SHIVER

SARS CoV-2 Historically Identified Variants in Epitope Regions

SHIVER: SARS CoV-2 Historically Identified Variants in Epitope Regions

SHIVER identifies variant forms of the SARS CoV-2 virus with a focus on the NTD and RBD neutralizing antibody epitope regions of the Spike protein, as well as sites related to furin cleavage; the forms are chosen to maximize coverage globally and/or on separate continents[*], depending on which of several strategies is employed.

In the Table of Variants, below, the first column is the pattern at sites where differences occur, relative to initial (Wuhan) sequence, with site numbers read down vertically.

Table of Variants

LPM = Local Pattern Matches = # of seqs in continent that match over epitope region GPM = Global Pattern Matches = # of seqs in world that match over epitope region
GSM = Global Sequence Matches = # of seqs in world that match over whole Spike protein

     1111122223333333334444444444444444444444455666
111114455544663345777780001344445555677788889900578
666694627859342966135623587501560256057813463815591 Name                    LPM    GPM    GSM  GSM/GPM [Mutations] (Lineage)
----TYHWFRHLAAIGRKSSSTVRDRKANLVGNLLFNASTNVEFQQNYHNP 1-Initial                 0      0      0     0.0% [] 
MPLFI-..SGN..DVHTTFPFA.KNSN.K.HSDWSLK.NKK-KP.RYHYKR 2-North-America-1      1772   2628    399    15.2% [+16MPLF,T19I,R21T,L24-,P25-,P26-,A27S,S31-,S50L,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,Q183H,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,R346T,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,V445H,G446S,N450D,L452W,L455S,F456L,N460K,S477N,T478K,N481K,V483-,E484K,F486P,Q498R,N501Y,Y505H,E554K,A570V,D614G,P621S,H655Y,N679K,P681R,N764K,D796Y,S939F,Q954H,N969K,P1143L] 
MPLFI-..SGN..DVH.TFPFA.KNSN.K.HSDWSLK.NKK-KPERYHYKR 3-Europe-1              905   3163   1579    49.9% [+16MPLF,T19I,R21T,L24-,P25-,P26-,A27S,S50L,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,V445H,G446S,N450D,L452W,L455S,F456L,N460K,S477N,T478K,N481K,V483-,E484K,F486P,Q493E,Q498R,N501Y,Y505H,E554K,A570V,D614G,P621S,H655Y,N679K,P681R,N764K,D796Y,S939F,Q954H,N969K,V1104L,P1143L] 
MPLFI-..SGN..DVHTTFPFA.KNSN.K.HSDWSLK.NKK..P.RYHYKR 4-Asia-1                 86     86      7     8.1% [+16MPLF,T19I,R21-,+22N,L24X,P25X,P26X,A27S,S50X,F59S,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,R346T,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,V445H,G446S,N450D,L452W,L455S,F456L,N460K,S477N,T478K,N481K,F486P,Q498R,N501Y,Y505H,E554K,A570V,D614G,P621S,H655Y,N679K,P681R,N764K,D796Y,S939F,Q954H,N969K,A1087S,P1143L] 
MPLFI-..SGN..DVH.TFPFA.KNSN.K.HSDWSLK.NKK-KP.RYHYKR 5-Oceania-1              58    497    117    23.5% [+16MPLF,T19I,R21T,L24-,P25-,P26-,A27S,S50L,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,V445H,G446S,N450D,L452W,L455S,F456L,N460K,S477N,T478K,N481K,V483-,E484K,F486P,Q498R,N501Y,Y505H,E554K,A570V,T572I,D614G,P621S,H655Y,N679K,P681R,N764K,D796Y,S939F,Q954H,N969K,P1143L] 
