COVID 19: Beyond the US and China

[tantalus]

Crucially Jonhson and Johnson and Astra Zenica are to report preliminary findings on the effect the south african strain are having on their vaccines shorthly. This is very important.

Lab studies in the last week have been mixed to disturbing. But the negativity around them will melt away if we find the variant doesnt significantly increase severe illness in respect to those vaccines.

The lab studies show the new strain has a few tricks up its sleeve in regard our best drugs and antibody protection provided by previous infection of the original virus. Potentially 1 out of every 2 patients not being provided with protection. This would dismiss the idea of natural herd immunity on a medium timescale if the effect translated to real world. There is alot of uncertainty in what these lab studies really show but they certainly don't show the vaccine doesnt't work. Thats far more complicated.

Leaked footage of the british health secreatry Hancock suggesting a 50% reduction in vaccine efficacy may just be poliical noise or his misunderstanding of the significance of the lab studies that came out the previous week. Or he may be privy to something not released. I hope not.

The UK variant may have a 30-40% higher mortality rate but they arent sure. It takes a sample size of tens of thousands of deaths over an extended period to try to detect a signal like that. The brits have the only real world sample that could show it. Counter-intuitively a higher transmission rate is far worse than an equivalent higher mortality rate as a less deadly virus makes up with fewer deaths by sheer volume of infections.

Its worth noting that the more transmissive variant always become the dominant variant. It does this if the virus is increasing, decreasing or stable in the population. In either of the 3 scenarios it doubles each week relative to the less transmissive variant if it about 50% more transmissive. It doesnt need to double in absolute numbers, just double against its less transmissive sibling.

if its at 1% it goes to 2, then 4, then 8, then 16, then 32 then over half in 5 to 6 weeks. Its probably a bit of a lottery how long it takes to get to 0.5% and then fairly predictable there after. The march from zero to 0.5% would take far longer then the march from stage of 0.5% to 50%. This means there is probably a disportionate value in trying to prevent or slow the south african strain than trying to slow the uk strain in continental europe and north america.

[DOR]

IMF World Economic Outlook, Jan 2021

Although recent vaccine approvals have raised hopes of a turnaround in the pandemic later this year, renewed waves and new variants of the virus pose concerns for the outlook. Amid exceptional uncertainty, the global economy is projected to grow 5.5 percent in 2021 and 4.2 percent in 2022. The 2021 forecast is revised up 0.3 percentage point relative to the previous forecast, reflecting expectations of a vaccine-powered strengthening of activity later in the year and additional policy support in a few large economies.

The projected growth recovery this year follows a severe collapse in 2020 that has had acute adverse impacts on women, youth, the poor, the informally employed, and those who work in contact-intensive sectors. The global growth contraction for 2020 is estimated at -3.5 percent, 0.9 percentage point higher than projected in the previous forecast (reflecting stronger-than-expected momentum in the second half of 2020).

The strength of the recovery is projected to vary significantly across countries, depending on access to medical interventions, effectiveness of policy support, exposure to cross-country spillovers, and structural characteristics entering the crisis.

Policy actions should ensure effective support until the recovery is firmly underway, with an emphasis on advancing key imperatives of raising potential output, ensuring participatory growth that benefits all, and accelerating the transition to lower carbon dependence. As noted in the October 2020 World Economic Outlook (WEO), a green investment push coupled with initially moderate but steadily rising carbon prices would yield needed emissions reductions while supporting the recovery from the pandemic recession.

Strong multilateral cooperation is required to bring the pandemic under control everywhere. Such efforts include bolstering funding for the COVAX facility to accelerate access to vaccines for all countries, ensuring universal distribution of vaccines, and facilitating access to therapeutics at affordable prices for all. Many countries, particularly low-income developing economies, entered the crisis with high debt that is set to rise further during the pandemic. The global community will need to continue working closely to ensure adequate access to international liquidity for these countries. Where sovereign debt is unsustainable, eligible countries should work with creditors to restructure their debt under the Common Framework agreed by the G20.



