Thread by @vinodscaria

What do we know about the B.1.1.529 variant of SARS-CoV-2 with a very large number of mutations
An updated thread on emerging evidence.

B.1.1.529 is a newly designated variant of SARS-CoV-2 github.com/cov-lineages/p…
This would not have been possible without the exemplary work of researchers in Africa who have sequenced and deposited the genomes in public domain which forms the basis of this variant designation.

The lineage (variant) is characterized by 32 conserved spike mutations A67V Δ69-70 T95I G142D/Δ143-145, Δ211/L212I ins214EPE G339D S371L S373P S375F K417N N440K G446S S477N T478K E484A Q493K G496S Q498R N501Y Y505H T547K D614G H655Y N679K P681H N764K D796Y N856K Q954H N969K L981F

Many of the spike mutations independently predict immune (Antibody) escape and transmissiblity.

Some of the mutations suggest possibility of S-gene droput, which means some primers targeting the Spike gene locus might not work, and could be used to detect the variant quickly.

3 mutations are in the S1/S2 furin cleavage site possibly suggesting better cell entry (and may be transmissibility)

Point to keep in mind: Properties of single mutations don't always add up when they occur in combination. Nevertheless they give potential directions to explore.

The sequences currently available in public domain are from South Africa, Hong Kong (South African traveler) and Botswana. Large nos of sequences are from Gauteng in South Africa.
For a quick update, there is this press statement

Gauteng saw a rapid increase in test positivity last week.
Notwithstanding the potential for bias in sequencing, the B.1.1.529 variant seemingly is becoming dominant (almost 0 to 75% in 2 weeks) in South Africa. More sequences and data is awaited over the coming days.

@rid1tweets has a wonderful plot mapping the waves of COVID-19 infection in South Africa, including the present outbreak.

https://twitter.com/rid1tweets/status/1463915525856280584?s=20

Eagerly awaiting more details as they emerge, especially the NICD SA and UKHSA reports on the emerging evidence

A useful map of literature on functional mutations in B.1.1.529 has been made available by @YYCist
people.ucalgary.ca/~gordonp/linea… also suggesting increase in B cell epitope mismatch residues compared to Delta

@jbloom_lab has a wonderful thread on immune escape mutations in B.1.1.529 variant.

https://twitter.com/jbloom_lab/status/1464005676842184705?s=20

The B.1.1.529 variants seemed to be spreading rapidly in South Africa, much faster than other VoCs we have seen in the past.

@FT has a wonderful plot putting the variants and waves of infection in South Africa. The previous waves has been dominated by Beta and Delta VoCs

@nextstrain has named the B.1.1.529 lineage as 21K to enable.easy comparison between the lineage nomenclature systems.

https://twitter.com/nextstrain/status/1464122912881872899?s=20

#Israel confirms its first case of B.1.1.529 in a traveller from Malawi
2 other suspected travellers being investigated as per the news report.
newsweek.com/nu-b-1-1-529-c…

Statement from #Botswana on the four cases of B.1.1.529 #COVID19 variant suggests all four were vaccinated. The same applies to 2 cases from #HongKong
This suggest the B.1.1.529 variant can indeed cause #vaccine #breakthrough infections.

At least one case of B.1.1.529 in #Israel seems to have received a #COVID19 vaccine #booster suggesting the variant can cause #vaccine breakthrough infections. The disease severity is yet to be known, which is the most important point to consider.

https://twitter.com/ariehkovler/status/1464190991204859919?s=20

#Belgium reports two suspected cases infected with B.1.1.529 variant of #SARSCoV2

https://twitter.com/BNODesk/status/1464195182279245852?s=20

🔴 While vaccine breakthrough infections per se is not the major concern (delta also caused V-BTs), transmissibility and clinical outcomes (severity and mortality) are the key points.

#Update
ECDC has designated B.1.1.529 as a variant of concern
ecdc.europa.eu/en/covid-19/va…

#Update
🔴 UKHSA designates B.1.1.529 as a Variant Under Investigation VUI-21NOV-01
gov.uk/government/pub…
No cases in 🇬🇧 yet.

🔴 @WHO designates variant B.1.1.529 as a Variant of Concern #VoC. Names it #Omicron
who.int/news/item/26-1…

🔴 @WHO statement on #Omicron #VOC designation for B.1.1.529

https://twitter.com/WHO/status/1464295764809637898?s=20

@trvrb on #Omicron B.1.1.529
The extremely long branch (>1 year) indicates an extended period of circulation or continual evolution in a chronically infected individual before spilling back into the population.

https://twitter.com/trvrb/status/1464353234420600835?s=20

The identification of the #Omicron / B.1.1.529 variant would not have been possible without the tireless efforts of clinicians and researchers in Africa who have provided timely alerts

@nicd_sa @Tuliodna @BWGovernment @discoverhk

https://twitter.com/Tuliodna/status/1464303232973484038?s=20

Sequencing coverage issues with #Omicron on Midnight assay on @nanopore and how to work around

https://twitter.com/freed_nikki/status/1464477513107730433?s=20

The structural context of the immune escape mutations in omicron / B.1.1.529 variant compiled by @mercy_rophina and colleagues in the ESC database. For accessing the database, please visit clingen.igib.res.in/esc

https://twitter.com/mercy_rophina/status/1464548645458440195?s=20

#Update
The B.1.1.529 / #Omicron variant has been found the UK

https://twitter.com/sajidjavid/status/1464594748795146240?s=20