COVID COVID-19 Coronavirus Containment Efforts

[collinsmark]

Perhaps PF members better versed in microbiology and epidemiology will have a better answer than mine. But for what it's worth, here's my take on it from watching the news and reading as much science on it as I could easily find.

Apologies if this has been addressed in this thread. What I understand is that the COVID-19 virus has a fairly short lifetime when in an open environment? I also understand this virus may be seasonal? If those understands are correct, my question is, how does this virus stay potentially infectious after the "off-season"?

o "What I understand is that the COVID-19 virus has a fairly short lifetime when in an open environment?"

Not too much is known about this, but certainly there's evidence that if an infected person were to cough up a loogie and spit it into a laboratory petri dish, and that sample were to be kept in ideal conditions (precisely controlling temperature, humidity, etc.), then the virus could survive many days.

For more practical situations, the survival time is on the order of hours. More hours for materials like metal and plastic, and less than that for materials like clothing. Probably. Maybe.

If instead we go by other similar viruses (for which we have more data), the virus tends to break down in conditions with high humidity and high temperature. They'll live longer in cold, dry conditions.

o "I also understand this virus may be seasonal? If those understands are correct, my question is, how does this virus stay potentially infectious after the 'off-season.'"

I wish we had more data on that for this particular virus. Some viruses are more susceptible to seasonal changes than others. That fact is we don't have a lot of data how well this virus does in summertime conditions (it's peaking pretty close to an equinox). It has seemed to survived well enough in countries that are presently hot and humid.

 

[collinsmark]

New 3Blue1Brown video.

 

[Astronuc]

I wish we had more data on that for this particular virus. Some viruses are more susceptible to seasonal changes than others. That fact is we don't have a lot of data how well this virus does in summertime conditions (it's peaking pretty close to an equinox). It has seemed to survived well enough in countries that are presently hot and humid.

COVID-19 may have peaked in China, possibly in S. Korea and few other countries. It has yet to peak in the US and parts of Europe. In one of my previous posts, I linked to one model that peaks in mid-April in the US, but that makes assumptions about current cases and deaths, and takes into account various measures, e.g., stay-at-home and social/physical distancing/isolation. Only 21 of 50 states have adopted stay-at-home, and many only in the last week or so. Let's see where we are in 1 week (7 days).

The model was predicting 1542 (1462-1629) by today, but Coronavirus Dashboard reports 1701 deaths in the US as of today; Covidtracking.com (3/27 20:49 ET) reports 1530 deaths (numbers subject to change). I hope we don't see 7000 deaths.

 

[Astronuc]

Another dashboard - https://gisanddata.maps.arcgis.com/apps/opsdashboard/index.html#/bda7594740fd40299423467b48e9ecf6

Looking at the US, in addition to concentrations in the regions associated with major international airports (SEA, SFO, LAX, EWR, JFK, ATL), concentrations show up in metropolitan areas with major airline hubs (e.g., Denver, CO (DEN, United), Salt Lake City, UT (SLC, Delta), Charlotte, NC (CLT, American), Dallas-Ft Worth, TX (DFW, American), Houston, TX (IAH, United)).

https://www.ncdhhs.gov/covid-19-case-count-nc
https://txdshs.maps.arcgis.com/apps/opsdashboard/index.html#/ed483ecd702b4298ab01e8b9cafc8b83Looking back to January 30, 2020, which seems like a long time ago,
https://www.who.int/docs/default-source/coronaviruse/situation-reports/20200130-sitrep-10-ncov.pdf

First confirmed cases of 2019-nCoV acute respiratory disease in Finland, India and Philippines; all had travel history to Wuhan City.

One of the first cases diagnosed in the US was a 35 year old man returning from Wuhan on January 14/15. He was diagnosed in hospital after 4 days of being ill, and confirmed on Jan 20/21. The virus was probably widespread at that point.

 

[atyy]

Question about immunity and two COVID-19 strains:

We've discussed immunity before on a broad level. -----> For those who contract the virus and survive, their bodies develop immunity from the virus' harms in the future.

With two strains - L and S - does anyone know if immunity is specific to just one strain? Thanks!

Whether the 2 strain idea is a useful concept remains to be seen.

 

[atyy]

BBC, March 17, 2020 - Coronavirus: US volunteers test first vaccine
https://www.bbc.com/news/health-51906604

So someone has already started on a vaccine for 2019-nCoV/SARS-CoV-2.

