Read on Twitter
The new “Kent” strain of SARS-CoV-2 (officially named VUI 202012/01 for Variant Under Investigation, year 2020, month 12, variant 01) was identified as have multiple spike protein mutations
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These include deletion 69-70, deletion 144-145, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H
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https://www.gisaid.org/references/gisaid-in-the-news/uk-reports-new-variant-termed-vui-20201201/
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https://www.gisaid.org/references/gisaid-in-the-news/uk-reports-new-variant-termed-vui-20201201/
Structural modelling suggests N501Y (orange in Fig) might affect host receptor and antibody binding
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Credit https://www.gisaid.org/references/gisaid-in-the-news/uk-reports-new-variant-termed-vui-20201201/
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Credit https://www.gisaid.org/references/gisaid-in-the-news/uk-reports-new-variant-termed-vui-20201201/
The deletions in cyan in above Figure are in positions contributing to potential spike surface variation (Y145del is where some antibodies like neutralizing 4A8 bind).
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It strain was identified by @PHE_uk monitoring during surge in cases in Kent and London.
Great work by Public Health England
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Great work by Public Health England
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Dr Susan Hopkins, Test and Trace and PHE joint medical adviser, said: "There is currently no evidence that this strain causes more severe illness"
Credit https://www.medscape.com/viewarticle/942643
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Credit https://www.medscape.com/viewarticle/942643
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Much remains unclear still, but such mutations are to be expected as the virus spreads. Most of the spike protein will “look” the same to the immune system, so current vaccine should continue to provide protection.
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Over time the vaccine might need modification, just as the flu jab does each year.
This is new so sincere apologies if there are errors. As these & new information come to light, I’ll update you.
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This is new so sincere apologies if there are errors. As these & new information come to light, I’ll update you.
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News briefing from @bmj_latest https://www.bmj.com/content/371/bmj.m4857
“At this point in time, there is no reason to believe that any of the mutations discussed here will affect vaccine efficacy” COG-UK
https://www.cogconsortium.uk/wp-content/uploads/2020/12/Report-1_COG-UK_19-December-2020_SARS-CoV-2-Mutations.pdf
https://www.cogconsortium.uk/wp-content/uploads/2020/12/Report-1_COG-UK_19-December-2020_SARS-CoV-2-Mutations.pdf
So far, 126,219 genomes from +ive samples generated by the COG- UK consortium. This identified 1,777 different amino acid changing mutations in Spike protein.
Of these, 37% (654) were only observed in a single sequence, while 5% (87) were observed in at least 100.
Of these, 37% (654) were only observed in a single sequence, while 5% (87) were observed in at least 100.
“5 amino acid replacements (D614G, A222V, N439K, Y453F and N501Y), 1 deletion (del) and co- occurrence of some of these changes are actively being investigated by COG-UK”
Some interesting details on individual mutations & presumed origins
Biological significance of some specific changes
And “A222V: It has been speculated that the increased transmissibility of the B.1.177 lineage may be associated with the presence of the A222V mutation, but more evidence is needed”
Recommended read!
“... a distinct phylogenetic cluster (named lineage B.1.1.7) was detected within the COG-UK surveillance dataset...[it’s] been growing rapidly over the past 4 weeks & since been observed in other UK locations, indicating further spread”
https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563
![Recommended read!“... a distinct phylogenetic cluster (named lineage B.1.1.7) was detected within the COG-UK surveillance dataset...[it’s] been growing rapidly over the past 4 weeks & since been observed in other UK locations, indicating further spread” https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563](https://pbs.twimg.com/media/EprpjZBXUAA9wFS.jpg "Recommended read!“... a distinct phylogenetic cluster (named lineage B.1.1.7) was detected within the COG-UK surveillance dataset...[it’s] been growing rapidly over the past 4 weeks & since been observed in other UK locations, indicating further spread” https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563")
“... a distinct phylogenetic cluster (named lineage B.1.1.7) was detected within the COG-UK surveillance dataset...[it’s] been growing rapidly over the past 4 weeks & since been observed in other UK locations, indicating further spread”
https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563
Interesting in vitro data from @GuptaR_lab — Δ69/70 twice as infectious https://twitter.com/guptar_lab/status/1340438930601242625
NERVTAG = New and Emerging Respiratory Virus Threats Advisory Group
1/n https://twitter.com/adamjkucharski/status/1340694809997160452
1/n https://twitter.com/adamjkucharski/status/1340694809997160452
Points discussed re transmission:
“Growth rate from genomic data which suggest a growth rate of VUI-202012/01 that
that is 71% (95% CI: 67%-75%) higher than other variants”
= By sequencing many samples of +ive tests, the rate of increase was compared to other strains
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“Growth rate from genomic data which suggest a growth rate of VUI-202012/01 that
