🦠Covid-19 - 01/03/20 US: 2 wars or is it one war? | 🤕89,074 | Deaths 3,050

📊 Daily Data Brief:

89,081 cases (+2,088)

New Cases outside China: 1,775 (+359)

New Cases in China:  313 (-220)

Total Death: 3,057 (+78)

Serious or Critical Cases:   7,375 (-194); 8.3% of Total Cases (-0.4%)

Source: https://www.worldometers.info/coronavirus/

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The main headline is cases continue to grow outside China and in particular US cases about to shoot up this week with new diagnostic capability following the FDA decision Saturday. The narrative in the US is changing fast and in a positive way but remains very politicised in an election year. There is the perception that there are two wars going on: war against Trump and war against the virus. Given that Trump’s reelection campaign narrative is based on stock market performance (he’s the Chief Index Officer in America), I believe that there’s actually one war. We cannot have a non-contained, non-mitigated COVID19 and not a recession.

🦠 We now have sadly recorded a second death in the US from the nursing home outbreak I reported yesterday in Kirkland, WA. Also 6 patients have now tested positive for COVID19 there. There was a growing concern yesterday with the first death and outbreak, that the virus had gone undetected in the Pacific Northwest. There is now some phylogenetic (think ancestry study but for genes) corroborating that fear. There has been some nifty and interesting work reported by Trevor Bedford whose lab works at the interface of evolution, epidemiology and virology at FredHutch in Seattle. Trevor and collaborators have looked at the gene sequences of the first case reported in Snohomish County, WA (sampled January 19) and that of a case reported in the same county two days ago (the genes are labelled WA1 and WA2 in the Twitter thread). They have detected only one variant from one gene to the other which suggested that they share ancestry. This variant has only appeared in 2/59 strains of COVID19 from China and therefore the probability that this is a coincidence is very low (probability 3%). He conclude that there has likely been cryptic (undetected) transmission of the virus in the Seattle area for the last 6 weeks and that more strains sequencing and work will help confirm his initial results and deepen understanding of the virus spread. I also want to stress, how the sharing of data between China and the rest of the world on these sequences, a hallmark of the scientific community, is making that type of work possible. A number of other areas of our society should embrace that type of data openness. (Twitter thread)

🔬 The US and the rest of the world needs to be prepared for the numbers of COVID19 in the US to shoot up following the FDA announcement of allowing academic labs to carry diagnostic tests in the US. Dr Scott Gottlieb, former FDA commissioner and physician, expects US testing capacity to ramp up to 10,000/day at the end of this week to 20,000/day at the end of next week. Given the undetected transmission likely to have happened in the US (as suspected by Trevor Bedford) due to faulty CDC test (more on this below) but also a very narrow criteria for CDC authorising to test a patient (travel to China initially) the extent of the lack of detection on current numbers will unfold over the next few days. However as Assistant Professor Caitlin Rivers from John Hopkins Center for Health Security and one to have carried excellent work on early detection from influenza-like illness data in the US argues in an excellent thread: we need to heighten hospital preparedness. There is actually a sobering (given the numbers) and hopeful (given that the analysis is being carried out and shared) paper by Eric Toner, MD, and Richard Waldhorn, MD (John Hopkins Center for Health Security) of different scenarios of overloading of the hospitals and ICU in the US in case of a severe pandemic. There has actually been some official planning assumptions already released by the US Department of Health and Human Services (HHS) depending on a Moderate Scenario (1968-like) or Very Severe Scenario (1918-like AKA Spanish Flu). The former requires 1M hospitalisations and 200,000 patients needing ICU (Intensive Care Unit), the latter requires 9.6M hospitalisations and 2.9M ICU units. And “there are about 46,500 medical ICU beds in the United States and perhaps an equal number of other ICU beds that could be used in a crisis”. The mismatch is clear event if a severe pandemic would likely be spread out over several months (Twitter thread)

🔎 The narrative has dramatically and positively changed in the US for better preparation of both the care ecosystem and the public. Dr Anthony Fauci (part of Trump’s task force on COVID19 and Director of the National Institute of Allergy and Infectious Diseases) has come out unequivocally publicly on TV that Coronavirus cases in US are becoming ‘community spread' and could be more prevalent. Similarly and at the opposite end of the political spectrum, there is a story in Axios that a top federal scientist had raised the alarm on the contamination in the Atlanta lab which the CDC was using to make the early batch of coronavirus diagnostic test. His alarm was ignored. There is a strong narrative in the anti-Trump camp that this administration is against science and does not listen to what it does not want to hear. This story will be developing over the next few days particularly if the early testing fiasco which significantly hampered COVID19 testing (only 456 test had been carried out in the US at the end of last week) can be traced back to this lab. Here is the Axios story (Link)

🌏 News in the RoW (excluding China and US) remains worrying with a number of stories around under-reporting of the diseases in South East countries due to lack of testing and perhaps as some suggest an over eagerness to protect their tourism industry. This has resulted in a reported rise of “viral pneumonia” cases rather that of the novel coronavirus (to be fair Caitlin Rivers had also looked at abnormal rise in reprint of Acute Respiratory Distress Syndrome in the US to detect under reporting). 28 people have been quarantined in Nigeria who had been traced to the Italian worker infected with COVID19. Cases in Iran and Middle East continue to rise significantly. The spread of the virus in countries with low containment (due to lack of testing for example) and mitigation capabilities (availability of hospital beds) is particularly worrying. In Europe, Italy now has 1,701 reported cases and is the third most infected country after China (80,026) and South Korea (4,212). France and Germany have both reported 130 cases and are being followed closely by the international community as the next likely surging countries. The UK announced a further 12 more cases yesterday in England and now have 36 reported cases. On a positive note, as we get more globally trusted data from countries outside China we will be able to get a better prognosis of the Case Fatality Rate (CFR) of COVID19. It is noteworthy that EVERY expert always give their gloomiest prognosis with the caveat IF containment and mitigation fail. It is also worth noting that a city-like state like Singapore with state-of-the-art ability and experience with SARS has thus far reported 106 cases, with 0 death and 7 patients in critical conditions. We will ultimately come up with a global CFR number for the epidemic, but if we were to carry CFR for region or countries these would very markedly differ. A lot of how we end up with this pandemic depend on the quality of government and infrastructure. Here is the Indonesia story: “A Silent Epidemic? Experts Fear the Coronavirus Is Spreading Undetected in Southeast Asia” (Link)

💰 Quality of containment and mitigation are not only a scientific and infrastructure capability question but also an affordability one. There are two stories (both in the New York Times) highlighting that success of containment efforts will be conditioned by health and sick leave benefits. The first story focuses on the fact that not all professions can practice remote work without losing pay. The other story is how a family faced with mandated government quarantine still have uncertainty about who will foot their $3,918 bill. Both of these stories relating to financial needs in countries with limited health and sick leave might impair containment efforts because of economic need (Link and Link)

🎬 Here is a short video of Dr Scott Gottlieb, former FDA commissioner and physician, on CBS “Face the Nation” talking about what the administration did wrong, what lies ahead and what we need to learn for the future. Of particular interest, given that he was the head of the FDA whose business is to approve drugs is his comments on timeline for vaccine and therapeutic: “… a therapeutic- a treatment is going to be more likely to be available in the fall. A vaccine is a much longer way off.”  (transcript is also available in the Link)