photo courtesy of engin akyurt and pixabay.com
These tidbits have come from a wide search of recent literature on COVID-19 (coronavirus disease 2019) and its causative agent, SARS-COV-2 (severe acute respiratory syndrome-coronavirus 2).
First, you should have blood type O positive. Not easy to do, but if you can arrange to be born this way, that would be nice. There is an association in multiple surveys between type O blood and less COVID (sorry, no reference at hand but there are several available).
Second, any diseases that you may have, such as asthma, high blood pressure, diabetes, kidney insufficiency, coronary heart disease, in fact any disease at all, even if it’s only a genetic tendency about which you are completely unaware, you should not have. If you do have it, keep it under rigid control. Now is the time to lose that weight, get your blood sugar down, lower your blood pressure, and take long-term asthma control medications like topical corticosteroids (inhaled cortisone and/or cortisone nasal spray)– but don’t take oral cortisone or other potent anti-inflammatories, unless your doctor tells you to do so. This is common sense, and many studies show an association between chronic diseases and high mortality in COVID.
Third, if you have a vitamin D deficiency, or even think you might, you should take replacement doses of vitamin D3. This is available over-the-counter– unfortunately, the research on all-cause mortality (death for any reason) is not conclusive (yet) but it is clear that even large doses of vitamin D3 are not bad for you (I’m gonna get dissed for saying that, but so be it). Many people are low in D and don’t know it because it is still not routinely evaluated with the widely available blood test. I won’t recommend a specific dose of D3, but you can ask your nutritionist.
On the other hand, vitamin A is potentially toxic and has not been seen to have any benefit in severe COVID-19 (see the above-referenced study again). Multivitamins are fine, but they haven’t been shown to lengthen your life in general, so they’re optional unless you have a terrible diet already.
Fourth, you should be young at heart. Try singing, the song that is. You don’t have to be chronologically young (again, see the above-referenced study). A positive mental attitude will help you no matter what else is happening. You can still get sick, but having a good attitude and not being a pain in the neck will help others around you to rally to your side.
Finally, if you should have the misfortune to be exposed to a patient with COVID, try to make sure it’s a very light exposure. I’m speculating here, but the experience with many other infectious diseases (like smallpox) is that small exposures can lead to mildly symptomatic disease, while massive exposures can be overwhelming. This aspect of the new coronavirus has not yet been studied, which is not surprising given that the disease is only four months old.
Until a vaccine is widely available or we have a positive blood antibody test, it is incumbent upon us (we are obligated to) be careful and try to stay healthy in case we are exposed despite physically distancing ourselves from other susceptible people.
Coronavirus by Engin Akyurt via pixabay.com (open access)
(Nota bene: This is an enlargement of my last post, with a title altered to be more specific and a few new sentences at the beginning about the initial stages of the outbreak. My statement about the size of the outbreak in China is merely speculation, but it is informed speculation.)
When COVID-19 was first detected in Hubei, China in late November or early December of 2019, it presented as an unusual outbreak of atypical viral pneumonia. Patients with this disease presented with fever, dyspnea, cough, and chest pain. They had negative tests for influenza, respiratory syncytial virus, and bacterial pneumonia, but their blood showed signs of raging infection: elevated C-reactive protein, abnormal white blood cell counts, and dropping oxygen saturation (blood oxygen levels). Their chest CAT scans (computer-assisted tomography) showed a characteristic pattern of hazy, “ground-glass” opacities (areas of increased density) in the lungs, usually bilaterally (on both sides). Some of these patients inexorably went downhill, stayed on the ventilator (a machine which pumps oxygenated air into the lungs through a tube inserted into the windpipe, while the patient is heavily sedated) for long periods of days and weeks, and developed multiple organ failure. Their kidneys, livers, brains, muscles, and finally hearts, broke down. Some of them died.
This was the picture of COVID-19 as it was presented to the world. No-one seemed to realize that the infection was in most cases completely asymptomatic (without any symptoms of illness) or trivially symptomatic (with a runny nose or fatigue). It was really looking at the tip of the iceberg to see the new virus as pneumonia. Within three months, the virus spread around the world, leaping country borders and side-stepping quarantines. It spread so fast that even our president was unprepared (although he later said that he had known it all along and was just making happy talk to keep people from panicking). /s
The Chinese government, once they realized (unwillingly) that they had a potential pandemic on their hands, reacted with draconian severity. Quarantines on patients were enforced by the police, who were used to keeping dissidents under close observation and applying all sorts of pressure to keep people under control. Contacts of known cases were separated from their families and put into rudimentary holding cells repurposed from hotels and inns. Eventually, the doctor who had sounded the warning about a new form of atypical pneumonia was vindicated– posthumously.
