COVID-19

[shpalman]

BREAKING NEWS: People can get infected from asymptomatic and pre-symptomatic carriers but we don't know how much

"Ought to figure it out and do something about it"

Brought to you by our "weird, this seems to have a timestamp from now and not from a year ago" desk.

[Woodchopper]

A majority of uninfected adults show pre-existing antibody reactivity against SARS-CoV-2

Pre-existing cross-reactivity to SARS-CoV-2 may occur in absence of prior viral exposure. However, this has been difficult to quantify at the population level due to a lack of reliably defined seroreactivity thresholds. Using an orthogonal antibody testing approach, we estimated that ~0.6% of non-triaged adults from the greater Vancouver area, Canada between May 17th and June 19th 2020 showed clear evidence of a prior SARS-CoV-2 infection, after adjusting for false-positive and false-negative test results. Using a highly sensitive multiplex assay and positive/negative thresholds established in infants in whom maternal antibodies have waned, we determine that more than 90% of uninfected adults showed antibody reactivity against the spike, receptor-binding domain (RBD), N-terminal domains (NTD) or the nucleocapsid (N) protein from SARS-CoV-2. This sero-reactivity was evenly distributed across age and sex, correlated with circulating coronaviruses reactivity, and was partially outcompeted by soluble circulating coronaviruses’ spike. Using a custom SARS-CoV-2 peptide mapping array, we found that this antibody reactivity broadly mapped to spike, and to conserved non-structural viral proteins. We conclude that most adults display pre-existing antibody cross-reactivity against SARS-CoV-2, which further supports investigation of how this may impact the clinical severity of COVID-19 or SARS-CoV-2 vaccine responses.

https://insight.jci.org/articles/view/146316

[bob sterman]

I wonder how James Annan will adjust the model he fits to ONS data in light of this (now deleted tweet from the company collecting data on behalf of the ONS)...

EyjZgVgXMAYc9-t.png (396.17 KiB) Viewed 6190 times

[tenchboy]

Aaaaaaand we are back to normal; pandemic obviously over; virus obviously gone home.
Why?
Cos I just had a royal mail recorded signed for delivery and t postie said sign this as he thrust an old fashioned neighbourhood flu spreader at me upon which to wipe my finger where everyone else had just wiped theirs.
I said no. Nicely of course.
That's why.

[Woodchopper]

COVID-19 epidemic in the Brazilian state of Amazonas was driven by long-term persistence of endemic SARS-CoV-2 lineages and the recent emergence of the new Variant of Concern P.1

https://www.researchsquare.com/article/rs-275494/v1

A good, perhaps important article.

Concludes:

These findings collectively support those lineage replacements could be a recurrent phenomenon in the local evolution of SARS-CoV-2 driven by ecological and virological factors. Moreover, our findings indicate that NPIs deployed in the Amazonas state in April 2020 were sufficiently effective to reduce the Re of early prevalent local SARS-CoV-2 clades. In contrast, NPIs were insufficient to bring the epidemic under control, allowing the establishment and local persistence of several endemic viral lineages and subsequent emergence of the VOC P.1 in late November 2020. The lack of efficient social distancing and other mitigation measures probably accelerated the early transmission of VOC P.1, while the high transmissibility of this VOC further fueled the rapid upsurge in SARS-CoV-2 cases and hospitalizations observed in Manaus following its emergence. The feeble adoption of non-pharmaceutical interventions as it occurred in Amazonas and other Brazilian states represents a significant risk for the continuous emergence and dissemination of new variants. Implementing efficient mitigation measures combined with massive vaccination will be crucial to control the spread of SARS-CoV-2 VOCs in Brazil.

[Woodchopper]

We show that a state of transient collective immunity (TCI) emerges well below the HIT during early, high-paced stages of the epidemic. However, this is a fragile state that wanes over time due to changing levels of social activity, and so the infection peak is not an indication of long-lasting herd immunity: Subsequent waves may emerge due to behavioral changes in the population, driven by, for example, seasonal factors. Transient and long-term levels of heterogeneity are estimated using empirical data from the COVID-19 epidemic and from real-life face-to-face contact networks. These results suggest that the hardest hit areas, such as New York City, have achieved TCI following the first wave of the epidemic, but likely remain below the long-term HIT. Thus, in contrast to some previous claims, these regions can still experience subsequent waves.

https://www.pnas.org/content/118/17/e2015972118

[Grumble]

Hopefully we’re seeing the end of covid in the U.K. We’ve now had a whole week of <50 reported deaths each day. Can’t wait for my jab when they get to my age group, which will be soon.

