U.S. Virologic Surveillance

Clinical Laboratories

The results of tests performed by clinical laboratories nationwide are summarized below. Data from clinical laboratories (the percentage of specimens tested that are positive for influenza) are used to monitor whether influenza activity is increasing or decreasing.

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Public Health Laboratories

The results of tests performed by public health laboratories nationwide are summarized below. Data from public health laboratories are used to monitor the proportion of circulating viruses that belong to each influenza subtype/lineage.

Nationally influenza B/Victoria viruses have been reported more frequently than other influenza viruses this season; followed by A(H1N1)pdm09 and A(H3N2) viruses. The predominant virus varies by region and the proportions of influenza B/Victoria and influenza A(H1N1)pmd09 viruses are increasing in some regions. Regional and state level data about circulating influenza viruses can be found on FluView Interactive. The predominant virus also varies by age group. Nationally, influenza B/Victoria viruses are the most commonly reported influenza viruses among children age 0-4 years (46% of reported viruses) and 5-24 years (59% of reported viruses), while A(H3N2) viruses are the most commonly reported influenza viruses among persons 65 years of age and older (47% of reported viruses). Among adults aged 25-64 years, approximately equal proportions of influenza A(H1N1)pdm09 and B/Victoria viruses (38% and 34%, respectively) have been reported. Additional age data can be found on FluView Interactive.

Additional virologic surveillance information for current and past seasons:
Surveillance Methods | FluView Interactive: National, Regional, and State Data or Age Data

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Novel Influenza A Virus:

One additional human infection with a novel influenza A virus was reported by Ohio. This person was infected with an influenza A(H1N2) variant (A(H1N2)v) virus and reported exposure to swine at an agricultural fair during the week preceding illness onset. The patient is a child < 18 years of age, was not hospitalized, and continues to recover from illness.

A total of 14 variant viruses have been reported to CDC during 2018. One of these has been an influenza A(H3N2) variant (A(H3N2)v) virus (Indiana [1]), and 13 have been A(H1N2)v viruses (California [6], Michigan [3], and Ohio [4]).

Early identification and investigation of human infections with novel influenza A viruses are critical so that the risk of infection can be more fully understood and appropriate public health measures can be taken. Additional information on influenza in swine, variant influenza infection in humans, and strategies to interact safely with swine can be found at http://www.cdc.gov/flu/swineflu/index.htm.

Additional information regarding human infections with novel influenza A viruses can be found at http://gis.cdc.gov/grasp/fluview/Novel_Influenza.html.

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Influenza Virus Characterization

CDC performs genetic and antigenic characterization of U.S. viruses submitted from state and local health laboratories using Right Size Roadmap submission guidance. These data are used to compare how similar the currently circulating influenza viruses are to the reference viruses used for developing new influenza vaccines and to monitor evolutionary changes that continually occur in circulating influenza. CDC also tests susceptibility of influenza viruses to antiviral medications including the neuraminidase inhibitors (oseltamivir, zanamivir, and peramivir) and the PA endonuclease inhibitor baloxavir.

CDC genetically characterized 369 influenza viruses collected in the U.S. from September 29, 2019 to December 7, 2019.

CDC antigenically characterizes a subset of influenza viruses by hemagglutination inhibition (HI) or neutralization based Focus Reduction assays (FRA). Antigenic drift is evaluated by comparing antigenic properties of cell-propagated reference viruses representing currently recommended vaccine components with those of cell-propagated circulating viruses. CDC antigenically characterized 61 influenza viruses collected in the U.S. from September 29, 2019 to December 7, 2019.

Influenza A Viruses

• A (H1N1)pdm09: Eighteen A(H1N1)pdm09 viruses were antigenically characterized by HI with ferret antisera, and all were antigenically similar (reacting at titers that were within 4-fold of the homologous virus titer) to cell-propagated A/Brisbane/02/2018-like reference viruses representing the A(H1N1)pdm09 component for the 2019-20 Northern Hemisphere influenza vaccines.
• A (H3N2): Seventeen A(H3N2) viruses were antigenically characterized by FRA with ferret antisera, and 12 (70.6%) were antigenically similar to cell-propagated A/Kansas/14/2017-like reference viruses representing the A(H3N2) component for the 2019-20 Northern Hemisphere influenza vaccines.

