COVID-19 Thoughts of a Scientist

Me: I have a Ph.D. in evolutionary genetics and am currently a professor in Microbiology & Statistics at the University of Manitoba. I’m not an epidemiologist or a virologist, but a lot of what a graduate degree in science teaches you is how to read, evaluate, and synthesize information. Here’s a round-up of my thoughts (with some links), posted approximately weekly.

Sunday, March 22

So here we are. I’ve been seeing a few things that made me think it was time for another (long) update from team microbiology, to try and speak to some of the misinformation I keep seeing passed around.

Anyone reading this has probably already had the critical need for social distancing beaten into their heads? It’s actually now been rebranded as physical distancing with social connection. Just because I have to, I’ll shout it one more time — you’re not doing it right if you’re not sitting at home (or alone in the woods or something — in which case, get off facebook!). A lot of official guidelines say no crowds of more than 50 and to maintain a 6 feet distance. I don’t know about everyone else, but I basically feel anxious anytime I’m in public anymore. So just stay home. And keep working on your boomer parents or your weird cousin. We have to do this right now, we just have to. FYI, Zoom (and apparently also HouseParty) is the best game in town for video conferencing and they’ve dropped some of the restrictions they previously had for free accounts.

What’s up with the testing? Why are there not test kits? The answer depends a bit on whether you’re talking about the US or another country, but the underlying idea is the same and some of the issues are the same. The current test is called a qPCR test, which is a really standard test in molecular biology to look for a particular bit of focal DNA or RNA sequence. Here are the basic steps for identification of SARS-CoV-2 (the bug that causes COVID-19; I may be missing a couple but this will give you a sense of the steps involved): nasopharyngeal swabs (swabs that go through the nostril) are used to collect the specimen. They’re put straight into something called “Universal Transport Medium”. That’s the part the clinician does. That sample (or multiple samples) then gets passed off to a clinical lab that has very specific regulations and criteria, so even though a lot of basic university research labs can physically do the work, they aren’t certified or trained for clinical work. Once in the lab, the genomic material (RNA) is extracted and then run through a specific kit (this is the part of science that involves transferring small volumes of liquid from one tube to another). Then the actual qPCR test is done. That test involves something called primers (sometimes called reagents in the media) that are short pieces of sequence that bind specifically to SARS-CoV-2, and not, say Influenza.

So where are the backlogs and why are tests being rationed? Well for step one, we seem to be globally running out of swabs and transfer medium. For step two, the WHO has a set of primers that work and are being used globally. For some unknown reason, the CDC in the US decided to develop their own primers. Those primers didn’t work properly because they produced a lot of false positives. That’s one backlog. At this point though a lot of places seem to also be running low on the kits that the clinical labs have been using for the early steps (to extract RNA), and also on personnel to staff the clinical labs. Science is moving **really** quickly in this area though and there is some reason for optimism. Some research is showing that the RNA extraction step (that uses the kit) might actually not be that necessary. It seems like some places are also rapidly certifying people to work in the clinical labs, which will help get tests through faster if physical labour is the issue. There have also been a few groups that seem to have created an altogether different type of test, that would be much faster and easy to do (the FDA just approved one). So hopefully, hopefully we’ll soon all be able to test more people because the ability to test is directly related to the ability to track infections and identify who might be infected. To be honest though, at this point I’m staying at home until “after”. So let’s focus on that.

About food. A plea has been made for everyone to restrict grocery shopping to once a week, either using a pickup service or going at an off-time (early morning, late at night). Some friends in various places are reporting that the Asian markets are much less crowded and better stocked than regular grocery stores. It’s also okay to use food delivery, and your small local restaurants will probably be appreciative of the business. Eating is not a majorly risky activity for COVID-19, it needs a route to your lungs (i.e., mouth, nose, eyes) and there has been no evidence that it spreads through food or food packaging. https://www.seriouseats.com/…/food-safety-and-coronavirus-a…