[jimbob]

COVID-19 epidemic in the Brazilian state of Amazonas was driven by long-term persistence of endemic SARS-CoV-2 lineages and the recent emergence of the new Variant of Concern P.1

https://www.researchsquare.com/article/rs-275494/v1

A good, perhaps important article.

Concludes:

These findings collectively support those lineage replacements could be a recurrent phenomenon in the local evolution of SARS-CoV-2 driven by ecological and virological factors. Moreover, our findings indicate that NPIs deployed in the Amazonas state in April 2020 were sufficiently effective to reduce the Re of early prevalent local SARS-CoV-2 clades. In contrast, NPIs were insufficient to bring the epidemic under control, allowing the establishment and local persistence of several endemic viral lineages and subsequent emergence of the VOC P.1 in late November 2020. The lack of efficient social distancing and other mitigation measures probably accelerated the early transmission of VOC P.1, while the high transmissibility of this VOC further fueled the rapid upsurge in SARS-CoV-2 cases and hospitalizations observed in Manaus following its emergence. The feeble adoption of non-pharmaceutical interventions as it occurred in Amazonas and other Brazilian states represents a significant risk for the continuous emergence and dissemination of new variants. Implementing efficient mitigation measures combined with massive vaccination will be crucial to control the spread of SARS-CoV-2 VOCs in Brazil.

The World Service had some sobering bits on Brazil. Bolsonaro has been working hard to hinder the vaccine rollout as well as the state governors' NPIs to the disease.

It's only just struck me, but it will disproportionately affect the poor (and indigenous peoples) so is this actually his intent? It is hard to oppose someone if you have long-term illness or are sole carer for a family due to others dying. It seems like a conspiracy theory, but he has advocated political violence and sterilisation of the poor.

[sTeamTraen]

From Facebook: "It's not fair, why are bars in <other parts of the country> open and those here aren't? We have far fewer cases than them!".

They're soooooo close to understanding...

[Woodchopper]

I've moved the discussion on new variants in India and Brazil to a separate thread.
viewtopic.php?f=19&t=2380&p=78521#p78512

[Herainestold]

Despite wide spread vaccination we are going to have to keep masking for some time yet.
Guide to double masking which reduces covid exposure by 95%. I double mask when I leave my flat as long as I am outside.

https://indianexpress.com/article/expla ... d-7283996/

Amid the battle against Covid-19, healthcare experts are encouraging the use of two face masks, a practice popularly called “double masking”. This, they say, could create a stronger barrier against the deadly disease. Double masking, with cloth and surgical masks, can prevent leakage of air and fit the contours of the face better, studies by the United States Centers for Disease Control and Prevention (CDC) has found.

Double masking reduced exposure to Covid-19 by nearly 95 per cent, according to the US CDC.

[Woodchopper]

Good news

SARS-CoV-2 antibodies remain detectable 12 months after infection and antibody magnitude is associated with age and COVID-19 severity

https://www.medrxiv.org/content/10.1101 ... 21256207v1

[Herainestold]

Environmental determinants of COVID-19 transmission across a wide climatic gradient in Chile

Chile covers 40º of latitude, so encompasses a number of climatic zones,researchers tried to correlate covid infection rate with various climate variables.

Several studies have examined the transmission dynamics of the novel COVID-19 disease in different parts of the world. Some have reported relationships with various environmental variables, suggesting that spread of the disease is enhanced in colder and drier climates. However, evidence is still scarce and mostly limited to a few countries, particularly from Asia. We examined the potential role of multiple environmental variables in COVID-19 infection rate [measured as mean relative infection rate = (number of infected inhabitants per week / total population) × 100.000) from February 23 to August 16, 2020 across 360 cities of Chile. Chile has a large climatic gradient (≈ 40º of latitude, ≈ 4000 m of altitude and 5 climatic zones, from desert to tundra), but all cities share their social behaviour patterns and regulations. Our results indicated that COVID-19 transmission in Chile was mostly related to three main climatic factors (minimum temperature, atmospheric pressure and relative humidity). Transmission was greater in colder and drier cities and when atmospheric pressure was lower. The results of this study support some previous findings about the main climatic determinants of COVID-19 transmission, which may be useful for decision-making and management of the disease.

https://www.nature.com/articles/s41598-021-89213-4

[jimbob]

I worry that we might be venturing into this territory:

How far outside Annan's credible intervals is the recent wobble?

