Influenza and SARS-CoV-2 Co-Infections in California, USA, September 2020–April 2021

Kyle R. Rizzo; Cora Hoover; Seema Jain; Monica Sun; Jennifer F. Myers; Brooke Bregman; Deniz M. Dominguez; Allison Jacobsen; Garrett J. Jenkins; Tamara Hennessy-Burt; Erin L. Murray


Emerging Infectious Diseases. 2021;27(11):2923-2926. 

In This Article

The Study

California laboratories and medical providers must report all positive and nonpositive (i.e., negative, inconclusive, or invalid) SARS-CoV-2 laboratory results to their local health jurisdictions (LHJs).[2] For influenza, only positive results that can be submitted electronically by laboratories are reportable. Most data are reported directly to CDPH's web-based platform, California Reportable Diseases Information Exchange (CalREDIE). CalREDIE assigns electronic laboratory reports a unique identifier, personID, that can be used to link the same person across different disease reports. CalREDIE is used by 59 of California's 61 LHJs for disease tracking and reporting. Two LHJs, Los Angeles and San Diego, which represent one third of California's population, do not use CalREDIE directly; we excluded data from those LHJs.

We matched positive molecular influenza test results reported during September 1, 2020–April 30, 2021, with positive and nonpositive molecular SARS-CoV-2 test results to identify co-infections. We matched positive influenza results with nonpositive SARS-CoV-2 results to determine whether persons infected with influenza were negative for SARS-CoV-2 or were potentially not tested for SARS-CoV-2. We deduplicated all positive influenza tests results and excluded antigen test results.

We matched laboratory results first using CalREDIE personID, then by name and date of birth, and finally by manual record review if positive influenza results did not match to SARS-CoV-2 results by personID or name and date of birth (Figure 1). If a person had both positive and nonpositive SARS-CoV-2 results within 7 days of a positive influenza result, we used the positive SARS-CoV-2 result in the analysis. Persons with both positive influenza and SARS-CoV-2 test results with ≤7 days between specimen collection dates met criteria for influenza and SARS-CoV-2 co-infection. We analyzed co-infection data by week of illness onset and geographic distribution. We summarized co-infected persons by age, race and ethnicity, sex, hospitalization, and survival status. We completed all analyses using SAS version 9.4 (SAS Institute, This study received a nonresearch determination from the California Committee for the Protection of Human Subjects.

Figure 1.

Matching process of influenza and SARS-CoV-2 molecular test results submitted to CalREDIE, California, USA, September 1, 2020–April 30, 2021. CalREDIE, California Reportable Diseases Information Exchange; DOB, date of birth; personID, CalREDIE individual identification code; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2

CDPH received 258 positive influenza test results during September 1, 2020–April 30, 2021, and >21.1 million SARS-CoV-2 total test results. Among positive influenza results, 255 (99%) matched with a SARS-CoV-2 test result (positive or nonpositive). From these matches, 58 (23%) persons were co-infected with influenza and SARS-CoV-2 and 197 (77%) were positive for influenza and negative for SARS-CoV-2 (Figure 1). Co-infections occurred sporadically in California beginning in mid-November 2020 (Figure 2). At least 1 positive influenza result was received from 35 (59%) of 59 reporting LHJs, and ≥1 co-infections were identified in 21 (36%) LHJs throughout all regions in California. Among the 258 persons with positive influenza tests, 170 (66%) had influenza B and 88 (34%) influenza A. Influenza B was predominant (n = 39; 67%) among co-infected persons. Fifty-two (90%) co-infected persons had influenza and SARS-CoV-2 test specimens collected on the same date.

Figure 2.

Number of influenza infections (n = 258) and co-infections with SARS-CoV-2 (n = 58) by week of onset, California, USA, September 1, 2020–April 30, 2021. SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.

Age distribution among co-infected persons was 5 (9%) who were 0–17 years, 23 (40%) 18–49 years, 12 (21%) 50–64 years, and 18 (31%) ≥65 years of age. Twenty-two (38%) persons were female and 35 (60%) were male; sex was unknown for 1 (2%) co-infected person. The racial/ethnic distribution of co-infected persons was 20 (34%) Latino, 20 (34%) White, 5 (9%) Asian, 3 (5%) African American, 1 (2%) American Indian or Alaskan Native, 1 (2%) Native Hawaiian or Pacific Islander, 2 (3%) other, 2 (3%) multirace, and 4 (7%) unknown. Among 28 (48%) co-infected persons with available hospitalization status data, 11 (39%) were hospitalized. Five (9%) co-infected persons died, including 2 who were hospitalized; all who died were >50 years of age.