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Health officials bump up Oklahoma flu outbreak to epidemic status

prepdeb

Moderator
http://www.tulsaworld.com/news/article.aspx?articleID=20080227_1__OKLAH15888

Health officials bump up Oklahoma flu outbreak to epidemic status

by: Associated Press
2/27/2008 12:00 AM


OKLAHOMA CITY -- Influenza activity has changed from "widespread" to "epidemic" in Oklahoma and conditions could get worse before they improve, health officials say.

"This epidemic is placing a significant strain on our health care systems, our workplaces and our schools due to high rates of absenteeism," state epidemiologist Dr. Kristy Bradley said Tuesday.

The Oklahoma Health Department's surveillance network of 35 health care providers, laboratories and ambulance services statewide has reported an increase in cases during the past four weeks, Bradley said.

"We have a high rate of people who are very ill and that's translated into more hospitalizations because of the flu," she said.

The change in the status of flu activity in Oklahoma -- "widespread" to "epidemic" -- occurred when more than 60 percent of patients treated for flu symptoms at surveillance network providers tested positive for influenza, Bradley said.

"The rate of confirmed illness is clearly above what we would expect -- three to four times above baseline expectations," she said.

Bradley is worried that the epidemic could lead to not only more flu cases, but more deaths related to the virus. Oklahoma did not have a flu epidemic in 2007, she said.

Dr. Pamela E. Ahearn, a physican in Madill, said the flu is rampant in southern Oklahoma.

"In fact, several of my staff and their family members have had it even though we were all immunized for it. The rest of us took Tamiflu so we wouldn't get it," Ahearn said.

"Each time I make the flu diagnosis, I treat family members in addition to treating the patient. My office has been overflowing with patients and so has our rural hospital. I wondered when we were going to actually start calling it an epidemic."

The antiviral medicine Tamiflu can lessen the flu's severity when taken early. Flu sufferers take the medicine twice a day for five days, while those who are trying to keep from getting the flu take it once a day for 10 days.

"We've been dispensing a lot of Tamiflu prescriptions, the capsules and the liquid," said Stephanie Lepard, manager of Sherry's Discount Drug in Edmond.

"Up until the last few weeks we had only seen a few cases. These last few weeks, though, we've been very, very busy."

Oklahoma City resident Ronna Hoffman said she began to feel ill on a Monday and didn't return to work until the following Saturday.

"I first thought it was a cold -- a little bit of scratchy throat -- thinking it was going to go away," said Hoffman, who added that she had fever for three nights and terrible body aches.

"I took seven baths one day because that's the only thing that halfway relieved it."

In western Oklahoma, "elderly and children" have been hit particularly hard by the flu, said Stephen Rhymer, a spokesman for Great Plains Regional Medical Center in Elk City.

"The biggest problem for those groups was dehydration. Emergency room visits have been up and doctors' offices are full of patients," Rhymer said. "The flu out here seems to be causing mostly upper-respiratory and upper GI (gastrointestinal) problems."

Rhymer said he had influenza symptoms for 21 days. "The cough would not go away," he said.
 
Re: Health officials bump up Oklahoma flu outbreak to epidemic status

"In fact, several of my staff and their family members have had it even though we were all immunized for it. The rest of us took Tamiflu so we wouldn't get it," Ahearn said.
...
In western Oklahoma, "elderly and children" have been hit particularly hard by the flu, said Stephen Rhymer, a spokesman for Great Plains Regional Medical Center in Elk City.

"The biggest problem for those groups was dehydration. Emergency room visits have been up and doctors' offices are full of patients," Rhymer said. "The flu out here seems to be causing mostly upper-respiratory and upper GI (gastrointestinal) problems."



Seasonal flu epidemic of a new type of strain out of the vaccine.
__________________________________________________________
Question:

Will it spread to pandemic, or isn't that the necessary future scenario?
____________________________________________________


WHO web site - NO MENTION ABOUT.

CDC web flu site weekly report - A unsubtyped

- why not subtyped in this report yet (fast tests?!?)?

___________________________________________________________

U.S. Flu Activity Report for Week Ending Feb 16 (Week 7)

- posted Feb 22


2007-2008 Influenza Season Week 7, ending February 16, 2008
(All data are preliminary and may change as more reports are received.)
Synopsis

During week 7 (February 10 - 16, 2008), influenza activity continued to increase in the United States.
  • Two thousand three hundred forty (34.0%) specimens tested by U.S. World Health Organization (WHO) and National Respiratory and Enteric Virus Surveillance System (NREVSS) collaborating laboratories were positive for influenza.
  • The proportion of deaths attributed to pneumonia and influenza was above the epidemic threshold for the sixth consecutive week.
  • The proportion of outpatient visits for influenza-like illness (ILI) and acute respiratory illness (ARI) was above national baseline levels. ILI increased in six of the nine regions compared to week 6, and was above region-specific baselines in all nine regions. All nine regions reported ARI at or above their region specific baselines.
  • Forty-nine states reported widespread influenza activity; one state reported regional influenza activity; and the District of Columbia reported local influenza activity.
<TABLE class=table cellSpacing=0 cellPadding=3 align=center border=0><CAPTION>National and Regional Summary of Select Surveillance Components

