Interim Estimates of 2019–20 Seasonal Influenza Vaccine Effectiveness

United States, February 2020

Fatimah S. Dawood, MD; Jessie R. Chung, MPH; Sara S. Kim, MPH; Richard K. Zimmerman, MD; Mary Patricia Nowalk, PhD; Michael L. Jackson, PhD; Lisa A. Jackson, MD; Arnold S. Monto, MD; Emily T. Martin, PhD; Edward A. Belongia, MD; Huong Q. McLean, PhD; Manjusha Gaglani, MBBS; Kayan Dunnigan, MPH; Angie Foust, MS; Wendy Sessions, MPH; Juliana DaSilva, MA; Shoshona Le; Thomas Stark, PhD; Rebecca J. Kondor, PhD; John R. Barnes, PhD; David E. Wentworth, PhD; Lynnette Brammer, MPH; Alicia M. Fry, MD; Manish M. Patel, MD; Brendan Flannery, PhD


Morbidity and Mortality Weekly Report. 2020;69(7):177-182. 

In This Article

Abstract and Introduction


During the 2019–20 influenza season, influenza-like illness (ILI)* activity first exceeded the national baseline during the week ending November 9, 2019, signaling the earliest start to the influenza season since the 2009 influenza A(H1N1) pandemic. Activity remains elevated as of mid-February 2020. In the United States, annual vaccination against seasonal influenza is recommended for all persons aged ≥6 months.[1] During each influenza season, CDC estimates seasonal influenza vaccine effectiveness in preventing laboratory-confirmed influenza associated with medically attended acute respiratory illness (ARI). This interim report used data from 4,112 children and adults enrolled in the U.S. Influenza Vaccine Effectiveness Network (U.S. Flu VE Network) during October 23, 2019–January 25, 2020. Overall, vaccine effectiveness (VE) against any influenza virus associated with medically attended ARI was 45% (95% confidence interval [CI] = 36%–53%). VE was estimated to be 50% (95% CI = 39%–59%) against influenza B/Victoria viruses and 37% (95% CI = 19%–52%) against influenza A(H1N1)pdm09, indicating that vaccine has significantly reduced medical visits associated with influenza so far this season. Notably, vaccination provided substantial protection (VE = 55%; 95% CI = 42%–65%) among children and adolescents aged 6 months–17 years. Interim VE estimates are consistent with those from previous seasons, ranging from 40%–60% when influenza vaccines were antigenically matched to circulating viruses. CDC recommends that health care providers continue to administer influenza vaccine to persons aged ≥6 months because influenza activity is ongoing, and the vaccine can still prevent illness, hospitalization, and death associated with currently circulating influenza viruses as well as other influenza viruses that might circulate later in the season.

Methods used by the U.S. Flu VE Network have been published previously.[2] At five study sites (Michigan, Pennsylvania, Texas, Washington, and Wisconsin), patients aged ≥6 months seeking outpatient medical care for an ARI with cough within 7 days of illness onset were enrolled once local influenza circulation was identified. Enrollment eligibility criteria included 1) age ≥6 months on September 1, 2019 (i.e., vaccine-eligible); 2) ARI with cough, with onset ≤7 days earlier; and 3) no treatment with influenza antiviral medication (e.g., oseltamivir or baloxavir) during this illness. Consenting participants or their proxies were interviewed to collect demographic data, information on general and current health status and symptoms, and 2019–20 influenza vaccination status. Nasal and oropharyngeal swabs (nasal swabs alone for children aged <2 years) were collected to obtain respiratory specimens; swabs were placed in a single cryovial with viral transport medium and tested at U.S. Flu VE Network laboratories using CDC's real-time reverse transcription–polymerase chain reaction (RT-PCR) protocol for detection and identification of influenza viruses.§ For interim estimates, participants (including children aged <9 years, who require 2 vaccine doses during their first vaccination season) were considered to be vaccinated if they received ≥1 dose of any seasonal influenza vaccine ≥14 days before illness onset, according to medical records, registries, or patient report. VE against all influenza virus types combined and against viruses by type/subtype was estimated as 100% x (1 − odds ratio). Estimates were adjusted for study site, age group, sex, race/ethnicity, self-rated health status, days from illness onset to enrollment, and month of illness using logistic regression. VE estimates by age group and influenza subtype are presented for strata with sufficient numbers of influenza cases to achieve adequate statistical power to detect a significant VE based on a priori sample size calculations.**