Influenza B Viruses

• B/Victoria: Sixteen B/Victoria lineage viruses, including viruses from both co-circulating sub-clades, were antigenically characterized by HI with ferret antisera, and 10 (62.5%) were antigenically similar to cell-propagated B/Colorado/06/2017-like reference viruses representing the B/Victoria component for the 2019-20 Northern Hemisphere influenza vaccines.
• B/Yamagata: Ten B/Yamagata lineage viruses were antigenically characterized by HI with ferret antisera, and all 10 (100%) were antigenically similar to cell-propagated B/Phuket/3073/2013-like reference viruses representing the B/Yamagata component for the 2019-20 Northern Hemisphere influenza vaccines.

CDC assesses susceptibility of influenza viruses to the antiviral medications oseltamivir, zanamivir, peramivir, and baloxavir using next generation sequence analysis supplemented by laboratory assays. Viruses collected in the U.S. since September 29, 2019 were tested for antiviral susceptibility as follows:

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• A (H1N1)pdm09: Phylogenetic analysis of the HA genes from 63 A(H1N1)pdm09 viruses showed that all belonged to clade 6B.1. Fifty-seven A(H1N1)pdm09 viruses were antigenically characterized, and 57 (100%) were antigenically similar (analyzed using HI with ferret antisera) to A/Michigan/45/2015 (6B.1), a cell-propagated A/Michigan/45/2015-like reference virus representing the A(H1N1)pdm09 component for the 2018-2019 Northern Hemisphere influenza vaccines.

• A (H3N2): Phylogenetic analysis of the HA genes from 64 A(H3N2) viruses revealed extensive genetic diversity with multiple clades/subclades co-circulating. The HA genes of circulating viruses belonged to clade 3C.2a (n=24), subclade 3C.2a1 (n=35) or clade 3C.3a (n=5). Thirty influenza A(H3N2) viruses were antigenically characterized by FRA with ferret antisera, and 28 (93.3%) A(H3N2) viruses tested were well-inhibited (reacting at titers that were within fourfold of the homologous virus titer) by ferret antisera raised against A/Singapore/INFIMH-16-0019/2016 (3C.2a1), a cell-propagated A/Singapore/INFIMH-16-0019/2016 -like reference virus representing the A(H3N2) component of 2018-2019 Northern Hemisphere influenza vaccines.

Influenza B Viruses

• B/Victoria: Phylogenetic analysis of 10 B/Victoria-lineage viruses indicate that all HA genes belonged to genetic clade V1A, however genetic subclades which are antigenically distinct have emerged. The majority of recent B/Victoria-lineage viruses belonged to a subclade of viruses with a 6-nucleotide deletion (encoding amino acids 162 and 163) in the HA (V1A.1, previously abbreviated as V1A-2Del). In addition, a small number of B/Victoria-lineage viruses have a three amino acid deletion (162-164) in the HA protein (abbreviated as V1A-3Del). Nine (90%) B/Victoria lineage viruses were well-inhibited by ferret antisera raised against cell-propagated B/Colorado/06/2017-like (V1A.1) reference virus, representing the B/Victoria lineage component of 2018-2019 Northern Hemisphere influenza vaccines. One (10%) B/Victoria lineage virus reacted poorly (at titers that were 8-fold or greater reduced compared with the homologous virus titer) with ferret antisera raised against cell-propagated B/Colorado/06/2017-like reference virus, and belonged to clade V1A.

• B/Yamagata: Phylogenetic analysis of 33 influenza B/Yamagata-lineage viruses indicate that the HA genes belonged to clade Y3. A total of 32 influenza B/Yamagata-lineage viruses were antigenically characterized, and all were antigenically similar to cell-propagated B/Phuket/3073/2013 (Y3), the reference vaccine virus representing the influenza B/Yamagata-lineage component of the 2018-2019 Northern Hemisphere quadrivalent vaccines.

