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Third sublineage in B.1.1.529 (Omicron-related) #367

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rambaut opened this issue Dec 11, 2021 · 5 comments
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Third sublineage in B.1.1.529 (Omicron-related) #367

rambaut opened this issue Dec 11, 2021 · 5 comments
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BA.3

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@rambaut
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@rambaut rambaut commented Dec 11, 2021 •
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A new diverse genome has appeared within the B.1.1.529 lineage that has all of the shared mutations of B.1.1.529, some of the mutations unique to BA.1 and some unique to BA.2 plus a few of its own.

Name: England/MILK-2D24AC9/2021, accession EPI_ISL_7526186, collected 2021-12-03

image

It seems likely this is an additional circulating member of the B.1.1.529 diversity and that recombination has occurred in its history (although this is likely to have occurred prior to the emergence of the BA.1 clade based on the pattern of mutations).

As a single genome it doesn't yet require a lineage designation and at the moment it will be classified as a member of B.1.1.529.
@cov-lineages cov-lineages locked as resolved and limited conversation to collaborators Dec 11, 2021
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@AngieHinrichs
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@AngieHinrichs AngieHinrichs commented Dec 13, 2021 •
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@amniewiadomska suggests these new sequences as well:

hCoV-19/South Africa/NICD-N22389/2021|EPI_ISL_7605590|2021-11-30
hCoV-19/South Africa/NICD-N22404/2021|EPI_ISL_7605591|2021-11-25
hCoV-19/South Africa/NICD-N22385/2021|EPI_ISL_7605772|2021-11-29
hCoV-19/South Africa/NICD-N22239/2021|EPI_ISL_7605589|2021-11-26
hCoV-19/South Africa/NICD-N22163/2021|EPI_ISL_7605713|2021-11-18

(posting on her behalf since comments are locked down)

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@cov-lineages cov-lineages unlocked this conversation Dec 14, 2021
@rambaut
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@rambaut rambaut commented Dec 14, 2021 •
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Yes - these are the same sub-lineage. A couple of the mutations listed above are unique to England/MILK-2D24AC9/2021 so will be removed from the defining list. But I think this qualifies as BA.3 now.

Table of mutations

mut (nuc) gene mutation (aa) B.1.1.529 BA.1 BA.2 BA.3 (proposed) notes
T670G ORF1ab S135R     Y Y  
C832T nuc C832T     Y  
C2790T ORF1ab T842I     Y    
A2832G ORF1ab K856R   Y      
C3037T nuc C3037T Y     Y B.1
T5386G nuc T5386G   Y      
G4184A ORF1ab G1307S     Y Y  
C4321T nuc C4321T     Y    
6513_6515del ORF1ab SL2083I   Y      
G8393A ORF1ab A2710T   Y      
C9344T ORF1ab L3027F     Y    
A9424G nuc A9424G     Y    
C9534T ORF1ab T3090I     Y Y  
C9866T ORF1ab L3201F     Y   Not in CERI-KRISP-K032307
C10029T ORF1ab T3255I Y     Y  
C10198T nuc C10198T     Y    
G10447A nuc G10447A     Y Y  
C10449A ORF1ab P3395H Y     Y  
C11235T nuc C11235T     Y
11288_11296del ORF1ab SGF3675del Y     Y The exact position of this deletion is ambigous in nucleotide coordinates
T11296G ORF1ab F3677L     Y Y depending on the position of the deletion
G11287T ORF1ab L3674F   Y     depending on the position of the deletion
A11537G ORF1ab I3758V   Y      
C12880T nuc C12880T     Y Y  
C14408T ORF1ab P4715L Y     Y B.1
C15240T nuc C15240T   Y      
C15714T nuc C15714T     Y Y  
C17410T ORF1ab R5716C     Y    
A18163G ORF1ab I5967V Y        
C19955T ORF1ab T6564I     Y    
A20055G nuc A20055G     Y    
C21618T S T19I     Y    
21633_21641del S LPPA24S     Y    
C21762T S A67V   Y   Y  
21765_21770del S HV69del   Y   Y  
C21846T S T95I   Y      
G21987A (outlier); 21987_21995 (main) S G142D Y        
21987_21995 S VYY143del   Y   Y  
22194_22196del S NL211I   Y   Y  
T22200G S V213G     Y    
22205GAGCCAGAAins S 215EPEins   Y      
G22578A S G339D Y     Y  
C22674T S S371F     Y Y  
T22673C, C22674T S S371L   Y      
T22679C S S373P Y     Y  
C22686T S S375F Y     Y  
A22688G S T376A     Y    
G22775A S D405N     Y Y  
A22786T S R408S     Y    
G22813T S K417N Y     Y  
T22882G S N440K Y     Y  
G22898A S G446S   Y   Y  
G22992A S S477N Y     Y  
C22995A S T478K Y     Y  
A23013C S E484A Y     Y  
A23040G S Q493R Y     Y  
G23048A S G496S   Y      
A23055G S Q498R Y     Y  
A23063T S N501Y Y     Y  
T23075C S Y505H Y     Y  
C23202A S T547K   Y      
A23403G S D614G Y     Y B.1
C23525T S H655Y Y     Y  
T23599G S N679K Y     Y  
C23604A S P681H Y     Y  
C23854A S N764K Y     ?  
G23948T S D796Y Y     Y  
C24130A S N856K   Y      
A24424T S Q954H Y     Y  
T24469A S N969K Y     Y  
C24503T S L981F   Y      
C25000T nuc C25000T Y        
C25584T nuc C25584T Y        
A26059G,C26060T ORF3a T223V       Y ACT->GTT
C26060T ORF3a T223I     Y   ACT->ATT (not fixed in BA.3)
C26270T E T9I Y     Y  
A26530G M D3G   Y     Not in CERI-KRISP-K032307
C26577G M Q19E Y     Y  
G26709A M A63T Y     Y  
C26858T nuc C26858T     Y Y  
A27259C nuc A27259C Y     Y  
G27382C, A27383T, T27384C ORF6 D61L     Y   (GAT->CTC)
C27807T nuc C27807T Y     Y  
A28271T nuc A28271T Y     Y  
C28311T N P13L Y     Y  
28362_28370del N ERS31del Y     Y  
G28881A, G28882A, G28883C N RG203KR Y     Y (B.1.1.1)
A29510C N S413R     Y Y  

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@rambaut rambaut changed the title New outlier in B.1.1.529 (Omicron-related) Third sublineage in B.1.1.529 (Omicron-related) Dec 14, 2021
chrisruis added a commit that referenced this issue Dec 14, 2021
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Added new lineage BA.3 from #367 with 5 new sequence designations
09d3a3b
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@chrisruis chrisruis commented Dec 14, 2021

Now added as BA.3 in v1.2.112

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@chrisruis chrisruis closed this Dec 14, 2021
@chrisruis chrisruis added this to the BA.3 milestone Dec 14, 2021
@zach-hensel
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@zach-hensel zach-hensel commented Dec 14, 2021

I don't think EPI_ISL_6906349 and EPI_ISL_4652284 qualify to be a sub-lineage but they might be worth reconsidering in light of overlap with all three of these in some places but only BA.1 in others, plus time/location information. I mentioned one of these elsewhere, but @c19850727 recently noted the additional one and also possibly related EPI_ISL_3838306.

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@kevinlibuit kevinlibuit mentioned this issue Dec 16, 2021
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