COVID19 update, June 30, 2020: droplet and aerosol transmission; herd immunity requires as little as 20%?

Been a very busy day at work, but let me just share with you two things:

(a) a long essay that Jeff Duntemann drew my attention to:

Aerosols, Droplets, and Airborne Spread: Everything you could possibly want to know by Justin Morgenstern MD, an emergency physician located in the greater Toronto area.

The essay is long but very much worth your while.

(b) Coronavirus: could it be burning out after 20% of a population is infected? We pointed earlier to a preprint that showed that, if susceptibility to the infection isn’t assumed to be all or nothing, that this leads to a second-order mathematical model that predicts much lower herd immunity thresholds than the common first-order model. See also (h/t: masgramondou): 

But it is unlikely that lockdowns alone can explain the fact that infections have fallen in many regions after 20% of a population has been infected – something that, after all, happened in Stockholm and on cruise ships. 

That said, the fact that more than 20% of people have been infected in other places means that the T-cell hypothesis is unlikely to be the sole explanation either. Indeed, if a 20% threshold does exist, it applies to only some communities, depending on interactions between many genetic, immunological, behavioural and environmental factors, as well as the prevalence of pre-existing diseases. 

Understanding these complex interactions is going to be necessary if one is to meaningfully estimate when SARS-CoV-2 will burn itself out. Ascribing any apparent public health successes or failures to a single factor is appealing – but it is unlikely to provide sufficient insight into how COVID-19, or whatever comes next, can be defeated.

COVID19 update, June 27, 2020: The Economist on how COVID-19 changed the office; reduced hospital fatality rates in the UK; initial infection rates may have been 80 times higher than reported

(1) The Economist has a video on how COVID-19 is changing the office building as we know it. Working from home used to be the exception — companies insisted that you show up in the office even for work that can be done from home very well

Now COVID-19 has forced companies to make a virtue of necessity — and it turns out this works pretty well. The video claims that 47% of all existing jobs in Switzerland can be done from home, with somewhat lower percentages for other developed economies, but much lower percentages for developing countries.

And guess what: considering how expensive office space in premium locations is (downtown Hong Kong, with about $250/mo/square meter, probably takes the case), companies can save a ton of money by letting WFH-feasible jobs be done from home and downsizing their office locations.

This will have a ripple effect: a WSJ journalist interviewed in the video claims that every Manhattan office job created employment for 5 people in the service industry (bars and restaurants, custodial,…) 

Of course, one man’s meat is another man’s poison, so it is quite possible that the lost jobs catering to downtown office worker may be partly or even wholly offset by other jobs created elsewhere — as people working from home will want to upgrade their housing arrangements, or will have more disposable income to spend on family amenities.

I would not say that COVID-19 will bring the end of the Dilbert cube farm as we know it: simply that it triggered a transformation that was waiting to happen, only delayed by managerial inertia.

(2) There are reports from various countries that hospital mortality rates have dropped considerably from the peak of the infection. The Daily Telegraph reports that mortality of COVID19 patients admitted to English hospitals has dropped fourfold, from 6% in April (the peak of the epidemic there) to 1.5% now. A number of explanations are proffered:

  • Doctors have gotten better at managing the disease and mitigating its severity
  • Hospitals have enough capacity now that milder cases can now be admitted that would have been sent home earlier: as these mild cases almost invariably recover, this drives down the statistics
  • The most vulnerable older people either have already died or recovered, or we have simply gotten better at shielding the elderly from infection. 
  • [not in the article] the better, sunnier weather reduces vitamin D deficiency

(2b) [Hat tip: Erik W.]

An epidemiological study from Penn State U. suggests that the initial COVID19 infection rate in the US may have been about 80 times the officially reported one. The paper can be read directly here:

Quoting from the abstract:

Detection of SARS-CoV-2 infections to date has relied heavily on RT-PCR testing. However, limited test availability, high false-negative rates, and the existence of asymptomatic or sub-clinical infections have resulted in an under-counting of the true prevalence of SARS-CoV-2. Here, we show how influenza-like illness (ILI) outpatient surveillance data can be used to estimate the prevalence of SARS-CoV-2. We found a surge of non-influenza ILI above the seasonal average in March 2020 and showed that this surge correlated with COVID-19 case counts across states. If 1/3 of patients infected with SARS-CoV-2 in the US sought care, this ILI surge would have corresponded to more than 8.7 million new SARS-CoV-2 infections across the US during the three-week period from March 8 to March 28, 2020. Combining excess ILI counts with the date of onset of community transmission in the US, we also show that the early epidemic in the US was unlikely to have been doubling slower than every 4 days. Together these results suggest a conceptual model for the COVID-19 epidemic in the US characterized by rapid spread across the US with over 80% infected patients remaining undetected.

Note that a “Dunkelziffer” of 80:1 is in the 50:1  – 85:1 range the [much-maligned] original version of the Santa Clara serological study (Ioannides et al.) had.

(3) “Covid toes” may actually not be a COVID-19 symptom or sequel after all, but simply result from lack of physical activity , reports UPI.

