🦠 COVID-19 | The magical thinking around re-opening

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 (+/-)

4,012,837 (+199,925cumulative cases 

Active cases: 2,351,486 (+94,868) (this is the number of currently infected patients)

Total Deaths:  276,216  (+12,039)

Serious/Critical Cases: 48,699 (+498)

Recovered:   1,385,135 (+93,018)

Source: Worldometers

1) Cumulative death curves (updated daily as ECDC releases). Major update with per country graphs now available (Link) (USUKFranceGermanySweden) (👈NEW❗️)

2) “Coronavirus tracked: has your country’s epidemic peaked?” from the Financial Times. Looking at seven-day rolling average of new deaths. You can compare two countries per chart by clicking on the Link. (NEW❗️)

3) U.S. states reopening risk map (Link)

There is magical thinking about re-opening and increasingly it appears that the conversation is at the very least getting polarised if not outright nasty. Epidemiologists are being pitted against economists, when in reality the sensible way forward aligns them as two Twitter threads and a plan put forward by Harvard T.H. Chan School of public health convincingly argue.

The solution from other successful countries involves at its core a test-trace-isolate-protect capacity. In most places, this capacity is building up but not to the level required to avoid another exponential spread of SARS-Cov-2. Re-opening prematurely would risk a second spike and putting the discipline and sacrifice of the current lockdown to waste. A second spike would be catastrophic for the long-term health of both our economy and society.

There are two very good articles in the Financial Times and the Atlantic, showing that consumer behaviour and worker risk-aversion have changed once COVID-19 was amongst us impacting the economy before the lockdowns were put in place. Similarly, as we have reported previously for South Korea (and as can be seen in early data from US states having partially re-opened) the uptick in economic activity is seriously dented by the persistent behavioural change of both consumer and workers post-pandemic. We have learned a lot but we still have knowledge gaps. A high level of distrust amongst the public towards the ability of their respective government to execute continue to significantly dent confidence with lockdown or not.

Contact tracing is improving as an article and mapping project from NPR is showing, research progress is benefiting from pre-print servers as shown in a Nature Biotechnology article. Important ethical work is being published to potentially accelerate vaccine trials, and more data is becoming available with the largest study of its kind being published by Ben Goldacre et al. in the UK.

Let us not succumb to magical thinking and ignore ethics. We should instead build the trust which our society needs to restart progressively and durably our economies.

NEW❗️I am open-sourcing my curated feeds and making them freely available below.

Free COVID-19 curated feeds

🦠A way forward: “Consilience, hope, and a path forward: A plan for saving lives and our economy has emerged. The only thing left to do is execute it.” by Harvard T.H. Chan School of Public Health.

A very sensible plan. (Link)

👐 Re-opening Threads: it’s getting nasty

Thread 1: Gregg Gonsalves (Assistant Professor of Epidemiology (Microbial Diseases); Associate (Adjunct) Professor of Law, Yale)

Gonsalves starts by laying out the insult and abuse he has received:

This is shocking but not surprising in the current environment. Gonsalves argues that his position should not been seen as one pitting epidemiologists against people who care about the economy, highlighting and referencing a paper by the “Economic Strategy Group” which demonstrates quite the opposite:

The list of people making up the Economic Strategy Group is pretty impressive to say the least. A must read thread. (Twitter Thread)

Thread 2: Caitlin Rivers (Assistant professor at Johns Hopkins Center for Health Security)

Rivers starts off with a tweet highlighting the unhealthy polarisation of the debate about timing of re-opening:

Rivers is a co-author of one of the first report on re-opening published on March 29 (National coronavirus response: A road map to reopening) and subsequently on April 7 of “A national COVID-19 surveillance system: achieving containment”. She has been both active and early in thinking about re-opening and yet she writes:

A must read thread. (Twitter Thread)

❗️Dereck Thomspon writes “It’s the Pandemic, Stupid” in the Atlantic.

The Corona Daily has consistently praised the intelligence of the public (“Underestimating the public” - March 15 edition) or remarked that policy makers would eat their marshmallow before the public would (“Failing the marshmallow test” - April 28 edition). Thompson runs the same argument with the support of a economics paper from Harvard:

“The White House and most Republicans seem to think that this crisis will be solved by loudly announcing the reopening of the economy. But this is a dangerous misunderstanding of what’s actually driving the recession: It’s the pandemic, stupid. The shutdowns themselves had “little or no impact on economic activity” according to an analysis by a team of economists at HarvardSeveral papers now show that the decline in spending and employment in most cases occurred before states officially shut down their economy. Governments didn’t close state economies on their own, and they can’t open the economies on their own, either.”