Spread on surfaces is definitely one thing that I’ve been worried about, e.g, how scared should I be of touching pizza boxes or food that was packed for me in the grocery store? From what I can tell we don’t really know. There have been studies that showed how long the virus will stay viable on different surfaces (that I posted before, scarily up to 3 days on things like steel, 1 day on cardboard etc.), but it’s not thought that this is a major way the virus spreads. A recent correspondence published in Lancet Infectious Disease from 76 patients in China showed that the mean viral load of severe cases was around 60 times higher than that of mild cases, suggesting that higher viral loads might be associated with severe clinical outcomes. At least, for now, I will interpret this as the risk of having a serious infection is likely much lower if you acquire it from a surface compared to, say, being sneezed or coughed on from someone that has COVID-19. If you have antibacterial wipes or some type of disinfectant it definitely doesn’t hurt to wipe things down as much as you can (if you’re using bleach remember that you have to mix up a fresh water:bleach solution every day or two), and to of course wash your hands after touching things that come into your house from outside. The negative mental health aspects of being suspect of every single thing are also real, though, and that bears taking into account.

re: Ibuprofen. The WHO “doesn’t recommend avoiding ibuprofen for COVID-19 symptoms.” Double negative yikes. If anyone remembers back to statistics 101, this is the same as “failing to reject the null hypothesis”. The anti-ibuprofen thing comes from the opinions of one doctor from France. Based on what I’ve seen, if I get a headache that might be a symptom of COVID-19 I’ll still take ibuprofen because that’s what usually works for me for headaches and there’s no good data that suggests I should do differently.

Another piece of crap science was published by French scientists this week and repeated by he who shall not be named. There was a paper published that suggests the drugs hydroxychloroquine and azithromycin can be used to treat COVID-19. This paper has a very, very small sample size of patients and the analysis done was pretty shoddy. It shouldn’t have made it through peer review. That doesn’t mean these drugs couldn’t be beneficial, but it does mean we don’t have good evidence that they are either. I can direct you to many commentaries of this if you’re interested in the nitty-gritty of this. People who need these drugs for their actual illnesses (e.g., lupus) are now reporting they can’t get them. Big sigh. I expect these types of miracle cures will continue to pop up. There is excellent work being done including a proper clinical trial out of the University of Minnesota. These things take time, but lots of people are working on it.

There are starting to be a number of ‘it’s not all that bad’ or ‘this will all resolve itself without taking drastic measures’ articles. Some by people with a lot of followers. Some that have a thin veneer of science-speak but underlying half-truths. I’m sorry to say this, friends, but talk to an epidemiologist or virologist or emergency room physician and they’re all bracing for war. We’re in this. It’s not going to magically disappear. There are no dolphins or swans in the canals in Venice or drunk elephants in rice fields. The water in the Venice canals is clearer though! And the air pollution over China has drastically been reduced! People are hearing birds singing where they haven’t been able to before because of the reduction of human noise. I don’t think our world will be the same “after”, and that’s okay. I have lots and lots of opinions about how we can build society back up to a place that works for the many and not the few. That’s not my domain expertise, though I look forward to organizing for a better world, and hope that this time we may be heard.

If you do have a decent stock of N95 masks, now is probably a good time to see if anyone is locally organizing a collection. If not, start one and then contact a local clinic or hospital. Canadian academics, we started a lab PPE inventory here: bit.ly/33y1gAQ, testing reagents are being inventoried by PHAC (message me if you need details). American academic friends, there’s a testing reagent inventory here: https://docs.google.com/…/1FAIpQLSc65mtobuntqco5Me…/viewform and lots of people are locally organizing PPE for donation.

Be well, friends. This is going to be a marathon, not a sprint.

March 15, 2020

March 13, 2020

March 8th feels like a year ago. A lot has happened quickly. A few people have told me they’re finding these posts helpful, so I thought I’d share some updated thoughts.

It just comes down to health care capacity. One of the primary factors that affects the mortality rate of COVID-19 is the availability of ventilators/intensive-care beds. Spoiler alert: we don’t have anywhere near the required capacity if the outbreaks take off. This is where “flatten the curve of infections” is critical. So.