I think we discussed earlier in this thread that Moderna's nucleic acid based vaccine is not the traditional route, and there is no vaccine used in humans that has previously used this approach. Others have mentioned more traditional approaches by Chinese and by Australian groups, but I'm not sure what the status of those are. My personal favourite (not for any scientific reason) that I've seen mentioned earlier in the thread is the MIGAL attempt - they happened to be working on a vaccine for chicken Coronavirus bronchitis, which they will now try to modify for humans.

 

[Ygggdrasil]

Question about immunity and two COVID-19 strains:

We've discussed immunity before on a broad level. -----> For those who contract the virus and survive, their bodies develop immunity from the virus' harms in the future.

With two strains - L and S - does anyone know if immunity is specific to just one strain? Thanks!

As @atyy mentioned, the paper making the claim about two different strains of the virus has been criticized by other researchers in the field:

An analysis of genetic data from the ongoing COVID-19 outbreak was recently published in the journal National Science Review by Tang et al. (2020) 84. Two of the key claims made by this paper appear to have been reached by misunderstanding and over-interpretation of the SARS-CoV-2 data, with an additional analysis suffering from methodological limitations. [...] Given these flaws, we believe that Tang et al. should retract their paper, as the claims made in it are clearly unfounded and risk spreading dangerous misinformation at a crucial time in the outbreak.

http://virological.org/t/response-to-on-the-origin-and-continuing-evolution-of-sars-cov-2/418

According to the Tang paper, the S and L strains they identify are primarily differentiated by two mutations, one in the orf1ab gene and the other in the ORF8 gene. Neither of these genes are expressed on the surface of the virion, so the mutations will not affect immunity to the virus, and I would expect immunity to one "strain" to confer immunity to the other "strain." The spike protein is the main protein on the surface of the virus, so scientists should monitor mutations in the spike protein to find potential mutations that could affect immunity against the virus.

So someone has already started on a vaccine for 2019-nCoV/SARS-CoV-2.

Again, as @atyy mentioned, neither Moderna nor any other company has been able to make a successful vaccine based on their new technology. Their technology leads to very rapid and flexible vaccine development (their main advantage over conventional techniques and why they have been first to start clinical trials), but their approach to vaccine development remains unproven. Here's a good article describing Moderna's technology as well as discussing where it has failed in past attempts to develop a vaccine: https://www.nature.com/articles/d41586-019-03072-8 [edit: original version had the wrong link]

Here's a good article updating progress towards development of COVID-19 therapies: https://www.statnews.com/2020/03/19...oronavirus-drugs-and-vaccines-in-development/

In addition to Moderna, CanSino Biologics (a Chinese company) has begun Phase I Clinical Trials to examine the safety of their vaccine candidate. Various other companies are developing vaccine candidates (based on both new technologies and traditional technologies), but these other efforts remain in the preclinical testing and development phases.

 

[Astronuc]

Just how bad is it?
New Jersey Department of Health - Volunteers with qualified medical training and experience needed. !
https://covid19.nj.gov/volunteer

 

[mfb]

Italy's new cases have been stable for a week now.

As expected, Italy prepares for a lockdown extension beyond April 3, but the situation could already improve by that time.

----

It's a reddit comment, so no way to check claimed credentials ("I am a physician"), but here is a discussion of mutation rate. In summary, it's expected that vaccines will work and re-infection is unlikely.

----

The state of New York has 1/3 the population of Italy, but already 1/2 the reported cases. I scaled Italy's numbers by the population ratio. Italy reached 149 adjusted deaths by March 8, New York reached 157 by March 23. I shifted Italy's numbers by 15 days and then plotted everything on a logarithmic scale. Too early to tell how the deaths evolve, especially as New York might have missed some earlier deaths. New York is accumulating confirmed cases quicker than Italy.

 

[atyy]

https://www.sciencemag.org/news/202...avirus-big-mistake-top-chinese-scientist-says
Not everyone will agree with the comments on masks, and probably the WHO messaging is somewhat inaccurate on this point (ie. the truth is probbaly quite nuanced and context dependent between both positions). But I am posting this link not so much for the mask comment (let's avoid revisiting that controversy), but for the rest of the interview which is well worth a read.

 

[wukunlin]

https://www.sciencemag.org/news/202...avirus-big-mistake-top-chinese-scientist-says
Not everyone will agree with the comments on masks, and probably the WHO messaging is somewhat inaccurate on this point (ie. the truth is probbaly quite nuanced and context dependent between both positions). But I am posting this link not so much for the mask comment (let's avoid revisiting that controversy), but for the rest of the interview which is well worth a read.

