COVID19 update, April 20, 2020: sensitivity to sunshine and humidity strongly suggests seasonality

(1) So how seasonal is COVID19? A preliminary technical report from the Department of Homeland Security’s scientific and technical division offers clues. Yahoo News obtained a copy https://news.yahoo.com/sunlight-destroys-coronavirus-very-quickly-new-government-tests-find-but-experts-say-pandemic-could-still-last-through-summer-200745675.html

To cut a long story short: the researchers exposed virus samples to artificial sunlight of varying intensity. The half-life of the virus in the equivalent of midday sun at mid-US latitudes was two minutes: that meant in practice that just 20 minutes, or ten half-lives, would kill 99.9% (or to be precise, 1023/1024) of the viruses. In weaker sunlight, the 

For influenza viruses, a 2009 PNAS paper (http://doi.org/10.1073/pnas.0806852106; editorial commentary at http://doi.org/10.1073/pnas.0900933106 ) showed an inverse relationship between absolute humidity and virus survival/transmission. From the preliminary findings of the DHS group, it appears that the same applies to coronaviruses. Cold and dry weather is best for virus ‘survival’, hot and humid worst; dry but abundant sunshine will still whack it.

These findings suggest that the COVID19 epidemic likely will exhibit similar seasonality as influenza, and that it will be less virulent in sunny climates. I notice Australia and South Africa got off pretty light this round, as these countries were in their antipodal summer and early fall: I assume many are bracing there for an antipodal winter resurgence at the same time as the epidemic might die out in the north. Hopefully, by the time we might see a second winter-spring wave of COVID19 in the Northern hemisphere, there should be a vaccine available.

(2) was the virus already in California in November? Via Erik Wingren, here is a Twitter thread by viral geneticist Trevor Bedford (Fred Hutch and U. Of Washington) that appears to debunk this theory, based on analysis of patient samples from the Seattle Flu Study. 

https://threadreaderapp.com/thread/1249414291297464321.html

“We confirmed that these samples from acute respiratory infections from Oct 2019 through Feb 2020 contained a variety of different viruses including influenza, RSV, rhinovirus, metapneumovirus and seasonal coronavirus. […S]easonal coronaviruses are responsible for ~30% of common colds and are easily distinguished from #SARSCoV2 (the virus responsible for COVID-19) in molecular assays. There is no chance of confusion between these in our assay.[…] If we restrict to viruses sampled in California (highlighted here as larger yellow dots) we see that they fall in with the rest of the US epidemic. There is no chance SARS-CoV-2 was circulating in California in fall 2019. Circulation in CA started in Jan or Feb 2020.Estimating total number of infections is difficult without serology[…] but I’d guess that we’re catching between 1 in 10 to 1 in 20 infections as a confirmed case.  

This would give 5-10 million infections in the US or about 2-3% cumulative prevalence. This is a long way from the 50% (R0 of 2) to 66% (R0 of 3) we’d need for herd immunity. I see #TestTraceIsolate as the only real solution to the problem we’re facing, alongside non-economically disruptive distancing and broad use of masks.”

(3) The “positivity rate” as a metric. This article https://www.theatlantic.com/technology/archive/2020/04/us-coronavirus-outbreak-out-control-test-positivity-rate/610132/ argues in favor of using the percentage of tested people who test positive as a metric for the severity of an epidemic. Seems a little bass-ackwards at first, since normally this will be influenced by how many test kits are available (if they are scarce, normally only people strongly suspected of being infected will get tested), but he does note an intriguing correlation between the positivity rate and the severity of an epidemic.

COVID19 update, April 14, 2020: vitamin D, zinc, testing; end of globalization as we know it?

(1) Roger Seheult MD in his latest update gives a clear discussion of RT-PCR (reverse transcriptase polymerase chain reaction) testing vs. antibody testing.

I spoke to an industry insider about why not more antibody testing yet? I was told that first-generation antibody testing kits achieved accuracies of around 30%, which are “worse than useless”. But accuracies are steadily improving, and we should soon be looking at something comparable in accuracy to a good RT-PCR.

In response to reader demand, Dr. Seheult also gives a link to a hydrotherapy regime that might be useful for prophylaxis and for treatment of mild cases — but only in addition to more conventional approaches: https://www.hydro4covid.com

(2) Nursing school instructor John Campbell, in his latest update, hammers a lot on the beneficial effect of vitamin D for the human immune system. In fact, he looks at the different mortality statistics for ethnic groups in NYC, and finds it fascinating that everybody comes up with socio-economic explanations while overlooking something obvious: at northern latitudes, vitamin D deficiency is quite common among dark-skinned people. (In fact, both the white and “yellow” skin types evolutionarily started as mutations that just happened to allow humans to thrive in less-sunny northern regions.)

He strongly recommends everybody who does not already enjoy abundant sunshine take vitamin D supplements to boost their immune systems — especially people with darker skin types.

On a related note, he looks at the surprisingly mild statistics of the epidemic in Australia, and notes that this militates in favor of seasonality — but again stresses the beneficial effect of vitamin D in the sunny Australian summer and early fall. (I note that South Africa too has so far dodged a major bullet.)

He also notes that homes for the elderly everywhere have appalling statistics — it takes only one or two cases to cause a major outbreak in one unless you really know what you are doing.

One more thing: out of 459 newly diagnosed cases in South Korea, 228 are imports from the USA. While he admits this will not be a representative sample of the US population (whoever still travels may be a businessman or some sort of expert), it does have implications for the Dunkelziffer/”dark case load” in the USA.