</CAPTION><TBODY><TR vAlign=top><TH vAlign=bottom width=85 rowSpan=2>
Region​
</TH><TH noWrap align=middle width=300 colSpan=4>Data for current week</STRONG></TH><TH noWrap align=middle width=276 colSpan=5>Data cumulative for the season</TH></TR><TR vAlign=top><TH align=middle width=72>Sentinel Provider ILI*</TH><TH align=middle width=72>DoD and VA ARI*</TH><TH align=middle width=60>% pos. for flu?</TH><TH align=middle width=96># jurisdictions reporting regional or widespread activity? </TH><TH noWrap align=middle width=48>A (H1)</TH><TH noWrap align=middle width=48>A (H3)</TH><TH align=middle width=60>A Unsub-typed</TH><TH noWrap align=middle width=48>B</TH><TH align=middle width=72>Pediatric Deaths</TH></TR><TR><TD align=left width=85>Nation</TD><TD noWrap align=middle width=72>Elevated</TD><TD noWrap align=middle width=72>Elevated</TD><TD noWrap align=middle width=60>34.0 % </TD><TD noWrap align=middle width=96>50 of 51 </TD><TD noWrap align=middle width=48>1266</TD><TD noWrap align=middle width=48>2156</TD><TD noWrap align=middle width=60>8956</TD><TD noWrap align=middle width=48>2457</TD><TD noWrap align=middle width=72>22</TD></TR><TR><TD align=left width=85>New England</TD><TD noWrap align=middle width=72>Elevated</TD><TD noWrap align=middle width=72>Elevated</TD><TD noWrap align=middle width=60>22.4 % </TD><TD noWrap align=middle width=96>6 of 6</TD><TD noWrap align=middle width=48>34</TD><TD noWrap align=middle width=48>17</TD><TD noWrap align=middle width=60>293</TD><TD noWrap align=middle width=48>235</TD><TD noWrap align=middle width=72>0</TD></TR><TR><TD align=left width=85>Mid-Atlantic</TD><TD noWrap align=middle width=72>Elevated</TD><TD noWrap align=middle width=72>Elevated</TD><TD noWrap align=middle width=60>21.7 % </TD><TD noWrap align=middle width=96>3 of 3</TD><TD noWrap align=middle width=48>57</TD><TD noWrap align=middle width=48>20</TD><TD noWrap align=middle width=60>339</TD><TD noWrap align=middle width=48>379</TD><TD noWrap align=middle width=72>3</TD></TR><TR><TD align=left width=85>East North Central</TD><TD noWrap align=middle width=72>Elevated</TD><TD noWrap align=middle width=72>Elevated</TD><TD noWrap align=middle width=60>50.1 % </TD><TD noWrap align=middle width=96>5 of 5</TD><TD noWrap align=middle width=48>119</TD><TD noWrap align=middle width=48>532</TD><TD noWrap align=middle width=60>347</TD><TD noWrap align=middle width=48>223</TD><TD noWrap align=middle width=72>3</TD></TR><TR><TD align=left width=85>West North Central</TD><TD noWrap align=middle width=72>Elevated</TD><TD noWrap align=middle width=72>Elevated</TD><TD noWrap align=middle width=60>26.3 % </TD><TD noWrap align=middle width=96>7 of 7</TD><TD noWrap align=middle width=48>62</TD><TD noWrap align=middle width=48>65</TD><TD noWrap align=middle width=60>851</TD><TD noWrap align=middle width=48>182</TD><TD noWrap align=middle width=72>0</TD></TR><TR><TD align=left width=85>South Atlantic</TD><TD noWrap align=middle width=72>Elevated</TD><TD noWrap align=middle width=72>Elevated</TD><TD noWrap align=middle width=60>31.8 % </TD><TD noWrap align=middle width=96>8 of 9</TD><TD noWrap align=middle width=48>191</TD><TD noWrap align=middle width=48>676</TD><TD noWrap align=middle width=60>2119</TD><TD noWrap align=middle width=48>424</TD><TD noWrap align=middle width=72>1</TD></TR><TR><TD align=left width=85>East South Central</TD><TD noWrap align=middle width=72>Elevated</TD><TD noWrap align=middle width=72>Elevated</TD><TD noWrap align=middle width=60>42.9 % </TD><TD noWrap align=middle width=96>4 of 4</TD><TD noWrap align=middle width=48>21</TD><TD noWrap align=middle width=48>301</TD><TD noWrap align=middle width=60>22</TD><TD noWrap align=middle width=48>14</TD><TD noWrap align=middle width=72>4</TD></TR><TR><TD align=left width=85>West South Central</TD><TD noWrap align=middle width=72>Elevated</TD><TD noWrap align=middle width=72>Elevated</TD><TD noWrap align=middle width=60>34.9 % </TD><TD noWrap align=middle width=96>4 of 4</TD><TD noWrap align=middle width=48>86</TD><TD noWrap align=middle width=48>304</TD><TD noWrap align=middle width=60>3999</TD><TD noWrap align=middle width=48>472</TD><TD noWrap align=middle width=72>7</TD></TR><TR><TD align=left width=85>Mountain</TD><TD noWrap align=middle width=72>Elevated</TD><TD noWrap align=middle width=72>Elevated</TD><TD noWrap align=middle width=60>27.7 % </TD><TD noWrap align=middle width=96>8 of 8</TD><TD noWrap align=middle width=48>325</TD><TD noWrap align=middle width=48>172</TD><TD noWrap align=middle width=60>567</TD><TD noWrap align=middle width=48>346</TD><TD noWrap align=middle width=72>2</TD></TR><TR><TD align=left width=85>Pacific</TD><TD noWrap align=middle width=72>Elevated</TD><TD noWrap align=middle width=72>Elevated</TD><TD noWrap align=middle width=60>17.5 % </TD><TD noWrap align=middle width=96>5 of 5</TD><TD noWrap align=middle width=48>371</TD><TD noWrap align=middle width=48>69</TD><TD noWrap align=middle width=60>419</TD><TD noWrap align=middle width=48>182</TD><TD noWrap align=middle width=72>2</TD></TR></TBODY></TABLE>

