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

2008-2009 Influenza Season Week 38 ending September 26, 2009

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


During week 38 (September 20-26, 2009), influenza activity remained elevated in the U.S

  • 2 126 (22,8 %) 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.
  • 99 % of 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 below the epidemic threshold.
  • Eleven influenza-associated pediatric deaths were reported and all eleven were associated with 2009 influenza A (H1N1) virus infection.
  • The proportion of outpatient visits for influenza-like illness (ILI) was above the national baseline. Regions 2 through 10 reported ILI above region-specific baseline levels; only Region 1 was below its region-specific baseline.
  • Twenty-seven states reported geographically widespread influenza activity, Guam and 18 states reported regional influenza activity, two states, the District of Columbia, and Puerto Rico reported local influenza activity, one state reported sporadic influenza activity, and the U.S. Virgin Islands and two states did not report.
  • The 2009-10 influenza season officially begins October 4, 2009.

National and Regional Summary of Select Surveillance Components

HHS Surveillance Regions*
Data for current week Data cumulative for the season
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 22,8 % 46 of 54 8 293 4 369 47 918 945 25 194 10 860 128
Region 1 Normal 5,4 % 4 of 6 586 304 3 064 15 1 717 816 4
Region 2 Elevated 2,9 % 2 of 4 290 228 1 831 21 2 400 713 20
Region 3 Elevated 18,2 % 5 of 6 1 250 224 5 121 26 1 086 1 366 11
Region 4 Elevated 24,5 % 8 of 8 1 078 784 8 784 104 5 044 1 318 16
Region 5 Elevated 20,1 % 6 of 6 1 594 215 9 165 221 1 087 1 385 18
Region 6 Elevated 27,3 % 5 of 5 830 312 4 748 15 7 276 2 716 21
Region 7 Elevated 22,9 % 4 of 4 536 85 1 588 171 711 540 2
Region 8 Elevated 21,3 % 5 of 6 542 219 2 335 80 2 619 510 12
Region 9 Elevated 38,5 % 3 of 5 1 200 1 680 8 159 77 2 697 810 21
Region 10 Elevated 27,1 % 4 of 4 387 318 3 123 215 557 686 3

* 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 38
No. of specimens tested 9 314
No. of positive specimens (%) 2 126 (22,8 %)
Positive specimens by type/subtype
  Influenza A 2 119 (99,7 %)
             A (2009 H1N1)              1 116 (52,7 %)
                          959 (45,3 %)
             A (unable to subtype)              35 (1,7 %)
             A (H3)              6 (0,3 %)
             A (H1)             3 (0,1 %)
  Influenza B 7 (0,3 %)

During week 38, seasonal influenza A (H1), A (H3) and influenza B viruses co-circulated at low levels with 2009 influenza A (H1N1) viruses. Over 99 % of 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. 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 - September 26, 2009, 16 174 hospitalizations and 1 379 deaths associated with influenza virus infection or based on syndromic surveillance for influenza and pneumonia, were reported to CDC. CDC will continue to use its traditional surveillance systems to track the progress of the remainder of the 2008-09 season, and for the 2009-10 influenza season, which officially begins October 4, 2009.

Aggregate Hospital and Death Reporting
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Antigenic Characterization:

CDC has antigenically characterized 2 209 seasonal human influenza viruses [1 219 influenza A (H1), 276 influenza A (H3) and 714 influenza B viruses] collected by U.S. laboratories since October 1, 2008, and 795 2009 influenza A (H1N1) viruses.

1 192 (98 %) of 1 213 seasonal influenza A (H1) viruses tested are related to the influenza A (H1N1) component of the 2009-10 Northern Hemisphere influenza vaccine (A/Brisbane/59/2007) and 27 (2 %) showed reduced titers with antisera produced against A/Brisbane/59/2007.

Two hundred twenty-nine (83 %) of 276 influenza A (H3N2) viruses tested are related to the influenza A (H3N2) 2009-10 Northern Hemisphere vaccine component (A/Brisbane/10/2007-like) and 47 viruses (17 %) tested showed reduced titers with antisera produced against A/Brisbane/10/2007. Many current viruses that demonstrated reduced titers with antisera produced against A/Brisbane/10/2007 are related to A/Perth/16/2009, a new reference virus that has recently evolved from A/Brisbane/10/2007. An A/Perth/16/2009-like virus was recommended by WHO as the influenza A (H3N2) vaccine strain for the 2010 Southern Hemisphere influenza vaccine.

