COVID COVID-19 Coronavirus Containment Efforts

[kadiot]

The officially compiled data on the number of infections and deaths caused by COVID-19 in the Philippines is too little to establish any correlation of infections and mortality rates relative to the size of our population. Simulation or forecasting models at this point is a better reference point on what could happen next or estimate the duration of the crisis.

The national circumstances and cultural practices are all pointing to high transmission and mortality rates. Based on projections it's possible the number of casualties will reach catastrophic numbers. However, there are certain factors that seem to be working in our favor: immunity and warm weather.

Viruses are comprised of a protein shell and either a DNA or RNA core. How does heat destroy the virus? I say destroy, because viruses are non-living, and thus, cannot be killed. I would love an explanation on how the heat from a blow dryer degrades the peptide bonds in the proteins. Also, not all blow dryers produce the same level heat either, so i’m curious on how one would even know whether their’s was at the proper heat?

As of now the CDC and the WHO state that there are no scientific direct cures or treatments for this novel coronavirus.

Anyway, the Philippines is not recording deaths by the hundreds in the range of Italy, Spain and other countries. Whether this low numbers is caused by under reporting or influenced by our unique factors. Virologists are still unsure to what extent the warm weather could affect the virus life cycle. With qualified optimism.

Although our national circumstances and cultural practices certainly will cause high transmission rates. The observed social practices of close contact, poor hygiene and high population density. Amazingly we're in the time period where the surge should have started and yet it's not happening - at least not yet.

 

[peanut]

Los Angeles Times reported "singing may have spread virus through the air at a church in Washington state". According to the Washington Examiner "it was a group of approximately 60 people singing in close proximity to each other for over an hour". I’m sure you’ve all experienced singing in a choir. When you sing, you drop your jaw much more than you do in a normal everyday conversation, you open your mouth and throat much wider, so the sound does not get trapped inside the mouth. Dr. Melfred L. Hernandez (The Voice Doctor), please feel free to correct me. When you sing, you project your voice. You spread DROPLETS, a LOT of droplets. So, imagine a group of people with strong and powerful vocal cords in a CLOSED room for hours SPREADING DROPLETS. The droplets fall everywhere (the floor, tables, chairs, sheet music, notes etc). The choir members take a break, sit on the chairs, exchange sheets / notes – these objects then become “fomites” objects that serve as vehicles for the spread of pathogens (in this case SARSCoV2 #coronavirus that causes COVID19) through indirect contact.

https://www.washingtonexaminer.com/...airborne-disease-as-experts-raise-possibility

 

[anorlunda]

How about a light-hearted piece for contrast.

Astrophysicist gets magnets stuck up nose while inventing Coronavirus device

https://www.theguardian.com/austral...ck-up-nose-while-inventing-coronavirus-device

 

[mfb]

Can Covid-19 antibody test be used as a standalone test to definitively diagnose Covid-19? Are they being used for mass testing in other countries?

It can be used to see if you had contact to the virus at least two weeks ago or so. It can't help finding people who got infected recently.

In addition to the antibody tests (post 1936) Germany aims at 200,000 virus tests per day by the end of April. German source.
Ideally this will be enough to test contacts of infected people again.

We'll get so many publications in the future analyzing the strategies of different countries. Will be very interesting to see once this pandemic is over and people have more time to study everything in detail.

 

[kyphysics]

Anyone here been tracking the development/availability of COVID-19 immunity tests?

We've mostly (or 100%?) talked about testing for the virus, but what about testing for immunity?

Are those supposed to be available widely anytime soon? And, if you got tested for having immunity, would that drastically change how you treated going out and your social activities? Would you do "favors" for others or volunteer, etc.?

 

[peanut]

It can be used to see if you had contact to the virus at least two weeks ago or so. It can't help finding people who got infected recently.

In addition to the antibody tests (post 1936) Germany aims at 200,000 virus tests per day by the end of April. German source.
Ideally this will be enough to test contacts of infected people again.

We'll get so many publications in the future analyzing the strategies of different countries. Will be very interesting to see once this pandemic is over and people have more time to study everything in detail.

