I wanted to share this Brazilian research article with you. It’s an analysis of the genomes of the SARS-CoV-2 viruses of the first two individuals identified as having contracted the disease in Brazil. You may already be familiar with it but it was new to me.
The TL;DR version of the article is that the disease originated from a different places in each of the cases, one from China to Italy to Germany and then to Brazil, the other from China to Australia to Brazil. I think there are several puzzling aspects to the results of this analysis.
For one thing I don’t see how the number of mutations expressed in these samples, collected at the end of February in Brazil, is consistent with the presumed mutation rate of SARS-CoV-2 and a start of community spread in China of late December. Maybe I’m missing something but it appears to me that either the mutation rate is wrong or the time when community spread is wrong or there’s something wrong with the analysis. IMO it throws some doubt on whether there was any possibility of containment of the disease outside the U. S. unless all foreign travel to or from the U. S. had been suspended no later than December which would have been controversial to say the least.
Small number of patients, 2. Would wait for confirmation before getting too sure about the results. That said, the general rule is that by the time you know you have the disease present it is always spread much further than you think.
The case of Korea suggests that travel bans aren entirely necessary if you quarantine everyone returning from an out of the country trip. But, it is really hard given how much international trade we have to completely cut off travel. In order from most effective to least effective I would list the following.
1) Complete travel ban
2) Complete quarantine of those arriving from another country.
3) Selective complete travel bans from chosen countries.
4) Complete travel ban from the country of origin, China.
5) Ban Chinese nationals and require US citizens returning to quarantine.
6) Banning only Chinese nationals while allowing Americans to contour traveling back and forth to China.
We chose the least effective option. It may have had some effect at slowing spread, but the 2 before it should have been more effective. The last option was a good one if the goal was a political one.
Steve
I think what this study suggests is that by the time China was acknowledging community spread it was already too late for any of those tactics to be effective.
And how did it get here? The biggest localized outbreaks are at Smithfield owned packing plants in S.D. and Mo. They continue to operate with one fourth of employees testing positive, agreeing to a two week “pause”, then offering a $500. “responsibility” bonus to employees who agree to work thru the pause.
https://www.bbc.com/news/world-us-canada-52311877
By the way, not that it should matter at all, Smithfield is a Chinese owned packer.
“too late for any of those tactics to be effective.”
Define effective. I dont think anything was going to completely stop spread. What we should have been hoping for was slowing the spread so we had time to prepare. Since that was largely wasted (at the federal level) maybe it didnt really matter anyway.
Steve
The unknown unknowns still far outweigh the knowns and even the known unknowns. I think by this time next year we’ll have a pretty good handle on who what when how etc., but post-mortems are only interesting to the general public when they’re in crime dramas and detective tales (would suspect that not to be the case for the posters on this site, especially the MD’s).
Considering how bananas the Democrats and the media went when option (6) was exercised I had to what their reaction would have been to even (4) or (5). Maybe POTUS should have said F**k it and done it anyway, but when you had the experts saying as late as late February that it’s not going to be a big deal, that’s asking a bit much from someone who isn’t an epidemiologist.
The CDC bear some responsibility for the delay in action due to their insistence on central control, including the faulty first run of test kits. Perhaps again POTUS should have overridden them and bought kits that worked from South Korea, but assuming SK would have been willing to sell them considering their own need I would also have to assume the CDC advised against doing that.
Steve: How’s the situation with you? Getting enough PPEs yet or is your used equipment sterilization process working good enough that getting new isn’t a major problem? How’s the status of the patients and your wards? Getting better or worse or the same? Are you getting any nursing home patients or are they just remaining mostly in place? And most importantly how you and your staff doing, since you’re at most risk from your patients than anyone?
I would define effective as containing the outbreak within China. I do not believe there was any prospect whatever of avoiding community spread within the United States without containing the outbreak to China.
“I think what this study suggests is that by the time China was acknowledging community spread it was already too late for any of those tactics to be effective.“
No shit. And as I’ve said from the start, the best would have been China cooperation from the start, and shut them off at our borders. The former is wishful thinking. The latter was rendered a politic football, mostly by Democrats. Steve is desperate to put it on the administration, but its on China, their apologists, mostly in the media or WHO, and the Disgusting politics of xenophobia.
Once the die was cast and the health care community was placed front and center all we had was chickens running around with their heads cut off.
Next up will be public unrest. People need to feed their families and certain governors are acting like, well, fascists. Either most of the country will say open up, and NYC your problems are self inflicted, or we will have state by state civil unrest.
Reading the paper, it is consistent with what other geneticists have found.
The second patient didn’t catch it from Australia — it was a similar strain to an Australian traveler to Italy.
If you go to https://nextstrain.org/ncov/global, it has the Brazilian genomes along with all others around the world. You can see the inferred date of the most recent common ancestor is Oct 25 – Dec 10, which matches SCMP reports that Chinese investigators think the earliest case from medical records was Nov 15th or so.
