the kits that can tell them if it is a coronavirus. Once that gets confirmed then it is sent to
NIV for confirmation on whether it is novel coronavirus or not,” said a senior scientists from ICMR who asked not to be named.
Since China, within weeks of the virus breaking out in the country last December, shared the genetic sequencing of the Sars-CoV-2 with WHO, laboratories globally are able to match the pieces of the Sars-CoV-2 virus’s gene code with the virus found in their sample.
The confirmatory test, performed by NIV and called reverse-transcription polymerase chain reaction (RT-PCR), is done to check the virus’s genetic sequence against the published Sars-CoV-2 sequence.
“There is a part of the gene that is constant in the virus, and is used for matching with the coronavirus found in our swab samples. This is a more sensitive test, and confirms positive Covid-19,” said the ICMR scientist quoted above.
The final test is next-generation sequencing, which relates the whole gene sequence of the virus in the sample with the virus that has been isolated in Wuhan (Sars-Cov-2).
“It is meant to compare the entire gene structure of SarsCov-2 with the coronavirus found in the swab sample. This is by far the most accurate and we do it if there’s even slightest of doubt about the test result,” said a senior scientist at NCDC.
The NIV lab not only confirms Sars-Cov-2 samples but also checks the quality of samples being tested by its network of laboratories. “NIV is also there for quality assurance; so labs are sending all positive samples and also 5% of all the negative samples that they have tested. These negative samples are randomly tested to check the quality of tests,” said the ICMR scientist.
Sars-CoV-2 is closely associated to two bat-drived Sars-like coronaviruses (bat-SL-Cov-ZC45 and bat-SL-Cov-ZXC21) collected in 2018 in Zhoushan, eastern China. It has 79% genetic affinity with Sars-CoV and 50% with Mers-CoV.
The Sars-CoV-2 receptor-binding domain structure, which allows a virus to latch on to and enter a cell, is similar to SarsCoV, despite amino acid variations at some key residues.
It usually takes about five hours to get the test result, with anywhere between 45-90 samples being tested in a machine session.
According to sources, the NIV lab can test about 750 samples in a day, and can scale this up to about three times, if required. The All India Institute of Medical Sciences in Delhi is also capable of performing at least 270 tests in a day, but these also need to be verified by NIV before reporting them as positive to WHO.
› There are seven types of coronaviruses, and the local laboratories use the kits that can tell them if it is a coronavirus. Once that gets confirmed, then it is sent to NIV for confirmation on whether it is novel coronavirus or not
AN ICMR SCIENTIST