Real economic growth (%)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2020 _ _ 2021_ _ 2022
Global GDP _ _ _ _ _ _ _ _ -3.5% _ _ 5.5% _ _ 4.2%
USA _ _ _ _ _ _ _ _ _ _ _ _ -3.4% _ _ 5.1% _ _ 2.5%
Euro Area _ _ _ _ _ _ _ _ _ -7.2% _ _ 4.2% _ _ 3.6%
China _ _ _ _ _ _ _ _ _ _ _ +2.3% _ _ 8.1% _ _ 5.6%
Japan _ _ _ _ _ _ _ _ _ __ -5.1% _ _ 3.1% _ _ 2.4%
India _ _ _ _ _ _ _ _ _ _ _ -8.0% _ _11.5% _ _ 6.8%
World Trade _ _ _ _ _ _ _ -9.6% _ _ 8.1% _ _ 6.3%

https://www.imf.org/en/Publications/...outlook-update

[kato]

Portugal is being extremely hard-hit by the British mutation strain. The country currently has 884 new cases per 100,000 citizens per week, the highest rate globally. The government estimates the British strain to cause 50% of all cases within the Lissabon metropolitan area, where it is currently particularly virulent. The contagion rate is expected to rise further and possibly reach its peak in two weeks.

As of yesterday, exactly 7 out of 850 ICU beds in the country reserved for Corona patients in the country were still free - and that's including field hospitals set up by the military (there's some more being built, but they're lacking equipment to outfit them). In addition 70% (!) of hospital staff in the country is infected, patients are being triaged in the ambulances, and bottled oxygen supplies are running low. They spent the last few days balancing patients so they'd at least have enough until the weekend, such as by flying patients to less-struck hospitals on islands in the Atlantic like Madeira. Austria will take in new patients from Portugal, the German Air Force is flying in a medical platoon and additional ventilators, other ICU equipment and supplies.


Spain is also being hit, although they're a bit behind the curve in comparison - 530 new cases/100,000 citizens per week, and estimating that the British strain will form the majority of new cases in about 6 weeks. Spain, though, has individual provinces where infection rates are downright abysmal - the island of Ibiza is at around 2,000 new infections/100,000 citizens per week.

[tantalus]

A question worth asking here is what would be going on without the new variant up to this point. There was a similar pattern in Ireland. My intepretation is slightly different to yours on weighting. I think most of this initial wave has been driven by the older variants. Portugal is at 40% today, presuming around 20% a week or 2 before that data was collected. With 2 to 3 weeks to hospitalization there isnt time for the new variant to significantly alter the first part of this wave. Its effects are still to come through.

Now with the variant said to make people more sick it needs fewer people to cause an increase in hospitalization rates so while my thinking has changed slightly I still think change in behaviour has been the biggest factor so far in cases such as Portugal and Ireland. This is compatible to your previous observations on communcation failures and framing in Europe and your prediciton of a spring wave, which you had already made prior to the variants emerging anyways.

I am curious to how other EU countires with low rates of the UK strain view the threat. The vaccines are highly effective, its spread throughout the EU without intra EU travel bans is inevitable. Should the focus be on the south african strain...

[kato]

I am curious to how other EU countires with low rates of the UK strain view the threat.

I actually just 5 minutes ago finished a lengthy discussion on that on the phone with someone working at a local hospital who pretty much says the hospital is pretty scared about a massive outbreak of the new strains.

Last week they got new SOPs for handling any patients with either the British or South African strains, and they pretty much run towards full quarantine in a full isolation ward with single-bed rooms for at least two weeks and at least daily full PCR testing of anyone - including hospital staff - who has had contact with them.

Statistic analysis of a couple hundred PCR tests in the neighboring state here found ~4% occurence of B.1.1.7 (British) and ~0.5% occurence of B.1.351 (South-African), so we're still pretty low on that.

The vaccines don't enter the equation with regard to handling the new strains at all due to 98% of the population not being vaccinated, and that being unlikely to change anytime in the next couple months...

[tantalus]

Feels like its worse for the poor medical community when they can see it coming but I was thinking more along the lines how the EU views the Uk variant in context of travel restrictions at this point.

I hadnt heard of South African variant rates anywhere near 0.5% anywhere in the EU. Iam hoping that is due to small sample size or linked to travel? Iam assumung that limited sequencing will be targetting suspected south african travellers and contacts. As well as the UAE. But ofcourse we need random sampling also. Definitely concerned we arent doing enough sequencing. Seems a major oversight in most countries from the outset.