That is not what it's for. It's just an immediate and easily understood picture.

This is the exam question all over again. Your smoke alarm doesn't need to bother with credible intervals, it just needs to sound an alarm the second it's the slightest bit worried. An immediate investigation follows. You don't want an alarm that studies the data over 7 minutes before determining the particles have exceeded standard norms.

"Simple" can often defeat "proper" - for example our simple spreadsheets one year ago were far better than the disastrous models used by the govt. "Four weeks behind Italy". The proper models were 8x worse than ours.

Bit of a derail, but this is almost exactly wrong about smoke alarms. My first job was designing fire detectors and there was lots of effort into reducing false alarms. At the time it was very standard to increase the sensitivity with temperature and even more so if the temperature started rising quickly. That meant that they could have lower sensitivity at normal room temperature. When I left the big thing was fuzzy logic to reduce false alarms.

[lpm]

I worry that we might be venturing into this territory:

How far outside Annan's credible intervals is the recent wobble?

That is not what it's for. It's just an immediate and easily understood picture.

This is the exam question all over again. Your smoke alarm doesn't need to bother with credible intervals, it just needs to sound an alarm the second it's the slightest bit worried. An immediate investigation follows. You don't want an alarm that studies the data over 7 minutes before determining the particles have exceeded standard norms.

"Simple" can often defeat "proper" - for example our simple spreadsheets one year ago were far better than the disastrous models used by the govt. "Four weeks behind Italy". The proper models were 8x worse than ours.

Bit of a derail, but this is almost exactly wrong about smoke alarms. My first job was designing fire detectors and there was lots of effort into reducing false alarms. At the time it was very standard to increase the sensitivity with temperature and even more so if the temperature started rising quickly. That meant that they could have lower sensitivity at normal room temperature. When I left the big thing was fuzzy logic to reduce false alarms.

That's a different sort of smoke alarm. One that needs to sit still for decades, waiting for an event that probably will never come.

The Covid analogy is more like a building where various hotspots are smouldering and there are a couple of hundred firefighters on site, all geared up and ready to rush to any place where a fire erupts. What you want then are over sensitive smoke alarms - false alerts cost you almost nothing, yet a single failure to detect an outbreak leads to the entire building burning down.

The UK was cursed by fantasies of false precision, particularly in March 2020, imagining it could fine-tune smoke detectors and damp down fires to the exact level wanted. And it nearly led to the building burning down - twice - when the speed of the virus raced ahead of fine tuning measures. E.g. the now almost forgotten "let's damp it down a touch by shutting pubs at 10pm" silliness.

[headshot]

That is not what it's for. It's just an immediate and easily understood picture.

This is the exam question all over again. Your smoke alarm doesn't need to bother with credible intervals, it just needs to sound an alarm the second it's the slightest bit worried. An immediate investigation follows. You don't want an alarm that studies the data over 7 minutes before determining the particles have exceeded standard norms.

"Simple" can often defeat "proper" - for example our simple spreadsheets one year ago were far better than the disastrous models used by the govt. "Four weeks behind Italy". The proper models were 8x worse than ours.

Bit of a derail, but this is almost exactly wrong about smoke alarms. My first job was designing fire detectors and there was lots of effort into reducing false alarms. At the time it was very standard to increase the sensitivity with temperature and even more so if the temperature started rising quickly. That meant that they could have lower sensitivity at normal room temperature. When I left the big thing was fuzzy logic to reduce false alarms.

That's a different sort of smoke alarm. One that needs to sit still for decades, waiting for an event that probably will never come.

The Covid analogy is more like a building where various hotspots are smouldering and there are a couple of hundred firefighters on site, all geared up and ready to rush to any place where a fire erupts. What you want then are over sensitive smoke alarms - false alerts cost you almost nothing, yet a single failure to detect an outbreak leads to the entire building burning down.

