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midtskogen
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Coronavirus (COVID-19) Thread

25 Apr 2020 12:59

I tried to look for the age distribution for US covid-19 deaths, but could not find any recent data.  Whether that looks similar to Scandinavian corresponding data could indicate how well other data data can be compared.
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Coronavirus (COVID-19) Thread

27 Apr 2020 12:11

midtskogen wrote:
A-L-E-X wrote:
Source of the post Did you see how he mentioned (on Earth Day) how the highest rates of it are in highly polluted areas, where the asthma rates are 3x worse?  Very much on point and exactly why we need tougher regulations.

The correlation may simply be that both pollution and virus spread are correlated with population density.  It means that the regulations need to be local.  There are many places where the toughest regulations will be pointless.

Watsisname wrote:
Source of the post Norway went more heavily toward total societal shutdown, while Sweden leaned towards keeping things open and trying to protect the more vulnerable. How well did it work? Well, their growth curves for cases started out at around the same time and for a while looked fairly similar, with the typical exponential growth that eventually flattens out toward something more linear. But now that more time has gone by we see the differences quite clearly. Norway's rate of new cases has been dropping -- now down to about 100 per day from a peak of about 300 per day around March 27. Sweden however has only just plateaued, at around 500 per day. It appears that Norway's strategy has proved more effective at flattening the curve.

Sweden has played a more dangerous game.  Protecting the vulnerable has not been very successful with many deaths in the >80 years group.  Their other goal, achieving herd immunity without collapsing healthcare, is yet to be judged.  If it turns out that herd immunity is hard to achieve for this virus, then the strategy is a big failure.  That remains to be seen.  The number of new cases in Norway and Sweden, even if you correct for roughly double the population in Sweden, is difficult to compare as the testing is different and many are asymptomatic.  It may well be possible that the cases in Sweden has passed the million mark, whereas in Norway it's just in the tens of thousand range.  In that case deaths in Sweden will drop, whereas Norway will simply slowly catch up with all the pain of strict regulations.  I think we need to look at the death numbers when this is over and all data are in to judge who where right.  Sweden does have a much higher number of deaths per million than Norway, but Norway may simply have postponed the problems.  Currently Norway has 125 people hospitalised with Covid-19, 33 of which getting breathing aid.  Many are above 80 who would not have received this kind of attention for similar symptoms in a normal situation, which raises some ethical questions concerning how elderly are treated.  The capacity is higher, and a lot of other appointments have been postponed to free up resources in case Covid-19 gets really nasty.  This is also bad, and premature deaths due to this are likely not counted.

Schools will partially reopen here on Monday.

EDIT 2020-04-24: Today the first deaths of anyone under 50 years were reported in Norway.   The current breakdown is:
40-49: 2
50-59: 6
60-69: 13
70-79: 44
80-89: 70
90+: 56

The average age is 83.  Life expectancy in Norway is also 83.

But the other correlation is asthma, which has been identified as a pre-existing condition.  In the JAMA study it was found that about 60% of coronavirus deaths were diabetics and 40% were asthmatics.  The areas with the higher level of air pollution (NO2) also had 3x the asthma rate.  This is why they've been talking about the bad diet and air pollution in urban areas, where fresh fruit and vegetables are not easily found in some communities (like the Bronx, which has a really high death rate compared to other areas.)
I agree with you about pop density being a major factor though, it leads to the higher pollution levels also.
 
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Coronavirus (COVID-19) Thread

27 Apr 2020 12:19

Watsisname wrote:
midtskogen wrote:
Source of the post You leave out one important factor: Of all infected a small percentage get seriously ill and their survival highly depends on whether they get good treatment.  That's the whole point of the flatten the curve mantra.  Healthcare in Sweden is very good and hospitals have not been seriously overwhelmed.

The flood on the health care system in NY has been very high. Even now, on the decline of the curve, about 1300 new COVID-19 patients still come in to hospitals statewide every day. But with the expansions of capacity and coordinating patient and equipment movement across all hospitals in the region, they managed to avoid being overwhelmed. Patients who required it have been put on oxygen, and those that continue to decline have been put on ventilators. So I do not think many deaths can be attributed to insufficient care, except for those who died at home, which we have not counted yet. Maybe another explanation is perhaps there is more use of effective antiviral remedies in Sweden than NY? Offhand I don't have good info about that besides this page for NYC hospitals.

