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INFLUENZA A (H1N1) "SWINE FLU": WORLDWIDE (04)
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A ProMED-mail post
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International Society for Infectious Diseases
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[1]
Date: Tue 28 Apr 2009
From: Raul Rabadan
<rabadan@dbmi.columbia.edu>
In relation to the questions posed by Prof. Morris [see: Influenza A
(H1N1) "swine flu": worldwide (03) archived as 20090428.1600]: My
group and I are analyzing the recent sequences from the isolates in
Texas and California of swine H1N1 deposited in National Center for
Biotechnology Information (NCBI) (A/California/ 04/2009(H1N1),
A/California/05/2009(H1N1), A/California/ 06/2009(H1N1),
A/California/07/2009(H1N1), A/California/ 09/2009(H1N1),
A/Texas/04/2009(H1N1) and A/Texas/05/2009(H1N1).
The preliminary analysis using all the sequences in public databases
(NCBI) suggests that all segments are of swine origin. NA and MP seem
related to Asian/European swine and the rest to North American swine
(H1N2 and H3N2 swine viruses isolated since 1998). There is also
interesting substratification between these groups, suggesting a
multiple reassortment.
We are puzzled about sources of information that affirm that the
virus is a reassortment of avian, human and swine viruses. It is true
that the H3N2 swine virus from 1998 and 1999 is a triple reassortant,
but all the related isolates are found since then in swine.
--
Raul Rabadan, PhD
Assistant Professor
Department of Biomedical Informatics
Center for Computational Biology and Bioinformatics
Columbia University College of Physicians and Surgeons
1130 St. Nicholas Ave
ICRC Bldg 8th Floor, Office 803B
New York, NY 10032
<rabadan@dbmi.columbia.edu>
[ProMED-mail thanks Raul Rabadan for the prompt response to Professor
Morris's query in the ProMED-mail post titled "Influenza A (H1N1)
"swine flu": worldwide (03), archived as 20090428.1600 requesting
information on the nature of the genome of the virus responsible for
the outbreak in Mexico and beyond. The analysis of Dr. Rabadan and
colleagues is surprising in view of previous statements which have
gained currency that the genome of this virus is comprised of
components derived directly from avian, human and swine sources. We
look forward to seeing a detailed account of this new analysis. -
Mod.CP]
*****
[2]
Date: Tue 28 Apr 2009
From: Declan Butler <declan.m.butler@gmail.com>
Source: GISAID Alert
<http://platform.gisaid.org/>
The below may be of interest to the list.
Please find below a list of new human-swine influenza virus sequences that
have been uploaded and are available on the GISAID Database immediately.
*Isolate name; passage history; segment; accession code; version
A/California/04/2009; C2; NA; EPI176609
*A/California/04/2009; C2; PB2; EPI176610
A/California/04/2009; C2; PA; EPI176611
A/California/04/2009; C2; NS; EPI176612
A/California/04/2009; C2; MP; EPI176613
A/California/04/2009; C2; NP; EPI176614
A/California/06/2009; M1; NS ; EPI177275
A/California/07/2009; C1; PB1; EPI176615
A/California/07/2009; C1; PB2; EPI176616
A/California/07/2009; C1; PA; EPI176617
A/California/07/2009; C1; NS; EPI176618
A/California/07/2009; C1; MP; EPI176619
