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South African hospital outbreak: at least 119 infected from one emergency room patient; 15 of 39 hospital patients died: Science magazine

2020-05-26

Durban, South Africa by Liesl Muhl courtesy of pixabay.com

Krisp.org published a story on May 22 (which is excerpted in Science magazine on May 25) about an outbreak in a Durban, South Africa hospital that started on March 9 with a patient who entered the emergency room with symptoms of COVID-19.  The infection jumped to another patient who was in the ED (emergency department) at the same time and was admitted to C-ICU (cardiac intensive care unit) with symptoms of a stroke.  From there, the virus spread, apparently mainly through “indirect contact and fomite transmission” to patients on at least five wards.  119 cases at the hospital (80 staff and 39 patients) were affected, and “smaller outbreaks” occurred at a nursing home (four cases) and an outpatient dialysis unit (nine patients and eight staff).  A total of up to 135 cases may have been seeded from one patient attending the emergency room.

Eighteen genomes were sequenced, and all had the same clade: type A2, associated with infections from Europe.  There was “limited genomic diversity” in these genomes, suggesting that all of them came originally from one infection.

Fifteen of the 39 patients infected died, all with multiple co-morbidities and all “elderly.”  “There was no evidence” that “any specific intervention” would have prevented their deaths once they were infected (none of the patients received remdesivir.)  The first opportunity for prevention of additional infections was when an 81 y/o woman (patient 3) (who turned out to have a “transient ischemic attack” (TIA), a precursor to stroke) developed an unexplained fever on March 13.  This woman was discharged from the medical ward to the nursing home on March 16 and readmitted with severe pneumonia on March 22.  During her time on the medical ward, she appears to have infected five other patients on the same ward, although she had no cough or other apparent symptoms except for the transient fever.

Around the same time, a 46 y/o woman (patient 4) (one of the five mentioned above) was admitted with an “acute respiratory illness” on March 21.  Two other patients and a nurse were infected by this patient.  On March 23, a nurse from the C-ICU (who had treated the TIA patient) was found to have confirmed COVID-19.

Patients 3 and 4 appear to have infected nine other patients when they were in the medical intensive care unit between March 22-27.  Patient 7, one of those nine, then infected eight other people on medical ward one.

Patient 8, from medical ward one, was moved to surgical ward one, where he infected two other patients and then died on April 1.  Patient 12 was moved from medical intensive care on March 31 (when it was closed because of the infection cluster) to the surgical intensive care unit, where he infected eight other patients.

A total of 1892 patients were recalled because they had been in the hospital in March; 191 were brought in for testing, and seven of these tested positive.  Some of these patients may have been infected outside the hospital, but it is also possible that some of the 1700+ patients who were not called in for testing had asymptomatic COVID-19 and were missed (that detail is not mentioned in the complete report.)

The case fatality rate among the confirmed COVID-19 cases who were patients (rather than staff) was 38.5%, with a median age at death of 79.  All of those who died had some co-morbidity, eleven with hypertension (high blood pressure), seven with diabetes mellitus (DM), and two with cancer.  None was known to be HIV positive.  In all but three cases, patients who died were not intubated because of their known poor prognosis at the time the decision was made.

A total of 1171 staff members were tested at least once, of whom 80 (roughly 5%) had positive tests.  The positive staff members were mostly from the medical intensive care unit and medical ward one; none of them came from the specialized COVID-19 intensive care unit, possibly due to the extra care taken there against infections.  All staff members eventually recovered; only fourteen were admitted to the specialized COVID-19 ward.

The nursing home involved took care of patient 3, and four other patients there developed COVID-19.  These were isolated in a separate building and no staff members at the home tested positive.  Nineteen COVID-19 cases (11 patients and eight staff) were found at the dialysis unit.  All patients and staff at the dialysis unit (133 and 36, respectively) were tested.  Five of the eleven cases in dialysis (45.5%) died.

