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SHIVER

SARS CoV-2 Historically Identified Variants in Epitope Regions

Last update: Mar 30, 2023

Dates of current data

Variants   Strategy   Reference

Variants: Delta and Omicron Variants
Strategy: Take turns
Reference strain: Wuhan reference
Early 2021 Variants color key
Delta Variants color key
Delta Omicron Variants color key

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

 11111112222223333333334444444444444444555666
144455554455553455677770011444456778899002578
946726783423679646813565807045620784608151591 Name                    LPM    GPM    GSM  GSM/GPM [Mutations] (Lineage)
TYHKWEFRALGDSGGRNKLSSSTDRIKNKVGLNSTEFFQNYPHNP 1-Initial                 0      0      0     0.0% [] 
I-Q.......V...HT..IFPFANS.NK.PS.KNKAPSRYH.YKH 2-North-America-1      7860  15245  10279    67.4% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
I..ER.L......SHT...FPFANS.NKT.SRKNKAS.RYH.YKH 3-Europe-1              587   2461    566    23.0% [T19I,L24-,P25-,P26-,A27S,G142D,K147E,W152R,F157L,I210V,V213G,G257S,G339H,R346T,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,K444T,G446S,L452R,N460K,S477N,T478K,E484A,F486S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
I-............DT...FPFANS.NKT..RKNKAV.RYH.YKH 4-United-Kingdom-1      182    857    454    53.0% [T19I,L24-,P25-,P26-,A27S,H69-,V70-,G142D,Y144-,V213G,G339D,R346T,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,K444T,L452R,N460K,S477N,T478K,E484A,F486V,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] (Omicron_BA.4andBA.5)
I..ER.L......SHT.T.FPFANS.NK..S.KNKA.SRYH.YKH 5-Asia-1                960   1106    635    57.4% [T19I,L24-,P25-,P26-,A27S,G142D,K147E,W152R,F157L,I210V,V213G,G257S,G339H,R346T,K356T,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,G446S,N460K,S477N,T478K,E484A,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
I..ER.L......SHT...FPFANS.NK..S.KNKAPSRYH.YKH 6-Oceania-1             174    720    415    57.6% [T19I,L24-,P25-,P26-,A27S,G142D,K147E,W152R,F157L,I210V,V213G,G257S,G339H,R346T,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,G446S,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
I-Q.......V...HT..IFPFANS..K.PS.KNKAPSRYH.YKH 7-South-America-1        54    311    155    49.8% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,N440K,V445P,G446S,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
I-Q.......V...HT..IFPFAN..NK.PS.KNKAPSRYH.YKH 8-Africa-1               16    153     74    48.4% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,K417N,N440K,V445P,G446S,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
I.............DT...FPFANS.NKT..RKNKAV.RYH.YKH 9-North-America-2       489    935    548    58.6% [T19I,L24-,P25-,P26-,A27S,H69-,V70-,G142D,V213G,G339D,R346T,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,K444T,L452R,N460K,S477N,T478K,E484A,F486V,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] (Omicron_BA.4andBA.5)
I-K.......V...HT..IFPFANS.NK.PS.KNKAPSRYH.YKH 10-Europe-2             173    786    526    66.9% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146K,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
I-.........G..DT...FPFANS.NKT..RKNKAV.RYH.YKH 11-United-Kingdom-2     136    178     52    29.2% [T19I,L24-,P25-,P26-,A27S,H69-,V70-,G142D,Y144-,V213G,D253G,G339D,R346T,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,K444T,L452R,N460K,S477N,T478K,E484A,F486V,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K,E1144Q] (Omicron_BA.4andBA.5)
I.............DT...FPFANS.NK...R.NKAV.RYH.YKH 12-Asia-2               631    712    305    42.8% [T19I,L24-,P25-,P26-,A27S,H69-,V70-,G142D,V213G,G339D,R346T,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,L452R,S477N,T478K,E484A,F486V,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] (Omicron_BA.4andBA.5)
I-...G----..L..S...FPFANS.NK..SR.NKAP.RYH.YKH 13-Oceania-2             58     58     48    82.8% [T19I,P25S,G142D,Y144-,E156G,F157-,R158-,P209L,L212S,D215H,A222V,A243-,L244-,S256L,R346S,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,G446S,L452R,S477N,T478K,E484A,F486P,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N703I,N764K,D796Y,Q954H,N969K] 
I-K.......V...HT..IFPFANS..K.PS.KNKAPSRYH.YKH 14-South-America-2       11     29     14    48.3% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146K,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,N440K,V445P,G446S,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
I-Q.......V...HT..IFP.AN..NK.PS.KNKAPSRYH.YKH 15-Africa-2              13     13      2    15.4% [T19I,L24-,P25-,P26-,A27S,D40X,K41X,V42X,F43X,R44X,S45X,S46X,V47X,L48X,H49X,S50X,T51X,Q52X,D53X,L54X,F55X,L56X,P57X,F58X,F59X,S60X,N61X,V62X,T63X,W64X,F65X,H66X,A67X,I68X,H69X,V70X,S71X,G72X,T73X,N74X,G75X,T76X,K77X,R78X,F79X,D80X,N81X,P82X,V83X,L84X,P85X,F86X,N87X,D88X,G89X,V90X,G142D,Y144-,H146Q,Y170X,V171X,S172X,Q173X,P174X,F175X,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,T376A,D405N,K417N,N440K,V445P,G446S,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
