Thread by @RajlabN

New #PANGO designations - BA.2.*

BA.2.4Alias of B.1.1.529.2.4, #Singapore lineage

BA.2.5Alias of B.1.1.529.2.5, lineage in #Portugal and other countries

BA.2.6Alias of B.1.1.529.2.6, lineage in #France and other countries

BA.2.7Alias of B.1.1.529.2.7, #USA lineage

These are new designations - branching from the BA.2 subvariant

more to follow ..... will update key mutational differences and transmission advantage (if any)

BA.2.4 (aka B.1.1.529.2.4) | prevalent in Singapore

Key mutation: ORF6:M58K

COV-spectrum predicts a growth advantage of 14% over BA.2 and 46% over BA.1.1 in #Singapore

BA.2 and BA.1.1 are currently the dominant lineages in circulation in Singapore

BA.2.5 (aka B.1.1.529.2.5) | prevalent in #Portugal and other countries (mostly Europe)

Key mutation: ORF1ab:P1018S

COV-spectrum predicts a global growth advantage of 2% over BA.2 and 49% over BA.1.1 in the #World

BA.2.5 (BA.2 + orf1ab:P1018S) is clearly distinct from BA.2.1 (yellow), BA.2.2 (orange), BA.2.3 (lime green)

BA.2.5 (uploaded sample - rendered in green)

BA.2.6 (aka B.1.1.529.2.6) | prevalent in #France and other countries

Key mutation: ORF3a:D27H

COV-spectrum predicts a global growth advantage of 11% over BA.2 and 62% over BA.1.1 in the #World

BA.2.7 (aka B.1.1.529.2.7) | Prevalent in #USA and other countries

Key mutation: Orf1ab:T2124I or NSP3 mutation in the group 2 marker domain

COV-spectrum predicts a global growth advantage of 13% over BA.2 and 67% over BA.1.1

Fully vaccinated individuals are better protected than the unvaccinated

Get #Boosted ASAP (especially >65 yr old; immune compromised)

Several of the current therapeutics should work - (#bebtelovimab, #paxlovid)

NPIs if you are in a hotspot

BA.2.8 (aka B.1.1.529.2.8) | Prevalent in #UnitedKingdom (#Scotland)

Key mutations: ORF3a: T9K and ORF3a: A31T

COV-spectrum predicts a global growth advantage of 34% over BA.2 and >100% over BA.1.1

#NewCoV2Lineages #Alert

Two new BA.1 lineages added to the #PANGO collection

BA.1.18 (BA.1 + ORF1a:T1822I)
BA.1.19 (BA.1 + ORF1b:L2523F)

spotted by @CorneliusRoemer

Globally both BA.1.18 & BA.1.19 are tending down

BA.1.18:cov-spectrum.org/explore/World/…
(slight increase in #France (~3%) recently)

BA.1.19: cov-spectrum.org/explore/World/…

#OmicronUpdates #NewLineageAlerts

XM - New recombinant lineage designated -BA.1.1/BA.2 #Recombinant (Prevalent in Germany, Netherlands and other countries)

Spotted by @JosetteSchoenma

more info: github.com/cov-lineages/p…

#OmicronUpdates #NewLineageAlerts

BA.2.9 alias of B.1.1.529.2.9
BA.2.10 alias of B.1.1.529.2.10
BA.2.3.1 alias of B.1.1.529.2.3.1
BA.1.17.2 B.1.1.529.1.17.2 and
XN - BA.1*/BA.2 recombinant

#Pango #Designations

BA.2.3.1 (aka B.1.1.529.2.3.1) | Prevalent in #Japan
Key mutations: Spike: Q677E

COV-spectrum predicts a growth advantage of 15% over BA.2 and 59% over BA.1.1 in Japan

Spotted by Takashi Abe | github.com/cov-lineages/p…

BA.2.9 (aka B.1.1.529.2.9) | Prevalent in #Denmark and other countries

Current Hotspots: #Poland #Germany

Key mutations: ORF3a: H78Y

COV-spectrum predicts a global growth advantage of -3% over BA.2 and 35% over BA.1.1

