DNA, RNA, RT-PCR, Testing Methods, Supply Chains… and Politics

What is Reverse Transcription Polymerase Chain Reaction?

Reverse transcription polymerase chain reaction (RT-PCR) is a laboratory technique combining reverse transcription of RNA into DNA (in this context called complementary DNA or cDNA) and amplification of specific DNA targets using polymerase chain reaction (PCR). It is primarily used to measure the amount of a specific RNA. This is achieved by monitoring the amplification reaction using fluorescence, a technique called real-time PCR or quantitative PCR (qPCR). Combined RT-PCR and qPCR are routinely used for analysis of gene expression and quantification of viral RNA in research and clinical settings.

Blah Blooh Bleeh Blah. Right?

Well, this is the test that will tell us if a person has got the corona virus or not. So listen up!

The corona virus is in the form of RNA:

Coronaviruses, so named because they look like halos (known as coronas) when viewed under the electron microscope, are a large family of RNA viruses. The typical generic coronavirus genome is a single strand of RNA, 32 kilobases long, and is the largest known RNA virus genome. Coronaviruses have the highest known frequency of recombination of any positive-strand RNA virus, promiscuously combining genetic information from different sources when a host is infected with multiple coronaviruses. In other words, these viruses mutate and change at a high rate, which can create havoc for both diagnostic detection as well as therapy (and vaccine) regimens.

But as best as I can tell, detecting the corona virus becomes pretty difficult unless it turns into DNA, which can be done by a process called Reverse Transcription.

With the newly formed DNA, replicate it – have it reproduce a lot, basically. That’s where PCR comes in. And with that (and a fluroscent dye that is added to make detection easier) you have a sample that you can check for the presence of the corona virus.

The first, PCR, or polymerase chain reaction, is a DNA amplification technique that is routinely used in the lab to turn tiny amounts of DNA into large enough quantities that they can be analyzed. Invented in the 1980s by Kary Mullis, the Nobel Prize-winning technique uses cycles of heating and cooling to make millions of copies of a very small amount of DNA. When combined with a fluorescent dye that glows in the presence of DNA, PCR can actually tell scientists how much DNA there is. That’s useful for detecting when a pathogen is present, either circulating in a host’s body or left behind on surfaces.

But if scientists want to detect a virus like SARS-CoV-2, they first have to turn its genome, which is made of single-stranded RNA, into DNA. They do that with a handy enzyme called reverse-transcriptase. Combine the two techniques and you’ve got RT-PCR.

So, here’s how it works, best as I can tell:

Coronavirus Detection Steps

 

That article I linked to from Wired has a more detailed explanation, including more detailed answers about the “how”, if you are interested. Please do read it fully!

Now, which kit to use to extract RNA from a snot sample, which dye to use, which PCR machine to use – all of these and more are variables. Think of it like a recipe – different steps, different ingredients, different cooking methods. Except, because this is so much more important than a recipe, the FDA wags a finger and establishes protocol.

That protocol doesn’t just tell you the steps, but it also tells you whether you are authorized to run the test at all or not. And that was, uh, problematic.

For consistency’s sake, the FDA opted to limit its initial emergency approval to just the CDC test, to ensure accurate surveillance across state, county, and city health departments. “The testing strategy the government picked was very limited. Even if the tests had worked, they wouldn’t have had that much capacity for a while,” says Joshua Sharfstein, a health policy researcher at Johns Hopkins School of Public Health and the coauthor of a recent journal article on how this testing system has gone awry. “They basically were saying, we’re going to use a test not only developed by CDC, but CDC has to wrap it up and send it to the lab, and it’s just going to be state labs doing it.”

The effect was that the nation’s labs could only run tests using the CDC’s kits. They couldn’t order their own primers and probes, even if they were identical to the ones inside the CDC kits. And when the CDC’s kits turned out to be flawed, there was no plan B.

By the way, if you want a full list of the various protocols that are listed by the WHO, they can be found here.

