The Washington Post says that there have been nearly 300,000 excess deaths between January 26 and October 3 this year. The average death rate by year in the US has been roughly 2.85 million for the last five years. Today, the CDC reported an excess of 299,000 deaths in eight months, with about 2/3 of those deaths accounted for by COVID-19 diagnoses. The total of excess deaths for this year (not necessarily directly due to the virus) will probably exceed 400,000.
The cause of death for about 200,000 of those people was COVID-19, according to CDC. The other 99,000? Unknown. Many of those excess deaths were reported as at-home or in a nursing home and attributed to Alzheimer’s Disease, coronary (heart) disease, stroke, or diabetes. How many such deaths were due to rapid deterioration because of the isolation precautions have not been concluded.
Weekly excess deaths were highest for the weeks ending April 11 (40%) and August 8 (23%.) The greatest excess death rate overall was for Hispanics, and peaks during those same periods were greater than 100% above normal. Figures showing the increases are presented in the CDC report.
The excess death rate for 25 to 44 year olds has gone up 26%; 5,707 of those deaths were confirmed to be due to the virus. How much suicide and homicide rates have increased has not been determined. The total excess deaths for whites increased 11%, while for Hispanics it increased 53%.
The good news is that, over the whole country, hospitalization rates have stayed flat even as daily case counts have increased. Hospitals in the upper Midwest have been swamped, but the rate has not increased commensurate with the increase in cases.
COVID-19 surges in previously untouched places: Poland, Czechoslovakia, Paraguay– even North Dakota.
The Washington Post on October 20 reported new surges in countries that had avoided the virus in the past: Eastern Europe, including Poland and Czechoslovakia were described in this new article. Multiple media have already reported that the northern Midwest US, including the states of North and South Dakota, Montana, Wyoming, and Wisconsin are particularly hard hit.
These areas were previously spared the effects of the pandemic. New measures include the transformation of the National Stadium in Warsaw, Poland into a field hospital. Wisconsin has also set up a field hospital (source: Wisconsin Public Radio) at the site of its state fair in a suburb of Milwaukee. The Wisconsin field hospital could hold about 500 people; nearly a thousand people are currently hospitalized in the state with COVID-19.
There are multiple reasons for the outbreak of pandemic in the northern Midwest. One reason is the Sturgis motorcycle rally in August, where over 400,000 people gathered for an annual event that featured mass parties, drinking, and concerts. One estimate suggested as many as a quarter of a million infections could have been spread by the motorcycle rally (multiple sources.)
Another example is a party held in Prague, Czechoslovakia in early July to “say farewell” to the virus, which was attended by over 12,000 people.
Small multi-family gatherings have been blamed for the spread of virus to many groups who have otherwise remained isolated until this summer.
In Asia, Sri Lanka (formerly Ceylon) developed an outbreak recently. Jordan and Lebanon have been forced to institute measures, including curfews and shutting down bars and nightclubs.
The novel coronavirus has inexorably spread throughout the world, reaching areas that seemed to have been spared in the spring and summer. This winter is almost certain to see continued spread and quite possibly worsening in the US and all over the world.
The US has been a “hot spot” during the entire pandemic. There has been no relief. Daily new cases are averaging over 50,000. Death rates, however, have gone down– a new estimate by the Centers for Disease Control states that the rate is now 0.65% including all asymptomatic and mild disease.
The death rates at the onset of the pandemic were as high as 7 percent, but have gradually trended downwards as many milder infections were found. No one is certain why the severity of illness seems to be less. Nonetheless, the US has seen an average of 700 deaths a day for the last month.
North Dakota, a tiny state of 762,062 people, has had 4 deaths a day recently, almost a 50% increase in the last two weeks, with a 70% increase in cases. People in this state are widely dispersed and don’t travel much; cases are spread from person to person in families and at lunch counters where farmers gather for coffee.
Very few people wear masks even now. I lived there for a couple of years, and I know how far apart people there naturally are– so it’s shocking to me to see an infectious disease travel in that state. There are very few hospital beds per capita and even fewer intensive care or isolation beds.
If North Dakota is being hit, that means that it’s everywhere. If you haven’t gotten it yet, you have been running between the rain drops.
