Re: UK Genetic Evaluation thread
I ran all the HA nucleotides of the UK sequences with gs's program and then grouped them together in a way that looked right. Keep in mind that I'm no scientist. Maybe someone else will see different clades; please feel free to offer opinions.
The severe and fatal cases are marked; notice that about half of them appear on clade B.
Clade A: 451,598,658,1408,1464
G451A,T598C,T658A,T933C,T1020C,T1191C,G1206A,C1245 T,T1374G,C1408T,C1464T(4)
G451A,T598C,T658A,T933C,T1020C,T1191C,G1206A,C1245 T,T1374G,C1408T,C1464T(4)
G451A,T598C,T658A,T933C,T1020C,T1191C,G1206A,C1245 T,T1374G,C1408T,C1464T(4)
G451A,T598C,T658A,T933C,T1020C,T1191C,G1206A,C1245 T,T1374G,C1408T,C1464T(4)
G451A,T598C,T658A,T933C,T1020C,T1191C,G1206A,C1245 T,T1374G,G1403A,C1408T,C1464T(4)
G451A,T598C,T658A,T933C,T1020C,T1191C,G1206A,C1245 T,T1374G,G1403A,C1408T,C1464T(4)
G451A,T598C,T658A,T879C,C1098T,A1172G,G1266A,C1408 T,C1464T,A1568G,G1577T,G1630A(4)
G451A,T598C,T658A,T879C,C1098T,A1172G,G1266A,C1408 T,C1464T,A1568G,G1577T,G1630A(4)
G451A,T598C,T658A,T858C,T879C,C1098T,A1172G,G1266A ,C1408T,C1464T,A1568G,G1577T,G1630A
G451A,T598C,G605A,T658A,A1172G,A1213G,G1266A,C1408 T,C1464T,G1577T,G1630A(4)
G451A,T598C,G610T,T658A,A1172G,G1266A,C1408T,C1464 T,G1577T,G1630A(4) F
G451A,G531A,T598C,T658A,C921T,A1131G,C1408T,C1464T (4)
Clade B: 340,658,1056,1171,1403,1408
G340A,G605C,T658A,T1056C,G1171A,G1403A,C1408T,T165 3C(4)
G340A,G605C,T658A,T1056C,G1171A,G1403A,C1408T,T165 3C(4)
G340A,G605C,T658A,T680C,T1056C,G1171A,G1403A,C1408 T,T1653C(4) F
G340A,G605C,C612T,T658A,T1056C,G1171A,G1403A,C1408 T,T1653C(4)
G340A,A579G,G605C,T658A,C704T,T1056C,G1171A,A1386G ,G1403A,C1408T(4)
G340A,A579G,G605C,T658A,T1056C,G1171A,A1386G,G1403 A,C1408T(4) S
G340A,A579G,G605C,T658A,T1056C,G1171A,A1386G,G1403 A,C1408T(4) S
G340A,A579G,G605C,A611G,T658A,T1056C,G1171A,A1386G ,G1403A,C1408T(4) F
G340A,A579G,G605C,T658A,A716G,T1056C,G1171A,A1386G ,G1403A,C1408T(4) S
G340A,A579G,G605C,T658A,A716G,T1056C,G1171A,A1386G ,G1403A,C1408T(4) S
Clade C: 40,207,605,658,1056,1171,1403,1408,1629
A40G,G207A,G302T,C573A,G605C,T658A,T1056C,G1171A,G 1403A,C1408T,G1629T(4)
A40G,G207A,G515R,G605C,T658A,C816T,T1056C,G1171A,G 1396A,G1403A,C1408T,G1629T(4)
A40G,G340A,A579G,G605C,T658A,C672T,T1056C,G1171A,A 1386G,G1403A,C1408T,G1624A(4)
A40G,G207A,G605C,T658A,T834A,T1056C,G1171A,G1403A, C1408T,G1473A,G1629T(4)
A40G,G207A,G605C,T658A,G832A,T1056C,G1171A,G1403A, C1408T,G1629T(4)
