New Covid Variants

Covid-19 discussion, bring your own statistics
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Woodchopper
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Re: New Covid Variants

Post by Woodchopper » Mon Jun 14, 2021 7:17 am

Increased household transmission of COVID-19 cases associated with SARS-CoV-2 Variant of Concern B.1.617.2: a national case-control study

Background
The SARS-CoV-2 B.1.617.2 variant (Delta) first detected in India, has rapidly become the dominant variant in England. Studies suggest this variant has increased growth rate and is more transmissible than the previous dominant B.1.1.7 (Alpha) strain. This study aimed to assess the difference in transmissibility in England between the emergent B.1.617.2 variant compared to B.1.1.7 variant.

Methods
A matched case-control study was conducted to estimate the odds of household transmission for B.1.617.2 index cases compared with B.1.1.7 SARS-CoV-2 index cases. Two-to-one matching was undertaken on the basis of geographical location of residence, time period of testing and property type, using a conditional logistic regression model.Findings3,765 genomically sequenced index cases in household clusters(≥ 2 cases in a household), were matched to 7,530 sporadic cases (single cases in a household). 5.8% (n=220) of index cases in household clusters had confirmed B.1.617.2 variant, compared to 4.7% (n= 351) of sporadic cases. The adjusted odds of household transmission was1.64 among index cases with B.1.617.2 variant (95%CI 1.26 to 2.13, p <0.001) compared to the B.1.1.7 variant after adjusting for age, sex, ethnicity, index of multiple deprivation (IMD) and vaccination status of index case.

Interpretation
Overall, we found increased household transmission of COVID-19 associated with B.1.617.2 compared to B.1.1.7. These findings show households are important settings for rapid transmission of the lineage B.1.617.2. With household settings being an important factor in wider community spread, strategies to prevent transmission in these settings are vital to control the COVID-19 pandemic.
https://khub.net/documents/135939561/40 ... a8ef7be9aa

Thread on the paper: https://twitter.com/DrZoeHyde/status/14 ... 04801?s=20
UK pre-print study showing people infected with the delta variant (B.1.617.2, first identified in India) were 64% more likely to transmit the virus to household members than those infected with alpha (B.1.1.7/UK).

Warning sign Children were 46% more likely to transmit than young adults.

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Re: New Covid Variants

Post by Woodchopper » Mon Jun 14, 2021 7:48 am

Covid: Is there a limit to how much worse variants can get?
https://www.bbc.com/news/health-57431420
"This virus has surprised us a lot. It is beyond anything we feared," said Dr Aris Katzourakis, who studies viral evolution at the University of Oxford. "The fact it has happened twice in 18 months, two lineages (Alpha and then Delta) each 50% more transmissible is a phenomenal amount of change."

It's "foolish", he thinks, to attempt to put a number on how high it could go, but he can easily see further jumps in transmission over the next couple of years. Other viruses have far higher R0s and the record holder, measles, can cause explosive outbreaks.

"There is still space for it to move higher," said Prof Barclay. "Measles is between 14 and 30 depending on who you ask, I don't know how it's going to play out."

[...]

"Ultimately there are limits and there isn't a super-ultimate virus that has every bad combination of mutations," said Dr Katzourakis.

[...]

"It is quite possible that changes in the virus that make it better at avoiding vaccines could end up compromising its ability to transmit in an absolute sense," said Dr Katzourakis.

He thinks the Beta variant - which has a mutation called E484K that helps evade the immune system but hasn't managed to take off - is an example of this. However, the Delta does have mutations that both help it spread and partially dodge immunity.

What will turn out to be the optimal strategy for coronavirus is still hard to predict. Different viruses use different techniques to keep on infecting. Measles is explosive, but leaves behind lifelong immunity so it always has to find someone new. Influenza has a much lower R0, barely above 1, but constantly mutates to side-step immunity.

"We're in a really interesting, intermediate and somewhat unpredictable phase, it is difficult to predict how that's going to play out a year from now," said Prof Barclay.

One thing that is often claimed, but attracts scientific scorn, is that the virus must get milder in order to spread more easily. There is very little evolutionary pressure on the virus for that to happen. The virus is already off into the next person long before it kills the person it infected. And the people who do the most spreading (younger people) are those who don't get very ill.

