To Vaccinate or Not---The Rat Flu Odyssey Continues

[jono]

Those slipped past me so I won't argue the results. I didn't see real world evidence that any variants spread faster than OG covid.

I would be surprised if R0 ever existed in the real world for any variant, since people started taking various levels of precautions after OG. In addition to increasing immunity. That said, the slope of the case count graph in the US was higher for longer at least 3 times: 11/2020, delta in '21 and then omicron, with omicron being the clear winner.

https://coronavirus.jhu.edu/region/united-states

[bodywhomper]

Wife told me today that one of her families (family of 6, including a grandma) just wrapped up their second round of infections since early December 2023. Meaning it entered their home after thanksgiving, made its way through the household, they had a little over a month of reprieve before they all caught it again. Testing, apparently, using RAT. Presumably, different variants. Fkna!

[LongShortLong]

eta: Damn I'm cruising toward my own wall of text thread

I would be surprised if R0 ever existed in the real world for any variant, since people started taking various levels of precautions after OG. In addition to increasing immunity. That said, the slope of the case count graph in the US was higher for longer at least 3 times: 11/2020, delta in '21 and then omicron, with omicron being the clear winner.

https://coronavirus.jhu.edu/region/united-states

I agree with you about the misuse of "R0," but it seemed to be common to misuse it in that way to create the study titles and article headlines of "variant R0 similar to measles!!1!11"The English language was a casualty of Covid, with plenty of opportunity for semantics, pedantry, and misunderstanding. Or maybe it was a collision of silos each with their own jargon that happened to use each others' words with different meanings.

I also accept your complaints about using R0 as a metric. Unstated complaints as well. Your thread contributions and many others' have been honest, truthful, and pushed the discussion forward. I pick nits because you're worthy.

That graph has a linear scale, so a 10x growth from 1000 cases to 10,000 cases over 10 days has a slope of 900 cases per day. That 10x growth looks kinda flat compared to a doubling of 100k cases to 200k cases over ten days with a slope of 10,000 cases per day, yet 10x growth is way faster than 2x. We need a logarithmic y-axis on that graph if we wish to visually compare growth rates.

So I'll mouseover and directly read values off the graph picking fortnights with roughly the steepest slopes. I contend that a more thorough treatment would produce similar results.
OG Covid 14 days 2020, Mar 18 - Mar 31, cases went from 3,300 to 27k, about 8x. Growth in China was similarly fast.*
11/2020 (also OG?) 14 days 2020, Nov 1 - Nov 14, cases went from 96k to 159k, less than 2x.
Omicron 14 days 2022, Dec 21 - Jan 3, cases went from 195k to 628k, a little more than 3x.
Delta left as exercise for the reader.

* I think it's fair to claim that Covid started spreading before we (or China) started counting cases, so we were getting better at finding cases while we were counting them. If you wanted to argue Covid spread cryptically over twice the time period then we should halve the estimated growth rate. Even so, OG covid spread very fast. 4x/fortnight instead of 8x if we use my crude estimate above.

The faulty argument I saw in papers and headlines went roughly like this: OG Covid's R0 was say 3, delta spread say twice as fast as OG when it took over, and omicron again say thrice as fast as delta. So multiply it all up and modern covid has R0 = 3 * 2 * 3 = 18, similar to measles, yikes. But not so fast - My contention is each variant would have spread about the same in a naive population, and instead we were seeing rising immunity to infection with the older variant, and all the variants have R0 somewhere between 2 and 3, possibly as high as 5.

[old goat]

In the middle of a measles outbreak, Florida surgeon general tells parents it's ok to not vaccinate your kids and send them to school.
https://wapo.st/49Gxfj9

[jono]

eta: Damn I'm cruising toward my own wall of text thread

Maybe a little. I wasn't so much complaining about R0 as pointing out that it's a "both can be true" situation: R0 values are estimates, but even if they're right, real world growth rates wouldn't match or even vary directly with it because of all the factors that turn it into R(/=0), several of which we've both acknowledged.

The other problem with that graph is that it's all variants combined, so it doesn't show where, for instance, omicron initially moves up from 0 because that's overlaid with the descending delta infections. So this is super rough.

And there may have been more patient zeroes in the US for omicron. Even so, 25x higher case count at the end of a spike is pretty hard to explain without a higher R0. Not impossible, but unlikely.

Some published estimates (no idea if they've been improved on by now):

"The original SARS-CoV-2 has an R0 of 2.5, while Delta variant had an R0 below 7. The Omicron variant is suspected to have an R0 value as high as 10..."

