Vaccine trials take 6 to 9 months: WHO Chief ScientistSoumya Swaminathan says candidate must meet efficacy and safety standards06/07/2020

Soumya Swaminathan

Days after the Indian Council of Medical Research issued a letter calling for fast-tracking the trial process of Bharat Biotech’s COVID-19 vaccine, Chief Scientist at the World Health Organisation Soumya Swaminathan said a vaccine trial usually takes at least six months to complete.

“A realistic (but very optimistic) timeline from the start of Phase-1 to the completion of Phase-3 [trials] could be about six to nine months (if all goes exactly according to plan),” Dr. Swaminathan told The Hindu, responding to questions via email.

On the specific question of whether Phase-3 trials can be skipped for making the vaccine available for public use in light of the pandemic, Dr. Swaminathan said: “Any vaccine must demonstrate efficacy and safety on a sizeable number of participants. The WHO has published target product profiles for a COVID vaccine [and] immunogenicity data alone would be insufficient for a vaccine use policy. It is possible to have protocols which flow seamlessly from Phase-2 to Phase-3 based on interim analysis of data.”

After scientists and experts raised serious concerns over the ICMR’s communication, the nodal agency issued a clarification saying the letter was meant only to “cut unnecessary red tape” and “speed up recruitment of participants”. Experts globally have been saying it would take at least 12 to 18 months to launch a vaccine for COVID-19.

Bharat Biotech has got an approval to conduct only the Phase-1 and Phase-2 trials.

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The impact of the Chinese apps banHow popular are these apps in India? Can the government’s move be challenged legally?05/07/2020

The story so far: In the wake of the face-off with Chinese forces on the India-China border in Ladakh, and a violent clash on June 15 that left 20 Indian soldiers dead, the Indian government on June 29 banned 59 apps of Chinese origin, citing data security and national sovereignty concerns. These include popular ones such as TikTok, SHAREIt, UC Browser, CamScanner, Helo, Weibo, WeChat and Club Factory.

Why were the Chinese apps banned?

The Ministry of Electronics and Information Technology in a press release asserted that it had received “many complaints from various sources, including several reports about misuse of some mobile apps available on Android and iOS platforms for stealing and surreptitiously transmitting users’ data in an unauthorised manner to servers which have locations outside India”.

The Ministry said it had decided to block the 59 apps to safeguard the “sovereignty and integrity of India”, invoking powers under Section 69A of the Information Technology (IT) Act read with the relevant provisions of the Information Technology (Procedure and Safeguards for Blocking of Access of Information by Public) Rules 2009.

The government also said that several citizens had reportedly raised concerns in representations to the Indian Computer Emergency Response Team (CERT-In) regarding security of data and loss of privacy in using these apps. In addition, the Ministry said it had also received “exhaustive recommendations” from the Home Ministry’s Indian Cyber Crime Coordination Centre.

And while the government did not name China openly in its action against the apps, public comments by officials including Ravi Shankar Prasad, the Union Minister for Communications, Electronics and Information Technology and Law and Justice — he asserted that the ‘digital strike’ was done “for safety, security, defence, sovereignty & integrity of India and to protect data & privacy of people of India” — signalled that it was aimed at Chinese economic interests.

How large is the user base in India for these banned apps?

Estimates by Sensor Tower show the video-sharing social networking app, TikTok, for instance, has seen about 611 million downloads in India over the app’s lifetime, while estimates of active users vary with the highest pegged at 200 million. According to media reports, file-sharing tool SHAREIt has about 400 million users. Statcounter places the Alibaba-owned UC Browser second in India market share at 10.19%, after Google Chrome (78.2%). Other reports estimate its user base at 130 million.

How will users be affected?

Installed apps may continue to exist on mobile devices. But now that the latest versions of the apps have been removed from Google’s Play Store and Apple’s App Store, users will not be able to access updated versions in future. If a notice goes out to internet service providers asking that data flow from these apps be halted, that could impact the functioning of existing, installed apps.

What are the alternatives and are they easy to find?

Users of banned browsers or video apps may find it easier to shift to similar offerings from elsewhere. Chingari, a competitor from India to TikTok, saw its downloads soar from 1 lakh to 1 crore-plus on Google Play Store soon after the ban on Chinese apps was announced.

