Science, Modelling (including actions and results of what top infected countries/states are doing)

[dixiegirl1035]

This thread is for focus on sharing and discussing Science, Modelling, spread, facts, information, studies, reports, preparation for us all (including actions and results of what top infected countries/states are doing) information, worldwide, state-wide, small towns and counties not excluded - as we did in the first 30 or so threads.

 

[dixiegirl1035]

In the above youtube, what I've not seen anywhere, is that 30 long term care facilities in King C0unty had at least one Covid19 case. If I had an elder, I would have pulled them out long ago. A consideration for sure as the staff travels to and fro from center to center. SCARY. This is why so important to learn from OTHER states it hits first MOO. 167 cases and 35 deaths from just the one index case identified as no contact tracing was done proactively to help prevent, only afterwards as reactive. SMH

 

[JerseyGirl]

Droplets carrying coronavirus can travel up to 27 feet, according to MIT researcher

An MIT researcher says that current CDC guidelines for proper social distancing might not be enough to stop coronavirus transmission.

Lydia Bourouiba, an associate professor at MIT who has done extensive research on the dynamics of exhalations, has found that some coughs or sneezes can create a cloud of gas that can travel up to 27 feet.

In an article published last week in the Journal of the American Medical Association, Bourouiba wrote that recent studies have shown that exhalations, sneezes and coughs are not solely made of mucosalivary droplets, “but primarily made of a multiphase turbulent gas (a puff) cloud that entrains ambient air and traps and carries within it clusters of droplets.”

The Centers for Disease Control and Prevention calls for six feet of space between individuals as an accepted space to enact social distancing, while the World Health Organization advises on three feet of space between people.

Bourouiba worries that such strategies might be outdated.

 

[10ofRods]

Here's my favorite dashboard:

Coronavirus Dashboard

And here's the fairly grim one:

IHME | COVID-19 Projections

The second one is worth spending some time with. It gives such data as when the 50 states went to stay at home, and has separate tables for projected cases of CoVid and beds needed vs beds available. It also projects death (and changes daily, showing where the state actually sits each day).

 

[Gardener1850]

I've been using this 1point3acres site for following case stats in US and Canada: COVID-19/Coronavirus Real Time Updates With Credible Sources in US and Canada | 1Point3Acres

And the worldometer site for the world stats: Coronavirus Update (Live): 849,432 Cases and 41,625 Deaths from COVID-19 Virus Outbreak - Worldometer

 

[Tadpole12]

New coronavirus study reveals increased risks from middle age


https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(20)30243-7/fulltext

Estimates of the severity of coronavirus disease 2019: a model-based analysis



https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(20)30257-7/fulltext

Likelihood of survival of coronavirus 2019

 

[dixiegirl1035]

Coronavirus outbreak: WHO “deeply concerned” as COVID-19 deaths near 50,000 worldwide

 

[10ofRods]

We are now closer to 150,000 known dead worldwide.

 

[10ofRods]

Here's an array of models, all of which contradict IMHE (keeping in mind that IMHE has never claimed to be accurate except for its cones of probability)

Where The Latest COVID-19 Models Think We're Headed — And Why They Disagree

Since the IMHE projection is once again askew, here are some other projections from various reputable scientists. The upshot is that by May 23, models predict that total deaths will be anywhere from 65,000 to 140,000. My prediction, above, if extended to May 23, is that it would be around 96,000, so pretty much in the middle of that range.

All of this dependent of course, on what happens next with testing, reporting and opening measures.

The prediction of 140,000 by May 23 sounded impossible, but as the states open up, that estimate may get increased.

 

[Henry2326]

"Scientists have identified a new strain of the coronavirus that has become dominant worldwide and appears to be more contagious than the versions that spread in the early days of the COVID-19 pandemic, according to a new study led by scientists at Los Alamos National Laboratory.
The new strain appeared in February in Europe, migrated quickly to the East Coast of the United States and has been the dominant strain across the world since mid-March, the scientists wrote.

In addition to spreading faster, it may make people vulnerable to a second infection after a first bout with the disease, the report warned."

“The story is worrying, as we see a mutated form of the virus very rapidly emerging, and over the month of March becoming the dominant pandemic form,” study leader Bette Korber, a computational biologist at Los Alamos, wrote on her Facebook page. “When viruses with this mutation enter a population, they rapidly begin to take over the local epidemic, thus they are more transmissible.”

https://www.latimes.com/california/...-original?_amp=true&__twitter_impression=true
This is the report....
Spike mutation pipeline reveals the emergence of a more transmissible form of SARS-CoV-2

 

[Henry2326]

This is a relatively new model....He did get an invite on CNN this weekend.

US deaths surpass: Most likely date:
70,000 May 5, 2020
80,000 May 12, 2020
90,000 May 19, 2020
100,000 May 28, 2020

COVID-19 Projections Using Machine Learning

 

[Henry2326]

Putting this here from Jerseygirl to keep close.

Coronavirus Latest: New University Of Penn Model Predicts 350,000 Deaths By End Of June If All States Fully Reopen – CBS Philly

Coronavirus Policy Response Simulator: Health and Economic Effects of State Reopenings — Penn Wharton Budget Model

They are buying in to the possibility of 3,000 deaths per day in June. The range here is
1,950 per day with STAY at home orders
2,700 with partial openings
5,833 per day with full openings.

 

[Henry2326]

233 new sequences added to Nextstrain from US. Notice how the CA strains cluster separately from the NY and New Orleans.