So the rapid antibody test kits can only be used in people who had onset of symptoms for at least two weeks. For people who got infected recently would probably be tested with an RT-PCR.

Are antibody-based test kits available over the counter or ONLY medical doctors can prescribe and interpret the use of it?

 

[jbriggs444]

I take it as an article of faith that no test is currently available over the counter at your corner drug store.

If they cannot keep toilet paper in stock, there is no way on this Earth that they can stock a test kit for COVID-19.

 

[peanut]

Anyone here been tracking the development/availability of COVID-19 immunity tests?

We've mostly (or 100%?) talked about testing for the virus, but what about testing for immunity?

Are those supposed to be available widely anytime soon? And, if you got tested for having immunity, would that drastically change how you treated going out and your social activities? Would you do "favors" for others or volunteer, etc.?

How about the IgG/IgM tests? We need it for our frontliners to know if they've been infected then recovered and whether they have developed some sort of immunity.

 

[atyy]

Anyone here been tracking the development/availability of COVID-19 immunity tests?

We've mostly (or 100%?) talked about testing for the virus, but what about testing for immunity?

Are those supposed to be available widely anytime soon? And, if you got tested for having immunity, would that drastically change how you treated going out and your social activities? Would you do "favors" for others or volunteer, etc.?

@kadiot (post #319) and @BillTre (post #406) mentiomed immunity tests early in this thread, and they've been mentioned several times since then.

Indonesia is doing rapid tests, which are antibody tests. I am not sure, but I believe the accuracy of these tests is low (relatively speaking), so they are used to rapidly identify people who need to take a confirmatory test.
https://www.thejakartapost.com/news...se-tb-test-kits-for-covid-19-doctor-says.html
https://www.channelnewsasia.com/new...avirus-cases-deaths-jakarta-measures-12585684

Antibody tests to allow people who are immune to continue or resume working have been mentioned by Trevor Bedford in this Twitter thread (posts 17 & 18), and it seems Germany is preparing to use them https://www.dailymail.co.uk/news/ar...00-000-people-coronavirus-antibody-tests.html

The antibody tests used by Indonesia and Germany are probably different, so they may have different false positive and false negative rates. A couple of interesting false positives occurred in Singapore, where a patient was thought to have dengue on the basis of an antibody test. Later these patients turned out to be Covid-19 positive by PCR tests. With the first case it was thought to be a probably extremely rare case of dengue and Covid-19 double infection. However, there was more than one case, and it turned out that Covid-19 antibodies cause the dengue test to be positive, even though patients are dengue negative. So these patients did not have two diseases, they had only Covid-19, which caused false positives on the dengue test.
https://www.thailandmedical.news/ne...to-false-positive-in-dengue-serological-tests
https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(20)30158-4/fulltext

 

[chemisttree]

In both tests, Delos Reyes said conclusions showed inhibition in viral replication, significant reduction of virus quantity, even the ability to selectively kill infected cells. Both drugs are approved by the Food and Drug Administration (FDA) in the Philippines and in the U.S.

This work builds on the thesis of Dr. Elbourakadi. Interesting read.

http://images-a.chemnet.com/suppliers/chembase/cas10/cas59-46-1.gif

PROCAINE
- also known as Novocain

DEXAMETHASONE

 

[peanut]

Indonesia is doing rapid tests, which are antibody tests. I am not sure, but I believe the accuracy of these tests is low (relatively speaking), so they are used to rapidly identify people who need to take a confirmatory test.
https://www.thejakartapost.com/news...se-tb-test-kits-for-covid-19-doctor-says.html
https://www.channelnewsasia.com/new...avirus-cases-deaths-jakarta-measures-12585684

So anyone who tested positive by antibody-based test should be tested with an RT-PCR to confirm the positive test. Maybe it's just me, but it seems redundant.

 

[chemisttree]

That might help distinguish between someone who is active vs recovered.

 

[mfb]

So anyone who tested positive by antibody-based test should be tested with an RT-PCR to confirm the positive test. Maybe it's just me, but it seems redundant.