MPLFI-Q.SGN..DVHTTFPFALKNSN.K.HSDWSLK.NKK-KP.RYHYKR 6-United-Kingdom-1        7     13     13   100.0% [+16MPLF,T19I,R21T,L24-,P25-,P26-,A27S,S31-,S50L,H69-,V70-,V127F,G142D,Y144-,H146Q,F157S,R158G,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,R346T,K356T,S371F,S373P,S375F,T376A,V382L,R403K,D405N,R408S,K417N,N440K,V445H,G446S,N450D,L452W,L455S,F456L,N460K,S477N,T478K,N481K,V483-,E484K,F486P,Q498R,N501Y,Y505H,E554K,A570V,D614G,P621S,H655Y,N679K,P681R,N764K,D796Y,S939F,Q954H,N969K,V1104L,P1143L] 
MPLFI-Q.SGN..DVHTTFPFA.KNSN.K.HSDWSLK.NKK-KP.RYHYKR 7-South-America-1         9    546    318    58.2% [+16MPLF,T19I,R21T,L24-,P25-,P26-,A27S,S31-,S50L,H69-,V70-,V127F,G142D,Y144-,H146Q,F157S,R158G,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,R346T,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,V445H,G446S,N450D,L452W,L455S,F456L,N460K,S477N,T478K,N481K,V483-,E484K,F486P,Q498R,N501Y,Y505H,E554K,A570V,D614G,P621S,H655Y,N679K,P681R,N764K,D796Y,S939F,Q954H,N969K,V1104L,P1143L] 
MPLFI-..SGN..DVHTTFPFA.KNSN.K.HSDWSVK.NKK-KP.RYHYKR 8-Africa-1                6     49     14    28.6% [+16MPLF,T19I,R21T,L24-,P25-,P26-,A27S,S31-,S50L,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,R190S,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,R346T,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,V445H,G446S,N450D,L452W,L455S,F456V,N460K,S477N,T478K,N481K,V483-,E484K,F486P,Q498R,N501Y,Y505H,E554K,A570V,D614G,P621S,H655Y,N679K,P681R,N764K,D796Y,S939F,Q954H,N969K,P1143L] 
MPLFI-..SGN..DVH.TFPFA.KNSN.K.HSDWS.K.NKK-KP.RYHYKR 9-North-America-2        97    141     38    27.0% [+16MPLF,T19I,R21T,L24-,P25-,P26-,A27S,S50L,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,V445H,G446S,N450D,L452W,L455S,N460K,S477N,T478K,N481K,V483-,E484K,F486P,Q498R,N501Y,Y505H,E554K,A570V,T572I,D614G,P621S,H655Y,N679K,P681R,N764K,D796Y,S939F,Q954H,N969K,P1143L,E1150D] 
....I-..SGN..DVH.TFPFA.KNSN.K.HSDWSLK.NKK-KPERYHYKR 10-Europe-2              62     91     28    30.8% [T19I,R21T,L24-,P25-,P26-,A27S,S31-,S50L,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,V445H,G446S,N450D,L452W,L455S,F456L,N460K,S477N,T478K,N481K,V483-,E484K,F486P,Q493E,Q498R,N501Y,Y505H,E554K,A570V,D614G,P621S,H655Y,N679K,P681R,N764K,D796Y,S939F,Q954H,N969K,V1104L,P1143L] 
MPLFI-Q.SGN..DVHTTFPFA.KNSN.K.HSDWSLK.NKK..P.RYHYKR 11-Asia-2                75     75     25    33.3% [+16MPLF,T19I,R21T,L24X,P25X,P26X,S31-,S50X,H69-,V70-,V127F,G142D,Y144-,H146Q,F157S,R158G,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,R346T,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,V445H,G446S,N450D,L452W,L455S,F456L,N460K,S477N,T478K,N481K,F486P,Q498R,N501Y,Y505H,E554K,A570V,D614G,P621S,H655Y,N679K,P681R,N764K,D796Y,S939F,Q954H,N969K,V1104L,P1143L] 
MPLFI-..SGN.VDVH.TFPFA.KNSN.K.HSDWSLK.NKK-KPERYHYKR 12-Oceania-2             17     33     29    87.9% [+16MPLF,T19I,R21T,L24-,P25-,P26-,A27S,S50L,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,N211-,L212I,V213G,L216F,H245N,A263V,A264D,I332V,G339H,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,V445H,G446S,N450D,L452W,L455S,F456L,N460K,S477N,T478K,N481K,V483-,E484K,F486P,Q493E,Q498R,N501Y,Y505H,E554K,A570V,D614G,P621S,H655Y,N679K,P681R,N764K,D796Y,S939F,Q954H,N969K,V1104L,P1143L] 
