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Details of Variant

General Information
                             
Omicron XBB => XBB.1.16.6 Spike
 
Pango Lineage XBB.1.16.6
Source Omicron XBB
Description In early March 2023, XBB.1.16 first appeared in India and caused a surge of hospitalizations. XBB.1.16.6 is a sublineage of XBB.1.16
Spike Mutation T19I LPPA24-27S V83A G142D VY143-144V H146Q E180V Q183E V213E G252V G339R G339D R346T L368I S371F S373P S375F T376A D405N R408S K417N N440K V445L V445A G446S F456L N460K S477N T478R E484A F486L F486S F490S Q498R N501Y Y505H D614G H655Y N679K P681H N764K D796Y D808 Q954H N969K D1146
Light blue cells indicate ACE2 binding sites.
Earthy yellow cells indicate therapeutic monoclonal antibody (mAb) resistance mutations.
Dark blue border cells with light blue background indicate both ACE2 binding site and resistance mutations.
Red border cells indicate conserved site in human coroviurs with conservation score > 0.5.
RBD Mutation Annotation
Position Mutation ACE2 Binding Site Mutation effect on expression by DMS, Δlog(MFI) Mutation effect on binding by DMS, Δlog10(KD) mAb Resistance Conservation Across HCoVs Conservation Score
339 G339R  -0.26  -0.1 0.2035
339 G339D  0.3  0.06 0.2035
346 R346T  0.15  0.06 0.0018
368 L368I  -0.17  -0.04 0.4908
371 S371F  -0.72  -0.19 0.3053
373 S373P  -0.22  -0.08 0.1018
375 S375F  -1.81  -0.55 0.5089
376 T376A  -1.1  -0.26 0.3053
405 D405N  -0.47  -0.1 0.1053
408 R408S  0.21  -0.06 0.1053
417 K417N  0.1  -0.45 0.0
440 N440K  -0.12  0.07 0.1053
445 V445L  -0.15  -0.03 0.1053
445 V445A  -0.08  -0.04 0.1053
446 G446S  -0.4  -0.2 0.0035
456 F456L  -0.49  -0.11 0.0035
460 N460K  0.16  0.09 0.0
477 S477N  0.06  0.06 0.0
478 T478R  -0.09  -0.04 0.0018
484 E484A  -0.23  -0.07 0.1839
486 F486L  0.03  -0.47 0.0437
486 F486S  0.13  -0.63 0.0437
490 F490S  -0.1  0.0 0.0
498 Q498R  -0.1  -0.06 0.3053
501 N501Y  -0.14  0.24 0.2035
505 Y505H  0.16  -0.71 0.1053

The table lists the mutations in the RBD of XBB.1.16.6 Spike. DMS represents expression changes as Δlog(MFI), the mean fluorescence intensity of each variant relative to the unmutated SARS-CoV-2 RBD, with a positive Δlog(MFI) indicating increased expression. And represents binding affinity as Δlog10(KD,app), with positive values indicating stronger binding. The DMS data is from Tyler N. Starr et al. Therapeutic monoclonal antibody (mAb) resistance mutations list can be found at Statistics page. Conservation scores can be found at Conservation page, and score above 0.7 is considered as a conserved site.