According to the LA Times on October 17, a survey by UC Davis found that, by mid-July, 110,000 new firearms were purchased in California; 57% of them were obtained by gun-owners and 43% by previously non-owners.
This is a dramatic increase and it overshadows the surges reported after other incidents that prompted new purchases, such as threats perceived to “Second Amendment Rights” that were prompted by media scares.
What possible use could a gun be for defense against a virus? Worse than using a cannon on a mosquito. Isn’t that irrational? Doesn’t it suggest that fear is overwhelming many people? Or does it mean that people will do anything they can when nothing can be done?
It seems that people fear unrest or the breakdown of law and order in the wake of the pandemic. One unintended consequence will be an increase in accidents, especially among those who have never owned a gun before and don’t know how to handle or store them.
Another unintended consequence will be an increase in suicides. The availability of a gun is a major factor in the increases in lethal suicide attempts that have been seen over the last twenty years. Most people don’t know that the suicide rate has increased over 50% in the new century.
Firearms are not inherently bad, but they are potentially dangerous, especially to their owners. Unfortunately, ownership of a gun seems to result in accidental and suicidal deaths far more than it does in deaths of home invaders or other miscreants.
Everyone who buys a gun should invest in secure, locked storage for their firearm to prevent misuse (especially by children, who seem to be unduly attracted to them) and keep the weapon out of sight when not needed.
This article from Science magazine, September 24, 2020, in which I have to look up a lot of words… IFN is short for interferon, for example, and TLR is short for toll-like receptor; IRF is short for interferon regulatory factor. That doesn’t clear it up, much. Here is the abstract:
Clinical outcome upon infection with SARS-CoV-2 ranges from silent infection to lethal COVID-19. We have found an enrichment in rare variants predicted to be loss-of-function (LOF) at the 13 human loci known to govern TLR3- and IRF7-dependent type I interferon (IFN) immunity to influenza virus, in 659 patients with life-threatening COVID-19 pneumonia, relative to 534 subjects with asymptomatic or benign infection. By testing these and other rare variants at these 13 loci, we experimentally define LOF variants in 23 patients (3.5%), aged 17 to 77 years, underlying autosomal recessive or dominant deficiencies. We show that human fibroblasts with mutations affecting this pathway are vulnerable to SARS-CoV-2. Inborn errors of TLR3- and IRF7-dependent type I IFN immunity can underlie life-threatening COVID-19 pneumonia in patients with no prior severe infection.
https://science.sciencemag.org/content/early/2020/09/29/science.abd4570
It’s not peer-reviewed yet, so the TLR3- and IRF7-dependent type 1 IFN immunity is not certain.. there’s only 3.5% of patients with severe disease who have loss-of-function genetic variants in specific areas; the other patients don’t have explanations for their severe illness in genetic variants, at least not those that were defined. One small step…
This tweet courtesy of Buzzfeed, dated October 17, 2020 at 5:48 AM.
During this period (since February) I have been using this blog mostly to document new things I have learned about the novel coronavirus. There is a lot that I don’t document. There may be things that I do document that seem trivial. Nonetheless, each post reflects new knowledge that strikes me as important.
This article in The Washington Post (dated October 15) is an example of reporting about things that strike me as important (even if they are not entirely new): a case report, published in Morbidity and Mortality Weekly Report (MMWR) on October 5.
The Post article states that a 13 year old girl who tested negative twice spread the virus to 11 of her relatives during a three week period during which she visited families in four states. Her only symptom was a stuffy nose. Three of her infected relatives with symptoms tested positive only on blood antibodies, not on the nasopharyngeal (NP) swab with reverse-transcriptase polymerase chain reaction (RT-PCR)– which has been described as the gold standard but was early on shown to be false-negative in as many as a third of patients with confirmed infections.
The MMWR reports that eleven relatives who stayed in the same house with the index patient (the 13 year old) developed symptoms and were diagnosed as having COVID-19. Two other relatives who stayed in the same house did not develop symptoms, and six other relatives who stayed outdoors and distanced from the others also remained asymptomatic.
The index patient was exposed in a large outbreak in June and had a rapid antigen test four days after exposure (while she was asymptomatic) that was negative. The test she had was only approved for use during the first five days after symptoms develop, not in asymptomatic patients. This is an example of improper or inadequate testing, followed by failure to isolate.