BA.2.9 (BA.2 + Orf3a:H78Y)

Spotted/Proposed by shay671, bitbyte2015, @JosetteSchoenma and @siamosolocani

github.com/cov-lineages/p…

BA.2.10 (aka B.1.1.529.2.10) | Prevalent in #India and other countries

Current Hotspots: #Australia #Singapore

Key mutations: ORF1b:S959P

COV-spectrum predicts a global growth advantage of -15% over BA.2 and 15% over BA.1.1

BA.2.10 (BA.2 + orf1b:S959P)

Designation proposed by @CorneliusRoemer

github.com/cov-lineages/p…

#NewCoV2Lineages #Alert

BA.2.10.1Alias of B.1.1.529.2.10.1, Prevalent in #Singapore and other countries

BA.2.3.2Alias of B.1.1.529.2.3.2, Prevalent in #Vietnam and #Japan

Summary of PANGO designations: pango.network/summary-of-des…

BA.2.3.2 (aka B.1.1.529.2.3.2) | Prevalent in #Vietnam #Japan and other countries

Key mutations: E:S55F

COV-spectrum predicts a global growth advantage of 12% over BA.2 and 64% over BA.1.1

#PANGO designations: pango.network/summary-of-des…

BA.2.10.1 (aka B.1.1.529.2.10.1) | Prevalent in #Singapore and other countries

Key mutations: S:G798D

COV-spectrum predicts a growth advantage of 11% over BA.2 and 43% over BA.1.1 in Singapore

#PANGO designations: pango.network/summary-of-des…

#OmicronUpdates #NewLineageAlerts

BA.4 alias of BA.1.1.529.4
BA.5 alias of BA.1.1.529.5
BA.2.11 alias of BA.1.1.529.2.11
BA.2.12 alias of BA.1.1.529.2.12
BA.2.12.1 alias of BA.1.1.529.2.12.1

#Pango #Designations

These are new #PANGO designations - BA.4 & BA.5 have key signature mutations that warrants a good closer look...

BA.2.11, BA.2.12 & BA.2.12.1 are branching from the BA.2 subvariant

more to follow ..... will update key mutational differences and transmission advantage (if any)

BA.2.11 (aka B.1.1.529.2.11) | Prevalent in #France

Key mutations: ORF1a:S2519P+S:L452R

COV-spectrum predicts a global growth advantage of 55% over BA.2 and 149% over BA.1.1 (sample size is low - these numbers are not reliable yet)

Spotted by vthibault35

#PANGO issue: #491

BA.2.12 (aka B.1.1.529.2.12) | Prevalent in #NorthAmerica, #Europe

Key mutations: Spike S704L

COV-spectrum predicts a global growth advantage of 3% over BA.2 and 47% over BA.1.1

Mutation spotted by
@nzm8qs, @CorneliusRoemer and others

#PANGO issue: #499

BA.2.12.1 (aka B.1.1.529.2.12.1) | Prevalent in #UnitedStates

Key mutations: Spike S704L, L452Q

COV-spectrum predicts a global growth advantage of 32% over BA.2 and 105% over BA.1.1

Mutation spotted by @nzm8qs and others

#PANGO issue: #499

BA.5 (aka B.1.1.529.5) | Prevalent in #SouthAfrica

Key mutations: Spike L452R, F486V, 493Q-reversion; M:D3N

COV-spectrum predicts a significant growth advantage over BA.1*/2* (sample size is low - these numbers are not reliable yet)

#PANGO issue: github.com/cov-lineages/p…

BA.4 (aka B.1.1.529.4) | Prevalent in #SouthAfrica

Key mutations: Spike L452R, F486V, 493Q-reversion; N:P151S

COV-spectrum predicts a significant growth advantage over BA.1*/2* (sample size is low - these numbers are not reliable yet)

#PANGO issue: github.com/cov-lineages/p…

Test positivity in #SouthAfrica is 5.8%

No significant increase in Hospitalizations or deaths
nicd.ac.za/diseases-a-z-i…

https://twitter.com/nicd_sa/status/1512095494943686668