COVID-19

[Woodchopper]

Also I think the natural R rate of flu is probably lower than for Covid, especially since there is a degree of past immunity to flu in the population.

As far as I remember, the natural R rate of influenza is below 2. Compare that with Delta which is 5-8.

This says that 2009 pandemic influenza had an R of 1.7: https://www.thelancet.com/pdfs/journals ... 0484-9.pdf

[shpalman]

Also I think the natural R rate of flu is probably lower than for Covid, especially since there is a degree of past immunity to flu in the population.

As far as I remember, the natural R rate of influenza is below 2. Compare that with Delta which is 5-8.

This says that 2009 pandemic influenza had an R of 1.7: https://www.thelancet.com/pdfs/journals ... 0484-9.pdf

This is why the use of software* for 'flu to model covid at the beginning of last year led to such a total f.ck-up.

* - software which was such a complicated mess that just adjusting some parameters to fit the actual data was considered too hard as compared to ignoring the data which didn't fit the model.

You also don't get hospitals overwhelmed with 'flu cases in the same way as has happened 2-3 times with covid so far.

https://blogs.scientificamerican.com/ob ... o-oranges/

tl;dr "Most of the physicians I surveyed couldn’t remember a single patient [dying of 'flu] over their careers. Some said they recalled a few."

[KAJ]

In previous waves, the UK's Tuesday case numbers were typically the closest or any day to the mean for the week (Mon-Sun) that contained that Tuesday, and there were big drops in recorded cases on Sunday and Monday. In the current wave there seems to be a bit of a dip on Sunday but otherwise it's fairly even. Presumably this represents some change in the patterns of who is getting tested, where and when.

Looking at the last 6 weeks...
Fitting log(cases) to quadratic in date + weekday factor...

Cases by publication date, Sunday-Tuesday a bit lower than the rest of the week

PubCases.png (16.54 KiB) Viewed 2525 times

Code: Select all

Coefficients:
               Estimate Std. Error t value Pr(>|t|)    
(Intercept)     8.67511    0.03988 217.526  < 2e-16 ***
poly(date, 2)1  4.33245    0.09904  43.745  < 2e-16 ***
poly(date, 2)2  0.25862    0.09772   2.647 0.012362 *  
dayMon          0.07643    0.05641   1.355 0.184629    
dayTue          0.01828    0.05645   0.324 0.748181    
dayWed          0.21361    0.05653   3.779 0.000628 ***
dayThu          0.26289    0.05653   4.650 5.15e-05 ***
dayFri          0.26063    0.05645   4.617 5.68e-05 ***
daySat          0.16398    0.05641   2.907 0.006478 ** 
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Residual standard error: 0.09768 on 33 degrees of freedom
Multiple R-squared:  0.9835

Cases by specimen date (which I prefer), zero weighting the last 5 data, Saturday-Sunday a bit lower than the rest of the week

SpecCases.png (17.23 KiB) Viewed 2525 times

Code: Select all

Coefficients:
               Estimate Std. Error t value Pr(>|t|)    
(Intercept)     8.51039    0.03561 238.969  < 2e-16 ***
poly(date, 2)1  4.93272    0.11336  43.512  < 2e-16 ***
poly(date, 2)2  0.21184    0.11393   1.859  0.07192 .  
dayMon          0.31170    0.04964   6.280 4.25e-07 ***
dayTue          0.32843    0.04967   6.612 1.61e-07 ***
dayWed          0.34343    0.04974   6.905 6.91e-08 ***
dayThu          0.26577    0.04983   5.334 6.89e-06 ***
dayFri          0.14977    0.04968   3.015  0.00492 ** 
daySat         -0.08624    0.04964  -1.737  0.09164 .  
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Residual standard error: 0.08595 on 33 degrees of freedom
Multiple R-squared:  0.9872

[Herainestold]

The CDC in America has re-iterated their position that vaccinated people dont need to wear masks indoors. This despite jurisdictions like LA reversing their earlier mandate in the face of the Delta variant.The CDC doesn't seem to realize that Delta is like a new pathogen, its more transmissible, deadlier and doesn't respond so well to vaccines. they should be calling for double masking as they are in India.

