FedeGueli
commented
3 years ago Now there is a list of mutations leading to each AY. lineageis published here: https://github.com/cov-lineages/pango-designation/commit/cb460cda1904270fd20ed26092d6b9a3a590f47f#diff-4aa5b85bab0b3961e769828e21af5c9cea2acfe841c9cfd60c6a30ac56d9aacf and here https://github.com/cov-lineages/pango-designation/tree/master/lineage_constellations
thx @chrisruis
To facilitate the work of the researchers i put here the list of AY.s this is competely unofficial . please always refers to this: Source: https://www.pango.network/summary-of-designated-ay-lineages/
and please double check there.
Updated 10/12/2021
AY.1 | Multiple | G22813T (S:K417N) AY.2 | USA | G22813T (S:K417N) AY.3 | USA | A11456G (Orf1ab:I3731V) AY.3.1 | USA | G3644T (Orf1ab:D1127Y), C18115T (Orf1ab:H5951Y) AY.4 | UK | C7851T (Orf1ab:A2529V) AY.4.1 | UK | A20374C (Orf1ab:I6704L),G22899T (S:G446V) AY.4.2 | Europe, particularly UK | T21995C (S:Y145H) AY.4.2.1 | UK, Germany | G28878T (N:S202I) AY.4.2.2| Uk | G25352C (S:V1264L) AY.4.2.3 | Italy ! G26526T (M:A2S) AY.4.3 | Europe | C21638T (S:S26P) AY.4.4 | Multiple European countries | G24348C (S:S929T) AY.4.5 | Lithuania | A14882C (Orf1ab:D4873A) AY.4.6| Europe | C20404T (Orf1ab:P6714S) AY.5 | UK | G24928T (synonymous) AY.5.1 | Portugal | C27143A (M:N207K) AY.5.2 | Portugal | C25572T (synonymous) AY.5.3 | USA | C7488T (Orf1ab:T2408I) AY.5.4 | Europe | C1191T (Orf1ab:P309L) AY.6 | UK | G17331T (Orf1ab:E5689D) AY.7 | UK | G11365T (synonymous), G12718T (Orf1ab:Q4151H), C27629A (Orf7a:A79D) AY.7.1 | Denmark | A18675G (synonymous) AY.7.2 | Europe | G25445T (Orf3a:G18V) AY.8 | UK | A14170G (Orf1ab:I4636V) AY.9 | UK | C22792T (synonymous) AY.9.2 | Europe | G1729A (synonymous) AY.9.2.1 | Canada | T6152C (synonymous),C16092T (synonymous) AY.10 | UK | C12756T (Orf1ab:T4164I), C13665T (synonymous) AY.11 | UK | C3486T (Orf1ab:A1074V), C18526T (Orf1ab:R6088C), C29509T (synonymous) AY.13 | USA | A17406G (synonymous) AY.14 | USA | G20718T (Orf1ab:M6818I) AY.15 | Canada | A16872G (synonymous), G27382C (Orf6:D61H) AY.16 | Kenya | T26076A (synonymous) AY.16.1 | France | A12417G (Orf1ab:N4051S),G12911A (Orf1ab:V4216I) AY.17 | Ireland, Northern Ireland | C17436T (synonymous) AY.18 | Canada | T23470C (synonymous), C27807T (synonymous) AY.19 | South Africa | G25019T (S:D1153Y), G25947T (Orf3a:Q185H) AY.20 | USA, Mexico | C2061T (Orf1ab:A599V) AY.20.1 | Czech Republic | C11173T (synonymous), G25481T (Orf3a:R30L) AY.21 | Italy, Switzerland | G28195T (Orf8:R101L), T28897C (synonymous), C29167T (synonymous) AY.22 | Portugal | T12496C (synonymous), G26062T (Orf3a:G224C) AY.23 | Indonesia, Singapore, Japan, South Korea | C1404T (Orf1ab:P380L), C4752T (Orf1ab:T1496I) AY.23.1 | Singapore | C25262A (S:L1234I) AY.23.2| Europe | T3718A (synonymous), A11903G (Orf1ab:R2880G) and A23667T (S:E702V) AY.24 | Indonesia | C25702T (Orf3a:P104S) AY.25 | USA | A27507C (synonymous) AY.25.1 | Peru' | G23948T (S:D796Y) AY.26 | USA, Mexico | A27345T (Orf6:K48N) AY.26.1 | Peru | S: E484Q,S:T1009S AY.27 | Canada | G29422T (synonymous) AY.28 | Sri Lanka | C8950T (synonymous), C9246T (Orf1ab:A2994V), G24794T (S:A1078S) AY.29 | Japan | T5514C (Orf1ab:V1750A) AY.29.1 | Japan | G22081T (S:Q173H) AY.30 | Thailand, Cambodia | A13482G (synonymous) AY.31 | Myanmar | T3306C (Orf1ab:M1014T), T23480C (S:S640P), G24872T (S:V1104L) AY.32 | South Africa | C9286T (synonymous) AY.33 | Europe | A21647G (S:T29A) AY.34 | France, UK, Germany, USA | G23593C (S:Q677H) AY.34.1 | Brazil,Africa,Usa | C28961T (N:L203F) AY.34.1.1| Brazil | G8017T (synonymous) AY.34.2| Martinique | G11417T (Orf1ab:V3718F) AY.35 | USA | G23012C (S:E484Q) AY.36 | Nigeria, UK, USA | T15628C (Orf1ab:C5122R), G18079T (Orf1ab:V5939L) AY.37 | Liberia, USA, France | T20911C (synonymous) AY.38 | South Africa | C2509T (synonymous) AY.39 | USA | G27604A (Orf7a:V71I) AY.39.1 | Australia, USA | A13482G (synonymous) AY.39.1.1 | New Zealand | G19563T (Orf1ab:L6433F) AY.39.2 | Peru | G5716T (Orf1ab:K1817N) AY.40 | Reunion | C28099T (Orf8:S69L) AY.41 | Europe | G1820A (Orf1ab:G519S), G22992T (S:S477I) AY.42 | Europe | C25872T (synonymous) AY.43 | Europe | A28299T (N:Q9L) AY.43.1 | Brazil | C12663T (Orf1ab:A4133V), C25433T (Orf3a:T14I) AY.43.2 | Brazil | G3728T (Orf1ab:G1155C) AY.43.3 |Chile| C19955T (Orf1ab:T6564I) (formerly proposed as ORF1b:T2163I) AY.43.4 | Suisse| C5241T (Orf1ab:P1659L) ( inner ORF1b:G1824C S:K356R) AY.43.5 | Portugal | A23064G (S:N501S) AY.44 | USA | C6040T (synonymous) AY.45 | South Africa | G13812T (Orf1ab:M4516I) AY.46 | Africa | C10977T (Orf1ab:A3571V) AY.46.1 | USA | T25673C (Orf3a:L94P) AY.46.2 | Germany, Turkey | A17799G (synonymous) AY.46.3 | Brazil | G28378T (synonymous) AY.46.4 | USA | G23545T (S:E661D) AY.46.5 | UK | T16242G (synonymous) AY.46.6 | Europe | C6310T (synonymous) AY.47 | USA | G22427A (S:V289I) AY.48 | USA | G27948T (Orf8:E19) AY.49 | USA | T5773C (synonymous),C10834T (synonymous),C23039G (S:Q493E),G24124T (S:K854N),A27979T (Orf8:Q29L) AY.50 | Ireland | C19554T (synonymous),G22484C (S:V308L),G28809T (N:G179V) AY.51 | Europe | G12223T,A25697T (Orf3a:E102V),G28248A (Orf8:D119N) AY.52 | USA | T25689C (synonymous) AY.53 | Europe | G1738T (synonymous),C18348T (synonymous) AY.54 | USA | A25806G (synonymous) AY.55 | Rwanda and other countries | A10978G (synonymous) AY.56 | USA | C25624T (Orf3a:H78Y) AY.57 | Vietnam | C1403T (Orf1ab:P380S) AY.58 | Europe | C5192T (synonymous) issue #286 AY.59 | Malaysia | T20391G (synonymous) AY.60 | Europe | C2919T (Orf1ab:P885L),T8634C (Orf1ab:I2790T) AY.61 | Italy | T25532C (Orf3a:I47T) AY.62 | USA, Mexico | A1045T (synonymous) AY.63 | Norway | A19126G (Orf1ab:I6288V),C25710T (synonymous),G29616T (Orf10:R20I) issue #286 AY.64 | USA | C5784T (Orf1ab:T1840I),C24130T (synonymous),G25691T (Orf3a:G100V) AY.65 | Bahrain and other countries | G14028T (Orf1ab:M4588I) AY.66 | Europe | T6496C (synonymous) issue #271 AY.67 | USA | A27368G (Orf6:Q56R) AY.68 | Europe | G105T (synonymous),C19524T (synonymous),T24499A (S:D979E) AY.69 | South Korea | A4838G (Orf1ab:I1525V),G9431A (Orf1ab:V3056I),G16864A (Orf1ab:V5534I),C27559T (synonymous) #260 AY.70 | Europe | G28899T (N:R209I),G28903T (N:M210I) AY.71 | Europe | C25317T (S:S1252F) AY.72 | Europe | G6080T (Orf1ab:D1939Y),A25856G (Orf3a:D155G) AY.73 | Europe | C6573T (Orf1ab:S2103F),C28409T (N:P46S),C28893T (N:P207L) AY.74 | Canada | G3994A (synonymous),C25413T (synonymous) AY.75 | USA | C21622T (synonymous) AY.75.2 | Philippines | G23611T (synonymous AY.75.3 | Japan | T19127C (Orf1ab:I6288T AY.76 | Malaysia | T7233C (Orf1ab:L2323S) AY.77 | USA | T27346C (Orf6:Y49H) AY.78 | Germany, Turkey | G14874T (Orf1ab:K4870N),G29227A (synonymous) AY.79 | Malaysia | T2125C (synonymous) AY.80 | Europe | G5017A (synonymous),G19735T (Orf1ab:D6491Y) AY.81 | USA | G11358A (Orf1ab:R3698K),A28032G (Orf8:I47V) AY.82 | Fiji | C9144T (Orf1ab:S2960F),C22783T (synonymous) AY.83 | USA | C5544T (Orf1ab:T1760I),A25491T (synonymous) AY.84 | Europe | G28086T (Orf8:A65S) AY.85 | Thailand | C1825T (synonymous),G16914T (synonymous),T17748A (synonymous) AY.86 | Canada, USA | G24095T (S:A845S),C29445T (N:T391I) AY.87 | UK | C832T (synonymous),G27556T (Orf7a:A55S) AY.88 | Ghana and other countries | G20709T (Orf1ab:M6815I) AY.89 | UK | C7851T (Orf1ab:A2529V) AY.90 | UK | G9251A (Orf1ab:V2996I) AY.91 | South Africa, Namibia | C28236T (Orf8:R115C) issue #246 AY.91.1 | Europe | C15540T (synonymous),C17010T (synonymous),C28310T (N:P13S) AY.92 | Europe | C28657T (synonymous) issue #290 AY.93 | Canada | C7262T (Orf1ab:L2333F) AY.94 | Europe | C15924T (synonymous) AY.95 | Maldives, Europe | T22293C (S:L244S) #209 AY.96 | Botswana | A28254C (Orf8:I121L) AY.97 | Europe | C6840T (Orf1ab:A2192V) AY.98 | UK | G526T (Orf1ab:E87D) AY.98.1 | Europe | C7768T (synonymous) AY.99 | South Africa, Nigeria | A3536G (Orf1ab:I1091V) issue #258 AY.99.1 | Brazil | C8994T (Orf1ab:T2910I) #258 AY.99.2 | Brazil | C4927T (synonymous),C12525T (Orf1ab:T4087I) #258 AY.100 | USA | G17122T (Orf1ab:A5620S) AY.101 | Brazil, Chile | C9474T (Orf1ab:A3070V) AY.102 | Peru, Chile | A27690T (synonymous) issue #272 AY.103 | USA | C24208T (synonymous) AY.104 | Sri Lanka | T13048C (synonymous),C23277T (S:T572I) issue #289 AY.105 | USA | C1063T (synonymous) AY.106 | Jordan and other countries | C22326T (S:S255F) issue #287 AY.107 | USA | A15012G (synonymous) AY.108 | Pakistan and other countries | C745T (synonymous),C823T (synonymous),C6828T (Orf1ab:S2188F) AY.109 | Nigeria and other countries | A14836G (Orf1ab:I4858V) AY.110 | USA | C912A (Orf1ab:S216Y) AY.111 | UK | C4456T (synonymous) AY.112 | Bahrain | A3997T [Orf1ab:E1244D] formerly: G28461A (N:G63D) AY.113 | USA, Mexico | A12772G (synonymous) then Orf1a:T2967I AY.114 | USA | G19677T (Orf1ab:Q6471H) AY.115 | Botswana | A10691G (Orf1ab:I3476V) AY.116 | Africa | A10691G (Orf1ab:I3476V) AY.116.1 | USA | G12071A (Orf1ab:D3936N) AY.117 | USA | C15810T (synonymous) AY.118 | USA | T826C (synonymous) AY.119 | USA | G19006T (Orf1ab:A6248S) AY.119.1 | Peru', Chile | G17338T (Orf1ab:A5692S),T24063C (S:I834T), G25552T (Orf3a:A54S) and G29392T (N:K373N) AY.120 | UK | C6408T (Orf1ab:S2048F) issue #293 AY.120.1 | USA | C11095T (synonymous) AY.120.2 | South Africa | C21758T (S:H66Y) #293 AY.120.2.1 | Europe | C13138T (synonymous) AY.121 | Europe | G25996T (Orf3a:V202L). AY.121.1 | Poland, Germany | C27737T (Orf7a:T115I) AY.122 | Europe | G1048T (Orf1ab:K261N) #320 AY.122.1 | Israel | C23934T (S:T791I) AY.122.2 | Estonia | S:411S AY.123| Belgium,France| G17790T (Orf1ab:Q5842H) and G27762T (Orf7b:E3) AY.124 | Portugal| C21301A (Orf1ab:P7013T), orf1a:K3353R AY.124.1 | Portugal | N:A119S AY.125 i| C745T (synonymous) which leads to the European clade. then Orf3a:D27Y then ORF1b:Q813H AY.126 | Denmark,Germany | A21137G (Orf1ab:K6958R) (formerly proposed starting from S:I850L) AY.127 | India,Europe | G25538T (Orf3a:G49V)