🦠COVID-19 | Great science and dismal politics

I am a scientist by education, banker at JPMorgan for a few years, then mature PhD student in Chemical Biology at Oxford under the supervision of Christofer Schofield (FRS) and Peter Ratcliffe (Nobel laureate in medicine in 2019). Founder and tech investor focusing on media and education. I care about science, learning and Democracy which are good bedfellows.

📊 Daily Data Brief: (❗️48 hours +/-)

Cumulative case: 4,666,736 (+171,900cumulative cases 

Active cases:  2,577,250 (+75,694) (this is the number of currently infected patients)

Total Deaths:  309,865  (+8,087)

Serious/Critical Cases: 44,984 (-508)

Recovered:  1,779,621 (+88,119)

Source: Worldometers

1) Seven-day rolling average of new deaths (updated daily as ECDC releases). Major update with per country graphs now available (Link) (Update❗️) (USUKFranceGermanySweden,  Nordic Comparison) (👈NEW❗️)

2) U.S. states reopening risk map (Link)
‘Elevated’ to ‘Moderate’:Arizona, Mississipi
‘Moderate’ to ‘Reduced’: West Virginia

A great paper published in Cell on SARS-CoV-2 reactive T Cells important for vaccine development, public policy and disease onset (added an explainer video on the difference between B Cells, cd4+ and cd8+ T Cells in the video section). At the other hand of ‘science’, a great piece of investigative journalism on JetBlue founder funding the controversial pre-print of the Santa Clara serology study published as a pre-print from professors at Stanford University. Inexcusable even if air travel is being particularly hard hit as observed in the article:

“One especially hard-hit sector is the airline industry, which stands to lose $314 billion this year as would-be travelers hunker down at home for the indefinite future.”

This is another case of politics/commercial interest interfering and attempting to instrumentalize science. It does a disservice to both, and continues to prolong the ‘Age of Distrust’ we live in. Instead, science should attempt to better interface with the public, policy makers and other non-scientific disciplines, rather than demean itself or be abused. The podcast from The Intercept, rather provocatively titled ‘Is Elon Musk a fraud?”, beyond its sensationalism also exposes how politics, public health and science can be influenced by commercial interest or someone like Musk (see below a tweet from him from 31s January):

This does not mean that science (or policy) should not be challenged beyond its peer-review process or that policymakers should ignore other non-scientific disciplines and socio-economic considerations (including ethics). It would however be really damaging to society that bullying, lying (or its milder form of sloganism) and provocation rule.

This is also an issue which Helen Branswell tackles on the vaccines and whether in a pandemic a country-first policy is optimal versus one based on global cooperation/coordination.

The food banks in the U.S. show us how by adapting they are currently able to provide better service, reduce waste whilst facing unprecedented surge in demand.

Encouraging result from the ‘Oxford vaccine’ trial with rhesus macaques.

An article looking at how safe it will be to go back to your gym as soon as it reopens.

Finally, an article from 2003 about funding of coronavirus research (including vaccine research) and the need to prepare for the next pandemic. A time for introspection.

NEW❗️I have open-sourced the curated feeds I use for my newsletter and made them freely available below.

Free COVID-19 curated feeds

🛑 Article of the day: Stephanie M. Lee writes “JetBlue’s Founder Helped Fund A Stanford Study That Said The Coronavirus Wasn’t That Deadly” (Link)

Lee write about the conflict of interest around a serology study from Professor Ioannidis (University of Stanford) which made headlines when it came out mid-April and was widely publicised:

“The study — released as a non-peer-reviewed paper, or preprint, on April 17 — made headlines around the world with a dramatic finding: Based on antibodies in thousands of Silicon Valley residents’ blood samples, the number of coronavirus infections was up to 85 times higher than believed. This true infection count was so high that it would drive down the virus’s local fatality rate to 0.12%–0.2% — far closer to the known death rate for the flu.”

It was heavily and immediately criticised by epidemiologists on Twitter. It turns out that it was partly funded by the JetBlue Founder, David Neeleman who believes lockdowns are not necessary as COVID-19 is not deadly enough.

A great piece of investigative journalism.

🦠 Mitch Leslie writes “T cells found in COVID-19 patients ‘bode well’ for long-term immunity” in Science. Leslie reports on a pre-print published by Andreas Thiel et al. (“Presence of SARS-CoV-2 reactive T cells in COVID-19 patients and healthy donors”) and one peer-reviewed paper published by Shane Crotty et al. in the prestigious Cell journal (“Targets of T cell responses to SARS-CoV-2 coronavirus in humans with COVID-19 disease and unexposed individuals”). These are both important papers with regards to vaccine development, the immunity that humans acquire once infected by SARS-CoV-2 and the general development of the disease in patient.