Users of some apps such as CamScanner may not be able to shift so easily. For example, it is not clear yet how say a pdf, or portable document format, created by a user via CamScanner a couple of years ago and backed up in Google Drive, could be transferred to another app such as the Adobe Scan or Microsoft Office Lens, unless individually downloaded and re-uploaded.

There are some alternative products such as the India-made Zoho Doc Scanner, which does offer users the option to import all files en masse from CamScanner.

How does the ban affect Chinese app providers?

The potential loss of advertising revenue impacts app-makers. Tik Tok’s parent ByteDance Ltd. recorded a doubling of global revenue to $17 billion in 2019, over the previous year, with $3 billion in profit.

Its India business may have yielded only $5.8 million in revenue for the year ended March 2019, but with quicker user adoption more recently, the stakes seem to be getting higher. When TikTok was banned briefly in India last year on the grounds that it reportedly promoted pornography, the company had told a local court that it was losing roughly $15 million a month due to the ban, according to a Reuters report. The app had subsequently been permitted to operate.

What has China’s response been to the ban?

China has said that it suspects India’s actions could be in violation of the World Trade Organization (WTO) rules. In a statement, the Chinese Embassy in New Delhi said, “India’s measure selectively and discriminatorily aims at certain Chinese apps on ambiguous and far-fetched grounds, runs against fair and transparent procedure requirements, abuses national security exceptions, and [is suspected] of violating the WTO rules. It also goes against the general trend of international trade and e-commerce, and is not conducive to consumer interests and the market competition in India.”

The Chinese government’s comments indicate that it could file a formal complaint at the WTO.

Will the move hurt India?

It could, in terms of investments and employment. ByteDance Ltd. had talked of upcoming investments worth $1 billion in India. That will probably remain suspended till further clarity emerges, potentially impacting job creation.

What legal options does the Indian government have?

In terms of process, there are two options available to the government under Section 69A of the IT Act to issue ban orders — normal and emergency. In the case of the ban on the 59 apps, based on the use of the phrase “interim order” in the statement issued by TikTok, it appears that the government may have adopted the emergency route. The emergency route allows content to be blocked on the directions of the Secretary, Department of IT, who must consider the impugned content and record his reasons for doing so. In the normal course, an order to block content requires: (a) a decision to be made by a government committee (b) relevant intermediaries to be given an opportunity to be heard by this committee.

These processes are not required when emergency provisions are used. However, in the case of emergencies, the order of the Secretary, Department of IT, must be placed before the government committee within 48 hours. Based on the recommendations of this committee, the order can then be finalised or vacated.

Does the government necessarily have to publish the order?

The legal order that empowers the designated authority to implement the ban is yet to be made public.

Rule 16 of the Blocking rules requires strict confidentiality to be maintained regarding blocking requests, complaints received, and actions taken. However, policy experts such as Rishab Bailey, a technology researcher with the National Institute of Public Finance and Policy, believe that this provision primarily applies to intermediaries (through whom blocking is implemented). He points out that the government ought to disclose the orders passed (subject to relevant redactions that may be required) in the interests of transparency and accountability.

Also, and as recognised by the Supreme Court recently in the Anuradha Bhasin case (in the context of Internet suspensions ordered under Section 144 of the The Code Of Criminal Procedure), publishing such orders is the only way in which the reasons and rationale for the decision can be judged. Challenging the decision-making process requires the reasoning to be made public, Mr. Bailey said.

Can the order be challenged in an Indian court?

Though it is unlikely that the companies concerned may take such a step immediately, either they or any affected individual in India could challenge the blocking orders in court.

The courts will then decide whether the government has provided sufficient explanation as to the nexus between what these apps are alleged to be doing and the reasons adduced by the government such as protection of national security and strategic interests. Courts will also consider if the ban is a proportionate and necessary step to be taken, given the facts at hand.

According to Mr. Bailey, another factor to be considered is whether the process for blocking under Section 69A of the IT Act contemplates blocking of content (or apps) on grounds of privacy violations.

