Coronavirus / COVID-19

[SurfD]

I have heard statements along the lines of something to the effect that Omicron picked up some elements of the common Flu in it's mutations, and part of me immediately went: FUCK, because if it is possible for Omicron to learn from the Flu, does this mean it could be possible for the Flu to learn from Omicron?  Like, literally the last thing we need right now is some kind of supercharged general Influenza running around that managed to pick up antibody evasion from Covid........

Or am I completely misunderstanding the context of how that is being discussed?

[Trippy]

I would need to see these statements in context to better understand what they are trying to say but flu viruses (influenza viruses) are different in structure and how they invade cells than coronaviruses. So they don’t really mutate in the same ways. If these statements were referring to things like infectiousness and deadliness in the general sense, rather than via specific mechanisms or mutations, then yes all infectious diseases can be ranked accordingly. I.e. influenza and corona viruses can both mutate into more or less infectious and / or deadly variants. E.g. the “Spanish Flu” H1N1 type A influenza virus subtype was a much more deadly version of the normal A type. On the flip side there are corona viruses that have very low lethality and are considered “common cold” viruses.

There is conflicting information about the lethality of the Omicron variant but it may be less lethal than Delta while also possibly being more infectious. Again it’s still too early to know for sure but assuming this holds true then SARS-CoV-2 is, in some sense, evolving to be more like our influenza viruses in effect, but not actual mechanics since they are still different viruses. And again on the flip side if you look at our most recent flu outbreaks that scared people because of their increased deadliness — I.e. the “bird flu” H5N1 type A outbreak and the “swine flu” H1N1 type A outbreak — those were variants and subtypes of the type A influenza virus that the Spanish flu also came from. In other words it’s likely in the future we’ll have another deadly influenza pandemic.

[01101010]

I would need to see these statements in context to better understand what they are trying to say but flu viruses (influenza viruses) are different in structure and how they invade cells than coronaviruses. So they don’t really mutate in the same ways. If these statements were referring to things like infectiousness and deadliness in the general sense, rather than via specific mechanisms or mutations, then yes all infectious diseases can be ranked accordingly. I.e. influenza and corona viruses can both mutate into more or less infectious and / or deadly variants. E.g. the “Spanish Flu” H1N1 type A influenza virus subtype was a much more deadly version of the normal A type. On the flip side there are corona viruses that have very low lethality and are considered “common cold” viruses.

There is conflicting information about the lethality of the Omicron variant but it may be less lethal than Delta while also possibly being more infectious. Again it’s still too early to know for sure but assuming this holds true then SARS-CoV-2 is, in some sense, evolving to be more like our influenza viruses in effect, but not actual mechanics since they are still different viruses. And again on the flip side if you look at our most recent flu outbreaks that scared people because of their increased deadliness — I.e. the “bird flu” H5N1 type A outbreak and the “swine flu” H1N1 type A outbreak — those were variants and subtypes of the type A influenza virus that the Spanish flu also came from. In other words it’s likely in the future we’ll have another deadly influenza pandemic.

 Well Influenza A is the most prevalent currently - H3N2 primarily so far. That said, we are still well below the average so far - based on the flu surveillance network at least. Seems to be spotty flair ups but nothing widespread. Strange world we live in.

[Trippy]

First large-scale study of Omicron from South Africa. I can't link to the Press Release directly because of their fucked up Web interface but you can get to it from here:

https://www.discovery.co.za/corporate/news-room

You want the article titled: "Discovery Health, South Africa’s largest private health insurance administrator, releases at-scale, real-world analysis of Omicron outbreak based on 211 000 COVID-19 test results in South Africa, including collaboration with the South Africa"

Here's the PDF link if you trust it:

https://discovery-holdings-ltd.mynewsdesk.com/pressreleases/discovery-health-south-africas-largest-private-health-insurance-administrator-releases-at-scale-real-world-analysis-of-omicron-outbreak-based-dot-dot-dot-3150697.pdf

Summary:

1. Vaccine effectiveness:
o The two-dose Pfizer-BioNTech vaccination provides 70% protection against severe complications of COVID-19 requiring hospitalisation, and 33% protection against COVID-19 infection, during the current Omicron wave.

2. Reinfection risk: For individuals who have had COVID-19 previously, the risk of reinfection with Omicron is significantly higher, relative to prior variants.