A failure of personal protective equipment and infection control procedures (IPC) led to the spread of the virus to a total of 135 people, with fifteen deaths.  It should be noted that there were only two known patients in South Africa with COVID-19 at the time the first patient was seen.

The article recommends separation of patients at low and high risk for COVID-19, with separate entrances.  They recommend environmental cleaning to reduce fomite transmission, “aligned with national COVID-19 IPC guidelines and the national IPC framework manual”, plus monitoring of cleaning with fluorescent markers and visual re-inspection.

In addition,  they recommend physical distancing within the hospital with floor markings and signs.  Finally, they recommend weekly PCR (polymerase chain reaction) (from sputum or nasopharyngeal swabs?) testing of all frontline staff.

The only difficult ask in this country would be weekly testing of frontline hospital staff, but the recent increased availability of test kits should be beneficial here.  Additionally, the throat/sputum test recently developed should make testing much easier and quicker to implement– with no need for staff involvement in specimen collection and a much less invasive procedure than the nasopharyngeal swab that has been the exclusive method so far.

This tragic series of events should be studied by infection control professionals in all hospitals and the lessons learned should be implemented universally if a recurrence with multiple fatalities is to be prevented.

A .pdf file of the comprehensive report is available here and makes for very interesting reading.  It has details of how each infected person interacted with the previous person, thus how the virus was passed on from person to person.

The article states, “KRISP has been created by the coordinated effort of the University of KwaZulu-Natal (UKZN), the Technology Innovation Agency (TIA) and the South African Medical Research Countil [sic] (SAMRC).”  One of the authors is the director of the Nelson R Mandela School of Medicine at UKZN in Durban, South Africa.

Multisystem inflammatory syndrome in children (MISC), a rare and underdiagnosed complication of COVID-19: LA Times

2020-05-25

Madagascar periwinkle–photo by PixArc courtesy of pixabay.com

The Los Angeles Times has an article in its May 22 science section about the Multisystem Inflammatory Syndrome in Children (MIS-C) that has been appearing since the pandemic started.  This condition is very rare but has killed at least three children recently.  It resembles Kawasaki disease (fever, rash, and swelling of hands and feet)– which occurs in about 5,500 children in the US every year– and occurs some three weeks after infection.  Kawasaki disease usually affects younger children, mostly under 5, but MIS-C can occur as old as adolescence.

The symptoms of MIS-C also include red eyes and tongue, abdominal pain, low blood pressure, and diarrhea.  In some cases, it resembles toxic shock syndrome (a condition that occurs when infection causes a reaction with low blood pressure, rash, and prostration) that happens rarely after a tampon is infected with toxin-generating bacteria.

Since the syndrome appears so long after SARS-COV-2 infection, most patients will test negative on the nasopharyngeal swab that detects the antigen.  Instead, an antibody test on the blood is required.  Four patients in Los Angeles had antibody-proven COVID-19 and later developed MIS-C.

Treatment of MIS-C is supportive, similar to treating Kawasaki disease.  First, intravenous immunoglobulin is given, just as plasma from recovered COVID-19 patients has been tried in adults.  Repeat doses of immunoglobulin are often needed.  Aspirin, steroids, and cytokine blockers are added.  Anticoagulants and platelet blockers are needed for the blood-clotting complications.

Three of the four patients treated at Children’s Hospital of Los Angeles have recovered.  The fourth is improving and out of the intensive care unit.  The condition was actually first noticed in the United Kingdom (UK) about a month after the pandemic started; it has not been described in China.  The second place it was found was in New York City, where the pandemic was raging last month.  Three children there have died.

The cause of Kawasaki Disease is unknown; some believe that it is due to some environmental element, such as an infection.  MIS-C is clearly related to the pandemic of COVID-19, but there is suspicion that a genetic element is at work making some children more susceptible.  Further study of the few cases that have appeared is ongoing.

