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

    111111112222222223333334444444444455666669
1111444455554445555553457771444577899900577785
3469334526783480134589661357069278436815557910 Name                    LPM    GPM    GSM  GSM/GPM [Mutations] (Lineage)
SQVTV-YYWEFRALYTPDSSWGRKSSSKNGYLSTEQGQNYHQQNPD 1-Initial                 3      3      1    33.3% [] 
...R.....G--...................R.K..........RN 2-United-Kingdom-1    78875 151585  48863    32.2% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (Delta)
...R...H.G--...................R.K..........RN 3-Europe-1             1261  20397   9907    48.6% [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] (Delta+Y145H,A222V)
...R.....G--...................R.K.......H..RN 4-North-America-1       434    650    274    42.2% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,Q675H,P681R,D950N] (Delta+FurinRelated)
...R.....G--...................R.K..........R. 5-Asia-1                 53    673    213    31.6% [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R] 
.....TSN..............K...........K...Y.....HN 6-South-America-1        11     12      6    50.0% [T95I,+143T,Y144S,Y145N,R346K,E484K,N501Y,D614G,P681H,D950N] (Mu)
...R.....G--...........Q.......R.K..........RN 7-Oceania-1               7      7      4    57.1% [T19R,T95I,E156G,F157-,R158-,K356Q,L452R,T478K,D614G,P681R,D950N] (Delta)
....-.--.............D..LPFNKS..NKARSRYHY..KH. 8-Africa-1               31     40     37    92.5% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
...R.....G--...................R.K........H.RN 9-United-Kingdom-2      819   1424    394    27.7% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,Q677H,P681R,D950N] (Delta+FurinRelated)
...R.....G--........R..........R.K..........RN 10-Europe-2             715    745    663    89.0% [T19R,G142D,E156G,F157-,R158-,W258R,L452R,T478K,D614G,P681R,D950N,A1078S] 
...R.....G--......F............R.K..........RN 11-North-America-2      151    314    145    46.2% [T19R,G142D,E156G,F157-,R158-,S254F,L452R,T478K,D614G,P681R,D950N] (Delta)
...R.....G--...I.............V.R.K..........RN 12-Asia-2                23     25     18    72.0% [T19R,T29A,E156G,F157-,R158-,T250I,G446V,L452R,T478K,D614G,P681R,D950N] (Delta+T29A,T95_,T250I)
...R.....G--.................V.R.K..........RN 13-South-America-2        6    347    133    38.3% [T19R,T95I,G142D,E156G,F157-,R158-,G446V,L452R,T478K,D614G,P681R,D950N] (Delta)
...R.....G--...................R.K..........RT 14-Oceania-2              2      2      1    50.0% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950T] 
...R.....G--...................R.KA.........RN 15-Africa-2               3    107     21    19.6% [T19R,E156G,F157-,R158-,G181V,L452R,T478K,E484A,D614G,P681R,D950N] 
T..R...H.G--...................R.K..........RN 16-United-Kingdom-3     592    593    476    80.3% [S13T,T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,V1264L] (Delta+Y145H,V1264L)
...R.....G--....L..............R.K..........RN 17-Europe-3             697   1264    576    45.6% [T19R,G142D,E156G,F157-,R158-,P251L,L452R,T478K,D614G,P681R,D950N] (Delta+T95_,P251L)
...R.....G--........L..........R.K..........RN 18-North-America-3      120    302     95    31.5% [T19R,G142D,E156G,F157-,R158-,W258L,L452R,T478K,D614G,P681R,D950N] 
...R.....G--.......F...........R.K..........RN 19-Asia-3                16    484    166    34.3% [T19R,T95I,G142D,E156G,F157-,R158-,S255F,L452R,T478K,D614G,P681R,D950N] (Delta)
...R.....G--.....V.............R.K..........RN 20-South-America-3        4      7      3    42.9% [T19R,T95I,G142D,E156G,F157-,R158-,D253V,L452R,T478K,D614G,P681R,D950N] (Delta)
...R.....G--..S................R.K..........RN 21-Oceania-3              2      3      2    66.7% [T19R,T95I,G142D,E156G,F157-,R158-,Y248S,L452R,T478K,D614G,P681R,D950N] (Delta)
......-.R...--................H..KK...Y.Y..K.. 22-Africa-3               3      3      2    66.7% [P9L,P25L,C136F,Y144-,W152R,R190S,D215G,A243-,L244-,Y449H,T478K,E484K,N501Y,D614G,H655Y,N679K,T716I,T859N,A879T] 
..FR.....G--...................R.K..........RN 23-United-Kingdom-4     339    499    113    22.6% [V16F,T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,I1179V] (Delta)
...R.....G--...I...............R.K..........RN 24-Europe-4             563    732    231    31.6% [T19R,T29A,G142D,E156G,F157-,R158-,T250I,L452R,T478K,Q613H,D614G,P681R,D950N] 
.H.R.....G--...................R.K..........RN 25-North-America-4      108    250     73    29.2% [Q14H,T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] (Delta)
...R...........................R.K..........RN 26-Asia-4                15    341     62    18.2% [T19R,T95I,G142D,L452R,T478K,D614G,P681R,D950N] 
...R.....G--...................RIK..........RN 27-South-America-4        3    186     64    34.4% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,S477I,T478K,D614G,P681R,D950N] (Delta)
...R....LG--...................R.K..........RN 28-Oceania-4              1     93     22    23.7% [T19R,G142D,W152L,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] (Delta+T95_,A222V)
.........G--...................R.K..........RN 29-Africa-4               3     56     18    32.1% [G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 

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 195708 sequences.

                Continent Name Coverage

                   Global T-1    0.0000
           United-Kingdom T-1    0.0000
Europe-w/o-United-Kingdom T-1    0.0000
            North-America T-1    0.0000
                     Asia T-1    0.0000
            South-America T-1    0.0000
                  Oceania T-1    0.0000
                   Africa T-1    0.0000

                   Global T-8    0.8858
           United-Kingdom T-8    0.8951
Europe-w/o-United-Kingdom T-8    0.8554
            North-America T-8    0.8983
                     Asia T-8    0.8774
            South-America T-8    0.9030
                  Oceania T-8    0.9609
                   Africa T-8    0.7265

                   Global T-15   0.9010
           United-Kingdom T-15   0.9056
Europe-w/o-United-Kingdom T-15   0.8833
            North-America T-15   0.9101
                     Asia T-15   0.8993
            South-America T-15   0.9291
                  Oceania T-15   0.9671
                   Africa T-15   0.7521

                   Global T-22   0.9146
           United-Kingdom T-22   0.9177
Europe-w/o-United-Kingdom T-22   0.9052
            North-America T-22   0.9172
                     Asia T-22   0.9103
            South-America T-22   0.9384
                  Oceania T-22   0.9712
                   Africa T-22   0.7778

                   Global T-29   0.9256
           United-Kingdom T-29   0.9243
Europe-w/o-United-Kingdom T-29   0.9276
            North-America T-29   0.9259
                     Asia T-29   0.9275
            South-America T-29   0.9478
                  Oceania T-29   0.9815
                   Africa T-29   0.8034

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 2021-11-03 to 2021-11-28. The number of sequences, broken out by continent is: Total: 195708, United-Kingdom: 109689, Europe-w/o-United-Kingdom: 48064, North-America: 34899, Asia: 1917, South-America: 536, Oceania: 486, Africa: 117. 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.