Mridul K. Thomas - Covid

ecology - phytoplankton - functional traits

26/11/201

26/4/2022

It's early days and there's lots of checking to be done. But the new variant detected in South Africa really could be the next Delta. Unless there's been some weird mistake or large bias in the data (not impossible), I expect some border closures & associated chaos in the coming weeks.

Also: just 10% of Africa has had at least one dose. We are continuing to fail them.

A helpful set of threads about the variant from scientists working on it already: https://twitter.com/AdamJKucharski/status/1464012926633840640?fbclid=IwAR1N6VBixJRHh7czxQg-ETrDCGqGZh15HyWRqycfg8H1_GNOcrevMUPbSiQ

EDIT: Just *hours* after I posted this, travel restrictions were being put in place. Wild.

31/07/2021

26/4/2022

You've probably seen lots of reports of 'breakthrough infections', people who have been vaccinated but have still been infected with Covid. The more alarming reports talk about vaccinated people being hospitalised and dying and suggest that we are on the cusp of losing protection. This is wildly misleading.

Vaccines are doing a fantastic job at protecting. The protection we are seeing in real life [EDIT: especially for serious cases & deaths] is very close to what was expected based on the vaccine trials. There is a modest decrease because the Delta variant is worse.

Imagine a population of 100 people, with 90 vaccinated and 10 unvaccinated. All get exposed to the virus. If 5 vaccinated people and 5 unvaccinated people get infected, the story is not "Half of all infected people are vaccinated!". It's that the infection rate is about 10 times higher among the unvaccinated: ~6% among the vaccinated (5/90) but 50% among the unvaccinated (5/10). This is roughly the situation developed countries are in now.

As vaccination increases, the proportion of new cases among the vaccinated will increase as well. If everyone was vaccinated, by definition 100% of all new cases would be among the vaccinated - but there would be very few cases and very few would die! Communicating this properly is desperately important to get the remaining unvaccinated on board, and to maintain some perspective when deciding on other protection measures.

Get your vaccines so that you are protected and protect those around you - especially the immunocompromised, many of whom cannot get vaccinated or get less protection from vaccines. And so we can finally focus on vaccinating the billions that are desperately waiting (less than 2% of Africa has been fully vaccinated) instead of this stupid personal liberty debate that is sucking up so much attention.

21/06/2021

26/4/2022

A handful of journalists are painstakingly collating data to calculate excess deaths in India. A few of the best-run states are showing excess deaths ~6 times higher than the official covid death count in the past year. That rises to ~40 times higher in some of the worse-run states.

If we treat those multipliers of 6 and 40 as lower and upper bounds and apply it to the whole country, that's between 2.4 million and 16 million excess deaths. The best-run states have a smaller fraction of the population, so the real number is probably closer to the upper end.

So perhaps 5-10 million deaths in India is what we are looking at, with values both below and above being plausible. For comparison, the official death toll for the whole world is about 4 million right now.

Caveats:
(1) this is a crude extrapolation from ~5 states to the country,
(2) the underlying data quality is unclear to me; these journalists seem diligent but I haven't investigated their methods in detail and there is more variation from year to year than I'd expect,
(3) some of these estimates actually end before the worst of the recent covid wave, so they are likely underestimates, but
(4) there are some other biases that cut the other way. And
(5) not all of these deaths would have been directly because of covid, but indirect deaths - such as through loss of access to medical services - matter too.

EDIT: The numbers above imply that in the last 15 months, about 50-100% more have died each day as compared to the pre-covid period. The 'normal' pre-covid death rate seems to be ~26000 per day. If you use my very crude estimate of 5-10 million deaths and assume that the pandemic has been in India since April 2020, there has been an additional ~11000 - 22000 deaths per day since then, a ~43-86% increase.

Updating this list of articles about those -level excess mortality estimation (h/t to Rahul for the UP link):
https://scroll.in/.../madhya-pradesh-saw-nearly-three... (Madhya Pradesh, 42X)
https://www.article-14.com/post/untitled-60cf605395758 (Uttar Pradesh, 43X)
https://www.thenewsminute.com/.../karnataka-recorded-102... (Karnataka, 5X)
https://www.thehindu.com/.../excess.../article34870624.ece (Karnataka, 6X)
https://scroll.in/.../assam-saw-28000-more-deaths-than... (Assam, 30X)
http://maths.mdx.ac.uk/.../modelling.../andhrapradeshifr/
https://scroll.in/.../andhra-pradesh-saw-400-increase-in... (Andhra Pradesh, 34X & Tamil Nadu, 7.5X)
https://www.thehindu.com/.../excess.../article35118826.ece
https://www.thehindu.com/.../exces.../article34834150.ece... (Tamil Nadu, 4X)
https://github.com/.../world.../tree/main/local_mortality
https://indianexpress.com/.../coronavirus-jharkhand-door.../ (Jharkhand, 2X)
https://www.thehindu.com/.../excess.../article34807214.ece
https://twitter.com/ChinmayTumbe/status/1407242935003803649 (Odhisha, 12-30X, not very clear)
https://www.thenewsminute.com/.../tnm-exclusive-kerala... (Kerala, 2X)
https://www.thehindu.com/.../chhat.../article35067172.ece... (Chhattisgarh, 4.8X)
https://www.thehindu.com/.../excess.../article35118826.ece (Rajasthan 5.4X, Andhra Pradesh 18X, Kerala ~1.3X, Madhya Pradesh 24X, Tamil Nadu ~5X, Karnataka ~4X)

21/05/2021

26/4/2022

16 months into this pandemic (!), I have now got my first vaccine dose. I was given moderna, but would have gladly taken almost* any of the vaccines out there.