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IITM: Converting written text to synthesised speechResearchers are developing the technology for 13 languages05/07/2020

Automated conversion: Changing text to speech is very useful, especially for online classes. Getty Imagesismagilov

Automated conversion of the written text to spoken form is very useful, especially in this time of online classes. Having lectures originally presented in English made available in all Indian languages has obvious uses. A group from the computer science department of Indian Institute of Technology Madras is working on this. The researchers are developing the technology to enable text-to-speech conversion for 13 Indian languages: Assamese, Bodo, Bengali, Gujarati, Hindi, Kannada, Malayalam, Manipuri, Marathi, Odia, Rajasthani, Tamil, Telugu and their corresponding Indian English flavours. A study on this was published in the journal IEEE/ACM Transactions on Audio, Speech,and Language Processing.

Indian languages

In order that the synthesised speech sound as natural as possible, and close to a sentence that has been read out by a human being, there is a need to convert punctuations into pauses of suitable lengths. This is the approach when converting English language text into synthesised speech. When applying this to Indian languages, the first difficulty one encounters is that there are no punctuations, save the period. There are many such differences, “The longest English sentence could be about 6 seconds long, while in Indian languages sentences can last as long as 30 seconds,” says Hema A. Murthy from the Computer Science and Engineering department of IIT Madras who led the study. Such long sentences are essentially phrase-based, the researchers found, and each phrase is almost a complete unit.

In the study, voice professionals – news readers and radio jockeys – were made to read out text carefully selected to be representative of various fields. “The audio signal and the text were aligned including pauses. Text was syllabified using rules, and syllables and pauses were identified in the audio using acoustic properties,” explains Prof. Murthy in an email to The Hindu. “Since the text and audio are aligned at the syllable-level, computing syllable-rate, number of syllables between pauses was straightforward,” she adds.

Domains covered

An hour of speech contains about 350-400 sentences. The researchers collected 10 hours of data for every language. “Five hours of data was used for hypothesising, and a set of held out sentences from the database was used for testing the hypothesis,” says Prof. Murthy. The text sentences were chosen in such a way that maximum domain coverage is ensured. “This includes news, sports, fiction, etc, as we work on open domain text-to-speech synthesis systems,” adds Jeena J Prakash from Uniphore Software Systems, IITM Research Park, Chennai, who is the first author of the paper.

Phrase-based synthesis

Using these inputs, the text is split into phrases using the findings. “A phrase location–based speech synthesis system was built [which delineates the first phrase, last phrase and middle phrases]. The phrases of the text were synthesised using the appropriate phrase-based synthesis systems.

The synthesised waveforms were concatenated,” explains Dr Prakash.

The results were tested on listeners to get a subjective evaluation. The original spoken sentences and the synthesised sentences were played out in random order. They found a uniform improvement across all Indian languages. “Currently we are part of a consortium on building speech-to-speech systems, where the objective is to replace the audio in the NPTEL/Swayam Lectures (in English) to vernacular,” says Prof. Murthy.

How a fungus grows inside a bug, goes on to kill and feed on itResearchers have now found these fungi for the first time in central India05/07/2020

Walking dead: The fruiting body sprouts out from between the insect’s thorax and head, and the fungus takes its nutrition.

When you are an Ophiocordyceps fungus, your life is straight out of a sci-fi movie: Infect a bug, eat from inside, kill it, sprout out and target the next bug. Researchers have now found this fungi (Ophicordyceps nutans) for the first time in central India and show how it infects a stink bug. They also explore the potential of using these fungi as biopesticide and medicine.

It was early summer in 2018 when a team from Pandit Ravishankar Shukla University in Raipur set out on a plant survey at the picturesque Kanger Valley National Park in Chhattisgarh. “By chance we stumbled upon the fungus and dead bug and wanted to study it further. Morphological studies showed that it was Ophicordyceps nutans which has been reported in India only from the Western Ghats,” says Jai Shankar Paul, from the University’s School of Studies in Bio-Technolog, the first author of the paper published in the Proceedings of the Zoological Society.

The fungus was found on its specific host insect Halyomorpha halys. Also called the stink bug, this insect is a pest to forest trees and agricultural crops. The simple but scary modus operandi of the fungi involves infecting the insect when alive, developing fungal mycelium inside its thorax, and when it is time for the spores to come out, kill the bug.

The fruiting body sprouts out from between the insect’s thorax and head, and it continues to take nutrition from the dead body. The fungi are very host-specific, so the spores travel and infect many more stink bugs.

