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FluView: A Weekly Influenza Surveillance Report Prepared by the Influenza Division

2009-2010 Influenza Season Week 40 ending October 10, 2009

All data are preliminary and may change as more reports are received.


During week 40 (October 4-10, 2009), influenza activity increased in the U.S.

  • 4,093 (29.4%) specimens tested by U.S. World Health Organization (WHO) and National Respiratory and Enteric Virus Surveillance System (NREVSS) collaborating laboratories and reported to CDC/Influenza Division were positive for influenza.
  • All subtyped influenza A viruses being reported to CDC were 2009 influenza A (H1N1) viruses.
  • The proportion of deaths attributed to pneumonia and influenza (P&I) was above the epidemic threshold.
  • Eleven influenza-associated pediatric deaths were reported. Ten of these deaths were associated with 2009 influenza A (H1N1) virus infection and one was associated with an influenza A virus, for which subtype is undetermined.
  • The proportion of outpatient visits for influenza-like illness (ILI) was above the national baseline. All 10 regions reported ILI above region-specific baseline levels.
  • Forty-one states reported geographically widespread influenza activity, Guam and eight states reported regional influenza activity, one state, the District of Columbia, and Puerto Rico reported local influenza activity, and the U.S. Virgin Islands did not report.

National and Regional Summary of Select Surveillance Components

HHS Surveillance Regions**
Data for current week Data cumulative since August 30, 2009 (Week 35)*
Out-patient ILI† % positive for flu‡ Number of jurisdictions reporting regional or widespread activity§ A (H1) A (H3) 2009 A (H1N1) A (unable to sub-type)¥ A(Subtyping not performed) B Pediatric Deaths
Nation Elevated 29.4 % 50 of 54 15 30 12,578 223 8,051 48 43
Region 1 Elevated 5.8 % 6 of 6 5 1 142 2 18 2 0
Region 2 Elevated 3.2 % 2 of 4 0 1 40 0 40 2 0
Region 3 Elevated 34.2 % 5 of 6 1 5 1,764 8 153 5 3
Region 4 Elevated 27.5 % 8 of 8 0 1 2,003 62 2,538 5 13
Region 5 Elevated 27.1 % 6 of 6 4 15 1,673 47 356 4 2
Region 6 Elevated 17.9 % 5 of 5 0 3 1,365 3 2,310 1 15
Region 7 Elevated 38.8 % 4 of 4 3 2 1,161 87 292 9 1
Region 8 Elevated 28.2 % 6 of 6 2 0 1,614 0 2,055 17 5
Region 9 Elevated 26.1 % 4 of 5 0 1 1,981 11 261 3 2
Region 10 Elevated 46.2 % 4 of 4 0 1 835 3 28 0 2

*Influenza season officially begins each year at week 40. This season data from week 35 will be included to show the trend of influenza activity before the official start of the 2009-10 influenza season.
**HHS regions (Region 1 CT, ME, MA, NH, RI, VT; Region 2: NJ, NY, Puerto Rico, US Virgin Islands; Region 3: DE, DC, MD, PA, VA, WV; Region 4: AL, FL, GA, KY, MS, NC, SC, TN; Region 5: IL, IN, MI, MN, OH, WI; Region 6: AR, LA, NM, OK, TX; Region 7: IA, KS, MO, NE; Region 8: CO, MT, ND, SD, UT, WY; Region 9: AZ, CA, Guam, HI, NV; and Region 10: AK, ID, OR, WA).
† Elevated means the % of visits for ILI is at or above the national or region-specific baseline
‡ National data are for current week; regional data are for the most recent three weeks
§ Includes all 50 states, the District of Columbia, Guam, Puerto Rico, and U.S. Virgin Islands
¥ The majority of influenza A viruses that cannot be sub-typed as seasonal influenza viruses are 2009 A (H1N1) influenza viruses upon further testing

U.S. Virologic Surveillance:

WHO and NREVSS collaborating laboratories located in all 50 states and Washington D.C. report to CDC the number of respiratory specimens tested for influenza and the number positive by influenza type and subtype. The results of tests performed during the current week are summarized in the table below.

Week 40
No. of specimens tested 13,921
No. of positive specimens (%) 4,093 (29.4%)
Positive specimens by type/subtype
  Influenza A 4,093 (99.6%)
             A (2009 H1N1)              2,505 (61.4%)
             A (subtyping not performed)              1,556 (38.2%)
             A (unable to subtype)              17 (0.4%)
             A (H3)              0 (0.0%)
             A (H1)             0 (0.0%)
  Influenza B 15 (0.4%)

During week 40, influenza B viruses co-circulated at low levels with 2009 influenza A (H1N1) viruses. All subtyped influenza A viruses reported to CDC this week were 2009 influenza A (H1N1) viruses.

