"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.

WFH - or "being at home trying to work when crisis going on"?

It's been four weeks for me being at home and not being allowed to go to "campus" (my office). so officially I'm "Working From Home" - WFH.

One of the things that I've been dealing with is the fact that I was SO proud I never got a proper organized work from home station organized at home. (I'll have a disclaimer here - since I'm a "straight A person" this has been stressful. Don't get me wrong, last few years in my job I've worked "being off campus/off hours on weekends" but it's always been my work laptop on my dining table, for a selective period of hours.) It has NOT been in what I call "my room" where I do crafts, write my blog posts, skype with my parents on the weekends, write my short stories - in short; where I do my hobbies and feel like I'm in my personal space (as an introvert).

It's been a temporary space when I pen my laptop on the dining table in the mornings or perhaps the few days I've been at home the entire day working but not going into the office)l.

Now?

Well, sorry sweethearts. My "hobby/relaxing/lovely 'my' room" is turned into "my office". I have my work monitor, a set up with the keyboard, headphones and all the work papers and books that I brought with me from work with special approval. On one level I understand that I should feel grateful that I not only can work from home, and also that we have a full extra room that I can call "my room" - another part of me was very annoyed that "my" room is no longer "my" room rather than "my work room". It might not be an issue for a lot of people, but for me - it's clearly a new thing, and something I have needed to take some time adapting and accepting.

It's similar to what a colleague of mine mentioned last week. They talked to me about issues that have come up with employees who have a though time adapting to working from home - mainly since they are lab workers and do lots of lab work - with out lab, what do they do? And that they are fortunate to get a pay check anyways (my work place is paying everyone so far, no furloughs of full time employees, regardless of "being able to do work from home or not").

For me I've mainly been dealing with the idea that I could technically work at least 12 hours a day, every day. There's a lot of things I need to do that's only me doing and once I'm done, we are done. So, part of my anxiety is to focus on that I "will not" do the work in 3 days, but I will do it in 4 days since I'm working 8 hours a day from home.

Trust me, it's not that easy and clear cut for a slightly over-working, over-achieving type A personality like myself.

Another way of looking at this situation - especially when talking to colleagues who are at home with children and therefore feel guilty that they aren't doing great in either place, their younger kids are upset "mommy/daddy doesn't play with me", nor that they get enough done at work - is looking at it slightly differently.

It's not "working from home" as we usually know it. It's "being at home and trying to work in a crisis". Sometimes giving the right frame to a picture makes you see the details in a clearer light and giving you an added understanding to your emotions and actions.

dealing with anxiety (safer-at-home edition 1)

I ran into my old kickboxing trainer today. I would say he looked more surprised to see me than I him. He apparently thought I had left town. No idea why. Apart from that he was the one leaving and cutting all of us off. I almost said "you took the heavy bag I paid for when you scooted out, and I would've really enjoyed it in my home now in Covid19 times". Of course I didn't say that. Because that would be ... I dunno, unnecessary? It's been almost 10 years.

Still though, it brought back an old conversation I had with a therapist during my divorce (even more years ago). I talked about how I handled anxiety and that I had noticed 5 different outlets that might not have been the best options all the time.
In no particular order;

• drinking (alcohol)
• eating (oh chips, carbs are faves, but really - beggars can't be choosers)
• getting into a fight (referring to verbal fights and slight screaming, since I wasn't a brawler)
• having sex
• working out (especially on a heavy bag with gloves, intervals so almost puking or sparring against someone bigger)

At the time, I was quite proud that I had moved away from the destructive ones and kept working out to keep calm and in control of feelings and stressors. This quarantine/safer-at-home deal makes it a little more complicated since I currently don't have a heavy bag at home. Sure, I have a few kettle bells and I jog/do intervals at times in the neighborhood. However, it's not the "all out endorphin looking kick" that I've chased over the years to mellow me out. 