She did develop a stuffy nose, but apparently was free of symptoms otherwise. This is an example of transmission from a relatively asymptomatic pediatric patient to numerous others, both children and adults. Eventually, she had a blood antibody test that was positive.
Three of the cases did not develop symptoms until two weeks or more after their first contact with the index patient. Two teenagers who were not counted as cases never developed symptoms (one tested negative by RT-PCR and the other was not tested.) Two teenaged cases developed symptoms late; one had a positive blood antibody test and the other was not tested. Both were counted as “probable” cases.
From the conclusion of the report:
This outbreak highlights several important issues. First,
https://www.cdc.gov/mmwr/volumes/69/wr/pdfs/mm6940e2-H.pdf
children and adolescents can serve as the source for COVID-19
outbreaks within families, even when their symptoms are mild
(2). Better understanding of transmission by children and
adolescents in different settings is needed to refine public health
guidance. Second, this investigation provides evidence of the
benefit of physical distancing as a mitigation strategy to prevent
SARS-CoV-2 transmission. None of the six family members who
maintained outdoor physical distance without face masks during
two visits to the family gathering developed symptoms; the four
who were tested for SARS-CoV-2 had negative test results. Third,
rapid antigen tests generally have lower sensitivity (84.0%–97.6%)
compared with RT-PCR testing; negative results should be
confirmed with RT-PCR if used for persons with high pretest
probability of infection, such as those with a known exposure
(4). Fourth, regardless of negative test results, persons should self-quarantine for 14 days after a known exposure (5) or after travel
when mandated by state, territorial, tribal, or local authorities (6).
Finally, SARS-CoV-2 can spread efficiently during gatherings,
especially with prolonged, close contact. Physical distancing,
face mask use, and hand hygiene reduce transmission; gatherings
should be avoided when physical distancing and face mask use
are not possible (7).
Thus, we see that rapid antigen tests are not as sensitive as RT-PCR and that a negative rapid test should be followed by RT-PCR when there is a high pre-test probability of infection. The CDC recommends that people in this situation should self-quarantine for 14 days regardless of the test results.
Equally important is the apparent absence of transmission of the virus to people who keep their distance and remain outdoors, even in the absence of face masking. This suggests that outdoor protest gatherings and even rallies are not likely to result in widespread virus transmission.
This blog post (which is like-fly-elephants-back or “like a fly on an elephant’s back”) is good to read if you need help with “framing” to get through your troubles today. “Framing” is a psychological technique for reducing the obsession we have with the things that are wrong right now.
The blog post explains that we are evolutionarily adapted to concentrate on and remember the things that are wrong, that is, the things we need to pay attention to and fix to get through and live another day (so we can have more children.) So, if we are depressed by thinking about the things that are wrong (that we can’t fix) we need to perform an exercise in framing.
Think hard about the positive things happening today. Fix them in your memory. The negative things will begin to recede. Remember what things were like a year ago– you may be able to think of the positive things, and if you can’t, think harder. The negative things about a year ago have mostly receded (I hope) already, and if they haven’t, think harder. If those negative things are too strong to forget, then you need to speak to a therapist.
Framing, in essence, is just thinking of the negative things as being like a fly on an elephant’s back. The positive things will (I hope) outnumber the negative things.
Here’s another blog I like: “Bits of DNA” and here is the latest post on that blog: “The lethal nonsense of Michael Levitt.” I myself have already contributed several comments to this post. If you have any doubts that trying to achieve “herd immunity” to the novel coronavirus before there is a vaccine is a bad idea, you should definitely read this post.
Finally, if you are really scientifically minded, you should follow “Retraction Watch”, which is a blog that keeps an eye on retractions of scientific papers. It has really blown up in the last several years, and some of its posts are fascinating. In fact, that is where I got the blog post that started this blog post– the one about the fly on the elephant’s back…
Genome sequencing of SARS-COV-2 can help with contact tracing for COVID-19: studies reported in WaPo
These reports in The Washington Post describe how genome sequencing can help speed contact tracing for COVID-19, an effort that is otherwise fraught with difficulty. Contact tracing is limited by tracers’ ability to get information from people who may not be willing to talk or who do not remember with whom they came into contact. Having an accurate sequence can narrow down the number of people who were potential contacts or were infected by the same person.