* Elevated means the % of visits for ILI or ARI is at or above the national or region-specific baseline
? National data is for current week; regional data is for the most recent 3 weeks.
? Includes all 50 states and the District of Columbia
Laboratory Surveillance

During week 7, WHO and NREVSS laboratories reported 6,889 specimens tested for influenza viruses, 2,340 (34.0%) of which were positive, including 47 influenza A (H1) viruses, 379 influenza A (H3) viruses, 1,432 influenza A viruses that were not subtyped, and 482 influenza B viruses.
Since September 30, 2007, WHO and NREVSS laboratories have tested a total of 109,089 specimens for influenza viruses and 14,835 (13.6%) were positive. Among the 14,835 influenza viruses, 12,378 (83.4%) were influenza A viruses and 2,457 (16.6%) were influenza B viruses. Three thousand four hundred twenty-two (27.6%) of the 12,378 influenza A viruses have been subtyped: 1,266 (37.0%) were influenza A (H1) viruses and 2,156 (63.0%) were influenza A (H3) viruses.
Although influenza A (H1) viruses predominated through mid-January, an increasing proportion of subtyped influenza A viruses are influenza A (H3) viruses. Influenza A (H3) viruses were reported more frequently than influenza A (H1) viruses during January 20?February 9. During week 6, influenza A (H3) became the predominant virus for the season overall. This season influenza A (H3) viruses have been reported more frequently than A (H1) viruses nationally, as well as in five of the nine surveillance regions (East North Central, East South Central, South Atlantic, West North Central, and West South Central). Influenza A (H1) viruses have predominated circulation this season in the remaining four regions (Mid-Atlantic, Mountain, New England, and Pacific).
<CENTER>
image071.gif

http://www.cdc.gov/flu/weekly/weeklyarchives2007-2008/data/whoAllregt07.htmView WHO-NREVSS Regional Bar Charts | View Chart Data | View Full Screen </CENTER>Antigenic Characterization:


CDC has antigenically characterized 280 influenza viruses [141 influenza A (H1N1), 70 influenza A (H3N2), and 69 influenza B viruses] collected by U.S. laboratories since September 30, 2007.
Influenza A (H1) [141]
  • One hundred twenty-four (88%) of the 141 viruses were characterized as A/Solomon Islands/3/2006, the influenza A (H1N1) component of the 2007-08 influenza vaccine for the Northern Hemisphere and the 2008 influenza A (H1N1) component for the Southern Hemisphere.
  • Seventeen (12%) of the 141 viruses showed somewhat reduced titers with antisera produced against A/Solomon Islands/3/2006.
Influenza A (H3) [70]
  • Twelve (17%) of the 70 viruses were characterized as A/Wisconsin/67/2005-like, the influenza A (H3N2) component of the 2007-08 influenza vaccine for the Northern Hemisphere.
  • Fifty-five (79%) of the 70 viruses were characterized as A/Brisbane/10/2007-like. A/Brisbane/10/2007-like viruses are a recent antigenic variant which evolved from, but are antigenically distinct from, A/Wisconsin/67/2005-like. A/Brisbane/10/2007-like virus is the recommended influenza A (H3N2) component for the 2008 Southern Hemisphere vaccine.
  • Three (4%) of the 70 viruses showed somewhat reduced titers with antisera produced against A/Wisconsin/67/2005 and A/Brisbane/10/2007.
Influenza B (B/Victoria/02/87 and B/Yamagata/16/88 lineages) [69]
  • Victoria lineage [4]
  • Four (6%) of the 69 influenza B viruses characterized belong to the B/Victoria lineage of viruses.
    • o Two (50%) of these 4 viruses were characterized as B/Ohio/01/2005-like. The recommended influenza B component for the 2007-08 influenza vaccine is a B/Malaysia/2506/2004-like virus, belonging to the B/Victoria lineage. B/Ohio/01/2005 is a recent B/Malaysia/2506/2004-like reference strain.
      o Two (50%) of these 4 viruses showed somewhat reduced titers with antisera produced against B/Ohio/01/2005 and B/Malaysia/2506/2004.
  • Yamagata lineage [65]
  • Sixty-five (94%) of the 69 viruses were identified as belonging to the B/Yamagata lineage of viruses.
Antiviral Resistance:

In the United States, two groups of antiviral drugs have been approved by FDA for use in treating or preventing influenza infections. These two groups of antiviral drugs are: neuraminidase inhibitors (oseltamivir and zanamivir) and adamantanes (amantadine and rimantidine). A description of these drugs can be found at: http://www.cdc.gov/flu/protect/antiviral/index.htm.
  • Neuraminidase Inhibitor Antiviral Drugs: Small numbers of influenza viruses resistant to the neuraminidase inhibitor oseltamivir have been detected in the United States. Of the 471 influenza A and B viruses tested for antiviral resistance so far this season, 27 (5.7%) have been found to be resistant to oseltamivir. Currently all of the resistant viruses are H1N1 viruses, with 27 (8.7%) of all H1N1 viruses exhibiting a genetic mutation that confers oseltamivir resistance. All tested viruses retain their sensitivity to zanamivir. Additional information on antiviral resistance can be found at: http://www.cdc.gov/flu/about/qa/antiviralresistance.htm
    Adamantane Antiviral Drugs: Resistance to the adamantanes continues to be high. Among 282 influenza A viruses tested, 88 (31.2%) are resistant to adamantanes, including 98.6% of H3N2 viruses and 7.2% of H1N1 viruses. The adamantanes are not effective against influenza B viruses: http://www.cdc.gov/mmwr/preview/mmwrhtml/rr5606a1.htm
    Based on the level of oseltamivir resistance observed in only one influenza subtype, H1N1, and persisting high levels of resistance to the adamantanes in both H3N2 and H1N1 viruses, CDC continues to recommend the use of oseltamivir and zanamivir for the treatment or prevention of influenza. Use of amantadine or rimantadine is not recommended. Guidance on influenza antiviral use can be found at: http://www.cdc.gov/mmwr/preview/mmwrhtml/rr5606a1.htm
Pneumonia and Influenza (P&I) Mortality Surveillance

During week 7, 8.2% of all deaths reported through the 122 Cities Mortality Reporting System were reported as due to P&I. This percentage is above the epidemic threshold of 7.2% for week 7. Including week 7, P&I mortality has been above threshold for six consecutive weeks.
<CENTER>
picurve07.gif

View Full Screen</CENTER>Influenza-Associated Pediatric Mortality

Twelve influenza-associated pediatric deaths were reported to CDC during week 7 from ten states [AR, CA, CO(2), FL, IL, IN, MS, NYC, TX(2), and WI]. Since September 30, 2007, CDC has received a total of 22 reports of influenza-associated pediatric deaths that occurred during the current season.
<CENTER>
IPD07_small.gif

View Full Screen</CENTER>Influenza-Associated Pediatric Hospitalizations

Laboratory-confirmed influenza-associated pediatric hospitalizations are monitored in two population-based surveillance networks: the New Vaccine Surveillance Network (NVSN) and the Emerging Infections Program (EIP).
During November 4, 2007-February 9, 2008, the preliminary laboratory-confirmed influenza-associated hospitalization rate reported by the NVSN for children 0-4 years old was 1.83 per 10,000.
<CENTER>
NVSN07_small.gif
</CENTER>
<CENTER>View Full Screen </CENTER>
During September 30 ? February 2, 2008, the preliminary laboratory-confirmed influenza-associated hospitalization rate reported by the EIP for children 0?17 years old was 0.36 per 10,000. For children aged 0-4 years and 5-17 years, the rate was 1.0 per 10,000 and 0.1 per 10,000, respectively.
<CENTER>
EIP07_small.gif

