Corona virus general questions mega thread

[MigL]

One factor which seems to be getting ignored during this outbreak, is the root cause.
Possibly because investigating it has racist overtones, but I think it can be discussed in a civil manner.

India is as overcrowded as China and probably even more insanitary in certain areas, yet no major diseases have originated there.
China, on the other hand has given us SARS in 2004, and now COVID-19. Both are thought to have originated in Chinese 'wet markets", where exotic animals are caged in close proximity, under stress, and slaughtered on the spot for customers who believe their consumption provides health, sexual, and other benefits. Both virus are common to bats, and while SARS made the jump to civet cats, and then to humans, COVID-19 is thought to have jumped from bats to pangolins ( scaly anteaters ) and then to humans. Mutating with each jump.
Turtles, snakes, cats, birds, bats, etc. in close proximity, and a great demand from wealthy Chinese for these exotic meats is the root cause ( what benefits does shark fin soup really bestow ? ).

These markets are common in China, Thailand, Vietnam, etc., where poor farmers can make good money by raising exotic animals that were never meant to be in proximity. China did close down some of these markets after the SARS outbreak, but they've looked the other way, as wet markets made a comeback ( as in Wuhan ).

Other diseases have also resulted from the overcrowded and unsanitary methods of raising pigs ( swine flu ) and chickens ( avian flu ).
Is it time that the world demands the ending of these wet markets ( especially the exotic animals part ), and other unsanitary livestock activities ?

[CharonY]

1 hour ago, MigL said:

India is as overcrowded as China and probably even more insanitary in certain areas, yet no major diseases have originated there.

I think there may a couple of wrong assumptions but I am not read enough in those areas to provide an immediate in-depth response.

Let's talk about zoonotic diseases first. One thing of note is that at high population densities and contacts with animals there is a higher likelihood of a pathogen crossing species barriers. But even then they may not cause large outbreaks, as they may have low transmission or low virulence and either exist invisibly in a given population or do otherwise do not garner a lot of traction. Many viruses re-assort in pigs transfer to humans and then change further (e.g. by grabbing genes from other viruses in their hosts) before they cause outbreaks. Take the H1N1pdm09 (swine-flu) pandemic, for example. That particular strain has a bit of a mosaic structure, probably originating from three parental pig viruses and emerged into humans somewhere in North America, some assume in Mexico. There is also the MERS epidemic, that came likely from camels but were sufficiently contained not to cause an epidemic. Hantavirus is a deadly virus that has a case fatality of ca. 40%. However, it is spread by mice and not human to human (luckily) and was found in the USA. There are also plenty of zoonotic diseases found in India, such NIpah virus and has been slowly spreading. However as there is no human-human transmission the spread is not as rapid. Likewise, we had a Zika pandemic not so long ago, a mosquito borne disease, originating from Africa. Japanese encephalitis likely originated in the Indonesia-Malaysia region and while it is also transmitted by mosquitos, it causes outbreaks every couple of years with about 13-20 thousand deaths each year. Again, lucky break that they need mosquitos as vectors.

So in a way to me the question is whether it is by chance that those originating from China have larger impact on global health and economy or whether there are factors contributing to it. I think one needs to think beyond sanitary issues, as you mentioned. One question could be for example how connected China is compared to India. But also for example how the meat industry looks like. Another perhaps simple question is also what types of potential zoonotic diseases are there that could for example mix with animals that come into close contact with humans. In India many are mosquito borne, but perhaps they are less relevant in China. In Europe and US industrial pig farming has a huge potential to recombine and spread viruses in pigs, but there are perhaps fewer animals around that can spread novel viruses into pigs. Regulating or closing those market can likely close some of the risk factors.

However, ultimately my thinking is that the world is shrinking, for better or for worse. There will be more contact between each of us and there are diseases that not zoonotic. What it means is that otherwise local disease have a much easier to become epidemic and even pandemic. Without the willingness for rapid responses to detect human-human spread, I think that most of the measures will be insufficient. And I think it is somewhat wrong to think that in the Western world our measures will keep us safe indefinitely. We had prion disease entering the food chain (sure it is not an infectious disease per se, but still). Farm animals often have to be culled due to various disease outbreaks. So far those have not managed to jump the species barrier, but it is not something that may so forever. On the other hand of course there is the tendency of diseases to become less virulent over time (as killing the host is generally not a good long-term strategy) but in the meantime a lot of harm can be done.

