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H3N2, 1976

gsgs

gsgs

Registered User
I just noticed this one, I hadn't examined H3N2 before.

-:not available or alignment-gaps
.:match
o:difference

A/Hong Kong/1/68(H3N2) PB1
A/Memphis/104/1976(H3N2) PB1

Code: 
------------------------------.............................
......o..o........o...........-...o.....o..o...........o....
.......o....................................................
..........o........o..o.................o..o........o.......
.o.....o............o.............o........o................
.o.....oo.............o.....................................
.o...o......................o........o.....o.o..............
.o...........o.....o..o..o.....o........o........o..o.......
.......o...........o..o...........o.....o.....o..o..........
.......o...........o..............o........o...........o....
.o.....o...........o..............o.........................
.o..............oo....o.....o.....oo.o...........o..oo......
.......o.................o.....o.....oo.o..o.....o........o.
....o.....o..o..o.................o.....o..o.....o.....o....
....o..o........o..o........o.....o........o.....o.....o..o.
......................o.....o...........o..o................
.o..o...........o.....o..............oo....o.....o.....o....
...o...o..............o.....o..oo....o..o..o..o..o..........
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.......o.................o.......--.........................
..................o..........................-------o......-
-------......................-----.......--.................
...............................o.................o..........
........o.....................o.............................
.o................-.......----------------------------------
--


A/Kiev/59/1979(H1N1),PB1
A/Memphis/104/1976(H3N2),PB1
Code: 
------------------------------.............................
.o....o..o..o.....o...........-...o.....o..o...........o....
.......o....................................................
..........o........o..o..........................o..o.......
.o..................o.............o........o................
.o.....oo.......o.....o........o............................
.o...o.......o..............o........o.....o.o......o.......
.o...........o.....oo.o..o.....o........o........o..o.......
.......o..o........o..o...........o.....o.....o..o..........
...................o..............o.....o..o...........o....
.o.....o...........o..............o.........................
.o.....o........oo....o.....o.....oo.o...........o..oo......
.......o.................o.....o.....oo....o.....o........o.
....o.....o..o..o.................o.....o..o.....o.....o....
....o..o........o..o........o.....o........o.....o.....o..o.
....o.................o.....o...........o..o................
.o..o..o........o.....o..............oo....o.....o.....o....
...o...o..............o.....oo..o....o..o..o..o..o..........
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..................o..........................-------o......-
-------......................-----.......--.................
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..................-.......----------------------------------
--


A/Memphis/104/1976(H3N2) , PB1
A/chicken/Dubai/338/2001(H9N2) , PB1

Code: 
-----------------------------------------------------------
-------------.................-.............................
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....o.......................................................
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...............................o............................
.....o......................................................
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.......o...............o.............................o.o....
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....o..............o........................................
.o.................o........................................
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......................o..o.o.......o.o..o..o..............o.
..........o...........o.....o...........o.....o.....o.......
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....o..o..........................o..o...........o........o.
....o..o.....o..oo.o..o..o..............o........o..o......o
.......o........o..............o..o....................o..o.
......................o........o.....o..o..o................
....o...........o.....o..............o..o..............o....
..........o..o........o.....o..o..o.....o.........o.o..o....
..........o......................................o.....o..o.
..........o...o..........o..o......o.o.................o....
....o..o.................o........o..o..o..o.....o.....o....
.......o.....o........o.....o..o.....o..o...............o...
.......o.............................o..o.....o........o..o.
....o..o........o..o..o........o.--.o.......................
............o.....o........o..o..o........o..-------o......-
-------..............o..o....-----.......--o........o.......
.......o........o.....o..oo...................oo.o..........
.......oo.o...................o.............................
.o................-.......----------------------------------
--
 
Re: H3N2, 1976

no, just working on my programs and updating my databases.
Most evident recombination in my PB1-database (all serotypes)

I found some laboratory work on recombination in 1976
(=swineflu-year) and even laws about it from that year,
so is it maybe a descendant or relative from a laboratory strain ?
 
