南アフリカで新たな変異株 B.1.1.529 感染者急増の原因か(2021.11.26作成) #オミクロン株 #Ο株 #B.1.1.529 (2ページ目)

B.1.1.529 Emmaさん @nextstrain 南アフリカは、ワクチン接種は進んでおらず、1回接種28%、2回接種24%とのこと。ワクチン回避能力は未知数ですね。 twitter.com/firefoxx66/sta…

2021-11-26 00:41:15

Dr Emma Hodcroft @firefoxx66

Important thing to keep in mind: - We don't know what other factors may be helping spread, for example, an event or recent behaviour change - SA has a low vax rate - 28% 1dose, 24% 2dose. Immune evasion may not be needed to spread. Fitness could differ in higher-vax countries.

2021-11-25 23:40:04

今晩、凄い話題に南アフリカ B.1.1.529 要約その2 多数の変異を持つ新しい株。これらの変異は免疫回避、感染性に関与するかもしれません。ゲノム判明数は、南ア(77)、ボツアナ(4)、香港(1、南アから) 特殊なPCRで検出可能。 (SGTF) Gauteng地方で急速に拡大し、、 twitter.com/EricTopol/stat… pic.twitter.com/og4jd550ts

2021-11-26 03:21:51

Eric Topol @EricTopol

Also worth reviewing @Tuliodna's valuable summary today twitter.com/Newzroom405/st… And @PeacockFlu's thread from 23 Nov that brought B.1.1.529 to our attention twitter.com/PeacockFlu/sta… pic.twitter.com/bseAVYByXm

2021-11-26 01:17:05

拡大

B.1.1.529 デルタ後継かもしれません。南アフリカを支援することが、将来の世界を救うことになるかもしれません！ G7各国は、至急支援を！各国1億ドルなら安い投資！調査研究資金、ワクチン無償提供、研究者の派遣etc. twitter.com/Tuliodna/statu…

2021-11-26 03:42:35

Tulio de Oliveira @Tuliodna

I would like to plea to all billionaires in this world @elonmusk @BillGates @JeffBezos @DrPatSoonShiong @WarrenBuffett to support Africa & South Africa financially to control and extinguish variants! By protecting its poor and oppressed population we will protect the world.

2021-11-26 01:44:54

B.1.1.529 PCRは、アルファ(B.1.1.7)のSGTFがそのまま使えるとのことです。欠損△69/70で検出。日本及び世界で既に検査追跡可能です。なお、アルファ他の変異株が多い地域では、確定にはゲノム解析が必要です。 twitter.com/Tuliodna/statu…

2021-11-26 03:53:49

Tulio de Oliveira @Tuliodna

Because this variant (B.1.1.529) can be detected by a normal qPCR due to deletion at Spike position 69-70 (like Alpha), it will make it easy for the world to track it. We estimate that 90% of the cases in Gauteng (at least 1000 a day are this variant, due to qPCR proxy testing) pic.twitter.com/QFU7javFA9

2021-11-26 01:44:52

Five quick tweets on the new variant B.1.1.529 Caveat first: data here is *very* preliminary, so everything could change. Nonetheless, better safe than sorry. 1) Based on the data we have, this variant is out-competing others *far* faster than Beta and even Delta did 🚩🚩 pic.twitter.com/R2Ac4e4N6s

2021-11-26 04:44:07

拡大

2) This is coinciding with a wider rise in cases in South Africa. Again, currently we’re talking about small numbers (both of B.1.1.529 and of cases in SA overall), but there’s a clear upward trend. This may be a blip, but this is how waves start. pic.twitter.com/sn9IIKtzUm

2021-11-26 04:44:08

拡大

3) Aside from its rapid rise in South Africa, the other key reason for concern here is that the specific mutations that B.1.1.529 has are — based on what we’ve seen with other variants — known to be associated with greater transmissibility & immune evasion twitter.com/miamalan/statu…

2021-11-26 04:44:09

Mia Malan @miamalan

[Thread] What is the potential impact of the new B.1.1.529 #COVID19 variant? @rjlessells: 1. It's relatively simple to detect some B.1.1.529 cases, as it's possible to use PCR tests to do this in some cases 2. B.1.1.529 = has many mutations across different parts of the virus pic.twitter.com/ytktqLzJUi