Other man-made reasons for outbreak are for example anti-vaccination campaigns. HIV/AIDS now is well controlled, and we get complacent again (in the 90s it was for a  time the leading cause of death in young adults). We have tons of pathogens that can mix, mutate and while there may be area with larger reservoirs than others, I do think it is dangerous to think it as an "elsewhere" problem. I think this is what lead to complacency when China was facing COVID-19 and that is why despite ample warnings the Western world only reacted when they had deaths in their midst.

It may not be quite what you are thinking of, but I do think that this change in mentality is necessary to combat the inevitable occurrence and re-occurrence of diseases (and I apologize for all the typo and rantiness, it is more flow of thoughts without proper editing, may try to express it clearer when I got time again). 

Edit: had so many unfinished thoughts but wanted to include that global warming is going to increase the likelihood of many, especially mosquito borne diseases, so that has to go in there also somewhere. 

[druS]

On 3/25/2020 at 1:17 PM, CharonY said:

You mean the origins? That is part of a large discussion with quite a bit of unknowns. I think most think that they are a version of mobile genetic elements, like transposons or plasmid, but more autonomous. However another line of thinking, especially among folks working on giant viruses think that they might be stripped-down cells from an unrecognized domain of life. I think the latter has some traction in certain areas but is still considered the less likely narrative by most folks, I would say.

 

CharonY you continue to fascinate on this thread. Should have started talking about virus a long time ago! Is this "unrecognised domain" part of what I have seen described as "phylum candidate radiata"?

By the way, don't plasmids self replicate? That would be a big difference to a virus I suspect. I will have to look up transposons.

 

 

Edited March 26, 2020 by druS
spelling

[CharonY]

11 hours ago, druS said:

CharonY you continue to fascinate on this thread. Should have started talking about virus a long time ago! Is this "unrecognised domain" part of what I have seen described as "phylum candidate radiata"?

No, I am not sure whether the community actually proposed a name (I think the evidence is not strong enough to warrant it, but folks still may have done so). Radiata is a historic term deep in the animal group. The idea was to group all animals with radial symmetry. However, as it turned out, animals with such body plans are not monophyletic (i.e. share the same common recent ancestor).

On the comment I made above, when we go away from viruses, I should also add that the various Cholera epidemics throughout history (including the one that is going since the 60s) have origins largely in India. Though due to the mode of transmission this is actually a sanitary issue (specifically lack of access to clean water).

[studiot]

In the meantime some good news, especially for the OP.

Free Fish and Chips for all.

https://www.bbc.co.uk/news/uk-england-oxfordshire-52047985

Edited March 26, 2020 by studiot

[MigL]

Don't misunderstand, I'm not necessarily picking on the Chinese, but any unhygienic form of animal farming and slaughter.
These Oriental wet markets bring all the worst circumstances together.
Different animals that are usually separated geographically, are kept in stressful/unsanitary conditions, in cages next to each other, and are then killed/skinned/cleaned in the same area, were bodily fluids of one specie may contaminate another.
If this isn't a best case scenario for viral transmission, I don't know what is.

I'm not saying this doesn't happen on pig farms, chicken farms, or in the water in India, and maybe we should be looking at the way pigs and chicken are farmed, as I'm sure most of the world's population is aware of not mixing drinking water with toilet water ( or at least, should be ).

Another question which comes to mind...
If you've had COVID-19, built up a supply of anti-bodies, and recovered so that you are now immune to re-infection, are these anti-bodies transferrable ? Would a blood transfusion give the receiver the anti-bodies developed by the donor ? and would these anti-bodies be effective ?
IOW are anti-bodies tailored to the invading virus, or the host cells ?
( go easy on me, Last biology class I had was Gr.10 )

[Strange]

!

Moderator Note

A few blatantly off-topic posts (and, I'm afraid, some responses) have been hidden. The perpetrator has been given some time in quarantine to think about following the rules of the forum in future.

 

[CharonY]

3 hours ago, MigL said:

 

Another question which comes to mind...
If you've had COVID-19, built up a supply of anti-bodies, and recovered so that you are now immune to re-infection, are these anti-bodies transferrable ? Would a blood transfusion give the receiver the anti-bodies developed by the donor ? and would these anti-bodies be effective ?
IOW are anti-bodies tailored to the invading virus, or the host cells ?
( go easy on me, Last biology class I had was Gr.10 )

Yes it is a possible treatment. If the recovered patients produced enough antibodies against the pathogen, it can help in alleviating the disease. It has been attempted with SARS and Ebola, mostly with modest success. And there are ongoing trials (i.e. treatments of patients with this approach) in China and Italy.  (side note- antibodies should be directed toward external targets, such as viruses and bacteria. Sometimes they react to host cell components, which can result in auto-immune diseases).

