SARS-CoV-2 Constellations
A constellation is a collection of mutations which are functionally meaningful, but which may arise independently a number of times. They are used to track important variants and lineages.
Learn more at the Constellations GitHub repository| Label | Description | Sources | Type | Sites | Rules |
|---|---|---|---|---|---|
| Omicron (BA.1-like) | BA.1 lineage defining mutations | variant | Pango_lineages: BA.1, WHO_label: Omicron, mrca_lineage: BA.1, lineage_name: BA.1, parent_lineage: B.1.1.529, PHE_label: VOC-21NOV-01, representative_genome: BA.1, VOC-21NOV-01 | orf1ab:K856R, nuc:T5386G, del:6513:3, orf1ab:A2710T, orf1ab:L3674F, orf1ab:SGF3675-, orf1ab:I3758V, nuc:T13195C, nuc:C15240T, spike:A67V, del:21765:6, spike:T95I, del:21987:9, del:22194:3, nuc:22205+GAGCCAGAA, spike:S371L, spike:G446S, spike:Q493R, spike:G496S, spike:T547K, spike:N856K, spike:L981F, nuc:C25000T, nuc:C25584T, m:D3G, n:RG203KR | default: [object Object] |
| Gamma (P.1-like) | Defining constellation for lineage P.1 | https://virological.org/t/586, https://cov-lineages.org/global_report_P.1.html | variant | nuc:T733C, nuc:C2749T, ORF1ab:S1188L, ORF1ab:K1795Q, del:11287:9, nuc:C12778T, nuc:C13860T, S:T20N, S:P26S, S:K417T, S:E484K, S:N501Y, S:T1027I, ORF8:E92K, nuc:28262+AACA, N:P80R | min_alt: 8, max_ref: 3 |
| Omicron (BA.2-like) | BA.2 lineage defining mutations | variant | Pango_lineages: BA.2, WHO_label: Omicron, mrca_lineage: BA.2, lineage_name: BA.2, parent_lineage: B.1.1.529, PHE_label: VOC-22JAN-01, representative_genome: BA.2, VOC-22JAN-01 | orf1ab:S135R, orf1ab:T842I, orf1ab:G1307S, nuc:C4321T, orf1ab:L3027F, nuc:A9424G, orf1ab:T3090I, orf1ab:L3201F, orf1ab:SGF3675-, nuc:C10198T, nuc:G10447A, nuc:C12880T, nuc:C15714T, orf1ab:R5716C, orf1ab:T6564I, nuc:A20055G, spike:T19I, del:21633:9, spike:V213G, spike:S371F, spike:T376A, spike:D405N, spike:Q493R, orf3a:T223I, nuc:C25000T, nuc:C25584T, nuc:C26858T, orf6:D61L, n:RG203KR, n:S413R | default: [object Object] |
| Theta (P.3-like) | Defining constellation for lineage P.3 | https://github.com/cov-lineages/pango-designation/issues/27, https://www.medrxiv.org/content/10.1101/2021.03.03.21252812v2 | variant | nsp3:D736G, nsp4:L438P, nsp6:D112E, nsp7:L71F, nsp13:A368V, del:21980:9, S:E484K, S:N501Y, S:P681H, S:E1092K, S:H1101Y, S:V1176F, ORF8:K2Q, nuc:C7564A, nuc:C12049T, nuc:T23341C, nuc:T24187A | min_alt: 9, max_ref: 3 |
| Alpha (B.1.1.7-like) | B.1.1.7 lineage defining mutations | https://virological.org/t/563 | variant | nuc:C913T, 1ab:T1001I, 1ab:A1708D, nuc:C5986T, 1ab:I2230T, 1ab:SGF3675-, nuc:C14676T, nuc:C15279T, nuc:T16176C, s:HV69-, s:Y144-, s:N501Y, s:A570D, s:P681H, s:T716I, s:S982A, s:D1118H, nuc:C26801T, 8:Q27*, 8:R52I, 8:Y73C, N:D3L, N:S235F | min_alt: 15, max_ref: 3 |
| Delta (B.1.617.2-like) +K417N | Defining constellation for lineage B.1.617.2 with the addition of spike K417N | https://github.com/cov-lineages/pango-designation/issues/49 | variant | S:T19R, S:K417N, S:L452R, S:T478K, S:P681R, S:D950N, ORF3a:S26L, M:I82T, ORF7a:V82A, ORF7a:T120I, N:D63G, N:R203M, N:D377Y | min_alt: 5, max_ref: 3, S:K417N: alt |