I.............D....FPFANS.NKT..RKNKAV.RYH.YKH 16-North-America-3      101    174     78    44.8% [T19I,L24-,P25-,P26-,A27S,H69-,V70-,G142D,V213G,G339D,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,K444T,L452R,N460K,S477N,T478K,E484A,F486V,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] (Omicron_BA.4andBA.5)
I-Q.......V...HT..IFPFAN..NK.PS.K.KAPSRYH.YKH 17-Europe-3             151    151     87    57.6% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,K417N,N440K,V445P,G446S,N460K,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
I..N..........DT...FPFANS.NKT..RKNKAV.RYH.YKH 18-United-Kingdom-3      33     47     20    42.6% [T19I,L24-,P25-,P26-,A27S,H69-,V70-,G142D,K147N,V213G,G339D,R346T,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,K444T,L452R,N460K,S477N,T478K,E484A,F486V,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] (Omicron_BA.4andBA.5)
I.............D....FPFANS.NK...R.NKAV.RYH.YKH 19-Asia-3               590    600    319    53.2% [T19I,L24-,P25-,P26-,A27S,H69-,V70-,G142D,V213G,G339D,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,L452R,S477N,T478K,E484A,F486V,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] (Omicron_BA.4andBA.5)
I..ER.L......SHT...FPFANS.NK..SRKNKAI.RYH.YKH 20-Oceania-3             45     73     45    61.6% [T19I,L24-,P25-,P26-,A27S,G142D,K147E,W152R,F157L,I210V,V213G,G257S,G339H,R346T,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,G446S,L452R,N460K,S477N,T478K,E484A,F486I,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
I-Q.......V...H...IFPFANS.NK.PS.KNKAPSRYH.YKH 21-South-America-3        2      4      2    50.0% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
I-Q.......V...HT..IFP..N..NK.PS.KNKAPSRYH.YKH 22-Africa-3               7      7      2    28.6% [T19I,L24-,P25-,P26-,A27S,D40X,K41X,V42X,F43X,R44X,S45X,S46X,V47X,L48X,H49X,S50X,T51X,Q52X,D53X,L54X,F55X,L56X,P57X,F58X,F59X,S60X,N61X,V62X,T63X,W64X,F65X,H66X,A67X,I68X,H69X,V70X,S71X,G72X,T73X,N74X,G75X,T76X,K77X,R78X,F79X,D80X,N81X,P82X,V83X,L84X,P85X,F86X,N87X,D88X,G89X,V90X,G142D,Y144-,H146Q,Y170X,V171X,S172X,Q173X,P174X,F175X,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,D405N,K417N,N440K,V445P,G446S,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,A570V,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
I-............D....FPFANS.NKT..RKNKAV.RYH.YKH 23-North-America-4       89    220     89    40.5% [T19I,L24-,P25-,P26-,A27S,H69-,V70-,G142D,Y144-,V213G,G339D,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,K444T,L452R,N460K,S477N,T478K,E484A,F486V,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] (Omicron_BA.4andBA.5)
I-Q.......V...HT..IFPFANSVNK.PS.KNKAPSRYHSYKH 24-Europe-4             115    118     85    72.0% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,I410V,K417N,N440K,V445P,G446S,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,P521S,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
I-Q........G..HT..IFPFANS.NK.PS.KNKAPSRYHSYKH 25-United-Kingdom-4      31    134     59    44.0% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146Q,Q183E,V213E,D253G,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,P521S,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
I............DDT...FPFANS.NK...R.NKAV.RYH.YKH 26-Asia-4               121    121     93    76.9% [T19I,L24-,P25-,P26-,A27S,H69-,V70-,G142D,V213G,G257D,G339D,R346T,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,L452R,S477N,T478K,E484A,F486V,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] (Omicron_BA.4andBA.5)
I-...G----..L......FPFANS.NK..SM.NKAP.RYH.YKH 27-Oceania-4             19     28     24    85.7% [T19I,P25S,G142D,Y144-,E156G,F157-,R158-,P209L,L212S,D215H,A222V,A243-,L244-,S256L,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,G446S,L452M,S477N,T478K,E484A,F486P,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N703I,N764K,D796Y,Q954H,N969K] 
I-Q.......V...HTK.IFPFANS..K.PS.KNKAPSRYH.YKH 28-South-America-4        2      2      2   100.0% [T19I,L24-,P25-,P26-,A27S,V83A,G142X,Y144-,H146Q,Q183E,V213E,G252V,G339H,R346T,N354K,L368I,S371F,S373P,S375F,T376A,D405N,R408S,N440K,V445P,G446S,N460K,S477N,T478K,E484A,F486P,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
I-K...........HT..IFPFANS.NK.PS.KNKAASRYH.YKH 29-Africa-4               1      1      1   100.0% [T19I,L24-,P25-,P26-,A27S,V83A,G142D,Y144-,H146K,M177T,K182E,Q183E,V213E,G339H,R346T,L368I,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,V445P,G446S,N460K,S477N,T478K,E484A,F486A,F490S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 

