Advances in Virology

Research Article

Rational Primer and Probe Construction in PCR-Based Assays for the Efficient Diagnosis of Drifting Variants of SARS-CoV-2

Table 2

SNP profiles in S gene of SARS-CoV-2 VOCs.
Common nameUK variantSouth African variantBrazilian variantIndian double mutantIndian double mutantOmicron
Country linked toUKSouth AfricaBrazilIndiaIndiaSouth Africa
Pango lineageB.1.1.7B.1.351P.1B.1.617.2AY.1BA.1
Variant a/c GISAIDVUI202012/01 GRY (B.1.1.7)GH/501Y.v2 (B.1.351)GR/501Y.V3 (P.1)GGGGGRA
WHO namesAlphaAlphaBetaBetaGammaGammaDeltaDeltaDelta (B.1.617.2-like) +K417NDelta (B.1.617.2-like) +K417NOmicronOmicron
Mutation/GISAID entry exampleEPI_ISL_601443EPI_ISL_581117EPI_ISL_678595EPI_ISL_660222EPI_ISL_792683EPI_ISL_792680EPI_ISL_2131567EPI_ISL_2441609EPI_ISL_2171265EPI_ISL_2479976EPI_ISL_11457659EPI_ISL_11655397
Spike L18F  L18F L18FL18F      
Spike T19R      T19RT19RT19R   
Spike T20N    T20NT20N      
Spike P26S    P26SP26S      
Spike A67V          A67VA67V
Spike H69delH69delH69del        H69delH69del
Spike V70delV70delV70del        V70delV70del
Spike K77T      K77T     
Spike D80A  D80AD80A        
Spike T95I        T95I T95IT95I
Spike D138Y    D138YD138Y      
Spike G142D      G142D G142D G142DG142D
Spike V143          V143delV143del
Spike Y144delY144delY144del        Y144delY144del
Spike Y145del          Y145delY145del
Spike E156G         E156G  
Spike 157del        F157del   
Spike R158del        R158del   
Spike R190S    R190SR190S      
Spike N211del          N211delN211del
Spike L212I          L212IL212I
Spike ins214EPE          ins214EPEins214EPE
Spike D215G  D215GD215G        
Spike L242del  L242delL242del        
Spike A243del  A243delA243del        
Spike L244del  L244delL244del        
Spike W258L        W258LW258L  
Spike G 339D          G339DG339D
Spike R346K          R346KR346K
Spike S371L          S371LS371L
Spike S373P          S373PS373P
Spike S375F          S375FS375F
Spike K417T  K417NK417NK417TK417T  K417NK417NK417NK417N
Spike N440K          N440KN440K
Spike G446S          G446SG446S
Spike L452R      L452RL452RL452RL452R  
Spike S477N          S477NS477N
Spike T478K      T478KT478KT478KT478KT478KT478K
Spike E484Q  E484KE484KE484KE484K      
Spike E484A          E484AE484A
Spike Q493R          Q493RQ493R
Spike G496S          G496SG496S
Spike Q498R          Q498RQ498R
Spike N501YN501YN501YN501YN501YN501YN501Y    N501YN501Y
Spike Y505H          Y505HY505H
Spike T547K          T547KT547K
Spike A570DA570DA570D          
Spike D614GD614GD614GD614GD614GD614GD614GD614GD614GD614GD614GD614GD614G
Spike H655Y    H655YH655Y    H655YH655Y
Spike N679K          N679KN679K
Spike P681HP681HP681H    P681RP681RP681RP681RP681HP681H
Spike A701V  A701VA701V        
Spike T716IT716IT716I          
Spike N764K          N764KN764K
Spike D796Y          D796YD796Y
Spike N856K          N856KN856K
Spike D950N      D950ND950ND950ND950B  
Spike Q954H          Q954HQ954H
Spike N969K          N969KN969K
Spike L981F          L981FL981F
Spike S982AS982AS982A          
Spike T1027I    T1027IT1027I      
Spike D1118HD1118HD1118H          
Spike V1176F    V1176FV1176F      
Not in the individual database but remarked as defining.