(3) Speaking of nutrition, a number of doctors advocate zinc supplements. [Full disclosure: I have been taking such since the beginning of the crisis.] This is emphatically not quack science: zinc is an essential nutrient, and in fact the most common transition metal in the body outside the bloodstream. (Iron in hemoglobin is the most common one if you include it.) Hundreds of physiological processes depend on zinc in the catalytic site of an enzyme, as a co-catalyst or modulator, or as a structural element. This includes the immune system too: I was struck between the similarity between some early COVID19 symptoms (such as loss of taste and smell) and those of zinc deficiency (presumably because Zn is mobilized in great amounts for the immune system). Here is an academic review article on the roles of zinc in the antiviral immune system.

Particularly people who live on vegetarian diets are at risk for Zn deficiency — those who primarily live on red meats or seafood least so.

(4) Urban geographer Joel Kotkin, in a must-read essay , explains how COVID19 (and whatever similar epidemics may lay in our future) will make dense urban centers less attractive to live in. He notes NYC accounts for nearly half of COVID19 mortality in the USA, greater Milan for half the cases in Italy and almost 3/5 of deaths,… “Simply put, pandemics are bad for dense urban areas, particularly those that are diverse and relatively free. This has been very much the case since antiquity. The more global and vital an urban system—Rome, Alexandria, Cairo, Venice, Florence, London, Paris—the more susceptible it is to the pandemics that seem to be occurring regularly over the past two decades. Cities no doubt will recover, particularly if real estate prices continue to fall, but the pandemics limit their upward trajectory and will continue to drive people elsewhere.”

On a related note, former director of the World Bank’s research department Branko Milanovic, https://www.standaard.be/cnt/dmf20200327_04904960 interviewed in De Standaard (in Dutch) argues that (my paraphrase) “We went for the extremes of globalization because technology enabled it. COVID19 showed such an economy is brittle.” He does see a return to some form of globalized economy the day after the crisis, but not again to this extreme extent.

It is noteworthy that such “the end of globalization as we know it” rhetoric is not the province of just the American populist “right”, but that one can hear similar voices around the globe and the political spectrum from the German establishment center-right to the left. I was (pleasantly) surprised to read a scathing article in The Guardian (!!) about the way some Chinese academic publications about the origins of the virus had to be airbrushed by CCP regime fiat. “Oceania is not at war with Eurasia.” [On a related note, Taiwan released an Email from December in which it warned the WHO about patients with a new, SARS-like lung disease.]

The American Interest looks at the long, hard road to decoupling from China. An article in De Standaard (in Dutch) entitled “[shoddy m]asks as a canary in the coalmine”, looks at the trend towards what it calls with an English neologism “reshoring” — bringing production back home to have better control over supply chain and especially quality. This process is said to have been going on for a while in Belgium, but is now being accelerated by COVID19.

Finally, feelgood story of the day: at age 107, a Dutch woman named Cornelia Ras is now the oldest person to survive a bout with COVID19 .

COVID19 update, April 5, 2020: Australia and the seasonality enigma

Australia is a very large country, sure enough, but human settlement is mostly limited to a coastal zone. Still, except perhaps for downtown Sydney and Melbourne, population densities are nowhere near what New Yorkers would take for granted.

According to worldometers., Australia has 5,687 cases, and thus far “only” 35 fatalities. Most cases are in the two most populous states, New South Wales (where Sydney is the largest city) and Victoria (with Melbourne as the largest population center), followed by Queensland (Brisbane being its largest city).

The country has been on what is locally denoted Level 2 lockdown. All arrivals to the country are mandated to self-quarantine for 2 weeks.

But this is possibly the most hopeful graph.

How is this possible? The mind wonders whether Australia coming out of an (unseasonably hot) summer could have something to do with it? After all, seasonality of flu viruses is a well-known phenomenon — but does that even apply to SARS-nCoV-2? To be sure, some things will apply to any viral infection — the vitamin D one gets from being in the sun sure is welcome to the immune system, and of course, in humid weather you don’t get the dried-out mucous membranes that are good ports of entry.

So what about hot and humid locales elsewhere? As of the time of writing, Hawaii has just several 351 cases and 3-4 deaths right now, despite the most populous island (Oahu) being densely populated. The tropical city-state of Singapore has coped well, but this could be explained by other factors without invoking the weather — particularly long-standing preparation since the 2003 SARS epidemic. Puerto Rico has so far just 475 cases with 20 deaths.
But then there is Ecuador, on the literal equator, currently being ravaged by the epidemic, with the largest city Guayaquil being completely overwhelmed. And in the US, despite its famously swampy weather, Louisiana has been hit very hard, particularly New Orleans with a death rate per capita twice that of NYC. (This has been attributed to “super-spread” events at Mardi Gras. I cannot help noting that Belgium’s largest outbreak also has been traced to a Carnival festival in the provincial town of Alken that was not canceled, and several infection foci in Israel have been traced to Purim celebrations.) In fact, hot and humid Florida has a similar number of COVID19 cases as Louisiana — despite having eight times the population!

Clearly, there is more here than meets the eye.

Meanwhile, in Belgium, for the first time during the epidemic, the daily hospital bed occupancy goes down, as the sum of discharged and deceased patients exceeds the number of new admissions.

And Instapundit links to a story about a team from Monash University that has found that the simple antithelmintic Ivermectin — which has been used in humans and animals for decades, in areas where parasitic worm infections are common — kills SARS-nCoV-2 in vitro within 48h.

Finally, Derek Lowe (h/t Cedar Sanderson) has a clear and informative discussion of antibody testing.