How strong could the effect be from the age distribution? Earlier we looked at South Korea and Italy, and found the difference in their population pyramids could account for about a 40% difference in mortality rate. For New York, the data from the antibody study as well as from hospitalizations do not suggest this would be very important. The former is a fairly uniform sampling by age, and it shows that for those interacting in society, the infection rate is also fairly uniform by age (within factor of 2). The latter shows that mortalities by age follow a consistent trend as what we expected.

Comorbidities can certainly be important. In NYC 34% of adults are overweight and 22% are obese. Asthma and diabetes factor in, too. I think that will surely change the calculus, but... will it change it by a factor of more than 2? That would really surprise me.

And of course the biggest caveat is this: These are preliminary data. The study is ongoing, so the data could change. Still, it's a sample size of 3000, which is a lot of data already and I think we can draw useful conclusions from them.

Anecdotally I have heard people in the US speculate that the true number of infected is so much higher than the reported cases that if we had all the numbers it'd turn out that this was no worse than a typical flu, or that some places have already hit or are very close to herd immunity, which if true would change the discussion about responses and reopenings. But these data do not show that to be true. The number of infections is higher, but not that much higher. I suspect that will be the case for most other countries so far, as well. I hope we can find out for sure by having similar antibody studies conducted elsewhere. The nice thing is it could soon be possible to do that in a more widespread manner -- we don't need to wait for the pandemic to play out to get those facts.

We dont know how accurate that antibody data is for NY yet, because some of these tests have a high false positive rate (I hope they gave them the PIXEL test which is the only one certified by the FDA.)
Do you think this experience will eventually lead to widespread reforms in our healthcare system, pollution levels in urban areas and trying to emphasize eating a more healthy diet to lower the high level of diabetes and high blood pressure in our society?  Cuomo and others keep talking about trying to achieve a level of equity in society, but that wont happen unless we make drastic changes.
https://www.pbs.org/wgbh/blood-sugar-rising/
That is PBS new blood sugar rising series about the diabetes epidemic and the rising costs of insulin.
https://jamanetwork.com/journals/jama/fullarticle/2733972

https://www.nih.gov/news-events/nih-research-matters/asthma-cases-dropped-when-air-pollution-declined

These are studies done last year which showed the close connection between asthma and air pollution.
Also been reading reports about more birds singing because of them not being stressed by so much traffic, the waters near Venice becoming more clear because of less marine traffic, and  turtles giving birth to many more offspring because of not being interfered with by humans at beaches.  Global greenhouse gas emission has been lowered by 6%?

Valuable lessons can be learned during this pandemic and the changes being made should be made to last even when it ends.  Pollution kills about 8 million people yearly.



Some good news coming out of all this (after being condemned by the UN) is both China and Vietnam are starting to close down those unsanitary wet markets.  Axios and PBS interviewed world renowned biologist Sir David Attenborough and he talked about the connections between biodiversity, pandemics and climate change and how poaching of elephants and other imported animals from Africa to Asia impacts deforestation (because these animals move seeds from one place to another in the African forests).  He is now 93 yrs old and he said that when he was growing up in the 30s, about 67% of the planet was wilderness, which was down to about 50% during the 90s, and now is down to only 25%.  These forests are integral because they act as carbon sinks.  He also mentioned that pandemics are becoming more common because of people cutting down more forests and venturing into areas where exotic animals live and coming into contact with new viruses.  Also mentioned was the release of once dormant microbes from under melting sea ice in Siberia.  He said that he thinks this pandemic will teach us lessons about how quick changes need to be made to thwart the oncoming climate crisis.  He also mentioned that giving urban areas access to more nutritious food is vitally important (less processed food, less sugar, etc-- sugary food and fast food can become addictive because of the release of dopamine and has been implicated in the quick rise of diabetes type 2, obesity and high blood pressure in young people, which, along with asthma from air pollution, have been shown to be major pre-existing conditions involved in covid19 deaths)  and reducing air pollution by continuing the switch to electric vehicles (no NO2 emission.)

