☣ Coronavirus ☣

[mopgoblin]

I doubt you got rid of it last year. You got down to the point where there were no known positive cases being tracked by your government, but that doesn't mean it wasn't still circulating undetected for a while. If you had really eradicated it, then you would not have seen new positives show up among people who had no contact with a known case and no contact with inbound travelers.

There were 102 days of no detected transmission between the outbreaks last year. That's a long time for a reservoir to go undetected - it's like seven cycles of transmission if they were really pushing the limits on how far out they could be spaced every time, and over a dozen with a more realistic mean interval. It just doesn't seem that plausible for it to go undetected for that many generations, not when border fuckups would provide a much more direct route to the same observations.

We've also completed sequencing on two of the three cases detected a few days ago (and I believe we sequence as many cases as we get enough usable viral bits for, though obviously these ones were prioritised as urgent). They're an overseas variant (one of the spready ones) and while this is not my area of expertise, I can't imagine we'd see sufficiently precise parallel evolution in a tiny hypothetical reservoir.

[Cipheron]

There were 102 days of no detected transmission between the outbreaks last year. That's a long time for a reservoir to go undetected - it's like seven cycles of transmission if they were really pushing the limits on how far out they could be spaced every time, and over a dozen with a more realistic mean interval. It just doesn't seem that plausible for it to go undetected for that many generations, not when border fuckups would provide a much more direct route to the same observations.

We've also completed sequencing on two of the three cases detected a few days ago (and I believe we sequence as many cases as we get enough usable viral bits for, though obviously these ones were prioritised as urgent). They're an overseas variant (one of the spready ones) and while this is not my area of expertise, I can't imagine we'd see sufficiently precise parallel evolution in a tiny hypothetical reservoir.

Australian here btw, similar situation. They test city sewage and traces of Covid may appear in that, and they get an idea if there is reservoir of untested cases from that too. So we did see readings from that in the tail end of some of the infection outbreaks in Australian cities, but there have been no new reports about that in quite a while.

Melbourne really proves that a broad mask mandate was effective. Even if not everyone follows the rules, just having the deadline to have a mask got a lot of people to go out and purchase then one. This includes myself. So a mask mandate, even temporarily is good for overcoming procrastination.

Cases were skyrocketing last year to over 700 new cases a day and growing, then they implemented the mask rule and it fell to zero within a couple of months of that, and had a run of 61 days, among others, with no new community cases reported.

Some people say it's more about "freedom" if you leave the mask wearing as optional. However the irony there is that I can now walk around most days without a fucking mask, and if we'd left is as "optional" then there's no way I'd be doing that now.

[Gryzemuis]

Cases were skyrocketing last year to over 700 new cases a day and growing ...

Skyrocketing? Australia has 26M people, and 700 new cases a day is skyrocketing? Hahaha. Amateurs.

[Vae]

Away from thee, COVID-19!

[heywood]

There were 102 days of no detected transmission between the outbreaks last year. That's a long time for a reservoir to go undetected - it's like seven cycles of transmission if they were really pushing the limits on how far out they could be spaced every time, and over a dozen with a more realistic mean interval. It just doesn't seem that plausible for it to go undetected for that many generations, not when border fuckups would provide a much more direct route to the same observations.

We've also completed sequencing on two of the three cases detected a few days ago (and I believe we sequence as many cases as we get enough usable viral bits for, though obviously these ones were prioritised as urgent). They're an overseas variant (one of the spready ones) and while this is not my area of expertise, I can't imagine we'd see sufficiently precise parallel evolution in a tiny hypothetical reservoir.

You had new, known positive cases entering the country throughout most of that period. The longest span I see between new positive cases was about a month, not 102 days. I think the fact that you just detected the variant that originated in SE England in a case of community spread proves that you aren't stopping this thing at the border. Likewise, the fact that you had a new cluster appear from community spread last August proves that you hadn't stopped the community spread when you thought you had.

My point, which you seem to overlook, is that you can't detect every case and can't trace every transmission. Tests are not 100% sensitive and only reflect single points in time. An infected person can transmit the virus and then test negative. An infected person can test negative due to a low viral load at the time of testing and then transmit the virus after. And you only require testing for people entering the country or if they are close contacts of a known positive. For the rest of the population who may be carrying the virus, you're depending on them to self-identify for testing based on a list of symptoms they may not have. Even if they have some of the symptoms they may just assume it's not COVID-19 because cases in your country are rare, like that pilot who had a cough but flew to Taiwan anyway and didn't wear a mask in the cockpit. And some who suspect they have COVID-19 may not want to be tested for other reasons.

