Outcomes of Contact Tracing in San Francisco, California—Test and Trace During Shelter-in-Place

Given the pressing need to reopen economic activity prior to the availability of a vaccine, the US and other nations are investing in contact tracing as a core component of the coronavirus disease 2019 (COVID-19) response.¹ An estimated 75% of infected contacts need to be quarantined to contain COVID-19.^2,3 We evaluated case investigation and contact tracing outcomes in San Francisco, California, during shelter-in-place restrictions.

San Francisco residents diagnosed with COVID-19 were routinely reported to the health department and assigned for case investigation and contact tracing.⁴ On May 5, 2020, universal testing for COVID-19 contacts was recommended, regardless of symptoms. This study included cases diagnosed during shelter-in-place from April 13 to June 8, 2020. Cases identified through outbreak investigations in long-term care facilities were excluded (10% of cases).⁵

To evaluate the outcomes of contact tracing, we calculated the proportion of people who were interviewed, identified close contacts, and had at least 1 contact notified, tested, and newly diagnosed with COVID-19. A deterministic match based on personal identifiers was performed between contact and testing databases to (1) exclude contacts who were known to have COVID-19, (2) deduplicate previously named household contacts, and (3) ascertain testing results. We report the median number of days (with interquartile range [IQR]) taken to process each step. Analyses were conducted in SAS, version 9.4 (SAS Institute). Bivariate tests including χ² tests to compare categorical variables and t-tests for continuous variables were conducted, as appropriate, and a P < .05 identified statistical significance. This work was conducted as part of San Francisco Department of Public Health COVID-19 surveillance; institutional review board approval and informed consent were not required.

Among 1633 cases reported, 1394 (85.4%) people were interviewed. Median (IQR) age was 37 (26-49) years; 972 (69.7%) were Latino (85% primarily Spanish-speaking), and 842 (60.3%) were male. Of the 603 (43.2%) interviewed people residing in a household with at least 5 persons, 510 (84.6%) were Latino. Half of interviewed people reported contact with someone diagnosed with COVID-19 (Table).

Among 791 people interviewed after recommending universal testing for close contacts, 404 (51.1%) identified a contact not previously diagnosed with COVID-19, 356 (45.0%) had at least 1 contact notified, 206 (26.0%) had at least 1 contact tested, and 72 (9.1%) had at least 1 contact test positive for COVID-19. Of people residing in a household with at least 5 persons, 10.7% named a contact who was newly diagnosed with COVID-19. Among 1214 contacts traced, 1017 (83.8%) were successfully notified, 457 (37.6%) were tested, and 120 (9.9%) were newly diagnosed with COVID-19 (Figure). The secondary attack rate (calculated as the percentage of contacts who tested newly positive for COVID-19) was higher among household compared with nonhousehold contacts (111 of 983 [11.3%] and 9 of 231 [3.9%], respectively; P < .001), despite similar testing rates.

The median (IQR) number of days was 3 (1-6) from symptom onset (or specimen collection date in asymptomatic cases) to testing, 2 (1-2) from testing to test result, 1 (0-1) from test result to case interview, and 1 (0-1) from case interview to notification of the first contact. Overall, median (IQR) time from the case’s symptoms to contact notification and testing was 6 (4-9) days and 6 (4-10) days, respectively.

San Francisco’s COVID-19 contact tracing program reached more than 80% of cases and contacts and identified secondary cases within a median time frame of 6 days from the case’s symptom onset. While Latinos comprise 15% of San Francisco residents, they represented 70% of interviewed cases. Ten percent of contacts were newly diagnosed with COVID-19 compared with citywide testing positivity of 2.2% during this period. Although the majority of people with COVID-19 were interviewed within 1 day of test result, the 5-day delay between case symptom onset and positive test result raises concern regarding the timeliness of tracing in preventing onward transmission. Because 90% of secondary cases were household contacts, presymptomatic transmission could have occurred such that infected contacts may have already transmitted the virus by the time they were notified.⁶ Limitations include underreporting of close contacts during shelter-in-place and inability to ascertain adherence to quarantine. Addressing testing delays and improving contact identification will be necessary to optimize COVID-19 contact tracing efforts.

Accepted for Publication: August 13, 2020.

Published Online: November 2, 2020. doi:10.1001/jamainternmed.2020.5670

Corresponding Author: Darpun D. Sachdev, MD, Population Health Division, San Francisco Department of Public Health, 356 Seventh St, San Francisco, CA 94103 (darpun.sachdev@sfdph.org).

Author Contributions: Drs Sachdev and Scheer had full access to all of the data in the study and take responsibility for the integrity of the data and the accuracy of the data analysis.

Concept and design: Sachdev, Reid, Cohen, Scheer.

Acquisition, analysis, or interpretation of data: Sachdev, Brosnan, Reid, Kirian, Cohen, Nguyen.

Drafting of the manuscript: Sachdev, Reid, Cohen, Scheer.

Critical revision of the manuscript for important intellectual content: Sachdev, Brosnan, Reid, Kirian, Cohen, Nguyen.

Statistical analysis: Sachdev, Brosnan, Kirian, Scheer.

Administrative, technical, or material support: Sachdev, Reid, Cohen, Nguyen.

Supervision: Sachdev, Reid, Cohen, Scheer.

Conflict of Interest Disclosures: None reported.