Centers for Disease Control and Prevention Director Rochelle Walensky said Wednesday that fully vaccinated people are "safe" from the current variants and do not need to wear masks, doubling down on CDC guidance as some others call for a return to mask wearing.

The question of mask wearing has come back to the forefront given recommendations from Los Angeles County health officials, and from the World Health Organization, that even fully vaccinated people should continue to wear masks indoors in public as a precaution due to the rise of the highly transmissible delta variant of the virus.

https://thehill.com/policy/healthcare/5 ... ed-to-wear

[shpalman]

I done a simple straight line fit on the semilog plot of the recent 7-day average* case (by date reported**) data and extrapolated it:

uk-cases-projection-20210701-log.png (24.99 KiB) Viewed 2450 times

(Today is day 497 after the Event.)

It looks reasonable?

On a linear scale it looks like this:

uk-cases-projection-20210701-lin.png (27.28 KiB) Viewed 2450 times

* - the average of a given day is that day's numbers plus the three before and the three after, i.e. I won't calculate it for today until I have the data all the way to the 4th of July. And while it predicts 30,000 cases per day on the 3rd, I won't be able to calculate that until the 6th.

** - the main difference between "by date reported" and "by specimen date" is a lag of a few days and a different day-of-the-week effect but the 7-day average deals with that such that it's just a slight systematic shift of the x-axis.

[lpm]

Hmm. I'll admit it's not bending as per my forecast.

We will be getting help from steadily vaccinating the young, so there must be something adverse offsetting.

Football socialising, as evidenced by the unusual male/female split? Or ideally better testing, increasing the % of total cases showing up in official case statistics?

[Grumble]

At my second jab yesterday, actually at Astra Zeneca in Alderley Park, there weren’t many people attending. Had expected it to be much busier. Hmm.

[Bird on a Fire]

f.ck. Portugal added over 2000 cases yesterday - it hasn't been that high since February, when we were still coming down from the Christmas/NYE wave.

Delta's dominant here now, and the Lisbon area is facing extra restrictions.

f.cking Brits (actually I largely blame the Portuguese government for being so keen to let them in.)

[wilsontown]

Hmm. I'll admit it's not bending as per my forecast.

We will be getting help from steadily vaccinating the young, so there must be something adverse offsetting.

Football socialising, as evidenced by the unusual male/female split? Or ideally better testing, increasing the % of total cases showing up in official case statistics?

Here's my version of test to case ratio. You can see we were doing nearly 500 tests for every positive one at the start of May, and now are down to about 50 tests for every positive. But I don't think that's telling us much, other than case numbers are really high, and we already knew that.

test_case_ratio_30062021.png (30.19 KiB) Viewed 2396 times

[shpalman]

Hmm. I'll admit it's not bending as per my forecast.

We will be getting help from steadily vaccinating the young, so there must be something adverse offsetting.

A point I was trying to make previously was that the amount of help you will be getting from that doesn't change much from one week to the next.

Football socialising, as evidenced by the unusual male/female split? Or ideally better testing, increasing the % of total cases showing up in official case statistics?

The "positive rate" is about 2%, stable but if anything it's been slightly increasing.

One complication with the UK daily case numbers is that they aren't just the difference between yesterday and today's cumulative total anymore. I think this is due to how rapid tests and the subsequent confirmatory PCR are handled.

[tom p]

f.ck. Portugal added over 2000 cases yesterday - it hasn't been that high since February, when we were still coming down from the Christmas/NYE wave.

Delta's dominant here now, and the Lisbon area is facing extra restrictions.

f.cking Brits (actually I largely blame the Portuguese government for being so keen to let them in.)

I would say the Portuguese government are solely responsible. They knew the risks but fancied a quick buck & now they may have f.cked the whole summer. tw.ts.

[shpalman]

10% of the covids in Lombardy in June were Delta

Lombardy's 7-day case rate is currently 114/100,000 when it was 412/100,000 at the beginning of June.

