Monthly Archives: June 2020

Nature India special issue on COVID-19 is out

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For most of us, 2020 will be marked as the year of great imponderables. We seem to know as much about the new coronavirus SARS-CoV-2 and its effects on the human body and societies at large, as we don’t. Ever since the virus broke out, ‘uncertainty’ is one of the most commonly used words in conversation, news reportage and emails.

Across the globe, very few lives have been untouched by the direct or indirect effects of the novel coronavirus. China, the most populous nation on Earth, bore its brunt as the virus jumped into human populations in the country’s Hubei province in late 2019. Though China reacted quickly to contain it, the contagion had spread via international travellers.

India, the world’s second most populous nation, reported the first case of the novel coronavirus on 30 January 2020. The number of people becoming infected by the virus began to rise quickly, prompting the government to impose a two-month complete shutdown of the country – the longest ever in its history.

An enormous population, a weak healthcare system, and traditionally meagre investments in scientific research and development meant there was enough reason to worry. However, the severe economic and social fallouts, like elsewhere in the world, forced the government to allow a regulated easing out of lockdown.

Nature India started reporting on COVID-19 in India from the outset. As the pandemic began unsettling every facet of life from healthcare to education and community life to businesses, our coverage embraced a new normal, going beyond pure science to a parallel reflection of its links with society, culture and life.

Nature India’s special issue on COVID-19, therefore, seeks to consider answers from the future. In a rapidly evolving pandemic, some of the articles in this special issue bear a time stamp. However, they will hopefully remain relevant for a long time to come as chronicles of the biggest human crisis any of us has faced in our lifetimes.

As we scrutinize India’s response to the mammoth healthcare challenge, we also look at vaccines and drugs being tested across the world in a hope to arrest the respiratory infection. We dive into the science of how the immune system responds to the virus and question if submitting genome sequences to global repositories at record speeds makes any sense without accompanying patient data. We explore how the packaging of the future would look like, and explain how to care for the elderly and critically ill in times when hospitals are struggling to accommodate COVID-19 patients.

Everyone has a COVID-19 story to tell. We feature some extraordinary everyday stories — a doctor on the frontline handling COVID-19 patients in a Delhi hospital, a scientist in the southern state of Kerala who hasn’t been able to start her dream laboratory due to the lockdown, and an Arctic explorer who endured months of darkness and isolation in the north pole before coming back to a world struck by a new virus.

This special issue also features the story of Ayurveda, and why it is time for India to apply scientific rigour to the study of the ancient system of medicine. We talk of the importance of socially influential groups, scientists, and religious leaders, in spreading the right messages and scotching misinformation in a public health emergency.
In many countries including India, the pandemic is testing the limits of science and of human perseverance. It is taking a toll on our mental health – how we live, work and communicate are set to change for a long time to come.

Science will hopefully find a solution to this unprecedented human suffering soon.

[Download the Nature India special issue “COVID-19 Crisis” free here.]

(For Nature India’s continuing coverage on the the novel coronavirus and COVID-19 crisis, please visit our special page.)

A peek into a COVID-19 testing facility

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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.

Outside the COVID-19 testing centre at IISER Pune.

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.

Putting together essential supplies for the centre.

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.

Inside the testing rooms.

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.

Data management

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.

Handling data.

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 shantik@iiserpune.ac.in and tweets from @skalipatnapu).

Nature India’s latest coverage on the novel coronavirus and COVID-19 pandemic here. More updates on the global crisis here.

Nature India 2019 annual volume is out

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Cover design: Marian Karam

Critics of India’s space programme have, in the past, demanded justification for sending rockets into space while the urgent issues of poverty, unemployment, illiteracy, and poor health cry for attention and funding. India has maintained that her space programme runs on less than a tenth of NASA’s budget, making it one of the most economical in the world and producing development-based benefits for the country’s environment, weather predictions, education, agriculture, and health.

Therefore, it was surprising when India’s ambitious, but unsuccessful, voyage to the far side of the Moon in 2019 did not publicly reignite that discussion. Instead, most of the 1.3 billion-strong nation stood in solidarity with the Indian Space Research Organisation (ISRO) when the Moon lander, Vikram, lost contact with the Earth station and later crash landed. A misty-eyed Prime Minister Narendra Modi consoled a tearful ISRO chief K Sivan. The country grieved, hoping and praying there would be a successful run to the Moon in the coming years.

We capture these tears, tribulations, nail-biting drama, and the science behind India’s shoe-string-budget space programme in this year’s cover story.

Talking of the science-economy relationship, we also analyse in one of our features the direct macro-deliverables from government research funding and look at the best ways in which a resource-poor country such as India can ensure tangible benefits from each rupee spent on scientific research.

Gender issues in science have always been important in India. In this issue, we reflect on why a better balance of men and women in leadership positions could lead to higher profitability in scientific enterprises; and also shine a light on India’s gender-skewed science awards. Two stories, about an anthropologist who made important revelations about indigenous Andamanese tribes, and a biologist working on pheromones of snow leopards and tigers, offer fascinating insights into the lives of pioneering women scientists and their science. We also speak to biologist Chandrima Shaha, the first woman elected president of the 84-year-old Indian National Science Academy (INSA) in January 2020, about her vision for mentoring more women in science.