that is 71% (95% CI: 67%-75%) higher than other variants”
= By sequencing many samples of +ive tests, the rate of increase was compared to other strains
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“Studies of correlation between R-values and detection of the variant: which suggest an absolute increase in the R-value of between 0.39 to 0.93”
Modelling seems to suggest this strain has higher R (remember, R is determined both by viral transmissibility AND our behaviour)
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Modelling seems to suggest this strain has higher R (remember, R is determined both by viral transmissibility AND our behaviour)
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“PCR ct values: which suggest a decrease of ct value of around 2 associated with the new variant”
In PCR testing, lower Ct values mean more starting RNA, so this suggests that ppl who swabbed +ive fir this strain may have had higher viral loads
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In PCR testing, lower Ct values mean more starting RNA, so this suggests that ppl who swabbed +ive fir this strain may have had higher viral loads
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“Viral load inferred from number of unique genome reads: which suggests 0.5 increase in median log10 inferred viral load in Y501 versus N501”
Suggests the mutation Y501 (one of several species n this new strain) is associated with 3-fold increase in viral load
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Suggests the mutation Y501 (one of several species n this new strain) is associated with 3-fold increase in viral load
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“ It was noted that VUI-202012/01 has demonstrated exponential growth during a period when national lockdown measures were in place”
Suggests stricter measures (and/or Bette adherence to them) required if we are to control this
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Suggests stricter measures (and/or Bette adherence to them) required if we are to control this
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“Antigenic escape. The location of the mutations in the receptor binding domain of the spike glycoprotein raises the possibility that this variant is antigenically distinct from prior variants”
Suggests the variant might be seen as “different” by our immune systems
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Suggests the variant might be seen as “different” by our immune systems
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“Four probable reinfections have been identified amongst 915 subjects with this variant but further work is needed to compare this reinfection rate with comparable data sets”
We knew reinfection is possible, so it isn’t clear if this is relevant. Time will tell.
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We knew reinfection is possible, so it isn’t clear if this is relevant. Time will tell.
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A very readable & informative article about the new strain, herein called B.1.1.7 https://www.sciencemag.org/news/2020/12/mutant-coronavirus-united-kingdom-sets-alarms-its-importance-remains-unclear
A note on naming the new strain
Viruses acquire mutations & diverge from each other. A group of strains sharing a common ancestor is called a clade
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Viruses acquire mutations & diverge from each other. A group of strains sharing a common ancestor is called a clade
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It is usually clear how to separate the clades, but sometimes minor disagreements arise about how to group the lineages (see grey in figure)
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The new strain can be called B.1.1.7 is unusual in the it “suddenly” appeared to acquire 17 mutations. This led to the hypothesis that it evolved in a chronically infected person.
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Sometimes when SARS-CoV-2 is detected in a swab, the entire viral genome is sequenced to provide the information shown above. This incidentally disproves the untrue claims that the tests are detecting non-SARS-CoV-2 viruses
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Looking at early sequences of B.1.1.7 collected since September to November, you see it was seen occasionally at first then repeatedly — this is what happens with exponential growth. It also shows why early on, its significance wasn’t obvious
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https://cov-lineages.org/lineages/lineage_B.1.1.7.html
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https://cov-lineages.org/lineages/lineage_B.1.1.7.html
Here’s a terrific thread from a real expert in this field of science
6/6 https://twitter.com/firefoxx66/status/1340359989395861506
6/6 https://twitter.com/firefoxx66/status/1340359989395861506
Regarding the gradual increase in B.1.1.7 since September (2 tweets up), this figure from the @ECDC_EU makes it even more clear ... exponential growth appears to grumble along then skyrockets
Now Variant Of Concern
Thanks @bealelab for the heads up
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https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/947048/Technical_Briefing_VOC_SH_NJL2_SH2.pdf
Thanks @bealelab for the heads up
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https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/947048/Technical_Briefing_VOC_SH_NJL2_SH2.pdf
This is such a complex report, I thought it needed its own thread. See the link...
2/2 https://twitter.com/Prof_Marciniak/status/1341317589922951168?s=20
2/2 https://twitter.com/Prof_Marciniak/status/1341317589922951168?s=20
