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http://www.deseretnews.com/article/7053 ... virus.html

Utah woman had mutated version of swine flu virus




A 28-year-old woman is believed to be the first Utahn known to carry a mutated version of the H1N1 virus. While health officials have not yet identified the woman, or the type of mutation she was carrying, they say the mutated virus more easily attacks the lungs, which often leads to death.

At this point officials are not overly concerned that the virus is spreading from person to person. They say they have no evidence that it can be easily transmitted.

Dr. Rachel Herlihy, deputy state epidemiologist, told the Deseret News that the Centers for Disease Control and Prevention notified her office earlier this week about the Utah case. The state routinely sends isolated H1N1 virus samples to the CDC for further testing, she said.

"This patient is not (a) new case. … We know it was likely a couple of months ago," she said. "We're looking through our records. At this point, we have more than 800 cases to sift through" of people who have been either hospitalized and/or died after contracting the virus.

Herlihy said she doesn't know at this point whether the woman died, or specifically when she contracted the virus.

As for the type of mutation, "there's been some confusion about whether it's 225 or 222. We're not positive on which one the patient had," she said

This patients is a 28F and the sample was collected in July. The change was at position 225 (also called 222 using H1 numbering), and the patient had D225N and D225G as described earlier

http://www.recombinomics.com/News/12060 ... _Utah.html

Utah sequences from July also had H274Y and a low reactor status, but these were all for different patients. The data are pretty much mixed up in the story, but the 28F did have D225G AND D225N (outcome not reelased in characterization sheet).

CDC has now released sequences at Genbank.

LOCUS GU290190 1701 bp cRNA linear VRL 09-DEC-2009
DEFINITION Influenza A virus (A/Utah/42/2009(H1N1)) segment 4 hemagglutinin
(HA) gene, complete cds.
ACCESSION GU290190
VERSION GU290190.1 GI:270358996
DBLINK Project:37813
KEYWORDS .
SOURCE Influenza A virus (A/Utah/42/2009(H1N1))
ORGANISM Influenza A virus (A/Utah/42/2009(H1N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1701)
AUTHORS Garten,R., Smith,C., Barnes,J., Xu,X., Klimov,A. and Cox,N.
TITLE Human infection with pandemic H1N1 influenza
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 1701)
AUTHORS Garten,R., Smith,C., Barnes,J., Xu,X., Klimov,A. and Cox,N.
TITLE Direct Submission
JOURNAL Submitted (09-DEC-2009) WHO Collaborating Center for Surveillance,
Epidemiology and Control of Influenza, Influenza Division, Centers
for Disease Control and Prevention, 1600 Clifton Road, N.E,
Atlanta, GA 30333, USA
COMMENT Swine influenza A (H1N1) virus isolated during human swine flu
outbreak of 2009. For more information, see http://www.cdc.gov/.

Some of the information does not have GenBank feature identifiers
and is being provided in the comment section.