View Full Screen </CENTER>Outpatient Illness Surveillance

Nationwide during week 7, 6.4% of outpatient visits reported through the U.S. Influenza Sentinel Provider Surveillance Network were due to influenza-like illness (ILI), which is above the national baseline of 2.2%. On a regional level, the percentage of visits for ILI increased in six of the nine regions compared to last week and ranged from 4.1% to 10.1%. All nine regions reported ILI above their region-specific baselines.
Starting in week 5, New York City began reporting ILI data collected electronically from emergency departments city-wide, adding approximately 60,000 additional patient visits per week to the U.S. Influenza Sentinel Provider Surveillance Network. Retrospective reports were submitted for all earlier weeks this season. While this change increases the total patient visits per week by approximately 15%, it is not expected to influence the national ILI outpatient visit percentage after population weighting, but may have a larger impact on the Mid-Atlantic regional ILI percentage.
During week 7, 3.7% of patient visits to Department of Veteran?s Affairs (VA) and Department of Defense (DoD) outpatient treatment facilities were for acute respiratory illness (ARI), which was above the national baseline of 3.2%. On a regional level, the percentage of visits for ARI ranged from 1.8% to 4.3%, and was at or above the region-specific baselines in all nine regions. The percentage of visits reported for ARI was at or above age-specific baselines in the 5-17 years, 18-49 years, 50-64 years, and >64 years age groups.
<CENTER>
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View Sentinel Providers Regional Charts | View Chart Data |View Full Screen
image073.gif

View Full Screen </CENTER>Geographic Spread of Influenza as Assessed by State and Territorial Epidemiologists


During week 7 the following influenza activity was reported:
  • Widespread activity was reported by 49 states (Alabama, Alaska, Arizona, Arkansas, California, Colorado, Connecticut, Delaware, Georgia, Hawaii, Idaho, Illinois, Indiana, Iowa, Kansas, Kentucky, Louisiana, Maine, Maryland, Massachusetts, Michigan, Minnesota, Mississippi, Missouri, Montana, Nebraska, Nevada, New Hampshire, New Jersey, New Mexico, New York, North Carolina, North Dakota, Ohio, Oklahoma, Oregon, Pennsylvania, Rhode Island, South Carolina, South Dakota, Tennessee, Texas, Utah, Vermont, Virginia, Washington, Wisconsin, West Virginia, and Wyoming).
  • Regional activity was reported by 1 state (Florida).
  • The District of Columbia reported local influenza activity.
...
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A description of surveillance methods is available at: http://www.cdc.gov/flu/weekly/fluactivity.htm
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Re: Health officials bump up Oklahoma flu outbreak to epidemic status

seems that the Texas/Oklahoma H3N2 is more distant to the vaccine
than other strains.

Do they measure how much percent of sick people had been vaccinated
in the several regions ? That's very interesting, easy to evaluate :
no blood-test, no PCR, just asking. Yet I never saw such a statistics.






current H3N2 strains compared to the current vaccine ("Wisconsin")
and next season's vaccine ("Brisbane")

note, that changes A<-->G or C<-->T at codon position 3 (blank)
are synonymous and thus irrelevant for the vaccine.


