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PostPosted: Mon May 03, 2010 10:51 am 
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NAMRU-3 is releasing HA and NA sequences from 12 2010 and 9 2009 isolates. Most recent is March 31, 2010.

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PostPosted: Mon May 03, 2010 1:18 pm 
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All HA sequences have 125del.

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PostPosted: Mon May 03, 2010 10:06 pm 
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All human H5N1 isolates in Egypt for the past year have been the 125del sub-clade. This is very unusual.

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PostPosted: Mon May 03, 2010 10:38 pm 
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NAMRU-3 has also released a 2007 seqence with S227N. This case preceded large scale hospitalizations of suspect H5N1 cases in early 2008.

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PostPosted: Mon May 03, 2010 10:47 pm 
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S227N

LOCUS CY062442 1317 bp cRNA linear VRL 30-APR-2010
DEFINITION Influenza A virus (A/Egypt/10217-NAMRU3/2007(H5N1)) segment 4
sequence.
ACCESSION CY062442
VERSION CY062442.1 GI:295443440
KEYWORDS .
SOURCE Influenza A virus (A/Egypt/10217-NAMRU3/2007(H5N1))
ORGANISM Influenza A virus (A/Egypt/10217-NAMRU3/2007(H5N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1317)
AUTHORS Elassal,E.M., Kandeel,A., Abdelghani,A.S., Elsayed,N.M.,
Gomaa,A.A., Younan,M., Earhart,K.C., Turner,M., Pimentel,G. and
Barthel,R.V.
TITLE Influenza A subtype H5N1 viruses from Egypt
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 1317)
AUTHORS Elassal,E.M., Kandeel,A., Abdelghani,A.S., Elsayed,N.M.,
Gomaa,A.A., Younan,M., Earhart,K.C., Turner,M., Pimentel,G. and
Barthel,R.V.
TITLE Direct Submission
JOURNAL Submitted (30-APR-2010) Viral and Zoonotic Diseases Research
Program, U.S. Naval Medical Research Unit No. 3, Extension of
Ramses Street, Nasr City, Cairo 11517, Egypt
FEATURES Location/Qualifiers
source 1..1317
/organism="Influenza A virus
(A/Egypt/10217-NAMRU3/2007(H5N1))"
/mol_type="viral cRNA"
/strain="A/Egypt/10217-NAMRU3/2007"
/serotype="H5N1"
/isolation_source="Throat Swab"
/host="human; gender F; age 30"
/db_xref="taxon:574652"
/segment="4"
/country="Egypt: Daqahleya"
/collection_date="29-Dec-2007"
gene 1..>1317
/gene="HA"
CDS 1..>1317
/gene="HA"
/function="receptor binding and fusion protein"
/codon_start=1
/product="hemagglutinin"
/protein_id="ADG21405.1"
/db_xref="GI:295443441"
/translation="MEKIVLLLTIVSLVKSDQICIGYHANNSTEQVDTIMEKNVTVTH
AQDILEKTHNGKLCDLDGVKPLILRDCSVAGWLLGNPMCDEFLNVPEWSYIVEKINPA
NDLCYPGNFNDYEELKHLLSRINHFEKIQIIPKSSWSNHEASSGVSSACPYQGRSSFF
RNVVWLIKKGNAYPTIKISYNNTNQEDLLVLWGIHHPNDAAEQTRLYQNPTTYISVGT
STLNQRLVPKIATRSKVNGQNGRMEFFWTILKSNDAINFESNGNFIAPENAYKIVKKG
DSTIMKSELEYGNCNTKCQTPIGAINSSMPFHNIHPLTIGECPKYVKSNRLVLATGLR
NSPQGERRRKKRGLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAID
GVTNKVNSIIDKMNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWT"
sig_peptide 1..48
/gene="HA"
mat_peptide 49..1038
/gene="HA"
/product="HA1"
mat_peptide 1039..>1317
/gene="HA"
/product="HA2"
ORIGIN
1 atggagaaaa tagtgcttct tcttacaata gtcagtcttg ttaaaagtga tcagatttgc
61 attggttacc atgcaaacaa ctcgacagag caggttgaca caataatgga aaagaacgtc
121 actgttacac acgcccaaga catactggaa aagacacaca acgggaaact ctgcgatcta
181 gatggagtta agcctctaat tttaagagat tgtagtgtag ctggatggct cctcgggaac
241 ccaatgtgtg acgaattcct caatgttccg gaatggtctt acatagtgga gaagatcaat
301 ccagccaatg acctctgtta cccagggaat ttcaatgact atgaagaact gaagcaccta
361 ttgagcagaa taaaccattt tgagaaaatt cagatcatcc ccaaaagttc ttggtcaaat
421 catgaagcct catcaggagt gagctcagca tgtccatacc agggaagatc ctcctttttt
481 agaaatgtgg tatggcttat caaaaagggc aatgcatacc caacaataaa gataagttac
541 aataatacca accaagaaga tcttttggta ctgtggggga ttcaccatcc aaatgatgcg
601 gcagagcaga caaggctcta tcaaaaccca actacctata tttccgttgg gacatcaaca
661 ttaaaccaga gattggtacc aaaaatagcc actagatcta aggtaaacgg gcaaaatgga
721 aggatggagt tcttttggac aattttaaaa tcgaatgatg caataaactt tgagagtaat
781 ggaaatttca ttgctccaga aaatgcatac aaaattgtca agaaagggga ttcaacaatt
841 atgaaaagtg agttggaata tggtaactgc aacaccaagt gtcaaactcc aataggggcg
901 ataaactcca gtatgccatt ccacaacatc caccctctca ccatcgggga atgccccaaa
961 tatgtgaaat caaacagatt agtccttgct actgggctca gaaatagccc tcaaggagag
1021 agaagaagaa aaaagagagg actatttgga gctatagcag gttttataga gggaggatgg
1081 cagggaatgg tagatggttg gtatgggtac caccatagca acgagcaggg gagtgggtac
1141 gctgcagaca aggaatccac tcaaaaggca atagatggag tcaccaataa ggtcaactcg
1201 attattgaca aaatgaacac tcagtttgag gctgttggaa gggaatttaa taacttagaa
1261 aggagaatag aaaatttaaa caagaagatg gaagacggat tcctagatgt ctggact

