MADURAI: Most providers of essential services risk being exposed to the coronavirus when they venture outdoors. For the seven-member team at the Viral Research and Diagnostic Laboratory (VRDL) at Madurai Medical College, however, the risk lies indoors. This team suits up daily to handle and test swab samples of patients suspected to have COVID-19. The number of tests to run is so high that most of the team members have stopped going home since the lab was authorised to test for SARS-CoV-2 on March 25.
The VRDL was the eighth lab in Tamil Nadu to receive permission from the National Institute of Virology to conduct the one-step real-time Reverse Transcription - Polymerase Chain Reaction (RT-PCR) tests for COVID-19.
A wing of the Indian Council of Medical Research (ICMR), the VRDL is normally engaged in research of communicable viral diseases like dengue, malaria and works from 10am to 4.30pm. Since it became a COVID-19 diagnostic lab, it functions round the clock, the team working in three shifts running screening and confirmatory tests of oropharyngeal swab samples collected in Madurai, Sivaganga, Virudhunagar and Ramanathapuram districts.
"Presently, three batches of screening tests and one batch of confirmatory tests are being performed one after another. So far, over 5,000 screening tests and over 2,000 confirmatory tests for COVID-19 have been performed at the VRDL," an official at the Government Rajaji Hospital (GRH) said.
‘Lab is now their home’
Comprising experienced microbiologists, the VRDL team includes the principal investigator, who is administrative head of the COVID-19 diagnostic lab, co-principal investigator who is technical in-charge of the COVID-19 lab, another technical in-charge of the lab, a research scientist, a research assistant and two laboratory technicians.
While the project staff and the laboratory technicians stay at a guest house inside the medical college premises, the administrative and technical heads take turns to go home for short breaks. The laboratory has become their home now, said another GRH official.
"Since the test report is the first and most critical step in effective management of the pandemic and as it puts the laboratory personnel first in line, delivering quality test reports becomes their prime responsibility. The strenuous work hours take a back seat. Interestingly, the laboratory is busier at night as nearly two-thirds of the samples are sent for testing in the evening," the official added.
On the risks the laboratory staff face, a retired microbiologist said they face ‘sample risk’ which is the risk of exposure to virus from the samples they test. "Thus, all samples are considered infectious since the time of receipt," the scientist said. For this reason, laboratory personnel are required to wear Personal Protection Equipment (PPE) kits throughout the two-hour extraction process and N95 masks and gloves while loading and unloading samples from the thermal cycler. The laboratory premises are also disinfected three times a day, GRH sources pointed.
"For experts at this VRDL, no special training is required to test for COVID-19. This is because Chinese scientists shared the genetic sequence of the coronavirus with all countries after they isolated the strain of the virus and the genetic sequence can be replicated globally in any laboratory. Generally, it is based on the genetic sequence that a few steps adopted during any RT-PCR technique are altered," explained the retired microbiologist. At a newly-established VRDL, the technicians would require hands-on training in Coronavirus testing for a month at least, he said. .
How are the swabs tested?
The swabs are collected by otorhinolaryngologists (ear, nose and throat specialists) and placed in a Viral Transport Medium (VTM). The VTM is placed in an ice box. That box is brought to the lab’s entrance where lab staff, wearing PPE, remove the VTM from the box and take it into a biosafety cabinet. The swab is then transferred to a test tube to begin the real-time RT-PCR test which involves extraction of the viral RNA. The first stage involves removing impurities. Once that is done, the swab is transferred to a PCR tube and more reagents are added. This entire process is carried out manually and takes about two hours.
Later, chemical reagents are added to the PCR tube containing the extracted RNA and the tube is loaded into an automated thermal cycler that carries out an amplification process for two hours. It also performs a documentation process (using pre-programmed software) for about 30 minutes. Manual data entry takes another 30-45 minutes.
Each time a result comes, the test reports are compiled in specific formats and are sent to the office of the GRH Dean, the COVID-19 control room at GRH, office of the Deputy Director of Health Services, office of the Joint Director of Epidemics (Chennai), the ICMR-NIE (Chennai) and the National Institute of Virology in Pune.
According to the retired microbiologist, as many as 12 reagents are used per COVID-19 test and the thermal cyclers require a break of at least an hour everyday for smooth operation.
The VRDL has two functional thermal cyclers (usually imported from countries like Germany and Japan, costing about Rs. 15-20 lakh each) and 144 samples can be tested at one go, an official at GRH said. While it takes about six hours for the results of the screening tests to be known, it takes another six hours to derive the results of confirmatory tests. Only samples that test positive in the screening test are subjected to a confirmatory test.
"If the result of a screening test is negative, the patient is declared to be free from Coronavirus infection. But, if the result is positive, the samples are again subjected to confirmatory tests. A patient is declared to be COVID-19 positive only if the result of the confirmatory test is also positive," the microbiologist explained.
After the tests, the sample vials, viral transport mediums and the test tubes are disinfected by soaking in sodium hypochlorite solution for three hours and autoclaved before disposal. Similarly, the suits are also disinfected separately in the same solution for three hours before being disposed of in yellow bins.
Wrapped in bags, the disinfected bio-medical waste is collected in a box, sealed and then handed over to the operator of the common bio-medical waste treatment and disposal facility (CBMWTDF). Notably, the operator of CBMWTDF, who handles all the biomedical waste generated at Madurai Medical College and at Government Rajaji Hospital, collects the bio-medical waste from COVID-19 wards and from the COVID-19 testing laboratory separately. Since poor dumping methods may become a source of infection, incineration of the bio-medical waste is recommended, say experts.
Dip in infection rate
While testing at VRDL has increased, the infection rate has shown a dip, sources said. "In the initial days, the infection rate of samples tested stood at 10 per cent. Now, the infection rate observed is less than 2 per cent," said an official at GRH.
The VRDL is currently engaged in training laboratory personnel from government hospitals in Sivaganga, Ramanathapuram and Virudhunagar districts where COVID-19 diagnostic labs are to be set up soon. Sources in the Department of Health and Family Welfare said that the laboratories at the three southern districts can begin COVID-19 testing only after validation from VRDL at Madurai and NIV at Pune.
How does RT-PCR work in COVID-19 testing?