outbreak! (ebola, sars, coronavirus, etc)

In honor of alpine static's backward glance, I bring you all the best reason for taking the same trip across those two months of posts:

We have no yard, and he must pee

Man Ellison just isn't trying anymore.

― Stoop Crone (Trayce), Tuesday, March 3, 2020

So France is requiring masks outdoors now too? That’s going to go over really well here when we can’t get half the population to wear then indoors.

Worth copying and pasting here from behind WaPo paywall:

‘Crazy’ omicron surge could peak soon, but the virus is unpredictable as the pandemic enters its third year

Columbia University researchers estimate infections could top out during the week of Jan. 9
—————————————

By Joel Achenbach
December 30, 2021 at 7:03 PM ET

The rapid surge of omicron infections in the United States may be relatively brief, measured in weeks rather than months, according to infectious-disease experts who have been astonished by the speed of the coronavirus variant’s spread — and who are hoping this wave ebbs just as quickly.

The idea of a rapid peak and swift decline has a precedent in South Africa, the country that revealed the presence of omicron in late November. Cases there spiked quickly and then dropped with unexpected speed after only a modest rise in hospitalizations. An especially transmissible virus tends to run out of human fuel — the susceptible portion of the population — quickly.

Some forecasts suggest coronavirus infections could peak by mid-January.
“Omicron will likely be quick. It won’t be easy, but it will be quick. Come the early spring, a lot of people will have experienced covid,” William Hanage, an epidemiologist at the Harvard T.H. Chan School of Public Health, said in an email Thursday.

But this has always been an unpredictable virus, going back to when it first appeared two years ago, on Dec. 31, 2019. The virus had probably been spreading for a month or more, but that was the day infectious-disease experts around the world began hearing by email and text about an outbreak of a mysterious pathogen causing pneumonia-like respiratory infections in Wuhan, China.

No one on that day could have known that this pathogen, initially called the “novel coronavirus” and later named SARS-CoV-2, would trigger the most brutal pandemic in a century. And no one today knows when it will be over.


Forecasts of how the pandemic will play out have repeatedly been incorrect, to the point that some modelers have stopped trying to make caseload projections four weeks out, instead limiting their forecasts to one week ahead.

Because beyond a week, who knows?

Forecasts of the current winter wave, in which omicron has come riding in atop an existing delta wave, are somewhat more plausible. Columbia University researchers have a model that projects a peak in cases during the week beginning Jan. 9, with about 2.5 million confirmed infections in that seven-day period — and potentially as many as 5 million.

Columbia epidemiologist Jeffrey Shaman said the infection numbers reported in recent days are already at the high-end of projections, and the peak could come sooner. Omicron is setting new daily records for infections with the virus. The seven-day average of new, officially confirmed daily cases soared to more than 300,000 Wednesday. Then came the eye-popping Thursday numbers from state health departments and the Centers for Disease Control and Prevention — 562,000 new cases, pushing the seven-day average to 343,000.

The official number captures only a fraction of the true number of infections. People who use rapid tests at home may not report positive results. Many others never get tested when sick. And some people are infected but asymptomatic or pre-symptomatic.

Shaman estimates the number of infections is four to five times the official count. Given that people remain infected for many days, that translates to many millions of active infections across the United States.

“We’re talking somewhere up to maybe 10 million people,” Shaman said. “Maybe not all of them are contagious yet. Crazy numbers. Crazy, crazy numbers.”

When infections begin to drop, hospitalizations could still rise for a period as the disease progresses among those most vulnerable to a severe outcome. Forecasts posted Monday by the CDC show national hospitalization rates rising steadily in the weeks ahead, with daily new hospital admissions topping 15,000 by mid-January — although the projections from different research teams varied widely.

The predictions of a short omicron surge are reflected in hopes expressed at the highest level of the federal medical bureaucracy.

“My hope is that we get a sharp peak with omicron, and it goes down to a very, very low level, and it just sort of stays there, and we don’t have any more really problematic variants,” Anthony S. Fauci, President Biden’s chief medical adviser for the pandemic, told The Washington Post on Wednesday.