The antibodies remove the virus from the body somewhat quickly. You can't confirm an antibody test with a test that looks for the virus particles. They are different things, for different times, with different purposes.

 

[Ygggdrasil]

It can be used to see if you had contact to the virus at least two weeks ago or so. It can't help finding people who got infected recently.

In addition to the antibody tests (post 1936) Germany aims at 200,000 virus tests per day by the end of April. German source.
Ideally this will be enough to test contacts of infected people again.

We'll get so many publications in the future analyzing the strategies of different countries. Will be very interesting to see once this pandemic is over and people have more time to study everything in detail.

I've seen reports of a test that can detect antibodies as early as 3 days after someone shows symptoms:

Introduction: SARS-Cov-2 (severe acute respiratory disease Coronavirus 2), which causes Coronavirus Disease 2019 (COVID19) was first detected in China in late 2019 and has since then caused a global pandemic. While molecular assays to directly detect the viral genetic material are available for the diagnosis of acute infection, we currently lack serological assays suitable to specifically detect SARS-CoV-2 antibodies.

Methods: 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.

https://www.medrxiv.org/content/10.1101/2020.03.17.20037713v1

As others have mentioned, the standard nucleic acid tests (RT-qPCR or the faster isothermal amplification test from Abbott) are probably the best for diagnosing new infections. Serological tests will have complementary functions in identifying those who were infected in the past (esp asymptomatic or mild cases that did not require hospitalization and were not tested) and are now immune (as well as monitoring whether immunity persists over time).

 

[DennisN]

I did two tables today concerning the current case fatality rates (CFR)* of Covid-19.

*

In epidemiology, a case fatality rate (CFR) — sometimes called case fatality risk — is the proportion of deaths from a certain disease compared to the total number of people diagnosed with the disease for a certain period of time. A CFR is conventionally expressed as a percentage and represents a measure of disease severity.

The left table contains the CFRs of the 25 countries with the largest numbers of confirmed cases.
The right table contains the CFRs of the 25 countries with the largest CFRs.

The total CFR for the world is currently 4,9 % (this is the total of all countries, not just the countries present in the tables).

Source: Covid-19 CSSE dashboard.
Date: 31 March 2020.
Notes: Please note that the numbers of cases are confirmed cases only which may also depend on the number of tests done in each country. Please also note that these numbers are a snapshot of the current situation, i.e. the numbers and thus the case fatality rates may change in the near future.

The tables:

 

[PeroK]

Poor Italy. It's not exactly La Dolce Vita there at the moment.

 

[bhobba]

I just saw an interview with a particle physicist who is using a synchrotron to get a more detailed look at the coronavirus. I know we have particle physicists here and am curios if they have been called upon to do that type of work.

Thanks
Bill

 

[Klystron]

{snip...}my physio keeps his distance and just guides me through the exercises, but there are some moments he gets close, such as when he attaches weights {snip...}

I always learn from reading posts from other countries and cultures. If 'physio' is similar to our 'physical therapy', then I schedule a grueling three visits a week prescribed by my primary care (PCP) and pain management doctors and approved by veteran's administration (VA) cardiologists.

While we have strap on weights at the physical therapy clinic, staff prefers we use calibrated stainless steel hand weights and appropriate weight machines that are easy to sanitize after each use. Healthy athletic people might scoff at 2 pound (less than 1 kilogram) hand weights and 15 pound leg lifts, but they give remarkable results for increased strength and mobility for people with physical disabilities.

We all differ but last year swimming 6 days a week plus 'physio therapy' twice a week kept me able to walk reasonably well. With pools and gyms closed, I am attempting Monday Wednesday Friday (MWF) physical therapy plus home exercise; but I workout much better with supervision even if the trainers remain distant. You mentioned safety equipment:

While swimming I wear long sleeved light synthetic shirt to protect from chill and sun and shaded face mask with snorkel to protect eyes and face. I also need foot fins plus plastic mesh leg braces, optional for most swimmers . The snorkel plus fins allows prone position with head level with spine, lots of air, no twisting, and regular slow movement. Let the water support you.