MPLFI-..SGN..DVHTTFPFA.KNSN.K.HSDWS.K.NKK-KP.RYHYKR 13-United-Kingdom-2       3     85     12    14.1% [+16MPLF,T19I,R21T,L24-,P25-,P26-,A27S,S31-,S50L,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,R346T,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,V445H,G446S,N450D,L452W,L455S,N460K,S477N,T478K,N481K,V483-,E484K,F486P,Q498R,N501Y,Y505H,E554K,A570V,D614G,P621S,H655Y,N679K,P681R,N764K,V785X,K786X,Q787X,I788X,Y789X,K790X,T791X,P792X,P793X,I794X,K795X,D796X,F797X,G798X,G799X,F800X,N801X,F802X,S803X,Q804X,I805X,L806X,P807X,D808X,P809X,S810X,K811X,P812X,S813X,K814X,R815X,S816X,F817X,I818X,E819X,D820X,L821X,L822X,F823X,N824X,K825X,V826X,T827X,L828X,A829X,D830X,A831X,G832X,F833X,I834X,K835X,Q836X,Y837X,G838X,D839X,C840X,L841X,G842X,D843X,I844X,A845X,A846X,R847X,D848X,L849X,I850X,C851X,A852X,Q853X,K854X,F855X,N856X,G857X,L858X,T859X,V860X,L861X,P862X,P863X,L864X,L865X,T866X,D867X,E868X,M869X,I870X,A871X,Q872X,Y873X,T874X,S875X,A876X,S939F,Q954H,N969K,P1143L] 
MPLFI-..SGN..DVHTTFPFA.KNSN.K.HSDWSLK.NIK-KP.RYHYKR 14-South-America-2        2      9      6    66.7% [+16MPLF,T19I,R21T,L24-,P25-,P26-,A27S,S50L,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,R346T,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,V445H,G446S,N450D,L452W,L455S,F456L,N460K,S477N,T478I,N481K,V483-,E484K,F486P,Q498R,N501Y,Y505H,E554K,A570V,D614G,P621S,H655Y,N679K,P681R,N764K,D796Y,S939F,Q954H,N969K,P1143L] 
MPLFI-..SGN..DVHTTFPFA.KNSNSK.HSDWSLK.NKK-KP.RYHYKR 15-Africa-2               2      3      2    66.7% [+16MPLF,T19I,R21T,L24-,P25-,P26-,A27S,S50L,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,R346T,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,A435S,N440K,V445H,G446S,N450D,L452W,L455S,F456L,N460K,S477N,T478K,N481K,V483-,E484K,F486P,Q498R,N501Y,Y505H,E554K,A570V,D614G,P621S,H655Y,N679K,P681R,N764K,D796Y,S939F,Q954H,N969K,P1143L] 
....I-..SGN..DVHTTFPFA.KNSN.K.HSDWSLK.NKK-KP.RYHYKR 16-North-America-3       76    128     27    21.1% [T19I,R21T,L24-,P25-,P26-,A27S,S31-,S50L,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,Q183H,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,R346T,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,V445H,G446S,N450D,L452W,L455S,F456L,N460K,S477N,T478K,N481K,V483-,E484K,F486P,Q498R,N501Y,Y505H,E554K,A570V,D614G,P621S,H655Y,N679K,P681R,N764K,D796Y,S939F,Q954H,N969K,P1143L] 
MPLFI-..SGNF.DVH.TFPFA.KNSN.K.PSDWSLK.NKK-KP.RYHYKR 17-Europe-3              55     66     52    78.8% [+16MPLF,T19I,R21T,L24-,P25-,P26-,A27S,S50L,A67V,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,N211-,L212I,V213G,L216F,H245N,L249F,A264D,I332V,G339H,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,V445P,G446S,N450D,L452W,L455S,F456L,N460K,S477N,T478K,N481K,V483-,E484K,F486P,Q498R,N501Y,Y505H,E554K,A570V,D614G,P621S,H655Y,N679K,P681R,N764K,D796Y,S939F,Q954H,N969K,P1143L] 
