D225G in Fatal Brazil Nasopharyngeal Swab

niman · **Posted:** Sat Jan 09, 2010 7:12 am

Most D225G isolates have come from fatal lung cases. New sequence at Genbank has D225G in nasal swab.

niman · **Posted:** Sat Jan 09, 2010 7:12 am

LOCUS CY054280 1701 bp cRNA linear VRL 08-JAN-2010
DEFINITION Influenza A virus (A/Rio de Janeiro/5826/2009(H1N1)) segment 4
sequence.
ACCESSION CY054280
VERSION CY054280.1 GI:283549135
DBLINK Project:37813
KEYWORDS .
SOURCE Influenza A virus (A/Rio de Janeiro/5826/2009(H1N1))
ORGANISM Influenza A virus (A/Rio de Janeiro/5826/2009(H1N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1701)
AUTHORS Motta,F.C., Born,P.S., Souza,T.M.L., Ferreira,S.S., Silva,P.C.R.,
Pinhao,A.T., Andrade,T.S., Mesquita,M.M.A., Lima,C.H.A.,
Andrade,D.S., Machado,D.B.B., Ferreira,D.A., Almeida,J.M.B.,
Cantarino,L.M., Krawczuc,M.M. and Siqueira,M.M.
TITLE Molecular evaluation of haemagglutinin (segment 4) sequences from
clinical samples of influenza A/H1N1pdm confirmed cases in Brazil
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 1701)
AUTHORS Motta,F.C., Born,P.S., Souza,T.M.L., Ferreira,S.S., Silva,P.C.R.,
Pinhao,A.T., Andrade,T.S., Mesquita,M.M.A., Lima,C.H.A.,
Andrade,D.S., Machado,D.B.B., Ferreira,D.A., Almeida,J.M.B.,
Cantarino,L.M., Krawczuc,M.M. and Siqueira,M.M.
TITLE Direct Submission
JOURNAL Submitted (08-JAN-2010) Respiratory Viruses and Measles Laboratory,
IOC/FIOCRUZ, Pav. Helio e Peggy Pereira, Av. Brasil, n. 4365, Rio
de Janeiro, RJ 21040-900, Brazil
FEATURES Location/Qualifiers
source 1..1701
/organism="Influenza A virus (A/Rio de
Janeiro/5826/2009(H1N1))"
/mol_type="viral cRNA"
/strain="A/Rio de Janeiro/5826/2009"
/serotype="H1N1"
/isolation_source="Nasopharyngeal secretion"
/host="human; gender M; age 32Y"
/db_xref="taxon:706446"
/segment="4"
/country="Brazil: RJ"
/collection_date="28-Jul-2009"
/note="deceased patient; deceased patient"
gene 1..1701
/gene="HA"
CDS 1..1701
/gene="HA"
/function="receptor binding and fusion protein"
/codon_start=1
/product="hemagglutinin"
/protein_id="ADB25319.1"
/db_xref="GI:283549136"
/translation="MKAILVVLLYTFATANADTLCIGYHANNSTDTVDTVLEKNVTVT
HSVNLLEDKHNGKLCKLRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETSSS
DNGTCYPGDFIDYEELREQLSSVSSFERFEIFPKTSSWPNHDSNKGVTAACPHAGAKS
FYKNLIWLVKKGNSYPKLSKSYINDKGKEVLVLWGIHHPSTSADQQSLYQNADAYVFV
GTSRYSKKFKPEIAIRPKVRGQEGRMNYYWTLVEPGDKITFEATGNLVVPRYAFAMER
NAGSGIIISDTPVHDCNTTCQTPKGAINTSLPFQNIHPITIGKCPKYVKSTKLRLATG
LRNVPSIQSRGLFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADLKSTQNAIDEI
TNKVNSVIEKMNTQFTAVGKEFNHLEKRIENLNKKVDDGFLDIWTYNAELLVLLENER
TLDYHDSNVKNLYEKVRSQLKNNAKEIGNGCFEFYHKCDNTCMESVKNGTYDYPKYSE
EAKLNREEIDGVKLESTRIYQILAIYSTVASSLVLVVSLGAISFWMCSNGSLQCRICI"
sig_peptide 1..51
/gene="HA"
mat_peptide 52..1032
/gene="HA"
/product="HA1"
mat_peptide 1033..1698
/gene="HA"
/product="HA2"
ORIGIN
1 atgaaggcaa tactagtagt tctgctatat acatttgcaa ccgcaaatgc agacacatta
61 tgtataggtt atcatgcgaa caattcaaca gacactgtag acacagtact agaaaagaat
121 gtaacagtaa cacactctgt taaccttcta gaagacaagc ataacgggaa actatgcaaa
181 ctaagagggg tagccccatt gcatttgggt aaatgtaaca ttgctggctg gatcctggga
241 aatccagagt gtgaatcact ctccacagca agctcatggt cctacattgt ggaaacatct
301 agttcagaca atggaacgtg ttacccagga gatttcatcg attatgagga gctaagagag
361 caattgagct cagtgtcatc atttgaaagg tttgagatat tccccaagac aagttcatgg
421 cccaatcatg actcgaacaa aggtgtaacg gcagcatgtc ctcatgctgg agcaaaaagc
481 ttctacaaaa atttaatatg gctagttaaa aaaggaaatt catacccaaa gctcagcaaa
541 tcctacatta atgataaagg gaaagaagtc ctcgtgctat ggggcattca ccatccatct
601 actagtgctg accaacaaag tctctatcag aatgcagatg catatgtttt tgtggggaca
661 tcaagataca gcaagaagtt caagccggaa atagcaataa gacccaaagt gaggggtcaa
721 gaagggagaa tgaactatta ctggacacta gtagagccgg gagacaaaat aacattcgaa
781 gcaactggaa atctagtggt accgagatat gcattcgcaa tggaaagaaa tgctggatct
841 ggtattatca tttcagatac accagtccac gattgcaata caacttgtca gacacccaag
901 ggtgctataa acaccagcct cccatttcag aatatacatc cgatcacaat tggaaaatgt
961 ccaaaatatg taaaaagcac aaaattgaga ctggccacag gattgaggaa tgtcccgtct
1021 attcaatcta gaggcctatt tggggccatt gccggtttca ttgaaggggg gtggacaggg
1081 atggtagatg gatggtacgg ttatcaccat caaaatgagc aggggtcagg atatgcagcc
1141 gacctgaaga gcacacagaa tgccattgac gagattacta acaaagtaaa ttctgttatt
1201 gaaaagatga atacacagtt cacagcagta ggtaaagagt tcaaccacct ggaaaaaaga
1261 atagagaatt taaataaaaa ggttgatgat ggtttcctgg acatttggac ttacaatgcc
1321 gaactgttgg ttctattgga aaatgaaaga actttggact accacgattc aaatgtgaag
1381 aacttatatg aaaaggtaag aagccagtta aaaaacaatg ccaaggaaat tggaaacggc
1441 tgctttgaat tttaccacaa atgcgataac acgtgcatgg aaagtgtcaa aaatgggact
1501 tatgactacc caaaatactc agaggaagca aaattaaaca gagaagaaat agatggggta
1561 aagctggaat caacaaggat ttaccagatt ttggcgatct attcaactgt cgccagttca
1621 ttggtactgg tagtctccct gggggcaatc agtttctgga tgtgctctaa tgggtctcta
1681 cagtgtagaa tatgtattta a

