🦠 COVID-19 | New surge, less will

📊 Daily Data Brief: June 25, 2020, 01:37 GMT (❗️Previous data: June 22, 2020, 23:20 GMT )

Cumulative case: 9,526,001 (+349,292) cumulative cases 

Active cases:  3,866,330 (+67,026) (this is the number of currently infected patients)

Total Deaths:  484,926  (+11,506)

Serious/Critical Cases: 58,417 (+558)

Recovered:  5,174,745 (+270,760)

Source: Worldometers

1) Seven-day rolling average of new deaths (ECDC data)

Showing a chart from the FT today highlighting the worrying situation in Brazil, Mexico, India and Russia and Iran (NEW❗️). Also the FT comparative charts now allow up to 6 countries.

2) Rt estimate per State (US) and per country (NEW❗️). This is a new resource link in the data section from a team which has led accuracy in modelling fatalities in the US for the past few weeks. (Link)

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According to the Washington post on Wednesday evening:

“Across the United States, 38,115 new infections were reported by state health departments on Wednesday — surpassing the previous single-day record of 34,203 set on April 25.”

This is a sad and worrying day in the pandemic, and yet one which seemed inevitable when I titled the Corona Daily edition of May 28 “A second spike is coming”.

The messaging then, and still now in the US and the UK, is about reopening without any risk warnings. It is solely about back to normal, when actually not having used the time afforded by lockdowns to prepare the needed test-trace-isolate infrastructure and further educate the public sadly puts the virus rather than the public in good position. It is a messaging which is detrimental to BOTH the economy and public health.

And as the article of the day advocates, the public at large, local decision makers and enterprises should take informed steps to prevent further deaths and pain rather than let distrust or politicisation drive their behaviour.

Dr Anthony Fauci in his testimony to the House committee on the administration's coronavirus response made clear that the next two weeks were critical. They always seem to be in the US. However, the risk now is that the public both loses faith and will, at a time when they are both most needed. This is what worries Caitlin Rivers in one of the Twitter threads of the day.

The second Twitter thread is by Natalie Dean who postulates different possible explanation for the recent lowering of the median age of infected patients in the US. The tweet of the day had already debunked one of her hypothesis and one which is often put forward by Trump in public.

The image of the day looks at the resurgence of cases in Israel despite the country having reopened with a daily case rate much lower that the ones we are currently witnessing in US states or the UK as they increasingly ‘reopen’ their economies. It should serve as a warning to the public if it is not heeded by their regional or national leaders.

One paper on the use of a CRISPR screen to discover new drug targets against SARS-CoV-2 and one article talking about the growing evidence that the virus could trigger Type I diabetes even in young patients. Finally, and echoing the last edition “The cost of distrust” a further example of this cost around contact tracing and the African-American community.

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🇺🇸😷 Article of the day: The editorial Board penned “Don’t listen to Trump, Mask wearing is essential” for the Washington Post. It is rather telling from the Editorial Board that it chose such a politicised title to depoliticise universal masking. Maybe, it wanted to highlight that the heavy politicisation of science around this pandemic laid more at the door of Trump and his supporters.

It is definitely the message conveyed in the article:

“In framing mask-wearing as a culture-war issue, Mr. Trump obscures and impugns what should be a straightforward and responsible act of personal protection and public hygiene.”

One has to question whether the title needed to be so outright political, but its conclusion remains sound advice:

“All Americans, and all businesses, want the country reopened. Mr. Trump has framed the issue falsely, as a choice between economic revival and public health. In fact, the goal is to reopen intelligently, without triggering a fresh tsunami of infections. That will require responsible decision-making by state and local leaders as well as companies and individuals. Wearing masks is an essential place to start.”

