COVID COVID-19 Coronavirus Containment Efforts

[Astronuc]

But I have to say, I always thought RNA is quite fragile. DNA is robust, which is why we can still analyze DNA from long long ago (like Jurassic Park - kidding, of course). @chemisttree @Ygggdrasil ?

There are four main groups of organic molecules that are preserved in the fossil record, and these include the following: nucleic acids (which include deoxyribonucleic acids (DNA) and ribonucleic acids (RNA)), proteins, carbohydrates, and lipids.

https://ucmp.berkeley.edu/paleo/fossilsarchive/molecu.html

 

[anorlunda]

Interesting. Sounds like they are never alive because they’re sort of in the middle of being alive (positive) and being dead (negative).

Nothing so mysterious. The result may be negative because there never was a virus at that location.

 

[chemisttree]

Is it safe to say that detecting DNA is not the same as detecting viable virus i.e. capable of infection?

I would say so, yes. Edit: By that I mean yes, detecting RNA is not the same as detecting viable virus.

 

[atyy]

https://ucmp.berkeley.edu/paleo/fossilsarchive/molecu.html

Really? Is that correct? There is RNA preserved in the fossil record? I think that'd be amazing. In principle, yes - but in practice, sure no?

 

[Ygggdrasil]

I realize we might not have good answers to all these questions right now. But a lot of people seem to be talking as though we do--for example, when people talk as though there will definitely be a second outbreak of COVID-19 if we let up on social distancing at some point in the future. So I'm wondering if anyone has actually seen hard evidence on these points.

Yes, there are documented cases that letting up on social distancing measures too early can lead to subsequent spikes in the disease. For example, from the 1918 flu pandemic:

(image source)

Even with successful measures to control the disease through stay at home orders, modeling from Imperial College London predicts that we will see periodic outbreaks of the disease into the future (see my post# 1322 for a discussion of this issue).

 

[PeterDonis]

from the 1918 flu pandemic

Yes, the second wave of that pandemic is the one I've seen referred to. But there were a lot of other variables that were also different then.

 

[Ygggdrasil]

But I have to say, I always thought RNA is quite fragile. DNA is robust, which is why we can still analyze DNA from long long ago (like Jurassic Park - kidding, of course). @chemisttree @Ygggdrasil ?

RNA is quite fragile and subject to degradation, however, the RT-qPCR method to test for viral RNA only looks for very small fragments of RNA (~80-200 nucleotides vs the 30,000 nt long viral genome) and RT-qPCR is very sensitive (CDC quotes the sensitivity of its test as being able to detect around one molecule of RNA per 1µL). Therefore, the test can detect fragments of RNA at very low concentration (which would not be infectious).

 

[peanut]

Yes, there are documented cases that letting up on social distancing measures too early can lead to subsequent spikes in the disease. For example, from the 1918 flu pandemic:
View attachment 259244
(image source)

Even with successful measures to control the disease through stay at home orders, modeling from Imperial College London predicts that we will see periodic outbreaks of the disease into the future (see my post# 1322 for a discussion of this issue).

I think it's the opposite. During the 1918 influenza pandemic, Philadelphia waited over 2 weeks after its first reported case to implement #socialdistancing. By this point, the city’s healthcare system was already overwhelmed. Philadelphia’s epidemiccurve — showing the number of deaths — had a tall peak.

In contrast, St. Louis implemented social distancing just 2 days after its first reported case. The city closed schools, playgrounds, libraries, courtrooms, even churches. Work shifts were staggered and streetcar ridership was strictly limited. St. Louis successfully flattened the curve.

 

[Ygggdrasil]

Yes, the second wave of that pandemic is the one I've seen referred to. But there were a lot of other variables that were also different then.

Sure, which is why I also linked to the recent Imperial College London report that deals with the current outbreak: https://www.imperial.ac.uk/media/im...-College-COVID19-NPI-modelling-16-03-2020.pdf

 

[Ygggdrasil]

I think it's the opposite. During the 1918 influenza pandemic, Philadelphia waited over 2 weeks after its first reported case to implement #socialdistancing. By this point, the city’s healthcare system was already overwhelmed. Philadelphia’s epidemiccurve — showing the number of deaths — had a tall peak.