Back to the Wired article:

Another in-demand approach would look for antibodies to the virus in the blood of patients, a so-called serological test. That’d be useful, because in addition to identifying people with Covid-19, it could tell you if someone was once infected but then recovered. “The better your surveillance, the more cases you’re going to catch, but even with perfect surveillance you won’t catch everything,” says Martin Hibberd, an infectious disease researcher at the London School of Hygiene and Tropical Medicine who helped develop one of the first tests for the coronavirus SARS in the early 2000s. “Until we’ve got a full test of this type of assay, we don’t know how many cases we’ve missed.”

A serological test would also probably be cheaper than a PCR-based one, and more suited to automation and high-throughput testing. A researcher in Singapore is testing one now.

Here’s an early paper on the topic, if you are interested.

Serological assays are of critical importance to determine seroprevalence in a given
population, define previous exposure and identify highly reactive human donors for the generation of convalescent serum as therapeutic. Sensitive and specific identification of Coronavirus SARS-Cov-2 antibody titers will also support screening of health care workers to identify those who are already immune and can be deployed to care for infected patients minimizing the risk of viral spread to colleagues and other patients.

As far as I can tell, this method has not been deployed at all thus far, and that applies to India as well. Here’s a Wikipedia article about the different methods of detecting Covid-19 – it’s about more than that, the first section applies here. Here’s an article from Science about a potential breakthrough.

But whether you use any variant of the RT-PCR or the serological test, given the sheer number of kits required, there is going to be crazy high demandand a massive supply chain problem.

Along with, what else, politics, and bureaucracy:

 


The Wired article is based on reporting in the US, obviously, but there are important lessons to be learned here for all countries, including India.

Here are some links about where India stands in this regard:

 

I’ll be updating the blog at a higher frequency for the time being – certainly more than once a day. Also (duh) all posts will be about the coronavirus for the foreseeable future.

If you are receiving these posts by email, and would rather not, please do unsubscribe.

Thanks for reading!

 

On India’s Constitution, Part II

I fear I have taken on more than I can handle, by starting the process of teaching myself more about India’s Constitution.

I started in the previous month with what I thought would be a rather more simple question: how did the constitution start off? What were its founding principles, its aims, its intentions? Why were these the principles, aims and intentions?

Well, if this is indeed a rather more simple question, I fear many more Mondays in the months years to come will be devoted to the entire task I have set myself: to learn more about India’s constitution.

But hey, the one thing we have is time!

So allow me to indulge myself, and devote one more Monday to the topic we covered in January 2020: understand better the founding of the Indian constitution, before moving on to other topics related to it.

I’d recommend you begin by watching this video of a speech given by Rohinton Nariman in the year 2013. It is nearly fifty minutes long, but all of those fifty minutes are worth your time. In my case, I ended up watching it twice, and if only I had time, I would watch it again. It raises many, many questions that make me want to learn more – and that is a good thing.

Here are just five things that I wanted to learn more about:

  1. B.N. Rau and the travels that he undertook before writing the Constitution,
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  2. The city of Danzig and the freedom of movement
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  3. The (to me, frankly amazing) right to property and its understanding and implementation in an Indian context
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  4. Dr. Ambedkar’s opinion about having no axe to grind as a member of the constituent assembly. It is a great way to start thinking about public choice theory, if you ask me
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  5. And how difficult the United States of America and even more so, Australia, have made the process for amending the constitution.

And believe me, I have cherry picked these five, more or less at random. There’s so much more to think about!

Second, in the post I wrote in January, I spoke about wishing I could learn more about how the constituent assembly was formed. Reading this article helped me understand that the people who wrote the constitution (the members of the constituent assembly) also were the people who ratified it!

An even more important point to note is that the Constituent Assembly was deeply involved in the drafting the Constitution itself. It met over 11 sessions and 166 days between 1947 and 1950 to discuss the Constitution. In contrast, in the US, there was a very clear separation between the drafting of the Constitution (done by the Philadelphia convention – a central body with representation from each state), and the state-level ratification conventions, which voted on it later.