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 31278 sequences.

                Continent Name Coverage

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

                     Global T-8    0.6667
              North-America T-8    0.7266
Europe-minus-United-Kingdom T-8    0.6501
             United-Kingdom T-8    0.7885
                       Asia T-8    0.4276
                    Oceania T-8    0.6243
              South-America T-8    0.7172
                     Africa T-8    0.6081

                     Global T-15   0.7534
              North-America T-15   0.8078
Europe-minus-United-Kingdom T-15   0.7042
             United-Kingdom T-15   0.8509
                       Asia T-15   0.5997
                    Oceania T-15   0.7321
              South-America T-15   0.8414
                     Africa T-15   0.7838

                     Global T-22   0.7871
              North-America T-22   0.8180
Europe-minus-United-Kingdom T-22   0.7293
             United-Kingdom T-22   0.8606
                       Asia T-22   0.7253
                    Oceania T-22   0.7834
              South-America T-22   0.8552
                     Africa T-22   0.8784

                     Global T-29   0.8071
              North-America T-29   0.8277
Europe-minus-United-Kingdom T-29   0.7529
             United-Kingdom T-29   0.8684
                       Asia T-29   0.7753
                    Oceania T-29   0.8100
              South-America T-29   0.8759
                     Africa T-29   0.8919

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 2023-02-28 to 2023-03-27. The number of sequences, broken out by continent is: Total: 31278, North-America: 11605, Europe-minus-United-Kingdom: 8053, United-Kingdom: 5480, Asia: 4984, Oceania: 937, South-America: 145, Africa: 74. 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.


 

last modified: Sun Jan 22 23:41 2023



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