Rhiza Labs FluTracker Forum

A/Mexico/InDRE2195/2011 has a mixture of D225N and D225G.

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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JOURNAL Unpublished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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www.twitter.com/hniman

Ukraine re-run, but on a novel background

http://www.recombinomics.com/News/01081 ... raine.html

_________________
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The genetic sequencing of the first three pandemic (H1N1) 2009 influenza cases (two fatal cases and one mild) reported that the virus is homologous to the one that is currently circulating worldwide. Thus far, there is no evidence that the influenza strains identified have mutations that confer greater virulence or antiviral resistance.

The above is more WHO disinformation. D225G is associated with severe and fatal cases and mixtures of D225G with D225N were common in autopsy lung samples in Ukraine.

_________________
www.twitter.com/hniman

D222G/N is transmitting efficiently on this background. At the same time, this subgroup is avoiding previous immunity so a new wave or major regional outbreaks are quite real for the coming weeks months.

The clinical presentation of some cases is clear signal of above.

Thank you, Henry.

It should be noted that this is an UPPER respiratory tract collection. In Ukraine the mixtures were in autopy lung samples. My guess is autopsy lung or BAL samples would find D225G and D225N in most samples from severe or fatal cases infected with the novel sub-clade.

Moreover, the presence of the same combinations as seen in Ukraine, but on a new genetic background signals recombination,

The partial sequence released for this patient matches the Chihuahua novel sub-clade. It has G386A, T462A, C681T and with nonsynonymous changes creating K149N, S165N, A189T, D225N, D225N, so D225G/N is on the novel genetic background.

_________________
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Yes, It's very significant that these samples were collected from the upper respiratory tract.

This background will allow D222N/G fixing as seen in a similar with H3N2.

Also, oseltamivir resistance might appear very rapidly.

This time I'm talking about serious pandemic concerns.