The majority of U.S. viruses submitted for characterization come from state and local public health laboratories. Due to Right Size Roadmap considerations, specimen submission guidance to laboratories is that, if available, 2 influenza A(H1N1)pdm09, 2 influenza A(H3N2), and 2 influenza B viruses be submitted every other week. Therefore, the numbers of each virus type/subtype characterized should be more balanced across subtypes/lineages but will not reflect the actual proportion of circulating viruses. In the figure below, the results of tests performed by public health labs are shown on the left and CDC sequence results (by genetic clade/subclade) are shown on the right.

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Antiviral Resistance:

During May 20-October 6, 2018, 156 specimens (61 influenza A(H1N1)pdm09, 51 influenza A(H3N2), and 44 influenza B viruses) collected in the United States were tested for susceptibility to the neuraminidase inhibitors (oseltamivir, zanamivir, and peramivir). All tested viruses were sensitive to all three recommended antiviral medications.

Antiviral Medication			Total Viruses	A/H1	A/H3	B/Victoria	B/Yamagata
Neuraminidase Inhibitors	Oseltamivir	Viruses Tested	2,547	1,183	969	215	180
		Reduced	2 (0.1%)	2 (0.2%)	0 (0%)	0 (0%)	0 (0%)
		Highly Reduced	4 (0.2%)	4 (0.3%)	0 (0%)	0 (0%)	0 (0%)
	Peramivir	Viruses Tested	2,547	1,183	969	215	180
		Reduced	0 (0%)	0 (0%)	0 (0%)	0 (0%)	0 (0%)
		Highly Reduced	4 (0.2%)	4 (0.3%)	0 (0%)	0 (0%)	0 (0%)
	Zanamivir	Viruses Tested	2,547	1,183	969	215	180
		Reduced	0 (0%)	0 (0%)	0 (0%)	0 (0%)	0 (0%)
		Highly Reduced	0 (0%)	0 (0%)	0 (0%)	0 (0%)	0 (0%)
PA Cap-Dependent Endonuclease Inhibitor	Baloxavir Marboxil	Viruses Tested	2,547	1,162	964	229	187
		Decreased Susceptibility	0 (0%)	0 (0%)	0 (0%)	0 (0%)	0 (0%)

While all of the recently circulating influenza viruses are susceptible to the neuraminidase inhibitor antiviral medications oseltamivir, zanamivir, and peramivir; rare sporadic instances of oseltamivir-resistant and peramivir-resistant influenza A(H1N1)pdm09 viruses and oseltamivir-resistant influenza A(H3N2) viruses have been detected worldwide. Antiviral treatment as early as possible is recommended for patients with confirmed or suspected influenza who have severe, complicated, or progressive illness; who require hospitalization; or who are at high risk for serious influenza-related complications. Additional information on recommendations for treatment and chemoprophylaxis of influenza virus infection with antiviral agents is available at http://www.cdc.gov/flu/antivirals/index.htm.

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Outpatient Illness Surveillance

ILINet

Nationwide during week 49, 3.2% 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%. The decrease in the percentage of patient visits for ILI during week 49 compared to week 48 may be influenced in part by a reduction in routine healthcare visits surrounding the Thanksgiving holiday (occurring during week 48) as has occurred during previous seasons.


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On a regional level, the percentage of outpatient visits for ILI ranged from 1.8% to 5.7% during week 49. All regions reported a percentage of outpatient visits for ILI which is equal to or above their region-specific baselines.

ILI Activity Map

Data collected in ILINet are used to produce a measure of ILI activity* by state.