##EpifluData-START##
Note human case of 2009 H1N1 Pandemic Influenza
Lab_ID 2009719859
Passage_history M1
Isolate A/Utah/42/2009
Subtype H1N1
Segment_name HA
Host_gender F
Host_age 28
Passage_history M1
Country United States
State/Province Utah
Collection_day 24
Collection_month 7
Collection_year 2009
EPI_accession EPI217237
Lineage swl
##EpifluData-END##
FEATURES Location/Qualifiers
source 1..1701
/organism="Influenza A virus (A/Utah/42/2009(H1N1))"
/mol_type="viral cRNA"
/strain="A/Utah/42/2009"
/serotype="H1N1"
/host="Homo sapiens"
/db_xref="taxon:698842"
/segment="4"
/country="USA"
/collection_date="24-Jul-2009"
/note="lineage: swl"
gene 1..1701
/gene="HA"
CDS 1..1701
/gene="HA"
/codon_start=1
/product="hemagglutinin"
/protein_id="ACZ81652.1"
/db_xref="GI:270358997"
/translation="MKAILVVLLYTFATANADTLCIGYHANNSTDTVDTVLERNVTVT
HSVNLLEDKHNGKLCKLRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETSSS
DNGTCYPGDFIDYEELREQLSSVSSFERFEIFPKTSSWPNHDSNKGVTAACPHAEAKS
FYKNLIWLVKKGNSYPKLSKSYINDKGKEVLVLWGIHHPSTSADQQSLYQNADAYVFV
GTSRYSKKFKPEIAIRPKVRGQEGRMNYYWTLVEPGDKITFEATGNLVVPRYAFAMER
NAGSGIIISDTPVHDCNTTCQTPKGAINTSLPFQNIHPITIGKCPKYVKSTKLRLATG
LRNVPSIQSRGLFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADLKSTQNAIDEI
TNKVNSVIEKMNTQFTAVGKEFNHLEKRIENLNKKVDDGFLDIWTYNAELLVLLENER
TLDYHDSNVKNLYEKVRSQLKNNAKEIGNGCFEFYHKCDNTCMESVKNGTYDYPKYSE
EAKLNREEIDGVKLESTRIYQILAIYSTVASSLVLVVSLGAISFWMCSNGSLQCRICI"
ORIGIN
1 atgaaggcaa tactagtagt tctgctatat acatttgcaa ccgcaaatgc agacacatta
61 tgtataggtt atcatgcgaa caattcaaca gacactgtag acacagtact agaaaggaat
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 gatttcattg attatgagga gctaagagag
361 caattgagct cagtgtcatc atttgaaagg tttgagatat tccccaagac aagttcatgg
421 cccaatcatg actcgaacaa aggtgtaacg gcagcatgtc ctcatgctga agcaaaaagc
481 ttctacaaaa atttaatatg gctagttaaa aaaggaaatt catacccaaa gctcagcaaa
541 tcctacatta atgataaagg gaaagaagtc ctcgtgctat ggggcattca ccatccatct
601 actagtgctg accaacaaag cctctatcag 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 agttgatgat ggtttcctag acatttggac ttacaatgcc
1321 gaactgctgg 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

LOCUS GU290188 1701 bp cRNA linear VRL 09-DEC-2009
DEFINITION Influenza A virus (A/Utah/42/2009(H1N1)) segment 4 hemagglutinin
(HA) gene, complete cds.
ACCESSION GU290188
VERSION GU290188.1 GI:270358991
DBLINK Project:37813
KEYWORDS .
SOURCE Influenza A virus (A/Utah/42/2009(H1N1))
ORGANISM Influenza A virus (A/Utah/42/2009(H1N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1701)
AUTHORS Garten,R., Smith,C., Barnes,J., Xu,X., Klimov,A. and Cox,N.
TITLE Human infection with pandemic H1N1 influenza
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 1701)
AUTHORS Garten,R., Smith,C., Barnes,J., Xu,X., Klimov,A. and Cox,N.
TITLE Direct Submission
JOURNAL Submitted (09-DEC-2009) WHO Collaborating Center for Surveillance,
Epidemiology and Control of Influenza, Influenza Division, Centers
for Disease Control and Prevention, 1600 Clifton Road, N.E,
Atlanta, GA 30333, USA
COMMENT Swine influenza A (H1N1) virus isolated during human swine flu
outbreak of 2009. For more information, see http://www.cdc.gov/.

Some of the information does not have GenBank feature identifiers
and is being provided in the comment section.