A40G,G207A,G605C,T658A,G1005A,T1056C,G1171A,G1403A ,C1408T,G1629T(4)
A40G,G207A,G605C,T658A,T1056C,G1171A,G1403A,C1408T ,G1629T(4) F
A40G,G207A,G605C,T658A,T1056C,G1171A,C1182T,G1403A ,C1408T,G1629T(4)
A40G,G207A,G605C,T658A,T834A,T1056C,G1171A,G1403A, C1408T,G1629T(4)
A40G,G207A,G605C,T658A,T1056C,G1171A,G1403A,C1408T ,A1435G,G1629T(4) (? F/S)
Odd Ones
C148T,G340A,A424G,A566G,T658A,G684A,C870T,T927C,G1 171A,A1230G,G1326A,C1408T,A1536G(4)
T216C,G340A,A424G,G435A,T658A,C672T,G1171A,C1408T( 4) F
T243C,G340A,A424G,C473T,T658A,G713A,A747G,G1171A,C 1408T,C1627A(4) F
C172T,G360A,A424G,T519A,T658A,G1171A,C1408T(4)
G154A,G207A,G605C,T658A,T1056C,G1171A,C1383A,G1403 A,C1408T,G1524K,G1629T(4)
T17C,G565A,T658A,A973G,G1171A,T1197C,G1395A,C1404T ,C1408T,G1524A,A1651G(4) F
G396A,G451A,G531A,T598C,T658A,A795G,C921T,A1131G,G 1407A,C1408T,C1464T,A1553G,A1579G(4)
G451A,T598C,T658A,T933C,T1020C,T1191C,G1206A,C1245 T,T1374G,C1408T,C1464T(4)
By areas
1 Coventry
4 Newcastle-upon-tyne
3 Oxford
1 Durham
2 Leeds
1 Manchester
4 Birmingham
1 Leicester
1 York
1 Cambridge (Fatal)
6 London
2 Nottingham
3 Whitechapel (2 Fatal)
1 Middlesex
1 North Yorkshire
8 Severe/fatal with no locations given
1 Possible severe/fatal no location
I ran all the HA nucleotides of the UK sequences with gs's program and then grouped them together in a way that looked right. Keep in mind that I'm no scientist. Maybe someone else will see different clades; please feel free to offer opinions.
The severe and fatal cases are marked; notice that about half of them appear on clade B.
Clade A: 451,598,658,1408,1464
G451A,T598C,T658A,T933C,T1020C,T1191C,G1206A,C1245 T,T1374G,C1408T,C1464T(4)
G451A,T598C,T658A,T933C,T1020C,T1191C,G1206A,C1245 T,T1374G,C1408T,C1464T(4)
G451A,T598C,T658A,T933C,T1020C,T1191C,G1206A,C1245 T,T1374G,C1408T,C1464T(4)
G451A,T598C,T658A,T933C,T1020C,T1191C,G1206A,C1245 T,T1374G,C1408T,C1464T(4)
G451A,T598C,T658A,T933C,T1020C,T1191C,G1206A,C1245 T,T1374G,G1403A,C1408T,C1464T(4)
G451A,T598C,T658A,T933C,T1020C,T1191C,G1206A,C1245 T,T1374G,G1403A,C1408T,C1464T(4)
G451A,T598C,T658A,T879C,C1098T,A1172G,G1266A,C1408 T,C1464T,A1568G,G1577T,G1630A(4)
G451A,T598C,T658A,T879C,C1098T,A1172G,G1266A,C1408 T,C1464T,A1568G,G1577T,G1630A(4)
G451A,T598C,T658A,T858C,T879C,C1098T,A1172G,G1266A ,C1408T,C1464T,A1568G,G1577T,G1630A
G451A,T598C,G605A,T658A,A1172G,A1213G,G1266A,C1408 T,C1464T,G1577T,G1630A(4)
G451A,T598C,G610T,T658A,A1172G,G1266A,C1408T,C1464 T,G1577T,G1630A(4) F