In media per tutte le varianti identificate, l’87,2% degli infettati non risultava vaccinato; era vaccinato con prima dose per l’8,1% e vaccinato dopo ciclo completo per il 4,7%”.

On average for all the variants, 87.2% of the infected were not vaccinated, 8.1% were vaccinated with the first dose, and 4.7% had "completed the cycle of vaccinations" i.e. had both.

lombardy-vax-demo-20210701.jpg (82.7 KiB) Viewed 2361 times

An overview of how Lombardy's rollout has gone so far, for each demographic. You can see that it's anyway the older demographics who are more likely to have had both doses.

In particolare, dopo il completamento del ciclo vaccinale e trascorsi 14 giorni dalla seconda e ultima somministrazione, la risposta al vaccino risulta pressoché uguale per tutte le varianti.

"14 days after the second and final dose, the vaccines work equally well against all the variants."

[raven]

What's your estimate for how many people aren't vaccinated yet but have immunity from having been infected?

Just to follow up on this from a few pages back, PHE reckons about 15%. From the weekly Flu&Covid report:

The impact of the vaccination programme is particularly notable in the seroprevalence data which indicates that approximately 84.2% of blood donors aged 17 and overhave antibodies to SARS-CoV-2 from either infection or vaccination, compared to 14.9% from infection alone. High levels ofseropositivity for vaccination or infection continue to be observed in those aged over 50, as well as increases in those aged 40 to 49and 30 to 39,following vaccination rollout.

[shpalman]

26,068.

Thanks to all who played.

27,989.

[Grumble]

Do infection acquired antibodies target the spike protein?

[wilsontown]

26,068.

Thanks to all who played.

27,989.

That's numberwang.

[jdc]

Do infection acquired antibodies target the spike protein?

Yes.

[shpalman]

This is why scientists are cautious about saying that we’re nearing the time when we can simply “live with the virus” and let it spread uncontrolled.

[Herainestold]

This is why scientists are cautious about saying that we’re nearing the time when we can simply “live with the virus” and let it spread uncontrolled.

What this opinion piece doesn't say is we are going to have to learn to live with travel restrictions and recurring lockdowns as well as masking and distancing for the forseeable future ( not forever, but...,)

[Millennie Al]

We will be getting help from steadily vaccinating the young, so there must be something adverse offsetting.

I'd guess it's people generally doing less to prevent the spread as they think it's less necessary.

[Herainestold]

We will be getting help from steadily vaccinating the young, so there must be something adverse offsetting.

I'd guess it's people generally doing less to prevent the spread as they think it's less necessary.

They are doing what worked before but Delta is a new pathogen the old rules dont apply.

[headshot]

We will be getting help from steadily vaccinating the young, so there must be something adverse offsetting.

I'd guess it's people generally doing less to prevent the spread as they think it's less necessary.

They are doing what worked before but Delta is a new pathogen the old rules dont apply.

No they aren’t. People are very clearly acting as if the pandemic is over.

I now regularly see large gatherings of people everywhere. Pubs, shops, cinemas and many other venues are open indoors, many people are back at work, families are mixing, schools are open and mask wearing is not required.

Barely anyone is abiding by the “old rules”. Delta is spreading because it’s more infectious and the rules that were followed for Alpha have been lifted/are being ignored.

Stop talking nonsense, take a breath and calm the f.ck down.

[Woodchopper]

Physical phenotype of blood cells is altered in COVID-19

Clinical syndrome coronavirus disease 2019 (COVID-19) induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is characterized by rapid spreading and high mortality worldwide. While the pathology is not yet fully understood, hyper-inflammatory response and coagulation disorders leading to congestions of microvessels are considered to be key drivers of the still increasing death toll. Until now, physical changes of blood cells have not been considered to play a role in COVID-19 related vascular occlusion and organ damage. Here we report an evaluation of multiple physical parameters including the mechanical features of five frequent blood cell types, namely erythrocytes, lymphocytes, monocytes, neutrophils, and eosinophils. More than 4 million blood cells of 17 COVID-19 patients at different levels of severity, 24 volunteers free from infectious or inflammatory diseases, and 14 recovered COVID-19 patients were analyzed. We found significant changes in lymphocyte stiffness, monocyte size, neutrophil size and deformability, and heterogeneity of erythrocyte deformation and size. While some of these changes recovered to normal values after hospitalization, others persisted for months after hospital discharge, evidencing the long-term imprint of COVID-19 on the body.