During week 49, the following ILI activity levels were experienced:

• High – Puerto Rico and 11 states (Alabama, Arkansas, Georgia, Mississippi, Nebraska, New Mexico, South Carolina, Tennessee, Texas, Virginia, and Washington)
• Moderate – New York City and 11 states (Arizona, Colorado, Connecticut, Hawaii, Kentucky, Maryland, Minnesota, Nevada, New Jersey, Oklahoma, and Oregon)
• Low – District of Columbia and nine states (California, Florida, Illinois, Kansas, Massachusetts, New York, North Carolina, Pennsylvania, and Wisconsin)
• Minimal – 18 states (Alaska, Delaware, Idaho, Indiana, Iowa, Maine, Michigan, Missouri, Montana, New Hampshire, North Dakota, Ohio, Rhode Island, South Dakota, Utah, Vermont, West Virginia, and Wyoming)
• Data were insufficient to calculate an ILI activity level from the U.S. Virgin Islands and Louisiana.

*Data collected in ILINet may disproportionally represent certain populations within a state, and therefore, may not accurately depict the full picture of influenza activity for the whole state. Differences in the data presented here by CDC and independently by some state health departments likely represent differing levels of data completeness with data presented by the state likely being the more complete.

Additional information about medically attended visits for ILI for current and past seasons:
Surveillance Methods | FluView Interactive: National, Regional, and State Data or ILI Activity Map

Geographic Spread of Influenza as Assessed by State and Territorial Epidemiologists

The influenza activity reported by state and territorial epidemiologists indicates geographic spread of influenza viruses but does not measure the severity of influenza activity.

During week 49 the following influenza activity was reported:

• Widespread – 23 states (Alabama, Arizona, California, Connecticut, Georgia, Idaho, Indiana, Kentucky, Louisiana, Maryland, Massachusetts, Nebraska, Nevada, New Mexico, New York, North Carolina, Oregon, Pennsylvania, South Carolina, Tennessee, Texas, Virginia and Washington)
• Regional – Puerto Rico and 14 states (Arkansas, Colorado, Florida, Illinois, Michigan, Minnesota, Mississippi, Montana, New Jersey, Ohio, Oklahoma, Rhode Island, Utah and Wisconsin)
• Local – 12 states (Delaware, Hawaii, Iowa, Kansas, Maine, Missouri, New Hampshire, North Dakota, South Dakota, Vermont, West Virginia and Wyoming)
• Sporadic – the District of Columbia, the U.S. Virgin Islands and one state (Alaska)
• Guam did not report.

Additional geographic spread surveillance information for current and past seasons:
Surveillance Methods | FluView Interactive

Influenza-Associated Hospitalizations

The Influenza Hospitalization Surveillance Network (FluSurv-NET) conducts population-based surveillance for laboratory-confirmed influenza-related hospitalizations in select counties in the Emerging Infections Program (EIP) states and Influenza Hospitalization Surveillance Project (IHSP) states.

A total of 1,139 laboratory-confirmed influenza-associated hospitalizations were reported by FluSurv-NET sites between October 1, 2019 and December 7, 2019. The overall hospitalization rate was 3.9 per 100,000 population. The highest rate of hospitalization was among adults aged ≥65 (9.4 per 100,000 population), followed by children aged 0-4 (7.5 per 100,000 population) and adults aged 50-64 (4.1 per 100,000 population). Among 1,139 hospitalizations, 627 (55.0%) were associated with influenza A virus, 499 (43.8%) with influenza B virus, 6 (0.5%) with influenza A virus and influenza B virus co-infection, and 7 (0.6%) with influenza virus for which the type was not determined. Among those with influenza A subtype information, 103 (70.5%) were A(H1N1)pdm09 virus and 43 (29.5%) were A(H3N2).