G451A,G531A,T598C,T658A,C921T,A1131G,C1408T,C1464T (4)
Clade B: 340,658,1056,1171,1403,1408
G340A,G605C,T658A,T1056C,G1171A,G1403A,C1408T,T165 3C(4)
G340A,G605C,T658A,T1056C,G1171A,G1403A,C1408T,T165 3C(4)
G340A,G605C,T658A,T680C,T1056C,G1171A,G1403A,C1408 T,T1653C(4) F
G340A,G605C,C612T,T658A,T1056C,G1171A,G1403A,C1408 T,T1653C(4)
G340A,A579G,G605C,T658A,C704T,T1056C,G1171A,A1386G ,G1403A,C1408T(4)
G340A,A579G,G605C,T658A,T1056C,G1171A,A1386G,G1403 A,C1408T(4) S
G340A,A579G,G605C,T658A,T1056C,G1171A,A1386G,G1403 A,C1408T(4) S
G340A,A579G,G605C,A611G,T658A,T1056C,G1171A,A1386G ,G1403A,C1408T(4) F
G340A,A579G,G605C,T658A,A716G,T1056C,G1171A,A1386G ,G1403A,C1408T(4) S
G340A,A579G,G605C,T658A,A716G,T1056C,G1171A,A1386G ,G1403A,C1408T(4) S
Clade C: 40,207,605,658,1056,1171,1403,1408,1629
A40G,G207A,G302T,C573A,G605C,T658A,T1056C,G1171A,G 1403A,C1408T,G1629T(4)
A40G,G207A,G515R,G605C,T658A,C816T,T1056C,G1171A,G 1396A,G1403A,C1408T,G1629T(4)
A40G,G340A,A579G,G605C,T658A,C672T,T1056C,G1171A,A 1386G,G1403A,C1408T,G1624A(4)
A40G,G207A,G605C,T658A,T834A,T1056C,G1171A,G1403A, C1408T,G1473A,G1629T(4)
A40G,G207A,G605C,T658A,G832A,T1056C,G1171A,G1403A, C1408T,G1629T(4)
A40G,G207A,G605C,T658A,G1005A,T1056C,G1171A,G1403A ,C1408T,G1629T(4)
A40G,G207A,G605C,T658A,T1056C,G1171A,G1403A,C1408T ,G1629T(4) F
A40G,G207A,G605C,T658A,T1056C,G1171A,C1182T,G1403A ,C1408T,G1629T(4)
A40G,G207A,G605C,T658A,T834A,T1056C,G1171A,G1403A, C1408T,G1629T(4)
A40G,G207A,G605C,T658A,T1056C,G1171A,G1403A,C1408T ,A1435G,G1629T(4) (? F/S)
Odd Ones
C148T,G340A,A424G,A566G,T658A,G684A,C870T,T927C,G1 171A,A1230G,G1326A,C1408T,A1536G(4)
T216C,G340A,A424G,G435A,T658A,C672T,G1171A,C1408T( 4) F
T243C,G340A,A424G,C473T,T658A,G713A,A747G,G1171A,C 1408T,C1627A(4) F
C172T,G360A,A424G,T519A,T658A,G1171A,C1408T(4)
G154A,G207A,G605C,T658A,T1056C,G1171A,C1383A,G1403 A,C1408T,G1524K,G1629T(4)
T17C,G565A,T658A,A973G,G1171A,T1197C,G1395A,C1404T ,C1408T,G1524A,A1651G(4) F
G396A,G451A,G531A,T598C,T658A,A795G,C921T,A1131G,G 1407A,C1408T,C1464T,A1553G,A1579G(4)
G451A,T598C,T658A,T933C,T1020C,T1191C,G1206A,C1245 T,T1374G,C1408T,C1464T(4)
By areas
1 Coventry
4 Newcastle-upon-tyne
3 Oxford
1 Durham
2 Leeds
1 Manchester
4 Birmingham
1 Leicester
1 York
1 Cambridge (Fatal)
6 London
2 Nottingham
3 Whitechapel (2 Fatal)
1 Middlesex
1 North Yorkshire
8 Severe/fatal with no locations given
1 Possible severe/fatal no location
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