In rich countries with good vaccination campaigns it is hoped the next variants won't be able to pose a major problem due to widespread immunity. But these progressively more transmissible variants are a nightmare for the rest of the world where they are making it harder and harder to stay on top of Covid.
https://www.bbc.com/news/health-57431420

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Re: New Covid Variants

Post by raven » Mon Jun 14, 2021 11:27 am

Woodchopper wrote:
Mon Jun 14, 2021 7:17 am
Thread on the paper: https://twitter.com/DrZoeHyde/status/14 ... 04801?s=20
UK pre-print study showing people infected with the delta variant (B.1.617.2, first identified in India) were 64% more likely to transmit the virus to household members than those infected with alpha (B.1.1.7/UK).

Warning sign Children were 46% more likely to transmit than young adults.
From that twitter thread:
While most older adults have been vaccinated (making them less likely to transmit if infected), less than half of younger adults have been vaccinated.

The higher risk of transmission by children is therefore unlikely to be entirely explained by the vaccination of adults.
But might be explained by kids being a)little snot monsters and b) dependent on adult care. Much harder to get a sick 7yr old to isolate from the rest of the household than it is an adult spouse.

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Re: New Covid Variants

Post by shpalman » Mon Jun 14, 2021 5:30 pm

shpalman wrote:
Sat Jun 12, 2021 6:12 pm
Delta variant involved in an outbreak at a gym in Milan

Well, one of the 10 cases is the Delta variant but they haven't sequenced the other 9 yet.
Apparently, one of these cases is someone who's had both vaccine doses, but we don't know which vaccine or indeed anything else about them.

Even if 140 members of the gym have been traced and tested I think the only positives were these 10, members of some sort of gymnastics class, but that could mean anything and I wonder if it's more likely to be the sort of gentle aerobics which older people do (tends to be known as ginnastica dolce here).
molto tricky

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Re: New Covid Variants

Post by shpalman » Tue Jun 15, 2021 5:08 pm

1 case in 100 is the Delta variant in Lombardy at the moment apparently (Lombardy is having 250 cases per day at the moment but it's halving every two weeks).

But then the Alpha variant started small and became dominant.
molto tricky

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Re: New Covid Variants

Post by shpalman » Sat Jun 19, 2021 7:07 am

99% of Covid cases in the UK involve the Delta variant
Figures show Delta is more transmissible and more resistant to vaccine than Alpha
Who knew!
The group cautions that since they're looking at data from two to three weeks ago, these figures represent the spread of Covid about two to three weeks ago.
While educational settings have recently been the most common settings for reported exposures, in the latest week the proportion linked to schools declined while that linked to hospitality settings and travel rose considerably.
molto tricky

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Re: New Covid Variants

Post by raven » Sat Jun 19, 2021 1:24 pm

While educational settings have recently been the most common settings for reported exposures, in the latest week the proportion linked to schools declined while that linked to hospitality settings and travel rose considerably.
Also who knew.

Education settings had a break for half term, during which everybody went on holiday/visited relatives/ate out.

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Re: New Covid Variants

Post by shpalman » Sat Jun 19, 2021 1:35 pm

Lombardy is currently sequencing 25% of the positive PCR swabs but intending to reach 100%.

At the moment, 68% are Alpha variant, 1.7% are Delta, 1.1% are Gamma and 0.3% are Beta.

Assuming Moratti is reporting correctly which she might not be.

https://www.espansionetv.it/2021/06/18/ ... a-e-all17/
molto tricky

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Re: New Covid Variants

Post by shpalman » Mon Jun 21, 2021 3:28 pm

shpalman wrote:
Sat Jun 19, 2021 1:35 pm
Lombardy is currently sequencing 25% of the positive PCR swabs but intending to reach 100%.

At the moment, 68% are Alpha variant, 1.7% are Delta, 1.1% are Gamma and 0.3% are Beta.

Assuming Moratti is reporting correctly which she might not be.

https://www.espansionetv.it/2021/06/18/ ... a-e-all17/
For example, instead of sequencing 25% of swabs and having about 2% as Delta, Eric Feigl-Ding has 2% sequenced and 26% Delta, from the FT, although obviously I find it incomprehensible without him having drawn over it in felt tip to point out what I'm supposed to see.