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PostPosted: Mon May 03, 2010 10:56 pm 
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12/12/2007 Yes, positive and mouth 30/12 Yes 26/43 Fatma Fathi Mohamed Mahdi was 30 Almansourprbp house Company 2 Rabiah - Dekrness Dakahlia 29

http://www.saidr.org/docs/pdf/Positive% ... %20(Arabic).pdf

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PostPosted: Mon May 03, 2010 11:30 pm 
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check link?


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PostPosted: Tue May 04, 2010 2:04 am 
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Posts: 1835
Location: germany
no Qinghai-genome since 2008

usually HA (and NA) may be enough, but at least one
full genome per year, would that be too much ?

Compare with 2005,2006,2007 where we have many genomes.
We want to follow the evolution, want to estimate what the
trend is, whether it may fade away, what wild birds harbour
and transport it

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PostPosted: Tue May 04, 2010 6:28 am 
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Tex wrote:
check link?

Above link can be accessed here

http://www.saidr.org/en/humans.php

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PostPosted: Tue May 04, 2010 6:37 am 
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gsgs wrote:
no Qinghai-genome since 2008

usually HA (and NA) may be enough, but at least one
full genome per year, would that be too much ?

Compare with 2005,2006,2007 where we have many genomes.
We want to follow the evolution, want to estimate what the
trend is, whether it may fade away, what wild birds harbour
and transport it

Please. Qinghai is clade 2.2 and all H5N1 in Egypt is clade 2.2.1 and always has been (see WHO tree at 2010 update)

http://www.who.int/csr/disease/avian_in ... Update.pdf

All human isolates for the past 12 months have the 3 BP deletion (125del), which was acquired vis recombination in early 2007. The vast majority of HA sequences have the characteristic Qinghai HA cleavage site GERRRKKR. New polymorphisms can be traced to wild birds, but they are acquired via recombination and are tacked onto the Qinghai clade 2.2.1 genetic background. NONE of this is new.

http://precedings.nature.com/users/3db4 ... 29dc49a780

More recent full sequences are at GISAID.

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