#1: It is time now to be social distancing, and encouraging everyone you know to do the same. Some of the official people are banning crowds > 250 or > 50. My number is somewhere around 5–6. And that’s 5–6 people that are also taking social distancing seriously. My university has cancelled in-person classes until the end of the semester. All of the conferences I was suppose to go to this summer are cancelled. I decided to pull my kid out of daycare starting today even though they’re still open. So what does that actually look like? It depends on who you ask, I liked this article: https://bit.ly/2xuHdXY

#2: Grocery stores are selling out of toilet paper and hand sanitizer is long gone. Ok. Soap works better anyways (cool biology here: https://bit.ly/39PK3Fp). A disinfectant would be good for surfaces (the virus can actually live for quite a while: up to 3 hours post aerosolization, up to 4 hours on copper, up to 24 hours on cardboard and up to 2–3 days on plastic and stainless steel). It seems totally okay (and actually preferable) to me to still get and cook fresh food. The toilet paper thing is … weird (this is not a thing that generally affects the GI tract!). I feel bad for the people that are terrified and it’s the only tangible thing they can think of to do.

#3: While everyone else is fighting at the grocery store, I’ve been calmly going to my local pharmacy and stocking up on the things that I hope will help alleviate symptoms. Here’s the prevalence of symptoms, from a WHO report:

• Fever: 88%
• *Dry cough: 68%
• Fatigue: 38%
• Coughing up sputum, or thick phlegm, from the lungs: 33%
• *Shortness of breath: 19%
• Bone or joint pain: 15%
• Sore throat: 14%
• Headache: 14%
• Chills: 11%
• Nausea or vomiting: 5%
• Stuffy nose: 5%
• Diarrhea: 4%
• Coughing up blood: 1%
• Swollen eyes: 1%

(* these are the three bullet points on the public health sites, so presumably most/all cases have at least one of these symptoms? — but note that in some cases fever is absent). I’m not a medical doctor or a nurse, so please someone out there correct what I’m about to say if there’s something better or missing! But I bought ibuprofen, acetaminophen, cough suppressant and vicks/halls. I also bought some soda and sparkling water. EDIT2: In a previous post I mentioned that I already bought a thermometer. And I’ve also been buying one bag of coffee each time I go to a grocery store. A lot of people who don’t routinely make their own coffee are soon going to be at home, many with small humans!

#4: Extrapolating from Canadian numbers, a lot of other illnesses are causing people to be worried they have COVID-19. As of a couple of days ago we had tested ~11000 people and only ~100 were positive (we’re at 152 now, which I’m actually thinking is okay, since that’s very much still in the linear rather than exponential/log growth). Flu is still a thing. If there are still flu shots available in your region (I’m told there aren’t in some places) it’s still recommended that you try and get one if you haven’t yet.

#5 There is an average incubation period of 5 days on average (doi:10.1016/s1473–3099(20)30144–4). I had previously thought that asymptomatic spread was uncommon, but there has been at least one published case. Data also show the viral load detected in an asymptomatic person can be similar to a symptomatic person. Hence the importance of social distancing. I really like the attached figure that plots the likelihood of someone having the virus by the number of people at an event

In my opinion, the best way not to get this thing is to generally #staythefuckathome

I know this is advice that has wildly different degrees of difficulty and hardship for different people. Our society sucks. We’re missing a lot of the social nets that should be in place. It’s breaking my heart and keeping me up at night. I’m going to start donating more money to my local foodbanks. And investigating other programs that get food to children, and house at-risk individuals. I’m happy to hear of other suggestions. I wish I had a good answer for people with precarious employment or those who are going to miss important paycheques. All I can suggest is to reach out to those around you and ask for help. We are all in this together. Truly.

I’ve been seeing other friends post some good things we can do while we’re isolated. Go to a virtual museum! https://bit.ly/2TPjcUs. Google doc list for kids activities: https://bit.ly/2w4Qm9p. Anyone have other ideas? Throw ’em in the comments.

Stay healthy, friends.

EDIT3 (20/03/14): for those who don’t know me, I have a PhD in Microbiology & evolutionary genetics. I teach microbiology and statistics. I’m not a medical doctor but I read a lot and have been training for a long time to evaluate the scientific literature. These are just my thoughts and opinions. We’re in “probability math” land. Nothing is certain. I’m very very concerned that the average person is not taking this seriously enough. This is not a drill. Talk to your friends and parents. Stay the fuck at home. When you go out be judicious about washing you hands and avoiding touching your face. Check your local Asian markets for supplies. We’ll get through this together. Be well.

March 11, 2020

March 8, 2020

Reminder that the AMA on my wall (or DMs) remains open to anyone with questions about COVID-19 (novel coronavirus). I have advanced training in microbiology and evolutionary genetics. I’m not an infectious disease physician. I have spoken directly with experts in global health preparedness and pandemics and the message from them is that it’s not too early to take reasonable action for ourselves and our loved ones. What that means to you depends on where you live and who you interact with on a daily basis.

