Citywide serosurveillance of the initial SARS-CoV-2 outbreak in San Francisco using electronic health records

Abstract

Serosurveillance provides a unique opportunity to quantify the proportion of the population that has been exposed to pathogens. Here, we developed and piloted Serosurveillance for Continuous, ActionabLe Epidemiologic Intelligence of Transmission (SCALE-IT), a platform through which we systematically tested remnant samples from routine blood draws in two major hospital networks in San Francisco for SARS-CoV-2 antibodies during the early months of the pandemic. Importantly, SCALE-IT allows for algorithmic sample selection and rich data on covariates by leveraging electronic health record data. We estimated overall seroprevalence at 4.2%, corresponding to a case ascertainment rate of only 4.9%, and identified important heterogeneities by neighborhood, homelessness status, and race/ethnicity. Neighborhood seroprevalence estimates from SCALE-IT were comparable to local community-based surveys, while providing results encompassing the entire city that have been previously unavailable. Leveraging this hybrid serosurveillance approach has strong potential for application beyond this local context and for diseases other than SARS-CoV-2.

A Scoping Review of the Health Impact of the COVID-19 Pandemic on Persons Experiencing Homelessness in North America and Europe

“…A number of included studies reported infection attack rates of SARS-CoV-2 among study participants: 29 studies measured positivity rates (i.e., current infection) [ 13 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 ], seven measured seroprevalence (i.e., prevalence of antibodies for SARS-CoV-2, indicating historic infection) [ 61 , 62 , 63 , 64 , 65 , 66 , 67 ], and four measured both positivity and seroprevalence rates [ 68 , 69 , 70 , 71 ]. Additionally, data regarding SARS-CoV-2 symptoms reported by study participants were provided by 32 articles [ 7 , 8 , 33 , 34 , 35 , 36 , 38 , 42 , 45 , 46 , …”

“…A number of included studies reported infection attack rates of SARS-CoV-2 among study participants: 29 studies measured positivity rates (i.e., current infection) [13,, seven measured seroprevalence (i.e., prevalence of antibodies for SARS-CoV-2, indicating historic infection) [61][62][63][64][65][66][67], and four measured both positivity and seroprevalence rates [68][69][70][71]. Additionally, data regarding SARS-CoV-2 symptoms reported by study participants were provided by 32 articles [7,8,[33][34][35][36]38,42,[45][46][47][48][49][50][51][52][55][56][57][58]61,62,[68][69][70][72][73][74][75][76].…”

Using sero-epidemiology to monitor disparities in vaccination and infection with SARS-CoV-2

“…As part of an existing serological survey 14 , residual serum samples from routine blood draws from the University of California, San Francisco (UCSF) and San Francisco Department of Public Health (SFDPH) inpatient and outpatient healthcare systems were sampled between February 4 and February 17, 2021 (Supplementary Fig. 5 ).…”

“…The characteristics of the samples are illustrated in Table 1 . The full inclusion and exclusion criteria and sampling algorithm are described previously 14 . Briefly, we included patients undergoing routine blood testing, defined as blood chemistries and tests for sexually transmitted infections and rubella.…”

“…To measure disparities in both infection rates and vaccination, we leveraged a SARS-CoV-2 serosurveillance platform launched in March 2020 that utilizes residual blood samples taken from two hospital networks in San Francisco. Estimates derived from this platform during the first wave of the pandemic showed seroprevalence in Hispanic/Latinx individuals to be nearly two times higher than in White individuals, and nearly two times higher in homeless individuals than the population average 14 . We collected samples from individuals undergoing routine blood draws between February 4 and February 17, 2021, capturing transmission during the first 11 months of the epidemic and the early roll-out of vaccination (primarily for those over 65 years old as well as workers in specific professions i.e., healthcare).…”