This separation meant that the ratifiers did not have their hands dirty in the document, with the exception of a small minority of members who were a common presence in both conventions. They had no emotional stake in the Constitution draft and could vote on it independently. It was up to the drafters of the Constitution to convince them of this document. This is what necessitated the “Federalist Papers” – a remarkable exercise in marketing the newly proposed law of the land.

No such marketing was required in India, given that the ratifiers were the drafters too.

Useful more for trivia buffs (and I enthusiastically plead guilty to the charge) than perhaps for the topic at hand, but an informative read nonetheless is this rather long article in Scroll. On the history of constitutionalism in India:

Knowing only too well that Englishmen only counted as knowledge what Englishmen declared to be so, when Rao wrote to Napier in March 1872 to decline the seat on the Viceregal Council, he appended the relevant sections from Bowring’s Eastern Experiences, adding that nothing could be more interesting than participating in the development of “something like a constitution” wherein “a Native Administration” might be brought under “a system of fundamental principles, derived from the advanced political wisdom of Europe” albeit “carefully adapted to the conditions of the Native society”.

I am somewhat ashamed to note that it took my reading of this article to know what I should have been aware of in any case, given that I teach at the Gokhale Institute of Politics and Economics:

The most vocal was Rao’s sometime protégé and collaborator, Mahadev Ranade, whose essay, “A Constitution for Native States”, which was published in the Quarterly Journal of the Poona Sarvajanik Sabha, generated much debate and discussion. It eventually prompted a series of remarkable works detailing indigenous forms of constitutionalism.

The most prominent of these works was Kashinath Telang and Ranade’s Rise of the Maratha Power, which carefully explained how much Shivaji’s success owed to the ‘constitutional’ nature of his rule (and concomitantly, how much Maratha decline owed to Shivaji’s descendants departing from such constitutional rule).

And finally, two book recommendations, with the caveat that I myself have as yet not read either. They’re both by the same author, who is currently coordinating with the Hindustan Times to publish a series on the same topic that I am writing about on these pages:

The two books are India’s Founding Moment, and  The Indian Constitution (Oxford India Short Introductions Series). As I said, I haven’t read them myself, but did purchase them today. Why then do I recommend them? Well, one, the relevance to the topic is obvious, but also, this article from Livemint a long time ago really helped.

 

The Constitution is inevitably shaped by and shapes politics. How it does so is a question far too ambitious for my book. But something I do try to gently do, wherever I could, is suggest how certain legal decisions were shaped by the political circumstances as well as how our overemphasis on politics has prevented us from appreciating the legal significance of particular aspects of our Constitutional law.

The good news, for me, is that I get a month to try and read these two books before I tackle the subject of the Indian Constitution once again.

Once again, a tip of the hat by way of thanks to Murali Neelakantan for helpful recommendations, and a request to my readers to help out along similar lines.

India: Links for 9th December, 2019

Five rather eclectic links from a variety of issues pertaining to India. Also, my apologies about the delay in posting today! I’m traveling a fair bit, and there may be some delay in posts this week.

  1. Surjit Bhalla and Karan Bhasin present the other side of the story when it comes to the release (or lack of it) of the NSO consumption survey.
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  2. The Scroll sheds light on a little known issue today: austerity in marriages in India in the years gone past – enforced by the government!
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  3. Anupam Mannur and Pranay Kotasthane make the important, but not well known point that Bangalore needs more firms (and more people!) not less.
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  4. Via Mostly Economics, a lovely write-up about the fish traders of Madras.
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  5. 18000 birds died in Rajasthan recently. Here’s why.