That link is behind a proxy in NUS

 

[Ygggdrasil]

It's a reddit comment, so no way to check claimed credentials ("I am a physician"), but here is a discussion of mutation rate. In summary, it's expected that vaccines will work and re-infection is unlikely.

I agree that most of the available data points to relatively few mutations accumulating in the virus, so viral mutation to avoid immunity is not a huge concern. In studies with monkeys, infection with COVID-19 provides immunity to the disease in the short term, so re-infection is unlikely and a vaccine should be able to produce immunity. Still, viral mutation can be unpredictable (especially if the disease becomes very widespread, providing more opportunities for mutation), so this is something that scientists are monitoring by sequencing the virus and looking for mutations in the spike protein.

However, a bigger concern may be that our body's immune response to the virus can wane over time. Our experience with the four other endemic coronaviruses suggests that immunity to these viruses wanes over time and studies on people who were infected by the similar SARS virus also suggests that levels of antibodies against the virus wane over the course of a few years. Of course, no data is available for COVID-19, but this is definitely a concern that scientists will need to monitor in the years to come.

 

[atyy]

That link is behind a proxy in NUS

Sorry, have edited the link.

 

[atyy]

It's a reddit comment, so no way to check claimed credentials ("I am a physician"), but here is a discussion of mutation rate. In summary, it's expected that vaccines will work and re-infection is unlikely.

Similar comments are made by Trevor Bedford in this Twitter thread.
"A thread on #SARSCoV2 mutations and what they might mean for the #COVID19 vaccination and immunity, in which I predict it will take the virus a few years to mutate enough to significantly hinder a vaccine."

 

[mfb]

I hope we have a good eradication campaign before that.

 

[bhobba]

My understanding is that South Korea does not screen asymptomatics. If they do test asymptomatics, they I suspect they only test the high risk subset, eg. those who are closed contacts of confirmed cases.

Here in Aus they have only recently started testing asymptomatics as part of better tracing protocols - if you have been in contact with a known case you are now tested regardless. As I mentioned in a post a politician was found asymptomatic, and even in quarantine feels perfectly well. But it has to be said saying you are feeling fine, and simple things like asking you to open your mouth and seeing your throat is hardly a thorough physical. So far the asymptomatics they have found are a small number - but that may change in time.

Thanks
Bill

 

[kyphysics]

As @atyy mentioned, the paper making the claim about two different strains of the virus has been criticized by other researchers in the field:

http://virological.org/t/response-to-on-the-origin-and-continuing-evolution-of-sars-cov-2/418

According to the Tang paper, the S and L strains they identify are primarily differentiated by two mutations, one in the orf1ab gene and the other in the ORF8 gene. Neither of these genes are expressed on the surface of the virion, so the mutations will not affect immunity to the virus, and I would expect immunity to one "strain" to confer immunity to the other "strain." The spike protein is the main protein on the surface of the virus, so scientists should monitor mutations in the spike protein to find potential mutations that could affect immunity against the virus.

Again, as @atyy mentioned, neither Moderna nor any other company has been able to make a successful vaccine based on their new technology. Their technology leads to very rapid and flexible vaccine development (their main advantage over conventional techniques and why they have been first to start clinical trials), but their approach to vaccine development remains unproven. Here's a good article describing Moderna's technology as well as discussing where it has failed in past attempts to develop a vaccine: https://www.nature.com/articles/d41586-019-03072-8 [edit: original version had the wrong link]

Here's a good article updating progress towards development of COVID-19 therapies: https://www.statnews.com/2020/03/19...oronavirus-drugs-and-vaccines-in-development/

In addition to Moderna, CanSino Biologics (a Chinese company) has begun Phase I Clinical Trials to examine the safety of their vaccine candidate. Various other companies are developing vaccine candidates (based on both new technologies and traditional technologies), but these other efforts remain in the preclinical testing and development phases.

I appreciate your answer and thoughts even if I do not understand the science behind it. I do, however, understand the broad gist of what you were saying. Thank you.

A follow-up for you or anyone else is whether we can still, in theory, get a mutated new strain in the future that would make survivors with immunity to the current strain once again susceptible to getting sick from that new strain?

If I'm not mistaken, the Spanish flu had a second wave that involved a mutated new strain, which was much more virulent than the first strain, no? What I am not sure of is whether those immune to the Spanish flu's first strain were still immune to the next wave.

 

[bhobba]

I hope we have a good eradication campaign before that.