The UK was cursed by fantasies of false precision, particularly in March 2020, imagining it could fine-tune smoke detectors and damp down fires to the exact level wanted. And it nearly led to the building burning down - twice - when the speed of the virus raced ahead of fine tuning measures. E.g. the now almost forgotten "let's damp it down a touch by shutting pubs at 10pm" silliness.

I might be misremembering, or misunderstanding, but I seem to remember you talking about payoffs within mitigations to allow some essential things to happen, by closing non-essential things, for example something like, "to open schools you have to close the pubs".

[lpm]

Yep. I had a proper priority list a year ago, the government only grasped it with their unlockdown plan of Feb 2021.

I gave each activity a value according to my personal opinions on worth, such as scoring health and family and funerals high, scoring beauty parlours and cinemas low. And I gave each activity a risk cost, saying that schools cost a huge number of points, indoor pubs quite a lot, tattoo places hardly any.

The idea was that a government should budget how many unlockdown points it could afford, then choose priorities of where to spend them according to value. And that there should be a national conversation on what we should value most.

This was my first draft at the approach, from 10 April 2020. If only I had been in charge of the country back then.
viewtopic.php?p=28011#p28011

Last summer the govt stated their number one priority was education - fair enough, they're the ones to choose, a fundamental purpose of government is to make choices about what to prioritise. It was immediately obvious under my system that this number one choice would cost almost all the unlockdown points the UK could budget. On 1 September 2020 we were all shouting that the government had overspent - schools and pubs and shops and gyms and tattoo parlours all open with total unlockdown points far beyond the safe limit. It should have shut a bunch of the most expensive elements, pubs and gyms say, in order to afford schools. We all know what followed.

The current unlockdown stages to the Summer Solstice date matches my 10 April 2020 scheme. The vaccine rollout has steadily increased the number of unlockdown points we can spend. The government choose schools first, taking the big cost of reopening in March, but didn't simultaneously spend points on pubs. In April they decided to spend the extra points on funerals, non-essential retail, pub gardens, hairdressers... In May the next batch of points will be spent on indoor pubs, indoor attractions, some outdoor festivals & sports... Then the final batch of points will be spent in June on nearly all the rest.

The precise ordering of values vs lockdown points isn't exactly what I'd have picked, but the fundamental approach is exactly as I laid out over a year ago - and the approach that should have been done in the summer of 2020. By ignoring me Boris Johnson unnecessarily killed at least 50,000 extra people and caused severe damage to the economy.

[Sciolus]

Yep. I had a proper priority list a year ago, the government only grasped it with their unlockdown plan of Feb 2021.

I gave each activity a value according to my personal opinions on worth, such as scoring health and family and funerals high, scoring beauty parlours and cinemas low. And I gave each activity a risk cost, saying that schools cost a huge number of points, indoor pubs quite a lot, tattoo places hardly any.

The idea was that a government should budget how many unlockdown points it could afford, then choose priorities of where to spend them according to value. And that there should be a national conversation on what we should value most.

This was my first draft at the approach, from 10 April 2020. If only I had been in charge of the country back then.
viewtopic.php?p=28011#p28011

I never got around to saying so last year, but this is what in the pollution reduction world is called a marginal abatement cost curve. You list the various control measures, assign a cost (usually in $) and a benefit (usually in tonnes of pollution saved; here it might be reduction in R), sort them by cost-effectiveness, plot them on a cumulative graph and you get something liked this. You can then read off what measures you need and what the cost is to achieve a certain reduction in pollution (or get R below 1). A very simple and effective tool but seems to be unknown outside the environmental field.

[Woodchopper]

South Africa excess deaths far higher than reported Covid deaths https://www.samrc.ac.za/reports/report- ... uth-africa https://www.samrc.ac.za/sites/default/f ... ay2021.pdf

In its latest report, published on Wednesday, the SAMRC said South Africa had seen 157,000 excess deaths in the past 12 months and estimated that 85% of them were caused by COVID-19, which means just over 133,000 people have died from the disease.

This compares to an official death toll of 54,968 since the start of the pandemic.

https://www.reuters.com/article/health- ... SL8N2N016W

[Grumble]

South Africa excess deaths far higher than reported Covid deaths https://www.samrc.ac.za/reports/report- ... uth-africa https://www.samrc.ac.za/sites/default/f ... ay2021.pdf

In its latest report, published on Wednesday, the SAMRC said South Africa had seen 157,000 excess deaths in the past 12 months and estimated that 85% of them were caused by COVID-19, which means just over 133,000 people have died from the disease.

