COVID-19

[raven]

So the government are only going to release infection figures once a week and redacted of geographical information.

https://twitter.com/DHSCgovuk/status/12 ... 4407802880

So there's 6 days for those in the know (IE ministers.) to do a nice little bit of insider trading on companies likely to be affected.

The tweet says...

"As of today, due to the number of new cases, we will no longer be tweeting information on the location of each new case. Instead, this information will be released centrally in a consolidated format online, once a week. We are working on this now and plan to share on Friday."

Doesn't this mean they will still tweet the numbers (perhaps each day) but just not tweet the locations.

Anyway they have done a U-turn and decided to carry on as before.

I caught a bit of the select committee this morning. Whitty (chief medical officer) said that they would still be releasing location data, but that if numbers increase there might be a 24hour delay so they can make sure they're putting out the right info.

He also said that other countries were being very open about this & pointed out that Singapore released location down to street level, and HongKong has an app that lets you know if you're within 100m of a case. Then he said that down to street level was probably not appropriate here. (Impication being because we can't be trusted not to abuse our neighbours who are ill, I think.)

I've been following the numbers. Cases in Hong Kong & Singapore seem to be increasing more slowly than elsewhere. Does anyone know why? Are they being stricter, are they not testing as many people, are people there being more sensible due to past experiences with SARs? Could the fine-grain location data be helping?

[bob sterman]

Yes - that's the bit that I don't think is very clear. E.g. using the term "aggressive" rather than clarifying whether they are referring to harm to the patient or transmissability.

I'm pretty sure they mean transmissability.

If so then their reasoning doesn't quite make sense. Surely, if you impose selection pressures that make it harder for a virus to be passed on, then this favours the most transmissable strains and these should become more prevalent. If you relax these selection pressures, then less transmissible strains can increase in prevalence.

[TimW]

At least Flybe are doing their bit to slow the spread of the virus.

[shpalman]

I can imagine how a strain of the virus which causes people to develop more obvious symptoms, and therefore get diagnosed and isolated, would allow a version which was more subtle to spread unnoticed.

[shpalman]

Thus far, we found that, although the L type is derived from the S type, L (~70%) is more prevalent than S (~30%) among the sequenced SARS-CoV-2 genomes we examined. This pattern suggests that L has a higher transmission rate than the S type. Furthermore, our mutational load analysis indicated that the L type had accumulated a significantly higher number of derived mutations than S type (P < 0.0001, Wilcoxon rank-sum test; Fig. S5). We propose that, although the L type newly evolved from the ancient S type, it transmits faster or replicates faster in human populations, causing it to accumulate more mutations than the S type. Thus, our results suggest the L might be more aggressive than the S type due to the potentially higher transmission and/or replication rates.

They then show that most of the viruses isolated in Wuhan were L type, with only one S type. Outside Wuhan the numbers were more equal.

If the L type is more aggressive than the S type, why did the relative frequency of the L type decrease compared to the S type in other places after the initial breakout in Wuhan? One possible explanation is that, since January 2020, the Chinese central and local governments have taken rapid and comprehensive prevention and control measures. These human intervention efforts might have caused severe selective pressure against the L type, which might be more aggressive and spread more quickly. The S type, on the other hand, might have experienced weaker selective pressure by human intervention, leading to an increase in its relative abundance among the SARS-CoV-2 viruses. Thus, we hypothesized that the two types of SARS-CoV-2 viruses might have experienced different selective pressures due to different epidemiological features. Of note, the above analyses were based on very patchy SARS-CoV-2 genomes that were collected from different locations and time points. More comprehensive genomic data is required for further testing of our hypothesis.

So it's still not clear but I think it makes sense if you assume that the more aggressive L type leads to more obvious symptoms so gets people put in isolation quicker.

[Woodchopper]

Very interesting, you got a link for that shpalman?

[shpalman]

Very interesting, you got a link for that shpalman?

The one time lpm actually posts a link:

Those guys from that link are pretty dismissive of this latest "new 2nd strain has emerged" theory.

I had a quick look at the paper - the part where they present an argument about selection pressures leading to a change in the prevalence of different strains is not very clearly written. So it's hard to follow their line of reasoning.

Paper here. S and L types.
https://academic.oup.com/nsr/advance-ar ... 36/5775463

Although the L type (∼70%) is more prevalent than the S type (∼30%), the S type was found to be the ancestral version. Whereas the L type was more prevalent in the early stages of the outbreak in Wuhan, the frequency of the L type decreased after early January 2020. Human intervention may have placed more severe selective pressure on the L type, which might be more aggressive and spread more quickly. On the other hand, the S type, which is evolutionarily older and less aggressive, might have increased in relative frequency due to relatively weaker selective pressure.