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8798788/

[bodywhomper]

In the middle of a measles outbreak, Florida surgeon general tells parents it's ok to not vaccinate your kids and send them to school.
https://wapo.st/49Gxfj9

Link to his memo

https://s3.documentcloud.org/documen.../file_1664.pdf

[PB]

.... failed to mention death as a symptom.

[californiagrown]

My wife is one of those people that judges the shit out of folks if they dont get the covid vaccine for political or conspiratorial reasons. Meanwhile, she hasnt gotten vaccinated for either flu or covid in more than a year because it hasnt been convenient, has basically been sick nonstop since November (we have a 2 yr old that started daycare last summer), and our monthly covid test budget is averaging $80/month. Frustrating.

Meanwhile i happily and naively let anyone in a white coat dose me up with whatever is available out of a sort of guilt from all the suspicious substances i haphazardly and enthusiastically ingested in my 20s. Its the opposite of my friend i had who in 2021 seamlessly transitioned from his story about enjoying blow and alcohol with a slutty girl the night before into a story about why he didnt trust the vaccine because he was worried about the lack of drug research and the effects the vaccine could have on his health.

[bennymac]

[Trackhead]

My wife is one of those people that judges the shit out of folks if they dont get the covid vaccine for political or conspiratorial reasons. Meanwhile, she hasnt gotten vaccinated for either flu or covid in more than a year because it hasnt been convenient, has basically been sick nonstop since November (we have a 2 yr old that started daycare last summer), and our monthly covid test budget is averaging $80/month. Frustrating.

Why are you even testing? If your not eligible for Paxlovid and otherwise healthy, why test?

[riser4]

I tested with my current cold because of a funny smell/lack of smell. Negative twice. I get sinus issues and usually a funny smell with sinus colds, it's normal for me. I tested because thing#1 works in a school and my wife is an LCMHC who sees some patients in person. If I had the 'rona, I'd want both people to know so they could mitigate their exposure to others. I tested because I think I'm eligible for the 'lovid if I test in time, right?

[bodywhomper]

We’ve tested to not be vectors spreading in our community, extended family, or places of work.

[Trackhead]

If you’re positive what is your protocol? And negative?

[bodywhomper]

I had a direct exposure at work in December. Coworker tested themself when they got home from work that day cuz they were symptomatic, informed our boss, boss informed the rest of the team. I appreciated knowing. It was right before the holidays and I altered behaviors. Never caught it, but was less than 1 month since receiving my booster.

Positive: Isolation in a room in the house (ie a sick room) and wearing mask when out of room for toilet use (it sucks). For the household, it would depend on who tested positive and symptoms of those testing negative. Those that are negative would change their social plans and wear masks in indoor spaces. We have not had to go through this process in my household. We’d also be blasting filters at home. Isolation ends when test is negative. I’d work from home if needed and call in sick for my side hustle at then ski hill. Wife (works at a school) would call in sick - her boss has long covid and would fully support not coming into work until testing negative.

Negative with symptoms: stay home as much as possible and wearing mask in public indoor spaces when have to be out and about. This is generally the protocol we’ve followed when there some other respiratory virus in our home (ie almost all of Xmas break. 2 of my nieces were sick on Xmas and spread it to everybody else cuz my in-laws ignored that their kids could get their entire family sick - it sucked). We tested one symptomatic person every few days at home during that time.

We’ve only tested when there are no symptoms in the house if we’re going to spend time with elderly family (one has T2D).

[Trackhead]

I only test healthy people in clinic if they are curious or encourage testing if someone like Grandma is coming to visit. Otherwise, if it won’t change treatment, I don’t test. I encourage testing only if in window for antivirals (Tamiflu/Paxlovid) and meet risk criteria for antivirals.

I never test for RSV unless it’s infant, or elderly with respiratory distress/hypoxia. But even then, doesn’t change much.

[bennymac]

it doesn’t change what happens in a clinic/ER between a healthy young patient and the clinician - but it could easily still change what that patient wants to do to protect others/prevent spread

[Trackhead]

it doesn’t change what happens in a clinic/ER between a healthy young patient and the clinician - but it could easily still change what that patient wants to do to protect others/prevent spread

Yup, which is why I offer testing to anybody that wants it, but also let them know if it will/ will not change treatment.

The thing with covid and home testing, you could be negative at home test, but easily have influenza, which is also nasty. So where's the ethical boundary for seeking an influenza test regarding isolation? Seems the ethical boundary only applies to covid, but influenza is pretty damn rough on elderly folks and some kids.

[californiagrown]

Why are you even testing? If your not eligible for Paxlovid and otherwise healthy, why test?

My buddy in the office next to me has a family member with respiratory issues that have them visiting the ER monthly so he appreciates knowing when I test positive for RSV/FLU/Covid.

