PlagueWatch 2020-23 - Coronavirus

[jimmymax]

Can't bear reading the whole thread, but this is from a friend's friend (sounds sketchy I know) at UCSD but it's a good read:


COVID-19
Some of my friends and family have asked me about this pandemic, and I have not answered, mostly because there is so much to say and so little attention span (in general, or actually I’m thinking of myself). But since I’ve published on the topic of disease ecology, and recently designed and delivered an entire course on the “Biology of Plagues” (30 hours of excruciating lecture), I thought I should share what I have learned. Besides, what good is being a professor if you can’t profess; however, if you’ve heard enough about SARS-CoV-2 virus and the COVID-19 disease, and the miserable American response to the epidemic, I emphasize. Go for a walk, sort your photographs, or even talk to your family (from a distance of 6 feet). I guess you can text and IG, but don’t share your germ-laden phone.

My prediction is that like most every other epidemic disease that has entered the human population, this one is not going away, probably ever. At least that has been the pattern throughout the long history of introduced diseases—they start as epidemics and pandemics and, short of a world-wide vaccination assault, remain as “childhood diseases”, meaning, everyone contracts the disease as a susceptible child, and either dies or retains immunity as an adult.

What I find fascinating is that these epidemics were inevitable given our ability to dominate and populate the entire earth[1].
[1] “Be fruitful and multiply and fill the earth and subdue it, and have dominion over the fish of the sea and over the birds of the heavens and over every living thing that moves on the earth.”

It is another way that we human beings are exceptional—in addition to be extraordinarily smart (or maybe too clever by half), we are disease-laden.

Short history.
This all started with domestication of plants and animals, several thousand years ago. With a stable source of food, people became situated and eventually aggregated in towns and cities, and tending their flocks and herds, sampled all of the bacteria and viruses from birds, pigs, cows, sheep, and horses—efficiency living, cheek to jowl. Germs and germ-theory were unknown. Toilets were not sanitized because there were no toilets, and nonetheless, poop happens. Multiple generations living in close quarters tend to share everything, including respiratory effluvia[2].
[2] mid 17th century: from Latin, from effluere: ‘flow out’

Introducing a new infectious agent (let me just focus on viruses, although similar principles apply to bacteria and other infectious agents) into such a population that has never before seen the disease is known as a “virgin soil epidemic”. Weird word usage, but it means that everyone is susceptible. The virus that is found in such an epidemic is the one that was able to spread most rapidly within a population. If the virus is too virulent (nasty), it kills its host before it can be transmitted. If it doesn’t replicate well in human beings, it cannot be effectively transmitted (virus numbers too low). In a high-density population where everyone is susceptible and spread is via casual contact, an infectious agent can be highly virulent, even deadly, and still find a new host before its previous host dies. On the other hand, if it kills its host before it can be transmitted effectively, it fades out of the population. An example of this is Ebola virus. It is extremely lethal but requires pretty intimate contact so that, prior to 2014, it periodically broke out and infected about 300 people and then faded away. Each outbreak probably involved a new human-animal interaction (and we think the reservoir species is fruitbats).

On the other hand, if an infectious agent lands in a low-density population or a population in which most people are already immune, the chances that it finds a new host goes down, and the only viruses that can persist are those that keep their host alive for a long time or actually remain with the host forever (herpes viruses come to mind). So that’s why the predecessors of our agrarian ancestors did not have these massive viral epidemics: small, dispersed bands of hunter gatherers could not have sustained virulent epidemic diseases. If one landed in a community, it would kill a few members of the group, and then fade away as it would lack new susceptible hosts.

So, sometimes, although it is unpredictable, an infectious agent from an animal is able to cross over and infect human beings, and this is known as a zoonosis. In the high-density human communities, highly virulent diseases took hold and remained within the population for centuries. This is what happened with the introduction of smallpox, measles, mumps, rubella, diphtheria, pertussis etc. and it is what continually occurs for influenza A and B (a special case reserved for another lecture). These diseases entered the human population only after 1) our population density increased such that they could be rapidly transmitted and 2) the size of our communities increased so that there was always a source of newborn susceptible hosts (measles requires an interacting population of 200,000-500,000 people). Thus, we have childhood diseases (as an ungraded exercise, describe what happened when ALL of the diseases that arose in Europe and Asia were introduced into the huge, naïve populations present in the Americas and Polynesia in the 15th and 16th centuries).

Such infections can be mild or lethal, we have no way of predicting, but the ones we notice cause serious disease. Influenza is a bird virus, usually does not cause disease in birds, but causes death in human beings, or at least makes people WANT to die. SIV causes some disease in chimpanzees, but as HIV in human beings, it is almost always fatal (without antiviral drug therapy). Rabies is found in healthy bats, and it is 100% lethal in people (without early vaccination). Hantavirus is found in wild mice, and causes lethal disease in humans, etc.