(Link)

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🇺🇸 Video of the day: Dr Anthony Fauci on the situation in the US (Link)

Aaron Rupar @atrupar

Fauci on coronavirus in US: "If you look at how we've been hit, we've been hit badly. We've had now over 120,000 deaths and 2.5 million infections. So it's a serious situation... the next couple weeks are going to be critical in our ability to address those surges we are seeing"

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🇺🇸 Tweet of the day: There has been a suggestion by Donald Trump that the high number of cases in the US was due to the high level of testing. The COVID tracking project put out a Tweet debunking that claim looking at data from the states currently leading the new surge in cases in the US:

The COVID Tracking Project @COVID19Tracking

And again, this is not just about testing more. Here's an updated chart from the one in this post: covidtracking.com/blog/its-not-j… Case growth is outstripping test growth in all of these states. And Florida has conducted fewer tests this week than last.

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🇮🇱 🇬🇧 Image of the day: Israel had its epidemic under control and went to a 7-day rolling average of new cases of around 10 cases. It reopened and yesterday declared 532 new cases.

The UK is re-opening almost fully on July 4 and its 7-day rolling average of new cases is currently above 1,000. The risk of it following on the footsteps of Israel’s new surge is very high. Netanyahu warns lockdown restrictions may be reimposed amid spike in Covid cases if Israelis do not change their behaviour.

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Twitter threads:

🇺🇸 Thread of the day 1: “New surge, less will” a good analysis by Caitlin Rivers (Assistant professor at Johns Hopkins Center for Health Security) (Twitter Thread)

The thread describes the worrying trend in the US, with the country having registered over 30,000 new cases in 3 out of the last 5 days. The more worrying part for Rivers is the will of the people to correct course:

Caitlin Rivers, PhD @cmyeaton

But even where transmission is intensifying, the will to correct course has seemingly waned. It’s hard to imagine how we will get to a better place. In some ways this feels worse than April bc at least then there was energy around gaining control. I sense less of that now. 5/

In the US, the “will to correct course” at an individual level is sadly linked to the ability to take sick days and/or get tested without suffering loss of income.

Rivers finishes with a ‘better news’ series of tweets almost to make the early part of the thread more bearable, and highlights the decline in deaths. She is quick to point out that this might not survive the test of time as deaths number lag cases number. It is an area which is also covered in the next thread.

🇺🇸 Thread of the day 2: “Why median age of infection declining is no reason for celebration” by Natalie Dean (Assistant professor of Biostatistics at University of Florida). (Twitter Thread)

Dean wants to answer as an ‘epidemiologist’ the question:

“What does it mean that the median age of new cases is dropping in some areas? I see three possible explanations, not all good. A thread on how to distinguish between them.”

There are 3 explanations: 1) More testing only, 2) Elderly people are more cautious and 3) Younger people are less cautious.

Dean then looks at what the implications for all three explanations would be data wise (i.e. what to expect in the data) and what they would imply for the epidemic going forward.

1) has already been debunked by the ‘Tweet of the day above’ on other grounds than the ones considered by Dean.

2) Looking at the data released from the COVID Tracking Project and charting seven-day average of both new cases and new hospitalisations, you do start to see a rise in hospitalisation in the US:

This is not what we should expect to see according to Dean in case of 2):

Natalie E. Dean, PhD @nataliexdean

If median age drops only because the elderly are more cautious, we expect: - Drop in number of new cases in the elderly - Drop in test positivity among the elderly (fever/illness is more likely due to other non-COVID causes) - Drop in hospitalizations (after a lag) 5/10

It appears then then 3) the most likely, and this is “the not good one” from an epidemiological point of view:

Natalie E. Dean, PhD @nataliexdean

Explanation 3 (the not good one): Young people are less cautious. This is distinct from the previous scenario. It means that young people are being infected even more than before. This could occur if there are many bar/nightclub or workplace outbreaks. 6/10

It is not the good one because:

Natalie E. Dean, PhD @nataliexdean

Besides the fact that young people can face unknown long-term outcomes of infection, they can also inadvertently spread the virus to their communities. So the median age could start to creep back up if it moves from bars out to coworkers, family members, etc. 8/10

Ultimately, Dean believes that it might be a combination of the three, and only further data granularity on age distribution of “cases, testing and hospitalisation” will allow us to distinguish or evaluate the contribution of each to the observed data.