I guess I know now that I have to up my milage (haven't done more than 6 miles since marathon in December) and start doing the horrid intervals/fartlek to see if that kicks in the "adrenalin get aways" and the endorphin kickoffs. It wasn't an issue in the fall when I averaged 22 miles a week (4, 3, 15 miles) when training for the marathon, and doing spinning intervalls and weights/boxing twice a week. Currently I'm more in the "walking 3-5 miles a day" and "jogging twice a week", but nothing over 6 miles (since I'm in my neighborhood and not the park where I used to go long distance running). It's not enough to keep the balance.

Why do I think about this?  Because the other options on the list aren't really great choices as outlets. And especially not as a grown up who should be honest with ones feelings and reactions - as I refer to myself right now. I know, it would be best if I learned to deal with anxiety as regular people. Now, what do regular people do when stressed??? (I really don't know. Please let me know)

a pandemic is inconvenient - and we are not used to that

If there is one thing I've been saying once it was clear that the virus situation in Wuhan was something extraordinary, it's "It's going to be inconvenient for many people. I mean, people complain about one snow storm stopping their plans. This is going to be more for longer time".

What I meant was that a lot of people didn't, and still don't, understand the basic concept of a pandemic. We have built a world where a lot of us think we have control. We decide. And if we want to do something, we do. (Of course there are a lot of people who don't have these choices. A lot of choices open up when you get from poor to middle class. Or higher.)

In reality though, the only way to stop a pandemic is to stop the spread of the infectious agent. In this case, Covid19, it's a virus that spreads mostly people to people, but also can't be ruled out as fomites (virus gets to a surface, you touch surface with hand, then touch hand to face/mouth, you might be infected).

So, now that WHO has declared a pandemic, a lot of countries will and have already done these curtailing measures. Most of these will be annoying for you in your everyday life. And it will be so for a while - most start with "for the next 2 weeks or 30 days". A lot of them will probably be longer. And it will affect a lot of businesses, family income and infrastructure.

It's important to remember, this is much better than the alternative - which would be a more chaotic, panicked world where people would be more hurt and dead.

What can you do to make this situation better?

Well, first of all - don't disregard the severity of the situation. Exponential growth is difficult to understand. When I started learning epidemiology and microbiology we had examples with peas and then one with a pond of water lilies (think Monet or Manet paintings).

In a pond grows water lilies. Every water lily gives rise to another water lily the next day. At day 48 the pond is full with water lilies. When is the pond half full?*

On top of this is - at least in the USA - a underreporting of cases since there is a lag in confirmed tested cases. That means that the confirmed cases is not the amount of people who are infected.

And to underscore the point with curtailing measures. It's not because we think the majority of people in society will die. It is because people who are in risk groups have NO OTHER way to protect themselves but for all of us to decrease the amount of people who walk around spreading the virus. There is no vaccine, no specific treatment and no immunity.

And the risk groups right now are pretty broad; older people (definitely over 70), immunosuppressed people (any former cancer and transplant patient), pre-existing conditions like diabetes, high blood pressure, obesity...

So please, let's repeat this to all of us who will get annoyed, bored, scared and inconvenienced in the weeks/months to come. It's because this is the better way than the alternative. It's not because it is fun and games. There will be no concerts, no sports events, no conferences, less/no travel and no vacations.

Staying at home doesn't mean play parties or drink parties. It means distancing yourself and your family to avoid spreading virus. It means, calling your grandmom on the phone or via skype, and not going to visit with your cute little child. School closings means that you can't put your child in after school activities since they are not supposed to be in a big group. And it means not going to a game of hockey to avoid thinking about this pandemic and worrying. Nope. It's you, at home, trying to keep hope that this to will pass and the world will learn, while washing your hands and avoiding touching your face.

Also, it will be imperative NOT to burden the (hospital and health care) system unnecessary. Most likely there will be longer wait times for everything and staff will either be fewer or they will be overworked. So please keep that in mind.

Food banks will need money and food for the poor who will lose income and jobs. And for the children who don't get their subsidized school lunch.