The “symptom” mirrors that of a condition called Chilblains, or perniosis, a painful inflammation of the small blood vessels in the skin that occurs after repeated exposure to cold air, they said.

(4) [Hat tip: Jeff Duntemann] A retired anesthesiologist on masks:

To protect yourself, you need an N95 respirator mask that is properly fitted.  Then you need to re-sterilize it every four hours using UV light or properly dispose of it and start over with a new one.  That is too expensive for most people.

The outside world is the safest place you can be.  The state of Florida has zero cases of COVID-19 that can be traced to outside transmission.  During the day, solar UV kills all viruses very quickly, and there’s always enough air movement to disperse aerosols, making them non-infective.  It has become clear that virtually all cases have been spread in closed spaces with prolonged (>10 minute) exposure.  And as the studies I’ve cited show, other than N95s, masks are no help there.  For that matter, six-foot spacing doesn’t help, either, since the aerosols that transmit the virus aren’t adequately dispersed.

COVID19 update, May 20, 2020: reinfection unlikely; correlation between HbA1C and vulnerability to severe disease; German RKI recommendations on masks

Just a quick update today, as workday has been pretty intense.

(1) Dr. John Campbell’s vlog has a special edition on a new report from the South Korean CDC. There have been a number of worrying reports that people tested positive again after recovering, fueling speculation that this could become a chronic disease, like HIV or Hepatitis B. (As he explains, these viruses slip into the cell nucleus and insinuate themselves into the human genome.[*]) Worse, that people could be infectious for life.

However, as it turns out, the tests were false positives. The RT-PCR test detects the presence of a short fragment of RNA that’s specific to the virus, but cannot tell whether this is a remnant of long-destroyed virus, or belongs to a viable virus particle. So when cured patients cough up worn-out lung cells in their sputum, such remnants will trigger a false positive test. This appears to have been the case here.

Just as I was typing today’s update, Dr. Seheult posted a video on the exact same study. He has the link to the English version of the Korean CDC report in the description. (Dr. Campbell had to go off second-hand reports, as only the Korean-language version had been released at the time.) Dr. Seheult’s video adds much more detail.

I believe this is the great COVID19 news of the day.

(2) Yesterday, the good doctor posted another video with a couple of different segments. One is about a recently published evaluation of four new antibody tests using arrays of known positive and negative samples. “Comparison of Four New Commercial Serologic Assays for Determination of SARS-CoV-2 IgG”

The second is about a paper in the Journal of Diabetes Research, showing a clear link between high levels of glycosylated hemoglobin (high HbA1C values) and severe COVID19. “Glycosylated Hemoglobin Is Associated With Systemic Inflammation, Hypercoagulability, and Prognosis of COVID-19 Patients”

Those of you who are struggling with diabetes (or are trying to avoid going there, as I am) will recognize HbA1C — while blood glucose gives an immediate picture, HbA1C gives an “integral”, as it were, of your blood sugar picture over the last few months, and is less prone to fluctuation due to exertion or recent food or drink intake. [**]

(3) Recently, the topic of face masks has generated extreme passions on both sides, at least in the US. (In Israel, the mask mandate came about as a compromise between the Ministry of Economics, which pushed for accelerated reopening of stores, and the Ministry of Health which wasn’t keen on that. The latter acquiesced in exchange for getting its way on masks. As far as I can tell in my Tel-Aviv borough, the mandate is not being enforced visibly, and indeed in some places is honored more in the breach than the observance.)
Now I would like to think that both sides in the US debate would agree that Germany doesn’t mess around in such matters. (Besides, its statistics in the epidemic speak for themselves.) So what does the Robert Koch Institute (RKI) — their infectious diseases authority — have to say on the matter? Here is their position paper on the subject, which may surprise both the “no masks!” and “must wear masks, because science!” sides. Summarizing in translation:

  • most important are good hand hygiene, sneeze-cough hygiene, and maintaining an effective distance of 1.5m (5ft)
  • high-grade multilayer masks are foreseen for healthcare workers
  • we recommend keeping a simple textile mask handy to wear in specific situation in public, namely where no 1.5m distance can be maintained (e.g., on public transit). [***]
  • that said, some people are unable to wear masks at all due to health conditions
  • links to “proper wear and care” recommendations for different mask types
  • notably absent: any recommendation, let alone requirement, that people need to wear masks in public at all times

[*] What Dr. Campbell skips over is that the RNA is first copied to a double strand of DNA using an enzyme called reverse transcriptase — yes, the RT of RT-PCR testing.

[**] Our red blood cells don’t last much longer getting pumped around our bodies, and hence are continuously replaced by newly manufactured ones, with an average turnover of about 4 months.

[***] I feel compelled to belabor the point that momentary passing-by at closer distance does not mean you are suddenly at risk of infection. Our own Ministry of Health, which recommends 2m (6ft6), only counts exposure as ‘closer than the safe distance for 15 minutes or longer.

