I posted the Blast below to the low reactor thread but I think this needs some discussion. N. Ireland and Perugia are so much like the early 2009 sequences that it seems like there must be an error somewhere. Gs thought maybe Perugia had been dated wrongly. Since Mill Hill was looking at N. Ireland pretty closely, a mis-date is doubtful for that one.
Is it possible for a late 2010 sequence to be almost identical to an early 2009 sample?
Here are the HA and NA mutations:
A/Northern Ireland/1/2010 2010-10-29 23
T298C(4),A517G(4),A716G(4),G891A(4),G1012A(4),
A1044G(6),
gs found this one at Genbank to compare it to; as you can see, they are almost identical in HA and are identical in NA:
A/CA/07/2009
T298C(4),G891A(4),G1012A(4)
A1044G(6)
Then I looked at Perugia and found it had strong Blast identity with '09 sequences, too
A/Perugia/1/2010 2010-11-24 19 M
T658A(4),T717A(4),C940T(4),C1408T(4),
G316A(6),A742G(6),G873A(6),A1186C(6),
gs found this one at Genbank to compare it to; again... they are so much alike:
A/Ancona/15/2009/07/17
T658A(4),T717A(4),C940T(4),C1408T(4),
G316A(6),A742G(6),G873A(6)
*********************************
34 new isolates were released at GISAID by Mill Hill today. Among those is A/Northern Ireland/1/2010 sampled on 10-29-10, noted in the Dec ECDC report to show a reduced level of reactivity with the majority of sera. It does have A517G (associated with low reactors)and A716G (D225G).
The other thing that stood out a bit with this one when I Blasted it was the close relation of the top 20 matches with the early 2009 sequences:
EPI301431 A/Northern Ireland/1/2010 (A/H1N1 swl) segment 4 (HA) 3142.3 0.00000
EPI182905 NIBRG-121 (A/California/07/2009 x PR8) (A/H1N1 swl) segment 4 (HA) 3133.0 0.00000
EPI273609 A/California/07/2009 (A/H1N1 swl) segment 4 (HA) 3131.2 0.00000
EPI243672 A/California/08/2009 (A/H1N1 swl) segment 4 (HA) 3131.2 0.00000
EPI240500 A/ENG/201/2009 (A/H1N1 swl) segment 4 (HA) 3131.2 0.00000
EPI223019 A/ENG/XFL00176/2009 (A/H1N1 swl) segment 4 (HA) 3131.2 0.00000
EPI186399 A/England/201/2009 (A/H1N1 swl) segment 4 (HA) 3131.2 0.00000
EPI185382 A/California/08/2009 (A/H1N1 swl) segment 4 (HA) 3131.2 0.00000
EPI177294 A/California/07/2009 (A/H1N1 swl) segment 4 (HA) 3131.2 0.00000
EPI177282 A/California/08/2009 (A/H1N1 swl) segment 4 (HA) 3131.2 0.00000
EPI176504 A/California/07/2009 (A/H1N1 swl) segment 4 (HA) 3131.2 0.00000
EPI176620 A/California/07/2009 (A/H1N1 swl) segment 4 (HA) 3129.3 0.00000
EPI259166 A/Hangzhou/04/2009 (A/H1N1 swl) segment 4 (HA) 3125.7 0.00000
EPI184369 A/Pennsylvania/09/2009 (A/H1N1 swl) segment 4 (HA) 3125.7 0.00000
EPI178457 A/California/04/2009 (A/H1N1 swl) segment 4 (HA) 3125.7 0.00000
EPI176470 A/California/04/2009 (A/H1N1 swl) segment 4 (HA) 3125.7 0.00000
EPI257201 A/California/07/2009 X-179A (A/H1N1 swl) segment 4 (HA) 3120.1 0.00000
EPI249806 A/reassortant/NYMC X-179A(California/07/2009 x NYMC X-157) (A/H1N1 swl) segment 4 (HA) 3120.1 0.00000
EPI225904 A/GUNMA/52/2009 (A/H1N1 swl) segment 4 (HA) 3120.1 0.00000
EPI184952 A/Kagoshima/1/2009 (A/H1N1 swl) segment 4 (HA) 3120.1 0.00000
EPI184229 A/Fukuoka-C/3/2009 (A/H1N1 swl) segment 4 (HA) 3120.1 0.00000
Is it possible for a late 2010 sequence to be almost identical to an early 2009 sample?