niman · **Posted:** Sat Jan 09, 2010 7:52 am

Updated D225G list (sequences at bottom of list are mixtures)

gb|GU371263.1| Influenza A virus (A/Bryansk/IIV2971/2009(H1N1... 36.2 0.76
gb|CY053907.1| Influenza A virus (A/Argentina/HNRG16/2009(H1N... 36.2 0.76
gb|GU367327.1| Influenza A virus (A/Salekhard/01/2009(H1N1)) ... 36.2 0.76
gb|GU367317.1| Influenza A virus (A/Tomsk/07/2009(H1N1)) segm... 36.2 0.76
gb|GU367315.1| Influenza A virus (A/Abakan/02/2009(H1N1)) seg... 36.2 0.76
gb|CY053695.1| Influenza A virus (A/Catalonia/NS092145684/200... 36.2 0.76
gb|GU290190.1| Influenza A virus (A/Utah/42/2009(H1N1)) segme... 36.2 0.76
gb|GU211219.1| Influenza A virus (A/Vladivostok/01/2009(H1N1)... 36.2 0.76
gb|GU189649.1| Influenza A virus (A/Zhejiang/DTID-ZJU03/2009(... 36.2 0.76
gb|GU112090.1| Influenza A virus (A/Zhejiang/DTID-ZJU02/2009(... 36.2 0.76
gb|GU108486.1| Influenza A virus (A/Zhejiang-Yiwu/11/2009(H1N... 36.2 0.76
gb|CY047074.1| Influenza A virus (A/Catalonia/NS1706/2009(H1N... 36.2 0.76
gb|GU014750.1| Influenza A virus (A/Hiroshima/201/2009(H1N1))... 36.2 0.76
gb|GQ915017.1| Influenza A virus (A/Sao Paulo/53206/2009(H1N1... 36.2 0.76
gb|GQ457487.1| Influenza A virus (A/Texas/05/2009(H1N1)) segm... 36.2 0.76
gb|GQ379822.1| Influenza A virus (A/Mexico/InDRE4114/2009(H1N... 36.2 0.76
gb|GQ374893.1| Influenza A virus (A/reassortant/IDCDC-RG18(Te... 36.2 0.76
gb|GQ280121.1| Influenza A virus (A/reassortant/NIBRG-121(Cal... 36.2 0.76
gb|GQ229348.1| Influenza A virus (A/swine/Hong Kong/NS857/200... 36.2 0.76
gb|GQ229261.1| Influenza A virus (A/swine/Hong Kong/NS837/200... 36.2 0.76
gb|GQ232076.1| Influenza A virus (A/Texas/11/2009(H1N1)) segm... 36.2 0.76
gb|GQ200237.1| Influenza A virus (A/Georgia/01/2009(H1N1)) se... 36.2 0.76
gb|GQ162194.1| Influenza A virus (A/Mexico/3955/2009(H1N1)) s... 36.2 0.76
gb|GQ160568.1| Influenza A virus (A/New York/04/2009(H1N1)) s... 36.2 0.76
gb|GQ132145.1| Influenza A virus (A/Mexico/InDRE4114/2009(H1N... 36.2 0.76
gb|CY053638.1| Influenza A virus (A/Mexico/InDRE43149/2009(H1... 32.2 12
gb|CY052399.1| Influenza A virus (A/Texas/42291877/2009(H1N1)... 32.2 12
gb|GU292341.1| Influenza A virus (A/Finland/614/2009(H1N1)) s... 32.2 12
gb|CY052019.1| Influenza A virus (A/Norway/3206-3/2009(H1N1))... 32.2 12
gb|CY051989.1| Influenza A virus (A/Norway/2924/2009(H1N1)) s... 32.2 12
gb|CY047083.1| Influenza A virus (A/Catalonia/NS2008/2009(H1N... 32.2 12
gb|CY047080.1| Influenza A virus (A/Catalonia/NS2001/2009(H1N... 32.2 12

