Brazil finds new strain of H1N1 virus - NOT

[Gert van der Hoek]

Brazil finds new strain of H1N1 virus



SAO PAULO (AFP) ? Brazilian scientists have identified a new strain of the H1N1 virus after examining samples from a patient in Sao Paulo, their institute said Tuesday.

The variant has been called A/Sao Paulo/1454/H1N1 by the Adolfo Lutz Bacteriological Institute, which compared it with samples of the A(H1N1) swine flu from California.

The genetic sequence of the new sub-type of the H1N1 virus was isolated by a virology team lead by one of its researchers, Terezinha Maria de Paiva, the institute said in a statement.

The mutation comprised of alterations in the Hemagglutinin protein which allows the virus to infect new hosts, it said.

It was not yet known whether the new strain was more aggressive than the current A(H1N1) virus which has been declared pandemic by the World Health Organization.

The genetic make-up of the H1N1 virus and its subvariants are important for scientists.

Pharmaceutical companies are working to mass produce a vaccine against the current A(H1N1) flu.

There are fears though that it could mutate into a deadly strain, much in the same way as the 1918 Spanish flu -- also an A(H1N1) virus type -- did when it killed tens of millions around the planet.

According to the WHO, 36,000 people in 76 countries have been infected with the H1N1 virus, causing 163 deaths.

http://news.yahoo.com/s/afp/20090616/hl_afp/healthflubrazilscience_20090616181146

[Giuseppe]

Re: Brazil finds new strain of H1N1 virus

GenBank: GQ247724.1
Influenza A virus (A/Sao Paulo/1454/2009(H1N1)) segment 4 hemagglutin (HA) gene, complete cds

<input name="EntrezSystem2.PEntrez.Sequence.Sequence_Sing leReportPanel.Sequence_ViewerPanel.Sequence_Viewer Title.Database" sid="1" id="Database" value="nuccore" type="hidden">
<script type="text/javascript" src="http://www.ncbi.nlm.nih.gov/core/ajax_loader/1.0/js/loadingbar.js"></script><script type="text/javascript" src="http://www.ncbi.nlm.nih.gov/core/ajax_loader/1.0/js/contentLoader.js"></script><link type="text/css" rel="stylesheet" href="http://www.ncbi.nlm.nih.gov/core/ajax_loader/1.0/css/loadingbar.css">

• Comment
• Features
• Sequence

LOCUS GQ247724 1701 bp cRNA linear VRL 08-JUN-2009
DEFINITION Influenza A virus (A/Sao Paulo/1454/2009(H1N1)) segment 4
hemagglutin (HA) gene, complete cds.
ACCESSION GQ247724
VERSION GQ247724.1 GI:239504533
DBLINK Project:37813
KEYWORDS .
SOURCE Influenza A virus (A/Sao Paulo/1454/2009(H1N1))
ORGANISM Influenza A virus (A/Sao Paulo/1454/2009(H1N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1701)
AUTHORS de Paiva,T.M., Santos,C.S., Silva,D.B., Correa,K.O., Ishida,M.A.,
Benega,M.A. and Sacchi,C.
TITLE Human infection with novel swine H1N1 influenza virus in Sao Paulo,
Brazil
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 1701)
AUTHORS de Paiva,T.M., Santos,C.S., Silva,D.B., Correa,K.O., Ishida,M.A.,
Benega,M.A. and Sacchi,C.
TITLE Direct Submission
JOURNAL Submitted (05-JUN-2009) Respiratory Virus Section, Adolfo Lutz
Institute, Av. Dr. Arnaldo 355, Sao Paulo, SP 01246/902, Brazil
COMMENT Swine influenza A (H1N1) virus isolated during human swine flu
outbreak of 2009.
FEATURES Location/Qualifiers
source 1..1701
/organism="Influenza A virus (A/Sao
Paulo/1454/2009(H1N1))"
/mol_type="viral cRNA"
/strain="A/Sao Paulo/1454/2009"
/serotype="H1N1"
/isolation_source="nasal swab"
/host="Homo sapiens; gender M; age 26"
/db_xref="taxon:650343"
/segment="4"
/country="Brazil"
/collection_date="29-Apr-2009"
/note="lineage: swl
first MDCK cell passage"
gene 1..1701
/gene="HA"
CDS 1..1701
/gene="HA"
/codon_start=1
/product="hemagglutin"
/protein_id="ACR78585.1"
/db_xref="GI:239504534"
/translation="MKAILVVLLYTFATANADTLCIGYHANNSTDTVDTVL EKNVTVT
HSVNLLEDKHNGKLCKLRGVAPLHLGKCNIAGWILGNPECESLSTASSWS YIVETSSS
DNGTCYPGDFIDYEELREQLSSVSSFERFEIFPKTSSWPNHDSNKGVTAA CPHAGAKS
FYKNLIWLVKKGNSYPKLSKSYINDKGKEVLVLWGIHHPSTSADQQSLYQ NADAYVFV
GSSRYSKKFKPEIAIRPKVRDQEGRMNYYWTLVEPGDKITFEATGNLVVP RYAFAMER
NAGSGIIISDTPVHDCNTTCQTPKGAINTSLPFQNIHPITIGKCPKYVKS TKLRLATG
LRNVPSIQSRGLFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADLKS TQNAIDEI
TNKVNSVIEKMNTQFTAVGKEFNHLEKRIENLNKKVDDGFLDIWTYNAEL LVLLENER
TLDYHDSNVKNLYEKVRSQLKNNAKEIGNGCFEFYHKCDNTCMESVKNGT YDYPKYSE
EAKLNREEIDGVKLESTRIYQILAIYSTVASSLVLVVSLGAISFWMCSNG SLQCRICI"
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 tgtggggtca
661 tcaagataca gcaagaagtt caagccggaa atagcaataa gacccaaagt gagggatcaa
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 agttgatgat 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

