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 Post subject: Re: El Paso deaths
PostPosted: Mon Apr 25, 2011 1:51 am 
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Joined: Wed Aug 19, 2009 10:42 am
Posts: 56044
Location: Pittsburgh, PA USA
gsgs wrote:
> D225N is not D225G (and Chihuahua sequences were direct and from
> the UPPER respiratory tract - D225N in pandemic H1N1 is at higher
> concentrations in lower respiratory tract).

yes, I thought you meant D225G. No D225G nor D225N at genbank
in Chi2

Please stop posting utter nonsense. D225N on Chihauhua sub-clade is well known and links to the relevant Genbank sequences are in recombinomics commentaries

A/Mexico/InDRE1945/2011
http://www.recombinomics.com/News/04031 ... Novel.html

A/Mexico/InDRE2195/2011
http://www.recombinomics.com/News/04141 ... Upper.html

Please go back to your babble boards. This board is about REAL DATA, not your clueless fantasy (or inability to even read a sequence).

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 Post subject: Re: El Paso deaths
PostPosted: Mon Apr 25, 2011 1:56 am 
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Joined: Wed Aug 19, 2009 10:42 am
Posts: 56044
Location: Pittsburgh, PA USA
niman wrote:
gsgs wrote:
> D225N is not D225G (and Chihuahua sequences were direct and from
> the UPPER respiratory tract - D225N in pandemic H1N1 is at higher
> concentrations in lower respiratory tract).

yes, I thought you meant D225G. No D225G nor D225N at genbank
in Chi2

Please stop posting utter nonsense. D225N on Chihauhua sub-clade is well known and links to the relevant Genbank sequences are in recombinomics commentaries

A/Mexico/InDRE1945/2011
http://www.recombinomics.com/News/04031 ... Novel.html

A/Mexico/InDRE2195/2011
http://www.recombinomics.com/News/04141 ... Upper.html

Please go back to your babble boards. This board is about REAL DATA, not your clueless fantasy (or inability to even read a sequence).

Actually, the claim that there is no D225N in the Chihuahua sequence reveals an inability to read English, since the TITLE of the Chihuahua sequence deposits at Genbank is :
Detection of D222N substitution in Pandemic Influenza A (H1N1) Virus in Chihuahua, Mexico
Your lack of understanding of the Chihuahua subclade is BEYOND profound.

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 Post subject: Re: El Paso deaths
PostPosted: Mon Apr 25, 2011 1:58 am 
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Joined: Wed Aug 19, 2009 10:42 am
Posts: 56044
Location: Pittsburgh, PA USA
gsgs wrote:
> D225N is not D225G (and Chihuahua sequences were direct and from
> the UPPER respiratory tract - D225N in pandemic H1N1 is at higher
> concentrations in lower respiratory tract).

