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


During May 2020–June 2021, the temporal pattern of SARS-CoV-2 positivity among CalSRVSS participants was largely consistent with overall California COVID-19 surveillance data, supporting the idea that sentinel surveillance can provide an accurate representation of trends.[3] However, CalSRVSS SARS-CoV-2 test positivity (total 19.6%, weekly range 0%–41.0%) was typically higher than that for general state surveillance data, which had a 7-day percentage positivity peak of 17.1% in late December 2020.[3] This difference was probably attributable to CalSRVSS testing of more symptomatic persons and focus on sentinel sites in communities disproportionately affected by COVID-19, such as those serving a high percentage of Latino persons, uninsured/underinsured or underserved populations, persons lacking sufficient access to testing, and persons working outside the home.

Similar to other rhinovirus/enterovirus data collected in California during 2020 and 2021, rhinovirus/enterovirus percentage positivity from CalSRVSS was lower than is typical in California during May–August 2020, which is often a peak time for viral transmission with maximums of 20%–30% positivity during May and June.[4,5] This decrease in rhinovirus/enterovirus activity might have been caused by widespread implementation of nonpharmaceutical interventions to curb the spread of COVID-19, including masking and the closure of schools and many workplaces. Competition with or interference by the SARS-CoV-2 virus, which peaked over the summer, might have also contributed.

Unlike the spring and summer months of 2020, rhinovirus/enterovirus activity during September–June 2021 (weekly median percentage positivity 15.1%, range 3.6%–31.1%) was only slightly below usual levels in California (typically ranging from ≈5% to 30%).[5] It is unclear why rhinovirus/enterovirus levels returned close to usual levels after the summer of 2020, although loosening of some COVID-19 restrictions or of adherence to restrictions might have contributed. Fall and winter peaks and troughs in rhinovirus/enterovirus activity were consistent with usual rhinovirus/enterovirus seasonality in California, peaking in October–November and again in May; however, these peaks and troughs occurred at opposite times as those for COVID-19, which peaked in August and December.[5] In general, nonoverlapping peak incidence between other respiratory viruses has been reported in previous studies; suspected contributing factors included replication conflicts and protective antibody interference.[10] It is not yet clear whether rhinovirus/enteroviruses and COVID-19 interact in this manner.

Other respiratory pathogen activity was much lower than usual in California, except for non–COVID-19 coronavirus activity during the spring of 2021. Typically, in California, non–COVID-19 coronavirus activity peaks in winter, decreasing to minimal levels over the late spring and summer.[5] CalSRVSS detected non–COVID-19 coronaviruses during May 2020–February 2021 in only 11 specimens, which increased to >100 specimens during March–June 2021. For all other respiratory pathogens, there were <10 detections of each (adenovirus, metapneumovirus, mycoplasma, parainfluenza, and RSV) during May 2020–June 2021.[5] No influenza virus was detected despite systematic testing of >7,000 specimens; these results were consistent with low influenza activity reported from other California surveillance systems and throughout the United States.[4] Similar to findings from other studies, these results showed limited evidence of co-infection between SARS-CoV-2 and other respiratory pathogens.[11]

This system focused primarily on testing mildly symptomatic or asymptomatic persons, which might have contributed to the absence of influenza detections and predominance of rhinovirus/enterovirus. In addition, the relatively small percentage of children included (13.2% <18 years of age) might account for some of the low incidence of other respiratory viruses that are typically detected among children, including RSV. It will be useful to clarify how influenza vaccination and continued use of nonpharmaceutical interventions to prevent COVID-19, such as mask wearing and staying home when sick, affects the incidence of respiratory illnesses, including influenza, during the winter of 2021–22.

For SARS-CoV-2 positivity, all non-White racial/ethnic groups, except Asian, showed potential increased risks when compared with White persons; aRRs ranged from 1.10 to 2.35. However, adjusted risk was only significant for persons reporting Latino ethnicity (aRR 2.35). Latino persons were the most common racial/ethnic group among persons positive for SARS-CoV-2 in both CalSRVSS (78.5%) and in general California COVID-19 surveillance data (56.2% as of June 12, 2021), although they make up only 38.9% of the California population.[3] The increased COVID-19 burden in Latino populations in California might also be associated with effects of structural racism that increase risk for COVID-19 incidence and illness, including underlying health conditions, higher rates of poverty, essential worker status, and crowded multigenerational households.[12,13]

This analysis provided additional evidence of the broad manifestations of mild and asymptomatic COVID-19, including a high proportion of patients who did not have fever or shortness of breath but instead had a limited number of more mild symptoms (e.g., cough, headache, muscle aches, sore throat). The commonly used ILI and CLI syndromic clinical case definitions were highly specific for COVID-19; however, they had low sensitivity. Syndromic surveillance systems using ILI or CLI case definitions are probably missing a large proportion of COVID-19 patients who have mild or asymptomatic disease.

Obesity, which has been established as a risk factor for COVID-19 and associated with severe outcomes, was strongly associated with SARS-CoV-2 positivity in CalSRVSS.[14] Asthma was associated with a decreased risk for showing positive test results in CalSRVSS, which is consistent with several other studies that found a negative association between asthma and SARS-CoV-2 positivity.[15]

Several occupations that are typically essential worker occupations, including transportation (significant in adjusted analysis), farming, fishing, forestry, construction of buildings, cleaning and maintenance of grounds, and production and manufacturing, showed potential increased SARS-CoV-2 positivity risk, and these occupations align with those identified as having highest excess mortality rates during the pandemic in California.[16] These occupations often require work outside the home in environments in which social distancing and effective workplace controls might be challenging, and they might also include high proportions of male and Latino workers, who are disproportionately affected by COVID-19.[17] On November 30, 2020, California approved California Division of Occupational Safety and Health emergency temporary standards for COVID-19 infection prevention requiring procedures such as physical distancing, use of face coverings, SARS-CoV-2 testing, and outbreak reporting in workplaces across the state.[18] Further studies to identify workplace risk factors and the effect of emergency standards on occupational disease burden in California are warranted.

The first limitation of our report is that data were obtained from a convenience sample and might be biased toward persons with health-seeking behaviors. Several sites specifically targeted areas with low testing volumes or areas with high-risk populations, so findings might not be generalizable. Sites were also asked to primarily enroll symptomatic patients (ideally ≤20% reporting no symptoms). Depending on site capacity, data were collected by using different methods (i.e., self- or clinician/interviewer-administered surveys conducted pretesting, onsite, or after testing), and some sites were not able to gather all requested variables. Respiratory panel testing was limited to mostly viral pathogens. Finally, because of low sample size for some characteristics, especially individual occupations, power to detect significant associations with SARS-CoV-2 positivity was limited.

CalSRVSS data have thus far paralleled overall statewide trends for SARS-CoV-2 and have provided insight into risk factors that are not available from routine surveillance, such as information about employment. Strengths of CalSRVSS include that it is an active sentinel system with prospective and enhanced data collection that occurs at time of specimen collection. In addition, CalSRVSS is the only COVID-19 surveillance system in California capable of integrating person-level enhanced data (demographic, clinical, exposure) with SARS-CoV-2 and other respiratory pathogen laboratory results. Starting in the summer and fall of 2021, we also began integrating California Immunization Registry COVID-19 vaccine status and SARS-CoV-2 whole-genome sequencing results into CalSRVSS data. As the pandemic continues, CalSRVSS will be a useful system for monitoring the trajectory of the pandemic, especially if routine SARS-CoV-2 testing and screening decreases and as another fall/winter respiratory illness season approaches.