....I-..SGN..DVH.TFPFA.KNSN.K.HSDWSLK.NKK-KP.RYHYKR 18-Asia-3                56     71     40    56.3% [T19I,R21T,L24-,P25-,P26-,A27S,S50L,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,V445H,G446S,N450D,L452W,L455S,F456L,N460K,S477N,T478K,N481K,V483-,E484K,F486P,Q498R,N501Y,Y505H,E554K,A570V,D614G,P621S,H655Y,N679K,P681R,N764K,D796Y,S939F,Q954H,N969K,P1143L] 
MPLFI-..SGN..DVH.TFPFA.KNSN.K.HSDWSLK.NKK-KPERYHYKH 19-Oceania-3             12     27     17    63.0% [+16MPLF,T19I,R21T,L24-,P25-,P26-,A27S,S50L,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,V445H,G446S,N450D,L452W,L455S,F456L,N460K,S477N,T478K,N481K,V483-,E484K,F486P,Q493E,Q498R,N501Y,Y505H,E554K,A570V,D614G,P621S,H655Y,N679K,P681H,N764K,D796Y,S939F,Q954H,N969K,V1104L,P1143L] 
MPLFI-..SGN..DVH.TFPFA.KNSN.K.HSDWSLK.NKK-KP.RYHYK- 20-United-Kingdom-3       3      9      4    44.4% [+16MPLF,T19I,R21T,L24-,P25-,P26-,A27S,S50L,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,V445H,G446S,N450D,L452W,L455S,F456L,N460K,S477N,T478K,N481K,V483-,E484K,F486P,Q498R,N501Y,Y505H,E554K,A570V,T572I,D614G,P621S,H655Y,N679K,P681-,+683W,N764K,D796Y,S939F,Q954H,N969K,P1143L] 
MPLFI-.RSGN..DVH.TFPFA.KNSN.K.HSDWSLK.NKK-KP.RYHYKR 21-South-America-3        1      1      1   100.0% [+16MPLF,T19I,R21T,L24-,P25-,P26-,A27S,S50L,H69-,V70-,V127F,Y144-,W152R,F157S,R158G,N185M,F186-,K187-,N188-,L189-,R190-,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,V445H,G446S,N450D,L452W,L455S,F456L,N460K,S477N,T478K,N481K,V483-,E484K,F486P,Q498R,N501Y,Y505H,E554K,A570V,T572I,D614G,P621S,H655Y,N679K,P681R,N764K,D796Y,S939F,Q954H,N969K,P1143L,E1150D] 
....I-..SGN..DVHTTFPFA.KNSN.K.HSDWS.K.NKK-KP.RYHYKR 22-Africa-3               1      5      1    20.0% [T19I,R21T,L24-,P25-,P26-,A27S,S50L,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,R346T,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,V445H,G446S,N450D,L452W,L455S,N460K,S477N,T478K,N481K,V483-,E484K,F486P,Q498R,N501Y,Y505H,E554K,A570V,T572I,D614G,P621S,H655Y,N679K,P681R,N764K,D796Y,S939F,Q954H,Q957X,T961X,L962X,N969K,P1143L,D1168E,E1195X,S1196X,E1202X] 
MPLFI-..SGN..DVHTTFPFA.KNS..K.HSDWSLK.NKK-KP.RYHYKR 23-North-America-4       32     35     14    40.0% [+16MPLF,T19I,R21T,L24-,P25-,P26-,A27S,S31-,S50L,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,R346T,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,N440K,V445H,G446S,N450D,L452W,L455S,F456L,N460K,S477N,T478K,N481K,V483-,E484K,F486P,Q498R,N501Y,Y505H,E554K,A570V,D614G,P621S,H655Y,N679K,P681R,N764K,D796Y,S939F,Q954H,N969K,K1086R,V1104L,P1143L,M1229I] 
MPVFI-..SGN..DVH.TFPFA.KNSN.K.HSDWSLK.NKK-KPERYHYKR 24-Europe-4              25     29     19    65.5% [+16MPVF,T19I,R21T,L24-,P25-,P26-,A27S,S50L,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,V445H,G446S,N450D,L452W,L455S,F456L,N460K,S477N,T478K,N481K,V483-,E484K,F486P,Q493E,Q498R,N501Y,Y505H,E554K,A570V,D614G,P621S,H655Y,N679K,P681R,N764K,D796Y,S939F,Q954H,N969K,V1104L,P1143L] 
