Day 392: Where Has All the Flu Virus Gone?

Scott Adams got into a kerfluffle on Twitter that led me to an interesting article about the disappearing flu virus:

If the wearing of masks was capable of almost entirely removing influenza from circulation, as has been observed, then this approach would also eliminate SARS-CoV-2. Indeed, SARS-CoV-2 virions, which range from ~50 to 200 nm, are similar in size to those of influenza (~80 to 120 nm), adenoviruses (~90 to 100 nm), and other endemic betacoronaviruses, such as HCoV-OC43 and HCoV-HKU1 (~118 to 140 nm), which share the same genus as the novel virus. Since SARS-CoV-2, influenza, and various other respiratory viruses are largely spread by fine-particle aerosols in indoor settings, an intervention that works for one should logically work for the other. But in spite of the stringency of interventions, SARS-CoV-2 cases have skyrocketed. At the same time, infections of endemic betacoronaviruses, which should respond to NPIs in the same manner as SARS-CoV-2, have also largely disappeared [though adenoviruses have not].

Massachusetts cases were up a third of a percentage point both yesterday and today.

Day 390: Herd Immunity

David Friedman suggests that we've already hit herd immunity, not from the rapid rate of vaccination but from the flood of holiday cases:

I have been looking at the number of new cases per day, both for Santa Clara County and for the U.S., and the pattern is striking. Over the past month, number of new cases per day in the U.S. has gone down by a factor of about 2.4, for the county by a factor of about 3.5. Death rates are also down, although by much less, but one would expect death rates to lag case rates by a few weeks. I don't think the explanation can be the weather, since it's still winter. I don't think it can be vaccination because there has not yet been enough of it to substantially affect the case rate.

He's pretty optimistic that this is the end, all vaccination aside.

Johnson & Johnson's one-shot vaccine has emergency FDA approval.

Massachusetts cases were up a third of a percentage point today.

Day 384: Covered Up

Loyal readers may recall that the true extent of New York State's nursing home deaths came out back around Day 363. One might think that counting is hard, even if it's your job, but one would (allegedly) be wrong; the New York Post reports that Melissa DeRosa, Cuomo's secretary, admitted to covering up the numbers for fear of federal prosecution.

In addition to stonewalling lawmakers on the total number of nursing home residents killed by COVID-19, Cuomo’s administration refused requests from the news media — including The Post — and fought a Freedom of Information lawsuit filed by the Empire Center on Public Policy.

Instead, it only disclosed data on the numbers of residents who died in their nursing homes.

But after state Attorney General Letitia James last month released a damning report that estimated the deaths of nursing home residents in hospitals would boost the grim tally by more than 50 percent, Health Commissioner Howard Zucker finally released figures showing the combined total was 12,743 as of Jan. 19.

In other cover-up/miscounting news, Taiwan News reports on 150,000 missing pensioners in Wuhan:

On Wednesday, RFA [Radio Free Asia] published government figures released by the Hubei Civil Affairs Department showing that 150,000 names had vanished from the list of pension recipients over the first three months of 2020, when the outbreak in Wuhan was at its peak. These subsidies are paid to elderly residents in Hubei over the age of 80 who are in need of financial assistance.

[...]

Given China's rapidly aging population, an academic who wished to remain anonymous told RFA that there should be an increase in the number of elderly collecting such subsidies, much less such a dramatic decrease. The scholar believed that the massive burden on the health care system brought on by the outbreak could have indirectly "led to an increase in the number of deaths from other diseases."

P.S. Massachusetts cases were up a third of a percentage point today.

Day 383: SSC and COVID Resurgent

Of 110 million coronavirus cases worldwide, 28 million have been in the US, with 500,000 deaths. India at #2 is nearing 11 million cases, and #3 Brazil is nearing 10 million (and also boasts its own strain these days). Russia and the UK are close as thieves with 4 million each, though some would say Russia's numbers are much higher, at least for deaths:

Russia’s official figures for the number of dead during the corona pandemic come from the Rospotrebnadzor authority and currently stand at 79,000 dead. However, on Monday the country’s statistics institute published data, revealing that the excess mortality in 2020 stood at 358,000, compared to the average deaths from the last couple of years.