COVID19 update, May 10, 2020: more on COVID19 outbreaks at German meat processing plants; BND drops bombshell about China and WHO; miscellaneous updates

(1) COVID19 outbreaks at meat processing plants are not just a US phenomenon anymore. Apropos the report yesterday of large outbreaks at two such plants at opposite ends of Germany (here and here, both articles in German): it was pointed out that many at these plants are foreign workers living in very tight quarters. But in addition, a friend who is a Ph.D. biologist as well as a volunteer EMT responded: “Meat packing is one of those physical jobs (so high respiration rate) which happens in close quarters, in a cool and air[-conditioned] environment. Most other airconditioned environments are probably not so close together and/or do not involve the level of physical labor. The other possible idea is that meat surfaces and the aerosols generated cutting with band-saws might be a good place for the virus to survive and thrive.”

(2) RedState, quoting German weekly Der Spiegel, has a bombshell: The BND (Bundesnachrichtendienst or Federal Intelligence Serivce, Germany’s equivalent of the CIA — in a report that is otherwise critical of Trump— says the following (my translation from the original German):

“Nevertheless, to the BND’s knowledge, China urged the World Health Organization (WHO) at the highest level to delay a global warning after the outbreak of the virus. On 21st January China’s Head of State Xi Jinping, during a telephone conversation with WHO leader Tedros Adhanom Ghebreyesus, asked the WHO to withhold information on human-to-human transmission and to delay a pandemic warning. According to the BND, China’s information policy has resulted in the loss of four to six weeks worldwide to fight the virus.” [*]

Confirmation of what was obvious to many of us.

(3) Miscellaneous updates:

{*] original wording: “Nach Erkenntnissen des BND drängte China die Weltgesundheitsorganisation WHO allerdings nach dem Ausbruch des Virus auf höchster Ebene dazu, eine weltweite Warnung zu verzögern. Am 21. Januar habe Chinas Staatschef Xi Jinping bei einem Telefonat mit WHO-Chef Tedros Adhanom Ghebreyesus gebeten, Informationen über eine Mensch-zu-Mensch-Übertragung zurückzuhalten und eine Pandemiewarnung zu verschleppen. [new paragraph] Nach Einschätzung des BND sind durch die Informationspolitik Chinas weltweit vier bis sechs Wochen für die Bekämpfung des Virus verloren gegangen.”

UPDATE: via masgramondou, a second analysis of Neil Ferguson’s COVID19 model code that is even “better” (ahem) than the first. I’ve encountered enough modeler hubris in my day job that I believe I recognize it when I see it.

COVID19 update, April 1, 2020: not April Fools edition

(1) Dutch scientists discovered that SARS-nCoV-2 can be detected in a city’s wastewater even before anybody realizes they are sick. “[Medema and coworkers] detected genetic material from the coronavirus at a wastewater treatment plant in Amersfoort on March 5, before any cases had been reported in the city, located about 50 kilometers (32 miles) southeast of Amsterdam. “

(2) Chemical and Engineering News, the house organ of the American Chemical Society, has more on remdesivir as well as on another antiviral discovered at Emory, EIDD-2081. While remdesivir needs to be administered intravenously, EIDD-2081 can be given orally. On the other hand, EIDD-2081 hasnever been tested in humans while remdesivir underwent safety testing back in 2015 (as a potential ebola drug.

(3) WIRED has a long story about masks. “Let’s face it: they work”. Most of the evidence concerns other respiratory viruses:

“A 2011 review of high-quality studies found that among all physical interventions used against respiratory viruses—including handwashing, gloves, and social distancing—masks performed best, although a combination of strategies was still optimal.”

Fortunately, the available evidence suggests that for most people in most situations, an N95 is not a necessary form of protection against Covid-19. If we eventually have a surplus of surgical masks, which are much more comfortable and affordable than respirators and still provide excellent protection, they would be an ideal choice for universal masking. In the meantime, homemade masks made from tightly woven yet breathable fabric are the best option and certainly better than nothing. A piece of cloth will never be as good as a manufactured filter, but it can still smother the brunt of a cough or sneeze and impede other people’s respiratory droplets.

Read the whole thing.

Seattle police during the 1918 “Spanish flu” pandemic

(4) According to a new epidemiological analysis in British medical journal THE LANCET: the infection fatality rate (IFR) of COVID-19 is 0.657% (confidence interval 0.389-1.33 %) and the adjusted case fatality ratio (CFR) is 1.38% (confidence interval: 1.23-1.53%). [mention in MSM: ]

(5) Beijing’s “mask diplomacy” appears to be backfiring, as many of the masks and test kits sent out turn out to be defective or substandard.

“Spain’s health ministry last Thursday said it had withdrawn around 58,000 Chinese-made test kits after it emerged that they had an detection accuracy of just 30 percent. The normal accuracy rate is more than 80 percent, local media reported.”

The story of a shipment of 600,000 mouth masks for healthcare workers being disapproved by the Dutch authorities as not meeting basic quality standards is all over the Dutch-language media, e.g., here in De Telegraaf.

(6) GenomeWeb reports that a genetic cancer testing company, that has seen demand slump as “non-urgent” medical tests are put off due to COVID-19, is now retooling for COVID-19 testing.

(7) Israel starts passive immune therapy experiment. This happened only today, as they needed a plasma donor who was not only cured, but had subsequently tested negative for the virus at least twice.