yes, I thought you meant D225G. No D225G nor D225N at genbank
in Chi2

LOCUS CY089387 1777 bp cRNA linear VRL 02-APR-2011
DEFINITION Influenza A virus (A/Mexico/InDRE1945/2011(H1N1)) hemagglutinin
(HA) gene, complete cds.
ACCESSION CY089387
VERSION CY089387.1 GI:327412375
DBLINK Project: 37813
KEYWORDS .
SOURCE Influenza A virus (A/Mexico/InDRE1945/2011(H1N1))
ORGANISM Influenza A virus (A/Mexico/InDRE1945/2011(H1N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1777)
AUTHORS Ramirez-Gonzalez,J.E., Alcantara-Perez,P., Rodriguez-Maldonado,A.,
Wong-Arambula,C., Del-Mazo,J.C., Esau,D., Olivera-Diaz,H.,
Barrera-Badillo,G., Lopez-Martinez,I., Guzman-Bracho,C. and
Alpuche-Aranda,C.
TITLE Detection of D222N substitution in Pandemic Influenza A (H1N1)
Virus in Chihuahua, Mexico
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 1777)
AUTHORS Ramirez-Gonzalez,J.E., Alcantara-Perez,P., Rodriguez-Maldonado,A.,
Wong-Arambula,C., Del-Mazo,J.C., Esau,D., Olivera-Diaz,H.,
Barrera-Badillo,G., Lopez-Martinez,I., Guzman-Bracho,C. and
Alpuche-Aranda,C.
TITLE Direct Submission
JOURNAL Submitted (02-APR-2011) Laboratorio de Genoma de Patogenos,
Instituto de Diagnostico y Referencia Epidemiologicos, Crpio 470
Col. Sto Tomas, Mexico, DF 11340, Mexico
FEATURES Location/Qualifiers
source 1..1777
/organism="Influenza A virus
(A/Mexico/InDRE1945/2011(H1N1))"
/mol_type="viral cRNA"
/strain="A/Mexico/InDRE1945/2011"
/serotype="H1N1"
/isolation_source="Pharyngeal swab"
/host="human; gender M; age 36"
/db_xref="taxon:1003291"
/segment="4"
/country="Mexico: Chihuahua"
/collection_date="Mar-2011"
gene 33..1733
/gene="HA"
CDS 33..1733
/gene="HA"
/function="receptor binding and fusion protein"
/codon_start=1
/product="hemagglutinin"
/protein_id="AEA74031.1"
/db_xref="GI:327412376"
/translation="MKAILVVLLYTFATANADTLCIGYHANNSTDTVDTVLEKNVTVT
HSVDLLEDKHNGKLCKLRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETSSS
DNGTCYPGDFIDYEELREQLSSVSSFERFEIFPKTSSWPNHDSNKGVTAACPHAGAKS
FYNNLIWLVKKGNSYPKLNKSYINDKGKEVLVLWGIHHPSTSTDQQSLYQNADAYVFV
GTSRYSKKFKPEIAIRPKVRNQEGRMNYYWTLVEPGDKITFEATGNLVVPRYAFAMER
NAGSGIIISDTPIHDCNTTCQTPKGAINTSLPFQNIHPITIGKCPKYVKSTKLRLATG
LRNVPSIQSRGLFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADLKSTQNAIDEI
TNKVNSVIEKMNTQFTAVGKEFNHLEKRIENLNKKVDDGFLDIWTYNAELLVLLENER
TLDYHDSNVKNLYEKVRSQLKNNAKEIGNGCFEFYHKCDNTCMESVKNGTYDYPKYSE
EAKLNREEIDGVKLESTRIYQILAIYSTVASSLVLVVSLGAISFWMCSNGSLQCRICI
"
sig_peptide 33..83
/gene="HA"
mat_peptide 84..1064
/gene="HA"
/product="HA1"
mat_peptide 1065..1730
/gene="HA"
/product="HA2"
ORIGIN
1 agcaaaagca ggggaaaaca aaagcaacaa aaatgaaggc aatactagta gttctgctat
61 atacatttgc aaccgcaaat gcagacacat tatgtatagg ttatcatgcg aacaattcaa
121 cagacactgt agacacagta ctagaaaaga atgtaacagt aacacattct gttgaccttc
181 tagaagacaa gcataacggg aaactatgca aactaagagg ggtagcccca ttgcatttag
241 gtaaatgtaa cattgctggc tggatcctgg gaaatccaga gtgtgaatca ctctccacag
301 caagctcatg gtcttacatt gtggaaacat ctagttcaga caatggaacg tgttacccag
361 gagatttcat cgattatgag gagctaagag agcaattgag ctcagtgtca tcatttgaaa
421 ggtttgaaat attccccaag acaagttcat ggcccaatca tgactcgaac aaaggtgtaa
481 cggcagcatg tccacatgct ggagcaaaaa gcttctacaa caatttaata tggctagtta
541 aaaaaggaaa ttcataccca aagctcaaca aatcctacat taatgataaa gggaaagaag
601 tcctcgtgct atggggcatt caccatccat ctactagtac tgaccaacaa agtctctatc
661 agaatgcaga tgcatatgtt tttgtgggga catcaagata cagcaagaag tttaagccgg
721 aaatagcaat aagacccaaa gtgaggaatc aagaagggag aatgaactat tactggacac
781 tagtagagcc gggagacaaa ataacattcg aagcaactgg aaatctagtg gtaccgagat
841 atgcattcgc aatggaaaga aatgctggat ctggtattat catttcagat acaccaatcc
901 acgattgcaa tacaacttgt cagacaccca agggggctat aaacaccagc ctcccatttc
961 agaatataca tccgatcaca attggaaagt gtccaaaata tgtaaaaagc acaaaattga
1021 gactggccac aggattgagg aatgtcccgt ctattcaatc tagaggccta tttggggcca
1081 ttgccggttt cattgaaggg gggtggacag gaatggtaga tggatggtac ggttatcacc
1141 atcaaaatga gcaggggtca ggatatgcag ccgacctgaa gagcacacag aatgccattg
1201 acgagattac taacaaagta aattctgtta ttgaaaagat gaatacgcag ttcacagcag
1261 taggcaaaga gttcaaccac ctggaaaaaa gaatagagaa tttaaataaa aaagttgatg
1321 atggtttcct ggacatttgg acttacaatg ccgaactgtt ggttctattg gaaaatgaaa
1381 gaactttgga ctaccacgat tcaaatgtga agaacttata tgaaaaggta agaagccagt
1441 taaaaaacaa tgccaaggaa attggaaacg gctgctttga attttaccac aaatgcgata
1501 acacgtgcat ggaaagtgtc aaaaatggga cttatgacta cccaaaatac tcagaggaag
1561 caaaattaaa cagagaagaa atagatgggg taaagctgga atcaacaagg atttaccaga
1621 ttttggcgat ctattcaact gtcgccagtt cattggtact ggtagtctcc ctgggggcaa
1681 tcagtttctg gatgtgctct aatgggtctc tacagtgtag aatatgtatt taacattagg
1741 atttcagaag catgagaaaa acacccttgt ttctact