Other countries have done much better than the US, not only in contact tracing by interviews, but also in sequencing the genomes of many more individual virus isolates.
The new article in WaPo (available free at the link) describes a fictional example of how sequencing helps with contact tracing, using novel graphics to help explain the process:
Imagine a place where politicians and public health experts use every tool at their disposal to contain the coronavirus.
Welcome to the fictional town of Scienceville.
https://www.washingtonpost.com/graphics/2020/health/coronavirus-genetic-code/
I strongly recommend this article to anyone interested in how we can use science to get out of this pandemic more quickly.
A concrete example of how the method works was described in this preprint published on MedRxiv on August 25, 2020. The preprint was also discussed in this story on WaPo. An outbreak in Boston that eventually spread to thousands of people was analyzed by looking at 772 viral genomes, all from within the first week of its spread. Over 80 separate introductions of the virus into Massachusetts were revealed.
Not only do viruses mutate as they are transmitted from person to person, but several variants of a virus may co-infect a single person. This preprint published on BioRxiv (updated on June 2, 2020) discusses significant variation of the virus within individual patients.
The recent tirade by the president includes the fantastic claim that Joe Biden is ineligible to run for president because the Crossfire Hurricane investigation was a coup attempt– and that Hillary Clinton should be in jail too, for her emails.
Of course, members of the current administration, including the presidential daughter, have been guilty of using private emails for official business. The current administration has done more treasonous things than trying to prevent the current president from taking power– which arguably is not treason, but an attempt to save the country from the disastrous “leadership” of the current president…
From this Washington Post story on October 9 comes this comment:
Or [redacted] himself talking loudly on a cell phone in a public place, about his extortion plot with Ukraine. This wasn’t on a government phone, but on a private cell phone.
Why is Hillary continually harassed by the media for doing something that was careless, but not a crime?
[redacted] has done far worse. The day after [redacted] fired Comey, he celebrated with the Russian Ambassador, even gave him classified information, face to face. Of course our news media was excluded, but we have a photographic record, courtesy of the Russian press, who were invited into the Oval Office celebration… that [redacted] had successfully removed the man in charge of the FBI and the Russian investigation. He removed Comey’s successor. He tried to remove Mueller, but since that failed, he fired AG Sessions and replaced him with Bill Barr. Who conveniently omitted the second chapter of the Mueller report in his “summary” to the public. The part where Mueller lays out multiple instances of obstruction of justice… and posts a final warning that we, as a nation, are in serious danger!
Now we are precariously dangling, over the edge, of a banana republic abyss. If [redacted] wins the election
not[even with– ed.] by popular votes, or votes from the electoral collage, but from his personal nominee at the Supreme Court. We are finished! America is done! This may very well be our last election, and the death knell of us all. To be at the mercy of an unrestrained, cruel and vindictive madman, and his henchmen… Nazi Germany ring a bell?… I sometimes wonder, if I am not already dead, and living in a constant state of purgatory. Out of all the month’s of Hair Fuhrer’s reign, this is the one I have feared the most. As well as the months leading up to inauguration day.[redacted] is losing, and he is desperate! No telling what sort of rabbit he will try to pull out of the hat.
https://www.washingtonpost.com/politics/trump-barr-durham-russia/2020/10/09/05ed9842-0a40-11eb-a166-dc429b380d10_story.html
Pray for us! We need all the help we can get, to rid ourselves of this abomination of a man!
To wordpress programmers: the following bugs need to be fixed: First, the () ‘ keys don’t always work; Second, when using ctrl-V to paste a multiparagraph bit of text into a “quote” block, the quote block disappears and has to be re-placed into each paragraph separately; then, the separate quote blocks have to be re-joined into a single block by going to the junction and pressing ‘back’ key, which joins two quote blocks together.
Thanks for fixing the bugs in the ‘insert link’ feature which changed the highlighted text after finishing the insert operation…
According to this article in The New York Times on October 7, 2020, the president called his illness “A blessing from G-d”, supposedly because he discovered the effectiveness of Regeneron’s experimental monoclonal antibody treatment.
