What evidence will tell us about the new strain? How are you updating?

post by Zvi · 2020-12-25T21:37:25.264Z · LW · GW · 5 comments

This is a question post.

Contents

  Answers
    Oskar Mathiasen
    TheMajor
    PPaul
    Gunnar_Zarncke
    Davidmanheim
None
5 comments

I didn't get into this question in the weekly post. The answer does not seem obvious to me.

Eventually, it will be obvious either way. Either the strain will spread rapidly across many locations, or it won't. But we would like to get the information as fast as possible, whatever the answer turns out to be. So the open question is, what numbers or other information can we use in the short term to generate useful evidence for or against the new strain being a lot more infectious than older ones?

The obvious first things to look at are England's case numbers, and how rapidly the new strain continues to outcompete the old strain. Certainly the percent dominance continuing to go up, or stabilizing, is evidence. 

Alas, tonight is Christmas, and I haven't been keeping up in detail with English reporting and testing dynamics. We saw only a small bump on Christmas Eve, after big jumps in the previous post-announcement days, and I can't tell how much of that was the holiday. Same will apply to today's number, to Boxing Day, and then there are issues of either lag or catchup, and then New Year's. Can anyone shed light on these details, and how seriously we should take them? Even if we get a new mix of strain results, should we worry about lags in the south versus the north, where different strains dominate, warping numbers?

What are good data sources to check for the strain in other nations? Who is checking enough that if it was present, we would notice, or we'd have a good handle on its numbers? Can we make this data happen somewhere? 'Has been spotted in' isn't much to work with.

Also making this a place for people to say how they're updating their estimates based on information that comes in.   

Answers

answer by Oskar Mathiasen · 2020-12-26T11:13:27.485Z · LW(p) · GW(p)

The countries that do the most sequencing (who also have a significant number of cases) is Denmark (10.9% of positives are sequenced) and the UK(5.61%).
The Danish data makes me slightly hopeful:
1. the virus has been found in Denmark.
2. But the numbers are surprisingly small, 9 confirmed cases by 20-12,  
3. The Danish government have not released statements regarding its effects on vaccines.
3-1. Denmark made such an announcement as soon as any evidence above baseline existed for cluster 5, so the lack of announcement is more significant than one might otherwise think.
4. Case numbers are not going up in Denmark

comment by orthonormal · 2020-12-27T00:53:22.546Z · LW(p) · GW(p)

Can't update on #4. Of course a rapidly growing new strain will have a negligible impact on total numbers early on; it's a question of whether it will dominate the total numbers in a few months.

comment by blob · 2020-12-27T09:52:57.480Z · LW(p) · GW(p)

On 2: This reports that Denmark has found 33 cases of the new variant, out of 7800 analysed between Nov 14 and Dec 14. Source: https://www.ssi.dk/aktuelt/nyheder/2020/statens-serum-institut-udgiver-opdaterede-tal-for-den-engelske-covid-19-virusvariant, English reporting: https://www.thelocal.dk/20201224/denmark

comment by Gunnar_Zarncke · 2020-12-27T21:05:23.273Z · LW(p) · GW(p)

I think a good indicator of whether the strain is picking up is Ireland which recently has done a good job containing the virus but is close to UK and they closed traffic between them only recently i.e. too late. If you eyeball this Our World in Data chart (sorry, can't embed pics im comments) you could guess that Ireland is about 10 days behind UK. For other countries like France or Germany, it is too early to say. I expect to see a clear signal (if there is one to be seen) by mid-January.

comment by Andrew_Clough · 2020-12-31T19:50:59.792Z · LW(p) · GW(p)

One thing that makes this disease hard to reason about is the high k.  That is, most people infect a very small number of people but some people infect large numbers. When case numbers are less than a thousand we should't expect a strong signal regardless of the underlying infectivity of the new strain.  This is evidence against it being significant but I fear its not very strong evidence.

answer by TheMajor · 2020-12-26T11:05:03.121Z · LW(p) · GW(p)

I can answer this one, or more specifically the PHE can. The tl; dr of this technical briefing is that the new strain tests positive on two assays (N, ORF1ab) and negative on a third (S), and that up to some noise this is currently the only strain to do so. So the number of PCR tests that are both S-negative and COVID-positive is a good indication of the spread of the new strain, without the need for genome sequencing. This document makes this argument precise, and then produces a painful graph on page 8 showing the 'S dropout' proportion at the Milton Keynes Lighthouse lab (Buckinghamshire). Mid December they show a proportion of over 60%.

This has led to me to update towards the new variant being as aggressive as previously feared, because unlike genome sequencing PCR test data does not lag several weeks behind. Combined with the fact that genome sequencing is done sporadically at best (if I understand correctly, nextstrain data explains the UK has sequenced 85 samples since September, with neighbouring countries showing similar numbers) I think it may already be more widely spread/beyond containment in a lot of European countries. Edit: Oskar Mathiasen gives a difference source with incompatible numbers, I am no longer confident in this point.