MPLFI-..SGN..DVH.TFPFA.KNSN.K.HSDW..KVNKK-KP.RYHYKR 25-Asia-4                22     23      8    34.8% [+16MPLF,T19I,R21T,L24-,P25-,P26-,A27S,S50L,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,V445H,G446S,N450D,L452W,N460K,A475V,S477N,T478K,N481K,V483-,E484K,F486P,Q498R,N501Y,Y505H,E554K,A570V,D614G,P621S,H655Y,N679K,P681R,N764K,D796Y,Q954H,N969K] 
MPLFI-..SGN..DVHTTFPFA.KNSN.K.HSDWSLK.NKK-KP.RYHYK- 26-Oceania-4              2     17      1     5.9% [+16MPLF,T19I,R21T,L24-,P25-,P26-,A27S,S50L,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,R346T,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,V445H,G446S,N450D,L452W,L455S,F456L,N460K,S477N,T478K,N481K,V483-,E484K,F486P,Q498R,N501Y,Y505H,E554K,A570V,D614G,P621S,H655Y,N679K,P681-,A684X,R685X,S686X,V687X,A688X,S689X,Q690X,S691X,I692X,I693X,A694X,Y695X,T696X,M697X,S698X,L699X,G700X,A701X,E702X,N703X,S704X,V705X,A706X,Y707X,S708X,N709X,N710X,S711X,I712X,A713X,I714X,P715X,T716X,N717X,F718X,T719X,I720X,S721X,V722X,T723X,T724X,E725X,I726X,L727X,P728X,V729X,S730X,M731X,T732X,K733X,T734X,S735X,V736X,D737X,C738X,T739X,M740X,Y741X,I742X,C743X,G744X,D745X,S746X,T747X,E748X,C749X,S750X,N751X,L752X,L753X,L754X,Q755X,Y756X,G757X,S758X,F759X,C760X,T761X,Q762X,L763X,N764X,R765X,A766X,L767X,T768X,G769X,I770X,A771X,V772X,E773X,Q774X,D775X,K776X,N777X,T778X,Q779X,E780X,V781X,F782X,A783X,Q784X,V785X,K786X,Q787X,I788X,Y789X,K790X,T791X,P792X,P793X,I794X,K795X,D796X,F797X,G798X,G799X,F800X,N801X,F802X,S803X,Q804X,I805X,L806X,P807X,D808X,P809X,S810X,K811X,P812X,S813X,K814X,R815X,S816X,F817X,I818X,E819X,D820X,L821X,L822X,F823X,N824X,K825X,V826X,T827X,L828X,A829X,D830X,A831X,G832X,F833X,I834X,K835X,Q836X,Y837X,G838X,D839X,C840X,L841X,G842X,D843X,I844X,A845X,A846X,R847X,D848X,S939F,Q954H,N969K,C1032X,V1104L,P1143L] 
MPLFI-..SGN..DVHKTFPFA.KNSN.K.HSDWS.K.NKK-KP.RYHYKR 27-United-Kingdom-4       2      2      2   100.0% [+16MPLF,T19I,R21T,L24-,P25-,P26-,A27S,S50L,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,R346K,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,V445H,G446S,N450D,L452W,L455S,N460K,S477N,T478K,N481K,V483-,E484K,F486P,Q498R,N501Y,Y505H,E554K,A570V,T572I,D614G,P621S,H655Y,N679K,P681R,N764K,D796Y,S939F,Q954H,N969K,P1143L,E1150D] 
MPLFI-..SGN..DVHTTFPFA.KNSN.KIHSDWSLK.NKK-KP.RYHYKR 28-South-America-4        1      1      1   100.0% [+16MPLF,T19I,R21T,L24-,P25-,P26-,A27S,S50L,H69-,V70-,V127F,Y144-,F157S,R158G,Q183H,N211-,L212I,V213G,L216F,A222T,H245N,A264D,I332V,G339H,R346T,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,L441I,V445H,G446S,N450D,L452W,L455S,F456L,N460K,S477N,T478K,N481K,V483-,E484K,F486P,Q498R,N501Y,Y505H,E554K,A570V,T572I,D614G,P621S,H655Y,N679K,P681R,N764K,D796Y,S939F,Q954H,N969K,P1143L] 
MPLFI-..SGN..DVH.TFPFA.KNSN.K.HSDWSLK.DKK-KPERYHYKR 29-North-America-5       23     23     19    82.6% [+16MPLF,T19I,R21T,L24-,P25-,P26-,A27S,S50L,H69-,V70-,V127F,G142D,Y144-,F157S,R158G,N211-,L212I,V213G,L216F,H245N,A264D,I332V,G339H,K356T,S371F,S373P,S375F,T376A,R403K,D405N,R408S,K417N,N440K,V445H,G446S,N450D,L452W,L455S,F456L,N460K,S477D,T478K,N481K,V483-,E484K,F486P,Q493E,Q498R,N501Y,Y505H,E554K,A570V,D614G,P621S,H655Y,N679K,P681R,N764K,D796Y,S939F,Q954H,N969K,V1104L,P1143L] 

