🌞 Good morning!
New @PHE_uk reports now published

Technical Briefing 15 on B.1.617.2/Delta

B.1.617.2/Delta risk assessment

Variant update 5
First up,

33,207 total cases of Delta variant this week

You may notice - a dramatic increase from 9,426 last week

Most of this is due to cases detected using *new* genotyping assay, which uses a highly specific mutation as an indicator of a Delta variant
What this means is we get Delta results faster.

Normal sequencing has a reporting delay 7-21 days

Genotyping assay has a ~36 hour turnaround

So we have a more accurate, real-time picture of the Delta variant spread.
What it also means is genotyping assay improves coverage of SARS-CoV-2 specimens

Rollout of the new assay has been super fast, and now ~88% of all new cases are genotyped

Adding ~20% more coverage to our already very high sequencing ~60% of cases

✅ Timeliness
✅ More cases
Ok - on to the data.

The good news is there is no new bad news.
The new data in the briefing largely confirms and updated previously published findings.

As expected, Delta has now almost killed off B.1.1.7 (Alpha) & any other variant

With genotyping data included we now see 96% of cases are Delta
One key finding is a new analysis of household transmission

This found 64% increased transmissibility associated with Delta variant Alpha

Full pre-print here (I will 🧵 this later...)
The severity analysis has been updated:

Findings largely the same

➡️ 2x risk of hospitalisation: Hazard Ratio 2.26 (1.32-3.89) England; HR 1.85 (1.39-2.47 Scotland

➡️ 1.5x risk of A&E attendance OR hospitalisation (a broader definition of severity) HR 1.45 (1.08-1.95)
Hospitalisation and deaths remain low considering case numbers

Though the majority of cases are recent and still under active follow up for these outcomes

3.7% (n=1,234) attended A&E
1.2% (n=383) admitted
0.1% (n=42) died
The great news is that vaccines are still working against infection & severe disease💉

📌 Of infections: 68% unvaccinated; 6% fully vaccinated

📌Of hospital admissions:
65% unvaccinated; 11% fully vaccinated

📌Of deaths: 55% unvaccinated; 29% fully vaccinated
Will leave the brilliant @JamesWard73 to estimate VE against those numbers

Of note is the high % of severe outcomes among people breakthrough infections.

Who are they & why is that happening?

Work ongoing to understand the profile of fully vaxxed people with severe outcomes.
Secondary attack rate (SAR) data from NHS Test & Trace is

41% ⬆️ transmissibility for Delta vs Alpha (community cases)

A decrease over the past couple weeks. Possible reasons: larger numbers reflect more recent cases, shifting demographic of Delta cases & ?some vaccine effect
Growth rate of Delta - 0.93

This has remained almost constant over the past 3 weeks

If Delta has real immune escape properties we would expect to see in real-world data more people to be reinfected.

We are not seeing that yet.

Yes reinfections rising in absolute number yes, but so are the number of cases...
If we focus on a cohort W/ frequent testing - NHS staff from SIREN study

We see very low numbers of reinfections (4 in the last week)

However this cohort also heavily vaccinated (96% of which 95% had Pfizer).

Encouraging but more data needed in vaccine naïve populations 🤔
New this week is an age/sex breakdown of Delta cases

We can see heavily concentrated in young people and children - ages 10-29.

Very few (<5%) of cases are in people aged 60 and over

This aligns with 2-dose vaccine coverage in older age groups & hospitalisations data
So given Delta is dominant in all England regions

What I find interesting is that we aren’t seeing huge increase in case rates in all areas. Delta cases arestill concentrated in a dozen or so areas

It spreads rapidly there in unvaccinated populations, driving up R nationally
By this point with B.1.1.7 (~8-10 weeks post-introduction)

We were seeing a much wider dispersion of cases

And of course much higher case rates generally

This is cause for optimism that vaccines are indeed slowing and in some populations halting the spread of #COVID19
Ps I would love if someone could map that against vaccine coverage rates by LTLA please and thank you!
A couple final notes

The briefing includes some epi on
Delta + spike protein mutation N417K

Also known as Delta-AY.1, first identified in travellers from Nepal

36 cases, most in South East & West Midlands. Not rapidly spreading.
Also, from Variant Data Update:

Two VUIs now declared provisionally extinct in England:

VUI-21FEB-01 (A.23.1 with E484K)
VOC-21FEB-02 (B.1.1.7 with E484K)

No new cases detected since 23 February and 1 March respectively

New cases of all non-Delta variants dropping

A silver lining of a highly transmissible and dominant new strain is it wipes out the competition.