In contrast, St. Louis implemented social distancing just 2 days after its first reported case. The city closed schools, playgrounds, libraries, courtrooms, even churches. Work shifts were staggered and streetcar ridership was strictly limited.

View attachment 259245

I agree that social distancing measures are an effective way of dealing with disease outbreaks and that instituting these measures early can have great benefits (I cited the same study in my post #1379). My point was that ending social distancing measures too early (as some US government officials are considering) can result in the return of the outbreak and wipe out any gains from the initial social distancing efforts.

 

[peanut]

I agree that social distancing measures are an effective way of dealing with disease outbreaks and that instituting these measures early can have great benefits (I cited the same study in my post #1379). My point was that ending social distancing measures too early (as some US government officials are considering) can result in the return of the outbreak and wipe out any gains from the initial social distancing efforts.

Sorry I misread your post. Yes, that's probably the reason why lockdown option is highly unlikely in Singapore. With the virus spreading in so many countries, it could also still be re-imported if they ended lockdown / physical distancing measures too early.

 

[PeterDonis]

which is why I also linked to the recent Imperial College London report that deals with the current outbreak

Yes, and I see that they predict that case numbers will quickly rebound if social distancing and other suppression interventions are relaxed, but that's because they assume that asymptomatic people are contagious from 4.6 days after infection onward--as far as I can tell, indefinitely. I see no evidence in the paper to back up that assumption; it is simply stated with no supporting argument. That does not seem to me to be a realistic assumption: if a person remains asymptomatic after being infected, that means their immune system is successfully fighting the virus, so they should not remain contagious indefinitely.

 

[Wrichik Basu]

A bit late into this thread, but here is the latest update from my country: Lockdown for the whole nation from tomorrow 0:00hrs to 14th April 23:59hrs IST. Only essential services shall be availabe. Some states are seeing a total curfew.

Almost all educational institutions have been closed by last week.

 

[peanut]

Yes, and I see that they predict that case numbers will quickly rebound if social distancing and other suppression interventions are relaxed, but that's because they assume that asymptomatic people are contagious from 4.6 days after infection onward--as far as I can tell, indefinitely. I see no evidence in the paper to back up that assumption; it is simply stated with no supporting argument. That does not seem to me to be a realistic assumption: if a person remains asymptomatic after being infected, that means their immune system is successfully fighting the virus, so they should not remain contagious indefinitely.

On asymptomatic carriers. More than 43,000 people in China had tested positive for Covid-19 without immediate symptoms by the end of February and were quarantined.

It is still unclear what role asymptomatic transmission is playing in the global pandemic.

https://www.scmp.com/news/china/soc...VvQmbLnoohfn6UcFKxeDjvkLyQcNRQdH3s779zwhhO_YU

 

[peanut]

King's College London is launching a new app that allows users to track Coronavirus symptoms, which it hopes will slow the outbreak.

About 5,000 twins and their families from across the UK have been recruited to test the app, which will help researchers identify:

How fast the virus is spreading in different areas
High-risk areas in the country
Which symptoms correspond to the coronavirus
Why some people are more at risk

Why twins? They "enable researchers to separate the effects of genes from environmental factors such as diet, lifestyle, previous illnesses and infections, and the microbes within the gut (microbiome)" the school said in a news release.

The twins will record information about their health on a daily basis, including temperature, tiredness and symptoms such as coughing, breathing problems or headaches. Any participants showing signs of Covid-19 will be sent a home testing kit.