The take-home message is that “crowd epidemic disease”[3], is an inevitable consequence of suddenly altering our human ecosystem from that of sparse groups of hunter-gatherers to high-density communities. Add in the continuous sampling of viruses from all the world’s wild animals, along with the invasion and disruption of tropical forests, and voilà, you have human beings, the most diseased species on earth.
[3] Guns, germs, and steel, Jared Diamond

21st century.
Coronaviruses account for a substantial percentage of what we experience as seasonal common colds. The present epidemic/pandemic is caused by a novel coronavirus that comes from bats, for sure. Whether it found its way into the live Chinese meat markets via an intermediate host is unknown. This is the 7th coronavirus to be found in the human population, and it is 80% identical to SARS-2003 (also from bats) and 96% identical to a bat coronavirus.

The previous SARS-2003 virus originated in horseshoe bats and somehow infected masked palm civets, the latter a delicacy in southern China. Until the present epidemic, wild animals, from snakes to civets were available at a wet market that is the origin of the present epidemic. A study from 2017 in which Chinese researchers sampled viruses from a cave of horseshoe bats found many variants of bat coronaviruses, some of which could grow in human cells. It was only a matter of time before one of these viruses, again caused a human epidemic. Slaughtering and eating wild animals, especially now that we know these animals can be contaminated by virus-harboring bats, risks starting an epidemic. It’s like having unprotected sex with multiple concurrent partners some of whom are i.v. drug users. Yea, it’s an infectious virus, but you’re askin’ for it. The Chinese government has officially closed these markets we are told, although I would not count on this being the last we hear of wet markets in China. Should we demonize China for starting this pandemic, well no, and we certainly should not blame Chinese people, but on this one very narrow issue the administration has a point. The pandemic was caused by highly risky cultural practices that made another epidemic inevitable. Note that there are examples the world over of human practices that make zoonotic infections likely, this is not limited to China.

COVID-19.
With the SARS-2003 virus, the epidemic was contained by isolation and quarantine. Since 2004 there have been no known cases of SARS-2003. It may be too virulent, as it killed or incapacitated its host at a rate of about 15%. It might have faded out of the population eventually unless it evolved to be transmitted more frequently. I don’t know. SARS-CoV-2 is unfortunately much better suited to causing widespread human misery. It seems to have an incubation period of about 4 days before the onset of symptoms and a long infectious period that includes 10 days before hospitalization (spread spread spread). The total time that a patient is contagious it is probably long, variable and not well characterized. The time between onset of symptoms and death ranges from 2-8 weeks. But lethality is less than that of SARS-2003 at between 1-3% (although this figure is an estimate because we do not know the real number of total infections).

The near future.
My guess is that there is little possibility that this virus will fade out of the human population without the widespread use of an effective vaccine. I hope I’m wrong, but as the virus has already found its way all over the earth, it may remain simmering in the population with the potential to break out at any time. Our present measures of isolation and quarantine should “flatten the curve”, that is limit the prevalence of disease at any one time in order not to overwhelm the medical system, but, unlike SARS-2003, we may not be able to contain it by isolation and quarantine. As I write this more than 5,500 Italians are testing positive every day. Their medical system had been overwhelmed, and their staff are forced to make choices about who will receive care. Why they seem to be hit so hard is unknown, at least to me. It may be that they have a particularly old population (demographic distribution), combined with multigenerational cohabitation. Perhaps they waited too long before mandating confinement. I can also imagine that the virus strain in Italy is more infectious.

One drug that was developed to treat influenza (another RNA virus) by Toyama Chemical (owned by Fujifilm), was tested in Shenzen, China and appears to greatly lessen the severity of the disease and shorten the length of infection. It is known by the trade name Avigan (favipiravir), but it is not presently available, although there was an internet blurb that Indonesia has ordered millions of doses. It targets RNA viruses, but I do not know whether there are plans to market it. The Chinese are ramping up production, but there are indications of serious side effects such that the Japanese are taking a more cautious approach. If this initial report is proven to be accurate, it can be used for patients showing initial symptoms, but it appears to be ineffective for patients with severe disease.

Gilead is testing an anti-viral called remdesivir that they were testing for use in Ebola infections, although it did not stack up well in a clinical trial last year. It is an RNA base analog that gets added by the virus trying to replicate itself. With the addition of remdesivir, the replication is cut short. It was used to treat a single COVID-19 patient that got well remarkably quickly. So, now Gilead has limited the drug’s availability except through clinical trials. Maybe it will work. Maybe not.