Well at least in Aus everything looks like its on track - we are still in level 2-3 measures, not a total level 4 lockdown everyone thought we would be in by now. It seems the rate of infection is slowing. But I still believe they have not handled this as well as they could have - look at Taiwan. If we did what they did we would be in much better shape, not necessarily much health wise, but certainly economically. Still Taiwan had the SARS experience to draw on - we didn't. The good news here is they are, finally, isolating in Hotels every single arrival from overseas and police, instead of just warning people that violate social distancing rules etc, are now fining them. But some are still ignoring rules eg a large group of people have been spotted ignoring social distancing outside a restaurant at Canungra. Nice place - the sort of not well known outside Aus tourist attraction those visiting should go to - but we all must follow the rules - takeaway only for restaurants:
https://www.mustdobrisbane.com/features/day-tripping-canungra

Thanks
Bill

 

[wukunlin]

But I still believe they have not handled this as well as they could have - look at Taiwan. If we did what they did we would be in much better shape, not necessarily much health wise, but certainly economically. Still Taiwan had the SARS experience to draw on - we didn't.

Not wanting to take anything away from the excellent job done by Taiwanese health workers, but if any country wants to look for a gold standard, they might want to know that citizens of PRC were not allowed to apply for individual travel visa to Taiwan since Augest last year (reasons being political shenanigans), so they could only travel to Taiwan in tour groups, and all tour groups in China were canceled on the 24th of Jan. After that the only people who could go to Taiwan from China, were Taiwanese returning. And all the Taiwanese in Wuhan were trapped there, because more political shenanigans.

 

[mfb]

Do we have some data what happens to asymptomatic cases over time? People who get sick seem to be infectious as long as they have symptoms and then a little bit beyond that. But that approach is meaningless for people who never develop symptoms.

 

[Rive]

With two strains - L and S - does anyone know if immunity is specific to just one strain? Thanks!

As far as I know the definition of 'strain' is not a really clear thing. If you ask somebody who works with genetics, then he/she might accept a few gene difference as two separated strain in case this distinction is useful to explain the actual topic.
If you ask a doctor (working with pandemics) he will require more: like the caused immunity not being valid for the other strain, or the ability to cause a new pandemic, or something like that - according to what's useful in his/her profession.

As far as I know the mentioned 'strains' right now are about genetics only: no evidence that it would have any effect on the scale of the pandemic.

Instead of those 'strains' the weak definition or strength of the 'immunity' and/or 'recovery' might be a https://www.msn.com/en-au/news/world/coronavirus-why-do-recovered-patients-test-positive-again/ar-BB10LACQ

 

[DennisN]

A follow-up for you or anyone else is whether we can still, in theory, get a mutated new strain in the future that would make survivors with immunity to the current strain once again susceptible to getting sick from that new strain?

That is a great question which I also would like to know the answer to. I've thought of asking it before in this thread, but I forgot to.

If I'm not mistaken, the Spanish flu had a second wave that involved a mutated new strain, which was much more virulent than the first strain, no?

Yes.

What I am not sure of is whether those immune to the Spanish flu's first strain were still immune to the next wave.

Another great question which I don't know the answer to.

 

[DennisN]

The state of New York has 1/3 the population of Italy, but already 1/2 the reported cases. I scaled Italy's numbers by the population ratio. Italy reached 149 adjusted deaths by March 8, New York reached 157 by March 23. I shifted Italy's numbers by 15 days and then plotted everything on a logarithmic scale.

That's a very interesting comparison (numbers/population ratio plotted against time) I've been thinking of doing myself for different countries. @mfb , do you mind telling where you got the numbers (with respect to time) from?

 

[BillTre]

Nice @Rive.

I would bet a lot of the genetic differences are probably the equivalent of single point mutations (one base changed) in the virus genome that are identified by whole genome sequencing. Sampling methods looking at smaller parts of the genome might not find them. This information is used as a forensic method to look at how the virus is moving around.

A new mutation originates locally and spreads within the local population but will not be found in other areas unless it gets transferred there (or if a second identical mutation occurs independently in another population (which might be identified by a second independent mutation (other new mutation) at other locations in the genome)). This kind of information can be used to track the origin of viral populations (and therefore the movement of the carriers).

You can name a strain in any way you want based on whatever level of detail you can want. Not all will be equally important for different uses.
The significance of different strains will differ based on for what purpose are examining them.
Very detailed differences (referred to by their "strain" name) can be used for mapping details of movement, or (as I think @Ygggdrasil said) differences more focused on the viral surface can be used for studying interactions with antibodies and the making of vaccines.
People studying their particular questions will name the strains that interest them for their significance for what they are studying.