[Woodchopper]

Sorry, on my phone. Didn’t scroll back more than a page.

[mikeh]

On the note of the location of patients, this is a summary taken by someone else who listened to Chris Whitty's comments. I imagine they are reflective of what he said. Am surprised the Singapore data is so detailed (on the geospatial aspects), for the reasons listed below. I wonder if the stigma is less in Singapore than it is here (in the UK).

What is rational for restricting location information?

We ARE intending to provide a dashboard as cases go up.
But we will have some delay of about 24 hours to make sure we get the details right.
We don’t want to give incorrect information.
In due course we will use maps.
But some people have had social problems and vilification on social media – we are against giving any patient-identifying information.
I am not in favour of going down to street level.

[FlammableFlower]

Ah, now Donald has weighed in to say it's fake news.

[bolo]

Identifying a street comes much closer to identifying a person when the density of housing is lower. Singapore is very densely populated compared to the UK.

[mikeh]

Identifying a street comes much closer to identifying a person when the density of housing is lower. Singapore is very densely populated compared to the UK.

True, but the data is so detailed, they're giving very specific location data, alongside age, sex, nationality. Can't imagine it would be hard to dig out identities with only a little bit of detective work.

Their data dashboard is at https://experience.arcgis.com/experienc ... fe67bd8b89. It's very impressive from the point of view of a public health tool. But not an equivalent that can be made publicly available in the UK.

[headshot]

Identifying a street comes much closer to identifying a person when the density of housing is lower. Singapore is very densely populated compared to the UK.

True, but the data is so detailed, they're giving very specific location data, alongside age, sex, nationality. Can't imagine it would be hard to dig out identities with only a little bit of detective work.

Their data dashboard is at https://experience.arcgis.com/experienc ... fe67bd8b89. It's very impressive from the point of view of a public health tool. But not an equivalent that can be made publicly available in the UK.

This sort of granular level data would make it possible to identify an individual, which would be in contravention of the GDPR.

[bolo]

I hadn't realized there was so much more than just "XXX Street". Thanks for the link.

[Boustrophedon]

Ah, now Donald has weighed in to say it's fake news.

What? I never.

Oh him.

[mikeh]

I hadn't realized there was so much more than just "XXX Street". Thanks for the link.

No worries, I was quite surprised at the granularity of it all when I went to take a peek.

Meanwhile, and apologies for those with no interest in UK-firsts, we have the first death in the UK. Fits into the typical demographic of elderly with co-morbidities, so not in itself a surprise. There'll be a few more of those before we're done. Hope we don't see an outbreak in care homes, infection prevention and control is difficult anyway, and not always impressive, in those settings.

[AMS]

Very interesting, you got a link for that shpalman?

The one time lpm actually posts a link:

I had a quick look at the paper - the part where they present an argument about selection pressures leading to a change in the prevalence of different strains is not very clearly written. So it's hard to follow their line of reasoning.

Paper here. S and L types.
https://academic.oup.com/nsr/advance-ar ... 36/5775463

Although the L type (∼70%) is more prevalent than the S type (∼30%), the S type was found to be the ancestral version. Whereas the L type was more prevalent in the early stages of the outbreak in Wuhan, the frequency of the L type decreased after early January 2020. Human intervention may have placed more severe selective pressure on the L type, which might be more aggressive and spread more quickly. On the other hand, the S type, which is evolutionarily older and less aggressive, might have increased in relative frequency due to relatively weaker selective pressure.

A fascinating implication is that the Chinese containment measures in Wuhan may have put a selective pressure on the virus that favoured the spread of a less aggressive virus. That may not have been their aim, but would be an amazing outcome.

Also, I'm intrigued by the S and L types. They actually refer to variants encoding Leucine and Serine, which are (biophysically speaking) very different amino acids.

[Sciolus]

On the note of the location of patients, this is a summary taken by someone else who listened to Chris Whitty's comments. I imagine they are reflective of what he said. Am surprised the Singapore data is so detailed (on the geospatial aspects), for the reasons listed below. I wonder if the stigma is less in Singapore than it is here (in the UK).

What is rational for restricting location information?

We ARE intending to provide a dashboard as cases go up.
But we will have some delay of about 24 hours to make sure we get the details right.
We don’t want to give incorrect information.
In due course we will use maps.
But some people have had social problems and vilification on social media – we are against giving any patient-identifying information.
I am not in favour of going down to street level.

This BBC report from South Korea seems a far more likely example of the societal effects of releasing detailed personally-identifiable information about people's contacts.