Dr. Paul adds that more studies are needed to understand in detail about the behaviour, mode of action, and exact interaction of the fungus with the insect.

Previous studies have shown that these fungi can be used as a biological pest control agent. The stink bug is known to damage the flower and fruits of soybean, green beans, apple, pear, and the team write that exploring these fungi as a pesticide will help reduce the harmful effect of chemicals in our fields.

“The more interesting and important point to note is that several species of the Ophiocordyceps fungi have medicinal properties. Reports have shown that China has been traditionally using it. Also, in the Western Ghats, the local people use these fungi as an immune stimulator,” adds corresponding author Professor S.K. Jadhav.

The authors say that studies from across the globe have noted that these fungi is rich in biologically active metabolites, vitamin C, phenolic compounds, and also has anti-inflammatory and antioxidant properties.

They also claim that it contains a component called ‘cordycepin’ which has anticancer properties. The fungi can be grownin lab settings and explored further, says the team.

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Detecting RNA virus in saliva samples using Raman spectroscopyThose positive for RNA virus can be tested using RT-PCR05/07/2020

Essential lines: Analysis of 1,400 spectra from each sample, showed that 65 Raman spectral features were adequate to identify the viral positive signal.

If Israel developed a spectroscopy-based one-minute breath-analyser to detect coronavirus, a team led by Amit Dutt from the Mumbai-based Tata Memorial Centre has turned to Raman Spectroscopy to detect RNA viruses present in saliva samples. It is a proof-of-concept study to analyse non-infectious RNA viruses using conventional Raman Spectroscopy without using any additional reagent to enhance the signal.

It has been reported that novel coronavirus is found in sufficient numbers in human saliva. For the study, the researchers spiked saliva samples with non-infectious RNA viruses and analysed it with Raman Spectroscopy. They analysed the raw Raman Spectroscopy data and compared the signals with both viral positive and negative samples. Statistical analysis of all the 1,400 spectra obtained for each sample, showed a set of 65 Raman spectral features was adequate to identify the viral positive signal. “Interestingly, most of the spectra were specific for the RNA molecule,” says Dr. Dutt. “We confirmed our finding by adding an enzyme that specifically degrades RNA molecule — the RNase — in presence of which the 65 spectra–based feature was completely abrogated that didn’t happen in presence of DNase or proteinase. We thus confirmed that the signal came from the RNA contributed by the intact virions,” says Dr. Dutt.

The signal set has 92.5% sensitivity and 88.8% specificity. The results are published in the Journal of Biophotonics. Dr. Sudeep Gupta, Director of TMC is a co-author of the paper.

Free downloads

To minimise variability and automate the analysis of the Raman spectra for RNA viruses, they developed an automated tool — RNA Virus Detector — using a graphical user interface. The tool can be used for detecting RNA virus from an individual or a group of samples in an unambiguous and reproducible manner, and is freely downloadable.

“This tool, the first of its kind, takes raw data from a Raman Spectrometer analysis based on the 65-spectra signature and provides an objective output if viral RNA is present or absent in the sample,” says Dr. Dutt.

“This conceptual framework to detect RNA viruses in saliva could form the basis for field application of Raman Spectroscopy in managing viral outbreaks, such as the ongoing COVID-19 pandemic,” they write.

Since the tool can only identify RNA viruses and not identify the specific one, it can be used only for screening. “The RNA virus detected could be a common cold virus as well or any other RNA virus such as HIV. It doesn't look for COVID-19 viral-specific signature,” he explains. The advantage is that the tool can be taken to the field and people who test positive for RNA virus can be quarantined while another sample may be sent for validation using RT-PCR.

“This whole process of data acquisition and analysis can be performed within a minute. Since no additional reagent is needed there is no recurring cost. A portable Raman spectrophotometer installed at the port of entry such as airports or any point of care can screen passengers within minutes,” he adds.

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Meta-analysis does not support continued use of point-of-care serological tests for COVID-19Governments should stop contemplating the use of serological tests to issue immunity certificates05/07/2020

Shaky base: A systematic review of 40 studies of antibody testing for novel coronavirus has found major weaknesses in the evidence base for serological tests.REUTERSTOM BRENNER

Serological tests to detect antibodies against novel coronavirus (SARS-CoV-2) could improve diagnosis of COVID-19 and be useful tools for epidemiological surveillance. These have been seen as a tool to issue immunity passports or certificates so that already-infected people can move around freely. There has been increasing number of serological tests, and many are being marketed for point-of-care use.