3. Severity: The risk of hospital admission among adults diagnosed with COVID-19 is 29% lower for the Omicron variant infection compared to infections involving the D614G mutation in South Africa’s first wave in mid-2020, after adjusting for vaccination status

4. Children: Despite very low absolute incidence, preliminary data suggests that children have a 20% higher risk of hospital admission in Omicron-led fourth wave in South Africa, relative to the D614G-led first wave.

I believe the variants with the D614G mutation that are referred to above are B.1.1.54, B.1.1.56 and C.1, as gleaned from this paper:

Nature: Sixteen novel lineages of SARS-CoV-2 in South Africa

So the relative numbers are relative to something(s) other than Delta (B.1.617.2).

[Khaldun]

#4 is a bit concerning.

[Tale]

Moderna's chief medical officer disagrees with initial interpretations of the South African findings.

Vaccine maker Moderna’s top medic has warned the world not to underestimate the threat from the COVID-19 omicron variant, saying it was “a severe disease” and could work in tandem with delta to create further “worrying mutations”.

“I actually do not think that omicron is a milder, less severe version of the current virus,” Moderna’s chief medical officer Paul Burton told a British parliamentary committee late on Tuesday (AEDT).

His biggest concern was that omicron and delta will co-exist in Europe for an extended time, during which people could be infected with both strains.

“This gives the opportunity for these viruses to further evolve and mutate, which is concerning and worrying,” he said.

“There are 50, 60, 70 thousand cases of delta a day in some European countries, including the UK. To bring omicron into that backbone, that background, of COVID is concerning.”

Dr Burton’s stark warning was in contrast to more upbeat evidence to the same committee from Angelique Coetzee, chairman of the South African Medical Association.

[schild]

Wife got it. Omicron, clearly. All upper respiratory. Thought it was normal allergies. Took test. Not allergies.

I tested negative.

She is now quarantined to the first floor.

[Hawkbit]

I hope she recovers as fast and easy as possible.

My 16yr old got a classroom exposure notification on Friday. Apparently the exposure happened somewhere on Mon-Wed. We got a test for her and it came back neg on Saturday, so hopefully no worries.

I will say that testing was far easier and faster this time around than last year this time. The swab didn't need to go deep and she used the swab on her own nose.

[slog]

My daughter works in one of the hospitals here, managing the people that draw blood from the patients (she also draws herself and drives to the area nursing homes).  She was telling me how the team things a certain bed is cursed because the COVID patients that get said bed always die.  That's not true about the other beds, but this one in particular seems to be cursed.  She's got a good disposition for that line of work, always so positive.

Edit: It's bed 372 and the most recent guy died last night.  My daughter only knew him as "the guy that said he just wants to feel better,"

[schild]

4 days after symptoms. I'm still negative, she's still positive.

[01101010]

4 days after symptoms. I'm still negative, she's still positive.

Interesting. Either those tests aren't that reliable or you are naturally immune. 

[Samwise]

4 days after symptoms. I'm still negative, she's still positive.

Interesting. Either those tests aren't that reliable or you are naturally immune. 

Or he'd already had it and gotten over it before taking the first test.   

[Trippy]

Or their quarantine setup is working.

[01101010]

Or their quarantine setup is working.

True too...

[Mandella]

4 days after symptoms. I'm still negative, she's still positive.

Interesting. Either those tests aren't that reliable or you are naturally immune. 

This happens a lot. I got it, wife didn't. We did divide the house up too, but only after I started showing symptoms. A friend of mine got it, husband never did, and they didn't even bother to divide the house -- I guess they are just more into sharing than I am.

Some folks just have a high natural resistance. Of course, there is no guarantee that will hold up across multiple strains.

[Trippy]

The US Food and Drug Administration has granted emergency use authorization to Pfizer's Paxlovid SARS-CoV-2 antiviral tablets treatment. I'm not sure, if like the SARS-CoV-2 vaccines, this also requires approval from the CDC before it can be prescribed but in any case it's good news since it was very effective in its trials and very safe (as safe as a placebo). Pfizer claims it's also effective against Omicron but that's based on lab tests and not trial data. However the protein that the treatment targets is not the mutating spike protein and is a separate intracellular protein involved with replication so Pfizer's claim will likely hold true.