http://www.ncbi.nlm.nih.gov/nuccore/239504533?ordinalpos=1&itool=EntrezSystem2.PEntrez.Sequence.Sequence_ResultsPanel.Sequence_RVDocSum

//</pre>

[Gert van der Hoek]

Re: Brazil finds new strain of H1N1 virus

See also this thread:

http://www.flutrackers.com/forum/showthread.php?t=110724

[Giuseppe]

Re: Brazil finds new strain of H1N1 virus

GenBank: GQ250156.1
Influenza A virus (A/Sao Paulo/1454/2009(H1N1)) segment 7 matrix protein 2 (M2) and matrix protein 1 (M1) genes, complete cds

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• Comment
• Features
• Sequence

LOCUS GQ250156 982 bp cRNA linear VRL 09-JUN-2009
DEFINITION Influenza A virus (A/Sao Paulo/1454/2009(H1N1)) segment 7 matrix
protein 2 (M2) and matrix protein 1 (M1) genes, complete cds.
ACCESSION GQ250156
VERSION GQ250156.1 GI:239586241
DBLINK Project:37813
KEYWORDS .
SOURCE Influenza A virus (A/Sao Paulo/1454/2009(H1N1))
ORGANISM Influenza A virus (A/Sao Paulo/1454/2009(H1N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 982)
AUTHORS de Paiva,T.M., Santos,C.L., Silva,D.B., Correa,K.O., Ishida,M.A.,
Benega,M.A. and Sacchi,C.
TITLE Human infection with novel swine H1N1 influenza virus in Sao Paulo,
Brazil
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 982)
AUTHORS de Paiva,T.M., Santos,C.L., Silva,D.B., Correa,K.O., Ishida,M.A.,
Benega,M.A. and Sacchi,C.
TITLE Direct Submission
JOURNAL Submitted (08-JUN-2009) Respiratory Virus Section, Adolfo Lutz
Institute, Av. Dr. Arnaldo 355, Sao Paulo, SP 01246/902, Brazil
COMMENT Swine influenza A (H1N1) virus isolated during human swine flu
outbreak of 2009.
FEATURES Location/Qualifiers
source 1..982
/organism="Influenza A virus (A/Sao
Paulo/1454/2009(H1N1))"
/mol_type="viral cRNA"
/strain="A/Sao Paulo/1454/2009"
/serotype="H1N1"
/isolation_source="nasal swab"
/host="Homo sapiens; gender M; age 26"
/db_xref="taxon:650343"
/segment="7"
/country="Brazil: Sao Paulo"
/collection_date="29-Apr-2009"
/note="lineage: swl
passaged in MDCK cells"
gene 1..982
/gene="M2"
CDS join(1..26,715..982)
/gene="M2"
/codon_start=1
/product="matrix protein 2"
/protein_id="ACR83533.1"
/db_xref="GI:239586243"
/translation="MSLLTEVETPTRSEWECRCSDSSDPLVIAANIIGILH LILWITD