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 Post subject: Re: El Paso deaths
PostPosted: Mon Apr 25, 2011 2:00 am 
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Joined: Wed Aug 19, 2009 10:42 am
Posts: 56044
Location: Pittsburgh, PA USA
gsgs wrote:
> D225N is not D225G (and Chihuahua sequences were direct and from
> the UPPER respiratory tract - D225N in pandemic H1N1 is at higher
> concentrations in lower respiratory tract).

yes, I thought you meant D225G. No D225G nor D225N at genbank
in Chi2

LOCUS CY089587 432 bp cRNA linear VRL 13-APR-2011
DEFINITION Influenza A virus (A/Mexico/InDRE2195/2011(H1N1)) hemagglutinin
(HA) gene, partial cds.
ACCESSION CY089587
VERSION CY089587.1 GI:328834648
DBLINK Project: 37813
KEYWORDS .
SOURCE Influenza A virus (A/Mexico/InDRE2195/2011(H1N1))
ORGANISM Influenza A virus (A/Mexico/InDRE2195/2011(H1N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 432)
AUTHORS Ramirez-Gonzalez,J.E., Alcantara-Perez,P., Rodriguez-Maldonado,A.,
Wong-Arambula,C., Del-Mazo,J.C., Rodriguez-Castillo,A.,
Olivera-Diaz,H., Barrera-Badillo,G., Lopez-Martinez,I.,
Guzman-Bracho,C. and Alpuche-Aranda,C.
TITLE Detection of D222N Substitution in the Pandemic Influenza (H1N1)
Virus in Chihuahua, Mexico 2011
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 432)
AUTHORS Ramirez-Gonzalez,J.E., Alcantara-Perez,P., Rodriguez-Maldonado,A.,
Wong-Arambula,C., Del-Mazo,J.C., Rodriguez-Castillo,A.,
Olivera-Diaz,H., Barrera-Badillo,G., Lopez-Martinez,I.,
Guzman-Bracho,C. and Alpuche-Aranda,C.
TITLE Direct Submission
JOURNAL Submitted (13-APR-2011) Laboratorio de Genoma de Patogenos,
Instituo de Diagnostico y Referencia Epidemiologicos, Carpio 470,
Colonia Santo Tomas, Mexico., Distrito Federal 11340, Mexico
FEATURES Location/Qualifiers
source 1..432
/organism="Influenza A virus
(A/Mexico/InDRE2195/2011(H1N1))"
/mol_type="viral cRNA"
/strain="A/Mexico/InDRE2195/2011"
/serotype="H1N1"
/isolation_source="Pharyngeal swab"
/host="human; gender M; age 41"
/db_xref="taxon:1006162"
/segment="4"
/country="Mexico: Chihuahua"
/collection_date="28-Mar-2011"
gene <1..>432
/gene="HA"
CDS <1..>432
/gene="HA"
/function="receptor binding and fusion protein"
/codon_start=1
/product="hemagglutinin"
/protein_id="AEB53032.1"
/db_xref="GI:328834649"
/translation="IDYEELREQLSSVSSFERFEIFPKTSSWPNHDSNKGVTAACPHA
GAKSFYNNLIWLVKKGNSYPKLNKSYINDKGKEVLVLWGIHHPSTSTDQQSLYQNADA
YVFVGTSRYSKKFKPEIAIRPKVRXQEGRMNYYWTLVEPGDK"
mat_peptide <1..432
/gene="HA"
/product="HA1"
ORIGIN
1 atcgattatg aggagctaag agagcaattg agctcagtgt catcatttga aaggtttgaa
61 atattcccca agacaagttc atggcccaat catgactcga acaaaggtgt aacggcagca
121 tgtccacatg ctggagcaaa aagcttctac aacaatttaa tatggctagt taaaaaagga
181 aattcatacc caaagctcaa caaatcctac attaatgata aagggaaaga agtcctcgtg
241 ctatggggca ttcaccatcc atctactagt actgaccaac aaagtctcta tcagaatgca
301 gatgcatatg tttttgtggg gacatcaaga tacagcaaga agtttaagcc ggaaatagca
361 ataagaccca aagtgaggrr tcaagaaggg agaatgaact attactggac actagtagag
421 ccgggagaca aa