INFLUENZA Virus Isolated
View WHO-NREVSS Regional Bar Charts| View Chart Data | View Full Screen

Pneumonia and Influenza Hospitalization and Death Tracking:

This new system was implemented on August 30, 2009, and replaces the weekly report of laboratory confirmed 2009 H1N1-related hospitalizations and deaths that began in April 2009. Jurisdictions can now report to CDC either laboratory confirmed or pneumonia and influenza syndromic-based counts of hospitalizations and deaths resulting from all types or subtypes of influenza, not just those from 2009 H1N1 influenza virus. To allow jurisdictions to implement the new case definition, counts were reset to zero on August 30, 2009. From August 30 – October 10, 2009, 4,958 laboratory-confirmed influenza associated hospitalizations, 292 laboratory-confirmed influenza associated deaths, 15,696 pneumonia and influenza syndrome-based hospitalizations, and 2,029 pneumonia and influenza syndrome-based deaths, were reported to CDC. CDC will continue to use its traditional surveillance systems to track the progress of the 2009-10 influenza season.

Aggregate Hospital and Death Reporting
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Antigenic Characterization:

CDC has antigenically characterized 94 2009 influenza A (H1N1) viruses collected since September 1, 2009. No seasonal A(H1N1), A(H3N2) or B viruses collected during this period were available for testing.

All ninety-four 2009 A (H1N1) viruses are related to the A/California/07/2009 (H1N1) reference virus selected by WHO as the 2009 H1N1 vaccine virus.

Annual influenza vaccination is expected to provide the best protection against those virus strains that are related to the vaccine strains, but limited to no protection may be expected when the vaccine and circulating virus strains are so different as to be from different lineages. Antigenic characterization of 2009 influenza A (H1N1) viruses indicates that these viruses are only distantly related antigenically and genetically to seasonal influenza A (H1N1) viruses, suggesting that little to no protection would be expected from vaccination with seasonal influenza vaccine.

Antiviral Resistance:

Since September 1, 2009, 89 2009 influenza A (H1N1) virus isolates have been tested for resistance to the neuraminidase inhibitors (oseltamivir and zanamivir). In addition, 317 2009 influenza A (H1N1) original clinical samples were tested for a single known mutation in the virus that confers oseltamivir resistance. Because of the low level of circulation of seasonal influenza A (H1N1), A (H3N2), and influenza B viruses, no samples collected since September 1, 2009 were available for antiviral resistance testing. Additional laboratories perform antiviral testing and report their results to CDC. The results of antiviral resistance testing performed on these viruses are summarized in the table below.

Antiviral Resistance Testing Results on Samples Collected Since September 1, 2009.

Samples tested (n) Resistant Viruses,
Number (%)
Samples tested (n) Resistant Viruses, Number (%)
Oseltamivir Zanamivir
Seasonal Influenza A (H1N1) 0 0 (0) 0 0 (0)
Influenza A (H3N2) 0 0 (0) 0 0 (0)
Influenza B 0 0 (0) 0 0 (0)
2009 Influenza A (H1N1) 406 2†‡ (0.5) 89 0 (0)

†Two screening tools were used to determine oseltamivir resistance: sequence analysis of viral genes or a neuraminidase inhibition assay.
‡Additional laboratories perform antiviral resistance testing and report their results to CDC.  Two additional oseltamivir resistant 2009 influenza A (H1N1) viruses have been identified by these laboratories since September 1, 2009, bringing the total number to 4.

Over 99% of all subtyped influenza A viruses reported during week 40 were 2009 influenza A (H1N1) viruses, and 100% of all 2009 H1N1 viruses tested since the virus emerged in April 2009 have been resistant to the adamantanes (amantadine and rimantadine). Currently, adamantane antiviral susceptibility testing has been suspended to allow a focus on neuraminidase inhibitors

Antiviral treatment with oseltamivir or zanamivir is recommended for all patients with confirmed or suspected influenza virus infection who are hospitalized or who are at higher risk for influenza complications. Additional information on antiviral recommendations for treatment and chemoprophylaxis of influenza virus infection is available at

2009 influenza A (H1N1) viruses were tested for oseltamivir resistance by a neuraminidase inhibition assay and/or detection of genetic sequence mutation, depending on the type of specimen tested. Original clinical samples were examined for a single known mutation in the virus that confers oseltamivir resistance in currently circulating seasonal influenza A (H1N1) viruses, while influenza virus isolates were tested using a neuraminidase inhibition assay that determines the presence or absence of neuraminidase inhibitor resistance, followed by the neuraminidase gene sequence analysis of resistant viruses.

The majority of 2009 influenza A (H1N1) viruses are susceptible to the neuraminidase inhibitor antiviral medication oseltamivir; however, rare sporadic cases of oseltamivir resistant 2009 influenza A (H1N1) viruses have been detected worldwide. Since September 1, 2009, four cases have been identified in the United States, and a total of 13 cases of oseltamivir resistant 2009 influenza A (H1N1) viruses have been identified in the United States since April 2009 (10 viruses identified by CDC and three viruses identified by additional laboratories). The 13 total cases represent an increase of one case over the previous week. All tested viruses retain their sensitivity to the neuraminidase inhibitor zanamivir. Eleven patients (including nine of the viruses detected at CDC and two viruses identified by the additional laboratories) had documented exposure to oseltamivir through either treatment or chemoprophylaxis, and the remaining two patients are under investigation to determine exposure to oseltamivir. Occasional development of oseltamivir resistance during treatment or prophylaxis is not unexpected. Enhanced surveillance is expected to detect additional cases of oseltamivir resistant 2009 influenza A (H1N1) viruses, and such cases will be investigated to assess the spread of resistant strains in the community

To prevent the spread of antiviral resistant virus strains, CDC reminds clinicians and the public of the need to continue hand and cough hygiene measures for the duration of any symptoms of influenza, even while taking antiviral medications (

Pneumonia and Influenza (P&I) Mortality Surveillance

During week 40, 6.7% of all deaths reported through the 122-Cities Mortality Reporting System were due to P&I. This percentage was above the epidemic threshold of 6.5% for week 40.

