COVID-19 symptoms and duration of direct antigen test positivity at a community testing and surveillance site, January 2021-2022

ImportanceCharacterizing clinical symptoms and evolution of community-based SARS Co-V-2 infections can inform health practitioners and public health officials in a rapidly changing landscape of population immunity and viral variants. ObjectiveTo characterize COVID-19 symptoms during the Omicron period compared to pre-Delta and Delta variant periods and assess the duration of COVID-19 BinaxNOW rapid antigen test positivity during the Omicron variant surge. Design, Setting, and ParticipantsThis public health surveillance study was undertaken between January 2021-January 2022, at a walk-up community COVID-19 testing site in San Francisco, California. Testing with BinaxNOW rapid antigen tests was available regardless of age, vaccine status, or symptoms throughout. Main Outcomes and MeasuresWe characterized the prevalence of specific symptoms for people with a positive BinaxNOW test during the Omicron period and compared it to the pre-Delta and Delta periods. During the Omicron period, we examined differences in symptoms by age and vaccine status. Among people returning for repeat testing during Omicron period, we estimated the proportion with a positive BinaxNOW antigen test between 4-14 days from symptom onset or since first positive test if asymptomatic. ResultsOf 63,277 persons tested, 18,301 (30%) reported symptoms and 4,568 (25%) tested positive for COVID-19. During the Omicron period, 41.6% (3032/7283) of symptomatic testers tested positive, and the proportion reporting cough (67.4%) and sore throat (43.4%) was higher than during Delta and pre-Delta periods. Congestion was higher during Omicron (38.8%) than during the pre-Delta period and loss of taste/smell (5.3%) and fever (30.4%) were less common. Fevers and myalgias were less common among persons who had received boosters compared to unvaccinated people or those who received the primary series. Five days after symptom onset, 31.1% of people with COVID-19 stated their symptoms were similar or worsening. An estimated 80.2% of symptomatic re-testers remained positive five days after symptom onset and 60.5% after ten days. Conclusions and RelevanceCOVID-19 upper respiratory tract symptoms were more commonly reported during the Omicron period compared to pre-Delta and Delta periods, with differences by vaccination status. Antigen test positivity remained high after 5 days, supporting guidelines requiring a negative test to shorten the isolation period. Key pointsO_ST_ABSQuestionC_ST_ABSDuring the Omicron period, are there differences in COVID-19 symptomatology compared to the pre-Delta and Delta periods and how long do rapid antigen tests remain positive? FindingsIn this community-based surveillance study we detected differences in symptomatology between the Omicron period and prior variant-periods, and by age and vaccination status. Five days after symptom onset, 80% remained positive with a BinaxNOW test. MeaningDuring the Omicron period, differences in symptomatology may be due to rising population immunity and a new variant. BinaxNOW positivity remained high among re-testers, which supports guidelines that use rapid tests to shorten the isolation period.

Direct Comparison of SARS Co-V-2 Nasal RT- PCR and Rapid Antigen Test (BinaxNOWTM) at a Community Testing Site During an Omicron Surge

In 731 persons seeking COVID-19 testing at a walk-up San Francisco community site in January 2022, simultaneous nasal rapid antigen testing (BinaxNOW) and RT-PCR testing was performed. There were 296 (40.5%) positive tests by RT-PCR; 98.5% of a random sample (N=67) were the omicron variant. Sensitivity of a single antigen test was 95.2% (95% CI 92-98%); 82.1% (95% CI 77-87%) and 65.2% (95% CI 60-71%) for Ct threshold of < 30, < 35 and no threshold, respectively. We also compared BinaxNOW to RT-PCR from oral cheek swabs to nasal swabs (N=75); oral cheek specimen was significantly less sensitive than nasal swab. A single BinaxNOW oral cheek rapid antigen test failed to detect 91% (20 of 22) of specimens that were BinaxNOW positive from the standard nasal sampling. In a separate direct comparison of BinaxNOW between specimens collected from nasal or throat (tonsillar) swab (N=115), sensitivity was 97.7% for nasal and 48.8% for throat swabs that were PCR-positive on nasal swab with a Ct threshold < 30. Among persons with either a nasal or throat RT-PCR positive swab with Ct<30, BinaxNOW sensitivity was 85.7% for nasal and 89.8% for nasal plus throat swabs. BinaxNOW continues to be a very useful diagnostic during the omicron surge; oral (throat or cheek swab) should not replace nasal swabs due to significantly reduced sensitivity compared to nasal. As currently recommended, repeat testing should be done for high-risk persons with an initial negative antigen test result.