But Fauci and other experts have consistently been surprised by the mutability of the virus. Some scientists did not think a variant with the number of mutations evident in omicron could be an effective transmitter.

“We are dealing with a virus that has a completely unanticipated level of transmissibility,” Fauci said. “We thought delta was very transmissible. This thing is like something we’ve never seen before.”

In the United States, vaccinations — including boosters — have blunted much of the impact of the latest wave of infections from the omicron variant, which appears to be innately less capable of generating severe disease.

That has led to a shift in the Biden administration’s strategy, with a new emphasis on keeping the economy running and shying away from top-down restrictions. All the while, the administration continues to push the available tools for fighting the pandemic, including testing, indoor masking, vaccinations for those reluctant to get the shots and boosters for those eligible for another dose.

But a more spontaneous shutdown has been underway since just before Christmas.

Airlines have canceled thousands of flights because of staffing shortages. The Smithsonian closed a few of its smaller museums. Some college football teams decided not to attend their bowl games. Broadway shows have gone dark. Actor Hugh Jackman, mildly sick with covid-19, is not anticipated back onstage in “The Music Man” until Jan. 6.

This is a new phase of the pandemic, one with sweeping disruptions but probably not the same level of fear and anxiety as earlier periods. Omicron appears milder. For many vaccinated people, it appears to present itself more like a bad cold than something capable of crippling the world economy — although the ramifications of the phenomenon known as “long covid” remain not well understood.

Scientists don’t know precisely why omicron tends to cause less severe illnesses than delta or other variants of the coronavirus. It is likely that immunity plays a role, as so many people have been infected previously or have been vaccinated.

That appears to have been the case in South Africa, hard hit by the virus in advance of the omicron wave.

A study of more than 7,000 people, posted online but not yet peer-reviewed, reported high levels of antibodies to the coronavirus in South Africa before the omicron wave. Omicron spread faster than previous variants, but rates of hospitalizations and excess deaths “did not increase proportionately, remaining relatively low,” the study found.

Research on mice and hamsters suggests that omicron is innately less dangerous, apart from population immunity. Although omicron appears to grow especially well in the nose and upper airways, leading to much higher viral loads and easier transmission, it may not invade the lungs as well as earlier variants.

“The dam has broken with a milder variant. Most people who made the correct choice to get vaccinated are protected from severe disease,” said David Rubin, director of PolicyLab at Children’s Hospital of Philadelphia.

Rubin predicts a swift recovery for much of the country in January but notes this is likely to vary geographically. The East Coast, including major cities along the Interstate 95 corridor, and the heavily populated states of Florida and Texas are seeing large spikes in cases, while parts of the country hit hard by delta, including the Upper Midwest, are already seeing improvements, he said.

“By the second week of January, we’re going to see the national declines, but there will be some areas struggling for sure,” Rubin said.

A model from the Institute of Health Metrics and Evaluation at the University of Washington puts the peak of this winter wave at Feb. 6, with 408,000 confirmed new daily infections.

Pandemic models are hampered by the difficulty of amassing reliable data. Testing is disrupted during the holidays. There are only rough estimates of how many people have already been infected.

The most urgent question is whether a spike in caseloads will lead to so many severe illnesses that hospitals are overwhelmed. Although some hospitals are stretched thin, the increase in hospitalizations has been modest so far compared with the rise in infections.

For now, the Biden administration is holding off on drastic measures to combat omicron, beyond common-sense efforts to get more tests in the hands of the public and to encourage vaccination. CDC has issued looser rather than tighter guidelines on the isolation time for people infected with the virus, reducing the recommendation from 10 days to five.
That covers people who are asymptomatic or are seeing their symptoms improve. The CDC’s guidance does not advise that people get a negative test before leaving isolation.

The virus has never been a static agent, nor is society a monolith, and so any forecast of what will happen in the coming weeks needs to be written with a pencil — not a pen.

Shaman, the Columbia epidemiologist, acknowledges that the model he and his colleagues have developed is based on incomplete data and must take into account a new variant that remains somewhat enigmatic.

And the virus itself may have new moves not yet anticipated.

“I’m not a betting person on this thing, ever,” Shaman said.