Deputy Prime Minister Tatiana Golikova announced that 31 percent of the excess mortality rate in 2020 was due to covid-19, in other words 111,000 deaths. But the official death toll sent daily to the WHO is still below 80,000 dead.

Independent Russian newspaper Meduza now states that the Ministry of Health for the Moscow region has estimated that 98-100 percent of the excess mortality is due to the corona pandemic.

Loyal readers may recall that the New York Times killed Slate Star Codex back in the summer, for having gotten too much right about COVID. Since then, Scott Alexander has recovered from being set upon by the bullies of the legacy media, and has started up a new blog (Astral Codex Ten), where he has made new predictions of more coronavirus from more strains and also written up his thoughts on the weak tea science behind Vitamin D for COVID. His humor is back, too:

If blacks get coronavirus more often because of socioeconomic reasons, and also have lower Vitamin D, anybody looking at coronavirus infection rate without adjusting for race is suspect. Merzon and the Israelis didn't control for race (and Israel is quite racially diverse). Kaufman and the Quest team say they adjusted for race, but if you look at their paper, they didn't have access to race data for any participants, so instead they looked at what zip code they were in, coded it as majority-black or majority-white or whatever, and adjusted for that. I live in a majority black zip code, so apparently I'm black now. And my lived experience as a person of color, which I hear is more trustworthy than any scientific study, tells me this is a big enough loophole to invalidate the entire paper.

On the home front, Massachusetts is back up to #15 in the country, though yesterday's numbers were up only a fifth of a percentage point.

P.S. Massachusetts cases were up a quarter of a percentage point.

Day 374: Even the Yanomamo

The Guardian reports that ten Yanomamo children died of COVID last month. It's unclear what the definition of "children" is in this case (it may include 20-year-olds), but they also report seven previous Yanomamo victims under the age of two out of 32 total deaths. So it's clear that real children are involved this time, though it's not as clear that these deaths were from coronavirus rather than some other communicable disease with similar symptoms. PlagueBlog speculates that this unusually high death rate among children may be related to the lack of off-target vaccine protection in the isolated population.

In other international news, WebMD reports the failure of AstraZeneca's vaccine against South Africa's variant coronavirus strain B.1.351. The CDC tracks variant strains in the US, only one of which (B.1.1.7) has reached Massachusetts.

Massachusetts' cases were up a quarter of a percentage point today, due to the usual Monday reporting lull (of Sunday's data).

Day 373 Retrospective: Football Stadiums

Superbowl Sunday saw the first anniversary of Li Wenliang's death. Earlier in the week, the NFL promised all its stadiums for vaccination sites. Here in Massachusetts, the Patriots' stadium is already in use for vaccine administration. It seems to PlagueBlog that an open-air football stadium is hardly the most appropriate spot for medical treatment, but it seems that efficiency outweighs everything in these crazy time—unless you're talking about software.

Here in Massachusetts the feel-good news of the weekend was about an Arlington mom who built a more convenient vaccination scheduling website than the state's (which was already better than the feds') while on maternity leave. Also, cases were up three fifths of a percentage point on Sunday.

Day 372: But Sweden...

Last June, Nature published a much-cited paper modeling the efficacy of lockdowns vs. other non-medical interventions, "Estimating the effects of non-pharmaceutical interventions on COVID-19 in Europe" (where "intervention" means the government did it), and concluding that lockdowns, acting alone, saved three million lives. PlagueBlog will not be publishing the authors' names because the math is too embarassing, but Philippe Lemoine had no such compunctions when he tore the paper a new one back in a December blog post: "Lockdowns, science and voodoo magic".

