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 Post subject: Re: India sequences
PostPosted: Fri Aug 19, 2011 10:04 am 
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Location: germany
early sequences with the UK-mutations from early Europe 2010/11
(markers 605,1056,1171,1403)

>A/Nanded/NIV29214,2010/05/21
>A/India/NIV29386,2010/06/02
>A/India/NIV29574,2010/06/14
>A/India/NIV30535,2010/07/12
>A/India/NIV30784,2010/07/16

and then many from Thailand, July 2010

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 Post subject: Re: India sequences
PostPosted: Tue Mar 13, 2012 12:22 pm 
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Location: germany
http://www.ncbi.nlm.nih.gov/pmc/article ... ool=pubmed


Surprisingly, NS nucleotide sequences of five A/H1N1 strains was highly
homologous (>97%) with the 1934 prototype strain [A/Puerto Rico/8/34(H1N1)]


nucleotide sequences of NS gene of
A/KOL/536/2007(H1N1),
A/KOL/596/2007(H1N1),
A/KOL/968/2007(H1N1),
A/KOL/230/2009(H1N1),
A/KOL/2086/2009(H1N1)
were nearly identical with A/Puerto Rico/8/34



To verify possible cross contamination, BLAST search of HA, NA, M1 and NS1 gene sequences showed only NS1 having sole identity with A/PR/8/34(H1N1). Thus, a chance of cross contamination with laboratory PR8 strain was ruled out


-----------------------------------------------------

who wants to bet ...

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 Post subject: Re: India sequences
PostPosted: Mon Apr 09, 2012 5:50 am 
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Location: germany
mutation tables here:
http://www.flutrackers.com/forum/showpost.php?p=449384

A/KOL/968/2007/07(H1N1) segment 2 (H3N2-like)
has C141T and A155G just as Perth-like/2009
but also C28A,T1887C,G2193A just like the other KOL-H1N1 sequences.
Looks like another "dirty-chromatogram"-pseudo recombination,presumably they
had sequenced other Perth-like H3N2s before with that machine/procedure.



A/KOL/1762/2008/07/(H3N2) and A/KOL/1819/2008/07(H3N2) had T386C in segment 8,
like 3 of the other KOL-2007 sequences, which however were the old Wisconsin/2005 strain
while the 2 former were the new 2007-strain.
This could be another "dirty-chromatogram"-pseudo recombination, but less clear with
just one mutation.

A/KOL/1690/2008/06/(H3N2) has A163G and C453T in segment 8 like 4 of the other KOL
non-Egypt/Iowa sequences from summer 2008, but then it also has the 3 Egypt/Iowa
mutations G404A,A416G,A735G, so this looks like another clear "dirty chromatogram"-
pseudo-recombination

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 Post subject: Re: India sequences
PostPosted: Mon Apr 09, 2012 6:16 am 
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Joined: Wed Aug 19, 2009 10:42 am
Posts: 40033
Location: Pittsburgh, PA USA
gsgs wrote:
mutation tables here:
http://www.flutrackers.com/forum/showpost.php?p=449384

A/KOL/968/2007/07(H1N1) segment 2 (H3N2-like)
has C141T and A155G just as Perth-like/2009
but also C28A,T1887C,G2193A just like the other KOL-H1N1 sequences.
Looks like another "dirty-chromatogram"-pseudo recombination,presumably they
had sequenced other Perth-like H3N2s before with that machine/procedure.



A/KOL/1762/2008/07/(H3N2) and A/KOL/1819/2008/07(H3N2) had T386C in segment 8,
like 3 of the other KOL-2007 sequences, which however were the old Wisconsin/2005 strain
while the 2 former were the new 2007-strain.
This could be another "dirty-chromatogram"-pseudo recombination, but less clear with
just one mutation.

A/KOL/1690/2008/06/(H3N2) has A163G and C453T in segment 8 like 4 of the other KOL
non-Egypt/Iowa sequences from summer 2008, but then it also has the 3 Egypt/Iowa
mutations G404A,A416G,A735G, so this looks like another clear "dirty chromatogram"-
pseudo-recombination

yada yada

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