While exercising out of the water I always wear long gym pants over or under my leg braces to protect my legs, long socks (UK stockings?), and light walking (cross-trainer) shoes. I wear a thin cotton long-sleeved shirt covered by a larger synthetic T-shirt, with a sweater when cold. This helps protect core, spine and arms. I always wear heavy synthetic gloves with padding, that cover fingers, sealed at the wrist over the long sleeve shirt to protect hands from damage and contamination.

I also wear prescription acrylic glasses* secured by a rolled bandanna (cotton scarf). I have used a second folded bandanna as an improvised face mask and also carry N95 masks in my gym bag and vehicle. I wipe surfaces before and after exercises. I also carry my own towels and yoga bands (canvas and rubber straps). Everything gets laundered and cleaned after each visit except shoes.

While I love exercise, I am not naturally a 'gym rat'. While the pain can be intense and fatigue difficult to master, the short and long term results of mild regular exercise are beneficial. Thanks

*also wear safety lenses over glasses or contact lenses or bare eyeballs for any activity that 'raises dust' or fragments or excessive light.

 

[DennisN]

@PeroK and others who get sad and/or anxious by the numbers:

I get sad and anxious too. I actually had to take a pause from working with the statistics. After I did the first two charts I posted previously in the thread, I did not feel good. I can't remember I've ever felt this before when doing statistics or analyzing numbers. Technology and science most often concerns numbers that are far away from the life and death of humans. This is very, very different, and it clearly affects me. So will take a pause from these statistics again.

On a more positive note:

Why I did the comparison was simply that I was interested in comparing countries to see which countries were doing well and what can possibly be learned from the countries that have been/are doing well.

This is the spirit I am hoping for:

"We shall defend our lives, whatever the cost may be, we shall fight the virus in the hospitals, we shall fight in the homes, we shall fight in the fields and in the streets, we shall fight in the hills; we shall never surrender."

...heavily influenced by Winston Churchill.

 

[Astronuc]

First 21 states to declare stay-at-home prior to March 25
https://www.physicsforums.com/threads/covid-19-coronavirus-containment-efforts.983707/post-6316586

Thirteen states declaring stay-at-home throughout state after March 25
Alaska, Stay at home, March 28 at 5 p.m.
Arizona, Stay at home, March 31 at 5 p.m.
District of Columbia, Stay at home, April 1 at 12:01 a.m.
Kansas, Stay at home, March 30 at 12:01 a.m.
Kentucky, Healthy at home, March 26 at 8 p.m.
Maryland, Stay at home, March 30 at 8 p.m.
Minnesota, Stay at home, March 27 at 11:59 p.m.
Montana, Stay at home, March 28 at 12:01 a.m.
New Hampshire, Stay at home, March 27 at 11:59 p.m.
North Carolina, Stay at home, March 30 at 5 p.m.
Rhode Island, effective March 28
Tennessee, Stay at home, March 31 at 11:59 p.m.
Virginia, Stay at home, March 30

Eleven states leaving stay-at-home declarations to cities and/or counties, some of which acted before March 25
Alabama - City of Birmingham Shelter in place, March 24 at 12 p.m.
Florida - limited parts of SE Florida
Georgia - Atlanta, Blakely, Carrolton, Savannah, Athens-Clarke County, Dougherty County issued stay-at-home or shelter-in-place
Maine - Portland, Stay at home, March 25 at 5 p.m.
Mississippi - Oxford, Stay at home, March 22
Oklahoma - Norman, March 25, Oklahoma City, Tulsa, March 28
Pennsylvania - stay-at-home orders for more than 20 counties in the state, varies by county
South Carolina - Charleston, March 26 at 12:01 a.m.; Columbia, March 29 at 12:01 a.m.
Texas - left to cities and counties; counties involving Houston, Dallas-Forth Worth and San Antonio issued stay-at-home declarations
Utah - Salt Lake County, Stay at home, March 30 and Summit County, March 27 at 12:01 a.m.
Wyoming - Jackson, Stay at home, March 28

