🦠 COVID-19 | Science at work

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: 

3,725,775 (+85,083cumulative cases 

Active cases: 2,225,817 (+29,883) (this is the number of currently infected patients)

Total Deaths:  258,271  (+6,433)

Serious/Critical Cases: 49,249 (-378)

Recovered:   1,241,687 (+48,767)

Source: Worldometers

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

Today, the Corona Daily does an in-depth into a pre-print published yesterday, the critical review which ensued, and the general question around science communication in the age of Twitter, ad-dependent publishers and pre-print servers.

The speed at which information is shared, cooperation is enabled and learning achieved is unprecedented. Nonetheless, we remain at the beginning of this journey with regards to COVID-19 knowledge and radical uncertainty remains. The extent to which researchers have embraced these new capabilities is to be lauded but there remains some learning and improvement on how that feeds and informs the urgent policy debate and the public. Cooperation needs to be more multidisciplinary given that the breadth of the virus’ impact on our society. To start it needs to include ethics and mental health more broadly in coming up with a defensible way forward.

Politicians are often all too ready to ascribe certainty to science and instrumentalize it. Such approach will do a disservice to both politicians and more importantly science and the public. The latter should not fall for it.

Until we know more, building testing-tracing-isolating-protect capacity is the best way forward out of the lockdown.

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

Free COVID-19 curated feeds

🇺🇸 Twitter Thread of the day: “On fire, oxygen and water” by Jeremy Konyndyk (Senior Policy Fellow at the Center for Global Development and expert in global outbreak preparedness) (First Tweet and Twitter thread)

In this thread, Konyndyk answers the question: “Why is reopening premature?

As Konyndyk compares SARS-CoV2 to a fire, his argument is that the lockdowns are depriving the virus of oxygen to spread. All the vulnerable (high oxygen) places (prison, nursing homes and meatpacking plans) have been hit hard whenever the virus was let in. If we were to open up too quickly without proportionate physically-distanced behaviour the virus would wreak havoc. For Konyndyk the water bucket is a robust testing-tracing-isolating-protect infrastructure.

💉🎬 Video of the day: Sir Jeremy Farrar, who is Director of the Wellcome Trust and on the government’s scientific advisory committee SAGE, is being interviewed on Channel4, talking about the ‘enormous global effort’ and ‘cooperation’ to have a vaccine in 12-18 months versus the normal 10 years. (Link)

🇺🇸 Jay Rosen (Professor of journalism at New York University) writes “The plan is to have no plan” for Press Think. There are some good referenced article in this short read as well.

In the preamble Rosen shares his purpose for writing the article:

“I will revise the text and add new links as more information flows in. My purpose in posting it is to challenge the American press to be a lot clearer in its descriptions.”

As much as it will be a pleasing read to the intellectual left, it will be a pleasant read for the popular right. It is astonishing how the liberal media has been so inept in focusing on what matters in the US even more so in an election year. (Link)

❗️In-Depth: the Bette Korber pre-print, reporting pre-prints in general and the Twitter peer-review

🧬 Bette Korber et al. published a pre-print (not peer reviewed) “Spike mutation pipeline reveals the emergence of a more transmissible form of SARS-CoV-2” in BioXRiv.

The preprint is significant and the area it researches is of great importance with potential implications (with further data) for vaccine development and anti-body testing (and the controversial immunity passport). It is also significant in the debate it stirred about pre-prints reporting - whether or not general media should report on them (or under what conditions), and more broadly science’s interaction with policy, the public, and commercial interests.

The paper is written by a well cited and solid scientist as Dr. Laura Boykin highlights and also can be deducted from looking at PubMed or Google Scholar:

Dr. Laura Boykin @laura_boykin
I think it’s important for people to know Dr Bette Korber has been in this viral evolution game a long time- leading the HIV sequence database (
hiv.lanl.gov) years and years. Her science and work is so so so solid. Let’s see.Time will tell but her experience is massive

Trevor Bedford @trvrb

I wanted to address the hypothesis put forward in Korber et al (https://t.co/ouM4IUyNrd) that the mutation in spike protein D614G causes an increase in transmissibility of SARS-CoV-2 virus. I find this hypothesis to be plausible, but far from proven. 1/16

The papers investigates the following area of interest as outlined in the abstract:

“We have developed an analysis pipeline to facilitate real-time mutation tracking in SARS-CoV-2, focusing initially on the Spike (S) protein because it mediates infection of human cells and is the target of most vaccine strategies and antibody-based therapeutics.”

It focused on a particular mutation D614G which is prevalent in Europe and which for the authors is of “urgent concern”. The paper postulate a strong hypothesis on the increased transmissibility of this strain which will require further epidemiological investigation, peer review and data. (Link)

📃 Denise-Marie Ordway writes Covering biomedical research preprints amid the coronavirus: 6 things to know” for Journalists Resource, an open-access online reference desk for journalists.

The article is based on interviews of Bill Hanage, an associate professor of epidemiology at Harvard, and John R. Inglis, who co-founded medRxiv and bioRxiv. Ordway addresses the concern expressed by researchers on the general media reporting on and misrepresenting pre-prints (non peer-reviewed research articles) as if pre-prints were only intended to accelerate and help “medical professionals, government leaders and others can respond more quickly to prevent, treat and control infections.”

The article provides sensible guidelines and knowledge which journalists should have about pre-prints to better report on them. As highlighted frequently by Bill Hanage on Twitter, he finds some of the reporting misleading, as he did today on pre-prints concerning virus mutations:

However, if we want to have a much needed and urgent Democratic debate regarding policy, an informed and educated public will be a pre-requisite. (Link)

💉 A Twitter thread from Bill Hanage reality checking the implication of Bette Korber paper (first tweet below):

It is more aimed in my opinion, at the reporting of the LA Times than the pre-print itself but nonetheless a good explainer to read. Hanage still downplays the significance of one SNP (single nucleotide polymorphism) for drug or vaccine development as per his last tweet in the thread.

🧬 A Twitter thread from Trevor Bedford (Fred Hutch) commenting on Bette Korber pre-print. It is a thorough thread which concurs with the importance of looking at this known mutation (the D614G one), highlights some of the confounders to worry about in relation to two of the arguments put forth by the paper to substantiate an increased transmissibility in the D614G strain.

Towards the end of the thread he references back the excellent long read from Ed Yong (previously shared in the Corona Daily) as well as disagrees with the other experts which have completely dismissed the paper:

In a very constructive way, he finishes by proposing a way forward to test the hypothesis put forward by Bette Korber et al.:

Science at work. (First tweet and Twitter thread)

🦠 Two articles reporting on the paper: an earlier one from the Los Angeles Times and one from the Washington Post.

The Los Angeles Times article first appear with the title: “A mutated coronavirus has emerged, even more contagious than the original, study says” as proven by the tweet below:

If you now click on the link (it might change again - or mutate 😏) it says: “Scientists say a now-dominant strain of the coronavirus could be more contagious than original”. The second title is more in line with the title of the pre-print, and this could potentially say more about the quality of this specific LA Times article or the clickbait temptation of the media in an ad-fuelled media world than the paper itself. (Link)

Sarah Kaplan and Joel Achenbach write Researchers hypothesize that a highly contagious strain of the coronavirus is spreading, but other experts remain skeptical”. This article is more in line with the guidelines which Bill Hanage and John R. Inglis have put forward in the article above about reporting about pre-prints in the general media (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 John 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)

  1. 💊 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)

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

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

  4. 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)

  5. 🌎 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)

  6. 🌎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)

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

  8. 🌎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)