This compares to an official death toll of 54,968 since the start of the pandemic.

https://www.reuters.com/article/health- ... SL8N2N016W

Not surprising tbh, the discrepancy is not as bad as some places.

[Herainestold]

Covid Surges In 4 Of 5 Most Vaccinated Countries—Here’s Why The U.S. Should Worry

Not just the US. UK should be cautious of further re opening in the face of new variants.

Countries with the world’s highest vaccination rates—including four of the top five most vaccinated—are fighting to contain coronavirus outbreaks that are, on a per-capita basis, higher than the surge devastating India, a trend that has experts questioning the efficacy of some vaccines (especially China’s Sinopharm) and the wisdom of easing restrictions even with most of the population vaccinated.

World leaders, including the head of the World Health Organization, issue frequent reminders that nobody is “safe until everyone is safe,” an issue underscored by the vast vaccine inequity between nations. New, potentially more dangerous, variants are emerging across the globe, some of which could potentially evade existing vaccines. The WHO classified the B.1.617 variant tearing through India as a variant of concern Tuesday, noting it may be more infectious.

https://www.forbes.com/sites/roberthart ... 3662fad677

[bob sterman]

Covid Surges In 4 Of 5 Most Vaccinated Countries—Here’s Why The U.S. Should Worry

Not just the US. UK should be cautious of further re opening in the face of new variants.

Definitely. Real-world data seems to suggest Pfizer is doing a better job than Sinopharm at stopping surges.

But UK (and myself) heavily reliant on Astrazenca - and I'm not sure there's enough "real-world" data on its performance against key variants yet - is there?

One thing that might help - NHS staff have been very widely Pfizered.

[Herainestold]

Covid Surges In 4 Of 5 Most Vaccinated Countries—Here’s Why The U.S. Should Worry

Not just the US. UK should be cautious of further re opening in the face of new variants.

Definitely. Real-world data seems to suggest Pfizer is doing a better job than Sinopharm at stopping surges.

But UK (and myself) heavily reliant on Astrazenca - and I'm not sure there's enough "real-world" data on its performance against key variants yet - is there?

One thing that might help - NHS staff have been very widely Pfizered.

AZ was rather disastrous against the SA variant, which luckily does not seem to be that prevalent at the moment. The jury is still out as to its efficacy against the Indian variant, lets keep our fingers crossed. I hope it works as I have one dose of AZ. Right now I am behaving as if un vaccinated, masking distancing, no social contact. I expect it will be like that for the summer or likely to the end of the year as we need full vaccination and likely bloosters against variants.

[shpalman]

Not just the US. UK should be cautious of further re opening in the face of new variants.

Definitely. Real-world data seems to suggest Pfizer is doing a better job than Sinopharm at stopping surges.

But UK (and myself) heavily reliant on Astrazenca - and I'm not sure there's enough "real-world" data on its performance against key variants yet - is there?

One thing that might help - NHS staff have been very widely Pfizered.

AZ was rather disastrous against the SA variant, which luckily does not seem to be that prevalent at the moment. The jury is still out as to its efficacy against the Indian variant, lets keep our fingers crossed. I hope it works as I have one dose of AZ. Right now I am behaving as if un vaccinated, masking distancing, no social contact. I expect it will be like that for the summer or likely to the end of the year as we need full vaccination and likely bloosters against variants.

Three weeks after the first AZ dose I think you're as protected as you're ever going to be. That protection starts to fade at about 12 weeks or so at which point you need the second dose to maintain it.

Maintaining masking and distancing isn't a bad idea though. It also helps to keep the idea of these things normalized in the population - "I'll wear a mask because everyone else is wearing one".

[headshot]

We've had two contractors come to our house this week to provide quotes. I had to ask them to put on masks before entering our house.

Both were overweight men in their 50s. You'd think they'd exercise a little caution...

When we moved house last week, I had to ask the removal men to wear masks, and even then they did it reluctantly and inconsistently.

Good luck getting folks to wear them after Johnson announces it's "Mission Accomplished" on June 21st.