We've also basically run out of the only anti-SARS-CoV-2 monoclonal antibody treatment that's effective against Omicron here in the US (GlaxoSmithKline’s sotrovimab) so we urgently need another way to treat serious Omicron infections right now.

FDA: Coronavirus (COVID-19) Update: FDA Authorizes First Oral Antiviral for Treatment of COVID-19

Pfizer PR: Pfizer’s Novel COVID-19 Oral Antiviral Treatment Candidate Reduced Risk of Hospitalization or Death by 89% in Interim Analysis of Phase 2/3 EPIC-HR Study

Fierce Biotech: Pfizer's COVID-19 antiviral is expected to work against the omicron variant

The Hill: Only one antibody treatment works against omicron — and it's running out

[schild]

Or their quarantine setup is working.

Multiple stories. She's on a story with no air recycling to the floors above it. While she's near the entryway, obviously with the garage and front door, that's the most airflow in the entire house. I'm not even sure you could catch norovirus on the first floor.

[pxib]

i was telling my dad, ever the skeptic, about corrupted blood back in March at the start of lockdown, and how the cdc studied it. how it can be used as a model for what to do and how people might act in the event of an unpredicted pandemic, and how people were playing out the same behavior during covid.

he said “so they fixed it, right? how did they fix it in the game?” and i told him the truth: they didn’t. they couldn’t control it. they had to reset the servers and roll them back to the time before the ZG encounter.

Some further discussion here.

Wikipedia on research into the Corrupted Blood incident.

[Sir T]

Brother and partner has it. Brother has headaches, fatigue and muscle pains, but he says he is alright. Partner was hit much harder, including vomiting. Brother is boosted, partner only double vaxxed.

[Mandella]

Second go round snuck up on me. I'm double vaxxed and boosted Moderna, and I honest to god thought I had a regular head cold. But then my daughter and her family started getting sick with the same starting symptoms so I took a home test and I got the second line right away.

Really sucks because since I have had the original Covid and the starting symptoms were nothing at all like what I felt like before I went a few days just ignoring what turned out to be Omicron, instead of quickly quarantining myself like I did back in 2020. So folks this is not the time to discard that abundance of caution.

But good news at least for me is that I appear to have been nearly over it when I tested, and never felt really bad. And looking at incubation times and encounters I'm probably not the one who infected my kid and grandkids, but I easily could have.

[slog]

One of my wife's coworkers just tested positive for the third time in two years.  He's been sick each time. 

Three times! That's got to really suck.

[01101010]

One of my wife's coworkers just tested positive for the third time in two years.  He's been sick each time. 

Three times! That's got to really suck.

Here we go.... 

[slog]

One of my wife's coworkers just tested positive for the third time in two years.  He's been sick each time.  

Three times! That's got to really suck.

Here we go....  

I will ask her more about it if you are interested.  I met him at the company Christmas party, here is what I know, he's a 45 year old dude who is about 5'7" and over 300 pounds.  Definitely a high risk candidate.  I don't know if he's vaccinated.  Covid is spreading rapidly in this dealership and a lot of the blue collar peeps are not vaccinated.

Edit: I asked anyway.  He's also a smoker who got the Johnson and Johnson shot, not boosted.

[eldaec]

I'm also now off sick with covid for the third time.

Have 3 shots of vaccine.

Rest of the family is fine happily enough. We aren't really isolating within the house. We have two young kids and I have no idea how people manage to isolate properly in a typical European size house if they have young kids.

Covid just hates me.

[slog]

My daughter (who lives in the in-law apartment at my house) just tested positive today at the hospital. We have all have what what feels like a cold (stuffy nose, headache, cough with no other symptoms. We did the at home tests and tested negative yesterday.  I did another at home test today, still negative.

[Samwise]

We did the at home tests and tested negative yesterday.  I did another at home test today, still negative.

After hearing a few stories like this (plus the FDA saying you need to do a PCR test if you have symptoms) I'm convinced the at-home tests just don't work on mild Omicron cases.  Curious what the result of a PCR is if you're able to get one.  I've also heard that the at-home tests work better if you swab your throat as well as your nose (I guess Omicron likes to hang out further back).

[eldaec]

Everything I've read suggests the lateral flows are really testing if you are infectious above a certain degree rather than whether you have it.

Which makes them useful even if not completely accurate.