Jacqueline Dupree contributed to this report.

Whatever our sufferings now at least they will be alleviated in the next life! (as long as you are good)

Good morning!

Don’t worry, Omicron won’t be around for long.

As we speak, an immunosuppressed person with chronic SARS-CoV-2 infection (or perhaps an animal!) is brewing up the next weird and wonderful #COVID19 variant to emerge in the next few months.

Have a great day 🙃

— Meaghan Kall (@kallmemeg) January 3, 2022

Apologies in advance for not confining Yglesias hot takes to the designated thread:

I feel like at this point 99 percent of the population is either vaccinated and safe, under 5 and safe, or doesn’t care about Covid and it’s time for non-pharmaceutical interventions to basically go away. https://t.co/ilrfyV2sVY

— Matthew Yglesias (@mattyglesias) January 3, 2022

god he is the worst

my best friend has a litany of symptoms that could either be chronic sinusitis or Omicron. the symptoms she describes match what I had when I had my last sinus infection, including yellow discharge, which isn't a COVID symptom. she's also the type that begins to feel phantom symptoms after reading the internet to see what symptoms to expect, so it's possible it's not COVID. she tested negative yesterday, and i'm giving her one of my home tests to re-test today.

since I was around her briefly last week, now I have to test multiple times, wound up wearing a mask in the house yesterday for my dad's sake. first test negative, taking second now (managed to find some at home tests after hours of searching store by store. found in each instance the ONE STORE that had a few in stock).

btw for US Folk - On/Go is selling their test directly from their website, and Walmart has BinaxNow back in stock for online ordering/shipping in many regions. the website SimplyMedical occasionally has the QuickVue for sale but have been out lately.

the annoying thing for folks with sinus issues/allergies is that sinus infections are a common thing and if you get a bacterial infection, you could get very COVID-like symptoms. and then you might not trust your negative tests and then you might not go to the doctor to get an antibiotic and might suffer a while longer than usual.

in 2019 I got what I assumed was COVID so I decided to wait it out cos I couldn't easily get a test, but it wasn't, it was a bacterial sinus infection. temp was 101 every day for over a week, massive headache, discharge, sore throat, malaise, chills.

after day 10, I saw a doc who was like "this sounds way more like a bacterial infection, here's an antibiotic", and it was gone in days. the doctor said if I hadn't gotten the antibiotic, I mighta been fending it off another week or more.

so i'm suggesting to my friend if she tests negative again to possibly get checked for that. (of course she might test positive, so who knows).

I had a bad bacterial sinus infection in late November after a four-day headcold, probably exacerbated by a dental issue, not Covid, and antibiotics took care of it almost from the first tablet.

2019???

sorry, 2020!

It was 10/2020, shortly after I got my second shot in the trial.

another PSA from former ilxor kate78 (who is an RN in Seattle):

PSA: If you're doing an rapid test, don't forget to swab your throat for 15 seconds before swabbing your nose.

There's a growing body of literature (and anecdata) suggesting that omicron virally sheds earlier in throat and saliva, relative to nasal secretions. I have told numerous folks to try this after testing negative with just a nasal swab and they've all tested positive with the throat.

I had heard that drinking sodas prior to the throat swab could lead to a false positive (by Edward Nirenberg, virologist). can she confirm if that's the case? (i drink a lotta diet sodas so i'll make sure to avoid doing that if so)

I personally wouldn't drink anything before a throat swab? will check tho.

yeah good point. maybe i'll just do it first thing in the morning tomorrow.

btw please pass along our thanks to kate!

You’re not supposed to eat drink or smoke for 30 minutes before saliva pcr test and I would assume the same applies to ersatz saliva rapid tests (which I wouldn’t recommend tbh) but ymmv

No drinking, eating or smoking 30 minutes before LFTs but to be on the safe side, I do the test immediately on waking up, before any of those things can happen.

(who is an RN in Seattle)

(also doing a masters in epidemiology and working as a covid vaccine researcher for one of the main covid vaccine manufacturers fwiw)

Not a lot of surprises from what I've been seeing over the last week, UK-wise, so I'm posting this tweet on the lack of vaccination means Omicron is killing more people in Africa.