The app will be available to the public without the home testing component, and to health professionals who want to contribute to the research.

https://www.kcl.ac.uk/news/new-symp...v-3Eul8eLUKu87KH0zHM2NxIEzHrthLSmJM2Vjhm6CSSg

 

[Astronuc]

Washington State Proportions of Confirmed Cases / Deaths by Age Group

Age Group     Percent of Cases     Percent of Deaths
   <19            2%                     0%
20-29            9%                     0%
30-39           14%                     0%
40-49           13%                     2%
50-59           17%                     5%
60-69           16%                    12%
70-79           15%                    30%
    80+          14%                    50%

I was looking at mortality rates in WA and NY. WA was between 4 to 5%, I believe because of the proportion of cases in the older population (60+ years), whereas in NY, the younger population (18-44) constitute 46% of cases, (45-64) 33%, (65-74) 11%, and (>75) only 8%. In WA, females represent 51% of cases (4% unknown), whereas in NY females are 43% of cases, which seems to reflect the elderly population in WA (e.g., Kirkland Life Care residents) who have a higher proportion of females.

On March 14, "Of the 40 deaths in Washington, 27 are now linked to the nursing home . . . " According to county health officials, 47 Life Care employees tested positive, 24 tested negative, one was inconclusive, five were still pending and 18 were pending specimen collection for Saturday. The total number of health care workers who are symptomatic is 95. At that time, 1/3 of the cases in King County were from Kirkland Life Care Center.
https://www.kiro7.com/news/local/li...cility-be-cleaned/EYNT43G5ZBH5BKZ3MATJOVVV5A/
As of March 23, "At least 37 deaths have been linked to the COVID-19 outbreak at the Life Care Center."
https://q13fox.com/2020/03/23/feds-release-results-of-inspection-at-virus-hit-kirkland-nursing-home/

https://www.seattletimes.com/seattle-news/times-watchdog/coronavirus-spread-in-a-kirkland-nursing-home-for-weeks-while-response-stalled/

https://www.vox.com/2020/3/23/21190033/coronavirus-covid-19-deaths-by-age

 

[atyy]

Yes, and I see that they predict that case numbers will quickly rebound if social distancing and other suppression interventions are relaxed, but that's because they assume that asymptomatic people are contagious from 4.6 days after infection onward--as far as I can tell, indefinitely. I see no evidence in the paper to back up that assumption; it is simply stated with no supporting argument. That does not seem to me to be a realistic assumption: if a person remains asymptomatic after being infected, that means their immune system is successfully fighting the virus, so they should not remain contagious indefinitely.

See The Hammer and the Dance where Pueyo discusses the second peak in the paper from Neil Ferguson and colleagues. Pueyo also references https://necsi.edu/review-of-ferguson-et-al-impact-of-non-pharmaceutical-interventions which discusses the second peak in the paper. Both of these think the second peak in Ferguson's paper is very much overestimated.

 

[mfb]

Measures to avoid a new outbreak can be looser than measures to cut down the number of cases in an existing outbreak. We also get better with testing and treatment over time.

 

[Ygggdrasil]

Measures to avoid a new outbreak can be looser than measures to cut down the number of cases in an existing outbreak. We also get better with testing and treatment over time.

Agreed. For the US, one could argue that the lack of sufficient testing resources necessitated the current stay at home orders. These social distancing measures should not be lifted at least until widespread testing is available so that we can isolate infected individuals and track their contacts, which could hopefully contain any new outbreaks without shutting down the economy.

 

[anorlunda]

I don't think we can demand answers on when to lift the social distancing measures until things play out more weeks or months first.

If 18 months of social distancing are needed, the supply chain for some critical infrastructures could be threatened. Collapse of any critical infrastructure introduces new risks to the public over and above the virus. Decisions would require a risk-versus-risk balance. In crude words, virus-versus-starvation, virus-versus-freezing ...

If the lockdown is short, there is a lot of inventory in the pipeline and not much risk of running out. So I expect that any risk-versus-risk balance would be a strong function of time. That's why we can't expect decisions or even hints in advance. It is necessarily a wait and see situation.

