Tag Archives: coronavirus

We Interrupt This Experiment

Today I made the decision to close the lab and temporarily suspend our experiments, including the LTEE, in light of the expanding SARS-CoV-2 outbreak.

I started to say it was a difficult decision, but really it was not all that difficult.  Several considerations led me to this decision.

1/ The SARS-CoV-2 outbreak appears to be taking off in many countries, including the USA, despite the substantial containment that has been orchestrated in Wuhan and elsewhere in China.

2/ The absence of evidence of any local cases is not as comforting as it might be, given the near-absence of testing here and in most of the USA.

3/ MSU students just returned from spring break today.  Some of the superb undergrads who work in my lab went to places that have confirmed cases. None of the places they went are among the locations with intense outbreaks, but the confirmed cases in at least one location have grown noticeably in the past week. They also flew on planes to and from their vacations.

4/ As a team, we’re connected not only to one another, but also to people who are health-care workers and others with increased vulnerabilities to infections. (Not to mention that I’m over 60 …) When you think about it, pretty much everyone has those connections.

5/ We’re very lucky because our work is easy to stop and re-start. Our study organisms can be frozen away and revived whenever we see fit.  In the meantime, everyone has classes to take, papers to read and write, data to analyze, etc.  And a little extra time, hopefully, to reflect on and maintain the health and well-being of our friends, families, and selves.  So, we will all be busy, but doing things a bit differently than we had planned.

6/ As we freeze away the long-term lines, the lab notebook will record:  “On this day, the LTEE was temporarily halted and frozen down for the coronavirus pandemic of 2020.”

Hopefully, some future historian of science will look back on today’s entry and say: “What the hell was that all about?”

Freezing LTEE for SARS

[Devin Lake putting the LTEE populations into the ultra-low freezer, where they will stay until they are called back into action … evolution in action.]


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More Words of Wisdom

I assume everyone is familiar with the concept of “going viral” and that you’re paying attention to the SARS-Cov-2 outbreak.  So you understand the importance of social distancing.  When it comes to conferences, they’re not quite what you’d call social distancing, are they?

Well then, Harvard’s Michael Baym puts 2 + 2 together in the way that physicists-turned-biologists seem able to to do with ease and elegance:

“The reason to cancel meetings and seminar visits is the same reason we have them in the first place: by establishing long-distance connections and high-connectivity nodes, we help ideas spread much faster through our social networks. It’s the same for a virus.”

Please see this post for more words of wisdom about pandemics. For suggestions to fellow scientists and lab teams on how to deal with this coronavirus outbreak, here are my thoughts.


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Global Dynamics of Coronavirus Spread

Almost a month ago, in my post on expert analysis, I highlighted a model by Richard Neher that looked at the possible global spread of SARS-CoV-2 infections based on numerous seeding events. At that time, many observers were reporting the good news that the rate of increase in the number of infections in Hubei province was declining.

That declining rate of increase was expected given the extreme quarantine measures taken in Wuhan and other cities. However, it was also clear that smaller outbreaks were being seeded elsewhere.

Neher ran simulations to get a handle on this scenario, using his educated guesses for the relevant parameters. He assumed then that many such outbreaks were already underway, and that they were running 2 or 3 months behind the Wuhan outbreak. With increased awareness among the public and health-care workers, he assumed that many of the new outbreaks would grow more slowly than Wuhan’s did and be contained. (As seems to have happened in Singapore.) And even those that grow large would, like Wuhan, slow down once they had become very large due to quarantines and other social distancing. (As seems to be be happening in South Korea.) Nevertheless, Neher found it was possible to envision total global cases in several months that would dwarf those seen in Hubei, even while it looked then as though the rate of increase was declining. I’ve re-posted a screen shot of Neher’s scenario below.

Nerer global scenario 09-Feb-2020

Here, for comparison, is a screenshot of a new graphic produced by CNBC using data from Johns Hopkins University. It’s still too early to say how the numbers will play out over time. Even right now, the total number of infections globally is very uncertain, with many countries (including the USA) lagging in testing for the virus. But qualitatively, at least, Neher’s model prediction is–unfortunately–looking all too real. 

ADDED:  As Richard Neher adds: “I want to point out that the simulations we did 4 weeks ago assumed limited infection control measures and essentially model unchecked growth. China has shown that drastic measures can change the course of a COVID-19 epidemic.”

Coronavirus in and out of China


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The Lenski Lab Health Plan for the New Coronavirus Outbreak

The future is unknown, as it always is.  We do know that the SARS-CoV-2 virus is spreading around the globe, but we don’t know how many people will be infected.  Some experts are predicting that something like half of the adult population will be infected, although not all at the same time.  We also know that many cases are relatively mild (like a cold or the usual flu), and some infections may be asymptomatic. However, we also know that some other cases—perhaps 20% or so—are very serious, and some of those are life-threatening.