Code:
recent strains normed to Wisconsin

                                     000000000000000000000000000000000000000000000011     
                                     000000111123344444444445555666667777788899999900     
                                     566899128997913466677991266027991237923803567858     
                                     505401402772320706728798157595095928280630407860     
-codon-position----------------------1 2  1  22   11 1121121221 22   1  1  21    21       
---Index-----------------------------CCAGCCCGGGATCGATTAAAAGTTAAATTCCCACCTAAGGTTTCACGG     
  1 >A/USA/AF1127/08                 .T.....A.A.A.A.CG.T......G.G....G........CC.....     
  2 >A/USA/AF1141/07                 .T.......A...A.CG.T......G.G....G........CC.....     
  3 >A/USA/AF1118/08                 .T.......A...A.CG.T......C.G....GT.......CC.....     
  4 >A/USA/AF1098/08                 .T.......A...A.CG.T......C.G....GT.......CC.....     
  5 >A/USA/AF1112/08                 .T.......A...A.CG.T......C.G....GT.......CC.....     
  6 >A/USA/AF1132/08                 .T.......A...A.CG.T......C.G....GT.......CC...--     
  7 >A/USA/AF1122/08                 .T.......A...A.CG.T......C.G....GT.......CC.....     
  8 >A/USA/AF1103/08                 .T.......A...A.CG.T......C.G....GT.......CC.....     
  9 >A/USA/AF1142/08                 .T.......A...A.CG.T......C.G....GT.......CC....-     
 10 >A/USA/AF1108/08                 .T.......A...A.CG.T......C.G....GT.......CC.....     
 11 >A/USA/AF1131/08                 .T.......A...A.CG.T......C.G....GT.......CC....-     
 12 >A/USA/AF1139/08                 .T.......A...A.CG.T......C.G....GT.......CC.....     
 13 >A/USA/AF1116/08                 .T.......A...A.CG.T......C.G....GT.......CC.....     
 14 >A/USA/AF1104/08                 .T.......A...A.CG.T......C.G....GTTC.....CC.....     
 15 >A/USA/AF1126/08                 .T.......A...A.CG.T......C.G....GTTC.....CC.....     
 16 >A/USA/AF1102/08                 .T.......A...A.CG.T......C.G....GT.......CC.....     
 17 >A/USA/AF1111/08                 .T.......A...A.CG.T......C.G....GT.......CC.....     
 18 >A/USA/AF1134/08                 .T.......A...A.CG.T......C.G....GT.......CC....-     
 19 >A/USA/AF1099/08                 .T.......A...AGCG.T......C.G....GT.......CC.....     
 20 >A/USA/AF1109/08                 TT.......AT..AGCG.T....C..TG....GT.......CC...T.     
 21 >A/USA/AF1140/08                 TT.......AT..A.CG.T....C..TG....GT.......CC...T.     
 22 >A/USA/AF1107/07                 TT.......AT..A.CG.T....C..TG....GT.......CC...T.     
 23 >A/USA/AF1128/08                 TT.......AT..A.CG.T....C..TG....GT.......CC...T.     
 24 >A/USA/AF1143/08                 TT.......AT..A.CG.T....C..TG....GT.......CC...--     
 25 >A/USA/AF1137/08                 TT.......AT..A.CG.T....C..TG....GT.......CC...T.     
 26 >A/USA/AF1145/08                 TT.......AT..A.CG.T....C..TG....GT.......CC...T.     
 27 >A/USA/AF1133/08                 TT.......AT..A.CG.T....C..TG....GT.......CC...T.     
 28 >A/USA/AF1110/08                 TT.......AT..A.CG.T....C..TG....GT.......CC...T.     
 29 >A/USA/AF1146/08                 TT.......AT..A.CG.T....C..TG....GT.......CC...T.     
 30 >A/USA/AF1117/07                 TT.......AT..A.CG.T..A.C..TG....GT.......CC...T.     
 31 >A/USA/AF1119/08                 TT.......AT..A.CG.T..A.C..TG....GT.......CC...T.     
 32 >A/USA/AF1100/08                 TT.......AT..A.CG.T....C..TG....GT.......CC...T.     
 33 >A/USA/AF1130/08                 TT.......AT..A.CG.T....C..TG....GT.......CC...--     
 34 >A/USA/AF1113/08                 TT.......AT..A.CG.T....C..TG....GT.......CCA..T.     
 35 >A/USA/AF1148/08                 TT.......AT..A.CG.T....C..TG....GT.......CC...--     
 36 >A/Colorado/UR06-0452/07         .T.......A...A.CG.T........G....G........CC.....     
 37 >A/Honduras/AF1136/07            .........A...A.CG.T........G....G........CC.....     
 38 >A/Honduras/AF1101/07            .........A...A.CG.T........G.............CC.....     
 39 >A/Honduras/AF1129/07            .........A...A.CG.T........G.............CC.....     
 40 >A/USA/AF1135/07                 .........A...A.CG.T........G....G.....A..CC.....     
 41 >A/Nepal/AF1106/07               .........A...A.CG.T........G....G.....A..CC.....     
 42 >A/Brisbane/10/07(egg),2/6/07    .........A...A.CG.T........GC...G.......CCC.....     
 43 >A/Brisbane/10e/07,2/6/07        .........A...A.CG.T........GC...G.......CCC.....     
 44 >A/Brisbane/10/07,2/6/07         .........A...A.CG.T........G....G.......CCC.....     
 45 >A/N.Mariana Islands/AF1121/07   .........A.C.A.CGC..G...G.GG.T..G.........CAG...     
 46 >A/N.Mariana Islands/AF1144/07   .........A...A.CGC..G...G..G.T..G.........C.G...     
 47 >A/Wisconsin/67/X-161/05         ................................................     
 48 >A/Wisconsin/67/05               ..............................................--     
 49 >A/Thailand/AF1114/07            ..T.TAT.A....A..G..G...C.G.G...TG...CG....C...--     
 50 >A/Thailand/AF1115/07            ..T.TAT.A....A..G..G...C.G.G...TG...CG....C...--     
 51 >A/USA/AF1147/07                 .T.A.....A..TA.CG.T...C..G.G...TG........CC.....     
 52 >A/USA/AF1120/08                 .T.A.....A..TA.CG.T...C..G.G...TG........CC.....     
 53 >A/USA/AF1123/08                 .T.......A..TA.CG.T........G....G......A.CC....A     
 54 >A/USA/AF1124/08                 .T.......A..TA.CG.T........G....G......A.CC....A     
 55 >A/USA/AF1125/08                 .T.......A...A.CG.T........G..T.G........CC..T.A     
 56 >A/USA/AF1105/08                 .T.......A...A.CG.T........G..T.G........CC..T.A     
 57 >A/USA/AF1138/08                 .T.....A.A.A.A.CG.T......G.G....G........CC...--     
                                                                                          