We are very lucky to live in the north of the globe.

The best illustration of this is Africa, where Covid deaths have passed 25% of their Delta peak in Mozambique and Angola, and are still rising.

In wealthy, well-boosted countries like the UK, deaths this wave may peak at 10-15% of the previous record. In others they may hit 50%. pic.twitter.com/toTRWLPNgp

— John Burn-Murdoch (@jburnmurdoch) January 4, 2022

thanks - Burn-Murdoch is one of the best at explaining the situation in South Africa.

I tried to swab my throat and wow was that hard but managed. I have the worst gag reflex in the world. doctors telling me to say "ahhhhhh" is the biggest source of anxiety during a dr appointment lol.

now...I wait ten mins.

xp -- that graph is a bit misleading tbh. Mozambique and Angola have among the lowest COVID death tolls per capita in the world, so even if their death rate doubled or tripled they wouldn't be anywhere close to the US, UK etc.

I don't know why that is. I would guess some of it is a mix of climate, population age, obesity levels, perhaps prevalence of heart disease and diabetes and other similar risk factors. But Angola with low vaccination could potentially still have lower per capita COVID deaths than the US with high vaccination rates. Obviously it's still long past time to get more vaccines to the rest of the world and there are plenty of poorer countries who aren't faring anywhere near as well.

Meanwhile, the Tennessee Department of Health has chosen now to begin reporting COVID data weekly rather than daily — right when Omicron has really taken off here. They made this decision in the fall, "in line with reporting of other infectious diseases," but the result is we're going to be a week behind on actually understanding what's going on.

So now "flurona" is a rhing.

thing too.

xxxpost Florida did that last summer and it utterly wrecked our data and ability to read it

another PSA from former ilxor kate78 (who is an RN in Seattle):

PSA: If you're doing an rapid test, don't forget to swab your throat for 15 seconds before swabbing your nose.

There's a growing body of literature (and anecdata) suggesting that omicron virally sheds earlier in throat and saliva, relative to nasal secretions. I have told numerous folks to try this after testing negative with just a nasal swab and they've all tested positive with the throat.

― chaos goblin line cook (sleeve), Monday, January 3, 2022 7:18 PM (yesterday)

FYI, rapid antigen tests are pH sensitive and throat pH is different than nose pH, so positives from a throat sample could be false

Yeah, seems like using a test in a way it hasn't actually been tested other than anecdotally could be problematic.

Rapid tests in the uk were both throat + nose to begin with (and 30mins to wait before reading your result). Different brands have been distributed more recently that are supposed to be nose-only - with a shorter swab stick! - and 15 min wait. One instructs you to leave the swab in the solution for 1 min before removing it, the others didn't.

would be interested to know if the tests mechanisms/ functions etc were significantly different.

I mean kate isn't the first (or even the 100th) physician to suggest this, and Michael Mina (the epidemiologist rapid test guru) has suggest there's nothing wrong with using them this way. that only saliva could hurt the results, but a throat/cheek swab is fine.

what I reject is the idea that these antigen tests can't get Omicron, as I see a lot of my friends suggesting today via gossip. my friend almost certainly has Omicron, and it detected it easily. the issue isn't that it won't detect Omicron - it's that it won't detect it 'early enough', is my understanding.

hence the throat swab

This is fairly standard in UK

Here is a how-to video

*In US it is NOT FDA authorized to do a throat swab

Does likely improve sensitivity. May potentially cause a slightly greater number of false positives. Don’t drink or eat for 30 mins beforehttps://t.co/D6lAYpwbJo

— Michael Mina (@michaelmina_lab) December 27, 2021

here's the UK guidance. the tests on sale in the US are not approved for this method. ymmv.

i'm not doing this, but i can see why you might.

good news for parents of under 5s after the pfizer fuck up (they reduced the dose so much they saw almost no response in the 2-5 group, it kind of worked in under 2s, they're now trialing a third dose):

https://www.wsaw.com/2021/12/30/moderna-vaccine-trial-young-children-nears-finish-line/

A lot of the LFTs in the UK are specifically nasal only and nobody I know who tested +ve (which is a lot of people!) needed a throat swab to do so. ¯\_(ツ)_/¯

8 w Covid in our house. We are all fine now (yay science! Thanks vaccines!!), but wanted to share our testing results in case it helps decision making. 🧵

TL;DR: antigen and PCR tests were both unreliable making it very difficult to know whom to quarantine from whom.