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 Post subject: Re: El Paso deaths
PostPosted: Mon Apr 25, 2011 2:03 am 
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User avatar

Joined: Tue Sep 01, 2009 11:54 pm
Posts: 1835
Location: germany
niman wrote:
gsgs wrote:
> D225N, which improves TRANSMISSION

who else says this ? give a source

Please. D225N is on SEASONAL H3N2 and was involved in the fixing of adamantane resistance (S31N). This data is old and quite well known to those in the field (just google D225N and S193F).
You spend too much time on babble boards and in a parallel universe.
You lack of understanding of receptor binding domain changes is PROFOUND.



you just can't compare H3 and H1. They are entirely different
If D225N did infer an advantage,if it were that easy,
then there was ample time
to develope already, but it didn't.

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 Post subject: Re: El Paso deaths
PostPosted: Mon Apr 25, 2011 2:04 am 
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Joined: Wed Aug 19, 2009 10:42 am
Posts: 56044
Location: Pittsburgh, PA USA
gsgs wrote:
niman wrote:
gsgs wrote:
> D225N, which improves TRANSMISSION

who else says this ? give a source

Please. D225N is on SEASONAL H3N2 and was involved in the fixing of adamantane resistance (S31N). This data is old and quite well known to those in the field (just google D225N and S193F).
You spend too much time on babble boards and in a parallel universe.
You lack of understanding of receptor binding domain changes is PROFOUND.



you just can't compare H3 and H1. They are entirely different
If D225N did infer an advantage,if it were that easy,
then there was ample time
to develope already, but it didn't.

Go away.

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 Post subject: Re: El Paso deaths
PostPosted: Mon Apr 25, 2011 2:10 am 
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Joined: Tue Sep 01, 2009 11:54 pm
Posts: 1835
Location: germany
> A/Mexico/InDRE1945/2011

G715R and A716R , mixed

> A/Mexico/InDRE2195/2011

G715A
OK, I missed that. Only mutations that occur more than once
are usually in my lists.

still 6 sequences from that strain from Mexico with 715G
and 5 from USA at genbank

11.5:1.5



--------------------------
Glycine,GLY,G,4,GGT,GGC,GGG,GGA
Asparagine,ASN,N,2,AAT,AAC
Aspartic Acid,ASP,D,2,GAT,GAC
D225G : GAT-->GGT
D225N : GAT-->AAT
----------------------------


