Covid Mutations

[2hats]

The US CDC has promoted B.1.427 and B.1.429, first identified in California, to be variants of concern. Both feature the L452R mutation (with D614G). The CDC estimate that they have around 20% greater transmissibility than earlier variant types (based on the study DOI: 10.1101/2021.03.07.21252647). Notably they also have introduced a variant of high consequence, though that category is currently unencumbered by entries.

 

[zahir]

Thread on the Brazilian variant

 

[zahir]

Thread on new variants in the UK

 

[ska invita]

Thread on the Brazilian variant

Thread on new variants in the UK

is the Brazillian variant in your first post the one in red in the second?

 

[zahir]

Yes, the second thread shows two variants from Brazil but as far as I know it's the P1 variant that matters.

 

[Riklet]

India isnt even on the red list, it's a mindboggling fucking disgrace.

I don't see any other solution but (free) mandatory quarantine for all UK arrivals for the next few months at least.

 

[elbows]

Its broadly the same approach as that taken in the early months of the pandemic - even though the standard template pandemic plan in this country has a phase called the 'contain phase', genuine attempts at full containment are just not part of the establishments plans.

 

[Mation]

I like the names for the changes

View attachment 256452

The names are excellent

I only saw this post and graphic a few minutes ago, and have been skin reading a couple of articles about variants since. Automatically reading as Eek and Nelly, etc. It's so much easier!

 

[elbows]

Where have you gone 2hats ?

 

[elbows]

Latest UK figures from Variants: distribution of cases data

 

[Supine]

Really interesting article on a new strain. It contains lots of info on mutations and how parts of them may change the way covid behaves.

New Tanzanian Variant Detected In Angola From An Entirely New Branch Of SARS-CoV-2

The versatility of SARS-CoV-2 to evolve new variants that increase transmissibility, virulence, and immune evasion is a new troubling feature of the Covid-19 pandemic. The recent discovery of a novel variant emerging from Tanzania adds a new chapter to this disturbing story.

www.forbes.com

 

[elbows]

Latest UK figures released yesterday, data up to April 21st:

Variants: distribution of cases data, 20 May 2021

www.gov.uk

 

[weltweit]

Worried by the VUI-21APR-01 from India, (IRCC it is working against young people) lots of Indian families living in the UK want to travel to and from India.

 

[elbows]

I find a lot of the claims about age groups severely affected by a particular variant to be hard to judge properly a lot of the time. eg when they are mostly coming via stories about the hospital and death situation in countries that are having a really huge wave of the disease in general.

I say that because of the 'a small percentage of a large number is still quite a lot of people' dynamic that we've seen in various ways in this pandemic. It certainly applies to younger people requiring hospital treatment as a result of this virus, as the risk to them is lower than for older people but it isnt zero, so when there are a huge number of cases there will be plenty of younger people needing treatment. And if the hospital is already full or lacking oxygen etc then there will be no shortage of terrible stories of some of those people dying.

This doesnt mean I discount stories about how a particular variant may be affecting younger people more, it might, its something to be alert for. But I need proper data, proper numbers and proportions before I can form a tentative opinion, and to form a more solid opinion than that I would need to read about proper clinical studies etc.

 

[elbows]

I'm rather late posting the last update to the UK figures. I see they've added other versions of the variant first detected in India.


From https://www.gov.uk/government/publi...e-numbers/variants-distribution-of-cases-data

 

[IC3D]

I'm with elbows quick Google median age in India 26, UK 40. Also stuff about low vit D there, plus many other factors I'm sure. Sadly data seems to emerge after txhe event.

 

[elbows]

No wonder B.1.617.2 was generating news stories recently.

Variants: distribution of cases data, 20 May 2021

www.gov.uk

 

[elbows]

I recommend looking at the data shown in this thread:

 

[2hats]

A new P.1 lineage variant, named P.1.2, originally seen in a cluster arising in late January in the state of Rio de Janeiro, thence spreading to other Brazilian states (São Paulo, Rio Grande do Sul). It has since been noted in the US, UK, Spain and Netherlands.

This has (amongst others) a D155Y mutation in the open reading frame (specifically ORF3a), which appears to downregulate caveolin-1, which may in turn avoid/delay cell apoptosis and so extend the asymptomatic phase, with obvious potential implications for transmission. Certainly a candidate VOI.