Buddhism versus the Dokkodo of Miyamoto Musashi

2020-05-25

Be Here Now– photo by Harald Lepisk courtesy of pixabay.com

The Dokkodo (The Way I go alone) of Miyamoto Musashi has many parallels to the Buddhist rules.  To take the most important example for me, the first of his  Nine Rules is “Do not think dishonestly.”  This is similar to “Don’t lie”, which is high on the Buddhist lists.  It doesn’t say, though, not to lie to other people, but what is more important to me, don’t lie to yourself.  Or, as another philosopher has said, first be true to yourself, then you can’t be untrue to anyone else.

There are also rules against sexual misconduct, although the Dokkodo has it in more personal terms.  There, he says, don’t have sexual thoughts, don’t crave things that are pleasurable.

I don’t see any rules in Musashi against killing people; that’s to be understood in relation to the Bushido (samurai code) of killing lots of people, especially your opponents in battle and commoners who annoy you.  Consistent with the killing philosophy, the Dokkodo says “Weapons are of the highest importance.”

Buddhists are clear that you’re not supposed to kill or harm anyone.  We see, however, many people who are nominally Buddhist attacking others in society who oppose them– so there is some hypocrisy there.

There is no rule in Musashi against stealing, but there are rules about not wanting things that you don’t need.  You don’t need to steal if you don’t want anything.

The Dokkodo says, in a distinct difference from Buddhism, “I will honor Buddha and the gods, but I will expect nothing from them.”

Even more important to me, Miyamoto Mushashi’s nine rules say: “Pay attention even to trifles” but “Do nothing which is of no use.”

Thus I’m ending this post now, to avoid doing something which is not really useful: talking too much.

A tale of two drugs: Hydroxychloroquine (HCQ) and Remdesivir. Remdesivir lowers death rates, but HCQ is associated with higher death rates.

2020-05-25

photo by Petra Goeschel courtesy of pixabay.com

Hydroxychloroquine (HCQ) has been relentlessly touted by a certain political figure, who even claimed to be taking the drug himself.  He also claims that there is support from doctors and that some studies show it is good.  This is unfortunately not true.  A VA study with 368 patients published on April 21 found an elevated death rate in the HCQ group as opposed to no drug or combined HCQ (HC) and azithromycin (AZ): “Rates of death in the HC, HC+AZ, and no HC groups were 27.8%, 22.1%, 11.4%, respectively.”  A large multicenter study published in Lancet on May 22  had similar results:

96 032 patients (mean age 53·8 years, 46·3% women) with COVID-19 were hospitalised during the study period and met the inclusion criteria. Of these, 14 888 patients were in the treatment groups (1868 received chloroquine, 3783 received chloroquine with a macrolide, 3016 received hydroxychloroquine, and 6221 received hydroxychloroquine with a macrolide) and 81 144 patients were in the control group. 10 698 (11·1%) patients died in hospital. After controlling for multiple confounding factors (age, sex, race or ethnicity, body-mass index, underlying cardiovascular disease and its risk factors, diabetes, underlying lung disease, smoking, immunosuppressed condition, and baseline disease severity), when compared with mortality in the control group (9·3%), hydroxychloroquine (18·0%; hazard ratio 1·335, 95% CI 1·223–1·457), hydroxychloroquine with a macrolide (23·8%; 1·447, 1·368–1·531), chloroquine (16·4%; 1·365, 1·218–1·531), and chloroquine with a macrolide (22·2%; 1·368, 1·273–1·469) were each independently associated with an increased risk of in-hospital mortality. Compared with the control group (0·3%), hydroxychloroquine (6·1%; 2·369, 1·935–2·900), hydroxychloroquine with a macrolide (8·1%; 5·106, 4·106–5·983), chloroquine (4·3%; 3·561, 2·760–4·596), and chloroquine with a macrolide (6·5%; 4·011, 3·344–4·812) were independently associated with an increased risk of de-novo ventricular arrhythmia during hospitalisation.
These findings are discouraging for proponents of HCQ.  The results for remdesivir are much better.  Gilead’s scientists released their most recent study details in the New England Journal of Medicine (NEJM) on May 22:
Preliminary results from the 1059 patients (538 assigned to remdesivir and 521 to placebo) with data available after randomization indicated that those who received remdesivir had a median recovery time of 11 days (95% confidence interval [CI], 9 to 12), as compared with 15 days (95% CI, 13 to 19) in those who received placebo (rate ratio for recovery, 1.32; 95% CI, 1.12 to 1.55; P<0.001). The Kaplan-Meier estimates of mortality by 14 days were 7.1% with remdesivir and 11.9% with placebo (hazard ratio for death, 0.70; 95% CI, 0.47 to 1.04). Serious adverse events were reported for 114 of the 541 patients in the remdesivir group who underwent randomization (21.1%) and 141 of the 522 patients in the placebo group who underwent randomization (27.0%).
It is important to note that the study was prematurely terminated because the time to recovery was significantly shorter for remdesivir, although the difference in mortality did not reach statistical significance.  The death rate was strikingly less with remdesivir: 7.1% versus 11.9% for placebo, a hazard ratio of 0.70– even though that result did not reach statistical significance because the study was stopped early.
There is strong data for the efficacy of remdesivir and the toxicity of HCQ based on these studies.  The mechanisms of action for these two drugs supports these conclusions.  With remdesivir, the drug is incorporated into the growing RNA chain as it is built and terminates it, (Wikipedia) damaging the virus’s genetic code.  HCQ only increases the pH of the vesicle (bag) (Wikipedia) that the virus creates when it fuses with the cell membrane; although this might help, it is not dispositive.  The side effects of HCQ overwhelm this mechanism and result in a higher death rate.
Remdesivir probably works better when it is given very early in the course of COVID-19, when there is active and uncontrolled virus replication.  It is less likely to help during the late phase of severe illness, when “cytokine storm” causes inflammatory reactions all over the body.  This hypothesis has not been confirmed by experiment, but is highly reasonable given experience with other viral infections.  For example, treating the shingles (varicella, or chickenpox) virus effectively requires starting acyclovir or valacyclovir early on (Mayo clinic webpage for shingles.)

Eighteen Bodhisattva Precepts

2020-05-22

Gandhara Buddha circa 1900 years ago, courtesy of wikimedia commons

More lists, this time precepts (from Wikipedia); most importantly, do not teach emptiness to those whose minds are unprepared.  Confusing; that might mean me, because I don’t think my mind is fully prepared.

Eighteen things NOT to do, still ascribed by Tibetan Buddhists and sworn to by monks:

  1. Praising oneself or belittling others due to attachment to receiving material offerings, praise and respect.
  2. Not giving material aid or (due to miserliness) not teaching the Dharma to those who are suffering and without a protector.
  3. Not listening to others’ apologies or striking others.
  4. Abandoning the Mahayana by saying that Mahayana texts are not the words of Buddha or teaching what appears to be the Dharma but is not.
  5. Taking things belonging to the BuddhaDharma or Sangha.
  6. Abandoning the holy Dharma by saying that texts which teach the three vehicles are not the Buddha’s word.
  7. With anger depriving ordained ones of their robes, beating and imprisoning them or causing them to lose their ordination even if they have impure morality, for example, by saying that being ordained is useless.
  8. Committing any of the five extremely negative actions: (1) killing one’s mother, (2) killing one’s father, (3) killing an arhat, (4) intentionally drawing blood from a Buddha or (5) causing schism in the Sangha community by supporting and spreading sectarian views.
  9. Holding distorted views (which are contrary to the teaching of Buddha, such as denying the existence of the Three Jewels or the law of cause and effect etc.)
  10. Destroying towns, villages, cities or large areas by means such as fire, bombs, pollution or black magic.
  11. Teaching emptiness to those whose minds are unprepared.
  12. Causing those who have entered the Mahayana to turn away from working for the full enlightenment of Buddhahood and encouraging them to work merely for their own liberation from suffering.
  13. Causing others to abandon their Prātimokṣa vows.
  14. Belittling the Śrāvakayāna or Pratyekabuddhayāna (by holding and causing others to hold the view that these vehicles do not abandon attachment and other delusions).
  15. Falsely stating that oneself has realised profound emptiness and that if others meditate as one has, they will realize emptiness and become as great and as highly realized as oneself.
  16. Taking gifts from others who were encouraged to give you things originally intended as offerings to the Three Jewels. Not giving things to the Three Jewels that others have given you to give to them, or accepting property stolen from the Three Jewels.
  17. Causing those engaged in calm-abiding meditation to give it up by giving their belongings to those who are merely reciting texts or making bad disciplinary rules which cause a spiritual community not to be harmonious.
  18. Abandoning either of the two types of bodhicitta (aspiring and engaging).