A systematic review and meta-analysis of 40 studies of antibody testing for novel coronavirus (SARS-CoV-2) has found “major weaknesses” in the evidence base for serological tests. The “evidence does not support the continued use of existing point-of-care serological tests for COVID-19”, says a study published in The British Medical Journal.

Risk of bias

The study found that the available evidence on the accuracy of serological tests is characterised by risks of bias, and estimates of sensitivity and specificity are unreliable and have limited generalisability. The evidence is “particularly weak” for point-of-care serological tests.

The team led by Dr F. Ahmad Khan from the Respiratory Epidemiology and Clinical Research Unit, Research Institute of the McGill University Health Centre, Montreal, Canada has said that caution is warranted while relying on serological tests for clinical decision making or epidemiological surveillance. And they say, “current evidence does not support the continued use of existing point-of-care tests”.

Immunity certificates

The study warns: “Our findings should also give pause to governments that are contemplating the use of serological tests — in particular, point-of-care tests — to issue immunity certificates or passports.”

A linked editorial also echoes the authors’ views on using serological tests for decision-making. The editorial says: “The key message of the review aligns with the conclusion of another systematic review published last week: serologic assays for SARS-CoV-2 antibodies, especially point-of-care tests, are not ready for widespread use by clinicians, the general public, or policy makers.”

Primary outcomes

The primary outcome of the analysis was to evaluate the overall sensitivity and specificity based on the method of serological testing — ELISA, lateral flow immunoassays (LFIAs), or chemiluminescent immunoassays (CLIAs), and immunoglobulin class (IgG, IgM or both).

The secondary outcomes of the analysis were to evaluate the sensitivity and specificity of the tests within subgroups defined by study or participant characteristics, including time since symptom onset.

The study found high risk of patient selection bias in 98% (48/49 studies) of assessments, and high or unclear risk of bias from performance or interpretation of the serological test in 73% (36/49) of studies. Only as little as 10% (4/40) of studies included outpatients.

Pooled sensitivity

However, the pooled sensitivity and specificity were estimated for each serological tests. The pooled sensitivity of ELISA measuring IgG or IgM was just 84.3%. But for all methods of serological testing, the sensitivity increased — 69.9% to 98.9% — when the testing was carried out at least three weeks after symptom onset compared with within the first week (from 13.4% to 50.3%).

But they warn that even when the sensitivity estimates were higher at later time points — third week or later — important false negative rates were found. “In people with COVID-19 who are tested three weeks after symptom onset, ELISA IgG will misclassify 18% as not having been infected and LFIA IgG will misclassify 30%,” they write.

“For each test method, the type of immunoglobulin being measured — IgM, IgG, or both — was not associated with diagnostic accuracy. Pooled sensitivities were lower with commercial kits and in the first and second week after symptom onset compared with the third week or later. Pooled specificities of each test method were high,” they write.

Word of caution

But the editorial cautions that pooling sensitivities makes it “difficult to determine how well tests perform at detecting antibody” in the course of illness whether undertaken early or late in the illness. The ability to identify individual tests that might perform well in testing algorithms is also hindered.

The study found many shortcomings in the case of LFIA serological tests, leading to say that LFIA should not be used beyond research and evaluation purposes.

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A sponge-like single-cell ancestorHow animals evolved from a simple life-form05/07/2020 The Smithsonian

 Institution, in the U.S., discussing the earliest form of life on earth, points out that an environment devoid of oxygen, and high in methane, was not fit for animal life, though it could ‘host’ microorganisms which could cope with the incoming sunlight and use it to generate energy for living. This was around 3.4 billion years (Byr)ago, about 1 Byr after the Earth itself was born. In the process, these microorganisms generated the gaseous waste product called oxygen. About 2 Byr later, thanks to this ‘great oxidation event’, the amount of oxygen on Earth became an important component of the Earths’ surface, and amenable for animal life.