| Zeta (P.2-like) | Defining constellation for lineage P.2 | variant | Pango_lineages: P.2, mrca_lineage: P.2, PHE_label: V-21JAN-01, WHO_label: Zeta, representative_genome: P.2, VUI-21JAN-01, VUI202101/01, V-21JAN-01 | ORF1ab:L205V, nuc:C11824T, S:E484K, nuc:A12964G, nuc:C28253T, N:A119S, N:M234I | min_alt: 5, max_ref: 1 |
| Omicron (XBB-like) | XBB recombinant lineage defining mutations | variant | Pango_lineages: XBB, WHO_label: Omicron, parent_lineage: XBB-parent2, mrca_lineage: XBB, lineage_name: XBB, representative_genome: XBB | spike:V83A, spike:Y144-, spike:H146Q, spike:Q183E, spike:V213E, spike:R346T, spike:L368I, spike:V445P, spike:F486S, spike:F490S, nuc:C15738T, nuc:T15939C, nuc:T17859C | min_alt: 5, max_ref: 3 |
| A.23.1-like+E484K | This is a variant of cA.23.1 that additionally contains E484K. | https://doi.org/10.1101/2021.02.08.21251393 | variant | nsp3:L741F, nsp6:M86I, nsp6:L98F, nsp6:M183I, S:R102I, S:F157L, S:V367F, S:E484K, S:Q613H, S:P681R, ORF8:L84S, ORF8:E92K, N:S202N | min_alt: 5, max_ref: 3, S:E484K: alt |
| Omicron (BA.4-like) | BA.4 lineage defining mutations | variant | Pango_lineages: BA.4, WHO_label: Omicron, mrca_lineage: BA.4, lineage_name: BA.4, parent_lineage: B.1.1.529, PHE_label: V-22APR-03, representative_genome: BA.4, V-22APR-03 | orf1ab:S135R, orf1ab:T842I, orf1ab:G1307S, nuc:C4321T, orf1ab:T3090I, nuc:C10198T, nuc:G10447A, del:11288:9, nuc:G12160A, nuc:C12880T, nuc:C15714T, orf1ab:R5716C, orf1ab:T6564I, nuc:A20055G, spike:T19I, s:HV69-, spike:V213G, spike:S371F, spike:T376A, spike:D405N, spike:L452R, spike:F486V, nuc:C25000T, nuc:C25584T, nuc:C26060T, nuc:C26858T, orf6:D61L, nuc:G27788T, n:P151S, n:RG203KR, n:S413R | default: [object Object] |
| Omicron (Unassigned) | B.1.1.529 lineage defining mutations | variant | Pango_lineages: B.1.1.529, WHO_label: Omicron, mrca_lineage: None, representative_genome: lineage_name: B.1.1.529, incompatible_lineage_calls: B.1.1.529 | nuc:C3037T, orf1ab:T3255I, orf1ab:P3395H, orf1ab:P4715L, orf1ab:I5967V, spike:G142D, spike:G339D, spike:S373P, spike:S375F, spike:N440K, spike:S477N, spike:T478K, spike:E484A, spike:Q498R, spike:N501Y, spike:Y505H, spike:D614G, spike:H655Y, spike:N679K, spike:P681H, spike:N764K, spike:D796Y, spike:Q954H, spike:N969K, e:T9I, m:Q19E, m:A63T, nuc:A27259C, nuc:C27807T, nuc:A28271T, n:P13L, del:28362:9 | default: [object Object], Probable: [object Object] |
| XE-parent1 | Majority parent of XE recombinant lineage | variant | mrca_lineage: , lineage_name: XE-parent1, parent_lineage: B.1.1.529, representative_genome: XE, GL2 | orf1ab:K856R, nuc:T5386G, del:6513:3, orf1ab:A2710T | default: [object Object] |
| Mu (B.1.621-like) | https://github.com/cov-lineages/pango-designation/issues/57 | variant | Pango_lineages: B.1.621, mrca_lineage: B.1.621, WHO_label: Mu, representative_genome: B.1.621 | nuc:C3037T, ORF1a:T1055A, ORF1a:T1538I, nuc:C6037T, ORF1a:T3255I, ORF1a:Q3729R, nuc:A13057T, ORF1b:P314L, ORF1b:P1342S, nuc:C18877T, nuc:T19035C, nuc:C20148T, spike:T95I, spike:Y145N, spike:R346K, spike:E484K, spike:N501Y, spike:D614G, spike:P681H, spike:D950N, ORF3a:Q57H, nuc:A26492T, ORF8:T11K, ORF8:P38S, ORF8:S67F, nuc:A28272T, N:T205I | min_alt: 19, max_ref: 3 |