The article notes that the president appeared to be more heavily made up than usual, in a darker shade of orange, and that he seemed to be out of breath at times. This is subjective, but it seems to jibe with other information that has come out: namely, the suspicion that he has COVID-19 pneumonia and his apparent well-being is a result of side-effects from his steroid treatments.
Regeneron’s monoclonal antibody therapy development has been supported by a $500 million grant from the federal government as part of its “Operation Warp Speed” program. The antibody is expensive, difficult, and time-consuming to make. About 50,000 doses have been produced, with the capacity to have 300,000 doses by the end of the year. There have been some statements that suggest that the president was given an extra-large dose; 8 grams intravenously was mentioned, but it is unclear whether that represents a normal dose or not.
A single dose of antibodies would last about a month in the body. An antibody is a large protein, not filtered from the blood by the kidneys, and thus would continue to circulate for some time before it would be degraded. There have been suggestions that it would be useful prophylactically as well as for therapy.
To be clear, this treatment was given in a “compassionate use protocol” as it has not been cleared by the Food and Drug Administration (FDA) for general use. While the president claims he wants “everyone” to get it free of charge, there is not likely to be enough available to treat more than a small fraction of patients who would need it. Regeneron announced that they will request an emergency approval for general use. This will short-circuit Phase III trials now in progress since no-one will want to enroll in a trial where they might get a placebo instead of the real thing.
In addition to the monoclonal antibody, the president was given remdesivir in a standard dose as well as dexamethasone. The dose of dexamethasone was not mentioned, but normally six milligrams daily is given, which is considered a modest dose for this drug. The president’s upbeat mood, energy, and lack of fever has been ascribed to side effects of dexamethasone. How long this would be continued is unclear, although it was mentioned that this is the only drug he is still getting.
Some critics have claimed that the president has been behaving in a particularly erratic fashion since his release from hospital. For example, he stopped negotiations on a coronavirus relief package in Congress which one would think would have helped his re-election chances. The president is normally hypomanic all the time, and the steroids would make him even more manic.
Just today, the president refused to participate in the debate October 15 after it was announced that it would be held virtually. His handlers claim that a virtual debate would allow his opponent to use a teleprompter, a truly absurd accusation. It appears that the president’s real fear is that the moderators would find it easier to cut off his microphone when his opponent is speaking– since he used his open mic to talk over and interrupt his opponent repeatedly during the last debate.
In addition, the president may fear another debate after his drop in the polls following the first debate. Apparently many people were put off by his behavior, calling it bullying and disruptive.
Some misleading statements have appeared, as well as a lack of transparency about the president’s overall condition. For example, the results of his lung scans have not been given; some experts have suggested that the president has pneumonia (which would explain why he was given dexamethasone, which is usually reserved for people with severe disease who are on continuous oxygen supplementation.)
Another example of misleading information was the statement that the president has tested positive for antibodies to SARS-COV-2. It was pointed out that the positive test would most likely be a “false positive” given that he has just received a dose of exogenous antibodies. In fact, we wonder why one would even test for antibodies after having given them, unless they have some way of distinguishing exogenous from endogenous antibodies. For example, a test for IgM antibodies might be performed (the exogenous antibodies are all IgG.) This was not explained.
A final example of lack of transparency that has been brought up: no results of testing for the presence of the SARS-COV-2 virus after the treatment have been given. This test would determine whether he is still contagious to others and help us to determine how well he has responded to treatment. This particular information is especially important.
At last, we have the question of when was the last time the president tested negative for the virus. People who came to the debate last Tuesday were supposed to be tested, but the Republican contingent arrived too late and they were not evaluated. This glaring lack of testing should have halted the debate, but instead the Republicans came in and refused to wear masks during the proceedings.
The lack of information about the president’s virus test results makes his positive test on Thursday night, about 48 hours after the debate, extremely concerning. Was he already positive or during the window of contagiousness at the time of the debate? A lack of information, which the president’s doctors have failed to clear up, has us all concerned about the exposure of others at the debate– especially the president’s challenger in the upcoming elections.
Fortunately, Joe Biden has tested negative so far, but he is, like the rest of us, still not out of the woods.
Conrad Theodore Seitz 