Re: H3N2, 1976

here is it again, but even clearer now and with the referrences.
Looks as if A/Memphis/104/1976 was created in the laboratory
by recombination of A/Memphis/103/1976 with another unpublished strain,
which was frozen and somehow reintroduced into Dubai in 2000.

edit: well, more likely IMO that they submitted the Dubai and the Memphis
sequences together last year and somehow mixed it up.


http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=CY006889
http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=CY012198
http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=EF063531

Code: 
>A/Memphis/103/1976(H3N2) segment 2
------------CAAACCATTTGAATGGATGTCAATCCGACTTTACTTTTCTTGAAAGTTCCAGCGCAAAATGCCATAAGCACCACATTCCCTTATACTGGAGATCCTCCATACAGCCATGGAACAGGAACAGGATACACCATGGACACAGTCAACAGAACACATCAATATTCAGAAAAAGGGAAGTGGACAACAAACACAGAGACTGGGGCGCCCCAACTTAACCCAATTGATGGACCACTACCTGAGGATAATGAGCCAAGCGGATATGCACAAACAGACTGTGTCCTGGAAGCAATGGCTTTCCTTGAAGAATCCCACCCAGGGATTTTTGAAAACTCGTGCCTTGAAACGATGGAAGTCGTTCAACAAACAAGGGTGGACAAACTGACCCAAGGTCGTCAGACCTATGACTGGACATTAAACAGAAATCAACCGGCCGCAACTGCATTAGCCAACACTATAGAAGTCTTCAGATCGAATGGTCTAACAGCTAATGAGTCGGGAAGGCTAATAGATTTCCTCAAGGATGTGATGGAATCAATGGATAAAGAGGAAATGGAGATAACAACACACTTCCAAAGAAAAAGAAGAGTAAGAGACAACATGACCAAGAAAATGGTCACACAAAGAACAATAGGAAAGAAGAAGCAGAGAGTGAACAAGAGAAGCTATCTAATAAGAGCATTAACATTGAACACAATGACCAAAGATGCAGAAAGAGGTAAATTAAAGAGAAGAGCTATTGCAACACCCGGGATGCAAATCAGAGGGTTCGTGTACTTTGTTGAAACTCTAGCTAGGAGCATTTGTGAGAAGCTTGAACAGTCTGGACTTCCAGTTGGAGGTAATGAAAAGAAGGCCAAACTGGCAAATGTTGTGAGAAAGATGATGACTAATTCACAAGACACAGAGCTTTCTTTCACAATTACTGGAGACAATACTAAGTGGAATGAAAATCAAAATCCTCGAATGTTCCTGGCGATGATTACATATATCACAAAAAATCAACCTGAATGGTTCAGAAACATTCTGAGCATCGCACCCATAATGTTCTCAAACAAAATGGCGAGACTAGGGAAAGGATACATGTTCGAAAGTAAGAGAATGAAGCTCCGAACACAAATACCAGCAGAAATGCTAGCAAGCATTGACCTAAAGTATTTCAATGAATCAACAAGAAAGAAAATTGAGAAAATAAGGCCTCTTCTAATAGATGGTACAGCGTCATTGAGTCCTGGAATGATGATGGGCATGTTCAACATGCTAAGTACGGTTTTAGGAGTCTCAATCCTGAATCTTGGGCAAAAGAAATACACCAAAACAACATACTGGTGGGATGGACTCCAATCTTCTGATGATTTTGCTCTCATAGTGAATGCACCAAATCATGAGGGGATACAAGCAGGAGTGGATAGATTCTACAGAACCTGCAAGTTAGTCGGAATCAATATGAGCAAGAAGAAGTCCTATATAAATAGAACAGGAACATTTGAATTCACAAGCTTTTTTTACCGCTATGGATTTGTAGCCAATTTTAGTATGGAGCTGCCCAGTTTTGGGGTGTCTGGAATTAATGAGTCAGCTGATATGAGCATTGGAGTAACAGTGATAAAGAACAACATGATAAACAATGACCTAGGACCAGCAACAGCCCAGATGGCTCTTCAACTGTTCATCAAAGACTACAGATATACATATCGGTGCCACAGAGGAGACACACAAATTCAGACGAGGAGATCATTCGAGCTAAAGAAGCTGTGGGAGCAAACCCGCTCAAAGGCAGGACTATTGGTTTCAGATGGAGGGCCAAACTTATACAATATCCGGAATCTTCACATCCCTGAAGTCTGCTTGAAGTGGGAGCTAATGGATGAGGACTATCAGGGAAGACTTTGTAATCCTCTGAATCCATTTGTCAGCCATAAGGAGATTGAATCTGTAAACAATGCTGTGATAATGCCAGCTCATGGTCCAGCCAAGAGCATGGAATATGACGCTGTTGCAACTACACACTCCTGGATTCCCAAGAGGAACCGCTCTATTCTCAACACAAGCCAAAGGGGAATTCTTGAGGATGAACAGATGTATCAGAAATGCTGCAACCTGTTCGAGAAATTTTTTCCCAGTAGTTCATACAGGAGACCGGTTGGAATTTCCAGCATGGTGGAGGCCATGGTGTCTAGGGCCCGGATTGATGCCAGAATTGACTTCGAGTCTGGACGAATTAAGAAAGAAGAGTTCTCCGAGATCATGAAGATCTGTTTCACCATTGAAGAGCTCAGACGGCAAAAATAATGAATTTAGCTTGTCCTTCATGA------------------
>A/Memphis/104/1976(H3N2) segment 2
------------CAAACCATTTGAATGGATGTCAATCCGACTTTACTCTTTTTGAAAGTGCCAGCGCAAAATGCTATAAGTACTACATTCCCTTACACTGGAGATCCCCCATACAGCCATGGAACAGGAACAGGATACACCATGGACACAGTCAACAGAACACATCAATACTCAGAAAAGGGAAAGTGGACAACAAACACAGAGACTGGAGCACCCCAACTCAACCCGATTGATGGACCATTACCTGAGGATAACGAGCCAAGCGGATATGCACAAACAGATTGTGTGTTGGAAGCAATGGCCTTCCTTGAAGAATCCCACCCAGGGATCTTTGAAAACTCATGTATTGAAACGATGGAAGTTGTTCAGCAAACAAGAGTGGATAAACTGACCCAAGGTCGCCAGACCTATGACTGGACTTTGAATAGAAACCAACCGGCTGCAACTGCTTTGGCCAACACTATAGAGGTCTTCAGATCTAACGGTCTAACAGCCAATGAATCGGGGAGACTAATAGATTTCCTCAAGGATGTGATGGAGTCAATGGATAAAGAAGAAATGGAAATAACAACACATTTCCAGAGAAAGAGAAGAGTAAGGGACAACATGACCAAAAAAATGGTCACACAAAGAACAATAGGGAAGAAGAAGCAGAGGCTGAATAAGAGGAGCTACTTGATAAGAGCATTGACCCTGAACACAATGACAAAAGATGCAGAAAGAGGCAAATTGAAGAGGCGGGCAATTGCTACACCCGGAATGCAGATCAGGGGATTTGTGTACTTTGTTGAAACGCTAGCGAGAAGCATCTGTGAAAAGCTTGAGCAATCTGGACTCCCGGTTGGAGGGAATGAGAAGAAGGCTAAACTAGCAAACGTCGTGAGAAAGATGATGACTAATTCTCAAGATACAGAGCTTTCCTTTACAATTACTGGAGACAACACCAAATGGAATGAGAATCAGAATCCTCGAATGTTTATGGCAATGATAACATACATCACAAGAAACCAACCTGAATGGTTTAGAAATGTCTTGAGTATTGCCCCTATCATGTTCTCAAACAAGATGGCGAGATTAGGAAAAGGATACATGTTCGAAAGTAAGAGAATGAAGCTCCGAACACAAATACCAGCAGAAATGCTAGCAAGCATTGACCTAAAGTATTTCAATGAATCAACAAGAAAGAAAATTGAGAAAATAAGGCCTCTTCTAATAGATGGTACAGCGTCATTGAGTCCTGGAATGATGATGGGCATGTTCAACATGCTAAGTACGGTTTTAGGAGTCTCAATCCTGAATCTTGGGCAAAAGAAATACACCAAAACAACATACTGGTGGGATGGACTCCAATCTTCTGATGATTTTGCTCTCATAGTGAATGCACCAAATCATGAGGGGATACAAGCAGGAGTGGATAGATTCTACAGAACCTGCAAGTTAGTCGGAATCAATATGAGCAAGAAGAAGTCCTATATAAATAGAACAGGAACATTTGAATTCACAAGCTTTTTTTATCGCTATGGATTTGTAGCCAATTTTAGTATGGAGCTGCCCAGTTTTGGGGTGTCTGGAATTAATGAGTCAGCTGATATGAGCATTGGAGTAACAGTGATAAAGAACAACATGATAAACAATGACCTAGGACCAGCAACAGCCCAGATGGCTCTTCAACTGTTCATCAAAGACTACAGATATACATATCGGTGCCACAGAGGAGACACACAAATTCAGACGAGGAGATCATTCGAGCTAAAGAAGCTGTGGGAGCAAACCCGCTCAAAGGCAGGACTATTGGTTTCAGATGGAGGGCCAAACTTATACAATATCCGGAATCTTCACATCCCTGAAGTCTGCTTGAAGTGGGAGCTAATGGATGAGGACTATCAGGGAAGACTTTGTAATCCTCTGAATCCATTTGTCAGCCATAAGGAGATTGAATCTGTAAACAATGCTGTGATAATGCCAGCTCATGGTCCAGCCAAGAGCATGGAATATGACGCTGTTGCAACTACACACTCCTGGATTCCCAAGAGGAACCGCTCTATTCTCAACACAAGCCAAAGGGGAATTCTTGAGGATGAACAGATGTATCAGAAATGCTGCAACCTGTTCGAGAAATTTTTTCCCAGTAGTTCATACAGGAGACCGGTTGGAATTTCCAGCATGGTGGAGGCCATGGTGTCTAGGGCCCGGATTGATGCCAGAATTGACTTCGAGTCTGGACGAATTAAGAAAGAAGAGTTCTCCGAGATCATGAAGATCTGTTTCACCATTGAAGAGCTCAGACGGCAAAAATAATGAATTTAGCTTGTCCTTCATGA------------------
>A/quail/Dubai/301/2000(H9N2) segment 2
AGCGAAAGCAGGCAAACCATTTGAATGGATGTCAATCCGACTTTACTCTTTTTGAAAGTGCCAGCGCAAAATGCTATAAGTACTACATTCCCTTACACTGGAGATCCCCCATACAGCCATGGAACAGGAACAGGATACACCATGGACACAGTCAACAGAACACATCAATACTCAGAAAAGGGAAAGTGGACAACAAACACAGAGACTGGAGCACCCCAACTCAACCCGATTGATGGACCATTACCTGAGGATAACGAGCCAAGCGGATATGCACAAACAGATTGTGTGTTGGAAGCAATGGCCTTCCTTGAAGAATCCCACCCAGGGATCTTTGAAAACTCATGTATTGAAACGATGGAAGTTGTTCAGCAAACAAGAGTGGATAAACTGACCCAAGGTCGCCAGACCTATGACTGGACTTTGAATAGAAACCAACCGGCTGCAACTGCTTTGGCCAACACTATAGAGGTCTTCAGATCTAACGGTCTAACAGCCAATGAATCGGGGAGACTAATAGATTTCCTCAAGGATGTGATGGAGTCAATGGATAAAGAAGAAATGGAAATAACAACACATTTCCAGAGAAAGAGAAGAGTAAGGGACAACATGACCAAAAAAATGGTCACACAAAGAACAATAGGGAAGAAGAAGCAGAGGCTGAATAAGAGGAGCTACTTGATAAGAGCATTGACCCTGAACACAATGACAAAAGATGCAGAAAGAGGCAAATTGAAGAGGCGGGCAATTGCTACACCCGGAATGCAGATCAGGGGATTTGTGTACTTTGTTGAAACGCTAGCGAGAAGCATCTGTGAAAAGCTTGAGCAATCTGGACTCCCGGTTGGAGGGAATGAGAAGAAGGCTAAACTAGCAAACGTCGTGAGAAAGATGATGACTAATTCTCAAGATACAGAGCTTTCCTTTACAATTACTGGAGACAACACCAAATGGAATGAGAATCAGAATCCTCGAATGTTTATGGCAATGATAACATACATCACAAGAAACCAACCTGAATGGTTTAGAAATGTCTTGAGTATTGCCCCTATCATGTTCTCAAACAAGATGGCGAGATTAGGAAAAGGATACATGTTCGAGAGTAAGAGTATGAAACTGCGGACACAAATACCAGCAGAAATGCTTGCAAACATTGACTTGAAATACTTCAATGAATCAACGAGAAAGAAAATAGAGAAAATAAGACCTCTCCTAATAGATGGCACAGCATCATTGAGTCCTGGAATGATGATGGGCATGTTCAACATGCTGAGCACCGTTTTAGGAGTCTCAATTCTGAACCTTGGGCAAAAGAGATACACCAAAACCACGTACTGGTGGGATGGACTCCAATCCTCTGATGATTTCGCCCTCATAGTGAATGCACCAAATCATGAAGGAATACAAGCAGGGGTGGATAGGTTCTATAGGACCTGTAAACTGGTTGGGATCAATATGAGCAAAAAGAAGTCTTACATAAATCGAACAGGGACATTTGAGTTCACAAGCTTTTTCTACCGCTATGGATTTGTAGCCAACTTCAGTATGGAGCTGCCCAGTTTTGGAGTGTCTGGGATTAACGAATCGGCTGATATGAGCATTGGAGTCACAGTGATAAAAAACAATATGATAAACAATGATCTTGGACCAGCAACAGCTCAGATGGCTCTTCAGCTATTCATCAAGGACTATAGGTACACATACCGATGCCACCGGGGTGACACCCAAATTCAAACGAGGAGATCATTCGAGCTAAAGAAGCTGTGGGAGCAGACCCGTTCGAAGGCAGGACTGTTGGTTTCAGATGGGGGACCAAACCTGTACAATATCCGGAATCTCCACATCCCAGAGGTCTGCTTGAAGTGGGAACTAATGGACGAAGATTACCAGGGCAGACTGTGTAATCCTCTTAATCCGTTTGTCAGTCATAAAGAAATTGAGTCCGTAAACAATGCTGTGGTAATGCCAGCCCATGGTCCAGCCAAGAGCATGGAATATGATGCCGTTGCCACTACACATTCATGGATCCCTAAGAGGAATCGTTCCATTCTCAATACTAGCCAAAGGGGAATTCTTGAGGATGAACAGGTGTACCAGAAGTGCTGCAATCTATTTGAGAAATTCTTCCCCAGTAGTTCATACAGGAGGCCAGTTGGAATTTCCAGCATGGTAGAGGCCATGGTGTCGAGGGCCCGAATTGACGCACGAATTGACTTCGAGTCTGGAAGGATTAAGAAAGAAGAGTTTGCTGAGATCATGAAGATCTGTTCCACCATTGAAGAGCTCAGACGGCAAAAATAGTGAATTTAGCTTGTCCTTCATGAAAAAATGCCTTGTTTCTA