Pneumonia And Influenza Mortality
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Influenza-Associated Pediatric Mortality

Eleven influenza-associated pediatric deaths were reported to CDC during week 40 (Arizona, Colorado, Idaho, Kentucky, Louisiana [2], North Carolina, Ohio, South Carolina, and Tennessee [2]). Ten of these deaths were associated with 2009 influenza A (H1N1) virus infection and one was associated with an influenza A virus for which the subtype is undetermined. These deaths occurred between August 30 and October 10, 2009. Since August 30, 2009, CDC has received 43 reports of influenza-associated pediatric deaths that occurred during the current influenza season (three deaths in children less than 2 years, five deaths in children 2-4 years, 16 deaths in children 5-11 years, and 19 deaths in individuals 12-17 years). Thirty-nine of the 43 deaths were due to 2009 influenza A (H1N1) virus infections. A total of 86 deaths in children associated with 2009 H1N1 virus have been reported to CDC.

Among the 43 deaths in children, 28 children had specimens collected for bacterial culture from normally sterile sites and seven (25.0%) of the 28 were positive; Staphylococcus aureus was identified in five (71.4%) of the seven children. One S. aureus isolate was sensitive to methicillin, three were methicillin resistant, and one did not have sensitivity testing performed. All seven children with bacterial coinfections were five years of age or older and four (57.1%) of the seven children were 12 years of age or older.

Influenza-Associated Pediatric Mortality
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Influenza-Associated Hospitalizations

Laboratory-confirmed influenza-associated hospitalizations are monitored using a population-based surveillance network that includes the 10 Emerging Infections Program (EIP) sites (CA, CO, CT, GA, MD, MN, NM, NY, OR and TN) and 6 new sites (IA, ID, MI, ND, OK and SD).

During September 1, 2009 – October 10, 2009, the following preliminary laboratory-confirmed overall influenza associated hospitalization rates were reported by EIP and the new sites (rates include influenza A, influenza B, and 2009 influenza A (H1N1)):

Rates [EIP (new sites)] for children aged 0-4 years and 5-17 years were 1.4 (1.8) and 0.7 (1.0) per 10,000, respectively. Rates [EIP (new sites)] for adults aged 18-49 years, 50-64 years, and ≥ 65 years were 0.4 (0.4), 0.4 (0.3) and 0.3 (0.3) per 10,000, respectively.

Influenza-Associated Pediatric Mortality

†Note: scales differ between age groups in the figure.
*2006-07 & 2007-08 (Oct 1–Apr 30); 2008-09 (Oct 1–Apr 14, limited due to emergence of 2009 H1N1).

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Outpatient Illness Surveillance:

Nationwide during week 40, 6.1% of patient visits reported through the U.S. Outpatient Influenza-like Illness Surveillance Network (ILINet) were due to influenza-like illness (ILI). This percentage is above the national baseline of 2.3%.

national levels of ILI and ARI
View ILINet Regional Charts | View Full Screen

On a regional level, the percentage of outpatient visits for ILI ranged from 1.8% to 12.9% during week 40, and increased in nine of the 10 surveillance regions compared to the previous week. All 10 regions reported a proportion of outpatient visits for ILI above their region-specific baseline levels.

Geographic Spread of Influenza as Assessed by State and Territorial Epidemiologists:

The influenza activity reported by state and territorial epidemiologists indicates geographic spread of both seasonal influenza and 2009 influenza A (H1N1) viruses and does not measure the severity of influenza activity.

  • During week 40, the following influenza activity was reported:
    • Widespread influenza activity was reported by 40 states (Alabama, Alaska, Arizona, Arkansas, California, Colorado, Delaware, Florida, Georgia, Idaho, Illinois, Indiana, Iowa, Kansas, Kentucky, Louisiana, Maryland, Minnesota, Mississippi, Missouri, Montana, Nebraska, Nevada, New Hampshire, New Mexico, New York, North Carolina, North Dakota, Ohio, Oklahoma, Oregon, Pennsylvania, South Dakota, Texas, Tennessee, Utah, Virginia, Washington, West Virginia, Wisconsin, and Wyoming).
    • Regional influenza activity was reported by Guam and eight states (Connecticut, Maine, Massachusetts, Michigan, New Jersey, Rhode Island, South Carolina, and Vermont).
    • Local influenza activity was reported by the District of Columbia, Puerto Rico, and one state (Hawaii).
    • The U.S. Virgin Islands did not report.

U. S. Map for Weekly Influenza Activity

Downloadable Version


A description of surveillance methods is available at:

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