Among 4,112 ARI patients enrolled during October 23, 2019–January 25, 2020, a total of 1,060 (26%) tested positive for influenza virus infection by real-time RT-PCR, including 691 (17%) for influenza B viruses and 374 (9%) for influenza A viruses (Table 1); five patients tested positive for both influenza A and B viruses. Of 673 influenza B viruses with lineage information available, 670 (>99%) belonged to the B/Victoria lineage, and three (<1%) belonged to the B/Yamagata lineage. Among 335 subtyped influenza A viruses, 326 (97%) were A(H1N1)pdm09 viruses, and only 11 (3%) were A(H3N2) viruses. The proportion of patients with influenza differed among study sites, age groups, racial/ethnic groups, self-rated health status, and days from illness onset to enrollment. The percentage of ARI patients who were vaccinated ranged from 38% to 61% among study sites and differed by study site, sex, age group, race/ethnicity, self-rated health status, and days from illness onset to enrollment.

Among influenza-positive participants, 37% had received the 2019–20 seasonal influenza vaccine, compared with 55% of influenza-negative participants (Table 2). Overall, the adjusted VE was 45% against influenza A and B virus types combined, 50% against influenza B/Victoria, and 37% against A(H1N1)pdm09. VE was higher among children and adolescents aged 6 months–17 years and lower among adults aged 18–49 years, especially against A(H1N1)pdm09 (VE = 5%; 95% CI = -45% to 37%).

As of January 25, 2020, CDC had genetically characterized 177 influenza B/Victoria viruses from U.S. Flu VE Network participants; 172 (97%) belonged to genetic subclade V1A.3, a different subclade from the V1A.1 subclade that includes the 2019–20 B/Victoria vaccine reference strain (B/Colorado/06/2017), and five (3%) belonged to V1A.1. All of the 32 genetically characterized A(H1N1)pdm09 viruses were from genetic group 6B.1A, which includes the 2019–20 A(H1N1)pdm09 vaccine reference strain (A/Brisbane/02/2018).

*Fever (temperature ≥100°F [37.8°C]) and a cough or a sore throat without a known cause other than influenza (
Study enrollment began at each site after local surveillance identified increasing weekly influenza activity or one or more laboratory-confirmed cases of influenza per week for 2 consecutive weeks. The U.S. Flu VE Network sites and the dates enrollment began are as follows: University of Michigan School of Public Health (partnered with the University of Michigan Health System, Ann Arbor, Michigan, and the Henry Ford Health System, Detroit, Michigan) (November 20, 2019); University of Pittsburgh Schools of the Health Sciences (partnered with the University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania) (November 25, 2019); Kaiser Permanente Washington, Seattle, Washington (November 25, 2019); Marshfield Clinic Research Institute, Marshfield, Wisconsin (December 30, 2019); and Baylor Scott and White Health, Texas A&M University College of Medicine, Temple, Texas (October 23, 2019).
100% x (1 − odds ratio [ratio of odds of being vaccinated among outpatients with CDC's real-time RT-PCR influenza-positive test results to the odds of being vaccinated among outpatients with influenza-negative test results]).
**Sample sizes to achieve an adequate number of influenza cases to estimate a significant VE with 95% confidence intervals that do not include zero were estimated by virus subtype and the following age groups: 6 months–17 years, 18–49 years, 50–64 years, and ≥65 years. Sample size calculations were based on a type I error probability of 5% and a type II error probability of 20% (power 80%) to detect 40% VE against any influenza, 50% VE against influenza A(H1N1) or influenza B, and 30% VE against influenza A(H3N2). Assumptions about vaccination coverage varied by age group as follows: 50% for children and adolescents aged 6 months–17 years, 45% for adults aged 18–49 years, 60% for adults aged 50–64 years, and 80% for adults aged ≥65 years. These VE and coverage assumptions were made on the basis of pooled estimates from the 2012–13 through 2018–19 influenza seasons in the U.S. Flu VE Network. Age strata with insufficient influenza cases were aggregated to provide VE estimates for larger strata when possible.