— Anne Carpenter, PhD (@DrAnneCarpenter) January 4, 2022

:shrug: what a mess.

Good op-ed from David Leonhardt about how kids continue to bear the heaviest burdens of COVID restrictions despite having the least health risk:

https://www.nytimes.com/2022/01/04/briefing/american-children-crisis-pandemic.html

i got unironically emotional watching the queer eye episode about a school prom under covid last night. (i have never seen this show. is it always like this?)

xxxpost I think people's mindset is less "antigen tests can't detect Omicron" but "antigen tests might not pick them up on the first few days of infectiousness", which....has kinda always been the case? I was told during all prior variants that a negative antigen didn't *necessarily* mean I wasn't infected, and almost all of the at-home tests here (other than On/Go I think) suggest re-testing in 24-36 hours to re-confirm (and to confirm positive results with PCRs).

the problem is, and continues to be, misuse of the results. If you are all rapid testing before a family gathering, the understanding should be "it looks like we're all not sick, but there is a non-zero risk that we are. We are accepting that risk by gathering". People instead are using it to say "WE are not at risk, now let's have a big household orgy".

Likewise, people WITH Omicron-like symptoms are testing once via antigen, getting a negative, and not re-testing (either because they CAN'T due to no appointments/at-home tests, or think they're in the clear), and they go out and think they're in the clear and test positive a few days later and scream B-B-BUT I JUST HUNG OUT WITH 30 PEOPLE.

when in reality, you should be isolating if you have those symptoms until you've had a second negative. these antigens reduce risk, they don't eliminate it, but perfect is always the enemy of good with the "elimination" folk.

It's just like the people who scream during hurricane season about the changing forecast over several days, but whose city has been in the cone of uncertainty for 3 days. They already gave you the warning that you might be hit - they gave you time to prepare! They didn't tell you to wait until they could give you GPS coordinates of where the hurricane would hit.

(with that being said - I swabbed my throat today and I see no issue if people want to do it to catch the infection earlier - there are good reasons why someone exposed but not symptomatic might want to do that if wanting to avoid exposing others).

i'm gonna say don't make up your own testing procedure because of anecdata but that's just me

@caek It's become a very touching show. Pretty much every episode gets to me.

xp that's my take.

my uk boy's whatsapp chat is now forwarding videos about how to use australian and american tests and saying they should do it like that and i'm like jfc just follow the instructions on *your* test.

Lol yes I was about to say that it’s often really emotional

Fwiw I have been doing both throat and nose since reading that is the best way to go.

xp i had to watch one of those F1 episodes to calm down!

xxxxxxpost I think this throat swab thing has the backing of prominent doctors/scientists at this point versus just internet randos, it's gotten mainstream. (https://slate.com/technology/2021/12/throat-swab-rapid-testing-omicron-effective.html, especially with Mina backing it).

but this is the fundamental problem with social media/Twitter. the news now moves too slowly, people want updates on things like hurricane forecasts, which sports players are injured/likely to start, the pandemic. so they go to Twitter/social media to get this "intermediate" data, which they get from a variety of people unqualified/qualified to give it, and entire new strategies get adopted by big pockets of people. often dispensed by cult-like personalities who attack the mainstream experts and implore you to adopt their strategy instead!

it's why people flock to this complete amateur asshole named Mike who lives in Oldsmar, FL, and runs Mike's Weather Pages. Thousands of people flock to him INSTEAD of the NHC to get HIS take on where the hurricane is REALLY going to go and insist that HE'S made the right call EVERY TIME and we should listen to him INSTEAD of the experts.

(btw, still seconding my thanks to kate for this tip - even if we don't all adopt it, it's good to hear about these suggestions. i'd rather get a false positive than false negative at this point)