| Beta (B.1.351-like) | Defining of lineage B.1.351 | https://www.medrxiv.org/content/10.1101/2020.12.21.20248640v1 | variant | NSP2:T85I, ORF1ab:K1655N, ORF1ab:K3353R, S:D80A, S:D215G, S:E484K, S:N501Y, S:A701V, ORF3a:Q57H, ORF3a:S171L, E:P71L, N:T205I, del:22280:9, del:11287:9 | min_alt: 6, max_ref: 3 |
| Epsilon (B.1.429-like) | variant | Pango_lineages: B.1.429, WHO_label: Epsilon, mrca_lineage: B.1.429, representative_genome: B.1.427 | variant | spike:S13I, spike:W152C, spike:L452R, orf1a:T265I, nuc:C3037T, orf1a:I4205V, orf1b:D1183Y, spike:D614G, orf3a:Q57H, nuc:T24349C, nuc:C26681T, nuc:G27890T, nuc:A28272T, n:T205I | min_alt: 6, max_ref: 3 |
| A.23.1-like | A.23.1 lineage defining mutations | https://doi.org/10.1101/2021.02.08.21251393 | variant | nsp3:L741F, nsp6:M86I, nsp6:L98F, nsp6:M183I, S:R102I, S:F157L, S:V367F, S:Q613H, S:P681R, ORF8:L84S, ORF8:E92K, N:S202N | min_alt: 5, max_ref: 3 |
| Eta (B.1.525-like) | This variant is a cluster of E484K containing genomes | variant | Pango_lineages: B.1.525, mrca_lineage: B.1.525, PHE_label: V-21FEB-03, WHO_label: Eta, representative_genome: B.1.525, VUI-21FEB-03, VUI202102/03, Eta, G/484K.V3, 20A, V-21FEB-03 | nuc:C1498T, nuc:A1807G, nuc:T8593C, nuc:C9565T, nsp12:P323F, nuc:C18171T, nuc:A20724G, S:Q52R, S:E484K, S:Q677H, S:F888L, nuc:C24748T, E:L21F, M:I82T, nuc:A28699G, nuc:G29543T | min_alt: 8, max_ref: 3 |
| Lambda (C.37-like) | C.37 lineage defining mutations | variant | Pango_lineages: C.37, mrca_lineage: C.37, WHO_label: Lambda, PHE_label: V-21JUN-01, representative_genome: Lambda, C.37, V-21JUN-01 | ORF1a:T1246I, ORF1a:P2287S, ORF1a:F2387V, ORF1a:L3201P, ORF1a:T3255I, ORF1a:G3278S, ORF1a:SGF3675-, ORF1b:P314L, S:G75V, S:T76I, S:RSYLTPG246-, S:L452Q, S:F490S, S:D614G, S:T859N, N:P13L, N:R203K, N:G204R, N:G214C | min_alt: 9, max_ref: 3 |
| Omicron (XBB.1.16-like) | XBB.1.16 lineage defining mutations | variant | Pango_lineages: XBB.1.16, WHO_label: Omicron, parent_lineage: XBB.1, mrca_lineage: XBB.1.16, lineage_name: XBB.1.16, representative_genome: XBB.1.16 | orf1b:D1746Y, spike:E180V, nuc:T28297C, nuc:A28447G, nuc:C29386T | min_alt: 3, max_ref: 1 |
| XBB-parent1 | Majority parent of XBB recombinant lineage | variant | mrca_lineage: , lineage_name: XBB-parent1, parent_lineage: BA.2, representative_genome: XBB | spike:G339H, spike:G446S, spike:N460K, e:T11A, nuc:C25416T | default: [object Object] |
| Omicron (XBB.1.5-like) | XBB.1.5 lineage defining mutations | variant | Pango_lineages: XBB.1.5, WHO_label: Omicron, parent_lineage: XBB.1, mrca_lineage: XBB.1.5, lineage_name: XBB.1.5, representative_genome: XBB.1.5 | nuc:T17124C, spike:G252V, spike:F486P | min_alt: 2, max_ref: 0, spike:F486: alt |