Chloroquine and its derivatives have broad antiviral and anti-parasitic activity. It works by interrupting the pathway by which many viruses enter the cell. It has not been demonstrated yet as an effective drug in the treatment of coronavirus infections, although after treating 100 patients, doctors noted that the treated patients appeared to experience a reduced fever and an improvement in lung images (CT scans). As Fauci said, this is anecdotal evidence, at best. There are numerous trials ongoing, but it is not a panacea. However, if you follow the President’s brand of magical thinking, which means he alone has answers to the world’s most pressing and difficult questions, it is a perfect drug.

There is reason to be optimistic that we can develop a safe and effective vaccine, but it is not trivial. The serum from infected patients contains neutralizing antibodies, that is, the antibodies bind to the virus and prevent it from infecting a human cell. This bodes well for production of a vaccine. The trouble is that there are instances when such vaccines work well in animals (technical name, pre-clinical models), but actually cause problems in human beings. The major problem we face is that sometimes, antibodies actually make a person MORE sensitive to a virus. This is the case for Dengue Fever; if you get one strain, you make antibodies that put you in real danger if exposed to one of the other three Dengue strains. There was some evidence for this in studies on a vaccine against the SARS-2003 virus. Nonetheless, a company called Moderna has sent an experimental vaccine to the National Institute of Allergy and Infectious Diseases (Tony Fauci, Chief) for clinical trials. Hope is fine, reality is better. My vote is to adequately test this or any vaccine before mass administration.

More new epidemics.
We have not seen the end of new or re-emerging diseases. In the past few decades we have seen the emergence of HIV infections, SARS, MERS, Lyme disease, Escherichia coli O157:H7 (E. coli), hantavirus, dengue fever, West Nile virus, and the Zika virus. So in addition to this new SARS-CoV-2 virus, there are many more that could potentially cause an epidemic. Prevention, preparedness, epidemiology, microbiology—science: because it works and wishful thinking doesn’t.

[left_hook_lacey]

Non-expert answering. Someone is working on a finger-prick test:

Found reference to others -- apparently 100+ companies have told the FDA they are working to develop antibody tests. Sounds like the wild West. Here's one article.

So is it a 7 minute test now?

I ask because someone I know got tested for antibodies and she said they had the results in 7 minutes.

[Dr. Rosenrosen]

^^^^ Thank you for sharing, Jimmymax. Very interesting and helpful in understanding and putting COVID-19 into historical context.

[BD80]

So is it a 7 minute test now?

I ask because someone I know got tested for antibodies and she said they had the results in 7 minutes.

[MChambers]

So is it a 7 minute test now?

I ask because someone I know got tested for antibodies and she said they had the results in 7 minutes.

Certainly are antibody tests with very quick results, like 15 minutes, but apparently their accuracy isn’t very good. https://www.palmbeachpost.com/news/2...-they-accurate

[left_hook_lacey]

Certainly are antibody tests with very quick results, like 15 minutes, but apparently their accuracy isn’t very good. https://www.palmbeachpost.com/news/2...-they-accurate

Thanks.

[PackMan97]

I have a recently met Nigerian friend that is importing rapid antibody tests that give results in 5 minutes. All I need is your bank account routing number and your address and we'll be able to ship them directly to your house.

PS. Please be wary of scammers, there are a lot of them trying to take advantage of people in this new world.

[DevilHorse]

I found this important measurement of the CarolinaVirus made in Chicago this morning on Twitter:
https://pbs.twimg.com/media/EVIAFJzX...g&name=900x900

Larry
DevilHorse

[Phredd3]

CarolinaVirus? Yikes. That just sounds scary. Full quarantine on that thing.

[OldPhiKap]

CarolinaVirus? Yikes. That just sounds scary. Full quarantine on that thing.

Hardest thing is — you can’t test for it. It is a no-test phenomenon.

[BD80]

Hardest thing is — you can’t test for it. It is a no-test phenomenon.

Just quarantine everything wearing carolina blue. Forever.

[aimo]

The Durham VA has been having daily conference calls led by the Director - informational discussions and Q&As for the employees on the current COVID-19 situation. Very informative. Anyway, yesterday his guest speaker was Coach K. Great motivational talk for the "frontline" employees. Even the 'hole fans were impressed. But great to have a Veteran who is also such a great motivational speaker with a local connection to boost the morale of the VA workers.

Thanks, Coach!

[Mtn.Devil.91.92.01.10.15]

The Durham VA has been having daily conference calls led by the Director - informational discussions and Q&As for the employees on the current COVID-19 situation. Very informative. Anyway, yesterday his guest speaker was Coach K. Great motivational talk for the "frontline" employees. Even the 'hole fans were impressed. But great to have a Veteran who is also such a great motivational speaker with a local connection to boost the morale of the VA workers.

Thanks, Coach!

