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Tag: covid19

I Watched Contagion: So Should You

Posted on by wotantx
Read Time:53 Second

This started as a Facebook post and a Twitter thread, but I decided to post it here as well.

If you haven’t ever watched Contagion, I urge you to do so. This movie is a very good portrayal of the world we live in. The science is very good. It depicts the very panic buying we have seen. About the only thing missing is the politicization of the pandemic. I don’t know who the technical advisor was, but he or she was allowed free reign, and it definitely shows.

The virus, dubbed MEV-1, had its origins in bats, just as the SARS-like coronaviruses, including the cause of COVID19, does. In the movie, it passed through pigs. Influenzavirus type A does sometimes pass through pigs from birds to humans. It is believed that SARS-CoV-2 passed through pangolins, though I’m not sure how well determined that is.

I’ve heard people say no one could see COVID19 coming. That’s very not true. Contagion came out in 2011. And others, myself included, have expected things like this.

Using ILINet to track COVID19

Posted on by wotantx
Read Time:2 Minute, 12 Second

In my first writing on the COVID19 Pandemic, I mentioned that flu surveillance can be used as a way to track the spread and severity of COVID19. Let me take you through some of what appeared in the Week 12 edition of FluView (the CDC’s influenza surveillance product). I originally wrote this on Twitter.

This first image shows the prevalence of influenza-like illness (or ILI) present in the country for the week ending March 20, 2020.

It shows flu-like illness is elevated across the country. The percentage of visits for ILI is almost to the levels of the peak of the current flu season, and the amount of confirmed flu (positive tests) is way down.

This next map shows the ILI activity in each state. Keep in mind that we are late in the flu season, and we are past peak. The map is ugly; it shouldn’t be so red. I also do not know why Florida is showing low levels of flu activity. It should be much higher than that. Perhaps the data is lagging.

More troublingly, perhaps, is that pneumonia and influenza mortality (P&I) was above the epidemic threshold for week 11, the week for which we have the most recent data. Since the CDC does not count the number of flu deaths (except for children), P&I mortality is one of the proxies used to determine that.

At this time of year, P&I mortality should be leveling off and then declining. This uptick could point to COVID19 deaths that are not being reported in the official case counts due to inadequate testing. This is one of the metrics that will be used to estimate the actual number of deaths once the epidemic is over.

I want to stress that the official case counts are far smaller than the number of actual infections, and the number of fatalities are as well, though I don’t think either can be quantified at this point.

I will continue to monitor FluView and see if it shows us anything that might be useful in determining if social distancing measures are helping.

Note that I am not a doctor, virologist, epidemiologist, or any other kind of expert. Infectious disease has long been an interest of mine, and here I am simply applying my interpretation of public data.

A future post may talk about what we know of serious illness in young people, including the prevalence of acute respiratory distress syndrome (ARDS). We seem to be seeing quite a lot of that, and but for modern medicine, we would probably be seeing a much different type of mortality.

Thoughts on the COVID19 Pandemic

Posted on by wotantx
Read Time:3 Minute, 1 Second

I haven’t really got the first clue why I have not started blogging on the COVID19 Pandemic. Some of you may be aware that infectious disease is one of my many interests, so I have certainly been following it closely since I first learned of the virus now known as SARS-CoV-2 sometime in January.

One of the truly distressing things about the pandemic is the seemingly willful ignorance of the progression of the disease. A large swath of the US population, particularly those of certain political persuasions, has decided that, somehow, we know the exact number of cases in this country as well as the exact number of deaths. This despite it being extremely well-documented that we have inadequate ability to test in this country. Even countries that have done a great job in their response to the COVID19 Pandemic, such as South Korea, are going to be significantly undercounting their caseload. This is because you simply will not find every single person who is infected, in part because you can be asymptomatic. As of this writing (3/16/2020), the US has about 3500 known cases. Known is the important word. Actual cases are going to be a few orders of magnitude higher. We will absolutely never know the true number.

People like to point to the number of seasonal flu cases and deaths to show that the COVID19 Pandemic isn’t as bad as flu. What they don’t understand, or don’t care to understand, is that those numbers are estimates. The United States, and probably the rest of the world as well, does not track cases of influenza, nor does it track fatalities, with the exception of pediatric influenza cases. The numbers that are reported are estimates based on incidents of Influenza-Like Illness (ILI) as well as Pneumonia and Influenza Deaths (P&I) that are tracked by various public health agencies in this country, including the CDC. A subset of cases is known through the administration of the Rapid Antigen test (the unpleasant swab of the nasal passages done in a Dr’s office) or through samples sent to a lab for Polymerase Chain Reaction (PCR) testing. One of the issues with this is that to Rapid Antigen test is notoriously unreliable. If memory serves, it has a false negative rate of about 50%. Now, as I will write about in a later post, the flu surveillance can be of importance in the tracking of COVID19 cases and fatality in this country, but most of that analysis will have to be done retrospectively once the epidemic in the US is over. It is worth noting that pandemics tend to come in waves of epidemics. For instance, the Spanish Flu had three distinct waves, with the second being the most lethal in the US.

The point of this post is to point out that we do not, and will never, know just how many people in the US will come down with the disease. Once it’s been established the community transmission has occurred, it is no longer possible to deny that there are uncounted cases precisely because we know we have a case not linked to anyone else. To ignore this is foolish at best, and very dangerous at worst. It leads to complacency, to people downplaying the severity of the disease, and this ultimately leads to further spread, and to people in high-risk groups, getting the disease.

Get your heads out of the sand and take reasonable precautions, including practicing social distancing to the extent possible. The life you save might well be a loved one.