Note: Genotyping assay data now available for Alpha (B.1.1.7) Beta (B.1.351) & Gamma (P.1)

That’s all for now!

Sorry so slow to thread but now we have a morning publication I’m not sure how @PHE_uk expects me to tweet & work at the same time 😉

Thanks as always to @meera_chand for whom I’m running out of adjectives to describe her greatness..
And as always - the amazing team of @PHE_uk & academic partners who work so hard produce this report weekly.

Give them a follow:

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More from @kallmemeg

6 Jun
Hard to believe that tomorrow it’s a whole month since @PHE_uk first published Tech Briefing 10 on B.1.617.2, now Delta variant when we had 509 cases.

That number has increased 20-fold in a month & case numbers are now increasing nationally...
Also over that time, vaccination rollout has been churning along & an additional:

➡️ 5 million people have had 1st dose
➡️ 10 million people have had 2nd dose
Read 12 tweets
3 Jun
✅ New @PHE_uk reports now published

Technical Briefing 14 on B.1.617.2/Delta

B.1.617.2/Delta risk assessment

Variant update
Will start this week with the risk assessment, which has some important changes:

1. Severity is now RED with low confidence (was insufficient info)
2. Vaccines is now RED with high confidence (was moderate)
This is due to 2 new analyses on severity, one from England and one from Scotland. They both found the same:

Increased severity of Delta (B.1.617.2)
- Risk of A&E attendance (Hazard Ratio 1.67)
- Risk of hospital admission (HR 2.61 England, 2.39 Scotland )
Read 18 tweets
1 Jun
Heard about Peru’s revised #COVID19 death count?

That thanks to my brilliant colleague @teozka who has worked behind the scenes on not one but TWO governments pandemic response: UK working for @PHE_uk and his home-country Peru as a technical advisor. 🧵
Early 2020, Mateo volunteered in @PHE_uk EpiCell as we rapidly developed the COVID-19 death data series

We combine 4 sources daily:
1️⃣ Death certs
2️⃣ NHS hospital deaths
3️⃣ Health record tracing link to + test
4️⃣ Community deaths reported by local teams

The daily number of deaths in people WITH Covid is used to rapidly inform the pandemic response

& closely aligns with the “gold standard” @ONS Death Certificate (published weekly on an 11day lag)

See below, the 2 stats mirror each other since widespread testing began mid-2020 Image
Read 6 tweets
27 May
New @PHE_uk variant reports published:

Technical Briefing 13 on B.1.617.2

Variant update 3

B.1.617.2 Risk Assessment
Data up to 25 May

VOC/VUI case numbers here

5,599 sequenced B.1.617.2 cases (double last week 2,854)

12 deaths in B.1.617.2 cases (double last week 6)
No vaccine effectiveness data this week, likely next week to be assured if any change in findings w/new data.

But - risk assessment updated to reflect moderate confidence in reduced vaccine efficacy. Analysis continue to show reduction for B.1.617.2 after 1 dose...
Read 16 tweets
27 May
New @PHE_uk report published today

Hospital-associated seeding of care home COVID-19 outbreaks

Data from the first wave - 30 January to 12 October 2020

This analysis requested by DHSC/SAGE to be submitted to the Public Accounts Committee (PAC) to inform their inquiry

It was prompted by the high number of COVID-19 outbreaks in care homes in Spring 2020

At this time COVID-19 was circulating in hospitals & the question is to what extent were the outbreaks due to resident being infected in hospital & discharged back to the care home
Read 11 tweets
23 May
To ppl asking why vaccine effectiveness for 2nd dose AZ in B.1.617.2 analysis differs from the summary table published this week:

- AZ 2nd dose after 28 days is 66%
- AZ 2nd dose after 12 weeks is 85-90%

Longer interval, more protection 👍
To clarify, from the paper - I am referring to longer follow-up time post-2nd dose, not interval between doses!

Apologies for confusion - I agree that interval wasn’t the best term to use!! No more 2am tweeting for me 😛
Cumulative proportion of 2nd doses
Read 5 tweets

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