[kato]

I hadnt heard of South African variant rates anywhere near 0.5% anywhere in the EU. Iam hoping that is due to small sample size or linked to travel?

In the district of my local public health agency we currently have four cases (out of 914 active cases) caused by a strain with "close similarity to B.1.351", all connected to each other. Infection path is still being traced, but travel or firsthand contact to travellers has already been excluded as a possible vector. The cases were published yesterday as a partial result from sequencing tests of 200 recent PCR test samples.

In the same sequencing test series of 200 samples in total 12 mutated Corona samples were found which are still being researched in details. They haven't published so far which variants these are specifically (other than the four cases "close to B.1.351", so the other 8 could be e.g. B.1.1.7 or B.1.1.28/P.1) - full genome sequencing for the samples will be finished early next week.

The local sequencing test series is also part of wider research on mutations of Corona, involving the European Microbiology Laboratory located on the hill across from my house. Similar 200-sample sequencing tests have been performed for other areas around here, in which the South-African variant usually pops up once per sample series recently.

[tantalus]

In the district of my local public health agency we currently have four cases (out of 914 active cases) caused by a strain with "close similarity to B.1.351", all connected to each other. Infection path is still being traced, but travel or firsthand contact to travellers has already been excluded as a possible vector. The cases were published yesterday as a partial result from sequencing tests of 200 recent PCR test samples.

In the same sequencing test series of 200 samples in total 12 mutated Corona samples were found which are still being researched in details. They haven't published so far which variants these are specifically (other than the four cases "close to B.1.351", so the other 8 could be e.g. B.1.1.7 or B.1.1.28/P.1) - full genome sequencing for the samples will be finished early next week.

The local sequencing test series is also part of wider research on mutations of Corona, involving the European Microbiology Laboratory located on the hill across from my house. Similar 200-sample sequencing tests have been performed for other areas around here, in which the South-African variant usually pops up once per sample series recently.

Thats pretty bad news. I wasnt aware of it.

[kato]

https://www.bbc.com/news/health-55900625
https://edition.cnn.com/2021/01/12/h...ant/index.html

The E484K mutation has been found in an evolved British B.1.1.17 variant (11 samples found). Apparently there is also a mainline SARS-CoV2 variant with E484K (32 samples found in the UK).

E484K lowers the chance of antigens succesfully docking on the virus to combat it - thus lowering the effectiveness of a immunoresponse trained by vaccination or previous infection. It is one main feature of the South African and Brazilian strains. Among the Brazilian strain it is particularly common and found in about 44% of virii across three of four lineages.

It is basically seen as a convergent evolution of a feature advantageous to propagation.

[tantalus]

https://www.bbc.com/news/health-55900625
https://edition.cnn.com/2021/01/12/h...ant/index.html

The E484K mutation has been found in an evolved British B.1.1.17 variant (11 samples found). Apparently there is also a mainline SARS-CoV2 variant with E484K (32 samples found in the UK).

E484K lowers the chance of antigens succesfully docking on the virus to combat it - thus lowering the effectiveness of a immunoresponse trained by vaccination or previous infection. It is one main feature of the South African and Brazilian strains. Among the Brazilian strain it is particularly common and found in about 44% of virii across three of four lineages.

It is basically seen as a convergent evolution of a feature advantageous to propagation.

For sure. its definitely showing that these are relatively easy finds for the virus in evolutionary space. Although we are giving it millions of opportunities to find these solutions with the amount of spread. But there are limitations in how it searches this space so it still has laws to follow even if we can't identitiy them. If we can get better tracking and sequencing globally we might be able to spot other future important mutations earlier. ofcourse that helps with containment but it can also inform vaccine and drug development. Admittedly we seem to be constantly playing catch up at the moment.

[kato]

Germany will be handing out a set of 15 FFP2/N95 masks within the next 5-6 weeks to anyone over age 60 or with certain preconditions (asthma etc). Not entirely free - co-pay will be 2 Euro on a nominal worth of 90 Euro. The federal government is investing 2.5 billion Euro.

