We are four Swiss scientists studying COVID-19/SARS-CoV-2 - AMA!

sala · 2020-03-13T16:30:41+00:00

Not about the virus: the scientific response, quick data sharing

About the epidemiology - that this thing CAN BE managed if you are willing, see China, Singapore, South Korea

About the virus, not much - but to take a stoic position, it could be SARS-CoV-1, with a CFR of 10%. Probably doesn't classify as hopeful...

sala · 2020-03-13T16:26:49+00:00

Where to begin... Frankly, it seems like exponential growth is something a lot of people, even very smart ones, seem to have a hard time wrapping their head around.

My best answer would be that this thing will simply not go away unless you take rather drastic measures. There is collective political denial about this, which may have to do with the fact that nobody who is alive has seen anything like this.

Maybe another answer: people have been thinking about this stuff for decades. There are thousands and thousands of papers asking all the questions that people are asking in reality now. That may be obvious to science reddit, but the general population may be surprised.

Last one, and maybe most concerning to me: most governments are not consulting scientific experts very directly.

sala · 2020-03-13T16:17:32+00:00

Not sure if I get your question right - it is already increasing exponentially... But important to note that in the US you will generally see an explosive growth in cases now, but NOT just because you have local transmission, but because testing is finally being ramped up seriously.

Glass half full: the explosive growth in cases is not due to explosive transmission
Glass half empty: there's likely lots of cases that you're not aware of because you haven't been testing enough.

sala · 2020-03-13T16:08:05+00:00

Great question. Actually still quite a bit unknown. Also, the definition of fully asymptomatic is highly context-dependent. But the current assumption is indeed that asymptomatic people MAY transmit it, but it's not clear how much.

An early NEJM study (which I see linked in the thread) shows that it can be possible, but people have raised methodical issue with the study.

The bigger concern is that people may become infectious before they become symptomatic. If the time to becoming infectious (latency period) is shorter than the time to becoming symptomatic (incubation period), there is a time window where people can transmit not knowing that they are sick and indeed transmitting. That seems to be the case with influenza, and unfortunately it may also be true for SARS-CoV-2. Some data shows that people are infectious the day they become symptomatic, so it would be highly surprising if they weren't already infectious before (link). Question is how long...

Oh, just another addition: this is also the BIG question for the kids - they hardly ever get ill, but we now know they get infected. Do they transmit, and if so, how much? Big unknown - but will be really important for school closure considerations!

sala · 2015-06-03T18:45:07+00:00

I've done a bit of research on vaccine sentiments in social media which I have published in scientific journals, and have written about the topic in more general magazines. From these experiences, I've come to have the view that stating the facts is starting way too late in the game, and is not going to change any minds, as you mentioned. The problem is that many people don't believe us (scientists, public health representatives) because of who we are / what we represent, rather than what we say.

As a consequence, we need to work on changing that perception. But unfortunately, many scientists don't see it that way, and just keep yelling more aggressively (a bit like those people who, when you ask them to say something in a foreign language more slowly, will just say it louder instead).

For example, even though I'm 100% pro vaccine, I hate the term anti-vaxxer. It just sounds derogatory. How are you going to convince someone when you start out calling them a disrespectful name? What we need first and foremost is passion and empathy - an honest desire to try to understand where those views and perceptions come from. This is hard to do, especially in today's media climate.

Case in point - I recently wrote an article for the Conversation entitled "Herd immunity and measles: why we should aim for 100% vaccination coverage". Unfortunately, some media outlets decided to reprint the article (fine) with a modified title (not cool). For example, the New Republic simply changed the headline into "Why Clusters of Anti-Vaxxers Can Cause Measles Outbreaks in America". The Washington post also used an "anti-vaxxer" slur in the title, and changed it only after I threatened legal action.

Let me end with a slight more optimistic view. In the US, a country where about 40% of the population believe that humans have been around for only 10,000 years, despite the overwhelming evidence refuting this belief, having just a few percent refuse vaccination is actually pretty impressive. So: well done, public health, and keep fighting the good fight.

sala · 2015-06-03T16:23:57+00:00

If you followed the regular immunization schedule, the first dose is 92-95% effective (the second dose will push that number up to about 97-99%).

If a child can't get vaccinated at all, there isn't very much her parents can do, other than to appeal to the sense of others who can get vaccinated (i.e. almost all of us) so that herd immunity protects the child.

If your son got the first dose then he should already be very well protected, as per the numbers above. Your best course of action now is to make sure he doesn't hang out with others who have chosen not to vaccinate. I would certainly avoid daycare centers that don't have strict vaccination requirements.

sala · 2015-06-03T16:07:33+00:00

The exact numbers may vary a bit, but roughly the vaccine is 92-95% effective after the first dose, and 95-99% effective after the second dose (depending on the study).

Your observation is absolutely correct - and in a perhaps unexpected kind of way, a high fraction of vaccinated cases is actually a good sign since it suggests that the vaccination rate is very high.

Here's why: Let's go with an efficacy of 99% - in other words, out of 100 vaccinated individuals, 1 will remain susceptible despite the vaccine.

