Coronavirus Sars-CoV-2/Covid-19 Megathread

[The Larch]

The thing I'm seeing attracting attention here is people noting that it works "remarkably" like the AZ vaccine which is interesting given that there were reports of state-sponsored hacking of Oxford and other vaccine developers through the year. Which may be nothing or may be something.

Both vaccines were developed using a similar methodology (modifying an existing virus, rather than employing RNA, as the Pfizer and Moderna ones). In fact AZ and the Russians were doing some kind of study to see how viable it was to combine them (ie, using one of them as 1st shot and the other as 2nd shot). It's no wonder if they work in a similar way.

[Sheilbh]

Oh that makes sense then.

Hancock announcing lots of other strains of concern which are mutations that are being monitored. I think 32 in Liverpool and 11 in Bristol.

How much of this is because the UK does a lot of gene sequencing in covid so is just more aware of mutations within its tests, or are there lots emerging here for some reason (possibly no border control and no quarantine are factors)?

[Tamas]

Oh that makes sense then.

Hancock announcing lots of other strains of concern which are mutations that are being monitored. I think 32 in Liverpool and 11 in Bristol.

How much of this is because the UK does a lot of gene sequencing in covid so is just more aware of mutations within its tests, or are there lots emerging here for some reason (possibly no border control and no quarantine are factors)?

I'd guess high level of infections are also a factor - lotsa' infections = lotsa' mutations.

[celedhring]

And I'm sure that if one starts looking there are probably hundreds of variants already, just that few will have true epidemiological significance.

[Sheilbh]

I'd guess high level of infections are also a factor - lotsa' infections = lotsa' mutations.

Yeah that's definitely key and celed's point makes sense.

I think the UK comms make a distinction between variants/mutations and variants of interest/concern (I can't remember the phrase).

I just freak out and wonder if there's loads of ones out there we don't know about - lurking

[The Larch]

I just freak out and wonder if there's loads of ones out there we don't know about - lurking

You can be sure of that. The issue is if they're epidemiologically relevant or not.

[Sheilbh]

On the other hand - good news about the delayed dose with AZ vaccine which matches some early data at the time of approval and recommendation of their CEO:

Scott Beasley
@SkyScottBeasley
44m
NEW: One dose of AstraZeneca/Oxford vaccine offers 76% protection after day 22 post vaccination - and offers sustained protection through a 3 month period until second dose
New analysis by Oxford University
vaccine shows sustained protection of 76% during the 3-month interval until the second dose
analyses shows single standard dose efficacy from day 22 to day 90 post vaccination of 76% with protection not falling in this three-month period
After the second dose vaccine efficacy from two standard doses is 82.4% with the 3-month interval being used in the UK
82.4% effective, with a 95% confidence interval of 62.7% - 91.7% at 12+ weeks
Oxford says this supports the extended time period between doses- AZ have always said longer was more effective:

Oxford: "Data supports the 4-12 week prime-boost dosing interval recommended by many global regulators"
Crucially, Oxford says the vaccine DOES stop transmission:

Oxford: "Analyses of PCR positive swabs in UK population suggests vaccine may have substantial effect on transmission of the virus with 67% reduction in positive swabs among those vaccinated"
Prof Andrew Pollard, Chief Investigator of Oxford Vaccine Trial,  co-author of the paper: "These new data provide an important verification of the interim data that was used by more than 25 regulators including the MHRA and EMA to grant the vaccine emergency use authorisation"
"It also supports the policy recommendation made by the Joint Committee on Vaccination & Immunisation for a 12-week prime-boost interval, as they look for the optimal approach to roll out, & reassures us that people are protected from 22 days after a single dose of the vaccine"
Crucially-as AZ & scientists have repeatedly said-extending interval INCREASES efficacy

Oxford: "the effect of dosing interval on efficacy is pronounced, with vaccine efficacy rising from 54.9% with an interval of less than six weeks to 82.4% when spaced 12 or more weeks apart"
This research is published by researchers at the University of Oxford in Preprints with The Lancet

You can find it here
https://papers.ssrn.com/sol3/papers.cfm?abstract_id=3777268
Increased efficacy with longer interval is not unusual-that's usual with many vaccines

Remember the AZ vaccine uses old fashioned technology- so they were always confident it would work this way

The mRNA vaccines (eg Pfizer) are new so we don't have years of data/experience
To be very clear: this analysis makes no mention or claims about new geographic variants

[Josquius]

The reduced transmission factor is a biggy.

[Legbiter]

Grandfather is getting vaccinated tomorrow.

[mongers]

Grandfather is getting vaccinated tomorrow.

Hope the whole family gets vaccinated soon. 

[Sheilbh]

On the signs from Israel - the share of cases from the over-60s (the vaccinated group in Israel):


It's been difficult to spot the effects of the vaccine because they went into lockdown at the same time as they rolled it out (a bit like the UK) but it does look like there's now a clear impact on the proportion of new cases in that group.

[Sheilbh]

Start of the Covax distribution/interim distribution - this depends on the AZ vaccine getting appropriate authorisations in countries - but it's basically 3.5% of the population on average which is enough to "cover the most vulnerable groups such as healthcare workers" in the first half of 2021. It's a start but nowhere near enough - in part this'll be fulfilling rich country contracts (plus "manufacturing" countries - India, South Africa, Argentina etc) first but I imagine part of it is also probably because of supply constraints as manufacturing is still being set up, although I read the Serum Institute in India is producing a lot (but mainly being used for India and South Africa at the moment). Hopefully it'll be far, far higher soon.

[Josquius]

Its not a number I normally pay much attention to...
But 2 million currently infected in the UK.
Thats just insane. 3% of the country have corona virus.

[celedhring]

In news of Sheilbh's interest, the analysis of sewage from a mountain town in the Pyrenees have bizarrely (or alarmingly) shown a 30% prevalence of the British Covid variant.

So far sequencing of PCR samples had shown rates of around 10% in both the Madrid and Barcelona areas.

[Sheilbh]

Interesting. Ski resorts maybe?

From the UK data it takes about 7-8 weeks for this variant to go from about 10% to 80+%:


The estimates are that in most of continental Europe the new UK variant is around about 5-10% at the moment. In Denmark they've got a little more (so does Geneva which is doing near real-time sequencing) and expect the UK variant to become dominant by March but I think in Europe it will be dominant by the end of March. This is why I keep worrying that Europe might need to lockdown hard now to avoid a big wave in late February/early March as this more transmissible variant really takes off - the same process will happen in the US I worry. I think the UK has offered spare sequencing capacity and also technical support/sharing expertise on sequencing this variant and I really hope that helps for some countries to start tracking it more closely.

On the upside from Switzerland, Ireland, the UK and Denmark it seems like the increased transmissibility is at the lower end of what was feared so it's around 30-50% not 50-70%.

Edit: And the key point on that UK data above is that in London, the East of England and the South-East this variant became dominant during a lighter lockdown when cases were declining.