He received an official apology for being called in to a police station and being told to shut his face– unofficially arrested for making a case report– and the officials who oversaw his silencing were dismissed. His relatives appreciated the gesture, but he had already died of COVID-19. We can assume that he faced massive exposure to the virus in the course of his work and succumbed to an overwhelming infection.
Even now, the true scale of the epidemic in China is unknown. Estimates of the actual number of patients involved have not been publicized, in part for fear of sounding alarmist. The government still reports only clinical cases of the viral illness that require significant intervention as “positive for viral RNA” although it has reflexively quarantined anyone who comes in contact with known cases. They do have a count of people known to be exposed and known to have tested positive, but they have not revealed these numbers.
While it is unfair to the rest of the world not to reveal the true figures for known infections, the Chinese have done the only thing that could have been effective against an infectious agent of this degree of “sneakiness”. The Chinese system routinely violates civil liberties, but it is effective against an agent that “flies under the radar” in about 90% of cases. I, personally, based on developments described below and in my last few posts, roughly estimate that the true case count in China is five to ten times as high as what has been officially reported.
A study published in BioRxiv on April 6 analyzes the reports from Iceland, where a community-wide voluntary random sampling program is underway. These studies are based on two sample sets, as the abstract explains:
The criteria for testing within the Icelandic medical system, processed by the National University Hospital of Iceland (NUHI), have also been targeted at high-risk individuals, but additionally most Icelanders qualify for voluntary testing through the biopharmaceutical company deCODE genetics.
Based on these samples, the authors of the BioRxiv study analyzed the data and found that:
Our primary estimates for the fraction of infections that are undetected range from 88.7% to 93.6%.
This report and the reports from California described in my previous posts reinforce my impression that we are massively underestimating the rate of SARS-COV-2 spread through the community. My own personal experience suggests that a wave of infections passed through our rural area in mid- to late-February, hitting medical staff at a community clinic through exposure to one or a few symptomatic patients before anyone realized what was happening. Now the infection is reaching shut-ins and chronically ill people who are relatively isolated from the rest of the community. These patients are the most susceptible to severe and overwhelming disease, and they will represent the largest percentage of deaths due to COVID-19.
Robust patients with inapparent disease who travel widely have spread the virus throughout the community; less than 10% of them have been detected. Now the isolated patients will begin to fall ill, and they will be detected with much greater frequency. More than 10% of them will die.
We need a massive rollout of blood antibody tests for everyone so those who have been infected and are now immune can go back to work. We need a smartphone app, like so many other countries already have, so that susceptible people can avoid known cases, self-isolation can be monitored, and immune people can advertise that fact. That is the way to get from behind the eight-ball.
Data from Iceland suggest that roughly 89 to 94% of infections have gone undetected: BioRxiv
Coronavirus by Engin Akyurt via pixabay.com (open access)
A study published in BioRxiv on April 6 analyzes the reports from Iceland, where a community-wide voluntary random sampling program is underway. These studies are based on two sample sets, as the abstract explains:
The criteria for testing within the Icelandic medical system, processed by the National University Hospital of Iceland (NUHI), have also been targeted at high-risk individuals, but additionally most Icelanders qualify for voluntary testing through the biopharmaceutical company deCODE genetics.
Based on these samples, the authors of the BioRxiv study analyzed the data and found that:
Our primary estimates for the fraction of infections that are undetected range from 88.7% to 93.6%.
This report reinforces my impression that we are massively underestimating the rate of SARS-COV-2 spread through the community. My own personal experience suggests that a wave of infections passed through our rural area in mid- to late-February, hitting medical staff at a community clinic through exposure to symptomatic patients before anyone realized what was happening. Now the infection is reaching shut-ins and chronically ill people who are relatively isolated from the rest of the community. These patients are the most susceptible to severe and overwhelming disease, and they will represent the largest percentage of deaths due to COVID.