Note: I'm not claiming it means something....only that it's different and smarter folks than me are trying to figure it out. Obviously, NY and New Orleans had a much more transmittable issue and virulent issue.

Nextstrain on Twitter

 

[Henry2326]

FL, GA, and SC sample sequences are found nested within a small USA cluster among otherwise mostly Asian sequences.......
Nextstrain on Twitter

 

[Henry2326]

Posting here also to keep under science.

This research paper confirms an early introduction into China of Oct 6, but do not yet have Italy genomes yet to understand initial introduction into Europe, other than multiple introductions occurred....definitely they give no credibility to a lab created virus and confirm late initiation of the epidemic at end of December in China with possible epidemic occurring in Europe at the same time.

Research Paper:
Emergence of genomic diversity and recurrent mutations in SARS-CoV-2 - ScienceDirect

Tweet from Francois Balloux:
It was a privilege and honour to lead with @LucyvanDorp a great team of scientists in the analysis of the first 7500 #COVID19 genomes. We searched for invariant targets for vaccines/drugs, and evidence for adaptation of #SARSCoV2 to its human host.
Emergence of genomic diversity and recurrent mutations in SARS-CoV-2 - ScienceDirect
(1/3) Prof Francois Balloux on Twitter
We confirm that #SARSCoV2 jumped into humans ~Oct/Nov 2019 in China. The emerging genetic diversity of the virus we found in many countries recapitulates its global diversity, indicating that several countries were seeded multiple times, sometimes early on in the pandemic.
(2/3) Prof Francois Balloux on Twitter
We identified subset of ~200 mutations that independently arose multiple times and that are candidates for adaptation of #SARSCoV2 to its novel human host. These need to be monitored as they may hold clues into transmission, virulence, as well as drug and vaccine escape.
(3/3) Prof Francois Balloux on Twitter
We don't know for sure whether they jumped into humans from bats. Related viruses circulate in all sorts of population of mammals and birds. I actually kind of suspect a reservoir in carnivores. The virus came into Europe very early in the pandemic, multiple times.
We have a good understanding of SARS-CoV-2's mutation rate. So far little genetic diversity has built up in the global viral population, but some of the emerging mutations are intriguing.
Prof Francois Balloux on Twitter

 

[Henry2326]

43 additional sequences for NY, Virginia, and DC analyzed by Nextstrain. Notice how they cluster at the top of the tree like the earlier one I shared several posts back.

Nextstrain on Twitter

 

[10ofRods]

43 additional sequences for NY, Virginia, and DC analyzed by Nextstrain. Notice how they cluster at the top of the tree like the earlier one I shared several posts back.

Nextstrain on Twitter

This is especially fascinating. This indicates that the branches at the top (all closely related) are "doing better" from the virus's point of view. They are probably the ones with the longest cryptic transmission. We're finding (in scientific research and many community studies conducted by epidemiological teams in the field, working alongside bio anthropologists who already have inroads into communities where blood can be taken) that some people are mildly to moderately symptomatic, but perceive their illness as allergies or colds. That's why the term "cryptic" is starting to be preferred.

I know you know that, Henry (and I so so appreciate your posts on this thread), but I thought in case others were reading they'd know that it seems more and more clear that while all infections produce some antibodies, not all CoVid infections trigger exactly the same antibodies in humans. In some field studies, anthropologists already have the human genomic information for some subjects, but no where near enough CoVid antibody data to make any correlations. The models for studying genes in the field are allied work between geneticists (Spencer Wells and I both knew Luca Cavalli-Sforza in graduate school - but Spencer was lucky to have been chosen for Luca's special training of a new generation of anthropologists - Luca is the Godfather of modern human genetics research, which almost never can accomplish random sampling - so the models in our field of anthropology are very helpful in epidemiology.)

Wells's work is on the Y chromosome - and our own phylogeny shows how much slower we evolve than this virus does:

Molecular Dissection of the Basal Clades in the Human Y Chromosome Phylogenetic Tree

 

[Henry2326]

Stanford University Covid forecast model can be found at

Extended Results COVID-19

Choose a state to see the coming forecast curve.

I compared this curve for Arizona after reading the ASU story. Appears that the curve here is consistent. Anything above 25% uptick in social distancing keeps them on the exponential curve.

This is the research paper discussing the forecast methodology.
https://web.stanford.edu/~chadj/sird-paper.pdf

 

[Henry2326]

NEXTSTRAIN

Many introductions to Russia
Highlighting samples from Russia, we see that they are scattered both geographically (across Russia) and genomically (across the tree).

This indicates that the epidemic in Russia was sparked by many separate introductions, rather than a single introduction followed by within-country spread.

While there are a few samples towards the bottom of the tree that are most closely related to Asian cases, the majority of Russian samples descend from European lineages.

auspice

Heterogeneous outbreak in Moscow
An example of frequent importation can be seen by zooming in on samples from Moscow.

There are a few clusters of cases which are most closely related to other samples from Moscow, indicating likely local transmission. However, most samples from Moscow are most closely related to samples from elsewhere, consistent with importation.

Given the number of confirmed cases in Moscow, it's likely that at least some of these introductions led to further local spread, but we don't yet have enough data to see this.

auspice

 

[Henry2326]

NEXTSTRAIN

Genomic epidemiology of novel coronavirus - Europe-focused subsampling

auspice

NOTE: Eventually the earlier genomes will be added to the dstabase..IMO