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🦠 Smriti Mallapaty writes “Mounting clues suggest the coronavirus might trigger diabetes” for Nature. Whilst it was known that people with diabetes were at higher risk when infected with SARS-CoV-2 there is now mounting evidence that the virus might actually damage pancreatic cells and trigger diabetes in infected patients.

The article just adds to the growing list of potential long term side effect caused by the virus. The article starts by talking about the onset of Type I diabetes in an infected individual aged…18. A stark reminder of the risk that the virus also poses to younger generation even though it might spare them death more often. (Link)

💊 Jin Wei et al. publish the pre-print “Genome-wide CRISPR screen reveals host genes that regulate SARS-CoV-2 infection” in BioRxiv. CRISPR screen is a recent technique which can be used to see which host genes are up regulate or down regulate a viral infection. It has been successfully used to determine Host Dependency Factors (HDF) for Influenza A (2020), Dengue and Hepatitis C (2016).

Apart from identifying the importance of well-known factors ACE2 and Cathepsin L, the screen identified other pro-viral host factors. The authors write in their abstract:

“We additionally discovered novel pro-viral genes and pathways including the SWI/SNF chromatin remodeling complex and key components of the TGF-β signaling pathway. Small molecule inhibitors of these pathways prevented SARS-CoV-2-induced cell death. We also revealed that the alarmin HMGB1 is critical for SARS-CoV-2 replication.”

The research which is yet to be peer-reviewed also highlighted that knocking out the H3.3 chaperone complex would trigger cell death upon virus infection.

This screen could help find novel therapeutics against SARS-CoV-2. Science at work.(Link)

🏛 Katelyn Esmonde writes “For contact tracing to work, public health authorities must regain the trust of Black communities” for VOX. Esmonde looks at how systemic racism in the US might negatively affect the ability to contact trace:

“Ultimately, systemic racism has undermined trust in our institutions when we need them the most. This is especially true for Black Americans, who have disproportionately been harmed by those charged with protecting them. Considerable damage has already been done, but it is not too late to take steps toward repair.”

At a time when preliminary data appears to show limited infections amongst individuals having attended the protests sparked by the death of George Floyd, the issues it has exposed might have a secondary and more lethal consequence on the containment of the pandemic in the US.

Esmonde outlines some steps to rebuild trust whilst acknowledging that distrust runs high in part cause by the Tuskegee study in which African-American who had contracted syphillis were left untreated long after penicillin had been identified as a treatment.

This historical distrust with public health will only have been exacerbated by 1) the difference police treatment white and black protesters experienced recently in the anti-lockdown and George Floyd protest respectedly, 2) as well as the fear that tracing data from COVID might be used by other public agencies. (Link)

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

1. 💉 (❗️NEW) “Coronavirus Vaccine Tracker” by Jonathan Corum and Carl Zimmerfrom the New York Times.

   “The status of all the vaccines that have reached trials in humans, along with a selection of promising vaccines still being tested in cells or animals.”

2. (Link)

3. 🇺🇸 (NEW❗️) “The COVID Racial Data Tracker”

   “The COVID Racial Data Tracker is a collaboration between the COVID Tracking Project and the Antiracist Research & Policy Center. Together, we're gathering the most complete race and ethnicity data on COVID-19 in the United States.”

   (Link)

4. 🦠  “Science Forum: SARS-CoV-2 (COVID-19) by the numbers” (Link)

   “The COVID-19 pandemic is a harsh reminder of the fact that, whether in a single human host or a wave of infection across continents, viral dynamics is often a story about the numbers. In this article we provide a one-stop, curated graphical source for the key numbers (based mostly on the peer-reviewed literature) about the SARS-CoV-2 virus that is responsible for the pandemic. The discussion is framed around two broad themes: i) the biology of the virus itself; ii) the characteristics of the infection of a single human host.”

5. 🇺🇸🌎 This model has led accuracy for several weeks in the US. It also does projection for Europe and Rest of the World. (Link)

6. 🇺🇸  “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)

7. 🌎 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)

8. 🇺🇸  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)

9. 💊 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)