Sunday, May 03, 2020

"let's wish the virus away" and other comments - from a microbiologist

The last couple of weeks (months if you are picky) it's been very clear to me that a lot of people are stating opinions and thoughts in regards to covid-19 that are not based on fact, nor knowledge. As I've been working from home and reading news, tweets, facebook posts and listened to a number of news shows and podcast - I've come to grow increasingly frustrated with a few very obvious limitations in what people really know in regards to viruses and pandemics.

This post is in no way covering all things that I would like to point out. It's mainly a try to state some of the bigger points that have been confused/forgotten/ignored/whathaveyou - in my opinion and knowledge as a trained microbiologist with training in viruses, bacteria and having been an active researcher at the time of the last pandemic (H1N1) where I was part of conferences and guideline preparations on what countries, companies and people could do to prepare for a situation that no one wanted to happen.

1) it's very important to remember that comparing countries - both in regards to "reported cases", "reported fatalities" and "actions suggested and legislation enforced" - are very different and difficult to compare to each other.
Example; one country only reports deaths in hospitals where the person have had a positive test for virus, another counts all deaths in a hospital where a person have been previously tested positive for the virus and people who died in nursing homes having a few symptoms associated with the virus.

2) the actions taken by various countries depend, not only on the way the various government have ability to enforce regulations, but also on when in a pandemic they encounter the virus that is spreading across the globe. If early, complete eradication might be possible, if later in the time line - mitigation might be the only opportunity.

3) reporting "positive tests" as a number on its own is not helpful unless presented in context of "how is testing done" and with numbers of "how many tests have been administrated". This is the long way of saying - know which part of population is being tested, how often and with which test.
Example; one country tests only people going to the hospital with symptoms, another country tests people who go to school regardless of symptoms.

4) as long as there is no vaccine nor treatment that will make an infected person better, there is no other option to stay healthy but not becoming infected. Any infected person will have to beat the infection on their own. Some people benefit from helpful interventions like ventilators, a lot of people don't necessarily get better as much as we would like from these interventions.

5) saying "it will go away" doesn't solve anything. The virus "will go away" when it is no longer present in the population by not having any more susceptible people to infect (either by everyone being immune due to earlier infection or by vaccination) or when we have successful treatments. This also implies that a lot of people will have become infected and either survived (immune) or not survived the infection (died) or a treatment has been found.
Example; very few infectious diseases have "gone away". Even when we have vaccines. They have decreased and for a lot of them they might "flare up" in a smaller part of the population and then we can successfully protect more people so they don't get infected. This is also where viruses are different from bacteria since for many of the infectious bacteria we have found an antibiotic that can treat the cause of infection. For viruses, viral infections, the only known "treatment" is a vaccine which technically is viewed as a prevention, rather than treatment, since you need to be vaccinated before being exposed to the virus and therefore avoid infection.

6) most airborne and droplet spread infections will be hindered by hand washing (the virus will not be present on your hands and therefore not spread when you put your hands in your face), wiping down shared surfaces you touch (with your hands) or by limiting the number of people you meet and talk, cough, hug, kiss or hand off infected stuff to.
Example; someone coughs in a room and droplets end up on a keyboard, you later touch the key board with your hand and then touch your face.... the virus spreads. If the keyboard is wiped down between different users, the virus will be removed/inactivated and the other user will not catch the virus on their hands.

7) masks limit the amount of virus particles you spread and that others spread to you when breathing/coughing. Proper mask handling is key for this to work. Improper mask handling will create a sense of false safety and therefore might increase the spread.

8) regardless of your political affiliation - the virus doesn't care about that - everyone in a society is susceptible to viruses (and other infectious diseases). Virus aren't sentient and therefore per definition "not smart" or "intelligent" or any other wording that's being used.

9) Actually, per strict biological definition a virus isn't alive since it can't replicate on its own. A virus needs to infect a cell to be able to replicate. That's why researchers make a distinction of "being able to replicate" or "infectious doses" and "RNA titers". Of course, this is detail that for much of the current (social and political) discussion isn't really relevant if it's not for the point that a test showing there is RNA present in someone doesn't automatically correlate to that person having a viable virus that can infect and then replicate (it's more likely than not that the virus titer indicates that there is a presence of virus being able to replicate - especially for this covid19 bullet point list that I'm writing here). For the sake of 99% of the conversation about covid19 though, this point is not key relevant since it's the weeds and details that many researchers take into consideration (mainly super important for the discussion of tests and their sensitivity and false negatives and false positives - see point 10).

10) the general understanding of what constitutes a "validated and confirmed biological test used in hospital setting/for medical purposes" is low. There are a lot of details going into validating a test. Two of the most important factors are sensitivity and specificity. The test needs to be specific enough to only pick up specific factors from the virus (microbe) in question to be positive. The test also needs to be sensitive enough to pick up factors even when in small quantities. There are more factors that are important but in general, I'd say these two factors are key when discussing "false negatives and false positives".
Example: currently there are a lot of antibody tests being deployed all over the world to investigate and confirm how many people have really been infected by SARS-CoV-2 (the virus that causes covid19). The antibody test need to be specific enough to ONLY give positive to people who have been infected by SARS-CoV-2 and not any other virus around. It also needs to be clear how sensitive it is - as in "how many antibodies/what level of immune response" will the test detect. This latter part is complicated since it's not known what kind of threshold is needed to be protected for future exposure nor what kind of immune response various individuals have had if they've been symptomatic or asymptomatic. (see, I'm in the weeds now... lots of details on the background on validation of these tests.)

11) microbiology, epidemiology and public health are specific areas of expertise where there are a lot of facts and previously collected knowledge that are helpful when determining what to do, when and how. There is a difference between non trained people and trained people in regards of this knowledge.

12) no situation is being helped by panic. Many situations involving "unknowns" and "large amount of people potentially afflicted" create panic reactions and knee jerk responses at the time they happen. This is why it's important to have a plan before a bad situation happens since then there is less second guessing or panic reactions but rather "following a plan previously vetted and laid out". Most health care workers have been trained in planned responses, so that when "panic situations" arise, the trained people don't panic but rather adapt well to the planned response and go through the situations many of us untrained people wouldn't handle as well. Trust well trained workers.

I'll stop here since I don't want to overthink or write more at this time. It's my vent and my thoughts and feelings. And hopefully someone who reads this will find it helpful. It was helpful for me to write it down. And possibly I'll make a blog post regarding number 10 - Validation of biological tests - later since I've created test validations under FDA (21 CFR part 11) and EU equivalent from EMA (EU Annex 11) requirements.

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