Update on the death figures- Johns Hopkins Hospital thinks that the number of people who have died from this virus in the US might be double the reported figures, because the number of people who have died at home has not been reported.  The estimate of 25% infection rate in NYC may also be an underestimate.  Research out of California indicates that if we loosen restrictions over the summer, the infection rate will become higher than it ever was by August.  They say if we keep the restrictions as they are now, the infection rate will rise to above 30% but if we loosen restrictions the infection rate will be around 95% in August.

The UK being slow to close things down, looks like PM Boris Johnson has changed his tune from being cavalier to much more cautious about opening things back up now that he's been hospitalized for the infection himself and is a newly minted father.  The nations that shut down fastest did the best (like New Zealand, Denmark, Norway, Germany, South Korea, Finland, Iceland, etc.)

The most likely scenario and the one which China and Vietnam are now starting to shut down are the unsanitary wet markets and the importation of exotic mammals with exotic viruses that humans haven't come into close contact with before.  60 Minutes did a great piece on this last Sunday and China has started to shut them down after the UN singled them out these wet markets as a source for exotic viruses.

The first infection of a dog was reported today in the US, it was a pet bulldog.
 
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Coronavirus (COVID-19) Thread

03 May 2020 14:54

Yes, There are many APIs with different data. This is very hard to find out which data is accurate for the exact cases of Corona Virus in USA. The total cases crossed a big figure now 1 billion. This is now a very serious concern, After Italy now USA is at a high risk. This corona virus causes the drop in economy as well, this needs to be end soon otherwise conditions will become even more worse. 
 
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Coronavirus (COVID-19) Thread

07 May 2020 10:27

Wat and others..... Cuomo's press conference from yesterday was highly interesting and very informative....I hope you and others get to see the video of it.  He mentioned that we are getting 600 new cases every day even with the shut downs in place.  He said that he has been sending questionnaires to hospitals to find out what kind of people these are who have been getting infections most recently (over the past 3 days).  The results were both what you would and would not expect.

1) the vast majority of new infections were NOT health care workers or other essential workers.

2) the majority were people who were staying at home , either retired, unemployed or working from home.  (66%)

3) the vast majority were older....51+ (75%)

4) the overwhelmingly vast majority had pre-existing conditions (asthma, obesity, diabetes or pre-diabetic and/or had high blood pressure)  (96%)!!!!!!!!!!

5) they were predominantly from downstate NY (Manhattan 21%, Long Island 18%)  Upstate 10% vs Downstate 90%

6) hospitalization rates are dropping in NY, but the above indicates the hospitalizations may continue at this rate for a long time.....if you take the NY numbers out, it looks like the rest of the country is still on the increase with new infection rate.

The other important section of the news conference was when he mentioned that he doesn't think this will be the last pandemic we face.  He always consults with a team of scientists (he did a 1 yr study before banning fracking, for example.)  He said that, like climate change is leading to more destructive coastal storms, he believes that pandemics are becoming more frequent (for the reasons we've already discussed in this thread.)  He said that both the healthcare and education systems will need to be overhauled so this result doesn't happen again.  He mentioned creating a public healthcare system that includes all the state's hospitals under one umbrella as well as a network of systems for doing both remote doctor consultations and remote learning.
 
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09 May 2020 21:37

A-L-E-X wrote:
Source of the post Wat and others..... Cuomo's press conference from yesterday was highly interesting and very informative....I hope you and others get to see the video of it.  He mentioned that we are getting 600 new cases every day even with the shut downs in place.

Yep, I saw, and it was a very good conference. That there are still 600 new hospitalizations per day in New York (down from a peak of around 3000 per day in early April) makes sense. Shutting things down doesn't mean that new infections will immediately stop, but rather that the R value (the basic reproduction number or how many more people an infected person infects on average), immediately decreases, because now there are fewer interactions between people. If the shutdown reduces R to less than 1, then the number of new infections per day will decline (exponential decay), which is exactly what we are observing. The farther below 1 it is, the faster the rate of decay. Or of course the higher above 1 it is, the faster the rate of exponential growth.

