Tuesday, March 31, 2020

Covid Update 3/31/20

There's some interesting news today, basically encouraging. The news appears to be especially encouraging for California--a matter Bebe and Ray SoCal have raised. In essence, it confirms my cautiously optimistic view--for the West Coast. On the West Coast, at least, Covid has been more of a localized thing, not a community spread thing. That's what I theorized early on--Covid was a bit of a late arrival in the US, compared to the rest of the world, and might be containable with aggressive action. That's not so much the case on the East Coast (NY), where it seems to be more on the loose in the community. And we don't really know about other hot spots like Michigan and Illinois. Here's what I'm talking about.

USAToday has an article--8 strains of the coronavirus are circling the globe. Here's what clues they're giving scientists--that explains what scientists have been able to learn through genomic sequencing. I won't attempt to explain that process, because I'd probably get it wrong, but here are the important points that have been learned. I'll leave out the ellipses, but you can go to the original for more:

While researchers caution they're only seeing the tip of the iceberg, the tiny differences between the virus strains suggest shelter-in-place orders are working in some areas and that no one strain of the virus is more deadly than another. They also say it does not appear the strains will grow more lethal as they evolve.  
The SARS-CoV-2 virus first began causing illness in China sometime between mid-November and mid-December. Its genome is made up of about 30,000 base pairs. Humans, by comparison, have more than 3 billion. So far even in the virus's most divergent strains scientists have found only 11 base pair changes.  
That makes it easy to spot new lineages as they evolve, said Chiu.  
“The outbreaks are trackable. We have the ability to do genomic sequencing almost in real-time to see what strains or lineages are circulating,” he said.  
So far, most cases on the U.S. West Coast are linked to a strain first identified in Washington state. It may have come from a man who had been in Wuhan, China, the virus’ epicenter, and returned home on Jan. 15. It is only three mutations away from the original Wuhan strain, according to work done early in the outbreak by Trevor Bedford, a computational biologist at Fred Hutch, a medical research center in Seattle.  
On the East Coast there are several strains, including the one from Washington and others that appear to have made their way from China to Europe and then to New York and beyond, Chiu said. 
“Remember, we’re seeing a very small glimpse into the much larger pandemic. We have half a million described cases right now but maybe 1,000 genomes sequenced. So there are a lot of lineages we’re missing,” he said.

The California experience is what I was hoping would be true of most of the US. It seems not true in metro New York City--including parts of New Jersey and Connecticut--and maybe some other East Coast areas. Hopefully we'll find out more about Michigan and Illinois soon.

Shelter in place working in California
Chiu’s analysis shows California’s strict shelter in place efforts appear to be working. 
Over half of the 50 SARS-CoV-2 virus genomes his San Francisco-based lab sequenced in the past two weeks are associated with travel from outside the state. Another 30% are associated with health care workers and families of people who have the virus. 
“Only 20% are coming from within the community. It’s not circulating widely,” he said. 
That’s fantastic news, he said, indicating the virus has not been able to gain a serious foothold because of social distancing. 
It's like a wildfire, Chiu said. A few sparks might fly off the fire and land in the grass and start new fires. But if the main fire is doused and its embers stomped out, you can kill off an entire strain. In California, Chiu sees a lot of sparks hitting the ground, most coming from Washington, but they're quickly being put out. 

So, good news for California.


  1. Tonite's Tucker show's first segment had much, about a Chinese scientific paper pubd. months ago, charging that the virus escaped from Wuhan *non-weapons* labs playing with, get this, BATS.
    He also charged, that the MSM has blacked out coverage of this Chinese paper, despite its utter relevance to this virus crisis.
    It sort-of figures, that the ChiComs would've cared more about solidly securing of *weapons* labs, more than non-weapons labs.

  2. I hope you are right on Ca. I'm still very pessimistic on the testing in CA debacle, and I have no idea why it's so horrible.

    CA - The number infected in testing ranges from 11% to a high of 23%. Average positive % is about 20% over the last 7 days. WA is at 7%. Good news is testing seems to be up to 2,000 a day, it was 1,000 a week ago.. Backlog is still 57,000 (supposedly the 60,000 was a lab mistake).