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Additional hospitalization surveillance information for current and past seasons and additional age groups:
Surveillance Methods | FluView Interactive

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FluSurv-NET data are preliminary and displayed as they become available. Therefore, figures are based on varying denominators as some variables represent information that may require more time to be collected. Data are refreshed and updated weekly. Asthma includes a medical diagnosis of asthma or reactive airway disease; Cardiovascular diseases include conditions such as coronary heart disease, cardiac valve disorders, congestive heart failure, and pulmonary hypertension; does not include isolated hypertension; Chronic lung diseases include conditions such as chronic obstructive pulmonary disease, bronchiolitis obliterans, chronic aspiration pneumonia, and interstitial lung disease; Immune suppression includes conditions such as immunoglobulin deficiency, leukemia, lymphoma, HIV/AIDS, and individuals taking immunosuppressive medications; Metabolic disorders include conditions such as diabetes mellitus; Neurologic diseases include conditions such as seizure disorders, cerebral palsy, and cognitive dysfunction; Neuromuscular diseases include conditions such as multiple sclerosis and muscular dystrophy; Obesity was assigned if indicated in patient’s medical chart or if body mass index (BMI) >30 kg/m2; Pregnancy percentage calculated using number of female cases aged between 15 and 44 years of age as the denominator; Renal diseases include conditions such as acute or chronic renal failure, nephrotic syndrome, glomerulonephritis, and impaired creatinine clearance; No known condition indicates that the case did not have any known high risk medical condition indicated in medical chart at the time of hospitalization.

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Pneumonia and Influenza (P&I) Mortality Surveillance

Based on National Center for Health Statistics (NCHS) mortality surveillance data available on December 12, 2019, 5.0% of the deaths occurring during the week ending November 30, 2019 (week 48) were due to P&I. This percentage is below the epidemic threshold of 6.5% for week 48.


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Additional pneumonia and influenza mortality surveillance information for current and past seasons:
Surveillance Methods | FluView Interactive

Influenza-Associated Pediatric Mortality

Four influenza-associated pediatric deaths were reported to CDC during week 49. One death occurred during week 47 (the week ending November 23, 2019) and was associated with an influenza A virus for which no subtyping was performed. Three deaths occurred during week 48 (the week ending November 30, 2019). One death was associated with an influenza B/Victoria virus, one was associated with an influenza B virus with no lineage determined, and one was associated with an influenza A(H1N1)pdm09 virus.

A total of 10 influenza-associated pediatric deaths occurring during the 2019-2020 season have been reported to CDC. Six cases tested positive for influenza B; three of these cases had the lineage determined and all were B/Victoria viruses. Four cases tested positive for influenza A. Two of these cases had subtyping performed and both were A(H1N1)pdm09 viruses.

 

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Additional pediatric mortality surveillance information for current and past seasons:
Surveillance Methods | FluView Interactive

Additional National and International Influenza Surveillance Information

FluView Interactive: FluView includes enhanced web-based interactive applications that can provide dynamic visuals of the influenza data collected and analyzed by CDC. These FluView Interactive applications allow people to create customized, visual interpretations of influenza data, as well as make comparisons across flu seasons, regions, age groups and a variety of other demographics. To access these tools, visit http://www.cdc.gov/flu/weekly/fluviewinteractive.htm

National Institute for Occupational Safety and Health: Monthly surveillance data on the prevalence of health-related workplace absenteeism among full-time workers in the United States are available from NIOSH at https://www.cdc.gov/niosh/topics/absences/default.html

U.S. State and local influenza surveillance:Select a jurisdiction below to access the latest local influenza information

Alabama	Alaska	Arizona	Arkansas	California
Colorado	Connecticut	Delaware	District of Columbia	Florida
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	West Virginia	Wisconsin
Wyoming	New York City	Puerto Rico	Virgin Islands

World Health Organization: Additional influenza surveillance information from participating WHO member nations is available through FluNet and the Global Epidemiology Reports.

WHO Collaborating Centers for Influenza located in Australia, China, Japan, the United Kingdom, and the United States (CDC in Atlanta, Georgia).

Europe: For the most recent influenza surveillance information from Europe, please see WHO/Europe and the European Centre for Disease Prevention and Control at http://www.flunewseurope.org/.

Public Health Agency of Canada: The most up-to-date influenza information from Canada is available at http://www.phac-aspc.gc.ca/fluwatch/

Public Health England: The most up-to-date influenza information from the United Kingdom is available at https://www.gov.uk/government/statistics/weekly-national-flu-reports