Genomic Surveillance of SARS-CoV-2 in the State of Rio de Janeiro, Brazil: technical briefing

There are certainly some interesting degrees of freedom in the ORF, with potential epidemiological and pathogenic implications, for the virus to explore and exploit.

 

[elbows]

This weeks numbers continue to demonstrate why B.1.617.2 is in the news quite a bit.

Variants: distribution of cases data, 20 May 2021

www.gov.uk

 

[2hats]

On Thursday evening Channel 4 news carried a brief interview with Ravi Gupta (Cambridge). With specific reference to "Indian" variants he mentioned the clear possibility that it could have a better degree of transmission amongst the vaccinated (compared to other variants).

The source of this is likely a paper he recently co-authored on the dynamics of B.1.617.x spread in vaccinated healthcare workers in India. That clearly hints at the possibility of increased transmission (or rather, lower degrees of reduction in transmission) of that lineage of variants by vaccines (perhaps related to the P681R mutation). Obviously that would necessitate additional/extended NPIs post vaccination to protect remaining vulnerable cohorts.
DOI: 10.1101/2021.05.08.443253

e2a: Noticed Harnden (deputy chair of the JCVI) has been reported as saying much the same.

 

[elbows]

I dont suppose you've seen any simple estimates of what range the 'natural, unimpeded R' of the India strain might be? Or for that matter what sort of range that would have been for the Kent variant?

 

[2hats]

DOI: 10.1126/science.abg3055 suggested B.1.1.7 had a "43 to 90% higher reproduction number (95CI: 38 to 130%) than preexisting variants".

SPI-M-O estimate that there is a realistic possibility (they have 40-50% confidence) that B.1.617.2 "could be 50% more transmissible" than B.1.1.7, but no harder numbers yet.

 

[elbows]

Thanks. I suppose I was looking for someone else to apply those percentage increases to R specifically, because I dont quite trust myself to do that and the R figures are something quite a lot of people are familiar with from earlier in the pandemic.

 

[elbows]

Ah I see from an earlier attempt to estimate the increase for B.1.1.7 that they are hesitant to apply such figures to the original, pre-restriction estimate for R. Which I suppose is understandable given that these exercises mostly rely on fitting real data from real places that still have real restrictions and changes in behaviour to models.

There is a consensus among all analyses that the VOC has a substantial transmission advantage, with the estimated difference in reproduction numbers between VOC and non-VOC ranging between 0.4 and 0.7, and the ratio of reproduction numbers varying between 1.4 and 1.8. We note that these estimates of transmission advantage apply to a period where high levels of social distancing were in place in England; extrapolation to other transmission contexts therefore requires caution.

(from https://www.imperial.ac.uk/media/im...2020-12-31-COVID19-Report-42-Preprint-VOC.pdf )

 

[elbows]

I think if I try to use the proper terminology, I was after some variants estimates for R0 rather that Rt

 

[2hats]

Haven't seen anything credible recently, which isn't surprising in the face of ever evolving, time dependent NPIs and, now, growing, PIs.

Interesting thread re-analysing latest Sanger sequencing data this morning from Tom Wenseleers. Aside from pointing out B.1.617.2 taking off, around Bolton one can see it being driven through community transmission in and across school age children and then, initially, being propagated up to people of their parents/teachers ages. The data indicate no link to particular ethnic groups. Growth advantage over B.1.1.7 appears to be 13±1%/day (might translate to around 60% or more transmission advantage over B.1.1.7). The sequencing based growth/decay curves fit well with the S dropout test data which suggests the latter is a good proxy for growth of B.1.617.2 (right now).

This is concordant with separate (GISAID) analysis by Henk-Jan Westeneng - looking at variants across a number of countries (12.5±2.5%/day growth advantage over B.1.1.7).

 

[Teaboy]

Johnson has been wittering on today about increasing confidence that the vaccines are effective against all known variants. There remains a suggestion that the pz one may be better at the SA variant. Anyway, it seems like decent news assuming he's not making shit up again.

 

[elbows]

The devil is on the detail and it might work out to be positive news in certain specific ways but they'll avoid drawing attention to other aspects that may be less positive, eg if vaccines ability to stop transmission of this variant is reduced.

 

[Supine]

Johnson has been wittering on today about increasing confidence that the vaccines are effective against all known variants. There remains a suggestion that the pz one may be better at the SA variant. Anyway, it seems like decent news assuming he's not making shit up again.

Always assume he is.

I’m not saying vaccines are ineffective, things are looking good in that department. I still wouldn’t trust Johnson though