Significant and sustained decrease in non-SARS-CoV-2 respiratory viral infections during COVID-19 public health interventions.

Public health interventions to decrease the spread of SARS-CoV-2 were largely implemented in the United States during spring 2020. This study evaluates the additional effects of these interventions on non-SARS-CoV-2 respiratory viral infections from a single healthcare system in the San Francisco Bay Area. The results of a respiratory pathogen multiplex polymerase chain reaction panel intended for inpatient admissions were analyzed by month between 2019 and 2020. We found major decreases in the proportion and diversity of non-SARS-CoV-2 respiratory viral illnesses in all months following masking and shelter-in-place ordinances. These findings suggest real-world effectiveness of nonpharmaceutical interventions on droplet-transmitted respiratory infections.

Race-ethnicity and Perceptional Determinants of COVID-19 Vaccination Intentions: A Cross-sectional Study Among Health Workers and the General Population in the San Francisco Bay Area

ObjectiveTo compare intention to receive COVID-19 vaccination by race-ethnicity, to identify perceptional factors that may mediate the association between race-ethnicity and intention to receive the vaccine, and to identify the demographic and perceptional factors most strongly predictive of intention to receive a vaccine. DesignCross-sectional survey conducted from November, 2020 to January, 2021, nested within two longitudinal cohort studies of prevalence and incidence of SARS CoV-2 among the general population and healthcare workers. Study Cohort3,161 participants in the Track COVID cohort (a population-based sample of adults) and 1,803 participants in the CHART Study cohort (a cohort of employees at three large medical centers). ResultsRates of high vaccine willingness were significantly lower among Black (45.3%), Latinx (62.5%), Asian (65%), multi-racial (67.2%), and other race (61.0%) respondents than among white respondents (77.6%). Black, Latinx, and Asian respondents were significantly more likely than white respondents to endorse reasons to not get vaccinated, especially lack of trust. Participants motivations and concerns about COVID-19 vaccination only partially explained racial-ethnic differences in vaccination willingness. Being a health worker in the CHART cohort and concern about a rushed government vaccine approval process were the two most important factors predicting vaccination intention. ConclusionsSpecial efforts are required to reach historically marginalized racial-ethnic communities to support informed decision-making about COVID-19 vaccination. These campaigns must acknowledge the history of racism in biomedical research and health care delivery that has degraded the trustworthiness of health and medical science institutions among non-white population and may continue to undermine confidence in COVID-19 vaccines.

Healthcare personnel knowledge, motivations, concerns and intentions regarding COVID-19 vaccines: a cross-sectional survey

BackgroundHealthcare personnel (HCP) are prioritized for earliest SARS-CoV-2 vaccine administration, yet relatively few data exist on HCPs knowledge, motivations, concerns, and intentions regarding COVID-19 vaccines. MethodsWe conducted a cross-sectional survey Nov.16-Dec.8, 2020 among HCP enrolled in a cohort study at three Northern California medical centers serving diverse roles including COVID-19 patient care. Eligible HCP were adult (age[≥]18) on-site employees of the University of California, San Francisco, San Francisco General Hospital, and Stanford Healthcare. A one-time electronically-administered survey was sent to cohort HCP on November 16, 2020 and responses analyzed. ResultsOverall, among 2,448 HCP invited, 2,135 completed the COVID-19 vaccine survey (87.2% response rate). HCPs had mean age 41 years, were 73% female, and had diverse jobs including COVID-19 patient contact. Enthusiasm for vaccination was overall strong, and more HCP (1,453, 69%) said they would definitely/likely receive vaccine if formally FDA-approved versus if approved via emergency use authorization only (785, 35%). While 541 (25%) respondents wanted to be among the earliest to receive vaccine, more desired vaccination after the first round (777, 36%) or >2 months after vaccinations began (389, 18%). Top factors increasing motivation for vaccination included perceiving risk from COVID-19 to self (1,382, 65%) or to family/friends (1355, 63%). Top concerns were vaccine side effects, cited by 596 (28%), and concerns about political involvement in FDAs approval process (249, 12%). ConclusionsHCP were enthusiastic about COVID-19 vaccination for individual protection and protecting others, but harbored concerns about vaccine side effects. Our data may inform emerging vaccine education campaigns. Key PointsAmong 2,135 healthcare personnel surveyed, we found enthusiasm for COVID-19 vaccination both for individual benefit and protecting others. However, healthcare personnel rated their knowledge of COVID-19 vaccines as only moderate and harbored concerns about vaccine side effects. Education raising awareness of vaccine efficacy and side effects may help maximize vaccine uptake.