Seven hundred ninety-four (99,9 %) of 795 2009 influenza A (H1N1) viruses are related to the A/California/07/2009 (H1N1)pdm reference virus selected by WHO as the vaccine strain for the 2009-10 influenza A (H1N1) vaccine for the Northern Hemisphere. One virus (0,1 %) demonstrated reduced titers with antisera produced against A/California/07/2009 (H1N1).

Influenza B viruses currently circulating can be divided into two distinct lineages represented by the B/Yamagata/16/88 and B/Victoria/02/87 viruses. Six hundred thirty-eight (89 %) of 714 influenza B viruses tested belong to the B/Victoria lineage, and of these, 630 (99 %) are related to the influenza vaccine component for the 2009-10 Northern Hemisphere influenza vaccine (B/Brisbane/60/2008), and the remaining eight (1 %) showed reduced titers with antisera produced against B/Brisbane/60/2008. Seventy-six (11 %) of 714 influenza B viruses tested belong to the B/Yamagata lineage.

Data on antigenic characterization should be interpreted with caution given that antigenic characterization data are based on hemagglutination inhibition (HI) testing using a panel of reference ferret antisera, and results may not correlate with clinical protection against circulating viruses provided by influenza vaccination.

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, as is seen with the two lineages of influenza B viruses. Antigenic characterization of 2009 influenza A (H1N1) viruses indicates that these viruses are antigenically and genetically unrelated to seasonal influenza A (H1N1) viruses, suggesting that little to no protection would be expected from vaccination with seasonal influenza vaccine.

Antiviral Resistance:

Since October 1, 2008, 1 148 seasonal influenza A (H1N1), 261 influenza A (H3N2), 654 influenza B, and 876 2009 influenza A (H1N1) virus isolates have been tested for resistance to the neuraminidase inhibitors (oseltamivir and zanamivir). In addition, 989 2009 influenza A (H1N1) original clinical samples were tested for a single known mutation in the virus that confers oseltamivir resistance. Also, 1 153 seasonal influenza A (H1N1), 261 influenza A (H3N2), and 526 2009 influenza A (H1N1) viruses have been tested for resistance to the adamantanes (amantadine and rimantadine). The results of antiviral resistance testing performed on these viruses are summarized in the table below. Additional laboratories perform antiviral testing and report their results to CDC.

Samples tested (n) Resistant Viruses,
Number (%)
Samples tested (n) Resistant Viruses, Number (%) Samples tested (n) Resistant Viruses, Number (%)
Oseltamivir Zanamivir Adamantanes
Seasonal Influenza A (H1N1) 1 148 1 143 (99,6 %) 1 148 0 (0) 1 153 6 (0,5 %)
Influenza A (H3N2) 261 0 (0) 261 0 (0) 261 261 (100 %)
Influenza B 654 0 (0) 654 0 (0) N/A* N/A*
2009 Influenza A (H1N1) 1 865 9†‡ (0.6) 876 0 (0) 526 526 (100 %)

*The adamantanes (amantadine and rimantadine) are not effective against influenza B viruses.
†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, bringing the total number to 11.

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, including 11 cases in the United States (nine viruses identified by CDC and two viruses identified by additional laboratories). All tested viruses retain their sensitivity to the other neuraminidase inhibitor: zanamivir. Ten patients (including the nine viruses detected at CDC and one identified by an additional laboratory) had documented exposure to oseltamivir through either treatment or chemoprophylaxis, and the remaining patient is currently 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 Additional information on antiviral recommendations for treatment and chemoprophylaxis of influenza virus infection is available at 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.

Four seasonal influenza A (H1N1) viruses collected between February 8 and August 12, 2009, were found to be resistant to both oseltamivir and the adamantanes (amantadine and rimantadine). All seasonal influenza A (H1N1) viruses tested retain their sensitivity to zanamivir. The four dually-resistant viruses represent less than 1 % of all seasonal influenza A (H1N1) viruses tested during the 2008-09 influenza season, and as a result, no changes to the influenza antiviral treatment or prophylaxis recommendations will be made at this time. CDC will continue to monitor trends in antiviral resistance throughout the upcoming 2009-10 influenza season.

