New Covid Variants

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

Post by lpm » Fri May 14, 2021 2:07 pm

Housing density / multi-generational households / English as a foreign language / have to go to work & no sick pay / poor local health facilities.
What ever happened to that Trump guy, you know, the one who was president for a bit?

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Woodchopper
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Re: New Covid Variants

Post by Woodchopper » Fri May 14, 2021 2:15 pm

lpm wrote:
Fri May 14, 2021 2:07 pm
Housing density / multi-generational households / English as a foreign language / have to go to work & no sick pay / poor local health facilities.
Yes, as correlates those look about right.

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Re: New Covid Variants

Post by jimbob » Fri May 14, 2021 2:23 pm

Woodchopper wrote:
Fri May 14, 2021 2:15 pm
lpm wrote:
Fri May 14, 2021 2:07 pm
Housing density / multi-generational households / English as a foreign language / have to go to work & no sick pay / poor local health facilities.
Yes, as correlates those look about right.
Which also correlate with low vaccine uptake, as far as I recall.

Probably difficulty in getting to a vaccine hub (my appointment there as opposed to the GP was a reasonable drive but rubbish on public transport) as well as distrust
Have you considered stupidity as an explanation

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Re: New Covid Variants

Post by Woodchopper » Sat May 15, 2021 6:23 am


Eighty-ninth SAGE meeting on COVID-19, 13 May 2021

[...]

Some local areas have had continued rapid growth in variants, and of particular concern is the B.1.617.2 variant (a variant first identified in India, where it is now widespread). There are now multiple fast-growing clusters of this variant in the UK, with the largest in the Northwest of England.

4. Transmission of this variant is currently faster than that of the B.1.1.7 variant most prevalent in the UK (high confidence). This is based on observed growth in sequenced cases, and in S-gene positive cases (S-gene positivity can now be used as a reasonable proxy for B.1.617.2, though not all labs are able to identify this). Observed doubling times are around a week or shorter for some of the largest clusters but slower in others.

5. This is unlikely to be wholly due to inherently higher transmission in the communities within which B.1.617.2 is currently circulating (i.e., this faster transmission cannot be explained entirely by contact patterns or behaviours). The places where transmission of this variant is occurring have different characteristics to each other, and do not appear to be experiencing similar growth of other variants (i.e., B.1.1.7).

6. It is therefore highly likely that this variant is more transmissible than B.1.1.7 (high confidence), and it is a realistic possibility that it is as much as 50% more transmissible. There are also plausible biological reasons as to why some of the mutations present could make this variant more transmissible.

7. It is unclear whether this same growth advantage that has been observed over recent weeks would apply to sustained wider community transmission regionally or nationally. The range of possible differences in transmissibility reflects the uncertainty around the number of imported cases, and the current relatively localised transmission.

8. In the areas where numbers of infections are increasing rapidly under the measures currently in place, an even faster increase can be expected if measures are relaxed (high confidence).

9. If this variant were to have a 40-50% transmission advantage nationally compared to B.1.1.7, sensitivity analyses in the modelling of the roadmap in England (SAGE 88) indicate that it is likely that progressing with step 3 alone (with no other local, regional, or national changes to measures) would lead to a substantial resurgence of hospitalisations (similar to, or larger than, previous peaks). Progressing with both steps 3 and 4 at the earliest dates could lead to a much larger peak. Smaller transmission advantage would lead to smaller peaks.

Early indications are that there is some antigenic distance between B.1.617.2 and wild-type virus, and that this distance is greater than that for B.1.1.7, but less than for B.1.351, and similar to that for B.1.617.1 (low confidence). This means that there may be some reduction in protection given by vaccines or by naturally acquired immunity from past infection, though data on this are still mixed.

11. Any such reduction is likely to affect protection against infection more than protection against severe disease or death. If protection against infection were reduced it could contribute to a transmission advantage over B.1.1.7. PHE has linked data on vaccinations and variants and is monitoring for any signals of an impact on vaccine efficacy.