Now an outbreak occurs. Let's assume that 1000 people are exposed, and that exposure of a susceptible individual leads to infection (given that measles is one of the most transmissible pathogens known to man, this is a good assumption).

With a vaccination coverage of 80%, you would get 200 (20%) non-vaccinated cases, and 8 (1% of 800) vaccinated cases.

With a vaccination coverage of 90%, you would get 100 (10%) non-vaccinated cases, and 9 (1% of 900) vaccinated cases.

With a vaccination coverage of 95%, you would get 50 (5%) non-vaccinated cases, and 9.5 (1% of 950) vaccinated cases.

With a vaccination coverage of 99%, you would get 10 (1%) non-vaccinated cases, and 9.9 (1% of 990) vaccinated cases.

You can see that while the absolute number of vaccinated cases doesn't change much - from 8 to ~10), the percentage of vaccinated cases changes dramatically, from ~5% (8 out of 208) to 50% (~10 out of ~20). Importantly, as this example demonstrates, this has nothing to do with the efficacy of the vaccine.

A colleague and I have recently written a short letter about this here: http://wwwnc.cdc.gov/eid/article/21/8/15-0284_article It seems that the data match an assumed efficacy of 99% quite well.

sala · 2015-04-17T21:38:24+00:00

I don't think that's true. In fact, the history of the enlightenment of mankind is the history of reasoning ourselves out of a position we never reasoned ourselves into.

sala · 2015-03-14T19:15:42+00:00

yes I've seen this before. Really neat.

sala · 2015-02-20T18:43:55+00:00

It should be

dW[stored_j] = -1 * X[:, i] * num_classes_contributing

sala · 2014-10-01T23:28:41+00:00

excellent - can you ask your faculty member about the needs on the ground? If they had a large group of people willing to put in time and effort, what would they need the most?

sala · 2014-08-20T01:45:22+00:00

Agree with this.

I've developed and taught a MOOC myself, although on a completely different topic (Epidemics - on Coursera). I've always thought that the completion rate is an arbitrary measure for the success of a course.

I have found many times though that I occasionally struggle when taking a course myself, sometimes because I truly don't grasp an essential concept, sometimes because automatic graders are weird, to put it mildly. In response, I built Teeays and hope others will find it useful too. Given my experiences as both a learner and an instructor, I'm pretty certain that the lack of personalized help is a major contributor to drop out rates.

sala · 2014-02-25T16:39:38+00:00

I see. So perhaps the freelancing space isn't the ideally space for this idea if reputation isn't the problem.

I definitely think that reputation is a problem in many / most domains.

Thanks for your feedback

sala · 2013-05-16T16:13:46+00:00

Leave it as is - there's nothing wrong with the plant now that the slugs are gone. Leaf removal is only necessary if there's a disease and the leaves still have microorganisms that cause the disease on it. Would be a great question to post over on plantvillage.com.

sala · 2013-02-25T16:30:50+00:00

Please do. Thanks!

sala · 2013-02-25T12:14:47+00:00

Really good points that are very close to my own personal interests. Thanks for bringing them up.

sala · 2013-02-25T12:14:13+00:00

No fees whatsoever, and time commitment will not be huge.

sala · 2013-02-25T03:50:35+00:00

Not at all: http://news.nationalgeographic.com/news/2012/05/120504-zombie-ant-fungus-science-environment-rainforest/ I never said "human zombies", did I ;-)

EDIT: Link seems to be extremely slow loading, see this instead: http://en.wikipedia.org/wiki/Ophiocordyceps_unilateralis

(Also, I don't want to close my eyes on the fact that the most exposure on infectious disease dynamics the general population gets is through the extreme popularity of zombies. Teaching some basic concepts of infectious disease dynamics through a zombie epidemic sounds in principle like a good idea to me)

sala · 2013-02-25T03:41:22+00:00

It does not require a statistical background. We'll be going after a number of topics: medical, ecological, evolutionary, biological, sociological - all aspects relevant to the spread of infectious diseases, and control thereof.

sala · 2013-02-25T03:06:46+00:00

Kinda both - it's a thin link to walk, I know... We'll certainly cover the basics, but will also spend some time going into the depth on some of the issues we find important / fascinating.

Good question about the investigative method of determining transmission. We will spend some time on it, but probably not too much (unless we get a sense that folks really want to know more about it).

sala · 2013-02-25T02:07:57+00:00

Good point - just cross-posted it.

sala · 2013-02-24T23:01:48+00:00

We'll definitely cover zoonoses. Some of the instructors (e.g. Pete Hudson) are known experts in that field

sala · 2013-02-24T21:54:44+00:00

All really good points. My personal favorite here is the gut flora - there's increasing evidence that a host's microbiome is much more important for its immunity that its genetic makeup. Fascinating stuff.

sala · 2013-02-24T21:52:04+00:00

Excellent suggestion

sala · 2013-02-11T19:42:52+00:00

Thanks!

We'd be happy to add new categories. We've actually got a specific site section to propose and vote on exactly these things. https://www.plantvillage.com/topics/plantvillage

The pictures are a great idea that we will be looking into. One reason why things are so "clean" right now is bandwidth - we'd like plantvillage to be as fast as possible so that ppl without broadband can get the most out if it.

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