So in NY we have been seeing a slow decline in new cases and deaths, which implies they succeeded in bringing R down below 1 -- but not by very much.

On that same note, I had recently coded up a simple SIR model to help myself to gain some intuition for the behavior of the pandemic, particularly for understanding better the relationship between changes in R over time and the spread or decline of the virus, and what possible scenarios for the future could look like depending on how R might change (e.g. with brief period of lifted restrictions). In this model I assume a 1% mortality rate (a guess based on antibody testing and possible biases) and a 17 day lag between infections and deaths on average (based on case progression records and the observed delay between shutdowns and deaths in multiple countries.) Then I manually define a piece-wise function for R(t) (basic reproduction number over time), so that the model's output fits the data for deaths. I also go by deaths and not cases, since deaths are generally more consistently reported across different regions. The downside is that the lag between infections and deaths is much greater, so the price I pay is that my reconstructions for R(t) are blind to changes in the last 17 days.

Applying this to New York has been interesting. Here it is:

Image

We see R(t) declining from an initial value of more than 2.5 down to around 0.9, with this shift beginning 60 days ago (from May 7th) and lasting for about 17 days. That would be from March 9 to March 27th. How well does this agree with when New York shut things down? Cuomo issued the statewide Stay at Home order on March 20th, but the "shutdown" really began much earlier than that. I found an article by Josh Marshall who dug up some data for New York City subway attendance, which shows a marked decline beginning on March 9 and going through March 23rd:

Image

Of course this data ends on the 23rd so we don't know how much it declined beyond that, but on the 23rd it was at only 13% of normal. So the timeframe for decreasing subway traffic and the reconstructed R(t) curves appear to match up rather well, which is reassuring.

Note also the grey shaded region in my figure, which represents the timespan where the model is "blind" to changes in R(t), because of that 17 day lag. Still, R has not changed significantly from 0.9 on that interval from 42 to 17 days ago. The decline in new hospitalizations (which also has less of a lag) confirms this, showing a fairly consistent exponential decay. The continued mitigation is continuing to work!

A caveat is that cases and deaths in New York right now are dominated by the urban areas which rose and peaked earlier, whereas rural areas upstate are still growing more rapidly. It could be the case that R in those areas is more than 1 while NYC is less than 1, so the "averaged R" that we derive from total deaths in the state could rise simply by virtue of those rural areas beginning to dominate the trends. As you noted, we see this across the whole US as well, where daily new cases are slowly declining, but if we subtract New York then we see them increasing:

Image

The virus spreads like a wave, more quickly in urban areas with more density, or wherever there happens to be a lot of people in close proximity (meat packing plants and agricultural centers are big problems now), and then reaching out into the rural areas. Now we are seeing that wave hitting the rural areas, and their response will be critical just as the shutdowns in the big cities were.
 
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Coronavirus (COVID-19) Thread

10 May 2020 01:41

Watsisname wrote:
Source of the post their response will be critical just as the shutdowns in the big cities were.

Rural areas can surely do fine with limited shutdowns, however.  Strict shutdowns are only meaningful in densely populated cities.  The Norwegian "shutdown" was limited to a few businesses (dentists, hairdressers, fitness centres), and schools, and people were encouraged to work from home and avoid public transport, and large events were prohibited.  Malls were still open and street life has appeared pretty normal, the main visible difference mainly that many cafes, museums and restaurants were closed.  I can count people that I've seen with masks on one hand.  R has now dropped to about 0.5, currently 59 people in the country (0.001% of the population) are getting treatment for Covid-19 at hospitals - well below the capacity, and the restrictions are gradually being lifted again.  We'll probably live with the disease for some time, however, but even if R approaches 1 again, the situation will be manageable.  Another thing is that social distancing is part of Norwegian mentality in general, so not much needs to change. :)
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Coronavirus (COVID-19) Thread

12 May 2020 00:39

Saw this on the news tonight and thought it was an excellent read, aimed especially for the American audience with staying safe as things begin to reopen. The author is a comparative immunologist at University of Massachusetts, Dartmouth.