| B.1.1.7-like+E484K | This is a variant of cB.1.1.7 that additionally contains E484K. This includes all independent instances of this. | https://virological.org/t/563 | variant | nuc:C913T, 1ab:T1001I, 1ab:A1708D, nuc:C5986T, 1ab:I2230T, 1ab:SGF3675-, nuc:C14676T, nuc:C15279T, nuc:T16176C, s:HV69-, s:Y144-, S:E484K, s:N501Y, s:A570D, s:P681H, s:T716I, s:S982A, s:D1118H, nuc:C26801T, 8:Q27*, 8:R52I, 8:Y73C, N:D3L, N:S235F | min_alt: 15, max_ref: 3, S:E484K: alt |
| Omicron (BA.3-like) | BA.3 lineage defining mutations | variant | Pango_lineages: BA.3, WHO_label: Omicron, mrca_lineage: BA.3, lineage_name: BA.3, parent_lineage: B.1.1.529, representative_genome: BA.3 | orf1ab:S135R, nuc:C832T, orf1ab:G1307S, orf1ab:T3090I, orf1ab:SGF3675-, nuc:G10447A, nuc:C11235T, nuc:C12880T, nuc:C15714T, spike:A67V, spike:Q493R, del:21765:6, del:21987:9, del:22194:3, spike:S371F, spike:D405N, spike:G446S, orf3a:T223V, nuc:C26858T, n:RG203KR, n:S413R | default: [object Object] |
| B.1.617.3-like | Defining constellation for lineage B.1.617.3 | https://github.com/cov-lineages/pango-designation/issues/49 | variant | nuc:C835T, nsp3:A1526V, nsp3:T1830I, nsp5:A194S, nsp6:A117V, nuc:C16293T, S:T19R, S:L452R, S:E484Q, S:P681R, S:D950N, nuc:T27384C, ORF7a:V82A, ORF8:T26I, N:P67S, N:R203M, N:D377Y | min_alt: 9, max_ref: 3 |
| B.1.1.318-like | Defining of lineage B.1.1.318 | https://github.com/cov-lineages/pango-designation/issues/15 | variant | nuc:C3961T, nsp3:K1693N, nsp4:T173I, nsp4:A446V, nsp5:T21I, del:11287:9, nsp15:V320M, S:T95I, del:21990:3, S:E484K, nuc:T23287C, S:P681H, S:D796H, nuc:C25276A, M:I82T, del:27887:15, ORF8:E106*, nuc:A28271G, del:28895:3 | min_alt: 11, max_ref: 3 |
| Omicron (XBB.1-like) | XBB.1 lineage defining mutations | variant | Pango_lineages: XBB.1, WHO_label: Omicron, parent_lineage: XBB, mrca_lineage: XBB.1, lineage_name: XBB.1, representative_genome: XBB.1 | spike:R408S, spike:K417N, orf8:G8* | min_alt: 2, max_ref: 0 |
| Omicron (XE-like) | XE recombinant lineage defining mutations | variant | Pango_lineages: XE, WHO_label: Omicron, parent_lineage: XE-parent2, mrca_lineage: XE, PHE_label: V-22APR-02, lineage_name: XE, representative_genome: XE, GL2, V-22APR-02 | nuc:C3241T, nuc:T5386G, nuc:C14599T, nuc:C12880T, nuc:A29510C, nuc:C14599T | min_alt: 3, max_ref: 0 |
| Delta (AY.4.2-like) | AY.4.2 lineage defining mutations | variant | Pango_lineages: AY.4.2, mrca_lineage: AY.4.2, lineage_name: AY.4.2, parent_lineage: AY.4, PHE_label: V-21OCT-01, representative_genome: AY.4.2, V-21OCT-01 | nuc:T17040C, spike:A222V, spike:Y145H | min_alt: 2, max_ref: 0 |
| Iota (B.1.526-like) | variant | Pango_lineages: B.1.526, mrca_lineage: B.1.526, WHO_label: Iota, representative_genome: B.1.526, Iota | variant | nuc:C3037T, ORF1a:T265I, ORF1a:L3201P, 1ab:SGF3675-, ORF1b:P314L, ORF1b:Q1011H, nuc:A20262G, S:L5F, S:T95I, S:D253G, S:E484K, S:D614G, S:A701V, ORF3a:P42L, ORF3a:Q57H, N:P199L, N:M234I, ORF8:T11I, S:S477N, S:Q957R, N:P13L, N:S202R, nuc:A28271- | min_alt: 11, max_ref: 7 |