---Index-----------------------------CCAGCCCGGGATCGATTAAAAGTTAAATTCCCACCTAAGGTTTCACGG     
-codon-position----------------------1 2  1  22   11 1121121221 22   1  1  21    21       
                                     000000000000000000000000000000000000000000000011     
                                     000000111123344444444445555666667777788899999900     
                                     566899128997913466677991266027991237923803567858     
                                     505401402772320706728798157595095928280630407860     

















recent H3N2-strains normed to Brisbane
--------------------------------------

                                     000000000000000000000000000000000000000000000011     
                                     000000111123344444444445555666667777788899999900     
                                     566899128997913466677991266027991237923803567858     
                                     505401402772320706728798157595095928280630407860     
-codon-position----------------------1 2  1  22   11 1121121221 22   1  1  21    21       
---Index-----------------------------CCAGCCCGGAATCAACGATAAGTTAAAGCCCCGCCTAAGGCCCCACGG     
  1 >A/USA/AF1127/08                 .T.....A...A.............G..T...........T.......     
  2 >A/USA/AF1141/07                 .T.......................G..T...........T.......     
  3 >A/USA/AF1118/08                 .T.......................C..T....T......T.......     
  4 >A/USA/AF1098/08                 .T.......................C..T....T......T.......     
  5 >A/USA/AF1112/08                 .T.......................C..T....T......T.......     
  6 >A/USA/AF1132/08                 .T.......................C..T....T......T.....--     
  7 >A/USA/AF1122/08                 .T.......................C..T....T......T.......     
  8 >A/USA/AF1103/08                 .T.......................C..T....T......T.......     
  9 >A/USA/AF1142/08                 .T.......................C..T....T......T......-     
 10 >A/USA/AF1108/08                 .T.......................C..T....T......T.......     
 11 >A/USA/AF1131/08                 .T.......................C..T....T......T......-     
 12 >A/USA/AF1139/08                 .T.......................C..T....T......T.......     
 13 >A/USA/AF1116/08                 .T.......................C..T....T......T.......     
 14 >A/USA/AF1104/08                 .T.......................C..T....TTC....T.......     
 15 >A/USA/AF1126/08                 .T.......................C..T....TTC....T.......     
 16 >A/USA/AF1102/08                 .T.......................C..T....T......T.......     
 17 >A/USA/AF1111/08                 .T.......................C..T....T......T.......     
 18 >A/USA/AF1134/08                 .T.......................C..T....T......T......-     
 19 >A/USA/AF1099/08                 .T............G..........C..T....T......T.......     
 20 >A/USA/AF1109/08                 TT........T...G........C..T.T....T......T.....T.     
 21 >A/USA/AF1140/08                 TT........T............C..T.T....T......T.....T.     
 22 >A/USA/AF1107/07                 TT........T............C..T.T....T......T.....T.     
 23 >A/USA/AF1128/08                 TT........T............C..T.T....T......T.....T.     
 24 >A/USA/AF1143/08                 TT........T............C..T.T....T......T.....--     
 25 >A/USA/AF1137/08                 TT........T............C..T.T....T......T.....T.     
 26 >A/USA/AF1145/08                 TT........T............C..T.T....T......T.....T.     
 27 >A/USA/AF1133/08                 TT........T............C..T.T....T......T.....T.     
 28 >A/USA/AF1110/08                 TT........T............C..T.T....T......T.....T.     
 29 >A/USA/AF1146/08                 TT........T............C..T.T....T......T.....T.     
 30 >A/USA/AF1117/07                 TT........T..........A.C..T.T....T......T.....T.     
 31 >A/USA/AF1119/08                 TT........T..........A.C..T.T....T......T.....T.     
 32 >A/USA/AF1100/08                 TT........T............C..T.T....T......T.....T.     
 33 >A/USA/AF1130/08                 TT........T............C..T.T....T......T.....--     
 34 >A/USA/AF1113/08                 TT........T............C..T.T....T......T..A..T.     
 35 >A/USA/AF1148/08                 TT........T............C..T.T....T......T.....--     
 36 >A/Colorado/UR06-0452/07         .T..........................T...........T.......     
 37 >A/Honduras/AF1136/07            ............................T...........T.......     
 38 >A/Honduras/AF1101/07            ............................T...A.......T.......     
 39 >A/Honduras/AF1129/07            ............................T...A.......T.......     
 40 >A/USA/AF1135/07                 ............................T.........A.T.......     
 41 >A/Nepal/AF1106/07               ............................T.........A.T.......     
 42 >A/Brisbane/10/07(egg),2/6/07    ................................................     
 43 >A/Brisbane/10e/07,2/6/07        ................................................     
 44 >A/Brisbane/10/07,2/6/07         ............................T...................     
 45 >A/N.Mariana Islands/AF1121/07   ...........C.....CA.G...G.G.TT..........TT.AG...     
 46 >A/N.Mariana Islands/AF1144/07   .................CA.G...G...TT..........TT..G...     
 47 >A/Wisconsin/67/X-161/05         .........G...G.TT.A........TT...A.......TTT.....     
 48 >A/Wisconsin/67/05               .........G...G.TT.A........TT...A.......TTT...--     
 49 >A/Thailand/AF1114/07            ..T.TAT.AG.....T..AG...C.G..T..T....CG..TT....--     
 50 >A/Thailand/AF1115/07            ..T.TAT.AG.....T..AG...C.G..T..T....CG..TT....--     
 51 >A/USA/AF1147/07                 .T.A........T.........C..G..T..T........T.......     
 52 >A/USA/AF1120/08                 .T.A........T.........C..G..T..T........T.......     
 53 >A/USA/AF1123/08                 .T..........T...............T..........AT......A     
 54 >A/USA/AF1124/08                 .T..........T...............T..........AT......A     
 55 >A/USA/AF1125/08                 .T..........................T.T.........T....T.A     
 56 >A/USA/AF1105/08                 .T..........................T.T.........T....T.A     
 57 >A/USA/AF1138/08                 .T.....A...A.............G..T...........T.....--     
                                                                                          
