key: cord-0825131-bu0pu6r5 authors: Adams, C.; Horton, M.; Solomon, O.; Wong, M.; Wu, S. L.; Fuller, S.; Shao, X.; Fedrigo, I.; Quach, H.; Quach, D.; Meas, M.; Lopez, L.; Broughton, A.; Barcellos, A. L.; Shim, J.; Seymens, Y.; Hernandez, S.; Montoya, M.; Johnson, D. M.; Beckman, K.; Busch, M. P.; Coloma, J.; Lewnard, J.; Harris, E.; Barcellos, L. F. title: Impact of individual-level characteristics and transmission mitigation behaviors on SARS-CoV-2 infection and seroprevalence in a large Northern California Bay Area cohort date: 2021-12-05 journal: nan DOI: 10.1101/2021.12.02.21266871 sha: d0ba48c05aa95d05caf4d74689b034fb851099ce doc_id: 825131 cord_uid: bu0pu6r5 Comprehensive data on transmission mitigation behaviors and SARS-CoV-2 infection and serostatus are needed from large, community-based cohorts to identify SARS-CoV-2 risk factors and impact of public health measures. From July 2020 to March 2021, {approx}5,500 adults from the East Bay Area, California were followed over three data collection rounds. We estimated the prevalence of antibodies from SARS-CoV-2 infection and COVID-19 vaccination, and self-reported COVID-19 test positivity. Population-adjusted SARS-CoV-2 seroprevalence was low, increasing from 1.03% (95% CI: 0.50-1.96) in Round 1 (July-September 2020), to 1.37% (95% CI: 0.75-2.39) in Round 2 (October-December 2020), to 2.18% (95% CI: 1.48-3.17) in Round 3 (February-March 2021). Population-adjusted seroprevalence of COVID-19 vaccination was 21.64% (95% CI: 19.20-24.34) in Round 3. Despite >99% of participants reporting wearing masks, non-Whites, lower-income, and lower-educated individuals had the highest SARS-CoV-2 seroprevalence and lowest vaccination seroprevalence. Our results demonstrate that more effective policies are needed to address these disparities and inequities. prevalence at each study round, and "probable COVID-19" prevalence at each study round. MRP 130 is a regression-based method for estimating population and sub-population averages from survey 131 data that has been shown to perform better than survey weighting, particularly with sparse data 132 (15, 16) . 133 In addition to estimation of regional prevalence of our outcomes, we estimated 134 prevalence within demographic groups and geographic areas in the study region. Variables of 135 . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted December 5, 2021. ; https://doi.org/10.1101 https://doi.org/10. /2021 interest were gender, age, race, Hispanic ethnicity, income, education, household size, and ZIP 136 code. We used a method described by Leeman and colleagues to generate a synthetic population 137 for poststratification using data from the 2018 American Community Survey (ACS) and the 138 Public Use Microdata Sample (PUMS).(16) Poststratification was done using binary sex because 139 gender is not reported by the ACS. Race and ethnicity were combined into a single variable to 140 reduce the number of poststratification strata. At each study round, binary SARS-CoV-2 outcomes were modeled as a function of 142 geographic and demographic characteristics using multilevel logistic regression models. Participant sex was included as a fixed effect. Vectors of random intercepts were defined for 144 each category of race/ethnicity, age, education, income, household size, and ZIP code and two-145 way interactions between ZIP code, race/ethnicity, educational attainment, income, and age. To 146 improve estimation of geographic effects we allowed for spatial correlations using the modified 150 We report populated-adjusted prevalence of SARS-CoV-2 outcomes across the study 151 region and within geographic and demographic groups of interest. To calculate prevalence 152 estimates, posterior distributions of the relevant poststratification stratum were aggregated. We 153 also estimated prevalence differences (PD) and prevalence ratios (PR) for the association 154 between populated-adjusted SARS-CoV-2 outcomes and race/ethnicity, education, and sex. For 155 each parameter of interest, the mean of the posterior distribution was the point estimate, and the 156 95% credible interval (CI) was the 2.5% and 97.5% quantiles of a posterior distribution. 158 . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted December 5, 2021. ; https://doi.org/10.1101/2021.12.02.21266871 doi: medRxiv preprint the net sensitivity and specificity of the SARS-CoV-2 antibody testing algorithm in each study 160 round (Supplement S-6). Transmission mitigation behavior analyses 162 In each round, participants were asked about physical distancing practices, recent close 163 contacts with others, mask wearing, and other behaviors and activities that might affect the risk 164 of SARS-CoV-2 infection. We classified participants into two behavior categories, "high-risk" 165 and "low-risk", with those responses using latent class analysis.(18) Crude associations between 166 behavior categories and characteristics such as sex, age, race/ethnicity, education, and income 167 were assessed with ! tests. Associations between high-risk vs. low-risk behavior and within 168 round SARS-CoV-2 seroprevalence and self-reported test positivity were estimated using the 169 MRP model described above with random intercepts for behavior categories and interactions 170 between the behavior categories and ZIP code, age, race/ethnicity, education, and income 171 (Supplement S-5 and S-6). Methods and at github.com/adams-cam/ebcovid_prev. Of the 16,115 residents who consented and completed the screening procedures between May-178 July 2020, 1,777 did not satisfy inclusion criteria and were excluded ( Figure 1 ). Characteristics 179 of participants are presented in Table 1 and Table S -1. Participation rates were high (Round 1: 180 76.8%, Round 2: 89.8%, and Round 3: 87.3%), and participants identified predominantly as 181 . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted December 5, 2021. ; https://doi.org/10.1101/2021.12.02.21266871 doi: medRxiv preprint female (~63%). Those aged 45-64 years were the largest age group of participants across all 182 study rounds (ranging from 37.3% to 39.4%). Most participants identified as White (52.5% to 183 63.3%), followed by Asian/Pacific Islander (13.9% to 15.7%), Hispanic (11.0% to 15.6%), two 184 or more races (6.9% to 9.1%), African American or Black (3.0% to 4.9%), and Native 185 American/Alaska Native or other (1.7% to 2.2%). Of those who completed the questionnaire, 87.3%, 95.3%, and 96.6% provided DBS and 187 93.6%, 98.1% and 98.% provided nasal swabs in rounds 1, 2, and 3, respectively (Table 2) . Antibodies against the SARS-CoV-2 spike protein were detected in 29 (0.6%) and 33 (0.6%) of 189 DBS in rounds 1 and 2, respectively. In Round 3, NC antibodies from natural infection alone . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted December 5, 2021. ; https://doi.org/10.1101/2021.12.02.21266871 doi: medRxiv preprint positivity (Table 5) , although the point estimates indicate that "low-risk" behavior was 250 associated with lower seroprevalence. In the current study, we investigated individual-level characteristics and behaviors that 253 contributed to SARS-CoV-2 related outcomes, including seroprevalence and self-reported 254 infection, in a large, population-based sample of over 5,500 participants from 12 East Bay 255 (Northern California) cities. During three time periods from July 2020 to March 2021, we 256 estimated the population-adjusted prevalence of SARS-CoV-2 outcomes across the study region 257 and within strata of age, sex, race/ethnicity, ZIP code, and household size. We then characterized 258 behaviors to mitigate transmission of SARS-CoV-2 and their effects on related outcomes. Overall, prevalence of SARS-CoV-2 outcomes for natural infection were low which may be 260 attributable to the high percentage of mask-wearing and other risk-mitigating behaviors among 261 our participants. COVID-19 vaccination seroprevalence estimates in Round 3 was greater than 262 20%, with non-Whites having much lower seroprevalence than Whites. Despite the low overall SARS-CoV-2 seroprevalence and infection observed in our study, 264 ZIP code of residence, age, racial/ethnic identification, education, and income all contributed to 265 differences in seroprevalence. Specifically, non-Whites, those without a college degree, and 266 lower income households, had higher seroprevalence. Further, ZIP codes with higher proportions 267 of Spanish speakers had higher populated-adjusted seroprevalence estimates ( Figure S-4) . These 268 differences persisted despite the high rates of mask wearing reported by our study sample, 269 further adding to strong evidence that the risk of COVID-19 is distributed unequally and that Another key finding was that almost all participants reported wearing masks. This CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted December 5, 2021. ; https://doi.org/10.1101/2021.12.02.21266871 doi: medRxiv preprint CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted December 5, 2021. Not reported 680 (12.4) 655 (11.7) 379 (7.9) *DBS, dried blood spot; QNS, quantity not sufficient. †Antibody assays specific to spike antibodies detect presence of antibodies induced by SARS-CoV-2 natural infection or vaccination. ‡Antibody assays specific to nucleocapsid antibodies detect presence of antibodies induced by SARS-CoV-2 natural infection. §As defined by the Council for State and Territorial Epidemiologists. . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted December 5, 2021. ; https://doi.org/10.1101/2021.12.02.21266871 doi: medRxiv preprint .64) *CI, credible interval; MOA, measure of association; PD, prevalence difference; PR, prevalence ratio †Populated adjusted prevalence estimated using multilevel regression and poststratification models; point estimate is the mean of a posterior distribution of the parameter, 95% credible interval estimated from 2.5% and 97.5% quantiles of a posterior distribution. ‡Defined as having detectable SARS-CoV-2 antibodies within a study round. . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted December 5, 2021. ; https://doi.org/10.1101 https://doi.org/10. /2021 . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted December 5, 2021. ; https://doi.org/10.1101/2021.12.02.21266871 doi: medRxiv preprint CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted December 5, 2021. ; https://doi.org/10.1101/2021.12.02.21266871 doi: medRxiv preprint CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted December 5, 2021. ; https://doi.org/10.1101/2021.12.02.21266871 doi: medRxiv preprint CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) The copyright holder for this preprint this version posted December 5, 2021. ; https://doi.org/10.1101/2021.12.02.21266871 doi: medRxiv preprint Figure 5 . Proportion of participants stratified by high-and low-risk mitigation behaviors in each 493 study round, A) overall, and B) according to specific behavior. . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) The copyright holder for this preprint this version posted December 5, 2021. ; https://doi.org/10.1101/2021.12.02.21266871 doi: medRxiv preprint SARS-CoV-2 Outcome Prev.% (95% CI) Prev. % (95% CI) Prev. % (95% CI) prevalence; V, vaccination. †Estimate of cumulative antibody prevalence from natural infection by SARS-CoV-2. ‡Population-adjusted prevalence estimated using multilevel regression and poststratification models. §Population-adjusted prevalence estimated using multilevel regression and poststratification models that included expressions for antibody assay sensitivity and specificity American Indian/Alaska Native/Other 18 81) Two or more races 15.74 (11.85, 19.94) -9.6 (-13.88, -5.28) All non-white 19 Prev, prevalence. †Population adjusted seroprevalence in round 3 estimated using multilevel regression and poststratification Assay used detects antibodies from natural SARS-CoV-2 infection or from COVID-19 vaccination. ‡Population adjusted COVID-19 seroprevalence difference in round 3 between each race/ethnicity group and Whites among race/ethnicity and between non-Whites and Whites within each age group. PDs estimated using MRP, and the PDs and 95% CIs are the mean and 2.5% and 97