A/California/07/2009; E2; HA; EPI176620
A/California/07/2009; E2; PA; EPI176621
A/California/07/2009; E2; NS; EPI176622
A/California/07/2009; E2; MP; EPI176623
A/California/07/2009; E2; NP; EPI176624
A/California/08/2009; C1; NS; EPI176625
A/California/08/2009; C1; MP; EPI176626
A/California/08/2009; E2; NS; EPI176627
A/California/08/2009; E2; MP; EPI176628
A/California/10/2009; ORIGINAL ; MP; EPI177273
A/Texas/04/2009; X; PB1; EPI176629
A/Texas/04/2009; X; PB2; EPI176630
A/Texas/04/2009; X; PA; EPI176631
A/Texas/05/2009; X; PB1; EPI176632
A/Texas/05/2009; X; PA; EPI176508;
A/Kansas/03/2009; ORIGINAL; HA; EPI176633
A/California/10/2009; ORIGINAL; HA; EPI176634
A/Ohio/07/2009; ORIGINAL; HA; EPI176635
A/Ohio/07/2009; ORIGINAL; NA; EPI176636
A/Ohio/07/2009; ORIGINAL-NP WASH ; HA; EPI176637
A/Ohio/07/2009; ORIGINAL-NP WASH ; NA; EPI176638
A/New York/19/2009; ORIGINAL; HA; EPI176640
A/New York/20/2009; ORIGINAL; HA; EPI176641
A/New York/20/2009; ORIGINAL; NA; EPI176642;
A/Mexico/4482/2009; ORIGINAL; HA; EPI176587
A/Mexico/4482/2009; ORIGINAL; NA; EPI176588
A/Mexico/4482/2009; ORIGINAL; MP; EPI176591
A/Mexico/4486/2009; ORIGINAL; HA; EPI176592
A/Mexico/4486/2009; ORIGINAL; NA; EPI176593
A/Mexico/4486/2009; ORIGINAL; MP; EPI176596
A/Mexico/4108/2009; ORIGINAL; HA; EPI176597
A/Mexico/4108/2009; ORIGINAL; NA; EPI176598
A/Mexico/4108/2009; ORIGINAL; MP; EPI176599
A/Mexico/4115/2009; ORIGINAL; MP; EPI176600
A/Mexico/4108/2009; C1; NA; EPI176601
A/Mexico/4108/2009; C1; NP; EPI176602
A/Mexico/4482/2009; C1; NP; EPI176603
A/Mexico/4603/2009; C1; HA; EPI176604
A/Mexico/4603/2009; C1; MP; EPI176605
A/Mexico/4603/2009; C1; NP; EPI176606
A/Mexico/4604/2009; C1; MP; EPI176607
A/Mexico/4604/2009; C1; NP; EPI176608
A/Mexico/4604/2009; C1; NS; EPI176646
A/Mexico/4604/2009; C1; PA; EPI176645
A/Mexico/4603/2009; C1; NS; EPI176644
A/Mexico/4604/2009; C1; PA; EPI176643
To access, visit the GISAID Platform at:<http://platform.gisaid.org/>
--
Declan Butler, PhD
Senior reporter, Nature
France
<d.butler@nature.com>
[see also:
Influenza A (H1N1) "swine flu": worldwide (03), 20090428.1600
Influenza A (H1N1) "swine flu": Worldwide (02) 20090427.1586
Influenza A (H1N1) "swine flu": Worldwide 20090427.1583
Influenza A (H1N1) virus, human: worldwide 20090426.1577
Influenza A (H1N1) virus, human - New Zealand, susp 20090426.1574
Influenza A (H1N1) virus, human - N America (04) 20090426.1569
Influenza A (H1N1) virus, human - N America (03) 20090426.1566
Influenza A (H1N1) virus, human - N America (02) 20090425.1557
Influenza A (H1N1) virus, human - N America 20090425.1552
Acute respiratory disease - Mexico, swine virus susp 20090424.1546
Influenza A (H1N1) virus, swine, human - USA (02): (CA, TX) 20090424.1541
Influenza A (H1N1) virus, swine, human - USA: (CA) 20090422.1516
Influenza A (H1N1) virus, swine, human - Spain 20090220.0715
2008
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Influenza A (H1N1) virus, swine, human - USA (TX) 20081125.3715
2007
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Influenza A (H2N3) virus, swine - USA 20071219.4079
2006
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Influenza, swine, human - USA (IA): November 2006 20070108.0077]
......................cp/ejp/lm
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