Despite this, I understand being a bit hesitant. Unless you have had some training/education in a relevant field and a lot of time to follow the development and testing process over the past year, you are being asked to take on faith that the Covid vaccines are good. That faith may be in short supply after the serious mistakes the scientific and health communities made, starting with the early claims that border closures and masks don't work. And there's a wealth of contradictory and alarming information that you encounter online and from friends and family, and no clear way to judge what information to trust.

So if you or any of your loved ones are hesitant about getting vaccinated for any reason - side effects, speed of development, the testing process, whatever - get in touch with me and I'd be happy to talk it over.
I for one am absolutely delighted to get vaccinated and celebrate each time one of my friends and family gets that same opportunity. I hope you and yours get that chance soon too, and take it.

*I am personally still moderately sceptical of the efficacy of the Russian, Chinese and Indian Covaxin vaccines, though I am glad they exist, would definitely take them if I didn't have alternatives, and am hopeful my concerns will prove to be misplaced.

02/05/2021

3/5/2021

Today in pandemic theatre: Bangalore is using drones to spray disinfectant around, including seemingly just directly into the air around buildings.

At the same time, the Indian central govt. ministry in charge of promoting bullshit boasts about traditional Indian medicine claims that a herbal concoction 'developed' to treat malaria in the 80s also cures Covid. Needless to say, there is absolutely nothing trustworthy about the 'study' and the claim should be treated like the garbage propaganda it is, not as science.

Meanwhile, hospitals overflow, oxygen supplies run low, people die in droves and the vaccination program stalls because of a lack of doses.

UPDATE:

The latest rage: steam inhalation in groups. Let's gather people in clusters, make them take off their masks, sit together for a while, and inhale deeply.

It's like the virus wrote this policy.

30/04/2021

3/5/2021

FYI: if you are in India and have Covid-like symptoms now or in the next few weeks, just assume you have Covid and isolate immediately. Testing your contacts is a priority at that point, testing yourself is not - you are extremely likely to have it. Monitor yourself to see if you need medical attention, of course.

28/04/2021

3/5/2021

India will now authorise vaccines approved by the US, UK, EU, Japan or WHO.

So in April 2021, Indian citizens will finally be allowed to get the Pfizer & moderna vaccines, which has been *illegal* till now. Pfizer actually withdrew its application for authorisation months ago after being asked to jump through hoops by the Indian government for no good reason.

The last year should make us much more sceptical of these regulatory bodies. India's is a stupidly extreme case, but every country's regulator has required a complex submission and evaluation procedure for these vaccines despite the burning pandemic and very strong evidence from other places. There's no good reason for the EU and US health regulators (for example) to not trust each other's judgement of the data. And there's even less reason for Indian regulators to think that their scrutiny is more rigorous and trustworthy.

26/04/2021

3/5/2021

Anyone with expertise in GIS & remote sensing who could help me figure something out?
This twitter thread made me think that we may be able to better estimate deaths across India using satellite imagery of funeral pyres. Would this be feasible? How would we go about it? What expertise/manpower would be needed to make this happen?

The reason I ask is that there's a very real chance that tens to hundreds of thousands will die uncounted and that it will all be forgotten. I'd like to help out with efforts to avoid that.

25/04/2021

3/5/2021

UPDATE on this situation: The US, EU, UK, and more have offered help! Oxygen and concentrators for immediate relief. And perhaps more importantly for the medium term, the US will undo the (effective) embargo on vaccine raw material export.

"The United States has identified sources of specific raw material urgently required for Indian manufacture of the Covishield vaccine that will immediately be made available for India."

23/04/2021

24/4/2021

The situation in India: 300k cases and 2000 deaths recorded per day and rising rapidly. Perhaps 10 times that number in reality, maybe more. The deceased being burnt in parking lots because there is no space for cremations. People dying in waiting lines outside hospitals, and inside crowded emergency rooms/ICUs because supplies have run out. Families desperately begging on social media for help in finding a hospital bed, an oxygen cylinder, or a drug that somebody has told them will cure their dying kin.

This is why so many of us were yowling since early last summer that every damned vaccine needed to have accelerated review and approval if it was even moderately protective. That we needed to plough mountains of money into creating manufacturing capacity even though many of the vaccines would not work out. That the months wasted on following standard review protocols were prioritising arse-covering over saving lives - possibly millions of lives. That slowing the whole vaccination process over every possible rare side-effect in the hope of maintaining faith in the system was dooming many to a horrible death while simultaneously wrecking confidence in vaccines globally, even in places without much prior antivax sentiment.

There's plenty of blame to go around for this present crisis. Pride of place certainly goes to the utterly incompetent and vile Indian government. But the US has made things worse by stopping the export of basic material needed for vaccine manufacturing. This has slowed down the rest of the world's ability to produce vaccines even as the US imports materials for its own vaccination program. If you can make your voice heard in the US about this, please urge your government to fix this!

Why I do this

I am not an expert on Covid, viruses, or vaccines, but I am a scientist with relevant training. I believe we have a responsibility to clearly communicate science to the public, especially in emergencies. So I started to write summaries of Covid developments on facebook in March 2020 to help friends and family understand the situation as it unfolded. This is an archive of those posts (created much later).

I also track the spread of alarming Covid variants at http://covidvarianttracking.com/ and map the consequences of faster variant spreading at https://tabsoft.co/2YwHCmZ.

Please do let me know if you find errors in the most recent posts.