https://www.sciencedirect.com/science/a ... 9521004549

[Woodchopper]

Pre-existing polymerase-specific T cells expand in abortive seronegative SARS-CoV-2 infection

Individuals with likely exposure to the highly infectious SARS-CoV-2 do not necessarily develop PCR or antibody positivity, suggesting some may clear sub-clinical infection before seroconversion. T cells can contribute to the rapid clearance of SARS-CoV-2 and othercoronavirus infections1–5. We hypothesised that pre-existing memory T cell responses, with cross-protective potential against SARS-CoV-26–12, would expand in vivo to mediate rapid viral control, potentially aborting infection. We studied T cells against the replication transcription complex (RTC) of SARS-CoV-2 since this is transcribed first in the viral life cycle13–15 and should be highly conserved. We measured SARS-CoV-2-reactive T cells in a cohort of intensively monitored healthcare workers (HCW) who remained repeatedly negative by PCR, antibody binding, and neutralisation for SARS-CoV-2 (exposed seronegative, ES). 16-weeks post- recruitment, ES had memory T cells that were stronger and more multispecific than an unexposed pre-pandemic cohort, and more frequently directed against the RTC than the structural protein-dominated responses seen post-detectable infection (matched concurrent cohort). The postulate that HCW with the strongest RTC-specific T cells had an abortive infection was supported by a low-level increase in IFI27 transcript, a robust early innate signature of SARS-CoV-2 infection16. We showed that the RNA-polymerase within RTC was the largest region of high sequence conservation across human seasonal coronaviruses (HCoV) and was preferentially targeted by T cells from UK and Singapore pre-pandemic cohorts and from ES. RTC epitope-specific T cells capable of cross-recognising HCoV variants were identified in ES. Longitudinal samples from ES and an additional validation cohort, showed pre-existing RNA-polymerase-specific T cells expanded in vivo following SARS-CoV-2 exposure, becoming enriched in the memory response of those with abortive compared to overt infection. In summary, we provide evidence of abortive seronegative SARS-CoV-2 infection with expansion of cross-reactive RTC-specific T cells, highlighting these highly conserved proteins as targets for future vaccines against endemic and emerging Coronaviridae.

https://www.medrxiv.org/content/10.1101 ... 1.full.pdf

[Herainestold]

People should start thinking about the next lockdown

If we keep reacting sluggishly to new waves, they will almost certainly result in national lockdowns. We also need to be honest with people. Our failure to vaccinate on a global scale will leave the virus out in the world, circulating and mutating for some time.

To avoid months of lockdown, we may need to accept earlier, smaller, more localised but harsh measures. Border controls still need to be tightened, with more effective quarantine and probably continued no-fly rules for much of the world. The government should be straight with the public and make it clear that foreign travel is off the menu for 2021 and consider what the implications for supporting those industries on the edge of the precipice would be.

What we do at the borders is irrelevant, however, if we don’t deal with what is going on within them. We need to urgently revisit and revise the system of support available for people to self-isolate. The UK may have as low as 18 per cent adherence to self-isolation(though there are always problems when surveys rely on self-reporting and ONS data has more recently put that figure higher). This should be worrying all of us and especially policy makers.

We need to move towards being able to rapidly shut down outbreaks ahead of widespread problems, a situation that should be possible in a vaccinated population. We will be living with the spectre of Covid-19 for some time yet and it is now time to accept this and start planning more long-term. We are in a better place, and it will get better still, but it is not a smooth path and the sooner we get this message out there the more time people will have to come to terms with it.

https://www.spectator.co.uk/article/are ... -lockdown-