As an aside, this is why c.nts whose reaction to Big Brother intrusiveness is "the innocent have nothing to fear" are c.nts.

[mikeh]

This BBC report from South Korea seems a far more likely example of the societal effects of releasing detailed personally-identifiable information about people's contacts.

Yeah, quoting from the BBC link

"A 43-year-old man, resident of Nowon district, tested positive for coronavirus," it says.

"He was at his work in Mapo district attending a sexual harassment class. He contracted the virus from the instructor of the class."

A series of alerts then chronicle where the men had been, including a bar in the area until 11:03 at night.

These alerts arrive all day, every day, telling you where an infected person has been - and when.

So much of that detail is completely unnecessary for the general public to know. If that kind of alert really has to be made, then it could simply be
"resident of Nowon district, tested positive for coronavirus"

Don't need to know the sex, age, their movements. People attending the sexual harassment class [ the what?? ] will be the subject of contact tracing anyway, everyone else passing by with a mere glimpse of the known case are not at risk anyway. I think it's phenomenally irresponsible. One of the downsides in the general and extensive trend of open data that we've seen used in this outbreak.

[Boustrophedon]

A fascinating implication is that the Chinese containment measures in Wuhan may have put a selective pressure on the virus that favoured the spread of a less aggressive virus. That may not have been their aim, but would be an amazing outcome.

Also, I'm intrigued by the S and L types. They actually refer to variants encoding Leucine and Serine, which are (biophysically speaking) very different amino acids.

So I wonder which type we have in the UK?

[Brightonian]

This BBC report from South Korea seems a far more likely example of the societal effects of releasing detailed personally-identifiable information about people's contacts.

Yeah, quoting from the BBC link

"A 43-year-old man, resident of Nowon district, tested positive for coronavirus," it says.

"He was at his work in Mapo district attending a sexual harassment class. He contracted the virus from the instructor of the class."

A series of alerts then chronicle where the men had been, including a bar in the area until 11:03 at night.

These alerts arrive all day, every day, telling you where an infected person has been - and when.

So much of that detail is completely unnecessary for the general public to know. If that kind of alert really has to be made, then it could simply be
"resident of Nowon district, tested positive for coronavirus"

Don't need to know the sex, age, their movements. People attending the sexual harassment class [ the what?? ] will be the subject of contact tracing anyway, everyone else passing by with a mere glimpse of the known case are not at risk anyway. I think it's phenomenally irresponsible. One of the downsides in the general and extensive trend of open data that we've seen used in this outbreak.

Agree, don't need to know sex and age, but I'd like to know movements, e.g. "on 5 March visited a bar on the High Street, a kebab shop on the Low Road, and used the no. 12 bus" just to alert me to the possibility I might have encountered them and become infected.

[lpm]

Those NextStrain.org people that Jimbob linked to yesterday - here's their response to the L and S thing:

http://virological.org/t/response-to-on ... -cov-2/418

Don't understand much of it, but I think they say:

- normal genetic drift is going to happen, there are 111 "nonsynonymous" mutations catalogued, with no evidence that these 111 mutations make any difference to transmission etc. Nonsynonymous means a difference that natural selection can act on, synonymous mutations don't
- not clear there's any reason to pick two mutations and call them two different types
- differences in transmission from mutations would get swamped by "stochastic epidemiological effects" - i.e. no way to get any signal amid the huge noise of randomness, plus the huge distortion of founder effects from a new spreader arriving in Fujian or Italy or Seattle
- small scale random variations at the very beginning of an outbreak lead to big differences downstream in the epidemic. I think this is like tiny differences shortly after the Big Bang leading to vast super clusters and empty voids today. Initial genetic drift drives the frequencies of variants today
- Tang et al f.cked up something in their maths, their two mutation types don't add up right, maybe because they mistakenly go back to the bat coronavirus ancestor instead of the first human in Wuhan to get SARS-CoV-2
- sequencing errors could be knocking their numbers awry
- some methodological issue with the software Tang et al used

Summary
Given these flaws, we believe that Tang et al. should retract their paper, as the claims made in it are clearly unfounded and risk spreading dangerous misinformation at a crucial time in the outbreak.

[lpm]

ETA not sure it is those nextstrain people, actually, not sure how they join up or how I got to this link...

[TopBadger]

So this is frightening...

What the 1918 flu's hidden history can teach the coronavirus era

https://flip.it/7._14u

[jimbob]

So this is frightening...

What the 1918 flu's hidden history can teach the coronavirus era

https://flip.it/7._14u

Yup, thanks