I tend to believe the genome analysis because it accurately inferred the majority of infections in the Seattle area started with a common ancestor on Jan 15. We know the index patient for Seattle came back around Jan 15th, and that most genomes sequenced in Seattle have distinct mutations from that index patient.
As to the possibility Lombardy was seeded multiple times — it is quite possible. Milan held its fashion week on the 3rd week of February, I imagine a huge influx of people from all around the world all throughout February.
Realistically — the time limit to cut travel outbound from China was Jan 7 or so. The first case was detected in Thailand on Jan 13 but it takes up to a week before becoming symptomatic.
Or, said another way, the choices were China being forthcoming, prescience, or spending upwards of $10 trillion and tens or hundreds of thousands of American lives.
Has anyone noticed that Singapore and Japan are having escalating outbreaks.
I believe that leaves Hong Kong and Taiwan as the two countries without an outbreak.
We should have a list of countries who
(A) prevented an outbreak
(B) crushed the curve while limiting deaths < 250.
I believe the list is very small.
I know of no compelling evidence that any country, including South Korea, Hong Kong, and Taiwan has “bent the curve” in any way that could not be explained by Farr’s Law, operating without other interventions.
“Considering how bananas the Democrats and the media went when option (6) was exercised ”
That was actually researched and in fact very few people claimed it was racist, mostly that it was kind of dumb. Besides, when did Trump start caring about what Democrats think?
“Steve is desperate to put it on the administration”
Ok self-declared man of science. Please explain how stopping Chinese people from coming to the US but not Americans flying back and forth was going to stop anything.
“Has anyone noticed that Singapore and Japan are having escalating outbreaks.”
You sure about that? I think man of science said those were two countries who had things under control without a lockdown.
Tars- We are having a small nursing home related surge. We now a have a UV sterilizer at every campus. If we receive a large shipment we have been promised this week then we are ok for another 12 weeks or more. If not we are OK for 8 weeks I think. Staff is doing OK. spirits are still pretty good. We have had quite a few asymptomatic people test positive so we are considering having everyone were KN 95 masks unless you are engaging in high risk procedures and then use N 95.
Steve
Professor Johan Giesecke, one of the world’s most senior epidemiologists, advisor to the Swedish Government , laid out these COVID pointers, as they related to the UK lock down policies, and indirectly to ours over here in the US.Â
“UK policy on lock down and other European countries are not evidence-based.T
The correct policy is to protect the old and the frail only.
This will eventually lead to herd immunity as a “by-product.”
The initial UK response, before the “180 degree U-turnâ€, was better.
The Imperial College paper was “not very good†and he has never seen an unpublished paper have so much policy impact.
The paper was very much too pessimistic.
Any such models are a dubious basis for public policy anyway.
The flattening of the curve is due to the most vulnerable dying first as much as the lock down.
The results will eventually be similar for all countries.
Covid-19 is a “mild disease†and similar to the flu, and it was the novelty of the disease that scared people.
The actual fatality rate of Covid-19 is the region of 0.1%.
At least 50% of the population of both the UK and Sweden will be shown to have already had the disease when mass antibody testing becomes available.”
I’m not sure I would agree with him about COVID-19 being necessarily a mild disease. However. I do think it’s possible, if not probable, that the virus was far more widespread via transmission by asymptomatic people, and consequently will have a final mortality percentage much lower than originally predicted by modeling.  Â
That’s basically been Guarneri’s argument for some time.
My own suspicion is that COVID-19 has a somewhat higher case mortality rate than the seasonal flu but not remotely what people have, apparently, feared.
My concern is that until the incentives change our political leaders will just double down on the strategies they’ve been using whether they work or not.
I’ve posed a number of questions over the last few weeks. Here’s another one. Why is having an unutilized capacity of 50% better than having an unutilized capacity of 20%?
You should look at what Sweden actually did before you comment upon it. They closed universities and schools for older kids. They banned gatherings over 50 people. Most of them live in singe person households (from memory). Their social distancing on a voluntary basis was probably as good as mandatory versions in the US. And they still ended up with a 50% higher death rate.
Steve
Sweden’s governmental hand was moderate, combining more voluntary restraint mixed in with mandates applied to larger groupings. Otherwise, they did not micromanage their economy to the extent that it would be crushed, like the US has done. To me, their numbers, identified infections and deaths (15,322/1,785), look proportionally similar to those from countries implementing more draconian measures.
You do realize people actually measure the data and dont just by their feelings? Sweden’s death rate is 50% higher than ours. Also, their “moderate” changes and what they did on a voluntary basis ended up being pretty much what we did by mandate. They left schools open for younger kids. Not quire as many businesses closed. They did ban large gatherings (over 50). Plus, over 50% of their people already live alone. When you look at what Sweden actually did, not just claim that they didnt lockdown, it isn’t that much different and they are having 50% more deaths.
But maybe the real comparison would be with similar countries since we arent a small fairly homogeneous country. If you compare them with other Scandinavian countries Sweden’s death rate is about 100% higher. They are expecting unemployment of about 15% I think, though cant remember where i read that.
Steve