Here are the HA and NA mutations:
A/Northern Ireland/1/2010 2010-10-29 23
T298C(4),A517G(4),A716G(4),G891A(4),G1012A(4),
A1044G(6),
gs found this one at Genbank to compare it to; as you can see, they are almost identical in HA and are identical in NA:
A/CA/07/2009
T298C(4),G891A(4),G1012A(4)
A1044G(6)
Then I looked at Perugia and found it had strong Blast identity with '09 sequences, too
A/Perugia/1/2010 2010-11-24 19 M
T658A(4),T717A(4),C940T(4),C1408T(4),
G316A(6),A742G(6),G873A(6),A1186C(6),
gs found this one at Genbank to compare it to; again... they are so much alike:
A/Ancona/15/2009/07/17
T658A(4),T717A(4),C940T(4),C1408T(4),
G316A(6),A742G(6),G873A(6)
*********************************
34 new isolates were released at GISAID by Mill Hill today. Among those is A/Northern Ireland/1/2010 sampled on 10-29-10, noted in the Dec ECDC report to show a reduced level of reactivity with the majority of sera. It does have A517G (associated with low reactors)and A716G (D225G).
The other thing that stood out a bit with this one when I Blasted it was the close relation of the top 20 matches with the early 2009 sequences:
EPI301431 A/Northern Ireland/1/2010 (A/H1N1 swl) segment 4 (HA) 3142.3 0.00000
EPI182905 NIBRG-121 (A/California/07/2009 x PR8) (A/H1N1 swl) segment 4 (HA) 3133.0 0.00000
EPI273609 A/California/07/2009 (A/H1N1 swl) segment 4 (HA) 3131.2 0.00000
EPI243672 A/California/08/2009 (A/H1N1 swl) segment 4 (HA) 3131.2 0.00000
EPI240500 A/ENG/201/2009 (A/H1N1 swl) segment 4 (HA) 3131.2 0.00000
EPI223019 A/ENG/XFL00176/2009 (A/H1N1 swl) segment 4 (HA) 3131.2 0.00000
EPI186399 A/England/201/2009 (A/H1N1 swl) segment 4 (HA) 3131.2 0.00000
EPI185382 A/California/08/2009 (A/H1N1 swl) segment 4 (HA) 3131.2 0.00000
EPI177294 A/California/07/2009 (A/H1N1 swl) segment 4 (HA) 3131.2 0.00000
EPI177282 A/California/08/2009 (A/H1N1 swl) segment 4 (HA) 3131.2 0.00000
EPI176504 A/California/07/2009 (A/H1N1 swl) segment 4 (HA) 3131.2 0.00000
EPI176620 A/California/07/2009 (A/H1N1 swl) segment 4 (HA) 3129.3 0.00000
EPI259166 A/Hangzhou/04/2009 (A/H1N1 swl) segment 4 (HA) 3125.7 0.00000
EPI184369 A/Pennsylvania/09/2009 (A/H1N1 swl) segment 4 (HA) 3125.7 0.00000
EPI178457 A/California/04/2009 (A/H1N1 swl) segment 4 (HA) 3125.7 0.00000
EPI176470 A/California/04/2009 (A/H1N1 swl) segment 4 (HA) 3125.7 0.00000
EPI257201 A/California/07/2009 X-179A (A/H1N1 swl) segment 4 (HA) 3120.1 0.00000
EPI249806 A/reassortant/NYMC X-179A(California/07/2009 x NYMC X-157) (A/H1N1 swl) segment 4 (HA) 3120.1 0.00000
EPI225904 A/GUNMA/52/2009 (A/H1N1 swl) segment 4 (HA) 3120.1 0.00000
EPI184952 A/Kagoshima/1/2009 (A/H1N1 swl) segment 4 (HA) 3120.1 0.00000
EPI184229 A/Fukuoka-C/3/2009 (A/H1N1 swl) segment 4 (HA) 3120.1 0.00000
