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Coronavirus’s Genetics Hint at its Cryptic Spread in Communities

Accepted submission by exec at 2020-03-07 03:57:46

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FeedSource: [TheScientist]

Time: 2020-03-06 22:21:43 UTC

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Title: Coronavirus’s Genetics Hint at its Cryptic Spread in Communities

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Coronavirus’s Genetics Hint at its Cryptic Spread in Communities

Arthur T Knackerbracket has found the following story []:

ABOVE: Scanning electron microscope image of SARS-CoV-2 (yellow) emerging from the surface of human cells (pink) cultured in the lab. WIKIMEDIA, NIAID ROCKY MOUNTAIN LABORATORIES (RML), US NIH []

Hodcroft decided to generate an infographic showing the connections between the traveler from Singapore and the other coronavirus cases emerging in Europe. “I thought, I’ll make an image and see if anyone else finds this useful,” she says. She posted the image on Twitter, and “somewhat unexpectedly, it got a lot of attention,” she says. “People were definitely really, really interested in this. So I kept that image updated over the next week or so.” As she updated it, the graphic showed that at least 21 people were exposed to the virus at the ski resort the traveler from Singapore visited; 13 of those people ended up developing COVID-19, the disease caused by the virus. After she’d finished the preliminary work, a colleague of Hodcroft saw it and suggested she write it up for publication. She posted the paper on February 26; the next day it appeared in Swiss Medical Weekly [].

Hodcroft talked with The Scientist about the work, how its conclusions have been supported by genetic testing of viral strains from patients, and what it tells us about the spread of the virus, SARS-CoV-2, in other countries.

The other thing that’s surprising is that, according to the patient statement that he released, the focal patient never had any symptoms. In his own words, he never felt sick. So he did all of this transmission without ever having any indication that he was unwell or that he should be taking any precautions to modify his behavior. It tells us that some infections might be from people who never even know that they’re sick. 

A few days ago, the research group called the Seattle Flu Study [], which is designed to take community samples from random people who have any kind of cough, runny nose, or cold-like symptoms and look for the flu—they pivoted and started testing some of the samples for coronavirus. They found a case in the Seattle area and sequenced the viral genome of the infected person [posted on NextStrain] and showed it links very closely with another case in the Seattle area that’s from mid-January. And so this strongly suggests (though we don’t yet know for certain) that there has been ongoing undetected transmission in Seattle since mid-January and wasn’t picked up because we weren’t looking for it. This has become clearer in the last few days, as more cases and even deaths have been reported in Washington State. That tells us the virus hasn’t just appeared in the last few days in the area.

When you have a very small number of cases of a disease, you can do this just through epidemiological contact tracing: you can go to everyone and ask questions and find out the connections between the cases. As the case numbers scale up, this becomes very hard to do. With genetic sequencing, we can do this without having to go and try and figure out where everyone was at the time of infection. We’ve had an influx of sequences from Brazil, Switzerland, Mexico, Scotland, Germany. These have clustered with sequences from Italy and have a travel history from Italy and so from that we can show that Italy really is now exporting cases around the world to multiple countries. 

One thing I would note is that studies have shown that limiting transportation really doesn’t make much of an impact for outbreaks. Quarantining particular cities, if they seem to be epicenters, can work as a preventive measure, but as the epidemic scales up, you move past being able to contain it in this sense, [and] what you end up doing is just disrupting supply routes, interrupting business, making all of these things much harder.

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