Patients with one foot in the grave will shuffle off the mortal coil and jump into their coffins when they are confronted with SARS-COV-2. I couldn’t resist using those stereotyped metaphors and similes to make a point: the most delicate patients will suffer the most from this virus. Robust patients with inapparent disease have spread the virus throughout the community; only 6 to 11% of them have been detected. Now the isolated patients will begin to fall ill, and they will be detected with much greater frequency. More than 10% of them will die.
Coronavirus by Engin Akyurt via pixabay.com (open access)
A study reported in BioRxiv on April 7 looked at using a combination of symptoms to predict infection with SARS-COV-2 and COVID in a UK (United Kingdom) community survey of 1,573,103 individuals, roughly 26% of whom said they had at least one symptom. They found that reports of multiple symptoms predicted infection with a greater likelihood than individual symptoms. Anosmia (loss of sense of smell and taste) was present in 59% of patients with confirmed infection; this symptom is a more recently recognized one. The group of symptoms that best predicted presence of the virus was the following:
… a combination of loss of smell and taste, fever, persistent cough, fatigue, diarrhoea, abdominal pain and loss of appetite is predictive of COVID-19 positive test with sensitivity 0.54[(range) 0.44; 0.63], specificity 0.86[(range) 0.80; 0.90] …
This specific combination of symptoms had not previously been reported to predict infection, but this large community survey confirms that there is a set of symptoms that together makes the diagnosis much more likely. Given that detection of the virus by nasopharyngeal swabs is not as sensitive as we would like (roughly 74% of victims have positive swabs on day eight after exposure) and depends on exactly when the test is done, we need a set of symptoms to guide us in presumptive identification of cases for isolation in the absence of universal testing.
Other symptoms, such as body aches (myalgia), headache, confusion, shortness of breath (dyspnea), chest pain, and productive cough, are also associated with COVID-19. They may relate to other manifestations such as pneumonia (possibly related to immune reaction) and brain infection (a feared but rare complication). The main symptoms of abdominal pain and diarrhea point to the presence of gastrointestinal (GI) (stomach and guts) infection as a primary factor in addition to the nasopharyngeal (nose and throat) route. GI infection has been suspected since fecal (stool) specimens have shown virus to be present in acutely ill patients.
This report suggests that patients with this combination of symptoms are the most likely to have the virus, although sensitivity is still poor at about 54%. RT-PCR testing of nasopharyngeal swab specimens to detect acute cases and blood antibody tests (a combination of IgG (chronic) and IgM (acute) antibodies) are needed to accurately outline the incidence and prevalence (new cases at any moment and overall number of cases) of COVID due to SARS-COV-2.
Other reports from early in the pandemic of wide community spread suggest that trivial or asymptomatic (no apparent illness) cases represent a major proportion of people with this virus, possibly as many as half. SARS-COV-2 may have been spreading widely on the West and East Coasts long before we realized that it was even present at all. Infected people without symptoms may have introduced the virus to the US early in January at the latest.
We were already far behind this virus when the first federal action was taken, a partial ban on travel from China, in late January. Warnings from the intelligence community in late December and early January were ignored. We have been playing “catch-up” ever since, a losing battle given the disorganized and tardy federal response. Even now, the administration is co-ordinating the sourcing of equipment through favored large companies and personal connections at great public cost. This is a subject for another post.
photo courtesy of pixabay.com and ErikaWittlieb
The New York Times reported on April 6 that a critical memo written by trade advisor Peter Navarro on January 29 warned of the coming pandemic, but was ignored by the White House. [redacted] later claimed that he had not seen it, despite evidence to the contrary. For six weeks after this memo, nothing serious was done. The White House cut off most travel from China on the 29th, but by then, people coming from China had already seeded the virus on the West Coast. Later, people from Europe brought the virus to the East Coast, long before travel from there was cut off. Finally, on March 13, a state of emergency was declared. The Defense Production Act has not been fully utilized, and organized preparations have been ignored and are still being ignored.
Numerous explanations have been given for this delay, from impeachment to distrust of the “deep state”, but none of these hold water. The only reasonable explanation is that [redacted] simply didn’t believe the warnings because they didn’t suit his narcissistic, sociopathic world view. Nothing could be allowed to upset his great economy– until it did.