-:not both available
.:match
o:difference



Code: 
>A/Memphis/103/1976(H3N2) segment 2
>A/Memphis/104/1976(H3N2) segment 2
------------...................................o..o........o
..............o.....o..o...........o...........o............
..................................................o........o
..o..........................o..o........o.....o............
o.............o..........................o.....oo...........
..o..........................o...........o..oo..............
..o.....o........o.....o.................o.................o
..o..o.....o........o........o..o..............o...........o
..o...........o.....o.....o..o.............................o
..............o........o...........o.....o.....o...........o
..............o..........................o..............oo..
..o.....o.....oo.o...........o..oo.............o............
.....o.....o.....oo.o..o.....o........o.....o.....o..o..o...
..............o.....o..o.....o.....o........o..o........o..o
........o.....o........o.....o.....o..o.....................
..o.....o...........o..o.................o..o..o........o...
..o..............oo....o.....o.....o.......o...o............
..o.....oo.oo....o..o..o..o..o..............o.........o....o
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.........................................-------------------
-
>A/Memphis/103/1976(H3N2) segment 2
>A/quail/Dubai/301/2000(H9N2) segment 2
------------...................................o..o........o
..............o.....o..o...........o...........o............
..................................................o........o
..o..........................o..o........o.....o............
o.............o..........................o.....oo...........
..o..........................o...........o..oo..............
..o.....o........o.....o.................o.................o
..o..o.....o........o........o..o..............o...........o
..o...........o.....o.....o..o.............................o
..............o........o...........o.....o.....o...........o
..............o..........................o..............oo..
..o.....o.....oo.o...........o..oo.............o............
.....o.....o.....oo.o..o.....o........o.....o.....o..o..o...
..............o.....o..o.....o.....o........o..o........o..o
........o.....o........o.....o.....o..o.....................
..o.....o...........o..o.................o..o..o........o...
..o..............oo....o.....o.....o.......o...o............
..o.....oo.oo....o..o..o..o..o..............o.........o....o
.................o........o.....o..o..o.....................
..o....o.......o.o..o..o..............o...........o.........
..o.....o...........o.....o.................................
........o..o..o.................o.....o.............o.......
.....o..o.......................o...........o..o............
..............o..o...........o........o.....o..o.....o..oo.o
..o..o..............o........o..o......o.......o........o...
...........o.......................o..o.....................
..o........o.....o..o..o....................o...........o...
..o..............o..o..............o..............o..o......
..o.....o..o..o.....o..o......o.o..o.....o........o.........
.............................o.....o..o...........o.........
.....o..o......o.o.................o........o..o............
.....o........o..o..o..o.....o.....o...........o.....o......
..o.....o..o.....o..o...............o..........o............
.................o..o.....o........o..o.....o..o........o..o
..o........o..o..............................o....o.....o...
.....o..o..o........o..o....................o..o............
........o..............o........o.....o..oo.................
...o.o.................oo.o...................o.............
.................o.......................-------------------
-
>A/Memphis/104/1976(H3N2) segment 2
>A/quail/Dubai/301/2000(H9N2) segment 2
------------................................................
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.................o........o.....o..o..o.....................
..o....o.......o.o..o..o..............o...........o.........
..o.....o...........o.....o.................................
........o..o..o.................o.....o.............o.......
.....o..o.......................o...........o..o............
..............o..o...........o........o.....o..o.....o..oo.o
..o..o..............o........o..o......o.......o........o...
...........o..o....................o..o.....................
..o........o.....o..o..o....................o...........o...
..o..............o..o..............o..............o..o......
..o.....o..o..o.....o..o......o.o..o.....o........o.........
.............................o.....o..o...........o.........
.....o..o......o.o.................o........o..o............
.....o........o..o..o..o.....o.....o...........o.....o......
..o.....o..o.....o..o...............o..........o............
.................o..o.....o........o..o.....o..o........o..o
..o........o..o..............................o....o.....o...
.....o..o..o........o..o....................o..o............
........o..............o........o.....o..oo.................
...o.o.................oo.o...................o.............
.................o.......................-------------------
-
 
Last edited:
Re: H3N2, 1976

sequences retracted now.

" The sample provider was unable to confirm the source of this sample.
The sequences associated with this virus are therefore suppressed in
GenBank now."
 
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