3 hours ago, MigL said:

Don't misunderstand, I'm not necessarily picking on the Chinese, but any unhygienic form of animal farming and slaughter.

I think that this is useful to limit. However, even conditions that we consider sanitary, we run risk of spreading zoonotic diseases. Animal farming is not a sterile process and pathogens are constantly evolving. In my mind, better processes can slow down the rate, but not stop the process.

[Casio]

19 hours ago, MigL said:

One factor which seems to be getting ignored during this outbreak, is the root cause.
Possibly because investigating it has racist overtones, but I think it can be discussed in a civil manner.

India is as overcrowded as China and probably even more insanitary in certain areas, yet no major diseases have originated there.
China, on the other hand has given us SARS in 2004, and now COVID-19. Both are thought to have originated in Chinese 'wet markets", where exotic animals are caged in close proximity, under stress, and slaughtered on the spot for customers who believe their consumption provides health, sexual, and other benefits. Both virus are common to bats, and while SARS made the jump to civet cats, and then to humans, COVID-19 is thought to have jumped from bats to pangolins ( scaly anteaters ) and then to humans. Mutating with each jump.
Turtles, snakes, cats, birds, bats, etc. in close proximity, and a great demand from wealthy Chinese for these exotic meats is the root cause ( what benefits does shark fin soup really bestow ? ).

These markets are common in China, Thailand, Vietnam, etc., where poor farmers can make good money by raising exotic animals that were never meant to be in proximity. China did close down some of these markets after the SARS outbreak, but they've looked the other way, as wet markets made a comeback ( as in Wuhan ).

Other diseases have also resulted from the overcrowded and unsanitary methods of raising pigs ( swine flu ) and chickens ( avian flu ).
Is it time that the world demands the ending of these wet markets ( especially the exotic animals part ), and other unsanitary livestock activities ?

I'm no expert in this subject at all, and if it were not so affecting humans to the degree it is worldwide, I'd probably of never had an interest to look in on the subject at all, however, that said, I think that some serious questions must be raised to ALL world leaders after this COVID-19 is resolved, if it can be resolved as Russian indicate that it might never be resolved. 

[Sensei]

On 3/26/2020 at 6:28 PM, studiot said:

In the meantime some good news, especially for the OP.

Free Fish and Chips for all.

https://www.bbc.co.uk/news/uk-england-oxfordshire-52047985

You made my day with this article.

This world needs true, honest, anonymous, not for likes, videos and public applause, generosity..

#fishandchips4all

 

Edited March 27, 2020 by Sensei

[Corey Bump]

Here's the problem, we are testing people for any strain of a Coronavirus. Not specifically for COVID-19. There are no reliable tests for a specific COVID-19 virus. There are no reliable agencies or media outlets for reporting numbers of actual COVID-19 virus cases. This needs to be addressed first and foremost. Every action and reaction to COVID-19 is based on totally flawed data and we simply can not make accurate assessments.

This is why you're hearing that most people with COVID-19 are showing nothing more than cold/flu like symptoms. That's because most Coronavirus strains are nothing more than cold/flu like symptoms. The few actual novel Coronavirus cases do have some worse respiratory responses, but still have a very promising recovery rate, especially for those without prior issues.

The ‘gold standard’ in testing for COVID-19 is laboratory isolated/purified coronavirus particles free from any contaminants and particles that look like viruses but are not, that have been proven to be the cause of the syndrome known as COVID-19 and obtained by using proper viral isolation methods and controls (not the PCR that is currently being used or Serology /antibody tests which do not detect virus as such). PCR basically takes a sample of your cells and amplifies any DNA to look for ‘viral sequences’, i.e. bits of non-human DNA that seem to match parts of a known viral genome.
The problem is the test is known not to work.
It uses ‘amplification’ which means taking a very very tiny amount of DNA and growing it exponentially until it can be analyzed. Obviously any minute contaminations in the sample will also be amplified leading to potentially gross errors of discovery. Additionally, it’s only looking for partial viral sequences, not whole genomes, so identifying a single pathogen is next to impossible even if you ignore the other issues.
The Mickey Mouse test kits being sent out to hospitals, at best, tell analysts you have some viral DNA in your cells. Which most of us do, most of the time. It may tell you the viral sequence is related to a specific type of virus – say the huge family of coronavirus. But that’s all. The idea these kits can isolate a specific virus like COVID-19 is nonsense. And that’s not even getting into the other issue – viral load.

