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New variant: omicron
#11
[url=
]Disturbing numbers out of South Africa[/url]:
7-day moving average of cases
16-Nov: 332
23-Nov: 1010
1-Dec: 4814
New cases on 2-Dec: 11,535
(Population of S. Africa: 60M; Total reported cases: 3M; Deaths: 90,000; total doses: 26.2M)

Look at the slides at 29:50 and subsequent. The disease is hitting the young significantly harder than before.
In particular, 0-4 yo are being hospitalized almost as likely as 60+.
0-15yo are being hit harder than their parents when compared to Delta.
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#12
A Hong Kong research letter published at the CDC documents two cases of Omicron, where the easiest explanation is that one case got it from the other, without any real contact, even at a distance.   Two tourists, arriving a day apart, were set up in quarantine in rooms in a quarantine hotel opposite one another.  Video indicates that neither left their room during quarantine.  PCR testing is done every 3 days, so they would not have been tested on the same day.  Other than testing, the only time they opened their doors was to get food dropped off at their door.  No one entered their rooms.  No items were shared.

Both tourists had two doses of Pfizer (late May/early June for 2nd dose).  Both had negative PCR tests within 3 days of arrival.
Nov 10.  Tourist A arrives from South Africa and is quarantined in a quarantine hotel.
Nov 11.  Tourist B arrives from Canada and is quarantined in the same quarantine hotel across the hall from Tourist A.
Nov 13.  Tourist A tests positive for COVID without symptoms.  He has a high viral load.
Nov 14.  Tourist A is hospitalized
Nov 17.  Tourist B develops mild symptoms.
Nov 18.  Tourist B tests positive for COVID with a high viral load and is hospitalized.

Both were infected with the Omicron variant.   The two virus sequence differ by 1 nucleotide.  Neither Tourist A nor Tourist B's virus sequence are exactly like any others previously reported.  Tourist A's differs by 1 nt from 2 other early sequences out of Botswana (from Nov. 11).

(I believe this was the first case of Omicron reported to WHO.)
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They don't go into detail about food delivery nor about ventilation of the hallway.  If Tourist A is highly infectious on Nov 13 (or 12), he may have introduced the virus into the hallway on that day when he opened his door for food (whether or not he was wearing a mask).   If Tourist B subsequently (and soon) opened his door, he may have inhaled some of the virus (if he wasn't wearing a mask).  He then shows up with symptoms 4 days later.

Alternatively, Tourist A's door was opened to take him to the hospital on the 14th, and possibly to clean his room. Tourist B was given a PCR test that day. When he took his mask off so he could be swabbed, he inhaled a nose full of virus still in the air of the corridor.



I think the 15 minutes within 6 feet arbitrary definition of "close contact" may soon go the way of the "You don't need a mask" advice.
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#13
Some very good posts, M_T.  THank you! 

Excerpt below really concerns me.  So far a huge "advantage" of Covid has been the comparatively low risk to younger people.   Despite this, the educational and psychological impact on young people is meaningfully negative.  If Omicron represents a health threat to young people that is an order of magnitude graver than what we have seen so far, I worry about the impact this winter on education and pray for rapid deployment of a tweaked vaccine


"Look at the slides at 29:50 and subsequent. The disease is hitting the young significantly harder than before.
In particular, 0-4 yo are being hospitalized almost as likely as 60+.
0-15yo are being hit harder than their parents when compared to Delta."
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#14
WSJ article this morning. Key points to me are that severity seems lower and scientists remain hopeful that existing vaccines will help prevent hospitalization. Still many open questions, obviously

https://www.wsj.com/articles/omicron-may..._lead_pos2
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#15
The UCSF Grand Rounds this past week (12/2) was about Omicron.

A friend interacted with the second speaker and found out he wasn't aware of the Dec. 2nd South African press conference & its material. So, recognize that there is more recent info out there.

I don't subscribe to the WSJ so I can't see their article. If that report is anything like this CNBC report, it is based on an extremely small number (which, by the way, wasn't specified) of COVID admissions. The report only looked at 166 all-reason admissions (not 166 COVID admissions).

