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

Disclosures

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

In This Article

Results

Of the 8,662 specimens collected during May 10, 2020–June 12, 2021, SARS-CoV-2 was detected in 1,696 (19.6%) specimens. Most specimens were from persons seen at participating testing sites in the San Francisco Bay Area (50.1%) and southern California (23.0%) (Figure 1). Of the 7,851 specimens tested by respiratory panel, rhinovirus/enterovirus was detected in 906 (11.5%) specimens, non–COVID-19 coronavirus in 126 (1.6%) specimens, adenovirus in 6 specimens, parainfluenza virus in 5 specimens, metapneumovirus in 3 specimens, M. pneumoniae in 2 specimens, and RSV in 1 specimen. A total of 7 specimens were positive for >1 pathogen in the respiratory panel (Appendix Figure, https://wwwnc.cdc.gov/EID/article/28/1/21-1682-App1.pdf). No influenza viruses were detected. Among 1,373 persons positive for SARS-CoV-2 with respiratory panel results, 23 (1.7%) co-infections were detected: 19 with rhinovirus/enterovirus, 1 with adenovirus, 1 with M. pneumoniae, 1 with parainfluenza virus type 4, and 1 with human coronavirus OC43 and parainfluenza virus type 1.

Figure 1.

Total specimens tested for SARS-CoV-2, by county of sentinel site, California, USA, from specimens collected through the California SARS-CoV-2 and Respiratory Virus Sentinel Surveillance program during May 10, 2020–June 12, 2021 (N = 8,662). SARSCoV-2, severe acute respiratory syndrome coronavirus 2.

Trends

SARS-CoV-2 percentage positivity first peaked at 30.0% during late July 2020, decreased to a low of 10.5% during October, and peaked at its highest point of 41.0% during early January 2021 (Figure 2). Percentage positivity then decreased to a plateau during February and March (weekly percentage range 10.0%–16.3%) before increasing again during early April (weekly percentage range 28.7%–33.3%) and then decreasing to ≈10% during June. The decrease from January through March 2021 is probably overestimated because data from the county with the highest consistent percentage positivity had to be excluded during that time due to issues with enrollment.

Figure 2.

Weekly specimens tested and percent positive for SARS-CoV-2 and for ≥1 other respiratory pathogen, California, USA, from specimens collected through the California SARS-CoV-2 and Respiratory Virus Sentinel Surveillance program during May 10, 2020–June 12, 2021 (SARS-CoV-2 tested, n = 8,662; other respiratory pathogen tested, n = 7,851). SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.

Respiratory panel positivity remained <5% from May 2020 through mid-August and then increased to a peak of 19.4% during November, decreased to a low of 4.2% during early January 2021, and then increased to 52.7% during late May (Figure 2). Before March 2021, rhinoviruses/enteroviruses made up 96.9% of respiratory panel–positive results. However, during March–June 2021, this value decreased to 72.2%, primarily because of an increase in non-COVID-19 coronaviruses during that time (Appendix Figure).

Demographic and Epidemiologic Characteristics

Among 8,662 participants tested for SARS-CoV-2, most (60.4%) were women; median age was 35 years (interquartile range 22–50 years), and 57.4% reported Latino ethnicity (Table 1). When we compared the CalSRVSS population with that of the general California population, children <18 years of age, male participants, and persons of most race/ethnicities other than Latino were underrepresented in CalSRVSS, whereas for persons 18–49 years of age, women and Latino persons were overrepresented in CalSRVSS (Figure 3).

Figure 3.

Percentage of persons tested for SARS-CoV-2 compared with percentage of persons in California by demographic group, California, USA, from specimens collected through the California SARS-CoV-2 and Respiratory Virus Sentinel Surveillance program during May 10, 2020–June 12, 2021 (SARS-CoV-2 tested, n = 8,662;. NHPI, Native Hawaiian/Pacific Islander; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.

Of those persons who had data, 22.2% of tested persons reported contact with a COVID-19 case ≤14 days before illness onset, and 19.5% reported travel outside of their county of residence in the month before illness onset. Among 7,729 patients ≥16 years of age who had data available for the related questions (numbers varied by county), 68.5% reported being employed, and 64.6% reported working in the month before onset, 76.1% of whom worked outside the home. Adequate data for occupational category coding were available for 2,384 employed persons (Table 1).

Percentage positivity of SARS-CoV-2 and the respiratory panel (primarily composed of rhinovirus/enterovirus–positive results) varied by demographic group (Figure 4; Appendix Table 1). The highest percentages of positivity for SARS-CoV-2 were among participants reporting to be 35–49 years of age (22.9%) and 5–17 years of age (22.1%), whereas respiratory panel percentage positivity decreased consistently with increasing age (range 41.9%–5.2%). Persons of Latino race/ethnicity had the highest SARS-CoV-2 percentage positivity (25.1%) and the second highest respiratory panel percentage positivity (14.3%), after other race (15.1%).