niman · **Posted:** Sat Jan 09, 2010 8:00 am

It is worth noting that prior samples from Brazil with D225G were from necropsy samples.

silvermaran · **Joined:** Tue Nov 24, 2009 7:10 pm **Posts:** 399

Where did the first samples from Brazil come from and why were their tests more efficient than the CDC's findings?

niman · **Posted:** Sat Jan 09, 2010 10:23 am

silvermaran wrote:

After watching the David Goldman fiasco for his son Sean last nite, I have no trust in the honor of truth and justice in anything coming from Brazil.

What does that have to do with sequences?

silvermaran · **Joined:** Tue Nov 24, 2009 7:10 pm **Posts:** 399

Scientists in Brazil say they have isolated and identified a new strain of the A(H1N1) swine flu virus from a patient who was hospitalized in São Paulo in April and who has since made a complete recovery. The scientists don't know if the new strain causes more severe infections.

The new strain came from a sample isolated from a 26-year old São Paulo man who started to have symptoms of flu shortly after returning from Mexico. He was hospitalized on 24 April and has since made a full recovery. While in hospital the patient gave a sample for analysis.

A team at the Instituto Adolfo Lutz in São Paulo, led by virologist Dr Terezinha Maria de Paiva, isolated the new strain, A/São Paulo/1454/H1N1, from this sample at the end of April.

Using electron microscopes, another team at Instituto Adolfo Lutz, led by Cecília Luiza Simões, looked at nucleotide sequences in the new strain.

They looked in particular at segments number 4 and 7. Segment 4 codes for the protein Hemagglutinin (HA) which is responsible for virus infectivity and triggers the production of antibodies in the human immune system. Segment 7 codes for the matrix proteins (MP) M1 and M2, which help the virus to develop and maintain its structure.

When they compared segment 4 and segment 7 of the new A/São Paulo/1454/H1N1 strain against the novel swine flu reference strain A/Califórnia/04/H1N1 they found that segment 7 appeared to be "completely conserved" while segment 4 showed a number of discrete alterations in nucleotide and amino acid sequences.

The complete nucleotide sequences for these HA and MP segments have been published in GenBank, the American open access gene sequence database, under access numbers GQ247724 (for the HA gene) and GQ250156 (for the MP).

For which the CDC denied. http://www.cidrap.umn.edu/cidrap/conten ... train.html

niman · **Posted:** Sat Jan 09, 2010 11:01 am

silvermaran wrote:

I feel like they can say and do whatever they want in Brazil. They have no respect for the international laws agreed upon by the UN, why would you believe they are honorable?
It was not until sanctions were threatened and US/Brazil relations were in jeopardy did they give the man his son.
Which took 5 years, after repeatedly denying him his rights to even see the boy after 11 visits there.
I would not believe anything they say. But that is just me.

What does this have to do with sequences? I think you are posting on the wrong thread/board.

silvermaran · **Joined:** Tue Nov 24, 2009 7:10 pm **Posts:** 399

Please don't be offended Dr. N. It is not you and your reports I question.

niman · **Posted:** Sat Jan 09, 2010 1:20 pm

silvermaran wrote:

Please don't be offended Dr. N. It is not you and your reports I question. They are great to finally feel truth.

It is the history I question. Not the here and now. But one cannot forge ahead without looking back.

I still see no relevance to the Brazil sequence, which is the subject of this thread.

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D225G in Fatal Brazil Nasopharyngeal Swab

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