In 2019, we used the term ‘Day Zero’ for the first time to denote the dystopic water emergency that the world is facing today. That’s the day when a city’s taps dry out and people have to stand in line to collect a daily quota of water. Climate change-triggered extreme heat, drying aquifers and extreme weather events have become the new normal for much of South Asia. We look at what this might mean for children, who will continue to endure the toll of climate change for a long time to come. On a more positive note, we explore how some undaunted farmer citizen scientists are finding new ways of adapting to climate-resilient crops.

The Nature India photo contest themed ‘food’ saw breath-taking entries from across the world that demonstrate the deep links between food, health, environment, nutrition, and happiness of communities. We present some of the top entries.

Nature India annual volumes select the best research highlights, news, features, commentaries and opinion pieces published through the year. Through this thoughtful selection, the editors at Nature Research bring to our readers a ready reference of the latest in India’s science.

We look forward to your feedback.

You will find more on our our archival annual issues here: 2018, 2017, 2016, 2015, 2014 and 2007-2013. To subscribe to the Nature India annual issues, please see here or write to natureindia at nature.com.

Building blocks of life from space

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Narendra Bhandari, a planetary scientist formerly with the Indian Space Research Organisation, recollects the time when he fortuitously became part of a meteorite detective team.

Narendra Bhandari with a meteorite fragment.

We spend crores of rupees trying to go to the Moon and other planets and bring back rocks. But nature is bountiful, even lugging space debris to our door step free of cost.

I regaled in one such gift a few summers back.

Just before sunrise at 5.15 a.m. on 6 June 2016, a rock of extraordinary type fell from the skies in the farm of Bishan Mehta of the Mukundpura village. The sound woke up the whole village, located in the outskirts of the pink city of Jaipur in Rajasthan.

I was driving down from Ahmedabad to Udaipur in Rajasthan when I heard about the meteorite fall on radio. I called Rajendra Prasad Tripathi, my friend who had recently retired from Jai NarainVyas University, Jodhpur and had settled in Jaipur. Tripathi immediately went to the site and surveyed the small foot-deep pit that the meteorite had created. To his dismay, the Geological Survey of India had swiftly collected all the pieces of the 2.5 kg meteorite. Not one to give up, Tripathi went home to fetch a kitchen sieve and filtered the sand from the bottom of the pit. He found two small pitch black chips, easily distinguishable as meteorite pieces owing to their colour.

Within a day, three of us – Tripathi, Ambesh Dixit of Indian Institute of Technology Jodhpur and I – measured the pieces using Mossbauer spectroscopy- to be sure the rocks were a rare type of carbon-containing meteorite, somewhat similar to the famous rock that fell at Murchison, in Australia, in 1969. About 2.5 per cent carbon content made this black, fragile, coal-like rock a scientific treasure.

A fragment of the Mukundpura rock , about 3 cm x 2 cm. The greyish surface on the left is due to heating in the Earth’s atmosphere. Dark black colour of the interior suggests presence of carbon, which contains organic molecules including amino acids, the building blocks of life. Mineral grains appear white.{credit}Anil Shukla{/credit}

When we analysed the minerals and chemical composition, it became clearer that this was going to be an important rock to study. Soon, we embarked on a detailed study with N.G. Rudraswami and colleagues at the National Institute of Oceanography, Goa, and found several amino acids in it. Amino acids, the chemical molecules from which biomolecules can be formed, are the building blocks of life.

We found evidence of water activity on various silicate minerals indicating the presence of abundant water on the asteroid where this rock had been lying for most of its life time, till it was kicked off by another space rock to come to Earth. Isotopes of carbon and nitrogen confirmed its extraterrestrial origin from the interstellar space.

M. S. Kalpana at the National Geophysical Research Institute, Hyderabad soon joined the effort, bringing a different set of expertise and technically sophisticated machines to complete the description of the extraterrestrial rocks. The team work paid off and using many techniques of mass spectrometry and gas chromatography, we were able to identify over 40 organic molecules of polyatomic aliphatic and aromatic hydrocarbons, including some fatty acids, and naphthalene.

These molecules are formed in the interstellar clouds from which our sun and planets were made 4.5 billion years ago. It is surprising that these organic molecules, easily destroyed at high temperature, survived the chaotic and complex processes in the severe environment that resulted in the formation of the Earth. Obviously the rock had not gone through much heating, may be it stayed below 100 degrees Celsius on the asteroid harbouring water, which saved the organic molecules, albeit with some alteration.

Hundreds of meteorites fall on the Earth every year, but what we received were among the rarest of rare rocks – only five such have fallen in India, the last one about 75 years ago. The Mukundpura rocks are now kept at Geological Survey of India museum in Kolkata.

These messengers from space packed with valuable information can tell us how life appeared on the earth. Together, we found over 15 heavenly rocks of different types in the past 30 years, many of which are described in my book Falling Stones and the Secrets of the Universe.

Strange rocks, like the ones that fell at Piplia Kalan and Lohawat in Rajasthan, tell different stories of their origin from different asteroids and their journeys to Earth. They increase our horizon of knowledge on space and fetch us extraordinary material for laboratory studies. These rocks tell us fascinating storiess of how it all began — the formation of the Sun, Earth, planets and life.

(Narendra Bhandari can be reached at nnbhandari@yahoo.com.)