    USA Total is increasing about 13% per day. # of tests in the US has leveled out at 100,000 per day. I hope this changes, and I think it will. % of positives in testing is around 18%. This indicates they are still testing high risk populations, and there are not enough test to use to get ahead of the virus.

    My guess is the stay at home order is being used as a sledge hammer to stop the spread of the coronavirus.

    New York is in really bad shape. 35% of people they tested has the virus in the last 4 days. They are doing around 16,000 tests in a day. NY Probably has a million infected, and has 41% of the deaths in the US.

    Interesting the article felt the need to state this is not an artificial virus. Logic / facts on that statement were lacking.

    1. Thanks for the analysis. You have to wonder whether this is an East Coast thing--in the sense that on the East Coast the transmission has moved from pockets to community spread. Perhaps spreading from NY to boston, to Philly, maybe further. People are starting to ask why flights are being allowed to leave NY. Looks bad all right.

  3. Here is a very interesting interview with Dr. Bob Wachter, who is also a professor at UCSF, about what they are experiencing in San Francisco, particularly at the UCSF Hospital.

    ‘How Do You Decide When to Open the World Back Up?’
    Wednesday: Dr. Bob Wachter of the University of California, San Francisco, talks about the numbers he’s tracking and what they say.

    An excerpt from the interview:

    The number of new cases diagnosed today in San Francisco is about two-thirds of what it was four or five days ago, which means the slope of the increase is lower than it was, which, to me, is reasonably good evidence of some flattening of the curve.

    If this thing was expanding in the way epidemics do when they’re not being mitigated or addressed, the growth is exponential.

    What about hospitalizations? What are you looking at there?

    My hospital made that number public early on and I think that was an incredibly smart decision, because data are better than what replaces data, which is rumors and speculation.

    I don’t pay that much attention to the number of patients under investigation — people who come in with Covid-19 symptoms. Most will turn out not to have Covid-19. A lot who come in will have pneumonia. On average, one out of 20 will be positive.

    The number of confirmed cases we have at any given time has gone up slightly from between eight and 10 last week, to now 13 to 15. But if we’re seeing 14 confirmed cases and a comparable hospital in New York has 150 to 200 cases, there’s something going on.

    A number that has shifted for us in the last several days is that about a week ago, if there were 10 Covid-19 patients at U.C.S.F., eight might have been on the main floor of the hospital while two were in intensive care. That ratio has flipped. Today, we have 14 total and nine in the I.C.U.

    I suspect that has a couple of factors associated with that. Once people are sick enough to be on a mechanical ventilator, many will die. Those who live will spend several weeks on a ventilator. Floor patients can come in and leave more quickly.

    He is also tracking COVID-19 on his very active Twitter thread:

    Here in our part of Southern California, we keep waiting for the other shoe to drop. So far, so good.

    1. Thanks. I really like this part (below), because transparency is the best policy, and we're not getting it for the most part:

      My hospital made that number public early on and I think that was an incredibly smart decision, because data are better than what replaces data, which is rumors and speculation.

    2. Here's another very important thing for people to understand. I've combined from the transcript above with some that wasn't in that transcript:

      Once people are sick enough to be on a mechanical ventilator, many will die. Those who live will spend several weeks on a ventilator. Floor patients can come in and leave more quickly.

      The second factor is that these patients can get very sick very quickly, ...

    3. "Once people are sick enough to be on a mechanical ventilator, many will die. Those who live will spend several weeks on a ventilator. Floor patients can come in and leave more quickly."

      I don't know if you had time to review Dr. Voung's YouTube video, but he said pretty much the same thing.

  4. I’m glad you picked up some more from that interview, Mark. I thought it was very informative. Dr. Wachter is an interesting guy. A little bio blurb off to the side on his Twitter page: “Career: What happens when a poli sci major becomes an academic physician.” He chairs the Department of Medicine at UCSF, a very highly rated program and hospital. You can see that other professionals are following his updates on his Twitter thread…

    His book The Digital Doctor: Hope, Hype and Harm at the Dawn of Medicine’’s Computer Age , about the transition from handwritten notes to digital recordkeeping, is now ready for me to read on my iPhone.

    1. I didn't read his bio but my interest perked up when I saw him ref Scott Gottlieb at AEI.