We are witness to a continuing failure to heed warnings and a continuing failure to mount an organized response to this pandemic. There were multiple warnings from many sources; what’s more, there are plans for just such an eventuality already laid out. We are in trouble, and there will be more loss of life and more economic hardships to come. The end result may be destruction of democracy if the November election cannot go forward with full participation of the electorate. People who don’t normally vote must be incentivized to vote this time, or democracy will end. Mark my words.
Coronavirus by Engin Akyurt via pixabay.com (open access)
An article in the LA Times published March 31 related the results of tests performed March 12-16 on a series of patients with “mild” flu-like illnesses. Of 131 patients screened, 7 came up positive on the RT-PCR test that indicates the presence of virus RNA in a person’s nasopharyngeal secretions. This test is generally believed to show about 2/3 to 3/4 of actual patients, that is, a sensitivity of roughly 60-80%. The sensitivity varies with the series and depends partly on the adequacy of sample collection, the type of swab used, and numerous other factors. Theoretically, the test should show virtually all of the actual patients secreting virus through their noses and throats, but there are numerous barriers to such sensitivity.
The point is that, on performing screening of some of the many patients who were treated at that center, 5% were positive. This would be described as a “point prevalence” (number of patients with illness at any one moment) in patients with symptoms– not necessarily with fever or shortness of breath. Six of the 131 had fever and one had a cough. All were described as “not so sick they would have stayed home.” None of them tested positive for influenza or RSV (respiratory syncytial virus), common causes of flu-like illness. Most importantly, none of them had travelled recently or had contact with a known case of the novel coronavirus.
In the article headlined in my last post, there is this nugget:
The California Department of Public Health and the CDC did not begin community surveillance for COVID-19 in Santa Clara County until March 5. Samples were collected from 226 coughing, feverish patients who visited four urgent care centers; 1 in 4 turned out to have the flu. The state tested samples from a subset of 79 non-flu patients. Nine of them had COVID-19.
These two screening studies performed a week or two apart in separate parts of California showed that the prevalence of COVID-19 in symptomatic patients was 5% and 4%. This was nearly a month ago. Imagine what the prevalence would be now. We desperately need studies of blood antibodies to SARS-COV-2 in order to determine who is immune and can come out of lockdown and who must stay isolated.
Coronavirus by Engin Akyurt via pixabay.com (open access)
An article in the LA Times published March 31 related the results of tests performed March 12-16 on a series of patients with “mild” flu-like illnesses. Of 131 patients screened, 7 came up positive on the RT-PCR test that indicates the presence of virus RNA in a person’s nasopharyngeal secretions. This test is generally believed to show about 2/3 to 3/4 of actual patients, that is, a sensitivity of roughly 60-80%. The sensitivity varies with the series and depends partly on the adequacy of sample collection, the type of swab used, and numerous other factors. Theoretically, the test should show virtually all of the actual patients secreting virus through their noses and throats, but there are numerous barriers to such sensitivity.
The point is that, on performing screening of some of the many patients who were treated at that center, 5% were positive. This would be described as a “point prevalence” (number of patients with illness at any one moment) in patients with symptoms– not necessarily with fever or shortness of breath. Six of the 131 had fever and one had a cough. All were described as “not so sick they would have stayed home.” None of them tested positive for influenza or RSV (respiratory syncytial virus), common causes of flu-like illness. Most importantly, none of them had travelled recently or had contact with a known case of the novel coronavirus.
In the article headlined in my last post, there is this nugget:
The California Department of Public Health and the CDC did not begin community surveillance for COVID-19 in Santa Clara County until March 5. Samples were collected from 226 coughing, feverish patients who visited four urgent care centers; 1 in 4 turned out to have the flu. The state tested samples from a subset of 79 non-flu patients. Nine of them had COVID-19.
These two screening studies performed a week or two apart in separate parts of California showed that the prevalence of COVID-19 in symptomatic patients was 5% and 4%. This was nearly a month ago. Imagine what the prevalence would be now. We desperately need studies of blood antibodies to SARS-COV-2 in order to determine who is immune and can come out of lockdown and who must stay isolated.
corona photo by mohamed Hassan courtesy of pixabay.com (creative commons)
The Los Angeles Times reports that Dr. Jeff Smith, chief executive of the Santa Clara County government, told county leaders in a briefing on Friday that “The virus was freewheeling in our community and probably has been here for quite some time”. He was also quoted as saying that data collected by the Centers for Disease Control and Prevention (CDC, a federal government body) indicated that the virus entered the state some time in December (presumably late December, but I’m guessing at that time frame).
