I've been drafting these blog posts about "sensitivity and specificity", "difference between antibody test (serotests) and PCR (RT-PCR)" and "timeline of pandemics". They are all still in the works. I got sidetracked though. Not by something fun. Not even by my work, even though I've managed to have two hard deadlines and another coming up within a few days, but by fighting this feeling that "throwing pearls for swine isn't worth it".
Nownow, I know the mistake of the analogy. First off, my blog readers are few and a lot of you I kinda know over the years. So, not "random", and most certainly not appropriate to have an analogy to "swine" as in the saying. For argument sake, let's disregard the saying and move on with the post.
It might just be the notion that writing explanations and trying to make sense of what is going on in the world from a microbiology point of view would be a good idea IF the posts were read in good faith by someone who might learn and even change their way of thinking.
Alas, and here comes the tiredness and the reason for the crude analogy, there's been quite a few interactions with people who go at things in bad faith. And also that they are so firmly lodged in the "other camp" that they have no interest, no semblance of idea, to learn or listen to facts.
And after the latest couple of weeks sharing borders with conspiracy theorist, "freedom seekers" and "God & Trump will protect us and the virus will go away with the heat in June" - I have spent a lot of energy not saying what I think. Not stating rude things. Not making over the top faulty "I want this to be true" signs posting them all over internet or calling people names. (Like they have done.)
Why? Because I was raised to be a behaved person. I was raised to respect and accept other opinions than my views. I was raised that "be above such muck".
However, I was also raised to stand up for what I believe in.
And I was raised to protect the people who couldn't protect themselves.
To think about and consider the people who didn't have a voice in the society.
To NOT only think about myself.
To be alright with having some discomfort IF it meant others were protected and it saved others.
To NOT put myself first all the time but to be humble and considerate of others.
To do the best thing for all of us, not only the best thing for me and mine.
Some of these things have been easier than others the last few months. I won't lie.
"First, do no harm"
I'm not a physician but the sentiment would be something that I was raised considering regardless. Got to be honest though, my experience with bullies - and I'm afraid I have more than I would've liked - is that you can turn the other cheek a lot of times, and not stoop to their level and be the better person.
Sadly (?) though, I would say that there was some experience of an effective way to stop and that was "to stoop at their level" and intimidate back. Threaten as the bully was threatening. Strike a punch and they got scared and thought it wasn't worth it. And to be the bigger person if finding a bully in the younger peer group, bullying the younger ones.
I don't like the experience the violence and threat "solved some bullying". I'm old enough now to see that it works for specific occasions. And that it is situational, like a four year old knows that mommy will be more likely to give the candy in the store if threatened with a full on temper tantrum and screaming and all the noise.
I had some hope that we were above being four year olds as adults. Or that it needed to be "brought to your own family for you to care". I'm now contemplating that a lot. I find myself looking back at my grandmother's teachings of being a lady, while running a secondary commentary in my head "let's go outside and solve this the old fashioned way".
But most of all I have had to fight my thoughts of "maybe, just maybe it's going to have to be really bad for these people to understand the errors of their ways" - also known as Burn it to the ground. It is a fairly common tactic in war after all (hello Russia in WWII and Germany on their Western front). Main issue is that there are A LOT of collateral damage. And again, the main issue here is that even if that would be a wakeup call for many "good faith" people, it wouldn't mean anything to "bad faith argument people". They see what they want to see. And collateral damage doesn't face them.
That means that the main thing getting hurt from that would be me and the collateral damage, and that wouldn't really help anything now would it?
TLDR:
Wash your hands.
It's helpful for vulnerable people (and you and others) if we keep social distancing.
Since we don't know everyone, if you are grocery shopping, in a closed space or on a public transportation, please wear a mask to save others like if you have the virus.
IF you feel sick, stay home and don't expose others.
It's the only way vulnerable people (and others like health care workers) will be able to go outside for the foreseeable future.
And also, if you still think this is a hoax - you are fooled by whatever outlet you watch, read or listen to. The virus and the consequences of being sick are real. And we don't even begin to know how being sick has affected people who have recovered.
Tuesday, May 26, 2020
Friday, May 15, 2020
interlude - canada geese
I mean, it's sort of a joke. Back in my home country (Sweden) we have a LOT of Canada geese. Especially congregating at the parks and places where we swedes would like to sit down and have picnics in the spring and summer. I might be slightly biased - as a young child, say 4 years old - I had a slightly less than terrific incident with regular geese (they are bigger and whiter than Canada geese but more tame and therefore less ferocious than wild Canada geese).
Anyway, it's funny for anyone else to notice that when I'm jogging around in my neighborhood during this "stay at home"/"stay safe" time in Covid-19, there is one new road that takes me to a ess than populated industrial area. I didn't know it existed before this "I need to find places to walk and jog since otherwise I will turn into more of a rotund person". However, I've explored a lot of places that are within a radius of 5 miles of my dwelling in the latests 6 weeks.
And there are these strange things like a congregation of Canada geese. Next by a road. Very little grass. And also, by another time when I went by, where there little alone cat used to hide.
Not sure what this means? Do someone feed the cat AND the Canada geese? Are the Canada geese going to eat the cat? (I don't think the cat can take on 5 Canada geese but sure, we could postulate I guess.)
Anyway, if anyone wants to leave a comment or email - feel free. I have a bunch of half made posts but I am trying to write them so that they are good (at least half decent) and not just venting based on the current situation in life and the world.
Here's a picture of the Canada geese. And yes, they are judging you. For sure! (the fifth one is one the street next to me on the left, outside of photo.)
Anyway, it's funny for anyone else to notice that when I'm jogging around in my neighborhood during this "stay at home"/"stay safe" time in Covid-19, there is one new road that takes me to a ess than populated industrial area. I didn't know it existed before this "I need to find places to walk and jog since otherwise I will turn into more of a rotund person". However, I've explored a lot of places that are within a radius of 5 miles of my dwelling in the latests 6 weeks.
And there are these strange things like a congregation of Canada geese. Next by a road. Very little grass. And also, by another time when I went by, where there little alone cat used to hide.
Not sure what this means? Do someone feed the cat AND the Canada geese? Are the Canada geese going to eat the cat? (I don't think the cat can take on 5 Canada geese but sure, we could postulate I guess.)
Anyway, if anyone wants to leave a comment or email - feel free. I have a bunch of half made posts but I am trying to write them so that they are good (at least half decent) and not just venting based on the current situation in life and the world.
Here's a picture of the Canada geese. And yes, they are judging you. For sure! (the fifth one is one the street next to me on the left, outside of photo.)
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.
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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