He mentioned during his interview on Colin Cowherd yesterday that he had that event next and was extremely complimentary of the front line healthcare workers.

[Indoor66]

Just quarantine everything wearing carolina blue. Forever.

And send them a case of Preparation H.

[left_hook_lacey]

CarolinaVirus? Yikes. That just sounds scary. Full quarantine on that thing.

Unfortunately, I have several family members that have been affected by this devastating disease. There is no known cure, and symptoms get worse over time.

[CrazyNotCrazie]

Three interesting updates:

- I personally am not very focused on the statistics and the statistical methods around coronavirus - I have too much else to worry about. I respect those who choose to discuss it at length here and on skimming their writing, I tend to agree with some more than others. Being in the middle of it all here in NYC, I get very aggravated by those who seem to be doubters of the the statistics and the severity of coronavirus. This article provides an good, fact-based counter to those arguments - admittedly the referenced sample size is just a few days, but there has been a huge spike in deaths in NYC and only a small percentage of those is being captured in the statistics being referenced. Long story short - a lot of people are dying at home and it is assumed that a decent amount of these deaths are caused by coronavirus, but most of those are not being counted.

https://www.nytimes.com/2020/04/10/n...ath-count.html

- Following up on that point, earlier today I saw a post on social media from the father of one of my son's friends here in NYC who is in his early 40s. He started showing symptoms in mid-March. He had a pretty bad case but not bad enough to need to go to the hospital - medical professionals in his family monitored him (I assume his wife and kids went to stay with his in-laws nearby) and he was fortunate to have a pulse oximeter that showed that his lung function was adequate. He tried to get tested but at that time tests were very infrequent so he could not get one, but the symptoms were obviously coronavirus. He has now recovered. So he is yet another unreported case.

- Finally, early on I think we had discussion of when anyone would know someone personally who died of it. I'm guessing someone beat me to it and I missed it or forgot, but I found out that my HS freshman history teacher died of coronavirus recently. He lived in NJ and was in his 80s, rehabbing from an injury at a nursing home - apparently he had been very healthy and active until a recent fall. He had not been formally tested at the time of death but the obituary states that this is the assumed cause of death and they are awaiting testing. He was an excellent teacher - very passionate and committed to his craft. I have not seen him in 25+ years.

[Bluedog]

Three interesting updates:

- I personally am not very focused on the statistics and the statistical methods around coronavirus - I have too much else to worry about. I respect those who choose to discuss it at length here and on skimming their writing, I tend to agree with some more than others. Being in the middle of it all here in NYC, I get very aggravated by those who seem to be doubters of the the statistics and the severity of coronavirus. This article provides an good, fact-based counter to those arguments - admittedly the referenced sample size is just a few days, but there has been a huge spike in deaths in NYC and only a small percentage of those is being captured in the statistics being referenced. Long story short - a lot of people are dying at home and it is assumed that a decent amount of these deaths are caused by coronavirus, but most of those are not being counted.

https://www.nytimes.com/2020/04/10/n...ath-count.html

- Following up on that point, earlier today I saw a post on social media from the father of one of my son's friends here in NYC who is in his early 40s. He started showing symptoms in mid-March. He had a pretty bad case but not bad enough to need to go to the hospital - medical professionals in his family monitored him (I assume his wife and kids went to stay with his in-laws nearby) and he was fortunate to have a pulse oximeter that showed that his lung function was adequate. He tried to get tested but at that time tests were very infrequent so he could not get one, but the symptoms were obviously coronavirus. He has now recovered. So he is yet another unreported case.

- Finally, early on I think we had discussion of when anyone would know someone personally who died of it. I'm guessing someone beat me to it and I missed it or forgot, but I found out that my HS freshman history teacher died of coronavirus recently. He lived in NJ and was in his 80s, rehabbing from an injury at a nursing home - apparently he had been very healthy and active until a recent fall. He had not been formally tested at the time of death but the obituary states that this is the assumed cause of death and they are awaiting testing. He was an excellent teacher - very passionate and committed to his craft. I have not seen him in 25+ years.

The only person I know of personally who has died is a co-worker's brother who was 31 years old...So, it's not just hitting older people as a PSA. I don't know if he had any underlying health conditions or not.

[BD80]

Unfortunately, I have several family members that have been affected by this devastating disease. There is no known cure, and symptoms get worse over time.

Fortunately, the symptoms encourage social distancing ...

[JasonEvans]

I found this important measurement of the CarolinaVirus made in Chicago this morning on Twitter:
https://pbs.twimg.com/media/EVIAFJzX...g&name=900x900

Larry
DevilHorse

For folks who have not clicked on this amazing link...

[budwom]

^ always good to see a Tarheel being dissed. The bloom sure went off that rose quickly.