12. There is not yet any clear evidence of any difference in disease severity following infection with this variant. The number of hospitalisations remains low in the affected areas, though this could be because the number of infections has only recently increased. As emphasised by SAGE previously rapid sequencing of hospitalised cases and infections post vaccination is important, and work is underway to increase the proportion of these cases sequenced.
https://assets.publishing.service.gov.u ... eeting.pdf

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Re: New Covid Variants

Post by Woodchopper » Sat May 15, 2021 6:31 am


SPI-M-O: Consensus Statement on COVID-19

[...]

18. SPI-M-O are particularly concerned about the increase in cases of the B.1.617.2 variant in some localities of England, for which S-gene positivity can now be used as a reasonable proxy. One modelling group’s assessment estimates that R for B.1.617.2 is approximately 1.64 (95% CI: 1.61 to 1.67). This analysis accounts for the importation of this variant from India in estimating R for onward community transmission. The model assumes that non- B.1.617.2 cases continue to decline at the same rate (3% per day) as they did in late April 2021, that the generation time for B.1.617.2 is the same as B.1.1.7, and there is no leakage of cases out of hotel quarantine.

19. This estimate is sensitive to the assumed number of imported cases; for example, if there were fewer importations, more local community transmission would be needed to give the outturn data seen or less community transmission if importations were higher. Timely data on traveller information, however, is limited, reflecting some of the uncertainty behind these estimates. Nonetheless, the principal result, that B.1.617.2 is growing more quickly than B.1.1.7, is robust to these sensitivities.

20. S-gene positivity and sequenced B.1.617.2 cases are regionally heterogeneous with clusters in Bolton, Blackburn and Hyndburn (North West cluster) as well as Sefton, Bedford, and London. Observed doubling times are short and getting shorter even under Step 2 restrictions (Figure 1). The diversity of locations and the difference between S-gene positive (such as B.1.617.2) and S-gene negative (such as B.1.1.7) variant growth rates suggests this apparent increase in transmissibility is unlikely to be wholly due to inherently higher transmission in the communities within which B.1.617.2 is currently circulating.

21. SPI-M-O is therefore confident that B.1.617.2 has a significant growth advantage over the UK’s currently dominant strain, B.1.1.7. The difference in growth rates between B.1.617.2 and B.1.1.7 is consistent with the former having a transmission advantage of more than 50%; this is based on observed growth that has already happened and it is unclear whether this same growth advantage would apply to sustained wider community transmission regionally or nationally. Resolving this question of the applicability of this growth advantage to the wider population will be difficult while the number of cases are small and relatively focussed.

22. Considering this, it is a realistic possibility that this scale of B.1.617.2 growth could lead to a very large increase in transmission. At this point in the vaccine roll out, there are still too few adults vaccinated to prevent a significant resurgence that ultimately could put unsustainable pressure on the NHS, without non-pharmaceutical interventions.

23. SPI-M-O would become more confident in this assessment of increased transmissibility advantage if any of these four possible situations were to arise. Any of these could happen extremely quickly, potentially even within days:
• Any emerging evidence of vaccine escape, such as more S-gene positive cases than expected in vaccinated people.
• More rapid increase in hospitalisations in areas with high or rising S-gene positivity compared to elsewhere, or higher than expected levels of B.1.617.2 cases in hospital.
• Other parts of the country reflecting similar situations to the North West cluster that cannot be easily identified as being linked to either that cluster or travel.
• If the North West cluster has another consistent doubling at the same speed (i.e. less than 1 week).

24. There is currently insufficient evidence to indicate that any of the variants recently detected in India cause more severe disease or render the vaccines currently deployed any less effective3. It is also too early to comment on the impact of B.1.617.2 on hospital admissions or deaths; reported COVID-19 hospitalisations in Bolton are concerning. Only accumulating more data on B.1.617.2 will provide this much needed clarity. If there were a time series of the total number of hospitalised B.1.617.2 cases according to their vaccination status, SPI-M-O would be much better placed to assess the threat that the variant poses.

25. SPI-M-O considered the implications of different characteristics of variants of concern in modelling to support Roadmap Step 3 decision making4. Both Warwick and London School of Hygiene and Tropical Medicine (LSHTM) performed sensitivity analyses for a variant of concern that was more transmissible than B.1.1.7, but without escape from immunity, in their modelling. If Step 3 alone were taken with a variant circulating in the population that is more than 40% more transmissible than B.1.1.7 with no increase in severity, a further resurgence in hospitalisations similar in size or larger than those seen in spring 2020 and January 2021 is likely (Figure 2, top right plot). If Steps 3 and 4 are taken (Figure 2, bottom plot) with such a variant, peaks could be double that seen in January 2021 if no interventions were taken.

