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strange sequences from Helsinki, 2013
similar to the vaccine strain from 1997 in some segments
but that's not all. Swine triple reassortant,
some segments like temporary seasonal flu, others (8)
just distant to any H3N2
closest neighbors from my list of human and swine H3N2-viruses:
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http://www.ncbi.nlm.nih.gov/nuccore/KF805680
Submitted (05-NOV-2013) Institute for Molecular Medicine Finland
(FIMM), P.O. Box 20, Helsinki, Uusimaa FI-00014, Finland
Assembly Method :: Interactive Genome Viewer IGV v. 2.0
Sequencing Technology :: Illumina
nasopharyngeal swab"
/country="Finland: Helsinki"
/collection_date="26-Feb-2013"
/note="passage details: MDCK 4"
--------------------------------------------------------------
looking at segment 8 ... it's so different from any other known segment 8
best match in flu,segment 8,full length,outside Helsinki is Texas,H1N1,Dec.2012
with 56(!) differences, the ****** index has 63 differences, 1918 Spainflu has
120 differences. The differences are not concentrated in some region
as in recombination, but scattered through the whole 838 nucleotides
of the coding region of segment 8.
The best explanation that I can find is, that they have some systematic error
that produces incorrect mutations, some severe confusion/mixing maybe, with
other sequences from the same run.
makes the other segments also dubitious, Sydney/1997
----------------------------------------------
genbank classifies these 11 Finnish H3N2-segments as pH1N1=******:
(thus making it H3N2-H1N1 reassortments)
8 times segment 2, 2 times segment 8, 1 time segment 7
>KF805634,A/Helsinki/716/2013,2013/02/16,Finland,H3N2,Human,2
>KF805636,A/Helsinki/716/2013,2013/02/16,Finland,H3N2,Human,8
>KF805642,A/Helsinki/798/2013,2013/02/20,Finland,H3N2,Human,2
>KF805650,A/Helsinki/823/2013,2013/02/21,Finland,H3N2,Human,2
>KF805658,A/Helsinki/824/2013,2013/02/21,Finland,H3N2,Human,2
>KF805674,A/Helsinki/897/2013,2013/02/26,Finland,H3N2,Human,2
>KF805676,A/Helsinki/897/2013,2013/02/26,Finland,H3N2,Human,8
>KF805679,A/Helsinki/897/2013,2013/02/26,Finland,H3N2,Human,7
>KF805682,A/Helsinki/941/2013,2013/02/27,Finland,H3N2,Human,2
>KF805690,A/Helsinki/942/2013,2013/02/27,Finland,H3N2,Human,2
>KF805706,A/Helsinki/991/2013,2013/03/02,Finland,H3N2,Human,2
similar to the vaccine strain from 1997 in some segments
but that's not all. Swine triple reassortant,
some segments like temporary seasonal flu, others (8)
just distant to any H3N2
closest neighbors from my list of human and swine H3N2-viruses:
Code:
30 >KF805633,A/Helsinki/716/2013,2013/02/16,Finland,H3N2 6: 27, 57, 13, 0, 4, 3, 57,129 A/Sydney/5/1997,1997//,Australia,H3N2 16:134, 37,158, 39,164, 16,120, 77 A/Sw/Index/triple-reassortant/1998(H3N2) 26: 53, 75, 31, 62, 33, 51, 51,137 Index/32g12f1.c2,10-37 31 >KF805641,A/Helsinki/798/2013,2013/02/20,Finland,H3N2 6: 24, 57, 17, 0, 15, 3, 40,107 A/Sydney/5/1997,1997//,Australia,H3N2 16:136, 37,157, 39,169, 16,111, 97 A/Sw/Index/triple-reassortant/1998(H3N2) 26: 49, 75, 32, 62, 27, 51, 31,103 Index/32g12f1.c2,10-37 32 >KF805649,A/Helsinki/823/2013,2013/02/21,Finland,H3N2 6: 37, 53, 46, 2, 35, 7, 27, 88 A/Sydney/5/1997,1997//,Australia,H3N2 16:130, 36,149, 41,172, 20,111,116 A/Sw/Index/triple-reassortant/1998(H3N2) 25: 53, 71, 36, 59, 8, 47, 22, 87 A/Czech Republic/121/2012,2012/03/06,Czech Republic 13: 49, 68, 38, 51, 9, 44, 23, 87 Index/2009/Egypt/Iowa 11: 47, 65, 42, 45, 12, 39, 22, 83 Index/Brisbane-like/2007 26: 54, 71, 36, 61, 9, 48, 21, 90 Index/32g12f1.c2,10-37 33 >KF805657,A/Helsinki/824/2013,2013/02/21,Finland,H3N2 25: 11, 61, 10, 14, 4, 4, 22, 13 A/Czech Republic/121/2012,2012/03/06,Czech Republic 16:152, 35,162, 90,176, 53,111,162 A/Sw/Index/triple-reassortant/1998(H3N2) 26: 11, 61, 10, 11, 5, 4, 19, 14 Index/32g12f1.c2,10-37 11: 17, 55, 18, 27, 9, 16, 20, 10 Index/Brisbane-like/2007 34 >KF805665,A/Helsinki/879/2013,2013/02/24,Finland,H3N2 26: 6, 2, 6, 3, 4, 4, 0, 2 Index/32g12f1.c2,10-37 25: 6, 3, 5, 6, 3, 4, 3, 3 A/Czech Republic/121/2012,2012/03/06,Czech Republic 