Code:
                                            0000000000000000000000000011111 
                                            0001122333445566667788889901224
                                            1693408029681305681204680585130
                                            6415272346296678315619553708538
-codon-position-----------------------------111 1        211  1   1       1
---Index------------------------------------GAGCAGCTCGTAAGGTACGGACGTTAGGATC
   1 >A/Mexflu/index/2009/02/01             ...............................
   2 >A/New Jersey/AF21791,2011/01/13       ....G..C.A...AAATT....ACGGA.---
   3 >A/Florida/AF21771,2011/01/12          A.A.G....A...AAA.T....A.GGA.---
   4 >A/North Carolina/AF21796,2011/01/18   AG..G...TA...AAA.T...TA.GGA.---
   5 >A/South Carolina/AF21803,2011/01/14   AG..G...TA...AAA.T...TA.GGAA---
   6 >A/Arizona/AF21768,2011/01/07          AG..G...TA..GAAA.T.A.TA.GGA.---
   7 >A/Mexico/InDRE1945,2011/03/           ...TGAT..AAC.AAA.TA...A.GGA.GCT
   8 >A/Mexico/InDRE1946,2011/03/22         ...TGAT..AAC.AAA.T....A.GGA.GCT
   9 >A/Mexico/InDRE1947,2011/03/23         ...TGA...AAC.AAA.T..G.A.GGA.GCT
  10 >A/Mexico/InDRE2192,2011/03/28         ---------AAC.AAA.T..-----------
  11 >A/Mexico/InDRE2195,2011/03/28         ---------AAC.AAA.TR.-----------
  12 >A/Mexico/InDRE2197,2011/03/28         ---------AAC.AAA.T..-----------
  13 >A/Mexico/InDRE2200,2011/03/29         ---------AAC.AAA.T..-----------
  14 >A/Mexico/InDRE2222,2011/03/31         ---------AAC.AAA.T..-----------
---Index------------------------------------GAGCAGCTCGTAAGGTACGGACGTTAGGATC
-codon-position-----------------------------111 1        211  1   1       1
                                            0000000000000000000000000011111
                                            0001122333445566667788889901224
                                            1693408029681305681204680585130
                                            6415272346296678315619553708538
                                                                           
.
.


.
.

_________________
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Last edited by gsgs on Mon Apr 25, 2011 2:31 am, edited 2 times in total.

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 Post subject: Re: El Paso deaths
PostPosted: Mon Apr 25, 2011 2:21 am 
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Joined: Wed Aug 19, 2009 10:42 am
Posts: 56044
Location: Pittsburgh, PA USA
gsgs wrote:
> A/Mexico/InDRE1945/2011

G715R and A716R , mixed

> A/Mexico/InDRE2195/2011

G715A
OK, I missed that. Only mutations that occur more than once
are usually in my lists.

still 6 sequences from that strain from Mexico with 715G
and 5 from USA at genbank

11.5:1.5



--------------------------
Glycine,GLY,G,4,GGT,GGC,GGG,GGA
Asparagine,ASN,N,2,AAT,AAC
Aspartic Acid,ASP,D,2,GAT,GAC
D225G : GAT-->GGT
D225N : GAT-->AAT
----------------------------

As I said, you remain clueless and can't even comprehend the title of the submissions (no genetic code required). D225N was in 2 of 8 Chihuahua sub-clade sequences which is VERY high and VERY well known by anyone remotely familiar with the Chihuahua sub-clade (and there are five more examples in withheld sequences from Chihuahua).

Stick to the babble boards where your nonsense might be belived by some (and your PROFOUND lack of knowledge or understanding might explain your absurd 20% GUESS on reassortment AFTER the sequences were published, which is not a guess, it is a BELIEF that is without a scientific basis or foundation).

Here it is both annoying and distracting (and NOT reality based).