Here are the Sixteen Soto Zen Precepts, some of which are basic to all Buddhism:

The Three Treasures

  • Taking refuge in the Buddha
  • Taking refuge in the Dharma
  • Taking refuge in the Sangha

The Three Treasures are universally known in Buddhism as the Three Refuges or Three Jewels.

The Three Pure Precepts

  • Do not create Evil
  • Practice Good
  • Actualize Good For Others

These are also known as the Three Root Precepts, and are mentioned in the Brahma Net Sutra as well.

The Ten Grave Precepts

  1. Respect life – Do not kill
  2. Be giving – Do not steal
  3. Honor the body – Do not misuse sexuality
  4. Manifest truth – Do not lie
  5. Proceed clearly – Do not cloud the mind
  6. See the perfection – Do not speak of others’ errors and faults
  7. Realize self and others as one – Do not elevate the self and blame others
  8. Give generously – Do not be withholding
  9. Actualize harmony – Do not be angry
  10. Experience the intimacy of things – Do not defile the Three Treasures

The first four of the ten grave precepts are straightforward and are mentioned in all the lists of prohibitions.  The next six are less clear.  “Do not cloud the mind”– does this mean not taking intoxicating substances?  The others show significant similarities to the previous lists I have posted.  All of this is highly preliminary and requires a lot more thought (on my part– it may be clear to you…)

Puzzling case in Snohomish County Washington: 64 y/o woman had flu-like symptoms starting December 27, now has positive SARS-COV-2 serum antibodies

2020-05-22

flu by Steve Buissinne courtesy of pixabay.com

The Seattle Times has reporting on a 64 year old woman patient who fell ill on December 27 with a persistent dry cough, fever, body aches, and eventually wheezing.  She finally had antibody testing a few weeks ago by a reliable lab at the University of Washington (an Abbott branded test) which was reported positive as of May 1.  Doctors who reviewed the case claim that she must have had an asymptomatic case of COVID-19 after this highly symptomatic illness.  The patient, who appears to be quite sophisticated (highly knowledgable), is not so sure.

If her illness at the end of December was due to the new virus, it would be the first in the US.  A similar date is definitely ascribed to a case in France that was diagnosed by re-examination of specimens taken at the time he was ill– December 27.  That man was a 42 year old fishmonger who complained of chest pain and shortness of breath.  At the time, doctors felt he had an unknown virus; they stored samples taken during his acute illness and he recovered.  Recently, an evaluation of many stored samples located his and found he was the first known case in France.

The French case came from unknown predecessors.  The man’s wife sold fish in a local market; she did not become ill, but the family’s children did.  Previously, the first known case in France had been January 24 and the first known case in the US had been reported January 21.  Cases of this nature are confusing and no firm conclusions may ever be drawn.