 

[DennisN]

We are getting new restrictions here in Sweden. From tomorrow Sunday and onwards, public gatherings including more than 50 people will be banned. Those who violate the rules can get fined or imprisoned up to six months. Our prime minister has also repeated the advice to avoid all unnecessary travels (including during Easter).

If you don't have to travel, stay home.
Things are serious now.
(my translation to English)

Source: Allmänna sammankomster med fler än 50 personer förbjuds (DN, 27 March 2020, Swedish only)

I personally welcome this restriction.

According to the CSSE Coronavirus dashboard Sweden has currently got 3069 confimed cases and 105 confirmed deaths (March 28, 2020).

 

[bhobba]

So, without testing it for efficacy in humans, this researcher now makes the bold claim that it would provide cross-protection! Interesting if true.

I do not think getting a vaccine is hard or time consuming with modern methods - after all UQ had theirs in 3 weeks. It's testing the thing to ensure its safe and effective - that, rightly so, is time consuming. The work around I have heard the UQ researchers will use is once animal testing has finished and human trials start (about mid year sometime I believe) they will in parallel manufacture it in quantity so if proven safe and effective it will be ready to go. They think, fingers crossed, end of the year sometime - if we are lucky - but most say 18 months or even 2 years. Moderna evidently skipped/reduced animal trials and went quickly to human testing:
https://www.statnews.com/2020/03/11...s-vaccine-trial-without-usual-animal-testing/

Not sure that's a good idea, especially if you want to start manufacturing before its completed full testing.

Thanks
Bill

 

[atyy]

https://www.spiegel.de/internationa...ssible-a-549d1e18-8c21-45f1-846f-cf5ca254b008
Interesting interview with a German ventilator maker

DER SPIEGEL: Given the number of contracts, you have little choice but to set priorities. Is "Germany First” the rule?

Dräger: No. At first, almost all of the devices went to China, where need was greatest. They needed a rather simple device, and we were able to produce 400 of them a week. The device turns ambient air into purified air, only requires an electrical socket and, if necessary, an oxygen cylinder, and requires no connection to a hospital's medical gas supply system.

 

[kyphysics]

Apologies if this has been addressed in this thread. What I understand is that the COVID-19 virus has a fairly short lifetime when in an open environment? I also understand this virus may be seasonal? If those understands are correct, my question is, how does this virus stay potentially infectious after the "off-season"?

I'll echo the previous poster who quoted you in that a person qualified in the relevant fields should give you a much better answer.

However, would it not be logical that the virus can survive in the summertime, due to summertime not being universal simultaneously for everyone? In other words, the entire globe does not experience summer at the same time. The U.S., for example, is in winter. But, countries like Australia are in the middle of summer. Or, they were: Dec. thru February. They are in fall right now technically.

Assuming you are correct and the virus cannot survive as long in heat and humidity, we would likely see less infections in the summer, but not have it go away. Other parts of the world could be in winter and the virus could be spreading there. If someone from a colder part of the world in July was infected and traveled to the U.S. during our summer. Would that person not potentially be able to infect someone here? So, we could still have infections - albeit at a lower rate.

That's my thought process anyways.

 

[PeroK]

March 20, 2020 - Young people appear to be at greater risk of serious illness from the Coronavirus than initially realized in the U.S. (A week ago) https://www.usnews.com/news/national-news/articles/2020-03-20/coronavirus-and-its-emerging-risk-to-the-young

That article looks like a meaningless, innumerate journalistic piece. Saying that "half of patients were between 20 and 64 years old" reveals typical journalistic innumeracy. That statement may be true if 1% of patients are under 50 and 49% of patients are 51-64. You could even argue that the 50+ age limit may even have been deliberately included in order to bump up the number and create a controversial, tendentious misconclusion.

It also ignores the relative percentage of the population who have been exposed. What if 90% of cases are in the 20-64 age group? Then the data would be fully consistent with younger people being less likely to be severely affected. To spell it out:

Total cases over 64: 10%
Total cases up to 64: 90%

With equal hospitalisation numbers, this would mean older people are nine times more likely to be hospitalised.

 

[mfb]

That's a very interesting comparison (numbers/population ratio plotted against time) I've been thinking of doing myself for different countries. @mfb , do you mind telling where you got the numbers (with respect to time) from?

From the graphs in the Wikipedia articles.
https://en.wikipedia.org/w/index.ph...ic_data/Italy_medical_cases_chart&action=edit
https://en.wikipedia.org/w/index.ph...ew_York_State_medical_cases_chart&action=edit

All the dashboards seem to focus on current numbers only, but at least Wikipedia keeps a history.