The Risks - Know Them - Avoid Them
 
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12 May 2020 12:53

Wat and Mid this was also very eyeopening, this scientist was on 60 Minutes the other night talking about the cut in NIH funding to his group which has been working in collaboration with the Wuhan lab to track down the sources of these pandemics and the exotic mammals they originate from.

https://www.cbsnews.com/news/trump-administration-coronavirus-vaccine-researcher-covid-19-cure-60-minutes/

An American scientist who collaborates with the Wuhan Institute of Virology had his grant terminated in the wake of unsubstantiated claims that COVID-19 is either manmade or leaked out of a Chinese government lab.

 

 

Peter Daszak is a British-born American Ph.D. who's spent a career discovering dangerous viruses in wildlife, especially bats.

In 2003, in Malaysia, he warned 60 Minutes a pandemic was coming. 

Peter Daszak in 2003 interview: What worries me the most is that we are going to miss the next emerging disease, that we're suddenly going to find a SARS virus that moves from one part of the planet to another, wiping out people as it moves along.

In the 17 years since that prophecy, Peter Daszak became president of the New York-based EcoHealth Alliance.

Peter Daszak: We're a nonprofit research organization that focuses on understanding where the pandemics come from, what's the risk of future pandemics and can we get in between this pandemic and the next one and disrupt it and stop it.

In China, EcoHealth has worked for 15 years with the Wuhan Institute of Virology. Together they've catalogued hundreds of bat viruses, research that is critical right now. 

Peter Daszak: The breakthrough drug, Remdesivir, that seems to have some impact on COVID-19 was actually tested against the viruses we discovered under our NIH research funding.


Wat, I saw the reality of what you stated in terms of rural areas in relative proximity to NYC still experiencing explosive growth of infection rates.  While the infection rate in NYC is going down, it is rising rapidly in eastern PA, where there is a meat processing plant in Hazleton, PA as well as Amazon not closing down its plant there which also has a high rate of infections.

https://www.cbs.com/shows/60_minutes/vi ... -pandemic/

They're firing workers who are speaking out about bad working conditions there.

On a different note, what is this new syndrome developing from this virus that is killing infants?  This virus is starting to sound more like HIV now (for which there still is no vaccine.)  100 children and infants infected in NY and 5 have died so far.

funding.
 
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14 May 2020 15:49

 
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17 May 2020 04:20

The app that was launched in Norway a month ago does pretty much exactly the opposite: gathering GPS data, storing everything centrally, closed source, and if the app is activated, the battery drains in no time.  Thanks for the effort, but no thanks.  The approach explained in the video isn't waterproof either, but is much better.  Your own device can track your locations and if you have other data, spreaders can be identified.  Phone or wifi providers could harvest information from the virus app and gather quite a bit of information.  Even if Google and Apple open source the app, you're not safe.  Other, closed source apps, could gather information from a large number of users.
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Coronavirus (COVID-19) Thread

20 May 2020 14:34

This new sterilizing system they're going to start using in the NYC subway system starting next week is like something right out of a sci fi movie..... based on research from Columbia that UV-C light kills bacteria and viruses (but doesn't harm humans), they're going to briefly flash UV-C light in subway cars starting next week.  First time it's been done in a subway system anywhere in the world.

https://talkingpointsmemo.com/news/in-p ... s-gov-says

Very sad but not a surprise because of the health inequalities we have.

This is a major reason why we need to stop chopping down rain forests and learn to manage our own population better (not just other animals.)  This is truly fascinating emerging research (well, it's been emerging for 17 years lol)..  This is also why there's been an outcry to end wet markets, which China is now starting to do.

 

https://www.cbsnews.com/news/nih-cancel ... 020-05-10/

 https://www.nature.com/articles/s41586-020-2012-7



Pelley and 60 Minutes first met Daszak for a 2004 report. At the time, scientists were still trying to determine the origin of the coronavirus that had caused a global outbreak of SARS, and ecologists like Daszak were among the virus hunters on the case. 