[Gryzemuis]

You are absolutely right, Heywood. Maybe NZ could theorectically control it, because they are an island and because they are so remote. But even then, it's almost impossible practically. Just think about the children. A few kids can carry it, have no symptoms, and nobody is aware. They can spread it amongst themselves. And suddenly, after weeks of going unnoticed, it can spread to adults and make them ill.

The only way to control it, maybe, is if we had a cheap, quick, reliable, easy test. So that everyone can test themselves before they step out the door in the morning, and test themselves again when they come home at night. But tests are not 100% reliable. Some people will deliberately not test themselves. And they are not cheap and easy. I hope vaccines are gonna do what we hope they will do.

[faetal]

Also most of the reliable indicators for background COVID are only practical when applied to large urban centers - no telling what the background level is out in the boonies.

[mopgoblin]

Likewise, the fact that you had a new cluster appear from community spread last August proves that you hadn't stopped the community spread when you thought you had.

The origin of the August cluster was never conclusively identified either way according to any credible source I've seen. I'm inclined to suspect that it got through the border some time after the initial outbreak (probably fairly close to the August outbreak being detected) because that's a simpler explanation than a cluster holding out that long without spreading to enough new people that it gets detected sooner.

My point, which you seem to overlook, is that you can't detect every case and can't trace every transmission. Tests are not 100% sensitive and only reflect single points in time. An infected person can transmit the virus and then test negative. An infected person can test negative due to a low viral load at the time of testing and then transmit the virus after. And you only require testing for people entering the country or if they are close contacts of a known positive.

I'm well aware of that*, but unless we're hypothesising an undetected chronic case, the virus needs to spread to survive. You might get a few false negatives, asymptomatic people, or people who don't go for a test despite symptoms, but to get at least one of those for each of roughly a dozen sequential transmissions, and for that tree to grow so narrow and tall (and be the only one) that you don't have an outbreak that gets detected earlier just doesn't seem plausible.

Like, I crunched some numbers and to get even a 1% chance of not finding it until 12+ hops of a perfectly non-branching chain of transmission you'd need a ~68% chance of each case going undetected (regardless of reason). To get to 5% you'd need ~77%, to get to 50% you'd need ~94%. As soon as you get any branching the needed chance of missing each case grows significantly. At a mean of 1.1 transmissions per case, the numbers become ~81%, ~87%, and ~97% respectively (with about 21 cumulative cases).

It is a quick-and-dirty model with a bunch of simplifications (assumption that the chances of detection are mutually independent, assumption that the time between transmissions in a branching spread pattern is a constant, being a model of a particular process rather than a whole system), but I think it still indicates that an undetected chain of transmission of that length would be peculiar enough that an undetected border link is usually a more plausible explanation.

So yeah, I still reckon it's quite possible to eliminate it locally, but not realistic to completely eliminate the risk at the border (short of, like, cutting off all international trade of physical things and shooting anyone who tries to enter at long range or something). So in the long run, everyone, meaning every country, has to do their part. But governments tend to grab onto a bunch of nasty ideas, including "other countries won't do their bit, so we'll still have risks at the border, so we shouldn't try to fully eliminate it locally either 'cause that's expensive", which is one hell of a self-fulfilling prophecy.

*I will note that in addition to multiple tests for people entering the country, and testing close contacts of known cases, we also do regular testing of anyone who works at the border

[lowenz]

https://www.sciencemag.org/news/2021...rs-coronavirus

[heywood]

Like, I crunched some numbers and to get even a 1% chance of not finding it until 12+ hops of a perfectly non-branching chain of transmission you'd need a ~68% chance of each case going undetected (regardless of reason). To get to 5% you'd need ~77%, to get to 50% you'd need ~94%. As soon as you get any branching the needed chance of missing each case grows significantly. At a mean of 1.1 transmissions per case, the numbers become ~81%, ~87%, and ~97% respectively (with about 21 cumulative cases).

I'm not sure what point you're trying to make. The longest span without any known positive cases was a month, not 102 days.

So yeah, I still reckon it's quite possible to eliminate it locally

I think it depends on what you mean by locally. Within an isolated community, sure. But in a country of 5 million where people are moving around, I don't agree. Nobody has been able to completely eliminate community spread. Your own experience demonstrates that. There were examples here too. Last May/June there were two US states that thought they had eliminated community spread, Hawaii and Vermont. And then they had clusters pop up out of nowhere. China and Taiwan also.

