Devising solutions in the wake of a pandemic

During the early months of 2020, researchers from TIFR Hyderabad began working on strategies to arrest the spread of COVID-19. Here, we list some of the research and training efforts.

Standardisation of a colour-based assay for visual detection of SARS-CoV-2 RNA

With an increase in the number of COVID-19 cases, a wide availability of quick and accurate diagnostic tests became the need of the hour. Sreejith R., Deepa Balasubramanian, Sunayana Sarkar and Manish Jaiswal standardised a colour-based LAMP assay that can detect the presence of SARS-CoV-2 RNA in 30 minutes. The results of this assay are determined by a characteristic change in colour after the reagents are added to the sample. This test addressed two bottlenecks: time and associated costs. RT-PCR based tests require around 6-8 hours for the reaction, in addition to an expensive experimental set up.

This team of researchers from TIFR Hyderabad collaborated with Dr. Madhumohan Rao K. from the Nizam’s Institute of Medical Sciences and ESIC Hospital-Medical College, Hyderabad.

Dr. Rao validated this LAMP-based assay against positive and negative samples.

Development of a low-cost rechargeable N95 mask and a testing device to determine the quality of masks

Conventional N95 masks have the capacity to filter out very small particles, around 0.3 microns in size, with 95% efficiency. Particles are trapped by the mask in two ways: a mechanical barrier created by the fibre and an electrostatic charge on the mask surface. The electrostatic charge on the surface erodes away with repeated usage, consequently reducing the ability of the mask to trap particles. A team of researchers- Stelbin Peter Figerez, Sudeshna Patra, G. Rajalakshmi and T. N. Narayanan- came up with a solution by modifying the commercial N95 mask to create a low-cost, rechargeable and thus, reusable N95 mask. This improvisation includes inserting a layer of graphene oxide based paint that allows the electrostatic charge on the mask surface to be regenerated via simple mechanical movements such as

when one moves their jaw. While developing this mask, the researchers (with the support of Aathif Ahmed) also directed their efforts towards building a user-friendly, low-cost mask testing device using sensors that are easily available in the market.

– Developing an open-source version of a fluorescence detector

RT-PCR based COVID-19 diagnostic tests, though most accurate, are time-consuming and expensive. One of the factors contributing to this cost is the expensive quantitative PCR (qPCR) machine. After signing up for the institute’s COVID-19 Diagnostic Training Programme, Parswa Nath, a graduate student in physics, started wondering why the qPCR machine was so expensive. The extent of diagnostic capabilities would depend on the availability of such machines and that prompted him to consider alternatives to the existing model.

A qPCR machine consists of two major components:
– a thermal cycler that amplifies segments of genetic material, and
– a detector which quantitates fluorescence emitted by processed samples in PCR tubes.

While an open-source version of the thermal cycler exists, there was no such equivalent for the fluorescence detector. With the help of his colleagues- G. Rajalakshmi and Pranav R. Shirhatti- Parswa used an LED as an excitation source and a general purpose photodiode to convert the fluorescence from the samples into an electrical signal. He used amplifiers to boost the strength of this signal. Finally, he programmed a microcontroller to perform ‘phase-sensitive detection’, a process by which one can single out the faint fluorescence emitted from the samples. This step confers sensitivity to this machine allowing it to detect the faint signal which is usually buried by other brighter sources (such as light from surroundings). Preliminary data shows that this detector is sensitive enough to quantitate different intensities of fluorescence. This seems to satisfy the requirements to monitor a typical PCR amplification even in ambient lighting conditions.

– COVID-19 diagnostic training programme

Training more professionals in COVID-19 diagnostic skills is crucial for expanding and strengthening India’s COVID-19 testing capabilities. TIFR Hyderabad, Foundation for Innovative New Diagnostics (FIND), PanIIT Alumni Reach for India (PARFI), and National Institute of Immunology (NII) worked together to form a well-rounded training module on COVID-19 testing methods and laboratory practices, especially biosafety protocols. This training module is being followed up by an assessment of acquired skills and a training experience at the COVID-19 diagnostic lab at ESIC Hospital, Hyderabad.

The institute appreciates the efforts of all the students and scientific officers (Sreejith R., Deepa Balasubramanian, Gopalakrishna R.) who have been involved in the COVID-19 related research and training initiatives and

have worked tirelessly with utmost sincerity throughout these challenging times.

*Descriptions modified from press notes released by the institute.