Pneumonia and Influenza (P&I) Mortality Surveillance

During week 38, 6,1 % of all deaths reported through the 122-Cities Mortality Reporting System were due to P&I. This percentage was below the epidemic threshold of 6,4 % for week 38.

Pneumonia And Influenza Mortality
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Influenza-Associated Pediatric Mortality

Eleven influenza-associated pediatric deaths were reported to CDC during week 38 (Arkansas, Colorado [3], Georgia, Kansas, South Carolina [2], Tennessee, and Texas [2]). These deaths were associated with 2009 influenza A (H1N1) virus infection and occurred between August 23 and September 26, 2009. Since September 28, 2008, CDC has received 128 reports of influenza-associated pediatric deaths that occurred during the current influenza season (26 deaths in children less than 2 years, 14 deaths in children 2-4 years, 38 deaths in children 5-11 years, and 50 deaths in individuals 12-17 years). Sixty of the 128 deaths were due to 2009 influenza A (H1N1) virus infections, and 14 of these have occurred since August 30, 2009.

Of the 56 children who had specimens collected for bacterial culture from normally sterile sites, 21 (37,5 %) were positive; Staphylococcus aureus was identified in 14 (66,7 %) of the 21 children. Six of the S. aureus isolates were sensitive to methicillin and eight were methicillin resistant. Nineteen (90,5 %) of the 21 children with bacterial coinfections were five years of age or older and 13 (61,9 %) of the 21 children were 12 years of age or older. Twenty-five (41,7 %) of the 60 children with confirmed 2009 influenza A (H1N1) infection had a specimen collected from a normally sterile site; seven (28 %) of the 25 children had a positive bacterial culture; five of which were positive for S. aureus. Two of the S. aureus isolates were sensitive to methicillin and three were methicillin resistant. Other bacteria identified include Streptococcus constellatus, Pseudomonas aeruginosa, Streptococcus, and Enterococcus.

Influenza-Associated Pediatric Mortality
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Influenza-Associated Hospitalizations

Laboratory-confirmed influenza-associated hospitalizations are monitored through the Emerging Infections Program (EIP), a population-based surveillance network.

During April 15, 2009 – September 26, 2009, the following preliminary laboratory-confirmed overall influenza associated hospitalization rates were reported by the EIP (rates include influenza A, influenza B, and 2009 influenza A (H1N1)):

Rates for children aged 0-23 months, 2-4 years, and 5-17 years were 3.3, 1.4, and 1.1 per 10,000, respectively. Rates for adults aged 18-49 years, 50-64 years, and ≥ 65 years, the overall flu rates were 0.7, 0.8, and 0.7 per 10,000, respectively.

Influenza-Associated Pediatric Mortality

*This value represents an age group-specific average influenza rate from October 1 to April 30 from the 2005-06, 2006-07, and 2007-08 influenza seasons.
**Note: The scales for the 0-23 month and the >= 65 years age groups differ from other age groups.

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Outpatient Illness Surveillance:

Nationwide during week 38, 4,2 % 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 2,4 %.

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

On a regional level, the percentage of outpatient visits for ILI ranged from 1,4 % to 7,4 %, and decreased in four of the 10 surveillance regions. Nine regions (Regions 2 through 10) reported a proportion of outpatient visits for ILI above region-specific baseline levels, while Region 1 reported a percentage of visits for ILI below its region-specific baseline. .

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 38, the following influenza activity was reported:
    • Widespread influenza activity was reported by 27 states (Alabama, Alaska, Arizona, Arkansas, California, Colorado, Delaware, Florida, Georgia, Illinois, Indiana, Kansas, Kentucky, Louisiana, Maryland, Minnesota, Mississippi, New Mexico, North Carolina, Ohio, Oklahoma, Pennsylvania, Texas, Tennessee, Virginia, Washington, and Wyoming).
    • Regional influenza activity was reported by Guam and 18 states (Idaho, Iowa, Maine, Massachusetts, Michigan, Missouri, Nebraska, New Hampshire, New Jersey, New York, North Dakota, Oregon, Rhode Island, South Carolina, South Dakota, Utah, West Virginia, and Wisconsin).
    • Local influenza activity was reported by the District of Columbia, Puerto Rico, and two states (Connecticut and Hawaii).
    • Sporadic activity was reported by one state (Vermont).
    • The U.S. Virgin Islands and two states did not report (Montana and Nevada).


A description of surveillance methods is available at:

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