I tracked down the original report.

The report says a lot in what it doesn't say. It was 166 admissions that were part of a "sharp increase". They don't say how many of those were admissions for COVID-like symptoms. Clearly they have that number. They compare the 9 adult deaths to the average death rate during the pandemic, rather than to recent death rates (COVID had really curtailed and deaths were still falling to a week or so ago). They speak of deaths as "best indicator of disease severity". And then later they indicate that they indicator doesn't apply yet. "The trend over the next two weeks will be clarified as the number of deaths is currently low, and sufficient time will have elapsed for the development of greater severity of disease and the number of deaths might be expected to increase"

The most encouraging statistic I saw was "A significant early finding in this analysis is the much shorter average length of stay of 2.8 days for SARS-CoV-2 positive patients admitted to the COVID wards over the last two weeks compared to an average length of stay of 8.5 days for the past 18 months." But then I realized if the patients they are putting in those wards are the patients that came in for other reasons but were found to have active COVID, then that statistic is distorted.

This variant was only identified about 3 weeks ago. For the original COVID, it took about a week after symptom onset before someone needed to go to the hospital.

It appears the authors are avoiding the data needed: how many were admitted for COVID symptoms, and what was their outcome - that can be correlated with detections a week earlier. They give outcomes for the entire patient population, not for those admitted for COVID. Their data is as of Dec. 2. A week earlier is Nov 25, the day after it was reported to WHO.

I hope they are right and this variant somehow doesn't cause the same symptoms. I wouldn't say this report gives me anything real yet.
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#16
Pfizer has a press release on results on neutralization titers against Omicron.
Quote:
  •     Preliminary laboratory studies demonstrate that three doses of the Pfizer-BioNTech COVID-19 Vaccine neutralize the Omicron variant (B.1.1.529 lineage) while two doses show significantly reduced neutralization titers
  •     Data indicate that a third dose of BNT162b2 increases the neutralizing antibody titers by 25-fold compared to two doses against the Omicron variant; titers after the booster dose are comparable to titers observed after two doses against the wild-type virus which are associated with high levels of protection
  •     As 80% of epitopes in the spike protein recognized by CD8+ T cells are not affected by the mutations in the Omicron variant, two doses may still induce protection against severe disease
  •     The companies continue to advance the development of a variant-specific vaccine for Omicron and expect to have it available by March in the event that an adaption is needed to further increase the level and duration of protection – with no change expected to the companies’ four billion dose capacity for 2022
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#17
Latest news conference from South Africa: Thursday 12/9 afternoon Pacific time
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#18
(12-10-2021, 02:34 PM)M_T Wrote: Latest news conference from South Africa: Thursday 12/9 afternoon Pacific time

Two Pfizer shots in February, a booster in October, and I still caught the Omicron variant.  Caught it at a Slava (Serbian celebration of patron saint).  Brother and sister in law (both caught it, both vaccinated, both exhibiting flu-like symptoms).  

I am asymptomatic.  Mrs. Mick (didn't get the booster), her parents, our sons all attended the event and currently test negative.
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#19
I don't know if I got Omicron or Delta, but 12 days ago I tested at home before travel and was positive.   Ended up with runny nose and nothing else.  Wife and other contacts all tested negative.  

Hope you are yours don't develop any serious symptoms, Mick!
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#20
How fast is the spread?  The CDC shows that 2.27% of NYC had a new positive test in the last week.  That would mean something like 8% next week (until all the tinder has been exhausted).  With that many positive tests, I have to wonder what the number of unreported, but known, cases are,  and then what all the undetected cases are.

1.5 years ago, I ran numbers for a lower R and found that the number of people sick at anyone time (not newly diagnosed, but diagnosed & in isolation) tended to top out in the 20-30% range for a completely vulnerable population.   As R drives the number sick higher, there are fewer and fewer vulnerable people.   

So, back of the envelope, I'd guess NYC will peak in 2 to 3 weeks.
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