##EpifluData-START##
Note human case of 2009 H1N1 Pandemic Influenza
Lab_ID 2009719859
Passage_history Original
Isolate A/Utah/42/2009
Subtype H1N1
Segment_name HA
Host_gender F
Host_age 28
Passage_history Original
Country United States
State/Province Utah
Collection_day 24
Collection_month 7
Collection_year 2009
EPI_accession EPI217234
Lineage swl
##EpifluData-END##
FEATURES Location/Qualifiers
source 1..1701
/organism="Influenza A virus (A/Utah/42/2009(H1N1))"
/mol_type="viral cRNA"
/strain="A/Utah/42/2009"
/serotype="H1N1"
/host="Homo sapiens"
/db_xref="taxon:698842"
/segment="4"
/country="USA"
/collection_date="24-Jul-2009"
/note="lineage: swl"
gene 1..1701
/gene="HA"
CDS 1..1701
/gene="HA"
/codon_start=1
/product="hemagglutinin"
/protein_id="ACZ81649.1"
/db_xref="GI:270358992"
/translation="MKAILVVLLYTFATANADTLCIGYHANNSTDTVDTVLERNVTVT
HSVNLLEDKHNGKLCKLRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETSSS
DNGTCYPGDFIDYEELREQLSSVSSFERFEIFPKTSSWPNHDSNKGVTAACPHAGAKS
FYKNLIWLVKKGNSYPKLSKSYINDKGKEVLVLWGIHHPSTSADQQSLYQNADAYVFV
GTSRYSKKFKPEIAIRPKVRXQEGRMNYYWTLVEPGDKITFEATGNLVVPRYAFAMER
NAGSGIIISDTPVHDCNTTCQTPKGAINTSLPFQNIHPITIGKCPKYVKSTKLRLATG
LRNVPSIQSRGLFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADLKSTQNAIDEI
TNKVNSVIEKMNTQFTAVGKEFNHLEKRIENLNKKVDDGFLDIWTYNAELLVLLENER
TLDYHDSNVKNLYEKVRSQLKNNAKEIGNGCFEFYHKCDNTCMESVKNGTYDYPKYSE
EAKLNREEIDGVKLESTRIYQILAIYSTVASSLVLVVSLGAISFWMCSNGSLQCRICI"
ORIGIN
1 atgaaggcaa tactagtagt tctgctatat acatttgcaa ccgcaaatgc agacacatta
61 tgtataggtt atcatgcgaa caattcaaca gacactgtag acacagtact agaaaggaat
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 gatttcattg 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 cctctatcag aatgcagatg catatgtttt tgtggggaca
661 tcaagataca gcaagaagtt caagccggaa atagcaataa gacccaaagt gaggrrtcaa
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 ggtttcctag acatttggac ttacaatgcc
1321 gaactgctgg 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

Both sequences at Genbank had D225G. A sequence at GISAID from the original sample also had mixed signals for D225, D225G, and D225N.

Correction. I loaded the same Genbank sequence twice. The Genbank sequences match the GISAID sequences. The original has mixed signals for D225G and D225N. The cloned sequence just has D225G.

Six Salt Lake County residents now have died after testing positive for H1N1 swine flu and nearly 100 have been hospitalized with the novel strain.

The past four deaths have occurred in the past week, as hospitals in the valley report being inundated with patients with flu-like symptoms and doctors race to understand more about the new virus.

Nathan Dean, chief of pulmonary critical care at Intermountain Medical Center in Murray and LDS Hospital in Salt Lake City, said about one patient a day has been admitted to the intensive care unit for the past three weeks.

Most ICU patients have been overweight, he said, which is puzzling: Their weight isn't causing other health conditions that the federal government says puts people at higher risk of severe influenza complications, such as cardiovascular disease or diabetes, he said.

"I really don't consider being overweight a disease, at least in the patients we're seeing," Dean said. "It's not like they're so [obese] they've gone into heart failure. Somehow, the disease is striking them."

About a fourth of the ICU flu patients have suffered from an inflamed airway, exacerbated by conditions like asthma or emphysema. Nationally, asthma is the most common condition causing hospitalizations.

Other patients end up in the ICU suffering from adult respiratory distress syndrome (ARDS) or septic shock, he said. ARDS is a lung condition that leads to low oxygen levels in the blood,


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which can harm organs, according to the U.S. Department of Health and Human Services.

And while septic shock, which can lead to low blood pressure and organ failure, is normally associated with bacterial infections, doctors aren't seeing such infections with flu patients.

"The virus itself seems to be initiating the septic shock cascade," said Dean, who said the virus reminds him of hantavirus, which is transmitted through rodent urine, droppings or saliva, and can cause acute respiratory distress.

The latest reported Salt Lake County deaths were a man between the ages of 25 and 50 who died Saturday and a woman who was 25 to 60 years old who died Monday. All six of the patients who have died had underlying health conditions that "may have put them at higher risk of complications or death, according to Salt Lake Valley Health Department spokeswoman Pam Davenport.

In two cases, those conditions have included obesity and sleep apnea and a liver condition, according to hospital officials or family members.

Additional deaths "are not unexpected," Gary Edwards, the department's executive director, said in a statement.

The continuing illnesses are surprising, since it was believed that the flu would take a summertime lull.

"Utah seems to be having a lot more of this than the rest of the country, in terms of severity of disease," Dean said. "It's partly because we have larger numbers of influenza than surrounding states. ... We're just trying to figure this out."

http://www.sltrib.com/ci_12603135?source=most_viewed

http://www.sltrib.com/news/ci_12999458

This could be the woman.