 

[nsaspook]

A possible immunity test for a get out of jail card.
https://www.medrxiv.org/content/10.1101/2020.03.17.20037713v1

Here we describe serological enzyme-linked immunosorbent assays (ELISA) that we developed using recombinant antigens derived from the spike protein of SARS-CoV-2. These assays were developed with negative control samples representing pre-COVID 19 background immunity in the general population and samples from COVID19 patients. Results: The assays are sensitive and specific, allowing for screening and identification of COVID19 seroconverters using human plasma/serum as early as 3 days post symptom onset. Importantly, these assays do not require handling of infectious virus, can be adjusted to detect different antibody types and are amendable to scaling. Conclusion: Serological assays are of critical importance to determine seroprevalence in a given population, define previous exposure and identify highly reactive human donors for the generation of convalescent serum as therapeutic. Sensitive and specific identification of Coronavirus SARS-Cov-2 antibody titers will also support screening of health care workers to identify those who are already immune and can be deployed to care for infected patients minimizing the risk of viral spread to colleagues and other patients.

 

[zoki85]

Is there any estimate of percentage of people that carry the virus but never get ill? I guess such individuals are less contagious than other infected people

 

[Astronuc]

It looks like NY may have slowed the spread of infection, but more data needed.

March 24, 2020 - 25,665 positive cases (and 210 deaths) of COVID-19, representing 4790 new cases compared with an increase of 5707 the previous day. NY City reported 14,904 positive cases, and 131 deaths. The numbers are still increasing.

https://coronavirus.health.ny.gov/county-county-breakdown-positive-cases
https://abc7ny.com/coronavirus-nyc-new-york-ny-news-update-cases-map/5989875/

However, cases in other states, e.g., Louisiana, may be on the rise.

 

[PeterDonis]

March 24, 2020 - 25,665 positive cases (and 210 deaths) of COVID-19, representing 4790 new cases compared with an increase of 5707 the previous day.

To quote Curly from City Slickers: "Day ain't over yet."

 

[Borg]

There is a Trader Joe's near our house that my wife and I plan to go to early tomorrow. We've both agreed that if there is a line of more than a few people, we will also abort.

So, we ended up going today. My wife called the store in advance and they said that they were stocked and maintaining safety protocols - no more than 20 customers in the store at once and they were treating carts with bleach as you entered. When we got there, the line was about 20 people long which put us about 100+ feet from the door - everyone was keeping their distance. All told, I felt comfortable that they were doing everything that they could to keep everyone safe.

 

[DennisN]

Two field hospitals are being built here in Sweden to be at standby in the two largest cities Stockholm and Gothenburg.
Source: http://www.dn.se/nyheter/sverige/har-ar-faltsjukhuset-som-ska-radda-svenska-liv/ (SVD, Swedish only)

 

[DennisN]

NY Times has published an interactive timeline with maps describing the spread of the virus:

• How the Virus Got Out (NYT, March 22, 2020) (scroll down on the page to go forward in the interactive timeline)

 

[Astronuc]

HARTFORD, Conn. (AP) — Connecticut Gov. Ned Lamont announced that the number of infections across the state jumped by more than 200 since Monday, to a total of 618 positive cases, with 62% in Fairfield County, which borders New York. So far, a total of 12 deaths have been reported.

It appears that the number of cases are surging in states that have reported low numbers so far.

Los Angeles County has reported what may be the first confirmed U.S. death of a child from coronavirus. The child lived in Lancaster north of Los Angeles.

Washington state reported late today. Positive COVID-19 cases are now 2469 with 123 deaths.

The US has now reported 54,141 positive cases including 789 deaths according to Coronavirus dashboard (ncov2019.live/data), while Covidtracking.com reports 51,970 positive cases with 675 deaths.

 

[Rive]

Is there any estimate of percentage of people that carry the virus but never get ill? I guess such individuals are less contagious than other infected people

I heard a 20-40% extra compared to the amount of people who does got ill, but this estimation was based on the behavior of other human Coronavirus and not on the actual Covid19. I think South-Korea might be a good reference, but I had no time to dig up real data.

 

[peanut]

Generally, that curve doesn't appear to be flattening at all. March saw the steepest climb. Is it due to the availability of testing kits?

Is this the first "realistic" presentation of the scale of the problem?