Leslie outlines early on, for non-immunologists, the difference between humeral and cellular immunity (there is also a short explainer video from Khan Academy in the video section today on B Cells and T Cells):

“The more than 100 COVID-19 vaccines in development mainly focus on another immune response: antibodies. These proteins are made by B cells and ideally latch onto SARS-CoV-2 and prevent it from entering cells. T cells, in contrast, thwart infections in two different ways. Helper T cells spur B cells and other immune defenders into action, whereas killer T cells target and destroy infected cells. The severity of disease can depend on the strength of these T cell responses.”

This is why these 2 papers carry significant importance, whilst not resolving the question of how long infected patient are immune to re-infection. Professor Shane Crotty also provided a helpful summary Twitter thread of the paper he is a senior co-author on. For a start it is good news on immunity:

There are three other findings which are interesting, two are actual findings and another one stems from the design of the study which enrolled “non-hospitalized COVID-19 cases” (i.e. mild cases).

One is that they found reactive T Cells in unexposed people in the study:

This might suggest that the population is not entirely naive towards SARS-CoV-2 and that previous exposure to the ‘common cold’ from other coronaviruses might confer immunity. The second finding is that while 100% of infected patients had T Cells that recognise the spike protein of SARS-CoV-2, they also found T Cells which reacted with other SARS-CoV-2 proteins. This points to the possibility of finding a vaccine which elicits T Cell response to a broader set of SARS-CoV-2 proteins rather than ones that focus solely on the spike proteins. Some will argue that it is more difficult to produce a vaccine eliciting such a broad response, but the study points that efficacy of such vaccine would likely improve patient’s immunity.

Finally, while the study was conducted on non-hospitalised patients (i.e. less severe than patients who require hospitalisation), it still observed high level of T Cell reactivity in these patients which is good news.

For comparison the pre-print paper from Andreas Thiel et al. also found 15 out of 18 infected patients (83.3%) had T Cells targeting the spike protein and only 34% (vs 50% in the Cell paper) of unexposed patients had T Cells reacting with SARS-CoV-2.

A very important paper. (Link)

🍔 Brett Anderson writes “To Fight Waste and Hunger, Food Banks Start Cooking” in the New York Times. Anderson’s article is both a stark reminder of the economic cost of the pandemic (36 million Americans are now unemployed), particularly in the hospitality sector, and a testament to the dedication and the adaptability of the food banks to better serve those in need during this pandemic, while fighting waste.

The surge in demand from food banks during this pandemic is unprecedented:

“Since March, demand for food has leapt by 600 percent at Feeding South Florida, the largest food bank in this agriculture-rich state. When the new kitchen opens, as early as next week, Ms. Benoit and her staff will begin preparing 10,000 hot meals a day.

At the same time, and as restaurants and schools have shut down during shelter-at-home orders, a bulk of the demand for produce has evaporated. Cooking at the food banks allows to:

  1. Process a lot more perishable food

  2. Cater to “a lot of single parents working two jobs. What they don’t have is time to cook a meal.”

Food banks across the country will continue to build up refrigerated and cooking capacity going forward planning for a prolonged demand for its produce and now service. (Link)

💉 Helen Branswell writes “Under an ‘America First’ president, will the U.S. corner the market on Covid-19 vaccine?” for STAT News. Branswell tackles the important issue of COVID-19 vaccine distribution when and if it becomes available.

Branswell writes the article on the back of President Trump publicly announcing “Operation Warp Speed” which aims for the US to have 300 million doses of vaccines by January 2021. Is it in the US interest to vaccinate all its population including low risk population, when the healthcare workers of countries it trades with would not have access to a vaccine?

Seth Berkley, CEO of Gavi, the Vaccine Alliance, argued the following:

“This is a global problem. It requires a global solution. It is the job of countries and political leaders to protect their own people and I certainly understand that. But it is also the job to have a longer-term view and understand the global nature of infectious diseases, as well as the global nature of science.”