Overall, it's going to be rough before it gets better. And we will need to overcome it together.



*the pond is half full with water lilies at day 47. It's very hard to grasp since it means "it grow so fast over night" but in reality it was same as always, one per one 1:1 spread. which in covid19 would be 1:2 or 1:3 plus the super spreaders who have been shown to infect as many as 1:100. pond fills very quickly.

"Best of" ... and one of my fave posts per year I've done this

Every once in awhile I get a bit surprised. I've kept this blog going for over 13 years.... not as many posts nowadays than when in the most productive times. I think it is a combination of "not as many blogposts as before for people in general" and "not as much time for blog posts as before". I was a little less private before.

It seems as the more people I know in person/with proper names and real life, the less I feel that this venting and writing is appropriate. Guess it is a part of being an introvert, but also a sane conclusion of being older and knowing that nothing on internet is really anonymous.

However, I read some of my older posts and and glad that I was this honest and wrote what I did. There are two of them that show some of the less fun parts of my life, but in context with some other ones, I am happy to read them. While they were written in times of turmoil and unknown life, they managed to capture how I felt, and how I wanted to get out of the feelings.

I thought I would make a list; best of the posts. And then in the end, the "most read posts" - which no surpose, aren't the same ;)

Top 5 - most read
1. Being a failure vs having failed at something

2. Most important for a woman, being likable

3. Rejection - part of life and grant writing
4. Feedback on resume - tough love
5. The importance of saying Thank you


My own favorites from the years are here (probably too many but there are various categories and it is one for each of the 13 years and one lagniappe*... )

My first of "two of them" - trying being poetic, hoping to be Sylvia Plath or Karin Boye. Of course failing but trying is better than not even giving it a chance.
http://chall-dreams.blogspot.com/2006/09/in-his-sleep-he-turns-to-her.html

The Second ot the two. An explanation of being in a less than optimal boat, drifting at sea but not accepting that it should be necessary to leave the boat and hop onto a bigger cruise ship....
http://chall-dreams.blogspot.com/2010/09/alone-on-ocean-in-dinghy-with-one-oar.html

Then there are gems (at least to me) where I pucker up and have feelings "of before" and go to work. This would be when I won a great negotiation
http://chall-dreams.blogspot.com/2008/08/seducing-boys-club.html

And this one why I am conflicted about the whole issue with engagement rings and diamonds a la America
http://chall-dreams.blogspot.com/2009/11/every-killing-begins-with-k_29.html

And the best title as a conversation starter.... just not best choice to do at work ;)
http://chall-dreams.blogspot.com/2012/11/ive-slept-with-more-people-than-k.html

Good reminder on what I felt like moving into the job after the post doc
http://chall-dreams.blogspot.com/2009/12/fat-girl-with-cookie.html

Moving on my career, when handing in a letter of resignation
http://chall-dreams.blogspot.com/2013/10/handing-in-my-letter_15.html

Six year anniversary of the blog
http://chall-dreams.blogspot.com/2012/08/six-year-anniversary.html

Again, I'm not a girl, I'm a woman. Or one of the guys. And these posts tell that story.
http://chall-dreams.blogspot.com/2012/07/im-not-girl.html
http://chall-dreams.blogspot.com/2010/09/that-is-doctor-girl-with-panties-in.html

My thoughts on being friends with coworkers
http://chall-dreams.blogspot.com/2015/02/being-friends-with-co-workers.html

Interesting posts about how I viewed my job after a few months
http://chall-dreams.blogspot.com/2014/01/job-transition-part-1.html
http://chall-dreams.blogspot.com/2014/01/job-transition-part-2.html

My dreams and feminist ideal
http://chall-dreams.blogspot.com/2008/05/why-men-would-benefit-from-having.html

Let me know which one, or some other post, you like or that touches you or something I should rewrite/do over! I'd like some feedback.

*one of those lovely words I've picked up in my new life :)