Mild cases of COVID-19 closely resemble the seasonal flu and would not have attracted any attention unless a CT scan (computer-assisted tomography scan) was performed and showed an unusual “ground-glass” appearance of a lung infiltrate. The Bay Area, of which Santa Clara County is a part, is an entry and exit site for visitors from China as well as people of Asian descent who have settled here for more than a century. Bruce Lee, one of the most famous actors ever from Hong Kong, was born in San Francisco.
Santa Clara County, according to the LA Times report, had its first two cases “almost a week” before the federal government approved testing for the virus on February 4. Both were returning from travel to Wuhan, a province of China. Testing was limited to “some health departments” with restrictions limiting testing to those who were sick from, or known to be exposed to, someone already known to have COVID-19. The Diamond Princess cruise ship was a focus of federal interest, and a passenger from that ship tested positive “five days after the ship’s January 20 departure from Japan”. A total of 712 people from that ship had positive test results, and nine people died. It was not until February 27 that a woman who had already been hospitalized for a week or more was tested on the insistence of her family. By then, community spread was evident when attempts were made to track down the source of the new infections that were reported.
Research is now focusing on banked blood samples in the search for earlier cases. This search will be for antibodies to the virus, which appear about two weeks after one falls ill. The National Institutes of Health (NIH, another federal group) is looking at samples from blood banks in Los Angeles, San Francisco, and elsewhere across the United States.
The LA Times story also details the case of the second death in that area, a woman who fell ill in mid-February and died March 9. She had been a stay-at-home daughter of 68, taking care of her elderly mother. By some eerie coincidence, she was of Iranian extraction; that country has seen a severe outbreak of the virus, with many deaths. She had not been tested until February 27, despite already being in the hospital for some days. Her family was unable to be at her bedside when she died because everyone had been isolated in the mistaken belief that she was the only one in the family with exposure. That cannot have been true, based on what we now know about community spread in the Bay Area.
ERROR: I stated that the case detailed was the second death in the area. On further review of the article, I realized that it stated that the case was actually the first reported death from COVID-19 in Santa Clara County.
Coronavirus by Engin Akyurt via pixabay.com (open access)
A new study published by the NEJM (New England Journal of Medicine) yesterday (Note: Virus research reports are free to all to read under rules agreed to by most media) revealed clinical data for 53 patients with severe COVID-19 due to SARS-COV-2 (the novel coronavirus, or just the virus). Over a thousand patients have been treated under the “compassionate use protocol” (a plan which allowed Gilead to provide remdesivir to selected patients upon individual application). Gilead sponsored and controlled this study, which makes sense given that they are the sole source for this still-investigational drug.
Originally, remdesivir was developed to treat Ebola virus, but it wasn’t successful there; most patients with Ebola died regardless of treatment, and the epidemic was stopped by careful contact tracing and isolation. In addition, Ebola appears to be attenuated (weakened) by serial transmission (in moving from one patient to the next) so that by the fifth successive patient infected, the clinical disease manifestation (the patient’s outcome) was manageable and survivable. Each jump of Ebola from animal (bats, probably) to man resulted in massive, fatal infection leaving a highly infectious corpse to be buried by traditional methods of washing and handling. Those who attended the funerals of Ebola victims frequently became the next to die. Now there are a few scattered cases of Ebola cropping up here and there, but there is no sustained outbreak. Traditional burial practices have changed, which has helped.
Gilead has a good drug, and it is still under patent, so they have an incentive to test and promote remdesivir for the next disease. This disease promises to be a real money maker for the pharmaceutical industry in general, or at least Gilead in particular. Therefore, they sponsored, paid for, supplied drug for, collated data for, and wrote up the first draft of the study I am referencing.
The results of this study are encouraging. It is not meant to be anything like conclusive, merely a demonstration that the drug is safe and appears to have a beneficial effect. Furthermore, stronger studies are likely to be in the pipeline. In keeping with the “compassionate use” idea, the patients selected for this study were mostly severely ill; over half were on ventilators and most had been sick for over ten days already.