In the Table of Variants, above, the first variant in the input alignment is taken as the reference sequence, and is the ancestral Wuhan variant to ensure epitope regions are chosen appropriately. The alignment on the left shows the positions that define unique common forms that are searched using SHIVER. The positions numbers are written vertically. The amino acids in the top row are taken from is the ancestral Wuhan variant. The epitope regions in Spike that are explored for a focused search for the common Spike variants are defined at the end of this document. The epitope and furin cleavage regions in Spike that are featured are defined below.

The basic NTD supersite sites selected are for inclusion are based on:

Sites 14-20, 140-158, and 245-264: McCallum, M. et al. N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2. Cell 184:9 2332-2347.e16 (2021)

Site 13: Impacts signal peptide cleavage and NTDss antibodies. McCallum, M. et al. SARS-CoV-2 immune evasion by the B.1.427/B.1.429 variant of concern. Science 373:648-654 (2021)

Sites 242-244: Impacts NTDss antibody potency SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma Wibmer, C. et al. Nature Med. 27(4): 622-625.

Toggling Sites: Site 18 is in the NTDss and toggles frequently between L and F, so we exclude it from the tallies of forms of the regions of interest as it splits the counts on otherwise distinctive forms. An analogous situation is a problem for site 142. Among Delta variants, every common variant within the Delta lineages includes both (the ancestral) G and D at site 142. This is because the ARTIC 3 primers can results in an erroneous call of the ancestral G at position 142. The G142D mutation is the common form, and this error is resolved by using the ARTIC 4 primers. By excluding both sites 18 and 142 from our NTDss definition, we group the forms of Spike that carry either form in our tallies.