It is not an easy issue, but the way the world tackles vaccine distribution, will inform us all on the direction the world is taking, at a time where we face other complex and global problems like nuclear proliferation and climate risk. (Link)

💉 Sarah C Gilbert, Vincent Munster et al. publish the pre-print “ChAdOx1 nCoV-19 vaccination prevents SARS-CoV-2 pneumonia in rhesus macaques” in BioRxiv. This was a trial of the ‘Oxford vaccine’ with rhesus macaques. Nine monkeys were part of the study. Six were given one dose of the ChAdOx1 nCoV-19 vaccine. The vaccinated monkeys also developed neutralising antibodies. The all monkeys were challenged (i.e. infected) with SARS-CoV-2. None of the vaccinated monkeys developed pneumonia while 2 of the 3 monkey in the control group did. (Link)

🏋🏻‍♂️ Casey Johnston writes “I Miss the Gym Like Hell, but I'm Not Going Back Anytime Soon” for Vice. Gym have re-opened in Germany and South Korea, and some might reopen in the US and elsewhere. Johnston believes that whatever precautionary measures are implemented by re-opening gyms, they will be insufficient in countries which (unlike Germany or South Korea) do not have a solid testing-tracing-isolating capacity. Johnson also raises the question of membership fees and wether they should fall due as soon as the gyms re-open. Looks like open air activity is set for a brighter future. (Link)

❗️A warning from the past and for the future:

📜 In 2003, Shibo Jiang; Lu Lu and Lanying Du wrote “Development of SARS Vaccines and Therapeutics Is Still Needed” in Future Virology. This is an important article to read to see why the authors’ warning was not heeded. Perhaps more importantly, will our societies exhibit the same complacency now about pandemics or other catastrophic events, as they did then.

As the authors write some of the funding pledged during SARS was actually never awarded:

“During the global 2002/2003 SARS pandemic, many foundations, pharmaceutical companies and governments provided abundant funds to support the development of anti-SARS vaccines and therapeutics. However, after the disappearance of SARS, these funds were either withdrawn or discontinued because of the lack of a sustainable market of the products to be developed.”

It is very likely that zoonotic epidemics will return, and we should make sure that funding does not cease when this current pandemic fades. The paper also raises then the questions about the ethics of human challenge trials for a coronavirus vaccine, as well as what could be have been done then to accelerate a future vaccine against a beta coronavirus:

“Apart from financial support, another main challenge for the clinical development of anti-SARS vaccines is the lack of endemic SARS and the lethal nature of the disease. It is not ethical to conduct human efficacy studies by exposing healthy human volunteers to a lethal agent like SARS-CoV.”

The latter point is a very live ethical point for the current trials and timetable of a COVID-19 vaccine.

🎬 Videos and podcast

🦠 A short video from Khan Academy explaining “B Cells, cd4+ and cd8+ T cells” (11 min 7 sec)

⚡️“Is Elon Musk a fraud?” in The intercept ‘Deconstructed’ podcast. (Link)

📊 A picture is worth a thousand words:  Global (🌎) and local (with relevant flag) visualisation and forecasting tool

  1. 🇺🇸 NEW❗️ “Is your community ready to reopen?”: A map of the US (50 states and 2,100+ counties) looking at reopening risks with metrics around 3 criteria: 1. Is COVID in retreat? 2. Are we testing enough? 3. Are our hospitals ready? (Link)

  2. 🌎 The Financial Times (visualisation) has a data tracking page which is in front of the paywall, looking at cases and fatality curves for selective countries and metropolitan areas/region. It is not as extensive as the Madlag link below, where you can see static as well as animated images for a greater number of individual countries. (Link)

  3. 🇺🇸  The Johns Hopkins University resource center was the first one I used back in January they have now made available in their latest iteration a county by county dashboard in the US including information about health capacity, insurance coverage, ethnicity and age breakdown of the populatio (Link)

  4. 💊 The "Map of Hope" provides a geographical overview of planned, ongoing and completed clinical trials. It is put together with data from WHO Clinical Trials Search Portal by the Heidelberg Institute for Geoinformation technology. (Link)

  5. 🌍 MRC Centre for Global Infectious Disease Analysis started to publish weekly death estimates for countries (Link)

  6. 🇺🇸 The US Center for Disease Control and Surveillance (CDC) publishes “A Weekly Surveillance Summary of U.S. COVID-19 Activity” (Link)

  7. Google has published a new website to “See how your community is moving around differently due to COVID-19”. They have a lot of data to do so… (Link)

  8. 🌎 Country by Country Curves: This is a GitHub made by my friend Francois Lagunas. He has written a script to scrape deaths and number of cases in order to visualise the rate of growth on a logarithmic scale.  Great resource (Link)

  9. 🌎A great resource put together by Ben Kuhn and Yuri Vishnevsky.  At a time when we need solidarity and cooperation, I prefer their subtitle “We need stronger measures, much faster” than their title. It’s a simulator on what case growth looks like depending on your community’s measures. Fantastic resource to stir communities and governments to action (Link)