Severe Acute Respiratory Syndrome Coronavirus 2 and Respiratory Virus Sentinel Surveillance, California, USA, May 10, 2020–June 12, 2021

Gail L. Sondermeyer Cooksey; Christina Morales; Lauren Linde; Samuel Schildhauer; Hugo Guevara; Elena Chan; Kathryn Gibb; Jessie Wong; Wen Lin; Brandon J. Bonin; Olivia Arizmendi; Tracy Lam-Hine; Ori Tzvieli; Ann McDowell; Kirstie M. Kampen; Denise L. Lopez; Josh Ennis; Linda S. Lewis; Eyal Oren; April Hatada; Blanca Molinar; Matt Frederick; George S. Han; Martha Sanchez; Michael A. Garcia; Alana McGrath; Nga Q. Le; Eric Boyd; Regina M. Bertolucci; Jeremy Corrigan; Stephanie Brodine; Michael Austin; William R. K. Roach; Robert M. Levin; Brian M. Tyson; Jake M. Pry; Kristin J. Cummings; Debra A. Wadford; Seema Jain


Emerging Infectious Diseases. 2022;28(1):9-19. 

In This Article

Abstract and Introduction


State and local health departments established the California Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and Respiratory Virus Sentinel Surveillance System to conduct enhanced surveillance for SARS-CoV-2 and other respiratory pathogens at sentinel outpatient testing sites in 10 counties throughout California, USA. We describe results obtained during May 10, 2020–June 12, 2021, and compare persons with positive and negative SARS-CoV-2 PCR results by using Poisson regression. We detected SARS-CoV-2 in 1,696 (19.6%) of 8,662 specimens. Among 7,851 specimens tested by respiratory panel, rhinovirus/enterovirus was detected in 906 (11.5%) specimens and other respiratory pathogens in 136 (1.7%) specimens. We also detected 23 co-infections with SARS-CoV-2 and another pathogen. SARS-CoV-2 positivity was associated with male participants, an age of 35–49 years, Latino race/ethnicity, obesity, and work in transportation occupations. Sentinel surveillance can provide useful virologic and epidemiologic data to supplement other disease monitoring activities and might become increasingly useful as routine testing decreases.


Coronavirus disease (COVID-19) was detected in California, USA, in January 2020, and community transmission was identified in February 2020. During March 2020, two pilot COVID-19 sentinel surveillance projects in California[1,2] detected severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) among outpatients who had mild influenza-like illness (ILI) and no known travel or COVID-19 contact, suggesting widespread community transmission. These sentinel detections helped support the decision to enact a shelter-in-place order in the San Francisco Bay Area on March 16, 2020, followed shortly by a statewide stay-at-home order issued on March 19, 2020. As of June 12, 2021, a total of 3,695,530 cases and 62,508 COVID-19–associated deaths had been reported in California.[3] Moreover, throughout the pandemic, far fewer cases of seasonal influenza occurred than would have been expected according to passive reporting systems in California from previous years.[4,5]

The California Department of Public Health (CDPH) routine statewide surveillance for COVID-19, which started during January 2020, is primarily a passive system, relying on retrospective reporting of cases from testing laboratories and local providers. Despite widespread efforts to conduct contact tracing and case investigations, the high volume of cases and testing made collection of enhanced epidemiologic information challenging during 2020 and early 2021. Moreover, data on additional respiratory pathogens are not available through the routine surveillance system.

In California, although influenza is a laboratory-reportable disease, limited data are available for cases.[6] Most other common respiratory infections, such as rhinovirus/enterovirus, parainfluenza viruses, other human coronaviruses, human metapneumovirus, adenovirus, and respiratory syncytial virus (RSV), are not reportable in California. Thus, CDPH does not receive reports on positive cases. As part of CDPH routine influenza surveillance program, laboratory data on influenza strains/subtypes and other respiratory viruses are reported in aggregate from a system of sentinel laboratories; results are not linked to patient data.[5]

As the COVID-19 pandemic emerged in California during early 2020, CDPH implemented an additional surveillance system to collect enhanced patient data and respiratory specimens for more comprehensive testing. The objectives of the California SARS-CoV-2 and Respiratory Virus Sentinel Surveillance System (CalSRVSS) are to monitor community transmission of SARS-CoV-2 in outpatient settings; provide enhanced patient data, including race/ethnicity, occupation, and concurrent conditions; and to concurrently monitor circulation of other respiratory viruses.