[...]

Until more data accumulates it will be difficult for SPI-M-O to give a confident plausible range for the transmissibility of B.1.617.2 in the wider population beyond that is it more transmissible than B.1.1.7 and that 50% more transmissible cannot be ruled out. Whilst there are clear observations that B.1.617.2 is currently spreading very fast in some places, numbers are still low and SPI-M-O cannot yet tell if that pattern will pertain across the whole population.

27. Testing of S-gene status by TaqPath assays is regionally heterogeneous with good coverage in those places that have clusters of concern now. There is a need, however, for better coverage with these assays, for example in South West England, to ensure any new hotspots are found early. Such capability allows the use of S-gene positivity as a leading indicator for B.1.617.2 cases.

28. B.1.617.2 is an urgent concerning issue due to its high levels of transmissibility. By contrast, B.1.351 continues to grow in the UK albeit much more slowly. There has been good localised control and extinguishing of clusters of B.1.351 and this will have contributed to its slower growth. As restrictions are eased further from 17th May, cases of both these variants of concern will increase.
https://assets.publishing.service.gov.u ... tement.pdf

See the link for figures etc

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Re: New Covid Variants

Post by shpalman » Sat May 15, 2021 11:00 am

We are responding calmly to Indian Covid variant, insists UK health minister

Well, I'm sure the variant will respect your gentlemanly behaviour.
Edward Argar, Minister of State for Health at the Department of Health and Social Care wrote:“As Chris Whitty said yesterday, it’s possible [it could be more transmissible], but equally it could be much less more transmissible, if that makes sense”
"it could be much less more transmissible"
The Guardian wrote:Edward Argar says the variant could be more – or less – transmissible
No that is not what he said.
molto tricky

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Re: New Covid Variants

Post by Woodchopper » Sat May 15, 2021 7:44 pm

Thread: UK govt delayed implementing travel restrictions for people coming from India. This was probably because Johnson wanted to make an official visit to India. The delay led to the spread of the B.1.671 in Britain

https://twitter.com/edconwaysky/status/ ... 67971?s=21

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Re: New Covid Variants

Post by Herainestold » Sun May 16, 2021 3:13 am

Grauniad:
Boris Johnson was under mounting pressure on Saturday to reconsider Monday’s relaxation of Covid rules in England because of the threat posed by the India variant. His own advisers and independent health experts raised fears that it could lead to a surge in hospital admissions, especially among young adults.
Meanwhile Professor Kit Yates, a member of the Independent Sage committee of scientific experts, told the Observer that Johnson should delay Monday’s unlocking by a fortnight to allow more people to be vaccinated. By pressing ahead, Yates said the prime minister would be breaching one of the government’s four key tests – that of risk assessment not being changed by a new variant – that he had previously insisted would guide all decisions on when and whether to ease restrictions.

“At this point the precautionary principle should kick in,” Yates said. “The more people we can vaccinate, the safer we become. Even a couple of weeks at this point could make a huge difference in the face of this seemingly more transmissible variant. A pause would also buy us time to understand more about the properties of the variant, which would put us in a better position to plan what comes next.”

He added: “The rapid rises in B.1.617.2 and the waves of hospitalisations that are predicted by the Sage modelling means that the risk has fundamentally changed and that the fourth test is not being met. The data suggesting a reassessment of the roadmap is there.”
If the roadmap is truly evidence based and not a political fiction, the Monday openings must not only be postponed, but cancelled.