The first known case in China fell ill December 1, and had no known connection to the Wuhan live animal or “wet” market which has been blamed for the virus’ jump from animals to humans– although this too is controversial.

Will this pandemic reduce inequality or exacerbate old divisions?

2020-05-22

Decebalus Rex by Erich Westendarp courtesy of pixabay.com

I was drawn to this question by the page one story in today’s Washington Post:  “‘I had to choose being a mother’: With no child care or summer camps, women are being edged out of the workforce”; this story was posted in the section “Lily Lines”, referring to stories that specifically involve women’s issues.  The problem is that parents of small children are forced to keep one parent, usually the mother, at home to raise them, as happened in the past when there was no community support for families.

Clearly, the pandemic has set us back by decades, if not a full century (I’m referring to women’s suffrage in particular, which recently celebrated its 101st anniversary here in the United States).  Historically subjugated minorities, particularly African- and Caribbean-Americans, are dying of the novel coronavirus at two or three times the rates of Caucasians (the reasons why are multifactorial, including high rates of being essential but underpaid in-person workers and high rates of co-morbid conditions).

Companies and people who were well-off are doing better than those who were struggling before, both intrinsically and in access to Congressionally-mandated financial support.  People who are technologically advanced both in their personal lives and at work are better able to ride out the lockdowns– by working from home (not possible for bus drivers and retail workers) and schooling from home, as well as accessing essential services like one’s bank account and entertaining oneself and one’s family.

All these factors are leading to greater suffering among those who had marginal lives before the pandemic struck.  This is particularly true in the US, where Depression-level unemployment has hit lower-paid, lower-technology workers disproportionately without significant relief from the federal government.  Contrast this situation with that in Denmark, where burger-flippers, who made the equivalent of $22 an hour and had sick leave plus medical insurance, have guaranteed jobs and most of their pre-pandemic pay preserved.  This is why people living there are happier than people living here.

In this country, we have a Secretary of State who sees fit to force government employees to do his dishes, pick up his dry cleaning, and walk his dog– when he could well afford to hire people to do this work, both from his government salary and his prior wealth.  These actions are clearly a violation of applicable federal laws against use of one’s government office for personal gain.  Does that have any immediate effect within this administration?  No.  Should we as a people do something about it?  Yes.  What should we do?  Vote the bums out.

To get back to where we were when we were so rudely interrupted by the knock-on effects of this virus, we will have to endure five years of concerted efforts.  That’s my opinion.  What is worse, by the time we get our heads above water, the world will have changed so that it is virtually unrecognizable to us.  China will be the world’s greatest economic power and the world’s greatest villain by virtue of its totalitarian government.  It’s not communism that is the villain; if anything, China is the victim of concerted exploitation by Western and even Japanese actors over the last two centuries– going back to the Opium Wars.  China’s government is not just communist, it is not even just authoritarian– it is totalitarian.  That is a reaction to all that has happened in the last two hundred years.

Even the pandemic virus is a result of the forces that have molded China.  There was a massive population explosion, which was partly the result of the economic misery that they endured because they were so ruthlessly exploited by other countries.  This population boom, which is only now just beginning to be controlled, has caused a scramble for calories, which has caused the human exploitation of animals for food.

The close quarters in which large numbers of food animals are kept and their proximity to humans has caused a fertile ground for micro-organisms, viruses in particular, to evolve into more dangerous human pathogens.  The novel coronavirus is just the latest evolution of viruses that exploits human overcrowding to spread.

Measures we have been forced to take, in order to slow its spread, have been essentially isolation of one human from another.  We are still waiting for more sophisticated methods of control, including vaccines, to help us get this virus under control.  That’s where we are today, and we will have to fight the same social battles all over again, especially here in the US, because retrogressive political parties run by retrogressive people are trying to prevent us from addressing this problem with the efficiency that we require.

That’s my opinion, and you’re free to disagree.  But don’t call me names or threaten me.  I’m just another human being trying to do my best to keep our species evolving together.