2021-11-25 21:26:24

4) Caveats • This variant wasn’t known about *last week*. V early days • Case rates v low when it emerged, so some of this could be a founder effect. Nonetheless it’s outcompeting Delta • Urgent search for more data means some growth could be due to targeted testing/sequencing

2021-11-26 04:44:09

5) But what data we do have is clearly cause for concern. Our preliminary story, from @donatopmancini @mroliverbarnes ft.com/content/57ccc9…

2021-11-26 04:44:10

And see this thread from @PeacockFlu that first raised the alarm twitter.com/PeacockFlu/sta…

2021-11-26 04:44:10

Tom Peacock @PeacockFlu

Small update: this lineage has now been assigned as B.1.1.529: github.com/cov-lineages/p…

2021-11-24 20:17:07

To be clear: • I dearly hope this turns out just to be a blip • If it does I’ll gladly walk thru the charts I’ve made here & talk thru why they looked alarming at the time despite not ending up to be significant, and what that would mean for future variant emergence charts/data

2021-11-26 04:49:13

Oh, and for people who’ve looked at this chart of cases in South Africa and their jaw hit the floor: that spike on Nov 23rd is an error in the data. It should be 868 cases, not 18,586 sacoronavirus.co.za/2021/11/23/upd… pic.twitter.com/tyilAqVtv5

2021-11-26 05:11:15

拡大

Nonetheless numbers are really rising. Tuesday 868, Weds 1,275, and since I posted the first tweet Thursday’s figure has come out: 2,465. Which means the wave chart now looks like this: pic.twitter.com/aUBktDmbQn

2021-11-26 05:11:16

拡大

Took a look at the spike mutations in B.1.1.529 this evening, and colour coded them (details below)...there is...not much green.🧵 pic.twitter.com/yNHM55oTTH

2021-11-26 05:59:42

拡大

First the obviously bad stuff (red): nine mutations seen in previous VOCs. There's a lot of overlap already among VOCs (convergent evolution), but this variant has an unprecedented sampling from mutations previously seen in Alpha, Beta, Gamma and Delta separately.

2021-11-26 05:59:43

In orange are three mutations that are probably meaningful biological changes for the virus, but not previously seen in VOCs. Two from VUI level lineages that likely had modest advantages over original virus, and E484A which is at a key site in the receptor binding domain.

2021-11-26 05:59:43

Next eleven things seen rarely or never before (blue) that may be functional and just new to us, or may be a side-effect of whatever process led to so many mutations in this lineage (i.e. either neutral or mildly deleterious). Need more data on these.

2021-11-26 05:59:44

In green is just D614G, which has been fixed in all SARS-CoV-2 since early 2020.

2021-11-26 05:59:45

Finally, three shades of purple which are new (not in previous VOCs) but have some other data to suggest they may be functional. First is a deletion/substitution/insertion hotspot in the N terminal domain, that may be further remodelling the protein structure there.

2021-11-26 05:59:45

Then there's a group of 4 nearby substitutions (3 in the space of 5 amino acids) that have not been seen before, but are so close together that I doubt its coincidence. They are also very close to the (previously conserved) binding site of sotrovimab, a therapeutic antibody. pic.twitter.com/3e4gVvpcqR

2021-11-26 05:59:46

拡大

Finally S477N and Q498R, predicted in an experimental evolution paper to substantially increase ACE2 binding together with N501Y, but only seen in the wild separately or rarely. Seeing this full combination now (along with everything else) is grim. nature.com/articles/s4156…

2021-11-26 05:59:47

There are also multiple (possibly funcitonal) mutations in genes other than spike: notably R203K and G204R in nucleocapsid, which were recently shown to be key in increasing transmissibility, and are present in all VOCs to date. science.org/doi/10.1126/sc…

2021-11-26 05:59:48

So the mutation profile is bad (as @PeacockFlu and others have already pointed out). We don't yet know how they act together, or how a virus with so many changes will behave.

2021-11-26 05:59:48