 

[OmCheeto]

Generally, that curve doesn't appear to be flattening at all. March saw the steepest climb. Is it due to the availability of testing kits?

View attachment 259293

Is this the first "realistic" presentation of the scale of the problem?

I suspect "confirmed" cases are under-reported by a factor of around 20.
Based on that suspicion, I focus on death trends.

The following graph I created, strikes me as interesting.

 

[mfb]

It looks like NY may have slowed the spread of infection, but more data needed.

March 24, 2020 - 25,665 positive cases (and 210 deaths) of COVID-19, representing 4790 new cases compared with an increase of 5707 the previous day. NY City reported 14,904 positive cases, and 131 deaths. The numbers are still increasing.

March 14: 198 new cases
March 15: 116 new cases
Don't interpret too much into a single day, especially as sometimes the reports are delayed, i.e. cases found on one day are only counted for the next update.

Generally, that curve doesn't appear to be flattening at all. March saw the steepest climb. Is it due to the availability of testing kits?

It's largely from the virus spreading nearly everywhere in March.

Italy still looks promising. The US will likely overtake Italy in the absolute confirmed case count in 3 days.

 

[peanut]

"(Coronaviruses) can be efficiently inactivated by surface disinfection procedures with 62–71% ethanol, 0.5% hydrogen peroxide or 0.1% sodium hypochlorite within 1 minute." Take note Clorox is 5% sodium hypoclorite so a 1:50 dilution will give 0.1%.

https://www.journalofhospitalinfect...LDuBv5Jvp5LV32vIgqy3kqxU#.Xnph1Fpyic0.twitter

 

[peanut]

Royal infection

BREAKING: Prince Charles has tested positive for coronavirus

 

[zoki85]

Royal infection

BREAKING: Prince Charles has tested positive for coronavirus

I'm not surprised. Too many social contacts & handshakes.

 

[peanut]

I'm not surprised. Too many social contacts & handshakes.

Unfortunate but at least he can afford the best medical care and his own ventilator. Feel for anyone getting this horrid virus. But scares me more how many people DO have it but don’t know it because of the difficulty getting tested unless you meet the strict criteria or are rich, famous and influential.

 

[bhobba]

The Italian death rate seems very high. Much higher than predicted for the virus and much higher than other countries. Is there any information on why this is?

Yes - they didn't do as much testing - only testing those as one doctor here in Australia called it - the worst cases at the top of the pyramid. Here in Aus when a case is found they trace everyone they have come in contact with. We have the highest testing rate in the world - now even higher than Singapore. Death rate now .33% here. We have discovered its quite likely people can have it and be asymptomatic. It even happened to a politician who had no symptoms or anything - they looked down his throat - saw nothing etc - but the rule was he should be tested. Guess what - he had it. He is in isolation and still the same as if he was not sick.

That said in some states here in Aus its growing exponentially - Queensland where I am is sort of on the verge - if you remove the Gold Coast it's reasonable - here the Gold Coast is a real hot spot. I live about 40 minutes from the Gold Coast at Redland Bay - we have our one and only case a couple of days ago - but that will likely increase.

On a positive note Nobel Prize winner Peter Doherty says the virus curve will flatten in 'couple of weeks':
https://www.smh.com.au/national/nob...atten-in-couple-of-weeks-20200324-p54dib.html

Please - if its not blocked by a paywall do read it - I subscribe to a paper and they have agreements with others so because I can see it does not mean you can. It's interesting and informative. Fingers crossed he is right.

Thanks
Bill

 

[peanut]

FYI:

https://www.sciencemag.org/news/2020/02/scientists-discover-virus-no-recognizable-genes

 

[bhobba]

I don't know how the following relates to the 80% don't know they have it, but . . .

From experience here in Aus, we are doing the most testing in the world, and while some cases have been found of people without symptoms having the disease its not common. But it has to be said the physical examination is not what you would call extensive - just looking down the throat etc.