RLFFKCIYRRFKYGLKRGPSTEGVPESMREEYQQEQQSAVDVDDGHFVNI ELE"
gene 1..759
/gene="M1"
CDS 1..759
/gene="M1"
/codon_start=1
/product="matrix protein 1"
/protein_id="ACR83532.1"
/db_xref="GI:239586242"
/translation="MSLLTEVETYVLSIIPSGPLKAEIAQRLESVFAGKNT DLEALME
WLKTRPILSPLTKGILGFVFTLTVPSERGLQRRRFVQNALNGNGDPNNMD RAVKLYKK
LKREITFHGAKEVSLSYSTGALASCMGLIYNRMGTVTTEAAFGLVCATCE QIADSQHR
SHRQMATTTNPLIRHENRMVLASTTAKAMEQMAGSSEQAAEAMEVANQTR QMVHAMRT
IGTHPSSSAGLKDDLLENLQAYQKRMGVQMQRFK"
ORIGIN
1 atgagtcttc taaccgaggt cgaaacgtac gttctttcta tcatcccgtc aggccccctc
61 aaagccgaga tcgcgcagag actggaaagt gtctttgcag gaaagaacac agatcttgag
121 gctctcatgg aatggctaaa gacaagacca atcttgtcac ctctgactaa gggaatttta
181 ggatttgtgt tcacgctcac cgtgcccagt gagcgaggac tgcagcgtag acgctttgtc
241 caaaatgccc taaatgggaa tggggacccg aacaacatgg atagagcagt taaactatac
301 aagaagctca aaagagaaat aacgttccat ggggccaagg aggtgtcact aagctattca
361 actggtgcac ttgccagttg catgggcctc atatacaaca ggatgggaac agtgaccaca
421 gaagctgctt ttggtctagt gtgtgccact tgtgaacaga ttgctgattc acagcatcgg
481 tctcacagac agatggctac taccaccaat ccactaatca ggcatgaaaa cagaatggtg
541 ctggctagca ctacggcaaa ggctatggaa cagatggctg gatcgagtga acaggcagcg
601 gaggccatgg aggttgctaa tcagactagg cagatggtac atgcaatgag aactattggg
661 actcatccta gctccagtgc tggtctgaaa gatgaccttc ttgaaaattt gcaggcctac
721 cagaagcgaa tgggagtgca gatgcagcga ttcaagtgat cctctcgtca ttgcagcaaa
781 tatcattggg atcttgcacc tgatattgtg gattactgat cgtctttttt tcaaatgtat
841 ttatcgtcgc tttaaatacg gtttgaaaag agggccttct acggaaggag tgcctgagtc
901 catgagggaa gaatatcaac aggaacagca gagtgctgtg gatgttgacg atggtcattt
961 tgtcaacata gagctagagt aa

http://www.ncbi.nlm.nih.gov/nuccore/239586241?ordinalpos=1&itool=EntrezSystem2.PEntrez.Sequence.Sequence_ResultsPanel.Sequence_RVDocSum

//</pre>


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[mixin]

Re: Brazil finds new strain of H1N1 virus

Ha was submitted on June 6, MP on June 9.

Where are all our FT sequencers, that we had to read about this in the news reports?!

[gsgs]

Re: Brazil finds new strain of H1N1 virus

nothing to see here, move along.

[Mamabird]

Re: Brazil finds new strain of H1N1 virus

Agreed. Just run of the mill Swine Flu like that in about 5 dozen other countries.