See MSU’s coronavirus page for University policy, information, and advice.

What can we do, as individuals and a lab group, to protect ourselves, our families, each other, our communities, and our research?  Here are my current thoughts, with an emphasis on activities related to our laboratory and our academic setting.

1/ If you haven’t done so already, get your flu shot. It won’t protect against the coronavirus, and it doesn’t provide perfect protection against the influenza virus, but it will reduce the chance of getting the flu (and save health-care resources for others in need).

2/ Make sure you and your household are prepared for a period of self-isolation or quarantine lasting 2 weeks, or perhaps longer.  This means stocking up on food staples and, importantly, any medicines that you and your household need.  For medicines, I suggest having at least a full month’s supply, maybe longer, in case there are disruptions to availability.  Talk to your doctor about extending prescriptions or any other special needs you might have.

3/ If you develop symptoms of a cold or flu—even mild symptoms—please stay at home and don’t come into the office or the lab.  We don’t want you to spread the infection.  Just email the group list to let us know what’s up, and work from home on your writing and reading if you feel up to it. You won’t impress me, or anyone, by trying to work while you’re sick.

4/ If a member of your household becomes ill, see and follow point 3 above.

5/ Let’s all start practicing more restrained physical interactions, and thus set good examples not only among ourselves but also for our colleagues and friends. That means skipping hugs and handshakes, for the time being.  Instead, you might put your own hands together and bow your head slightly to greet or congratulate someone. Or maybe an elbow bump, if you really must make contact.  Foot bumps are apparently another new thing, too.

6/ Be prepared to stop your lab work on short notice.  In the meantime, I guess March might be a good time to get a week-long or two-week experiment done, before the epidemic grows too large (if it does).  However, I suggest holding off, for the time being, on any plan to start a large and/or long experiment.

7/ Speaking of long experiments, you will recall that we have a certain long-term experiment in our lab.  The LTEE will soon hit 73,500 generations, at which time the samples will be frozen as usual.  After that date, I’d like population samples to be frozen more often, say, every 2 or 3 weeks.  Just freeze away a copy of each population (no need to plate cells)—basically, so we have samples to restart in the event that people get sick, or if the university should at some point curtail certain activities for a while.

8/ Be prepared to cancel your attendance at scientific conferences and other academic or social events as new information arises. Even if an event organizer decides to push ahead, you don’t have to go if you feel it is risky for you personally. As an aside, I recommend delaying purchases of airfares until an event is closer in time, given the current uncertainty.  (Refundable tickets on most airlines are very expensive, and other tickets have restrictions.)  Hotel reservations can usually be cancelled on shorter notice (a day or week, check to be sure), but not if they were booked through a discounter.

9/ And maybe the hardest advice of all is to practice good personal hygiene. Cover your mouth with your forearm or the inside of your elbow when you cough or sneeze unexpectedly.  (If you know you’re sick, then you should have disposable tissues handy. Use those to cover your nose and mouth completely, and dispose of a tissue after one use.) If you find yourself coughing or sneezing repeatedly, see point 3 above. Wash your hands thoroughly [Click that link, with the sound on, and stay for the end!] after you’ve touched shared surfaces, especially before eating. And most difficult of all, avoid touching your own face.  This coronavirus can survive for hours as tiny droplets on surfaces, which we may inadvertently touch (“fomite transmission”). Then, when we touch our mouth, nose, or eyes, we can infect ourselves.

10/ ADDED: Follow the news, and get your news from trustworthy, reliable sources. If it becomes clear that infections are spreading locally, or even if you are just concerned about that possibility, then avoid crowded public venues. (But this does not mean that you should follow the news obsessively, as that can be exhausting. h/t Carl Bergstrom.)

11/ ADDED: If you do isolate yourself, whether because of illness or concern, make sure to maintain frequent social contact with your family, friends, and the lab via phone, email, or whatever works best for you. Don’t let physical isolation and loneliness make you feel miserable. We are all stronger together, even if we might have to be physically apart.

12/ ADDED: Please read these Words of Wisdom, regarding preparedness for infectious disease outbreaks, from Michael Leavitt, a former Secretary of Health and Human Services.

13/ ADDED:  This one is for those of you in science or other relevant scholarly fields.  Do you have data in your lab notebooks and/or on computers accessible only in the lab?  Are the datasets ones that you might need for your analyses and writing if, say, you end up confined at home for a few weeks?  If so, I recommend that you copy it (but only if it’s allowed in the case of certain types of sensitive data!) by scanning it and/or copying it to your personal computer. That way, you can use it while working from home if you decide, or are required, to do so.

Take care everyone.  Please let me know of any errors, omissions, and practical suggestions.





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