Outdoor masking and a reversion to previous restrictions must be implemented immediatelt to avoid an India style catastrophe

https://www.theguardian.com/world/2021/ ... 1621113401
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Re: New Covid Variants

Post by shpalman » Mon May 17, 2021 5:11 pm

molto tricky

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Re: New Covid Variants

Post by wilsontown » Mon May 17, 2021 6:00 pm

shpalman wrote:
Mon May 17, 2021 5:11 pm
If we loosen restrictions too early, there is a real risk of a third wave in the UK, freely comments Devi Sridhar.
Just been reading that, and the comments BTL, and it looks like overall the great British public has had enough of restrictions.
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Re: New Covid Variants

Post by shpalman » Mon May 17, 2021 8:12 pm

India variant will be dominant UK Covid strain within days
Johnson is now set to delay plans to announce an end to social-distancing rules, postponing the conclusion of a review expected by the end of the month, casting significant doubt over the wider plan to relax most lockdown rules on 21 June.
molto tricky

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Re: New Covid Variants

Post by Bird on a Fire » Tue May 18, 2021 11:08 am

So in summary, India has been asking to be permitted to manufacture vaccines via a relaxation of patent law since last year. The UK has been the major holdout on this, to protect the financial interests of Big Pharma.

Now, entirely predictably, cases have got out of uncontrol amongst unvaccinated Indians, leading - again entirely predictably - to dangerous new variants, undermining the UK's own aggressively-defended vaccination program.

Obviously this is a catastrophic moral failure, as noted previously. But I think it's also fair to adopt an Indian phrase, and describe it is Big Karma.
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Re: New Covid Variants

Post by headshot » Tue May 18, 2021 11:14 am

***womp, womp***

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Re: New Covid Variants

Post by shpalman » Tue May 18, 2021 11:30 am

The UK's vaccination programme which involved India making vaccines for the UK in a kind of reverse-covax...
molto tricky

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Re: New Covid Variants

Post by hakwright » Tue May 18, 2021 12:11 pm

Woodchopper wrote:
Sat May 15, 2021 6:31 am

SPI-M-O: Consensus Statement on COVID-19

[...]

25. SPI-M-O considered the implications of different characteristics of variants of concern in modelling to support Roadmap Step 3 decision making4. Both Warwick and London School of Hygiene and Tropical Medicine (LSHTM) performed sensitivity analyses for a variant of concern that was more transmissible than B.1.1.7, but without escape from immunity, in their modelling. If Step 3 alone were taken with a variant circulating in the population that is more than 40% more transmissible than B.1.1.7 with no increase in severity, a further resurgence in hospitalisations similar in size or larger than those seen in spring 2020 and January 2021 is likely (Figure 2, top right plot). If Steps 3 and 4 are taken (Figure 2, bottom plot) with such a variant, peaks could be double that seen in January 2021 if no interventions were taken.

[...]
https://assets.publishing.service.gov.u ... tement.pdf

See the link for figures etc
Only just digested all the info here - really interesting and a fairly frightening assessment. The figures/stats from the model predictions for hospitalisations is the key area, IMHO. As in the above quote, as things stand (having already progressed through step 3 in the unlock plan), and with the estimate that the B.1.617.2 variant is likely to be 40-50% more transmissible than the UK variant, we will probably hit a peak of hospitalisations similar or slightly higher than previous UK waves. That's already pretty bad news.

If we progress through step 4 in late June, then hospitalisations will be much higher than previous waves. Surely the step 4 change will be postponed?

I guess the good news is that the number of deaths should remain much, much lower than before (older and more vulnerable people are mostly vaccinated), but the hospitals will likely fill up with younger people (or people who turned down the jab), and they will stay there for some time with non-fatal but possibly nasty health complications.

I also saw some indications that the vaccines help reduce symptoms of long covid, which is another sliver of good news.

Presumably Portugal, Greece and other countries keen to get tourists will likely be hit by similar problems in the coming months?

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Re: New Covid Variants

Post by Bird on a Fire » Tue May 18, 2021 12:50 pm

One advantage in south Europe is the climate - it's reliably sunny and hot all summer, and most tourists from the north want to take advantage of that.

We've (PT) been largely unlocked for a few months now, with café/restaurant tables spread out outside etc, and staff come and disinfect tables and chairs between customers and so on. Obviously beaches are safe. The main pinch points are toilets and potentially hotel corridors.

Requiring negative tests on arrival helps a fair bit too. (Does the UK do this?)