The northern and western parts of my state had near zero community spread throughout the summer, which is also when we had the most visitors because it was tourism season. And then suddenly in October/November, after travel season was well over, cases blossomed everywhere simultaneously around the state. In hindsight, the virus was more widespread than we thought all along, but through the summer it was circulating at a vanishingly low level, staying mostly under the radar until people started gathering indoors instead of outdoors.

Your country has demonstrated that aggressive containment, tight travel restrictions, and a cooperative population can lower the risk to a minimal level. And China has done it on an even bigger scale than NZ. But there's no way this virus can or could be eradicated. China was much more aggressive in containing SARS-CoV-2 than SARS-CoV-1, but the latter was eradicated after only ~8000 cases while SARS-CoV-2 is at 110M and counting. It even found it's way to Antarctica, which has the most tightly restricted travel in the world. It's been everywhere but the space station.

I think even if mass vaccinations get this thing to die down, it's likely to be with us forever and continue coming back much like some influenza strains do.

[Pyrian]

It's been everywhere but the space station.

Don't jinx them, man!

[mopgoblin]

I'm not sure what point you're trying to make. The longest span without any known positive cases was a month, not 102 days.

The 102 days was a span last year with no known community transmission, and community transmission is the thing I'm talking about. There were still cases at the border that were acquired overseas during that time, but that's not relevant to what I'm saying because the existence of border cases is about the circumstances/behaviour/competence of other countries. There were also a few cases in isolation hotels at the tail-end of the previous outbreak, but that's not community transmission either.

Like, since we got rid of the first outbreak, people coming into the country spend 14 days in one of a set of hotels that the government has arranged to use for that purpose. There are new cases related to that on the regular - most are people who caught the virus overseas, and occasionally someone catches it during those 14 days or while working there as a cleaner or the like. These are border cases and border-related cases*, and it doesn't make sense to consider them when looking at the efficacy of a strategy for eradicating the virus in the community because their existence is determined by other nations' efforts, not ours.

Those cases in June and July that you're talking about? They were all confirmed to be border-related. Every known case during the 102 day gap was either border-related or already in isolation; for the start of the August outbreak no definitive link was established either way. The point I'm making is that the source of the August outbreak was most likely border-related, not a sequence of local cases that had gone undetected since the previous outbreak, because the conditions needed for the latter are relatively implausible.

If you really want to count the last transmission in an isolation hotel as the start of the gap between outbreaks, that would still be 86 days, and using the high estimates from studies of the serial interval for the variants around at the time, that still means it takes an average of 14 undetected hops for a chain of transmission to span that period under normal conditions; you'd have to posit something fairly esoteric for it to be much shorter than that, and there's still the question of getting such a tall and narrow transmission tree.

* When there are new cases, we do contact tracing and testing and genetic sequencing of virus samples to try to determine the source and the chain of transmission (and especially whether it's linked to the border), and to stop the spread. Sometimes there's an overlooked contact, sometimes there's not enough material in a sample to sequence the entire genome, sometimes there might be esoteric transmission methods that complicate matters, but generally it works pretty well to identify the source.

[Starker]

Limbaugh might be dead, but his legacy continues:

https://apnews.com/article/ap-norc-p...1d8615eb176b2d

NEW YORK (AP) — About 1 in 3 Americans say they definitely or probably won’t get the COVID-19 vaccine, according to a new poll that some experts say is discouraging news if the U.S. hopes to achieve herd immunity and vanquish the outbreak.

[nickie]

I got a phone call on Thursday and had my first dose of Astrazenica vaccine yesterday. Side effects: not a lot, a bit sleepy but there's definitely an unexpected one. 12 weeks till the 2nd dose so there'll be no changes to my lifestyle at all at the moment but I feel really different, much lighter in spirit and kind of happy which isn't like me at all. 'Course that could be because it isn't raining, the sun is shining and my fig twig isn't dead after all.

[Azaran]

I think it's possible that long covid may be due to hypoxia.

The virus silently damages the lungs and insidiously lowers sufferers' blood oxygen to dangerous levels, which in turn impairs organ function. It would make sense that some people who are initially fine, then start having debilitating symptoms for no apparent reason.

It’s vital that people seek medical assistance for low oxygen levels, as if left unchecked, it could cause further damage to the body.

“When the oxygen in the blood starts to fail, if we can then put oxygen on, it means we can protect the rest of the body from the effects of low oxygen,” says Dr Strain, “and hopefully that may be one of the steps of preventing long Covid and some of the longer term symptoms.

“Some of the symptoms of long Covid are because of the fact the brain, or the body, has suffered for periods without oxygen.”