[AlaskaDenise]

Re: Brazil finds new strain of H1N1 virus

Of the 4 sequences from Brazil with M1 and M2 sequences posted, the M1 are identical, but Sao Paulo has a change in (position 43?) the M2 (but not the E16G and S20N that Mamabird said need to be monitored):

Positions from 1 till 60
Consensus sequence M S L L T E V E T P T R S E W E C R C S D S S D P L V I A A N I I G I L H L I L W I L D R L F F K C I Y R R F K Y G L K
ACR08493 A/Minas Gerais/65/2009(H1N1) - - - - - - - - - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - - - - - - - - - - - - - -
ACR83533 A/Sao Paulo/1454/2009(H1N1) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . T . . . . . . . . . . . . . . . . .
ACR09350 A/Rio de Janeiro/118/2009(H1N1) - - - - - - - - - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - - - - - - - - - - - - - - - - -
ACR09348 A/Rio de Janeiro/125/2009(H1N1) - - - - - - - - - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - - - - - - - - - - - - - - - -

Positions from 61 till 97
Consensus sequence R G P S T E G V P E S M R E E Y Q Q E Q Q S A V D V D D G H F V N I E L E
ACR08493 A/Minas Gerais/65/2009(H1N1) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
ACR83533 A/Sao Paulo/1454/2009(H1N1) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
ACR09350 A/Rio de Janeiro/118/2009(H1N1) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
ACR09348 A/Rio de Janeiro/125/2009(H1N1) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -




.

[AlaskaDenise]

Re: Brazil finds new strain of H1N1 virus

Of the 3 South American NA postings (not from Sao Paulo) only 1 has 2 changes, but not the ones Mamabird recommends to monitor.

.

[mixin]

Re: Brazil finds new strain of H1N1 virus

It's a relief to know our resident experts aren't overlooking anything

Another non-news report bites the dust.

[The Mountains Voice]

New Mutant Strain Identified in Brazil

http://www.news.com.au/couriermail/story/0,23739,25649013-5003402,00.html

South America bears swine flu
Print From correspondents in Buenos Aires
June 17, 2009 07:40am

THE swine flu deaths of two people in Argentina and a mutation of the H1N1 virus detected in Brazil have added to fears that South America is entering a harsh winter beset by the flu pandemic.

While big pharmaceutical firms are ramping up efforts to mass-produce a vaccine for H1N1, they are still months away from having enough stocks - too late for the Southern Hemisphere's winter flu season.

South America has already recorded five deaths from the disease: two in Chile, one in Colombia last week and, most recently, those of a three-month-old girl and a 28-year-old man with leukemia in Argentina's capital Buenos Aires.

The number of infected cases is outstripping figures put out regularly by the World Health Organisation.

According to the latest statistics from national health authorities, Chile has 2355 patients confirmed with H1N1 flu, Argentina has 733, Peru has 113, Brazil 69, Ecuador 84, Venezuela 44, Uruguay 36, Paraguay 25 and Suriname 13.

Those figures are far overshadowed by the data from North America and Central America, the apparent source of the pandemic.

Mexican authorities say they have had 109 deaths and 6,294 infected cases. The United States today added a nine-year-old boy to its death toll, bringing it to 47, alongside 17,855 infected cases. Canada has six deaths and 3515 infections.

Central America and the Caribbean have also been hit, registering nearly 800 infections and three deaths (one each in Costa Rica, the Dominican Republic and Guatemala).

Although the A(H1N1) virus has been classed as relatively mild since first being detected in April, its unusually strong effect on the young, on those with other underlying health problems, and on the poor have made it a redoubtable challenge.

Some major drug companies have started producing a vaccine for pre-clinical testing, but one of them, Switzerland's Novartis, told the Financial Times it did not intend to give it away to poor countries.

US rival Baxter said today it should have its H1N1 vaccine commercially available in July.

But there were underlying fears that the virus currently spreading around the world through human-to-human contact might mutate further, possibly into a more deadly form, as happened with the 1918 Spanish flu which killed tens of millions.

Those fears heightened a little today, when a Brazil's Adolfo Lutz Bacteriological Institute said its researchers had identified and isolated a new strain of the A(H1N1) virus in a Sao Paulo patient.