Based on what I have seen by playing a bit more with simulations, it seems that the model tends to ascribe most of the reduction in R_t to whatever intervention took place after the peak of infections and was closest to that peak or, if no intervention took place after the peak, to the last intervention. This makes sense when you think about it. Indeed, if you assume that one intervention is responsible for the overwhelming majority of the reduction in R_t, the peak of the infections curve you infer is going to be located at the time this intervention took place. So both the infections curve and the deaths curve you infer are going to be shifted to the left or to the right depending on whether you assume that R_t collapsed sooner or later. Moreover, since both the infection curve and the distribution of the delay between infection and death are right-skewed, the death curve, on which the model is fit, is also going to be right-skewed. Now, when a curve is right-skewed, the fit is going to be worse if the peak of infections, hence also the peak of deaths, inferred by the model is to the left of the actual peak than if it’s to the right. So the model is better off ascribing most of the reduction in R_t to the intervention that happened closest to the peak of infections but after it, unless that intervention happened really too late after the peak.

It seems that it’s those purely mathematical considerations and the fact that lockdowns were implemented last and before or not too late after the peak of infections in every country, not the fact that lockdowns really are the only intervention that have a meaningful effect on transmission, which explain why the model reached that conclusion.

Well, not quite every country. Sweden never had a lockdown, so the model instead ascribes all non-medical efficacy to their last intervention, the cancellation of public events—a measure that had no effect elsewhere because it was followed by the supremely effective lockdowns, but was truly miraculous in Sweden. The paper doesn't show this explicitly because all European data has been pooled together, so Lemoine had to run his own unpooled calculations to see the Swedish miracle. Much of his post is devoted to the alleged malfeseance of the original authors in omitting this damning per-country calculation:

I actually think that not mentioning this fact about the country-specific effect in Sweden comes very close to scientific malpractice. It makes their main conclusion, which as [I] just noted can be seen to be implausible without any complicated modeling, very hard to maintain and I have a hard time believing they weren’t aware of that and that it’s not why they carefully avoided the topic in describing their results. In any case, what is clear is that, once you realize that the model was only able to find that no intervention except lockdowns had a meaningful effect on transmission by estimating a huge country-specific effect for Sweden, it becomes impossible to take that conclusion seriously.

The blog post was not the end of the story. A few weeks later, Nature finally published a Swedish response to the paper that it had been sitting on for six months and that largely agrees with Lemoine. (He discussed it and other responses in a second blog post.) It also inspired Lemoine to come up with his own theory about Swedish deaths, that the disease had progressed further there than elsewhere in Scandinavia. We at PlagueBlog still prefer the "dry tinder" theory of Sweden (that, rather than having an outsized number of deaths due to the lack of lockdowns, Sweden had more deaths because, after two mild flu seasons, they had an outsized population of fragile old people hanging on by the proverbial thread), but both may very well be true.

If you enjoyed that takedown, Lemoine also takes on the hydroxychlorquine question. In any event, PlagueBlog recommends that you check whether Sweden immediately disproves your theory before you publish it in a respectable scientific journal.

Day 368: Groundhog Year

So the groundhog saw its shadow, which means we'll be having six more months of COVID. PlagueBlog regretfully welcomes you to Year 2, Day 2 of COVID in Massachusetts.

In other annual news, the WHO has finally gone to Wuhan, more than a year after the outbreak began.

Despite the abysmal failure of the CDC's vaccine scheduling software, the new COVID year brings us more vaccinations than victims:

As of Monday afternoon, 26.5 million Americans had received one or both doses of the current vaccines, according to data compiled by the Bloomberg Vaccine Tracker. Since the first U.S. patient tested positive outside of Seattle a year ago, 26.3 million people in the country have tested positive for the disease, and 443,000 have died, according to data from Johns Hopkins University.

For reasons related to different software and general wariness, Massachusetts is behind in administering the vaccine:

The rollout in Massachusetts fell behind from the start. Other states, including Vermont, New Hampshire, Maine, and Connecticut began vaccinating nursing home residents and staff a week before Massachusetts started on Dec. 28. Since then, both of the required rounds of doses have been given at nursing homes in other New England states. In Massachusetts, which has one of the nation’s highest virus death rates in long-term care, most nursing homes have just completed their first round.

On the variant front, a travel ban against the South African variant strain continues to expand.

P.S. Massachusetts cases were up four ninths of a percentage point today.