Just got my vouchers. In order to prevent people from copying them they went as far as having the vouchers printed by the Federal Printing Service on security paper, complete with anti-counterfeiting watermarks and UV-only imprint (which apparently shows a N95 mask on two-thirds of the voucher and the Federal Eagle on the rest).

[kato]

Definitely concerned we arent doing enough sequencing. Seems a major oversight in most countries from the outset.

RKI today released a report on that for Germany:

For this mutation spot tests were performed between Jan 22nd and Jan 29th (4th calendar week) on 34,000 samples taken that week for mutation of N501Y and delH69/V70. Both mutations within one samples were detected in 5.8% of samples (*), with four particular hotspots for it in Germany (**). Within that week some laboratories involved also observed a day-to-day rise in occurence, i.e. wider spreading with time.

Results are officially not fully representative as they did not fully cover all positive tests taken in the week, nor were samples evaluated weighte to population. But they're very indicative - the data actually closely matches relevant full genome sampling, in which 5.73% of a far smaller sample set within the same week were evaluated to be variant B1.1.7 (British).

These mutation spot tests are apparently far easier and faster to perform compared to full genome sequencing. RKI recommends a widespread implementation in order to perform surveillance on spread of known mutated variants, in addition to performing more full sequencing to find new variants.

(*) About 1.1% further samples showed N501Y without delH69/V70, which i personally find the interesting part. N501Y itself is an indicator for one of the British/South-African/Brazilian variants, presence of delH90/V70 is considered confirmation of B.1.1.7 (British).

(**) The hotspots are all "known" ones with wider outbreaks of the British variant.

[tantalus]

(*) About 1.1% further samples showed N501Y without delH69/V70, which i personally find the interesting part. N501Y itself is an indicator for one of the British/South-African/Brazilian variants, presence of delH90/V70 is considered confirmation of B.1.1.7 (British).

(**) The hotspots are all "known" ones with wider outbreaks of the British variant.

Because it indicates south african/brasilian instead of british?

[kato]

Because it indicates south african/brasilian instead of british?

There was a variant circulating in the UK that has the N501Y mutation but lacks delH69/V70 between September and November 2020 - i.e. basically just this variation. In the UK it was barely present outside Wales - and even there after peaking at 10% of positive infections mid-October pretty much vanished in mid-November to be replaced by other variants This variant is assumed to be about 10% more infectious than standard SARS-CoV2. Offhand there was also a similar variant with only a N501Y mutation in North Italy last summer, presumably similarly vanishing after a short run as it was not successful enough.

Those 1.1% in Germany represent these intermittent variants plus south african and brazilian.

The delH69/V70 mutation specifically also does not occur in South African and Brazilian variants, but does appear in the Danish variant infecting minks. It is also a known mutation in other coronaviruses that successfully sidestep an immunoresponse in immunosuppressed patients.
The South African and Brazilian variants are not related to this intermittent variant, in case that thought comes up - there are about half a dozen mutations involved that do not match for such lineage.

[tantalus]

The Mystery Of India's Plummeting COVID-19 Cases

Last September, India was confirming nearly 100,000 new coronavirus cases a day. It was on track to overtake the United States to become the country with the highest reported COVID-19 caseload in the world. Hospitals were full. The Indian economy nosedived into an unprecedented recession.

But four months later, India's coronavirus numbers have plummeted. Late last month, on Jan. 26, the country's Health Ministry confirmed a record low of about 9,100 new daily cases — in a country of nearly 1.4 billion people. It was India's lowest daily tally in eight months. On Monday, India confirmed about 11,000 cases.

"It's not that India is testing less or things are going underreported," says Jishnu Das, a health economist at Georgetown University. "It's been rising, rising — and now suddenly, it's vanished! I mean, hospital ICU utilization has gone down. Every indicator says the numbers are down."

Scientists say it's a mystery. They're probing why India's coronavirus numbers have declined so dramatically — and so suddenly, in September and October, months before any vaccinations began.

They're trying to figure out what Indians may be doing right and how to mimic that in other countries that are still suffering.

"It's the million-dollar question...

Full article lnked...


https://www.npr.org/sections/goatsan...=1612738701103