And we test at first symptoms. So really it's a way for us to see if it's COVID (we've both had COVID with real mild symptoms before) or just a mild cold. If we start feeling worse than a mild cold, we are shutting 'er down anyways and yeah, there isn't much point in testing other than to put a name to it at that point.

[bennymac]

Home testing kits for the flu aren’t as available - but they’re out there. Nothing is perfect of course - you could be covid positive or flu positive and test negative giving you a false sense of security. But maybe out of covid will come a better understanding of when people need to temporarily isolste to prevent infecting other people - especially vulnerable people. But maybe that’s too optimistic!

[Trackhead]

Looks like FDA approved home covid/flu test last year. Interesting…

[bennymac]

These reportedly have sensitivity and specificity approaching PCR - powered by a AA battery and for home use. I have two of them but haven’t had to use them (knocks on wood)

[LongShortLong]

Some published estimates (no idea if they've been improved on by now):

"The original SARS-CoV-2 has an R0 of 2.5, while Delta variant had an R0 below 7. The Omicron variant is suspected to have an R0 value as high as 10..."

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8798788/

That's an example of the inflated R0's. One referenced paper (Burki, 2021) presents the high R values but no evidence. The other (Ito et al., 2021) defines a relative reproduction number, their value is 3.19 for omicron vs delta. Presumably Burki or their source multiplied relative reproduction numbers (determined similar to Ito) to calculate reproduction numbers of each variant - the R's of 7, 10, etc. That's an error, as I described. They assume the same epidemiological conditions are present, but they are not. The population under study certainly has some immunity to delta infection and none to omicron. As a counterexample, why didn't beta surge again? It couldn't, as the population resists it. In reproduction terms, beta's R was below one. Dying delta's R was likely near 1 as well. So the proper multiplication for omicron is about one, times 3.19. That's why I contend covid's R is nowhere near measels'.

To be fair, they are experts, and I'm a crank who's good at math, decent at reasoning, can read a paper, and has an inflated sense of his ability to form an opinion.

It's an interesting question what would happen if covid didn't change. We may all have sufficient herd immunity against OG covid so that it can no longer spread. Maybe all old variants are as dead as smallpox. Is herd immunity lifelong, or just long enough to suppress the old variant while the new one takes over?

Graph here of variant prevalence over time. Old variants appear dead.
https://nextstrain.org/ncov/gisaid/n...orth%20America

[jono]

Dying delta's R was likely near 1 as well. So the proper multiplication for omicron is about one, times 3.19. That's why I contend covid's R is nowhere near measels'.

R << R0 though. R0 only happens when a naive population takes no precautions. Which is why measles outbreaks are so small: no naive population. R0 estimating requires looking at the fastest spread and then backing out factors that slowed it down to estimate the higher number.

By the time delta was dying it faced a cautious population (delta had been the deadliest to date and omicron was a fast-spreading unknown) with widespread immunity to delta: prior delta infections, some cross immunity from pre-delta exposures and strong cross immunity from omicron infections, on top of effective vaccines that became highly effective against delta with boosters. Even with heterogeneity, sub-populations got to choose their own immunity. The graphic you linked is really stark (at least for North America) but it's not very surprising given all those factors.

So no post-OG variant ever really had a chance to show off its R0. I'm not sure how much this effects the rest of your reasoning and I've got no opinion about the measles comparison. They look kinda roughly similar if I squint at a wind coming out of the sun. Maybe. IDK

[summit]

In the middle of a measles outbreak, Florida surgeon general tells parents it's ok to not vaccinate your kids and send them to school.
https://wapo.st/49Gxfj9

What a fucking piece of shit

.... failed to mention death as a symptom.

Death is a sign

[Thaleia]

My wife is one of those people that judges the shit out of folks if they dont get the covid vaccine for political or conspiratorial reasons. Meanwhile, she hasnt gotten vaccinated for either flu or covid in more than a year because it hasnt been convenient, has basically been sick nonstop since November (we have a 2 yr old that started daycare last summer), and our monthly covid test budget is averaging $80/month. Frustrating.

Meanwhile i happily and naively let anyone in a white coat dose me up with whatever is available out of a sort of guilt from all the suspicious substances i haphazardly and enthusiastically ingested in my 20s. Its the opposite of my friend i had who in 2021 seamlessly transitioned from his story about enjoying blow and alcohol with a slutty girl the night before into a story about why he didnt trust the vaccine because he was worried about the lack of drug research and the effects the vaccine could have on his health.

The biggest anti vacc guy in my circles drinks heavily (and drives), smokes cigarettes and black market shatter (weed processed with butane).