SARS-CoV-2 Community Transmission During Shelter-in-Place in San Francisco

BackgroundWe characterized SARS-CoV-2 infections in a densely-populated, majority Latinx San Francisco community six-weeks into the citys shelter-in-place order. MethodsWe offered SARS-CoV-2 reverse transcription-PCR and antibody (Abbott ARCHITECT IgG) testing, regardless of symptoms, to all residents (>4 years) and workers in a San Francisco census tract (population: 5,174) at outdoor, community-mobilized events over four days. We estimated SARS-CoV-2 point prevalence (PCR-positive) and cumulative incidence (antibody or PCR-positive) in the census tract and evaluated risk factors for recent (PCR-positive/antibody-negative) versus prior infection (antibody-positive/PCR-negative). SARS-CoV-2 genome recovery and phylogenetics were used to measure viral strain diversity, establish viral lineages present, and estimate number of introductions. ResultsWe tested 3,953 persons: 40% Latinx; 41% White; 9% Asian/Pacific Islander; and 2% Black. Overall, 2.1% (83/3,871) tested PCR-positive: 95% were Latinx and 52% asymptomatic when tested. 1.7% of residents and 6.0% of workers (non-census tract residents) were PCR-positive. Among 2,598 census tract residents, estimated point prevalence of PCR-positives was 2.3% (95%CI: 1.2-3.8%): 3.9% (95%CI: 2.0-6.4%) among Latinx vs. 0.2% (95%CI: 0.0-0.4%) among non-Latinx persons. Estimated cumulative incidence among residents was 6.1% (95%CI: 4.0-8.6%). Prior infections were 67% Latinx, 16% White, and 17% other ethnicities. Among recent infections, 96% were Latinx. Risk factors for recent infection were Latinx ethnicity, inability to shelter-in-place and maintain income, frontline service work, unemployment, and household income <$50,000/year. Five SARS-CoV-2 phylogenetic lineages were detected. ConclusionSARS-CoV-2 infections from diverse lineages continued circulating among low-income, Latinx persons unable to work from home and maintain income during San Franciscos shelter-in-place ordinance.

Management and Outcomes of Critically-Ill Patients with COVID-19 Pneumonia at a Safety-net Hospital in San Francisco, a Region with Early Public Health Interventions: A Case Series

BackgroundFollowing early implementation of public health measures, San Francisco has experienced a slow rise and a low peak level of coronavirus disease 2019 (COVID-19) cases and deaths. Methods and FindingsWe included all patients with COVID-19 pneumonia admitted to the intensive care unit (ICU) at the safety net hospital for San Francisco through April 8, 2020. Each patient had [≥]15 days of follow-up. Among 26 patients, the median age was 54 years (interquartile range, 43 to 62), 65% were men, and 77% were Latinx. Mechanical ventilation was initiated for 11 (42%) patients within 24 hours of ICU admission and 20 patients (77%) overall. The median duration of mechanical ventilation was 13.5 days (interquartile range, 5 to 20). Patients were managed with lung protective ventilation (tidal volume [≤]8 ml/kg of ideal body weight and plateau pressure [≤]30 cmH2O on 98% and 78% of ventilator days, respectively). Prone positioning was used for 13 of 20 (65%) ventilated patients for a median of 5 days (interquartile range, 2 to 10). Seventeen (65%) patients were discharged home, 1 (4%) was discharged to nursing home, 3 (12%) were discharged from the ICU, and 2 (8%) remain intubated in the ICU at the time of this report. Three (12%) patients have died. ConclusionsGood outcomes were achieved in critically ill patients with COVID-19 by using standard therapies for acute respiratory distress syndrome (ARDS) such as lung protective ventilation and prone positioning. Ensuring hospitals can deliver sustained high-quality and evidence-based critical care to patients with ARDS should remain a priority.