[slog]

We did the at home tests and tested negative yesterday.  I did another at home test today, still negative.

After hearing a few stories like this (plus the FDA saying you need to do a PCR test if you have symptoms) I'm convinced the at-home tests just don't work on mild Omicron cases.  Curious what the result of a PCR is if you're able to get one.  I've also heard that the at-home tests work better if you swab your throat as well as your nose (I guess Omicron likes to hang out further back).

Soonest I can get a test is Sunday,  I'll be sure to provide an update.

[Trippy]

There are results at-home PCR tests now too. Expensive but might be worth getting if you can't easily get a PCR test elsewhere.

E.g.: https://www.amazon.com/Lucira-COVID-19-Single-use-Quality-Molecular/dp/B092KGQT2Y

[Hammond]

Caught something, seems like a really mild head cold. Waiting on results from a covid test just to be sure. There has been a bunch of people with head colds around that have tested negative from what the nurse said. So you never know. Was going to do a at home test but everywhere is sold out.

I have been pretty safe and not around anyone that was obviously sick. Although 2 years into this without catching Covid I figured my number would come up sometime. Vaxed with Pfizer and got the booster in early December.

[Mandella]

Both my wife and son-in-law tested too early, right when they started to have symptoms (wife was home test, son-in-law was at a clinic) and both came out negative, and then obviously were sick. Son-in-law got a later test that showed positive (he needed it for work benefits).

Both my wife and I really just had head colds, although worrisome because COVID. Son-in-law ran a bit of a fever and felt more like he was having a bad flu. He's vaccinated, but I don't know if he got boosted.

So I would suggest don't trust the tests, at least not early on, and just assume if you have the symptoms you got it. Good news is it really does seem like a much milder variant, although long term effects, if any, are as yet unknown.

[Tale]

The PCR testing system in Australia has utterly broken down. My state NSW officially had 35,000 cases today (22,000 yesterday) but it's surely far more.

Numerous PCR testing places have closed until they deal with a backlog of results. Neighbours tested on Boxing Day are still waiting for results. One major PCR testing company has actually said "fuck this" and quit the business entirely, closing all of its doors. Rapid antigen tests have sold out and nobody can find any. The government has thrown up its hands and said basically "call your doctor if you feel sick".

None of my family have it yet. Closest confirmed case is my boss's husband (I haven't worked in the office since March 2020). My father is in a locked-down hospital and was a casual contact of a case, but has been cleared. My wife, my toddler son and I drove back from Melbourne (17,000 cases today) to Sydney over the previous two days and we're healthy. I did a week's grocery shopping at 7:30am today and the shops were very quiet, but many shelves are bare and fresh produce is going bad because too many staff are in isolation after being exposed. To keep things running, they're changing the definition of close contact to something like "sticking tongue down infected person's throat for four hours".

I'm scheduled for my booster shot tomorrow morning (Thursday). I'm spending my days on the phone trying to get my dad moved from hospital to aged care, but the nursing home that wanted to take him last week is in lockdown this week due to a positive case, so I'm chasing plan B. It's a fucking nightmare and all I can do is phone him and talk down his paranoid dementia. We likely won't be able to visit him even if he gets moved, and I can only hope he outlives this outbreak to see my son again. Dad's anti-lockdown sister is sending furious emails from Scotland.

[Sir T]

Ya the Testing system has pretty much gone kaboom here in Ireland too. They simply cannot keep Antigen tests stocked in Chemists, and the PCR testing system has maxed out.

https://waterford-news.ie/2022/01/04/out-of-hours-gp-services-overwhelmed-as-pcr-testing-maxed-out/

[HaemishM]

No at-home tests to be had here in Jackson, MS for 20 miles, and I booked the literal last appointment for the metro area at the drive-in testing site on Saturday. Testing has just failed completely because of our lack of attention to it. I can understand back in say March or April thinking we didn't need to ramp up testing capability since we had vaccines. By June, though, it should have been abundantly clear that the anti-vaxx Chuds were going to overwhelm testing capacity at some point, and we have reached that point.

[Hammond]

Thankfully up here in Washington UW has partnered with quite a few hospitals to provide testing. The test site I visited had nobody waiting and I just breezed through.

I am treating myself like I have covid even if I don't. Working from home is fine with my company and myself so its not like I am not getting my work done anyway.