---Index-----------------------------CCAGCCCGGAATCAACGATAAGTTAAAGCCCCGCCTAAGGCCCCACGG     
-codon-position----------------------1 2  1  22   11 1121121221 22   1  1  21    21       
                                     000000000000000000000000000000000000000000000011     
                                     000000111123344444444445555666667777788899999900     
                                     566899128997913466677991266027991237923803567858     
                                     505401402772320706728798157595095928280630407860



1118,1112,1111,1145,1146,1119,1117,1113 are from Texas,
1122,1109,1143 from Oklahoma
 
Re: Health officials bump up Oklahoma flu outbreak to epidemic status

Thank you for the data gsgs.

"Do they measure how much percent of sick people had been vaccinated
in the several regions ? That's very interesting, easy to evaluate :
no blood-test, no PCR, just asking. Yet I never saw such a statistics."

I think (I hope I'm not telling the wrong) that they evaluate the statistics in backwards, when the "seasonal flu battle" is finished, by collecting searched epid. flu regional reports from the field gp's, who can connect the data from their vaccinated patients, and those of them who suffering the flu (only those who contacted the gp).

That official report procedure (like stated in an FT posted CDC doc), can be over only 2-3 months after the start of the epidemic (like said above).

For earlier statistics during the flu epidemic they probably can give only "asking statistics".

Without minimizing the sci. bodies current outputs (thanks all of you), obviously for an fast response policy, which want to distribute enaugh exact vaccines more than 1 time a year for a half-globe, must to be implemented some "on the edge" virus strains infection simulation prediction models with real time informations from the field (the technology exist).
 
Re: Health officials bump up Oklahoma flu outbreak to epidemic status

OK, I found this from last season at CDC:

> Of the 63 cases for which the influenza virus type was known, 47 were influenza A and 16 were
> influenza B viruses. Of the 53 cases 6 months of age and older for whom the vaccination
> status was known, 50 (94%) were not vaccinated against influenza.

that's for children and only the positive cases and only 2006/7, I couldn't find it for earlier seasons,
and only USA.
Links to more data are appreciated.


the rate of ILI-suspected people who had been vaccinated as compared to the vaccine coverage
rate should be a good and easily obtained indicator of vaccine efficiency.
 
Re: Health officials bump up Oklahoma flu outbreak to epidemic status

http://www.ktul.com/news/stories/0208/499802.html?ref=home

Oklahoma Girl Dies From Flu Complications
posted 9:48 am Thu February 28, 2008 - Oklahoma City

A 3-year-old Midwest City girl has died from complications of the flu a week after she was taken to a Midwest City urgent care clinic. Dusti Gann says she took her daughter Afton to the clinic where she was seen briefly by a doctor who diagnosed her with an ear infection and tonsillitis and sent her home with an antibiotic.

Gann says the next afternoon the girl began breathing hard and grabbing at her then collapsed. The child fell into a coma and died a week later from pneumonia related to influenza.
 
Re: Health officials bump up Oklahoma flu outbreak to epidemic status

http://www.ktul.com/news/stories/0208/499802.html?ref=home

Oklahoma Girl Dies From Flu Complications
posted 9:48 am Thu February 28, 2008 - Oklahoma City

A 3-year-old Midwest City girl has died from complications of the flu a week after she was taken to a Midwest City urgent care clinic. Dusti Gann says she took her daughter Afton to the clinic where she was seen briefly by a doctor who diagnosed her with an ear infection and tonsillitis and sent her home with an antibiotic.

Gann says the next afternoon the girl began breathing hard and grabbing at her then collapsed. The child fell into a coma and died a week later from pneumonia related to influenza.
In flu epidemic times it's time to insert fast lab tests (same day) for influenza, when ORL/pneumo/ARDS patients came to the emergency, or to the clinic. If this cannot be payed by insurance, but is welcomed by the patient, the tests must be gived to the patient by paying.

Anyone implemented that?
 
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