G396A

EPI310173 A/Wisconsin/02/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.19077
EPI310136 A/Vermont/04/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.19077
EPI310133 A/Utah/08/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.19077
EPI310130 A/Texas/07/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.19077
EPI310103 A/Pennsylvania/02/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.19077
EPI310093 A/Oregon/03/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.19077
EPI310069 A/North Carolina/03/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.19077
EPI310055 A/New York/02/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.19077
EPI310049 A/New Jersey/03/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.19077
EPI310002 A/Massachusetts/06/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.19077
EPI309970 A/Maryland/04/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.19077
EPI309946 A/Maine/03/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.19077
EPI308933 A/South Carolina/AF21803/2011 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI308926 A/North Carolina/AF21796/2011 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI308923 A/New Jersey/AF21791/2011 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI308912 A/Florida/AF21771/2011 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI308910 A/Arizona/AF21768/2011 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI307981 A/swine/Hubei/101/2009 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI306130 A/Denmark/111/2010 (A/H1N1 swl) segment 4 (HA) 27.0 6.19077
EPI302745 A/Canada-AB/RV2811/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.19077
EPI301814 A/Aragon/RR6925/2010 (A/H1N1 swl) segment 4 (HA) 27.0 6.19077
EPI301401 A/England/118/2010 (A/H1N1 swl) segment 4 (HA) 27.0 6.19077
EPI295399 A/El Salvador/798/2010 (A/H1N1 swl) segment 4 (HA) 27.0 6.19077
EPI294682 A/England/118/2010 (A/H1N1 swl) segment 4 (HA) 27.0 6.19077
EPI294254 A/VANIMO/7/2010 (A/H1N1 swl) segment 4 (HA) 27.0 6.19077
EPI292008 A/swine/Iowa/H03US3/2003 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI288290 A/Boston/672/2009 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI281663 A/Egypt/N00238/2010 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI281264 A/swine/Nebraska/02013/2008 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI280320 A/Pennsylvania/07/2010 (A/H1N1 swl) segment 4 (HA) 27.0 6.19077
EPI278736 A/swine/Germany-NI/R369/09 (A/H1N2) segment 4 (HA) 27.0 6.19077
EPI278184 A/Korea/AF2394/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.19077
EPI273062 A/swine/Belgium/196/1992 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI273037 A/swine/Belgium/230/1992 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI273017 A/swine/Belgium/74/1995 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI266020 A/St.Petersburg oblast/CRIE-SEV/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.19077
EPI257680 A/Ningxia-Xixia/SWL116/2010 (A/H1N1 swl) segment 4 (HA) 27.0 6.19077
EPI255672 A/swine/Hong Kong/2990/2009 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI255664 A/swine/Hong Kong/2896/2009 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI245759 A/ENG/686/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.19077
EPI242895 A/swine/Germany/8533/91 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI242892 A/swine/Arnsberg/6554/79 (A/H1) segment 4 (HA) 27.0 6.19077
EPI242880 A/swine/Germany/2/81 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI240217 A/swine/Italy/671/1987 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI240209 A/swine/Italy/670/1987 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI239826 A/swine/Schleswig-Holstein/1/92 (A/H0) segment 4 (HA) 27.0 6.19077
EPI239405 A/swine/Italy/France/2111/95 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI233009 A/MIE/123/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.19077
EPI227618 A/Alabama/04/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.19077
EPI217091 A/Saint Lucia/7178/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.19077
EPI216866 A/Idaho/08/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.19077
EPI181734 A/swine/Parma/1997 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI177645 A/swine/Hong Kong/NS29/2009 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI175940 A/swine/France/WVL8/1992 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI175932 A/swine/England/WVL7/1992 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI175924 A/swine/Spain/WVL6/1991 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI175908 A/swine/France/WVL4/1985 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI175900 A/swine/France/WVL3/1984 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI175892 A/swine/Belgium/WVL2/1983 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI175861 A/swine/England/WVL14/1996 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI175854 A/swine/France/WVL13/1995 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI175847 A/swine/England/WVL12/1995 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI175831 A/swine/England/WVL10/1993 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI171769 A/swine/Germany/Vi5698/1995 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI131268 A/turkey/Germany/2482/90 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI131100 A/swine/Schleswig-Holstein/1/93 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI131096 A/Swine/England/195852/92 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI130755 A/mallard/Tennessee/11464/85 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI130747 A/swine/Netherlands/12/1985 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI125425 A/swine/IDT/Re230/92 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI98455 A/swine/Potsdam/194/90 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI98451 A/swine/Schwerin/182/87 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI98449 A/swine/Schwerin/103/89 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI98447 A/swine/Potsdam/15/81 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI98445 A/swine/Potsdam/123/81 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI98443 A/swine/Bad Langensalza/59/84 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI97658 A/swine/Bakum/5/95 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI86680 A/mallard duck/ALB/965/1979 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI24835 A/swine/IDT/Re230/92 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI14633 A/swine/Dongen/6T/96 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI14631 A/swine/Dongen/6J/96 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI14629 A/swine/Dongen/6D/96 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI14627 A/swine/Dongen/6B/96 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI14609 A/swine/Leende/15S/96 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI14607 A/swine/Leende/15R/96 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI14605 A/swine/Leende/15Q/96 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI14603 A/swine/Leende/15E/96 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI14601 A/swine/Leende/15C/96 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI14599 A/swine/Someren/14M/96 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI14597 A/swine/Someren/14J/96 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI14595 A/swine/Someren/14C/96 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI14593 A/swine/Someren/14A/96 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI14591 A/swine/Nederweert/13O/96 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI14589 A/swine/Nederweert/13I/96 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI14587 A/swine/Nederweert/13H/96 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI14585 A/swine/Nederweert/13G/96 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI14583 A/swine/Nederweert/13A/96 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI12352 A/swine/Cotes d'Armor/1482/1999 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI11954 A/swine/Italy/1511/98 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI11952 A/swine/Finistere/2899/1982 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI11940 A/swine/Italy/1390-5/95 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI11938 A/swine/Italy/1456-1/96 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI11928 A/swine/Belgium/117/96 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI11926 A/swine/Cotes d'Armor/1515/1999 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI8390 A/Swine/Netherlands/477/93 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI8388 A/Swine/Netherlands/386/86 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI8386 A/Swine/Netherlands/609/96 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI8384 A/Swine/Netherlands/1743/93 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI8382 A/Swine/Netherlands/1/87 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI8380 A/swine/Netherlands/12/1985 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI8376 A/Swine/France/525/94 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI8374 A/Swine/France/4510/86 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI8372 A/Swine/France/4203/85 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI8370 A/Swine/France/3614/84 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI4917 A/swine/Netherlands/12/1985 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI4915 A/swine/Belgium/1/83 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI4913 A/swine/Italy-Virus/671/87 (A/H1N1) segment 4 (HA) 27.0 6.19077
EPI4905 A/mallard/Tennessee/11464/85 (A/H1N1) segment 4 (HA) 27.0 6.19077

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T462A

EPI310133 A/Utah/08/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.19077
EPI310130 A/Texas/07/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.19077
EPI310103 A/Pennsylvania/02/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.19077
EPI310093 A/Oregon/03/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.19077
EPI309970 A/Maryland/04/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.19077

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K149N

EPI310133 A/Utah/08/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.19077
EPI310130 A/Texas/07/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.19077
EPI310103 A/Pennsylvania/02/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.19077
EPI310093 A/Oregon/03/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.19077
EPI309970 A/Maryland/04/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.19077
EPI266546 A/Boston/115/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.19077
EPI218962 A/Wisconsin/629-D02206/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.19077

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