Using this oxygen as external energy, animal cells can produce their food for growth and multiply. In order to do so, their body anatomy and biology needed to change. (An excellent summary of the origin and the need for ‘multicellularity’ is given by T. Cavalier-Smith in Proceedings of the Royal Society B, February 5, 2017,). He also points out why a unicellular organism, Choanoflagellate, can be used as the model to study the evolution and diversification of animals such as humans, consisting of multi-cell body parts such as tissues and organs. Choanoflagellates are the closest living relatives of animals that appeared nearly a billion years ago. Thanks to recent genome sequencing efforts, they have been shown to possess some key processes, such as cell signalling, cell–cell adhesion, that were thought to be present only in multicellular animals.

Avoiding mistranslation

Over time, animal cells also evolved to produce increased amounts of molecules called reactive oxygen species (ROS), which are involved in many essential cell activities but toxic at high levels. The ROS play an essential role as signalling molecules in processes such as immunity, stress response and development. In addition, more complexity necessitates a substantial increase in the genome size of the animal with concomitant increase in all transactions in the cell: DNA, the genetic material in the cells of the various organs, their transcription of the information to messenger RNA (mRNAs), then translation of these into the amino acid sequences that make individual proteins in the cells through what are called tRNAs — at least one per amino acid. These increased number of tRNAs, from around 50 in a typical bacterium to a few hundred or more in animals, means they must be selected carefully with minimal errors.

If a wrong interpretation of the genetic code at the protein level occurs, it will lead to functional disorders and even diseases. (For example, substitution of one ‘wrong’ amino acid in place of the right one can change the shape, size or the solubility of the protein, leading to what Linus Pauling has called ‘molecular disease’. One amino acid change in haemoglobin can lead to anaemia, one wrong amino acid in the proteins of the eye lens can lead to cataract). In order to avert such ‘mistranslation’ into the wrong amino acids in the resultant protein, cells do contain enzymes that help remove the incorrect amino acid. It is on this aspect of ‘proofreading’ enzymes in animal cells that a recent publication by Rajan Sankaranarayanan and his colleagues from the Centre for Cellular and Molecular Biology (CCMB), Hyderabad, has focused on. Their research findings titled: “Genomic innovation of ATD alleviates mistranslation associated with multicellularity in Animalia”, are published in the journal eLife, on May 28, 2020 (Kuncha et al. eLife2020;9:e58118. DOI: https://doi.org/10.7554/eLife.58118).

Proofreading enzyme

This intriguing title made me talk to Dr Sankaranarayanan, and here is how he explained it. His group has found such a proofreading enzyme which is Animalia-specific called ATD, which removes the amino acid alanine (A) from tRNAs which are supposed to carry another amino acid threonine (T), thus restoring proper protein synthesis and hence normal function in the cell. They further showed that animal cells also carry another enzyme called ThrRS which performs similar activity as ATD, though at high ROS levels in the cell, this enzyme loses its activity. The enzyme, ATD, appears to be stable even at high ROS levels in cells.

These results were confirmed by them in the laboratory, using human kidney cells and mouse embryonic stem cells. Knocking out this gene from cells, using the newly available genome editing technology called CRISPR-Cas9, resulted in global protein misfolding leading to cell death. Strikingly, they could also identify the molecular reasoning behind the above phenomenon.

They show that indeed alanine was wrongly substituted for threonine in multiple places in proteins that are made in cells devoid of ATD. They will now have to check the specific role of ATD in tissues with high levels of ROS, such as testes and ovaries. The group points out that the increased number of a particular group of tRNAs, which resulted in the mistranslation problem in animals, may even have evolved the potential to be involved in other functions beyond translation, such as epigenetics, programmed cell death (apoptosis) and even fertility. These are to be examined in greater detail.

Shaping evolution

Lastly, does the proofreader ATD exist in the model animal Choanoflagellate and perform a similar function? The answer is yes, as Kuncha and coworkers write: “One such enzyme,called ATD, is only found in animals. ... Further studies found that ATD originated around 900 million years ago, before Choanoflagellates and animals diverged, indicating these enzymes might have helped to shape the evolution of animals”. In other words, this sponge-like single cell is the ancestor of all animals on earth, including us, humans. Truly a humbling thought!

What about plants and trees? That is another story.

dbala@lvpei.org

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