Last summer tourism didn't seem to cause much trouble - didn't get a second wave till the government decided to allow everyone to go and kill each other at Christmas, and then again at New Year, when everyone was indoors.
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Re: New Covid Variants

Post by Millennie Al » Wed May 19, 2021 2:23 am

Bird on a Fire wrote:
Tue May 18, 2021 11:08 am
So in summary, India has been asking to be permitted to manufacture vaccines via a relaxation of patent law since last year. The UK has been the major holdout on this, to protect the financial interests of Big Pharma.
Explain how patent waivers would help. Take into account the fact that vaccines can be licensed while still protected by patent and that India has the world's largest vaccine producer and it is already producing vaccine as fast as it can. Also take into account the fact that India is a soverign nation which can impose compulsory licensing (or even abolition of patents) without reference to anyone else. And finally, should India be required to waive patents on its own vaccine (Covaxin) as part of benefiting from patent exemptions its gets on foreign vaccines?
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Re: New Covid Variants

Post by RoMo » Thu May 20, 2021 8:00 am

A couple of good websites for epidemiology and genomic surveillance:

https://outbreak.info/

https://covid19.sanger.ac.uk/lineages/raw

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Re: New Covid Variants

Post by shpalman » Thu May 20, 2021 8:59 am

Ministers consider relaxing the plan to relax Covid rules as India variant surges
The delay in lifting rules on social distancing, mask-wearing and work from home guidance may mean in practice that little would change on 21 June, apart from the opening of some high-risk venues on the condition of prior vaccination or testing on entry.
Diluting the government’s plans is likely to infuriate Conservative MPs who presumably have covid living in their brains as a kind of mind-control parasite.
molto tricky

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Re: New Covid Variants

Post by Woodchopper » Thu May 20, 2021 9:15 pm

3,424 B.1.617.2 cases in a week, an increase of 2,111 cases in a week. Not good.

https://www.gov.uk/government/publicati ... cases-data

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Re: New Covid Variants

Post by badger » Thu May 20, 2021 9:58 pm

Woodchopper wrote:
Thu May 20, 2021 9:15 pm
3,424 B.1.617.2 cases in a week, an increase of 2,111 cases in a week. Not good.

https://www.gov.uk/government/publicati ... cases-data
3,424 cases to date, no? And 2,111 of them identified in the last week (12-19 May)? Or am I reading their table incorrectly?

Still not good, of course...

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Re: New Covid Variants

Post by Woodchopper » Thu May 20, 2021 10:39 pm

badger wrote:
Thu May 20, 2021 9:58 pm
Woodchopper wrote:
Thu May 20, 2021 9:15 pm
3,424 B.1.617.2 cases in a week, an increase of 2,111 cases in a week. Not good.

https://www.gov.uk/government/publicati ... cases-data
3,424 cases to date, no? And 2,111 of them identified in the last week (12-19 May)? Or am I reading their table incorrectly?

Still not good, of course...
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Re: New Covid Variants

Post by badger » Thu May 20, 2021 10:59 pm

And of course an underestimate: PHE says the majority of samples relating to the new total date to around 10-14 days ago

Also
“Accounting for the proportion of samples that have been sequenced, we are likely to have had over 11,000 cases up to 15 May due to the Indian variant,” said Paul Hunter, a professor in medicine at the University of East Anglia.

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Re: New Covid Variants

Post by Woodchopper » Fri May 21, 2021 4:23 pm

Potential community transmission of B.1.617.2 inferred by S-gene positivity - briefing note, 11 May 2021
https://www.gov.uk/government/publicati ... 1-may-2021

CMMID COVID-19 Working Group: Modelling importations and local transmission of B.1.617.2 in the UK, 12 May 2021
https://www.gov.uk/government/publicati ... 2-may-2021

Both published 21 May

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Re: New Covid Variants

Post by jdc » Fri May 21, 2021 6:06 pm

Apparently, a "strange combination of mutations" has been spotted in Yorkshire. https://www.bbc.co.uk/news/uk-england-57199475

Looks like it might be a bit meh as far as variants go:
"So far the people that we have identified are not particularly infectious, they're not really getting more sick than other cases of coronavirus and we're not seeing anything particularly worrying about it," he added.

Dr Smith said that PHE had classified it as a "variant under investigation" and would continue monitoring its spread through extra testing.

"At the moment, we don't think it's more infectious than the other coronaviruses that we are seeing around."
VUI-21MAY-01 or AV.1 if you want to keep an eye on it.

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