The charts in the Harvard paper are worth taking a look at.

Martin Wolf made a similar case in “People cannot just be ordered back to work and to spend” for the Financial Times. Both are urgent reads to counter the magical thinking around reopening. (Atlantic Link and Financial Times Link)

🧪 Selena Simmons-Duffin writes “States Nearly Doubled Plans For Contact Tracers Since NPR Surveyed Them 10 Days Ago” for NPR. This is a hopeful article and also an initiative which can only accelerate the contact tracing in the US as Alexis Madrigal et al. did for testing with their COVID-19 Tracking Project (which now attempts to provide the most comprehensive data on COVID-19).

Simmons-Duffins reports a 30,000 increase in the numbers of tracers planned by states from the 36,000 planned only 10 days ago. The estimate of how many contact tracers will need to be hired and trained vary from 100,000 to 300,000. It will also require funding from the federal government. Progress is being made.

It is doable and this work by NPR can only help accelerate accountability, state level effort and federal funding to urgently reach the needed capacity. NPR will continue to provide a state-by-state for constituents on tracing levels and readiness (see below).

💉 Seema Skah et al. publish “Ethics of controlled human infection to study COVID-19” in Science. Controlled human infection studies (CHIs) are also known as “human challenge trials”, and are when participants agree to be infected with a pathogen generally in a vaccine or drug trial. The article lays out a comprehensive ethical framework to assess CHIs in the context of SARS-CoV-2 trials. A worthy read to understand the ethical considerations given the social and economical cost of the pandemic and the state of our knowledge about COVID-19. (Link)

🦠 Ben Goldacre et al. write “OpenSAFELY: factors associated with COVID-19-related hospital death in the linked electronic health records of 17 million adult NHS patients” on MedRxiv.

Goldacre rightly tweeted about the study with a sense of great achievement:

“Factors associated with COVID-19-related hospital death in the linked electronic health records of 17 MILLION adult NHS patients.

Largest study of its kind ever, anywhere.

The power of UK / NHS data, realised.”

There was one piece of data which was counterintuitive and which seem to imply that smokers were better protected than non-smokers. There is a critical thread on this and the pre-print by Ellie Murray (Assistant Professor of epidemiology at Boston University School of Public Health). It is once again “Science at work.

(Pre-print Link and Twitter Thread from Goldacre)

📃 “All that’s fit to preprint” is an editorial in Nature Biotechnology journal. It is supportive of the emergence of pre-print servers like BioRxiv and MedRxiv to accelerate the dissemination of research information on the outbreak and generally. COVID-19 pre-prints represent a far greater proportion of papers published than in other areas:

“This last statistic is notable because the number of COVID-19 preprints (2,449) as a proportion of peer-reviewed papers (7,136) published since the beginning of the year is high (34%). In comparison, preprints from these archives represented only 2.2% of papers indexed in PubMed last year (30,627 preprints versus 1,401,413 papers). Thus, preprints represent a larger proportion of SARS-CoV-2-related research than is typical for other research.”

Pre-prints have not come without their controversies with some being published and retracted, other being mis-reported by general media with click-bait headlines and others being severely critiqued. The latter is what we need to improve on, and Twitter is already providing a great platform for not only academics, but also policymakers and the public to see a live peer-review happening. It is definitely more bruising that the mediated and lengthier one organised by peer-reviewed journals. Twitter is also being complemented by more structured and vetted grassroots initiative like PREreview.

This new information ecosystem is emerging, in which science can ultimately win in accelerating its discoveries but also being more in conversation with the public and policymakers. (Link)

Video and podcasts:

🎙 Dark Horse PodCast: “The Evolutionary Lens with Bret Weinstein & Heather” Heying (Evolutionary biologist)

Looking at the “herd immunity as strategy” which 🇸🇪Sweden is pursuing (or re-opening now versus later).

“It is far better if you are going to get [COVID-19], to get it later, than to get it now. And so trying to fast forward herd immunity right now is a much more dangerous prospect.”


🎬 Bob Wachter (Chair, UCSF Dept of Medicine) leads the following Grand Rounds (99 minutes):

(Twitter Thread by Bob Wachter; 10 minutes read)

📊 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 population (New York example below) (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)

  10. 🇩🇪 The COVID19 dashboard for Germany is one of the best around. (Link)

  11. 🌎Data and chart regularly updated by the  Centre for the Mathematical Modelling of Infectious Diseases at the London School of Hygiene & Tropical Medicine. It maps the effective reproduction number (also known as R0) of COVID19. You want to get it below 1 as fast as possible to contain an epidemic. (Link to see charts and more data about your country)