Thanks
Bill

 

[atyy]

So, we ended up going today. My wife called the store in advance and they said that they were stocked and maintaining safety protocols - no more than 20 customers in the store at once and they were treating carts with bleach as you entered. When we got there, the line was about 20 people long which put us about 100+ feet from the door - everyone was keeping their distance. All told, I felt comfortable that they were doing everything that they could to keep everyone safe.

Which part of the US are you in? Is it warm enough to wait outside the store if the line is long?

 

[anorlunda]

Which part of the US are you in? Is it warm enough to wait outside the store if the line is long?

You mean warm enough but not too warm. Temperatures here in Florida will exceed 95F (35C) this weekend. Standing out in the blazing sun is not healthy, especially seniors.

 

[TeethWhitener]

Interesting C&E News article about Coronavirus protease inhibitors under development:
https://cen.acs.org/pharmaceuticals...letter&utm_medium=Newsletter&utm_campaign=CEN

 

[Borg]

Which part of the US are you in? Is it warm enough to wait outside the store if the line is long?

Northern Virginia. Temp was in the high 50s. The line went quickly - no more than 15 minutes.

 

[Ygggdrasil]

Interesting C&E News article about Coronavirus protease inhibitors under development:
https://cen.acs.org/pharmaceuticals...letter&utm_medium=Newsletter&utm_campaign=CEN

While targeting the protease is a promising direction for a new drug, developing new drugs is a very long process and unlikely to produce anything that could help with the current outbreak. Indeed, the article writes:

Hilgenfeld hopes this lead compound will be developed by a consortium set up by the European Union to fight COVID-19, but he expects that the road from this molecule to a functional drug could take years, perhaps ready in time for the next Coronavirus that pops up.

Still, given that we've had three coronaviruses emerge in the past 20 years (SARS, MERS and COVID-19), having good anti-coronaviral drugs in the pipeline is going to be helpful (e.g. many of the drugs currently being tested against COVID-19 now were originally developed for other outbreaks, like how Remdesivir was originally developed for the Ebola outbreaks).

In terms of potential therapies, maybe in a few months we'll have information about which existing drugs show efficacy against COVID-19. In the 1-1.5 year range, we would potentially have new biological drugs like vaccines and monoclonal antibody therapeutics.

 

[collinsmark]

 

[Astronuc]

March 14: 198 new cases
March 15: 116 new cases
Don't interpret too much into a single day, especially as sometimes the reports are delayed, i.e. cases found on one day are only counted for the next update.

Hence the comment, " . . . , but more data needed."

 

[peanut]

I suspect "confirmed" cases are under-reported by a factor of around 20.
Based on that suspicion, I focus on death trends.

The following graph I created, strikes me as interesting.

View attachment 259303

Covid-19 death rate - a calculation that divides the number of deaths by the total number of confirmed cases.

You mentioned that "confirmed" cases are under-reported due to certain factors e.g. country's testing policy etc.

Therefore, death rate varies widely by country and it is not accurate because of unreported / untested cases.

 

[peanut]

Pneumonia is one of the main causes of death in Covid-19. The pneumonia is a bacterium right? Am I correct in saying Covid-19 may cause an opportunist pneumonia?

 

[chemisttree]

...These social distancing measures should not be lifted at least until widespread testing is available so that we can isolate infected individuals and track their contacts, which could hopefully contain any new outbreaks without shutting down the economy.

The course of the outbreak is what Dr. Birx refers to as “granular” in nature at this time. This means that some parts of the country where infection rates are low can contact trace while other parts of the country have accepted an endemic presence of the virus and have given up on tracing . LA isn’t contact tracing cases anymore, for example. Korea was able to do this because they acted very early... when they only had confirmed cases in the single digits!

Our window in the US for a S. Korea type solution is long past. We are committed to a mitigation strategy like Italy now. It will always be so. Contact tracing is history now except in places far removed from the outbreak’s centers in New York, Washington, California AND for only a short time, since there are currently few travel restrictions into and out of those locations.

 

[Rive]

The pneumonia is a bacterium right?

No. For this, it is the virus itself...