If it’s of interest, here’s what I’m personally doing in my own life in Winnipeg, Canada (0 confirmed cases):

- If I or anyone in my family has symptoms of a respiratory infection (fever, cough) we will all self-quarantine immediately and contact health officials (Government of Canada coronavirus info line: 1–833–784–4397)

- I am way better at washing my hands properly and not touching my face than I was 2 weeks ago

- I started carrying hand sanitizer and try to remember to use it when I’m out and about away from soap and water

- I went to the drug store and got an extra ventolin inhaler (I have super mild asthma typically and rarely use an inhaler). I also bought extra ibuprofen, including for my kid, and extra vicks cough drops. I encouraged my parents to similarly get an extra supply of the medications they may need for 2–4 weeks. I have a digital thermometer at home, if I didn’t I would buy one.

- The last two times I went to the grocery store I bought a couple of extra things that I don’t typically buy (a couple of frozen pizzas, extra cheese and crackers, some chocolate bars, gatorade powder, jello, extra large bag of carrots). I’m fortunate to live in Winnipeg and participated in a grain CSA so have enough lentils, beans, oats and flour to last for 12 months … if I didn’t have those things I probably would have made a point to buy some. I also already had a stock of rice and pasta and pasta sauce on hand. I also married a hunter, and we have a freezer full of meat.

- I went to my fave used kids store and bought a couple ‘just in case’ puzzles and games to stash in case daycare gets closed. Same with art supplies.

- I’m working with other academics in North America to petition our universities to prepare to move classes online and be community leaders. That means training faculty to use new software and possibly purchasing specialized electronic equipment (e.g., I probably need an iPad for the document camera I use). It’s been crickets from my university so far (except with respect to travel to/from China) and I’m really disappointed about that.

It is not time to panic but I also don’t think it’s time to do nothing. The time from first infection to significant social impact (closing businesses and schools) has been 1–2 weeks in multiple places. There is an interactive map of cases available here: https://www.arcgis.com/apps/opsdashboard/index.html#/bda7594740fd40299423467b48e9ecf6

The yellow curve (infections outside of China) is in exponential growth, that means the number of cases doubles very, very rapidly.

There is a ton of information available from the daily briefings of the WHO Director General, published daily here: https://www.who.int/dg/speeches/detail

From the past week:

This is not a drill.

This is a time for pulling out all the stops.

If countries act aggressively to find, isolate and treat cases, and to trace every contact, they can change the trajectory of this epidemic.

Slowing down the epidemic saves lives, and it buys time for preparedness and for research and development.

Every day we can slow down the epidemic is another day hospitals can prepare themselves for cases.

Every day we slow down the epidemic is another day governments can prepare their health workers to detect, test, treat and care for patients.

Every day we slow down the epidemic is another day closer to having vaccines and therapeutics, which can in turn prevent infections and save lives.

There have been a lot of questions about how this compares to influenza, which kills many, many people a year, but we don’t seem to talk about it. We should (and gosh darn it, get the flu vaccine every year).

Here’s what the WHO has to say (summary from the March 3rd briefing, more details if you read the whole thing): COVID-19 spreads less efficiently than flu, transmission does not appear to be driven by people who are not sick, it causes more severe illness than flu, there are not yet any vaccines or therapeutics, and it can be contained — which is why we must do everything we can to contain it. That’s why WHO recommends a comprehensive approach.

As a healthy person I am not particularly concerned for my own mortality, should I be infected. I remain much more likely to die while driving in my car. But the mortality rate for older adults (>60 and especially >80) and those with underlying health issues (heart disease, diabetes) is much higher. To me, a society is only as successful as its ability to protect the most vulnerable. We can all work, now, to flatten the curve of the infection rate.

Government of Canada website with **tons** of information: https://www.canada.ca/en/public-health/services/diseases/2019-novel-coronavirus-infection.html

“Everything we do before a pandemic will seem alarmist. Everything we do after a pandemic will seem inadequate. This is the dilemma we face, but it should not stop us from doing what we can to prepare.” — Michael O. Leavitt, 2007 [Leavitt is a former Secretary of the US Department of Health and Human Services.]