No stay-at-home: Nevada, Nebraska, North and South Dakota, Iowa and Arkansas

Ref: https://www.nytimes.com/interactive/2020/us/coronavirus-stay-at-home-order.html

 

[Astronuc]

Washington State Department of Health has delayed reporting data for positive and negative cases since March 28. They issued the following statement:
https://www.doh.wa.gov/Portals/1/Documents/1600/coronavirus/DelayDataPosting.pdf

The Department of Health is committed to continued data transparency. We are working to ensure daily numbers are posted on time. Here’s some context about recent challenges:

• The Washington Disease Reporting System (WDRS) is used to report notifiable conditions.
• Outside a pandemic, only positive results would be reported.
• WDRS is now tracking negative results for COVID-19. This volume is overwhelming the tool.
• We have worked with the vendor supporting WDRS to increase capacity.
• We are also investigating additional solutions, which may include:
  • A separate reporting tool for negative results (roughly 93% of the data at this time).
  • Automating deduplication work performed manually each day. One day last week, more than 2,000 duplicate results were removed to ensure accurate, reliable numbers.

DOH will share additional updates if this problem persists. We cannot provide an estimate for the next release of numbers, but are working diligently toward that goal.

Washington DOH had revised their website on March 28 and changed how they report data, and they have not updated the numbers since. So positive and deaths are currently under-reported.

https://www.doh.wa.gov/Emergencies/Coronavirus
The number of cases by date were also changed/revised for the month of March.

Washington state Gov. Jay Inslee on Monday raised questions about some alarming new COVID-19 test results coming out of a handful of rural counties.
https://komonews.com/news/local/experts-try-to-understand-rural-spike-in-positive-covid-19-tests
Um, people travel! And testing rates are lower than in high population (metropolitan) areas.

More on the Skagit Valley Chorale choir. 28 of 45 people who fell ill have tested positive for COVID-19, so 17 others are presumptive cases.
https://komonews.com/news/coronavir...-choir-killing-2-members-and-infecting-others

 

[mfb]

I just saw an interview with a particle physicist who is using a synchrotron to get a more detailed look at the coronavirus. I know we have particle physicists here and am curios if they have been called upon to do that type of work.

The synchrotron machines are not directly connected to particle physics. They are normally closed, but they keep the ability to restart quickly if the medical field is interested in a study.
http://www.esrf.eu/home/news/general/content-news/general/covid-19-update.html
Situation at DESY - they had a request already

Italy's last daily update matched the day before, i.e. notably lower than the 10 days before that.

 

[scarlett zou]

About 35 companies and academic institutions are racing to create such a vaccine, at least four of which already have candidates they have been testing in animals. The first of these – produced by Boston-based biotech firm Moderna – will enter human trials imminently.

 

[peanut]

I did two tables today concerning the current case fatality rates (CFR)* of Covid-19.

*The left table contains the CFRs of the 25 countries with the largest numbers of confirmed cases.
The right table contains the CFRs of the 25 countries with the largest CFRs.

The total CFR for the world is currently 4,9 % (this is the total of all countries, not just the countries present in the tables).

Source: Covid-19 CSSE dashboard.
Date: 31 March 2020.
Notes: Please note that the numbers of cases are confirmed cases only which may also depend on the number of tests done in each country. Please also note that these numbers are a snapshot of the current situation, i.e. the numbers and thus the case fatality rates may change in the near future.

The tables:

View attachment 259739

Thanks for the nice tables on top 25 Countries: Current Confirmed Cases (CCC) vs Current Case Fatality Rate (CFR).

I would like to add the following factors on your notes for everyone's consideration and deliberation.

1. Age structure of the population: Italy has the second oldest population in the world, after #Japan, which may partly explain the high mortality observed.
2. Health care availability (number of hospitals, intensive care beds) and accessibility (free vs. paid): Low death rates in Germany and SouthKorea are partially due to the relatively high number of hospital beds per capita. Differences in death rates within the same country, for example Hubei province (location of Wuhan, where the outbreak emerged) and other parts of China are mainly because of the rapid increase in cases in Hubei (strain on health care resources).
3. How long the virus has been circulating: COVID19 has had longer to affect Italy and spread within the population compared to other countries.
4. Country’s systems of death registration / coding. Are deaths reported as COVID-19 / as the underlying medical condition with COVID-19 as secondary cause? Countries (even provinces / states) may vary in this respect too.
5. Country’s testing policy. Testing more patients increases the denominator (people who have a positive SARSCoV2 test); reduces the death rate.

