COVID COVID-19 Coronavirus Containment Efforts

[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...

 

[chemisttree]

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?

Yes, you are correct. The virus produces an environment where opportunistic bacterial infections cause pneumonia.

 

[chemisttree]

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

Nope!

 

[peanut]

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

Do you mean pneumonia can be caused by a virus? And in Covid-19 case, it is.

 

[Borg]

https://en.wikipedia.org/wiki/Pneumonia

 

[peanut]

The virus produces an environment where opportunistic bacterial infections cause pneumonia.

Virus and bacterial (co-infection?)

 

[chemisttree]

Virus and bacterial (co-infection?)

Yep!

 

[jbriggs444]

Virus and bacterial (co-infection?)

Pneumonia is the condition -- alveoli being filled with fluid and, hence, non-functional. The cause can be either viral or bacterial.

noun

1. lung inflammation caused by bacterial or viral infection, in which the air sacs fill with pus and may become solid. Inflammation may affect both lungs ( double pneumonia ), one lung ( single pneumonia ), or only certain lobes ( lobar pneumonia ).

 

[peanut]

Yep!

Thank you. But having been vaccinized by pneumo though not a guaranty can mitigate the effect?

 

[Rive]

Do you mean pneumonia can be caused by a virus? And in Covid-19 case, it is.

Yes. You can get bacterial bonus too, but in case of Covid19 the primary cause of the pneumonia is the virus (in a possible alternative explanation: your own immune system).

 

[Dullard]

Mold, fungus, particulates, chemicals...

 

[Astronuc]

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?

Pneumonia is inflamed or swollen lung tissue due to infection with a germ.
Viral pneumonia is caused by a virus.

https://medlineplus.gov/ency/article/000073.htm

Bacterial pneumonia is an inflammation of the lungs due to bacterial infection. Different types of bacteria can cause pneumonia. This type of pneumonia can occur in both lungs, one lung, or one section of a lung.

https://www.medicalnewstoday.com/articles/312565

Pneumonia is an infection that inflames the air sacs in one or both lungs. The air sacs may fill with fluid or pus (purulent material), causing cough with phlegm or pus, fever, chills, and difficulty breathing. A variety of organisms, including bacteria, viruses and fungi, can cause pneumonia.

https://www.mayoclinic.org/diseases-conditions/pneumonia/symptoms-causes/syc-20354204
According to the Mayo Clinic, "The most common cause of bacterial pneumonia in the U.S. is Streptococcus pneumoniae. "

Pneumonia may also be caused by a mycoplasma, which is what I had several years ago. I had a persistent dry cough, which might have started with one of several cold viruses. I had no fever, then got better (two weeks from the time I felt a cold), but I still had a mild cough. Then I got worse, developed a fever and productive cough. I went to the doctor and he put me on antibiotics, and the illness resolved in 4 days.

https://www.cdc.gov/pneumonia/atypical/mycoplasma/index.html

https://www.cdc.gov/pneumonia/atypical/mycoplasma/index.html

One could have both viral and bacterial pneumonia, with the bacteria being an opportunistic or secondary infection.

 

[PeterDonis]

The pneumonia is a bacterium right?

"Pneumonia" is not a name for a single disease. It's a general term for "diseases that fill the lungs with fluid, impairing lung function". Even apart from COVID-19, there are multiple varieties of bacteria and viruses that can cause pneumonia.

 

[chemisttree]

Thank you. But having been vaccinized by pneumo though not a guaranty can mitigate the effect?

Probably not. The virus itself can cause the pneumonia. It’s going to be a co-infection. The bacteria at the back of your throat are going to find a way into the lungs.

 

[Ygggdrasil]

From the WHO:

https://www.who.int/emergencies/diseases/novel-coronavirus-2019/advice-for-public/myth-busters

 

[Ygggdrasil]

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.

I agree that we need suppression strategies at the moment, such as social distancing and stay at home orders, but these measures should not need to continue indefinitely. These suppression strategies should be able to stop the spread of the virus so that there are new cases, and reduce the level of cases so that we can go back to a situation where contact tracing is a viable strategy (see the analysis from Tomas Pueyo for more discussion).

Here's a report from the MRC Centre for Global Infectious Disease Analysis providing preliminary evidence that China has been able to contain the spread through their lockdowns and has been successful (so far) in beginning to lift social distancing measures. Hopefully as stay at home orders continue in the US and we move towards containing the outbreak, analysis of the situation in China can inform how we plan to ramp down social distancing measures:

The COVID-19 epidemic was declared a Global Pandemic by WHO on 11 March 2020. As of 20 March 2020, over 254,000 cases and 10,000 deaths had been reported worldwide. The outbreak began in the Chinese city of Wuhan in December 2019. In response to the fast-growing epidemic, China imposed strict social distancing in Wuhan on 23 January 2020 followed closely by similar measures in other provinces. At the peak of the outbreak in China (early February), there were between 2,000 and 4,000 new confirmed cases per day. For the first time since the outbreak began there have been no new confirmed cases caused by local transmission in China reported for five consecutive days up to 23 March 2020. This is an indication that the social distancing measures enacted in China have led to control of COVID-19 in China. These interventions have also impacted economic productivity in China, and the ability of the Chinese economy to resume without restarting the epidemic is not yet clear. Here, we estimate transmissibility from reported cases and compare those estimates with daily data on within-city movement, as a proxy for economic activity. Initially, within-city movement and transmission were very strongly correlated in the 5 provinces most affected by the epidemic and Beijing. However, that correlation is no longer apparent even though within-city movement has started to increase. A similar analysis for Hong Kong shows that intermediate levels of local activity can be maintained while avoiding a large outbreak. These results do not preclude future epidemics in China, nor do they allow us to estimate the maximum proportion of previous within-city activity that will be recovered in the medium term. However, they do suggest that after very intense social distancing which resulted in containment, China has successfully exited their stringent social distancing policy to some degree. Globally, China is at a more advanced stage of the pandemic. Policies implemented to reduce the spread of COVID-19 in China and the exiting strategies that followed can inform decision making processes for countries once containment is achieved.

https://www.imperial.ac.uk/media/im...ID19-Exiting-Social-Distancing-24-03-2020.pdf

 

[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.

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

Update: Two sites I've used for aggregated data are showing different numbers. I normally wait to verify data from WA and NY, but they release data late in the afternoon and WA has been much later since yesterday.

As of 3/25 14:04 ET, Coronavirus Dashboard (https://ncov2019.live/data) has US with 54,428 positive cases and 846 deaths, while Covid Tracking (https://covidtracking.com/data/) has 60,443 positive cases (5,625 hospitalized) and 826 deaths. The sources of data for CD are not clear, whereas CT seems to get it from the state health departments and media releases.

New York released their number earlier today: 30,811 positive cases including 285 deaths and 3,805 hospitalizations. So New York has slightly more than 50% of the positive cases in the US. The number of positive cases has increased by 5146 compared to an increase the previous day of 4790, but less than the increase of 5707 two days ago. So one day, and even two days, doesn't make a trend.

https://covidtracking.com/data/#NY
https://covidtracking.com/data/state/new-york/
https://coronavirus.health.ny.gov/county-county-breakdown-positive-cases (link needs refreshing after loading)

New Jersey has second highest number of cases passing Washington (Wa) and California (Ca). There are many commuters between NJ and NY City, and infected travelers likely arrived at Newark airport (EWR) returning to parts of NJ and NY.

The surge of cases in Louisiana (La) seems to be tied to Mardi Gras celebration in New Orleans, February 25. New Orleans attracts people from all over the country, so folks likely took infections back home, as well as the virus spreading through New Orleans.
https://www.fox8live.com/2020/03/24...used-many-cases-coronavirus-new-orleans-area/
https://www.nbcnews.com/news/us-new...us-mardi-gras-could-be-blame-doctors-n1167741

 

[Borg]

Has any raw data made available for those who would like to perform analysis? We've all seen the many charts about the spread and charts showing that older people are more susceptible to the virus but I would like to see the data for myself. I'm also hoping that there might be other variables in the data such as blood type as was mentioned in another thread.

EDIT: I should do my searches before posting. Found this right away:
https://catalog.data.gov/dataset?q=covid
Not what I'm looking for though.

 

[Rive]

Good read.
Well, kind of...

 

[Astronuc]

Has any raw data made available for those who would like to perform analysis? We've all seen the many charts about the spread and charts showing that older people are more susceptible to the virus but I would like to see the data for myself. I'm also hoping that there might be other variables in the data such as blood type as was mentioned in another thread.

EDIT: I should do my searches before posting. Found this right away:
https://catalog.data.gov/dataset?q=covid

In the US, one can go to the state health department websites. I've been using the official numbers for Wa and NY from their respective sites. However, one will find that each state reports different age groups. Wa reports by 10 year, e.g., 20-29, while NY reports 18-44. Even then, details of patients are not reported due to respect of privacy.

Each site updates daily but at different times. And formats/details are different.
https://www.doh.wa.gov/Emergencies/Coronavirus
https://coronavirus.health.ny.gov/home
https://coronavirus.health.ny.gov/county-county-breakdown-positive-cases
https://www1.nyc.gov/assets/doh/downloads/pdf/imm/covid-19-daily-data-summary.pdf

I've looked at other states, but they do not necessarily report their data, or at least it's not readily accessible.

Hospitalizations is even more difficult to find.

https://covidtracking.com/data/ gives US and each state for each day and historically, but do not separate out male/female or age group. Blood type is not publicly available, and is usually only available select medical/scientist researchers.

https://covidtracking.com/us-daily/
https://covidtracking.com/data/#NY (click on the state name (link) to get to historical data
https://covidtracking.com/data/state/new-york/

Example of NJ: https://covid19.nj.gov/ (dashboard at bottom of page)
Note that Newark Airport spans the east side of Essex and Union Counties. Bergen county is north of Essex county.

And verify with the state health department.

Early on I found the CDC numbers were 24 to 48 hours behind individual states, and apparently, they don't work on weekends.

 

[Borg]

Awesome. Thanks!