It was not yet known whether that variant, called A/Sao Paulo/1454/H1N1, was more aggressive than the more common type.

The institute said in a statement the mutation comprised alterations in the Hemagglutinin protein which allows the virus to infect new hosts.

[HenryN]

Re: Brazil finds new strain of H1N1 virus

Identical HA sequences


gb|GQ247724.1| Influenza A virus (A/Sao Paulo/1454/2009(H1N1)... 3068 0.0
gb|GQ232060.1| Influenza A virus (A/North Dakota/04/2009(H1N1... 3068 0.0
gb|GQ232035.1| Influenza A virus (A/Wisconsin/11/2009(H1N1)) ... 3068 0.0
gb|GQ168620.1| Influenza A virus (A/Texas/19/2009(H1N1)) segm... 3068 0.0
gb|GQ162197.1| Influenza A virus (A/Mexico/4575/2009(H1N1)) s... 3068 0.0
gb|GQ162191.1| Influenza A virus (A/Mexico/4595/2009(H1N1)) s... 3068 0.0
gb|GQ162190.1| Influenza A virus (A/Mexico/4482/2009(H1N1)) s... 3068 0.0
gb|GQ160605.1| Influenza A virus (A/Wisconsin/08/2009(H1N1)) ... 3068 0.0
gb|GQ149684.1| Influenza A virus (A/Mexico/4603/2009(H1N1)) s... 3068 0.0
gb|GQ149677.1| Influenza A virus (A/Mexico/4482/2009(H1N1)) s... 3068 0.0
gb|GQ149674.1| Influenza A virus (A/Mexico/4482/2009(H1N1)) s... 3068 0.0
gb|GQ149671.1| Influenza A virus (A/Mexico/4482/2009(H1N1)) s... 3068 0.0
gb|GQ149634.1| Influenza A virus (A/Mexico/4604/2009(H1N1)) s... 3068 0.0
gb|GQ149630.1| Influenza A virus (A/Mexico/4603/2009(H1N1)) s... 3068 0.0
gb|GQ117112.1| Influenza A virus (A/Michigan/02/2009(H1N1)) s... 3068 0.0

[The Mountains Voice]

Re: New Mutant Strain Identified in Brazil

http://www.straitstimes.com/Breaking%2BNews/World/Story/STIStory_391477.html

June 17, 2009
H1N1 FLU PANDEMIC
New H1N1 strain found

SAO PAULO - BRAZILIAN scientists have identified a new strain of the H1N1 virus after examining samples from a patient in Sao Paulo, their institute said on Tuesday.

The variant has been called A/Sao Paulo/1454/H1N1 by the Adolfo Lutz Bacteriological Institute, which compared it with samples of the A(H1N1) swine flu from California.

The genetic sequence of the new sub-type of the H1N1 virus was isolated by a virology team lead by one of its researchers, Terezinha Maria de Paiva, the institute said in a statement.

The mutation comprised of alterations in the Hemagglutinin protein which allows the virus to infect new hosts, it said.

It was not yet known whether the new strain was more aggressive than the current A(H1N1) virus which has been declared pandemic by the World Health Organization.

The genetic make-up of the H1N1 virus and its subvariants are important for scientists.

Pharmaceutical companies are working to mass produce a vaccine against the current A(H1N1) flu.

There are fears though that it could mutate into a deadly strain, much in the same way as the 1918 Spanish flu - also an A(H1N1) virus type - did when it killed tens of millions around the planet.

According to the WHO, 36,000 people in 76 countries have been infected with the H1N1 virus, causing 163 deaths. -- AFP

[HenryN]

Re: New Mutant Strain Identified in Brazil

http://www.straitstimes.com/Breaking...ry_391477.html

June 17, 2009
H1N1 FLU PANDEMIC
New H1N1 strain found

The mutation comprised of alterations in the Hemagglutinin protein which allows the virus to infect new hosts, it said.

AFP

Nonsense

http://www.flutrackers.com/forum/showpost.php?p=249633&postcount=11

[hongkonger]

Re: New Mutant Strain Identified in Brazil

I am not a biologist. Could you explain why it's nonsense and how they came up with the nonsense?