Re: Questions on the Virus and Some of the Genetics of Tested Isolates
Link to the Genetic Sequences of various viral isolates from the CDC. Time to study these....
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Questions on the Virus and Some of the Genetics of Tested Isolates
Via Promed.....
[1] Some questions
Date: Tue 28 Apr 2009
From: Roger Morris <R.S.Morris@massey.ac.nz>
Some questions
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For those of us who are involved in international work on influenza
epidemiology and control and responding to the many media enquiries,
there is a very large information gap in relation to diagnosis and
epidemiology of the Mexican influenza. What is known of the genetic
structure of this virus? It has been called a swine flu, but no
evidence has been put forward to allow this statement to be
evaluated. I have received information that it is a reassortant,
which has genetic components from 4 different sources, but nothing
official has been released on this. Where does it fit
phylogenetically? Is there any genetic variation of significance
among the isolates investigated? Would this help to explain the
difference in severity of disease between Mexico and other countries?
It is also stated that it should be diagnosed by RT-PCR, without
clarifying which PCR. I have received information that the standard
PCR for H1 does not reliably detect this virus. Is this true? What is
an appropriate series of diagnostic steps for samples from suspect
cases? Could we have an authoritative statement on these issues from
one of the laboratories, which has been working with the virus?
- --
Professor Roger Morris
Emeritus Professor of Animal Health
Massey University EpiCentre, PN623
Institute of Veterinary, Animal and Biomedical Sciences
Massey University, Palmerston North
New Zealand
<R.S.Morris@massey.ac.nz>
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]
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