Etc: Links for 8th November, 2019

  1. “Munch would have probably seen any marks from this period of the painting’s life as part of its artistic development. He wanted people to see how his works evolved and changed over their lifetime, and saw any damage they incurred along the way as a natural process, even leaving artworks unprotected outdoors and in his studio, stating ‘it does them good to fend for themselves’.”
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    I cannot for the life of me remember how I chanced upon this link – all that I remember is that it came out of an interesting Twitter thread. 10 factoids about The Scream.
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  2. “It’s called the “dinner party problem”: A table of four or fewer people may happily converse as one, but a party of five or more will splinter fairly quickly into separate conversations of two or three four people each. What is it about the number four?”
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    It really should be called the panel discussion problem. The conclusion to the short article deserves to be highlighted!
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    “It’s possible our brains evolved to manage only the conversations in which we have a chance of swaying the group to our side. Otherwise, what’s the point of talking?”
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  3. I’ll happily admit to the fact that the math is way beyond my capabilities – but it made for enjoyable viewing, if nothing else. The Mandelbulb, or the 3D version of the Mandelbrot set. This is via Navin Kabra, who should immediately be followed on Twitter.
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  4. “Are Indigenous and Western systems of knowledge categorically antithetical? Or do they offer multiple points of entry into knowledge of the world, past and present?”
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    A very interesting article in the Smithsonian on what is knowledge, and how is to be gleaned, understood and used.
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  5. A rather old, but nonetheless interesting article from Scroll on the Salim-Javed partnership breaking up.

RoW: Links for 30th October, 2019

  1. Who, exactly, are the Rohingyas? A short explainer from Wikipedia.
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  2. “With repatriation stalled, Bangladesh is now exploring relocation. The country has thus far been patient and welcoming, but its willingness to host such a large refugee population is wearing thin. Dhaka now plans to relocate about 100,000 Rohingya to a remote island at the mouth of the Meghna river in the Bay of Bengal. Known as Bhasan Char, or “Floating Island” in Bengali, the islet is made up of accumulated silt and is hard to reach—aid workers worry that anyone moved there would be vulnerable to floods, cyclones, and traffickers.”
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    A problem that the world would rather not acknowledge.
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  3. “Myanmar, which United Nations officials say should be tried on genocide charges over the orchestrated killings that began on Aug. 25, 2017, is keen to prove it is not a human rights pariah.Bangladesh, struggling with overpopulation and poverty, wants to reassure its citizens that scarce funds are not being diverted to refugees.

    But the charade at Nga Khu Ya, with its corroded buildings devoid of any Rohingya presence, proves the lie in the repatriation commitment. The place is so quiet that a dog snoozes at the main entrance, undisturbed.

    Even the repatriation center’s watchtowers are empty of soldiers. There is no one to watch.”
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    They, the Rohingyas, are to be sent back to Myanmar. Except not.
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  4. “One day in the 1980s, my maternal grandfather was sitting in a park in suburban London. An elderly British man came up to him and wagged a finger in his face. “Why are you here?” the man demanded. “Why are you in my country??”“Because we are the creditors,” responded my grandfather, who was born in India, worked all his life in colonial Kenya, and was now retired in London. “You took all our wealth, our diamonds. Now we have come to collect.” We are here, my grandfather was saying, because you were there.”
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    Suketu Mehta in fine form on this topic.
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  5. “I want you to think of free movement across borders as not just a matter of humanitarianism, not just a matter of good policy, but as an issue of civil rights, in the same tradition as those of Milk, and King, and Stanton, and indeed others yet to come.”
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    A short blog post on a longer essay, which argues about instituting immigration as a civil right.

Etc: Links for 13th September, 2019

  1. The filmy divide in India.
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  2. Man or woman?
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  3. “Bau once told Rahul Bhattacharya, in an encounter for the ages from the book Pundits from Pakistan, that the action was “all artificial”, part of a carefully created persona built to defeat batsmen. It wasn’t the bowler or the ball that beat batsmen, it was this persona. They say that about Shane Warne too, about how batsmen were dead just from the theatre of Warne at the top of his mark, but man, did it ring true with Bau.”
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    Osman Samiuddin on Abdul Qadir.
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  4. “When we seek Western fads at Indian levels of income, the economic cost of our perceived moral rectitude will be borne by the poor.”
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    On opportunity costs.
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  5. On food, history, India and Asia.