It’s a race against time to produce accurate and efficient diagnostic results, says Shanti Kalipatnapu, as she walks through IISER Pune’s testing centre, one of the 1047 across India checking samples for the novel coronavirus.
Mridula Nambiar, a biologist at the Indian Institute of Science Education and Research (IISER) Pune, begins her day early to be at the COVID-19 testing centre, on a rather deserted campus of her institute – most students went home just before India’s two-month national lockdown that began 25 March 2020.
Nambiar is one of the 30-odd volunteers at the testing centre at IISER Pune approved by the Indian Council for Medical Research (ICMR) among the 21 in the city of Pune. It is unlike any other diagnostic centre since the institute, primarily engaged in undergraduate science education and research in the natural sciences, does not handle clinical or infectious samples on a normal day. However, some researchers at IISER Pune use the RT-PCR assay to decipher the inner workings of fundamental biological processes. This assay is also the key diagnostic tool for COVID-19.
Setting up a COVID-19 testing centre
Owing to this core RT-PCR expertise, when IISER Pune began to explore the possibility of setting up a testing centre, a group of faculty members from the institute’s biology department formed a COVID-19 action team. They used national guidelines to draft the standard operating procedures for the Centre. Team members used help from engineering colleagues to remodel some rooms at the institute to minimise the corridor and building space that the hospital samples would have to pass through.
Health and biosafety protocols firmly in place, the institute drew from the experiences of other already established testing centres in Pune – National Institute of Virology (NIV), Armed Forces Medical College (AFMC), National Centre for Cell Science (NCCS) – and elsewhere, to fine tune procedures and safety guidelines, and to ensure an efficient testing pipeline.
Supplies needed to create a mini-research lab of sorts – protective equipment, gloves, masks, tubes, tips, small and medium-sized lab equipment – were procured, backed by an organized inventory. A call for volunteers saw over 570 PhD scholars, undergraduate students, postdoctoral fellows, and faculty and staff members of the institute signing up. A nodal officer was appointed to coordinate the process from receipt of samples to timely submission of results and effective communication with hospitals.
Within a month and after a few dry runs, volunteer training sessions and a formal approval from the ICMR, the centre was all set to begin testing samples on 21 May 2020. Nodal Officer Anjan Banerjee says by the end of June, the centre had tested over 4400 samples.
India has tested about 8.3 million samples (by June 2020) since the beginning of the pandemic. It is widely acknowledged that more testing is essential to combat the spread of COVID-19.
How tests are done
Five teams of volunteers work in shifts of four hours. Each team of three members carry out a specific set of tasks. Hospitals send in throat and nasal swab samples in sealed tubes with a small bit of buffer solution to extract the sample into. These samples are collected from a designated location just outside the centre and handled by volunteers in room 1, equipped with level 2 biosafety (BSL-2) norms. Their task is to retrieve the buffer solution which would have extracted the essence of the swab, transfer the solution into fresh tubes, and release the viral RNA, should any virus be present in the sample. This is done by dissolving the outer lipid coat of the virus using detergents.
This RNA is then handled by volunteers in rooms 2 to 4, first to convert it into complementary DNA (cDNA) and then to amplify the cDNA to make enough material for detection. Primers that specifically bind to the COVID-19 virus are used, so that amplification (and thereby detection) occurs only if the sample originally contained the virus.
Since room 1 deals with samples that could potentially contain live virus, volunteers mandatorily wear a full set of personal protective equipment (PPE) — cover-alls, safety goggles, head and feet covers, and two layers of hand gloves. It takes them about 15 minutes to don this protective gear. In spite of the temperature and humidity controllers in the room, it gets rather hot inside the suit. Nambiar says they try and coordinate the transitions between the shifts in a way that volunteers need not be in PPE for any longer than they need to.
Since the virus is inactivated, processing of the samples beyond Room 1 is less risky and requires lesser protection. Nevertheless, it still needs utmost care as RNA is a notorious molecule to handle, with high chances of degradation and contamination.
Following RT-PCR runs, large datasets are carefully analyzed and validated by faculty members before the results are shared. A few faculty members from Savitribai Phule Pune University (SPPU) have joined the testing efforts with two more RT-PCR machines. The team tests about 250 samples every day, and plans to enhance capability by automating some steps in the testing pipeline.
The data management room of the testing centre is a great collaboration between technical expertise and administrative prowess. Managing data does not require the technical know-how of performing the tests; it however requires a keen eye to handle a screen full of lists.
From the time the samples come in to delivery of results to the hospitals, it works like a relay race. The baton needs to be passed on to the next player, with no room for error.
Volunteers in room 1 receive the hospital data sheets along with the samples. They assign a code to each sample, scan the information sheets and send them to the data room where volunteers digitize them and keep the files ready for recording the final results later in the night. When final results become available, they share it with the hospitals and feed the information onto government portals that maintain detailed records of each test conducted.
The day ends rather late for Nambiar, as it does for many of her fellow volunteers at the Centre working into the night to relay the test results to hospitals. Insitute faculty Sudha Rajamani, who has been supervising this massive exercise, says the same team of 4 to 5 members has been working seven days of the week, late into the night, with steadfast alertness keeping in mind the huge implication of accurate data for patients.
Each day, the testing centre presents a grim reminder of the lurking virus. But, it is also an exemplar of the power of collaboration, the human bond that shines through in times of crises, of what people in a community can stand up for beyond the confines of their everyday jobs.
Pictures courtesy: COVID-19 Action team, IISER Pune
(Shanti Kalipatnapu is the Head of Research Communications at IISER Pune. She can be reached at firstname.lastname@example.org and tweets from @skalipatnapu).