According to the protocol, remdesivir was given intravenously once a day for ten days. No other investigational drugs (including hydroxychloroquine) were given during remdesivir treatment. Antibiotics and other supportive medication were given as desired by the individual doctors treating each patient. 68% of patients showed significant improvement after eighteen days, and 84% by twenty-eight days. Seventeen of thirty patients on mechanical ventilation were extubated (had their endotracheal tubes removed) and three of four patients stopped ECMO (extra-corporeal membrane oxygenation, or passing the blood through a membrane filter which supplies oxygen to substitute for the lungs). Eighteen percent of patients on ventilators died and thirteen percent died overall. These figures compare favorably with the numbers in patients not treated with remdesivir, who were not directly included in the study (there was no matching of placebo or control patients due to the compassionate use protocol).
This study is far superior to the reported studies of hydroxychloroquine for several reasons. First, it included many patients who were severely ill at the outset of treatment, with low oxygen saturation (oxygen blood levels), older, and generally sicker before they were infected. Second, only patients with severe kidney failure and liver inflammation were excluded; mild renal insufficiency, diabetes, hypertension (high blood pressure), and other diseases were allowed.
Controlled studies comparing the outcomes in similar patients who were not given remdesivir will soon follow. An advantage of the patent protection and profit motive afforded Gilead for this drug is that they are sure to collect data and publicize it as quickly as possible, to benefit from the demand for more of this drug.
Whether the profit motive ends up being beneficial for humanity in this case is still open to question. Much depends on who will pay and how much. If rich governments like the United States pay for widespread treatment, then Gilead’s profit will wind up being a rounding error in the overall federal stimulus plan, which exceeds $2 trillion already.
If private patients in the US are forced to pay for remdesivir treatment, then the results will be widening inequality, bankruptcies, and pressure on Medicaid (the federal program which pays for some indigent patients to receive medical care). The pandemic has already resulted in widening income inequality as most workers in service-sector jobs are becoming unemployed. Those who live paycheck-to-paycheck are suddenly coming up short in food, rent, and emergency expenses. Inequalities in exposure to the virus (service-sector employees cannot work from home), infection, and outcomes (death or recovery) are already becoming starkly apparent.
These inequalities will lead to a further drive towards authoritarianism. This is so because income and wealth inequality is a prime source of public unrest, and authoritarian leaders thrive on popular discontent.
It gives anti-democratic bosses an excuse for cracking down on dissent, blaming the usual suspects, and aggrandizing their powers. Fortunately for the US, the man nominally in charge is as incompetent as he is narcissistic, as scatter-brained as he is sociopathic, and is as obvious a liar as he is nepotistic.
photo courtesy of pixabay.com
Paul Krugman, in his latest column, warns that the latest authoritarian moves by [redacted] may lead to the death of democracy as we know it. He points to what has happened under the rule of Viktor Orban, the leader of Hungary. He was headed for authoritarian rule all along, and now he has used the excuse of the pandemic to create rule by decree, censor and shut down the free press, and throw opposition leaders in jail.
The debacle in Wisconsin in Tuesday is a perfect example of the playbook by which the Republicans can suppress the vote. Under cover of people’s fear of exposure to the virus, all but five of the state’s 180 polling places were shut down. Absentee balloting was restricted, and many people who applied for ballots weeks ago never received them. As a result, a hyper-conservative supreme court justice appears to have won re-election to further stack the high court. In the 2018 elections, the voting districts were so heavily gerrymandered that, despite getting 53 percent of the vote, Democratic state representatives only got 36 percent of the seats.
The same thing could happen in numerous red states and even in swing states, setting up the Republicans to win in November despite their numerical inferiority among registered voters.
The answer to this onslaught on democracy is for every Democrat to work tirelessly to obtain “certificates of immunity” from the new antibody tests for SARS-COV-2. In this way, they can vote in person without fear of being infected or exposing others. This is of the highest priority, and there are only six months to get this done.
The alternative is the re-election of [redacted] and the collapse of American democracy. The country will be fragmented into red and blue territories, and civil war will be the next result. Democrats cannot take this assault on democracy lying down, for the good of the lower 99% of the population. Whether they like it or not, the best interests of the 1/3 of people who are die-hard Republican cultists would be better served by their loss at the polls. They are blindly voting against their own interests and if the new virus doesn’t open their eyes, nothing will.
Conrad Theodore Seitz 