If you remember the PCR works by amplifying minute amounts of DNA. It therefore is useless at telling you how much virus you may have. And that’s the only question that really matters when it comes to diagnosing illness. Everyone will have a few virus kicking round in their system at any time, and most will not cause illness because their quantities are too small. For a virus to sicken you you need a lot of it, a massive amount of it. But PCR does not test viral load and therefore can’t determine if a osteogenesis is present in sufficient quantities to sicken you.
If you feel sick and get a PCR test any random virus DNA might be identified even if they aren’t at all involved in your sickness which leads to false diagnosis. And coronavirus are incredibly common.

A large percentage of the world human population will have covi DNA in them in small quantities even if they are perfectly well or sick with some other pathogen. Do you see where this is going yet? They are incredibly common and there’s tons of them. A very high percentage of people who have become sick by other means (flu, bacterial pneumonia, anything) will have a positive PCR test for covi even if you’re doing them properly and ruling out contamination, simply because covis are so common.

There are hundreds of thousands of flu and pneumonia victims in hospitals throughout the world at any one time.

All you need to do is select the sickest of these in a single location – say Wuhan – administer PCR tests to them and claim anyone showing viral sequences similar to a coronavirus (which will inevitably be quite a few) is suffering from a ‘new’ disease.

Since you already selected the sickest flu cases a fairly high proportion of your sample will go on to die.

You can then say this ‘new’ virus has a CFR higher than the flu and use this to infuse more concern and do more tests which will of course produce more ‘cases’, which expands the testing, which produces yet more ‘cases’ and so on and so on.
Before long you have your ‘pandemic’.

The point is –sick people from other causes, are being misdiagnosed, thus producing misleading case numbers

[iNow]

3 minutes ago, Corey Bump said:

Here's the problem

There’s so much wrong in your post it’s hard to know where to start. There are multiple kinds of tests so you cannot generalize about them all. There may be a handful of false positives, but those are orders of magnitude lower than the number of infected who can never get tested at all. 

[Strange]

7 minutes ago, Corey Bump said:

Here's the problem, we are testing people for any strain of a Coronavirus. Not specifically for COVID-19. There are no reliable tests for a specific COVID-19 virus. There are no reliable agencies or media outlets for reporting numbers of actual COVID-19 virus cases. This needs to be addressed first and foremost. Every action and reaction to COVID-19 is based on totally flawed data and we simply can not make accurate assessments.

You need to provide some evidence for this. (Or, to put it another way: I don't believe you.)

 

Your claim that "There are no reliable tests for a specific COVID-19 virus" appears to be false. For example:

Quote

The workflow reliably detects 2019-nCoV, and further discriminates 2019-nCoV from SARS-CoV. Through coordination between academic and public laboratories, we confirmed assay exclusivity based on 297 original clinical specimens containing a full spectrum of human respiratory viruses. Control material is made available through European Virus Archive – Global (EVAg), a European Union infrastructure project.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6988269/

Quote

These assays have been evaluated using a panel of controls and only the positive control (SARSCoV RNA) is tested positive in these assays.

https://www.who.int/docs/default-source/coronaviruse/peiris-protocol-16-1-20.pdf?sfvrsn=af1aac73_4

Quote

Using DNA plasmids as positive standards, the detection limits of these assays were found to be below 10 copies per reaction. All negative control samples were negative in the assays.

https://academic.oup.com/clinchem/advance-article/doi/10.1093/clinchem/hvaa029/5719336

 

[CharonY]

There is also several fundamental misunderstandings of the methods, it is a RT-PCR (which along with viral cultivation is considered a gold standard but has mostly replaced the latter),primers provide target specificity, detection of antibodies is useful for rapid testing (but suffers more false negatives than RT-PCR), current tests look at two targets and inconclusive tests are validated via Sanger sequencing.

[PhilGeis]

On 3/26/2020 at 12:11 AM, MigL said:

 

Other diseases have also resulted from the overcrowded and unsanitary methods of raising pigs ( swine flu ) and chickens ( avian flu ).
Is it time that the world demands the ending of these wet markets ( especially the exotic animals part ), and other unsanitary livestock activities ?

China wet market are not only an important source of urban food, they also provides a source of fresh food.  Tho' the communist regime has extensive power (recall the temporary ban on  Beijing automobile travel during Olympics) permanently shutting down may lead to social unrest in cities.  The world has made many demands on China - why would another have any substance? 

[StringJunky]

1 hour ago, PhilGeis said:

China wet market are not only an important source of urban food, they also provides a source of fresh food.  Tho' the communist regime has extensive power (recall the temporary ban on  Beijing automobile travel during Olympics) permanently shutting down may lead to social unrest in cities.  The world has made many demands on China - why would another have any substance? 