Analysis of the ARTIC version 3 and version 4 SARS-CoV-2 primers and their impact on the detection of the G142D amino acid substitution in the spike protein. Davies et al. bioRxiv 10.1101/2021.09.27.461949 (2021)

Sites 330-521: the RBD region includes positions 330-521, based on a synthesis of the literature from early 2020.

Furin related sites: mutations that add positive charge to near the furin cleavage site can enhance Spike cleavage and infectivity. Also, the change at H655Y (Alba2021) has been shown to impact furin cleavage, and we include site 950 as it accompanies P681R in Delta and P681H in Mu, to variants that were particularly fast spreading, though Delta became prevalent. SARS-CoV-2 spike P681R mutation, a hallmark of the Delta variant, enhances viral fusogenicity and pathogenicity. Saito et al. bioRxiv 10.1101/2021.06.17.448820 (2021) SARS-CoV-2 variants of concern have acquired mutations associated with an increased spike cleavage. Alba et al. bioRxiv 10.1101/2021.08.05.455290 (2021)

Table of Coverages

In table below, T-n refers to a batch of the first n variants. Coverage is defined as fraction of sequences in the continent with an exact match (over the region NTDss-18-142+RBD+furin) to one of the first n variants. (Here, 'T' corresponds to the 'Taketurns' strategy.) The coverage table is based on 8946 sequences.

                Continent Name Coverage

                     Global T-1    0.0000
              North-America T-1    0.0000
Europe-minus-United-Kingdom T-1    0.0000
                       Asia T-1    0.0000
                    Oceania T-1    0.0000
             United-Kingdom T-1    0.0000
              South-America T-1    0.0000
                     Africa T-1    0.0000

                     Global T-8    0.7805
              North-America T-8    0.8102
Europe-minus-United-Kingdom T-8    0.7799
                       Asia T-8    0.6062
                    Oceania T-8    0.8632
             United-Kingdom T-8    0.8289
              South-America T-8    0.8214
                     Africa T-8    0.8571

                     Global T-15   0.8293
              North-America T-15   0.8501
Europe-minus-United-Kingdom T-15   0.8271
                       Asia T-15   0.6955
                    Oceania T-15   0.9116
             United-Kingdom T-15   0.8717
              South-America T-15   0.9107
                     Africa T-15   0.9524

                     Global T-22   0.8636
              North-America T-22   0.8712
Europe-minus-United-Kingdom T-22   0.8619
                       Asia T-22   0.7902
                    Oceania T-22   0.9389
             United-Kingdom T-22   0.9037
              South-America T-22   0.9286
                     Africa T-22   1.0000

                     Global T-29   0.8782
              North-America T-29   0.8856
Europe-minus-United-Kingdom T-29   0.8752
                       Asia T-29   0.8116
                    Oceania T-29   0.9453
             United-Kingdom T-29   0.9144
              South-America T-29   0.9464
                     Africa T-29   1.0000

This run uses the T=taketurns strategy for identifying further variants. Each continent, in turn, chooses the next variant, based on which is the most common variant in that continent that has not already been chosen. The order of the continents is based on number of samples available in those continents.

Sequence sample dates range from 2024-06-05 to 2024-07-03. The number of sequences, broken out by continent is: Total: 8946, North-America: 4843, Europe-minus-United-Kingdom: 2244, Asia: 1120, Oceania: 475, United-Kingdom: 187, South-America: 56, Africa: 21. The focus here is specifically on the epitope region: NTDss-18-142+RBD+furin Sites: 13-17,19,20,140,141,143-158,242-264,330-521,655,675,677,679,681,950

[*] Note that the UK is treated as a separate continent because so much of the sequencing has been from the UK.