Delta variant begins to spread, threatening EU’s Covid progress
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molto tricky

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Re: New Covid Variants

Post by shpalman » Tue Jun 22, 2021 6:24 am

molto tricky

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Re: New Covid Variants

Post by Brightonian » Tue Jun 22, 2021 2:23 pm

Cases of transmission of Delta just by fleeting exposure:
Eric Feigl-Ding thread.

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Re: New Covid Variants

Post by shpalman » Thu Jun 24, 2021 6:12 am

molto tricky

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Re: New Covid Variants

Post by Woodchopper » Fri Jun 25, 2021 11:42 am


Israel Renews Indoor COVID Mask Mandate as Delta Variant Spreads
Coronavirus czar, Dr. Nachman Ash, says that while cases are rising, he does not believe that Israel is entering a fourth wave and doesn't plan on imposing new lockdowns

Israel's Health Ministry reinstated the indoor mask mandate beginning Friday at 12:00 P.M., following a recent rise in coronavirus infections attributed to the delta variant.

The Health Ministry also recommends that Israelis wear masks during mass public events, even if they are held in the open air, "like the Pride events that will take place this weekend across the country."

Israel's coronavirus czar Dr. Nachman Ash said Friday that Israel is seeing a sharp rise in infections, as 227 new cases were diagnosed on Thursday, though he does not believe Israel is entering a fourth wave of the virus.
https://www.haaretz.com/israel-news/isr ... -1.9939962

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Re: New Covid Variants

Post by raven » Fri Jun 25, 2021 8:50 pm

Woodchopper wrote:
Fri Jun 25, 2021 11:42 am

Israel Renews Indoor COVID Mask Mandate as Delta Variant Spreads

Israel's Health Ministry reinstated the indoor mask mandate beginning Friday at 12:00 P.M., following a recent rise in coronavirus infections attributed to the delta variant.
Caught that on Al-Jazeera this morning. They'd only relaxed it 10 days ago too. One of the guests made a point of how good it is that that they've reacted so quickly, I think he said on only 4 days worth of data.

Compare that to Johnson, and the outbreaks here which have been going on for weeks.

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Re: New Covid Variants

Post by shpalman » Sat Jul 03, 2021 10:41 am

A couple of quick screengrabs from the "news" since I can never figure out how to actually get the data out of the ISS
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molto tricky

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Re: New Covid Variants

Post by headshot » Sat Jul 03, 2021 2:37 pm

As soon as I saw that top image, this music started playing in my head:

https://youtu.be/sxu6E8OHHF4

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Martin Y
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Re: New Covid Variants

Post by Martin Y » Sat Jul 03, 2021 2:48 pm

headshot wrote:
Sat Jul 03, 2021 2:37 pm
As soon as I saw that top image, this music started playing in my head:

https://youtu.be/sxu6E8OHHF4
Well that's a much more fun symptom than a persistent cough or loss of smell.

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Re: New Covid Variants

Post by shpalman » Sun Jul 04, 2021 5:47 pm

shpalman wrote:
Sat Jul 03, 2021 10:41 am
Image
Given the above, I thought I'd also plot the case rate in Friuli-Venezia-Giulia to see if there's an obvious effect from having Delta so dominant.
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Well, not obviously. Not yet, at least.

(I know it's the weekend so therefore not a particularly meaningful number, and I'll wait for the 7-day rates to settle down, but today Italy recorded fewer deaths (12) than England (15).)
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Re: New Covid Variants

Post by shpalman » Mon Jul 05, 2021 6:55 am

Starting to go up in France now
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Re: New Covid Variants

Post by Grumble » Mon Jul 05, 2021 8:46 am

That’s because the U.K. is world leading. France just copies us.
You’ve got no chutzpah, your organisational skills are lacklustre and your timekeeping is abysmal.

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Re: New Covid Variants

Post by hakwright » Mon Jul 05, 2021 12:26 pm

After a long period of declining cases, the numbers are suddenly starting to go up in many European countries. Pretty dramatic upwards trajectory in Spain and Greece, also going up in France and the Netherlands, Belgium is heading upwards (though wobbling a bit, so less clear).

Delta is taking over in many EU countries, as we knew would happen. The fact it is happening in the middle of summer, with lots of fresh air and mostly outdoor interactions, just shows how easily it can be transmitted compared to Alpha.