I also share shminux' fears that this more aggressive strain may be difficult to contain with just the measures we have taken so far.

comment by Oskar Mathiasen (oskar-mathiasen) · 2020-12-26T11:26:59.829Z · LW(p) · GW(p)

85 seems incongruent with this source https://covidcg.org/?tab=global_sequencing
 

Replies from: TheMajor
comment by TheMajor · 2020-12-26T12:06:29.507Z · LW(p) · GW(p)

Good point, I'm likely misinterpreting nextstrain website then.

answer by PPaul · 2020-12-28T11:20:37.612Z · LW(p) · GW(p)

Here is a preprint of a simulation study fitting observed data to various models. (dated 23-12-2020) Best fit is increased transmission. I lack the qualification to judge its quality, but update towards higher transmission.

"We estimate that VOC 202012/01 is 56% more transmissible (95% credible interval across three regions 50-74%) than preexisting variants of SARS-CoV-2."

comment by PPaul · 2020-12-29T13:57:32.123Z · LW(p) · GW(p)

The updated PHE report found:

228,361 (9.9% attack rate) of all contacts notified by cases in this period became cases:

  • 15.1% among those whose index case was confirmed to have the VOC [variant of concern] 202012/01
  • 9.8% among those whose index case was sequenced and confirmed with other variants
answer by Gunnar_Zarncke · 2020-12-27T20:48:47.839Z · LW(p) · GW(p)

Hi, I'm just sharing some more relevant links and documents from experts and official sources relating to the new variant of the virus. The new variant is designated VOC-202012/01 (VOC=Variant of Concern, previously VOI - Variant of Investigation). I found this by following links from CellBioGuy [LW · GW].

The variant is designated here:

https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/947048/Technical_Briefing_VOC_SH_NJL2_SH2.pdf 

I found a quite interesting Twitter COVID-19 Actuaries Response Group which linked to this bulletin with an in-depth analysis of the variant. Key findings:

The growth rate of this variant based on genomic data is 71% (95% CI, 67% - 75%) higher than other variants. 

Correlation studies on reproduction number (R) suggests an absolute increase in R between 0.39 and 0.93. 

There is “moderate confidence that VUI-202012/01 demonstrates a substantial increase in transmissibility compared to other variants.” 


 

answer by Davidmanheim · 2020-12-30T08:39:42.019Z · LW(p) · GW(p)

'Has been spotted in' isn't much to work with.


Agreed, but note that the US just found its first case, and it is community-acquired, plus we aren't doing anything to stop importation, so I'm assuming it's everywhere already, and just starting the exponential phase. 

(Note that I cannot find good public data for spread within the UK, which would be the key way to update about the strain.)

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comment by shminux · 2020-12-26T03:47:05.293Z · LW(p) · GW(p)

My main worry is whether the usual protection measures, masks and distancing, will prove inadequate against the new strain. Certainly the way the humanity has been behaving, "stay just at the limit of transmission" is favoring more contagious mutations. Or maybe it's less variability and more transmissibility/infectivity. I wonder if there is any data on those. Probably a good idea to increase the margin of safety until we know for sure.

comment by arunto · 2020-12-26T10:46:31.894Z · LW(p) · GW(p)

When it comes to the UK the changes in this weekly map are quite interesting: Interactive Map Coronavirus UK

Until mid November the most infections happened in the Northern parts of England, went down there and took off in the South (ignoring Wales and N. Ireland for simplicity's sake). Now, I see two possible scenarios:

  1. With increased countermeasures in the South the case increase there is stopped and slowly recedes. Maybe a larger increase in the North due to less restrictions.
  2. The cases in the South increase even more in spite of the countermeasures, followed by cases in the North.

So, what I would be watching is the ratio of the case rates per 100,000 in the South vs. in the North. If it continues to increase that's a bad sign because in that case the increase in the South is quite likely caused by a more infectious strain and not merely the coincidence in time between a mutation and different behaviour.

comment by Bucky · 2020-12-26T09:25:48.672Z · LW(p) · GW(p)

For people not in England it probably helps to say that restrictions were loosened somewhat at the beginning of December (following 3 weeks of stricter lockdown which ended on the 3rd IIRC) and are being tightened significantly today (26th). Worst affected locations were already tightened on the 20th.

The November lockdown was probably marginally stronger than the one now in place but comparing end of November drop rates to whatever happens over the next few weeks will probably be a good indicator as the December growth rates are confounded by different levels of lockdown and results being a mixture of the two strains.

comment by Annapurna (jorge-velez) · 2021-01-05T23:45:08.441Z · LW(p) · GW(p)

Have you looked at this preprint? 

https://www.medrxiv.org/content/10.1101/2020.12.24.20248834v1

I found it linked from here: https://blogs.sciencemag.org/pipeline/archives/2021/01/04/variants-and-vaccines

Replies from: Zvi
comment by Zvi · 2021-01-06T15:52:14.322Z · LW(p) · GW(p)

Yes. Seems like a consensus finding.