Disqus - Latest Comments for marken206

Re: Influenza A/Mexico/2009 (H1N1) – Questions and answers

marken206 — Wed, 06 May 2009 18:02:48 -0000

Are you aware of efforts to make the virus strain nomenclature more informative? Understanding what segments/genes are related historically and sequence wise to what is confusing using the 'serological' definitions like H1N1. What about the other segments? What about subtyping further the HA and NA genes?

Is there a good way to get a statistical handle on the relative rates if H1N1 isolate detection vs. others currently, particularly coinfection? Related to a question above, it will be interesting to see what happens with the flu species population and what the interaction of H1N1 in the background of other species will be.

Re: Influenza A/Mexico/2009 (H1N1) update

marken206 — Tue, 05 May 2009 23:05:23 -0000

Cool. Good to know. Thanks. There is a little bit of seq drift but probably essentially the same.
Really enjoy your web site. Learning lots. Thank you.

BTW, did finally get my account this afternoon. I did complain directly. Interesting email exchange:>)They are hyper worried about the whole IP thing, kind of anti industry, but I understand.

Keep up the good work!
Best regards John Marken

Re: Nucleotide sequences of influenza A/Mexico/2009 (H1N1) viruses available

marken206 — Tue, 05 May 2009 12:05:00 -0000

I'm actually running into difficulties with registration. GISAID is still a bit of a 'gate'. The data isn't truly available to the public until they decide to redeposit sequences into the normal databases. To understand, I found this wiki site a nicer summary than their own web site.
http://en.wikipedia.org/wik...

It seems there are issues of IP (avoiding patent aps filed using the data by unauthorized entities) and unfortunately priority concerns, ie who gets to publish the paper first.

Re: Influenza A/Mexico/2009 (H1N1) update

marken206 — Mon, 04 May 2009 17:14:32 -0000

From CDC: Recomended test is 1) qPCR, 2) Viral culture
http://www.cdc.gov/h1n1flu/...

From WHO: same tests at designated labs in approved countries
http://www.who.int/csr/dise...

Read that China is working on and will deliver improved PCR based assays, claimed speed, specificity, ease of use. I have a suspicion that this might be why the first sequences (from Mexio) were not deposited at NCBI, to give Chinese companies first access to develop these kits.

Re: Influenza A/Mexico/2009 (H1N1) update

marken206 — Mon, 04 May 2009 13:23:38 -0000

If it hasn't been commented on yet:
I wonder why the CDC chose to deposit the Mexico sequences at the GSAID instead of the much more useful NCBI?
http://platform.gisaid.org
And why have the GSAID chosen to 'protect' the sequences by requiring approved registration/login accounts?

Re: Influenza virus RNA genome

marken206 — Fri, 01 May 2009 19:06:39 -0000

Taubenberger and Morens note a similar phenomenon of a "W" shaped mortality histogram and discuss some similar hypothesis with regards to the 1918-19 pandemic.
http://www.cdc.gov/ncidod/e...
article

Re: Influenza virus RNA genome

marken206 — Fri, 01 May 2009 14:16:57 -0000

Thank you for helping to educate non virologists like myself.
It seems to me there needs to be further nomenclature/classification modification. The A/H1N1 classification of this 2009 version does not differentiate clearly from the 1918 virus or the swine/human H1N1 viruses that have been identified before. The concern is that this is a 'new' cross over virus that is human transmissible , where we do not yet know what will be the epedemiology or morbidity/mortaility rates. The nomenclature should reflect the sequence differences that make it 'new'. Some of the comments on phylogeny by the CDC relative to what has been said about the deposited sequences are a bit confusing.

Could you please summarize the differences? A graphical mutation table showing the genes (seqments) compared to related viruses would be most helpful. Are the Polymerase genes the old 'avian' link? What is unique about the H1 subtype that 'puts it in a lonely branch'?

obviously I don't care for the 'Serology' classification method. These days it should be all about sequence.