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Re: New Covid Variants

Post by Herainestold » Mon Jul 05, 2021 7:59 pm

hakwright wrote:
Mon Jul 05, 2021 12:26 pm
After a long period of declining cases, the numbers are suddenly starting to go up in many European countries. Pretty dramatic upwards trajectory in Spain and Greece, also going up in France and the Netherlands, Belgium is heading upwards (though wobbling a bit, so less clear).

Delta is taking over in many EU countries, as we knew would happen. The fact it is happening in the middle of summer, with lots of fresh air and mostly outdoor interactions, just shows how easily it can be transmitted compared to Alpha.
Well if they are 95% double dosed they will be okay. Of course no country will reach 95%, so we will see rising cases, hospitalizations and death.
Delta changes everything.

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Re: New Covid Variants

Post by Woodchopper » Mon Jul 05, 2021 9:12 pm


COVID Vaccine Effectiveness Drops to 64% in Israel, Health Ministry Says; Experts Differ
The ministry says, however, that the COVID vaccine is 93 percent effective in preventing hospitalizations and severe symptoms

The Pfizer-BioNTech coronavirus vaccine has dropped to 64 percent effectiveness in preventing infection in Israel as the delta variant continues to spread across the country, the Health Ministry said on Monday.

According to Israeli data published in March, two weeks after the vaccine was given, it had 99 percent efficacy in preventing symptomatic COVID-19 and 91.2 percent in preventing infection.

The ministry added that the vaccine is 93 percent effective in preventing hospitalizations and severe symptoms.

[...]

The data was presented on Sunday by members of the Health Ministry's epidemiology team. However, experts have expressed doubt regarding the analysis of infection rates in Israel in recent weeks and the ministry's epidemiology team has also questioned it.

Nevertheless, health sources believe that the inoculation's efficacy against the delta variant is much lower than initially presumed.
https://www.haaretz.com/israel-news/.pr ... -1.9971842

Not that different from the UK numbers linked to earlier in the thread.

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Re: New Covid Variants

Post by Herainestold » Mon Jul 05, 2021 10:04 pm

Woodchopper wrote:
Mon Jul 05, 2021 9:12 pm

COVID Vaccine Effectiveness Drops to 64% in Israel, Health Ministry Says; Experts Differ
The ministry says, however, that the COVID vaccine is 93 percent effective in preventing hospitalizations and severe symptoms

The Pfizer-BioNTech coronavirus vaccine has dropped to 64 percent effectiveness in preventing infection in Israel as the delta variant continues to spread across the country, the Health Ministry said on Monday.

According to Israeli data published in March, two weeks after the vaccine was given, it had 99 percent efficacy in preventing symptomatic COVID-19 and 91.2 percent in preventing infection.

The ministry added that the vaccine is 93 percent effective in preventing hospitalizations and severe symptoms.

[...]

The data was presented on Sunday by members of the Health Ministry's epidemiology team. However, experts have expressed doubt regarding the analysis of infection rates in Israel in recent weeks and the ministry's epidemiology team has also questioned it.

Nevertheless, health sources believe that the inoculation's efficacy against the delta variant is much lower than initially presumed.
https://www.haaretz.com/israel-news/.pr ... -1.9971842

Not that different from the UK numbers linked to earlier in the thread.
Vaccinated population vs Delta is like unvaccinated vs wild strain


"Well, in our country," said Alice, still panting a little, "you'd generally get to somewhere else—if you run very fast for a long time, as we've been doing."

"A slow sort of country!" said the Queen. "Now, here, you see, it takes all the running you can do, to keep in the same place. If you want to get somewhere else, you must run at least twice as fast as that!" [1]
Delta changes everything.

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Re: New Covid Variants

Post by Bird on a Fire » Tue Jul 06, 2021 10:34 am

Not sure if that's a deliberate reference to the Red Queen hypothesis, but it's certainly apposite https://en.m.wikipedia.org/wiki/Red_Queen_hypothesis

Evolution is constant. We cannot rest on our laurels just because older people in richer countries are now vaccinated. There will be more variants for sure, and partially-vaccinated populations are the biggest risk for something nasty to emerge.
He has the grace of a swan, the wisdom of an owl, and the eye of an eagle—ladies and gentlemen, this man is for the birds!

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