For this earlier report, Pelley traveled to Malaysia, where Daszak and a colleague were trying to find the source of another deadly virus, Nipah, which had killed 40 percent of the people it infected. The ecologists eventually traced the virus to bats, which ate the fruit from trees farmers had planted over their pigsties for shade. Pigs then ate bits of tainted fruit the bats had dropped near them. 

But even as he was trying to figure out how Malaysian pig farmers had contracted Nipah, Daszak had his eye on future outbreaks.

"What worries me the most is that we are going to miss the next emerging disease," Daszak told Pelley at the time, "that we're suddenly going to find a SARS virus that moves from one part of the planet to another, wiping out people as it moves along."

 

As part of his efforts to predict and prevent future pandemics, Daszak subsequently became president of EcoHealth Alliance, which researches where pandemics come from and how to stop them. Much of his work involves bats, which have become breeding grounds for deadly viruses. 

As Daszak explained to 60 Minutes, no one knows for sure why bats are such adept hosts for disease, but one theory is that bats are the only mammal naturally capable of sustained flight. Flying, Daszak explains, burns a lot of oxygen and puts a lot of stress on bats' cells. As a result, their immune system kicks in. 

"Bats can't live with that sort of immune response all the time, so they dampen down their immune response. That's been shown," Daszak said. "And in dampening down their own immunity, they allow viruses to proliferate. So bats carry a higher amount of virus and a higher diversity of viruses than other mammals."

Bats, Daszak and a team of international scientists discovered, were the origin of the 2003 SARS outbreak. While scientists do not yet know the origin species of COVID-19, the closest match has been found in a bat coronavirus in China's Yunnan province that shared 96 percent of its genetic material with the virus that's known to cause COVID-19. 
 
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20 May 2020 17:24

A-L-E-X wrote:
Source of the post based on research from Columbia that UV-C light kills bacteria and viruses

That's really not a new piece of science. The sterilizing effects of shortwave ultraviolet light have been known for a very long time. Photons in the UV-C range have high enough energy to be considered ionizing radiation, because they can knock electrons free from atoms and even photodissociate some molecules. UV-C is an important part of the Sun's spectrum that splits apart oxygen molecules to form ozone in the stratosphere.

A-L-E-X wrote:
Source of the post (but doesn't harm humans)


It surely does harm humans. This is the same part of the EM spectrum that gives you sunburn and increased risk of skin cancer from long exposure, and it's not a healthy wavelength of light to look at with your eyes, either. So you would not want to be standing around without protection while one of these devices is being used to sterilize an area. After it has been used, though, there's no danger from being in that area. It's not like nuclear radiation which may make things radioactive.
 
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20 May 2020 23:22

Watsisname wrote:
Source of the post  It's not like nuclear radiation which may make things radioactive.

Yes, but usually, what makes people or things radioactive is the contamination by radioactive dust or material, not the radiation itself.  For that, the radiation needs to change the nucleus of atoms to form new isotopes.  Neutron radiation does that.
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28 May 2020 17:45

Watsisname wrote:
A-L-E-X wrote:
Source of the post based on research from Columbia that UV-C light kills bacteria and viruses

That's really not a new piece of science. The sterilizing effects of shortwave ultraviolet light have been known for a very long time. Photons in the UV-C range have high enough energy to be considered ionizing radiation, because they can knock electrons free from atoms and even photodissociate some molecules. UV-C is an important part of the Sun's spectrum that splits apart oxygen molecules to form ozone in the stratosphere.

A-L-E-X wrote:
Source of the post (but doesn't harm humans)


It surely does harm humans. This is the same part of the EM spectrum that gives you sunburn and increased risk of skin cancer from long exposure, and it's not a healthy wavelength of light to look at with your eyes, either. So you would not want to be standing around without protection while one of these devices is being used to sterilize an area. After it has been used, though, there's no danger from being in that area. It's not like nuclear radiation which may make things radioactive.

ah, the Mayor's presser was wrong then-- he stated that UV-C doesn't harm humans.  The fact that they were wearing protective visors when applying it should show that it can indeed harm eyesight.

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