35 >KF805673,A/Helsinki/897/2013,2013/02/26,Finland,H3N2 6: 39, 54, 14, 0, 0, 0, 77,119 A/Sydney/5/1997,1997//,Australia,H3N2 16:124, 34,159, 39,168, 14,130, 88 A/Sw/Index/triple-reassortant/1998(H3N2) 25: 60, 72, 32, 61, 32, 53, 69,122 A/Czech Republic/121/2012,2012/03/06,Czech Republic 36 >KF805681,A/Helsinki/941/2013,2013/02/27,Finland,H3N2 6: 25, 54, 29, 7, 30, 21, 31, 79 A/Sydney/5/1997,1997//,Australia,H3N2 5: 41, 53, 42, 38, 37, 45, 35, 81 1989//,7852,CHN,A/Beijing/353/89 26: 36, 72, 27, 59, 14, 34, 27, 78 Index/32g12f1.c2,10-37 25: 35, 72, 28, 58, 13, 33, 28, 77 A/Czech Republic/121/2012,2012/03/06,Czech Republic 10: 33, 67, 29, 45, 16, 39, 30, 73 2007/02/06,14278,AUS,A/Brisbane/10/07 37 >KF805689,A/Helsinki/942/2013,2013/02/27,Finland,H3N2 25: 12, 67, 6, 26, 4, 7, 16, 30 A/Czech Republic/121/2012,2012/03/06,Czech Republic 16:151, 35,163, 79,176, 50,109,151 A/Sw/Index/triple-reassortant/1998(H3N2) 26: 12, 68, 7, 24, 5, 7, 13, 32 Index/32g12f1.c2,10-37 11: 17, 62, 15, 34, 9, 17, 14, 28 Index/Brisbane-like/2007 38 >KF805697,A/Helsinki/951/2013,2013/03/01,Finland,H3N2 26: 3, 1, 6, 7, 5, 5, 2, 3 Index/32g12f1.c2,10-37 ------------------------------------------------------ 40 >A/******/index/2009/02/01 2280 2274 2151 1701 1497 1410 982 838 30:135, 7,155,722,168,630, 89, 63 KF805633,A/Helsinki/716/2013,2013/02/16,Finland,H3N2 31:137, 7,153,722,171,630,108, 91 KF805641,A/Helsinki/798/2013,2013/02/20,Finland,H3N2 32:129, 9,142,721,174,629,110,106 KF805649,A/Helsinki/823/2013,2013/02/21,Finland,H3N2 33:154, 15,162,714,180,632,116,175 KF805657,A/Helsinki/824/2013,2013/02/21,Finland,H3N2 34:159, 67,168,717,178,632,130,189 KF805665,A/Helsinki/879/2013,2013/02/24,Finland,H3N2 35:123, 4,155,722,171,630, 69, 75 KF805673,A/Helsinki/897/2013,2013/02/26,Finland,H3N2 36:143, 6,151,719,172,628,106,113 KF805681,A/Helsinki/941/2013,2013/02/27,Finland,H3N2 37:154, 8,164,715,180,632,122,159 KF805689,A/Helsinki/942/2013,2013/02/27,Finland,H3N2 38:160, 69,164,713,180,633,132,188 KF805697,A/Helsinki/951/2013,2013/03/01,Finland,H3N2 39:156, 29,167,717,178,631,126,181 KF805705,A/Helsinki/991/2013,2013/03/02,Finland,H3N2
http://www.ncbi.nlm.nih.gov/nuccore/KF805680
Submitted (05-NOV-2013) Institute for Molecular Medicine Finland
(FIMM), P.O. Box 20, Helsinki, Uusimaa FI-00014, Finland
Assembly Method :: Interactive Genome Viewer IGV v. 2.0
Sequencing Technology :: Illumina
nasopharyngeal swab"
/country="Finland: Helsinki"
/collection_date="26-Feb-2013"
/note="passage details: MDCK 4"
--------------------------------------------------------------
looking at segment 8 ... it's so different from any other known segment 8
best match in flu,segment 8,full length,outside Helsinki is Texas,H1N1,Dec.2012
with 56(!) differences, the ****** index has 63 differences, 1918 Spainflu has
120 differences. The differences are not concentrated in some region
as in recombination, but scattered through the whole 838 nucleotides
of the coding region of segment 8.
The best explanation that I can find is, that they have some systematic error
that produces incorrect mutations, some severe confusion/mixing maybe, with
other sequences from the same run.
makes the other segments also dubitious, Sydney/1997
----------------------------------------------
genbank classifies these 11 Finnish H3N2-segments as pH1N1=******:
(thus making it H3N2-H1N1 reassortments)
8 times segment 2, 2 times segment 8, 1 time segment 7
>KF805634,A/Helsinki/716/2013,2013/02/16,Finland,H3N2,Human,2
>KF805636,A/Helsinki/716/2013,2013/02/16,Finland,H3N2,Human,8
>KF805642,A/Helsinki/798/2013,2013/02/20,Finland,H3N2,Human,2
>KF805650,A/Helsinki/823/2013,2013/02/21,Finland,H3N2,Human,2
>KF805658,A/Helsinki/824/2013,2013/02/21,Finland,H3N2,Human,2
>KF805674,A/Helsinki/897/2013,2013/02/26,Finland,H3N2,Human,2
>KF805676,A/Helsinki/897/2013,2013/02/26,Finland,H3N2,Human,8
>KF805679,A/Helsinki/897/2013,2013/02/26,Finland,H3N2,Human,7
>KF805682,A/Helsinki/941/2013,2013/02/27,Finland,H3N2,Human,2
>KF805690,A/Helsinki/942/2013,2013/02/27,Finland,H3N2,Human,2
>KF805706,A/Helsinki/991/2013,2013/03/02,Finland,H3N2,Human,2