| XE-parent2 | 3' parent of XE recombinant lineage | variant | mrca_lineage: , lineage_name: XE-parent2, parent_lineage: XE-parent1, representative_genome: XE, GL2 | nuc:C15714T, nuc:C12880T, orf1ab:R5716C, orf1ab:T6564I, nuc:A20055G, spike:T19I, del:21633:9, nuc:T22200G, spike:S371F, spike:T376A, spike:D405N, spike:R408S, nuc:C25000T, nuc:C25584T, nuc:C26060T, nuc:C26858T, orf6:D61L, n:S413R | default: [object Object] |
| Omicron (BA.5-like) | BA.5 lineage defining mutations | variant | Pango_lineages: BA.5, WHO_label: Omicron, mrca_lineage: BA.5, lineage_name: BA.5, parent_lineage: B.1.1.529, PHE_label: V-22APR-04, representative_genome: BA.5, V-22APR-04 | orf1ab:S135R, orf1ab:T842I, orf1ab:G1307S, nuc:C4321T, orf1ab:T3090I, nuc:C10198T, nuc:G10447A, del:11288:9, nuc:G12160A, nuc:C12880T, nuc:C15714T, orf1ab:R5716C, orf1ab:T6564I, nuc:A20055G, spike:T19I, s:HV69-, spike:V213G, spike:S371F, spike:T376A, spike:D405N, spike:L452R, spike:F486V, nuc:C25000T, nuc:C25584T, nuc:C26060T, m:D3N, n:RG203KR, n:S413R | default: [object Object] |
| AV.1-like | AV.1 lineage defining mutations | variant | Pango_lineages: AV.1, mrca_lineage: AV.1, PHE_label: VOC-20DEC-01, representative_genome: AV.1, VOC-20DEC-01 | s:D80G, s:T95I, s:G142D, s:Y144-, s:N439K, s:E484K, s:D614G, s:P681H, s:I1130V, s:D1139H, M:A63T, M:H125Y, N:I157V, N:R203K, N:G204R | min_alt: 7, max_ref: 3 |
| Delta (B.1.617.2-like) | Defining constellation for lineage B.1.617.2 | https://github.com/cov-lineages/pango-designation/issues/49 | variant | S:T19R, S:G142D, S:L452R, S:T478K, S:P681R, S:D950N, ORF3a:S26L, M:I82T, ORF7a:V82A, ORF7a:T120I, N:D63G, N:R203M, N:D377Y | min_alt: 5, max_ref: 3 |
| Delta (AY.4-like) | AY.4 lineage defining mutations | variant | Pango_lineages: AY.4, mrca_lineage: AY.4, lineage_name: AY.4, parent_lineage: B.1.617.2, incompatible_lineage_calls: AY.4.2, representative_genome: AY.4 | del:28271:1, del:22029:6, del:28248:6, orf1a:A1306S, orf1a:P2046L, orf1a:P2287S, orf1a:A2529V, nuc:C8986T, orf1a:V2930L, orf1a:T3255I, orf1a:T3646A, nuc:A11332G, orf1b:P314L, orf1b:G662S, orf1b:P1000L, orf1b:A1918V, nuc:C27874T, n:G215C, nuc:G29742T | min_alt: 12, max_ref: 3, orf1a:A2529V: alt |
| XBB-parent2 | Minority parent of XBB recombinant lineage | variant | mrca_lineage: , lineage_name: XBB-parent2, parent_lineage: XBB-parent1, representative_genome: XBB | orf1b:S959P | default: [object Object] |
| Epsilon (B.1.427-like) | variant | Pango_lineages: B.1.427, WHO_label: Epsilon, mrca_lineage: B.1.427, representative_genome: B.1.427 | variant | spike:S13I, spike:W152C, spike:L452R, nuc:C241T, orf1a:T265I, nuc:C3037T, orf1b:D1183Y, spike:D614G, orf3a:Q57H, nuc:C26681T, n:T205I, nuc:G13713A, nuc:A28272T | min_alt: 5, max_ref: 3 |
| B.1.617.1-like | Defining constellation for lineage B.1.617.1 | https://github.com/cov-lineages/pango-designation/issues/38, https://www.telegraphindia.com/india/covid-double-mutation-variant-fuels-fears/cid/1809715 | variant | nuc:C3457T, nsp3:T749I, nsp6:T77A, nsp13:M429I, nsp15:K259R, S:L452R, S:E484Q, S:P681R, ORF3a:S26L, ORF7a:V82A, N:R203M | min_alt: 5, max_ref: 3 |