Figure 4.

Percentage positive for SARS-CoV-2 and for ≥1 other respiratory pathogen, by demographic group, California, USA, from specimens collected through the California SARS-CoV-2 and Respiratory Virus Sentinel Surveillance program during May 10, 2020–June 12, 2021 (SARS-CoV-2 positive, n = 1,373; other respiratory pathogen positive, n = 1,002; total N = 7,476). Results included are not mutually exclusive; there were 23 co-infections between SARS-CoV-2 and another respiratory pathogen included. Included are only participants with test results for SARS-CoV-2 and for other respiratory pathogens. NHPI, Native Hawaiian/Pacific Islander; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.

Clinical Manifestations

At the time of specimen collection, 6,542 (77.7%) persons reported >1 symptom, of whom 1,498 (22.9%) had a positive SARS-CoV-2 result. Among these symptomatic persons with a positive SARS-CoV-2 result, 36.0% reported contact with a COVID-19 case. SARS-CoV-2 was also detected in 9.8% of specimens from persons without symptoms, of which 43.9% reported contact with a COVID-19 case.

For participants with a positive SARS-CoV-2 result only, 87.3% reported >1 symptom; the most common symptoms were cough (55.6%), headache (48.6%), muscle aches (44.5%), sore throat (37.4%), and fever (35.3%) (Figure 5). Among participants positive for rhinovirus/enterovirus or a non–COVID-19 coronavirus, 93.5% and 99.1%, respectively, reported >1 symptom; the most common symptoms for persons with either pathogen were cough, sore throat, and runny nose. Although loss of taste and smell was most common among patients with a positive SARS-CoV-2 result (26.6%), this symptom was also reported among persons positive for rhinovirus/enterovirus or non–COVID-19 coronaviruses (≈9% for both groups). Shortness of breath was reported among ≈13%–16% of patients who had a positive result for SARS-CoV-2, rhinovirus/enterovirus, or non–COVID-19 coronavirus and by persons who had negative results for any pathogen tested.

Figure 5.

Percentage of participants who had each collected symptom and meeting clinical case definitions for influenza-like illness and COVID-like illness among persons infected with SARS-CoV-2 and select respiratory panel pathogens, California, USA, from specimens collected through the California SARS-CoV-2 and Respiratory Virus Sentinel Surveillance program during May 10, 2020–June 12, 2021 (SARS-CoV-2 positive, n = 1,350; other respiratory pathogen positive, n = 973; total, N = 7,447). Results included are mutually exclusive: a SARS-CoV-2–positive person was negative for all other respiratory pathogens and vice versa. Coinfections between SARS-CoV-2 and other respiratory pathogens (n = 23) and multiple respiratory pathogen infections (n = 7) were excluded. Included are only participants with test results for SARS-CoV-2 and for other respiratory pathogens. Non–COVID-19 coronavirus, coronaviruses other than SARS-CoV-2; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.

Among the SARS-CoV-2–positive persons, 29.0% met the ILI clinical case definition and 25.4% met the CLI definition (Appendix Table 2). A smaller proportion of persons positive for non–COVID-19 coronavirus met the ILI (21.1%) or CLI (17.4%) criteria, and even less of those positive for rhinovirus/enterovirus met either definition (17.2% for ILI and 13.6% for CLI). Specificity, however, exceeded 80% for the ILI and CLI definitions for SARS-CoV-2, rhinovirus/enterovirus, or a non–COVID-19 coronavirus.

Risk for SARS-CoV-2 Positivity

Adjusted regression analyses showed that risk for a positive SARS-CoV-2 test result was greater for persons who reported being male (adjusted RR [aRR] 1.16, 95% CI 1.05–1.29) compared with persons who reported being female, persons 35–49 years of age (aRR 1.27, 95% CI 1.12–1.44) compared with persons 18–34 years of age, or Latino persons (aRR 2.35, 95% CI 1.99–2.77) compared with White persons (Table 2). SARS-CoV-2 risk was lower among persons reporting asthma (aRR 0.76, 95% CI 0.61–0.95) and higher among those reporting obesity (aRR 1.24, 95% CI 1.03–1.48). The occupation category for transportation, which includes truck drivers, delivery workers, and passenger transportation drivers, was the only occupation strongly associated with SARS-CoV-2 positivity in the adjusted analysis (aRR 1.60, 95% CI 1.09–2.35). However, persons reporting several other occupations had aRRs >1, including persons involved in farming, fishing, forestry, construction and extraction, building, grounds cleaning and maintenance, and production and manufacturing.

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