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 Post subject: Re: El Paso deaths
PostPosted: Mon Apr 25, 2011 2:27 am 
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Joined: Wed Aug 19, 2009 10:42 am
Posts: 56044
Location: Pittsburgh, PA USA
gsgs wrote:
> A/Mexico/InDRE1945/2011

G715R and A716R , mixed

> A/Mexico/InDRE2195/2011

G715A
OK, I missed that. Only mutations that occur more than once
are usually in my lists.

still 6 sequences from that strain from Mexico with 715G
and 5 from USA at genbank

11.5:1.5



--------------------------
Glycine,GLY,G,4,GGT,GGC,GGG,GGA
Asparagine,ASN,N,2,AAT,AAC
Aspartic Acid,ASP,D,2,GAT,GAC
D225G : GAT-->GGT
D225N : GAT-->AAT
----------------------------

You have mixed up the sequences. 1945 was the FIRST sequence from Chihuahua (and has the LOWEST sample number) and was part of the reason the submissions had D225N (D222N in H1 numbering) in the TITLE (the other part is the D225N in the withheld sequences). The sequence was NOT a mixture. It had D225N and was from the UPPER respiratory tract.
Your posts are NOT reality based.
You continue to post your FANTASY, which has NOTHING to do with the real DATA.

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 Post subject: Re: El Paso deaths
PostPosted: Mon Apr 25, 2011 2:35 am 
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Joined: Wed Aug 19, 2009 10:42 am
Posts: 56044
Location: Pittsburgh, PA USA
gsgs wrote:
> A/Mexico/InDRE1945/2011

G715R and A716R , mixed

> A/Mexico/InDRE2195/2011

G715A
OK, I missed that. Only mutations that occur more than once
are usually in my lists.

still 6 sequences from that strain from Mexico with 715G
and 5 from USA at genbank

11.5:1.5



--------------------------
Glycine,GLY,G,4,GGT,GGC,GGG,GGA
Asparagine,ASN,N,2,AAT,AAC
Aspartic Acid,ASP,D,2,GAT,GAC
D225G : GAT-->GGT
D225N : GAT-->AAT
----------------------------


Code:
                                            0000000000000000000000000011111 
                                            0001122333445566667788889901224
                                            1693408029681305681204680585130
                                            6415272346296678315619553708538
-codon-position-----------------------------111 1        211  1   1       1
---Index------------------------------------GAGCAGCTCGTAAGGTACGGACGTTAGGATC
   1 >A/Mexflu/index/2009/02/01             ...............................
   2 >A/New Jersey/AF21791,2011/01/13       ....G..C.A...AAATT....ACGGA.---
   3 >A/Florida/AF21771,2011/01/12          A.A.G....A...AAA.T....A.GGA.---
   4 >A/North Carolina/AF21796,2011/01/18   AG..G...TA...AAA.T...TA.GGA.---
   5 >A/South Carolina/AF21803,2011/01/14   AG..G...TA...AAA.T...TA.GGAA---
   6 >A/Arizona/AF21768,2011/01/07          AG..G...TA..GAAA.T.A.TA.GGA.---
   7 >A/Mexico/InDRE1945,2011/03/           ...TGAT..AAC.AAA.TA...A.GGA.GCT
   8 >A/Mexico/InDRE1946,2011/03/22         ...TGAT..AAC.AAA.T....A.GGA.GCT
   9 >A/Mexico/InDRE1947,2011/03/23         ...TGA...AAC.AAA.T..G.A.GGA.GCT
  10 >A/Mexico/InDRE2192,2011/03/28         ---------AAC.AAA.T..-----------
  11 >A/Mexico/InDRE2195,2011/03/28         ---------AAC.AAA.TR.-----------
  12 >A/Mexico/InDRE2197,2011/03/28         ---------AAC.AAA.T..-----------
  13 >A/Mexico/InDRE2200,2011/03/29         ---------AAC.AAA.T..-----------
  14 >A/Mexico/InDRE2222,2011/03/31         ---------AAC.AAA.T..-----------
---Index------------------------------------GAGCAGCTCGTAAGGTACGGACGTTAGGATC
-codon-position-----------------------------111 1        211  1   1       1
                                            0000000000000000000000000011111
                                            0001122333445566667788889901224
                                            1693408029681305681204680585130
                                            6415272346296678315619553708538
                                                                           
.
.


.
.

You left out A716R to create D225G in A/Mexico/InDRE2195,2011 (and it is the lower set of sequences, from Mexico and generated by DIRECT sequencing, that has the high frequency of D225N). Your posts are NOT reality based (and you are data analysis CHALLENGED as demonstrated by post after post, including the one quoted above).

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