 

[atyy]

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.

Not an answer to your question, but it may be possible this will result in some data.

China starts to report asymptomatic COVID-19 cases
https://www.channelnewsasia.com/news/asia/coronavirus-covid-19-china-asymptomatic-cases-12597704#cxrecs_s

I suppose from the context, some of these could be pre-symptomatic.

Also, the word "asymptomatic" has been used in some reports to mean no symptoms as noticed by the patient (which is a practically important definition). However, they did have symptoms when examined by a CT scan. For example, patient 5 in this report was aymptomatic but did have abnormalities in the CT.
"For the two asymptomatic children (patients 5 and 6), patient 5 had ground-glass lung opacities identified by CT scan. Unlike patient 5, who was aged 10 years and non-compliant to parental guidance, patient 6, who was aged 7 years and reported by her mother to wear a surgical mask for most of the time during the period in Wuhan, was not found to be infected by virological or radiological investigations."
https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)30154-9/fulltext

 

[kyphysics]

Case Fatality Rate - the likelihood a person diagnosed with the viral infection will die
Infection Fatality Rate - the likelihood a person will die after contracting the virus (whether diagnosed or not)

Since most infections are mild and go unreported, the former is higher than the latter.
It looks like the table reports CFR for the novel coronavirus, and IFR for the influenza.

Possibly a dumb question, but how do we know the IFR?

If someone is never diagnosed, how do they even show up in the statistics? Thanks.

 

[jbriggs444]

Possibly a dumb question, but how do we know the IFR?

If someone is never diagnosed, how do they even show up in the statistics? Thanks.

You can infer it by measuring the infection rate in a reduced sample and measuring the fatality rate over the population.

[Not my field, but that's how I'd do it]

 

[jim mcnamara]

@jbriggs444 Yep that is a reasonable way to do it. You have to wait for deaths, and with an example 2% death rate in a small population this can take time.

 

[anorlunda]

This is what China did to beat coronavirus. Experts say America couldn't handle it

In late February, as Coronavirus infections mounted in Wuhan, China, local authorities went door-to-door for health checks – forcibly isolating every resident in makeshift hospitals and temporary quarantine shelters, even separating parents from young children who displayed symptoms of COVID-19, no matter how seemingly mild.

Caretakers at the city's ubiquitous large apartment buildings were pressed into service as ad hoc security guards, monitoring the temperatures of all residents, deciding who could come in, and implementing inspections of delivered food and medicines.

Outside, drones hovered above streets, yelling at people to get inside and scolding them for not wearing face masks, while elsewhere in China facial-recognition software, linked to a mandatory phone app that color-coded people based on their contagion risk, decided who could enter shopping malls, subways, cafes and other public spaces.

"We couldn't go outside under any circumstances. Not even if you have a pet,"
...
More draconian steps are needed in the U.S., these officials say, although they also cast doubt on whether Americans could do what the Chinese did, for a mixture of reasons: political will and deep-rooted cultural inclinations, among them.
...
"Lockdowns, bans on gatherings, basic quarantines, testing, hand-washing, this is not enough, You need to isolate people on an enormous scale, in stadiums, big exhibition halls, wherever you can. It seems extreme. It works,"

I expect what the article says about the USA culture also applies in Europe, South America, and many other places.

 

[Ygggdrasil]

Possibly a dumb question, but how do we know the IFR?

If someone is never diagnosed, how do they even show up in the statistics? Thanks.

This is where a serologic test becomes useful. A serologic test will detect if someone has antibodies against the virus, which is a sign that they were infected in the past. As others have mentioned, you can use the test to sample a population after the outbreak to estimate the real infection rate (which also tells you the fraction of undiagnosed mild/asymptotic cases).