Considering how China was, it is a lot more transparent now and needs to progress at its own rate. I'm sure that regime will change it, if it's feasible to them, in time.

Edited March 28, 2020 by StringJunky

[CharonY]

Even if feasible, one should not believe that this would remove the threat of zoonotic or other diseases. It is not a matter of if just of when new diseases will emerge. As such implementing mechanisms and plans to stop their spread are crucial and one should not assume that removing single sources (wet market or even animal farming as a whole) would magically erase the risk.

[StringJunky]

8 hours ago, CharonY said:

Even if feasible, one should not believe that this would remove the threat of zoonotic or other diseases. It is not a matter of if just of when new diseases will emerge. As such implementing mechanisms and plans to stop their spread are crucial and one should not assume that removing single sources (wet market or even animal farming as a whole) would magically erase the risk.

Yes, evolution will do its thing.

[Airbrush]

Is there anything to fear walking one's dog if you keep a good distance from other people and dogs?  Dogs are attracted to the scent of urine of other dogs.  Can dogs get Covid9-19 from another dog by smelling where the other dog urinated?  The other question is can dogs get Coronavirus from people, and vice versa?

[Strange]

3 minutes ago, Airbrush said:

Is there anything to fear walking one's dog if you keep a good distance from other people and dogs?  Dogs are attracted to the scent of urine of other dogs.  Can dogs get Covid9-19 from another dog by smelling where the other dog urinated?  The other question is can dogs get Coronavirus from people, and vice versa?

There is no evidence that dogs can either transmit the virus or become ill from it: https://www.cdc.gov/coronavirus/2019-ncov/daily-life-coping/animals.html

[Airbrush]

2 minutes ago, Strange said:

There is no evidence that dogs can either transmit the virus or become ill from it: https://www.cdc.gov/coronavirus/2019-ncov/daily-life-coping/animals.html

Thank you!

[MigL]

17 hours ago, CharonY said:

Even if feasible, one should not believe that this would remove the threat of zoonotic or other diseases.

That is ultimately true, charonY.
But we practice social distancing to reduce the threat of infection.
Would not interspecies distancing also reduce the threat of interspecies infection/mutation ?
Especially when the differing species do not co-habitate in nature.

[CharonY]

2 hours ago, MigL said:

That is ultimately true, charonY.
But we practice social distancing to reduce the threat of infection.
Would not interspecies distancing also reduce the threat of interspecies infection/mutation ?
Especially when the differing species do not co-habitate in nature.

I think it would reduce one source. Though again, the same could be said about most animal farming. Several aspects make those market more likely to be a threat, but what I fear is that folks will just say think that banning those practices (especially those that they do not engage in, as it is the least annoying for them) is enough. For example, the current US administration tries to lay blame of the pandemic entirely on China, mostly to distract from their own failings (which had plenty of warning beforehand plus the active dismantling of mechanisms that could have given them even more intel). If we phrase overall pandemic readiness in terms of "those guys need to do XYZ" I fear that the overall result is that folks then lapse their own preparedness. I think this is what has happened now. Too many countries thought they were immune from biology and waited up to the last minute to get prepared. Countless folks suffer from it now and in the foreseeable future. Also, it creates the illusion that own practices (and I feel a little bit about that in the initial question) are somehow safe and sanitary. Yet, intensive animal farming does carry significant risks of spreading disease to the environment. In fact, the rise of antibiotics resistance bacteria is largely driven by agriculture.

Certainly, it is not a zero-sum game, but regardless whether those markets are banned or not, it must be done in addition, not instead of disease preparedness.

[MigL]

If in 15 years time we have another outbreak that originated in a South-east Asian wet market, I don't know if I'm a big enough person to be able to resist saying "I told you so."
Assuming we're both still here  .

[CharonY]

1 hour ago, MigL said:

If in 15 years time we have another outbreak that originated in a South-east Asian wet market, I don't know if I'm a big enough person to be able to resist saying "I told you so."
Assuming we're both still here  .

Well, we already had plenty that did not originate there (as well as a few pandemics) and we will have plenty of outbreaks within the next few years. It is mostly the confluence of factors that make a disease more likely become a pandemic, which includes e.g. effective human-human transmission, long incubation time, late/difficult detection, outbreak in areas with high connections to rest of the world etc.

This time a lot of folks dropped the ball which resulted in a rather unprecedented situation. The question is whether the next one (which will come) will be contained better or not.