Performance characteristics of a rapid SARS-CoV-2 antigen detection assay at a public plaza testing site in San Francisco

We evaluated the performance of the Abbott BinaxNOW Covid-19 rapid antigen test to detect virus among persons, regardless of symptoms, at a public plaza site of ongoing community transmission. Titration with cultured clinical SARS-CoV-2 yielded a human observable threshold between 1.6x104-4.3x104 viral RNA copies (cycle threshold (Ct) of 30.3-28.8 in this assay). Among 878 subjects tested, 3% (26/878) were positive by RT-PCR, of which 15/26 had a Ct<30, indicating high viral load. 40% (6/15) of Ct<30 were asymptomatic. Using this Ct<30 threshold for Binax-CoV2 evaluation, the sensitivity of the Binax-CoV2 was 93.3% (14/15), 95% CI: 68.1-99.8%, and the specificity was 99.9% (855/856), 95% CI: 99.4-99.9%.

Supervised self-collected SARS-CoV-2 testing in indoor summer camps to inform school reopening

Background and ObjectivesTesting strategies for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in school settings are needed to assess the efficacy of infection mitigation strategies and inform school reopening policies. We hypothesized that supervised serial self-collected non-nasopharyngeal testing in summer camp settings would be acceptable and feasible. MethodsWe performed a cohort study at two urban day camps for kindergarten-8th graders in June and July 2020. Eligible participants were campers, up to two adult household contacts, and camp staff. We assessed participation rates for providing, at two time points, supervised, self-collected anterior nares samples for reverse transcription polymerase chain reaction (RT-PCR) and saliva samples for antibody testing. We qualitatively assessed testing feasibility and adherence to stated camp infection mitigation strategies. Results76% (186/246) of eligible participants consented. The cohort completing both rounds of testing (n=163) comprised 67 campers, 76 household contacts, and 20 staff. Among those present, 100% of campers and staff completed test collection at both time points. Testing was feasible to implement, including staff participation supervising camper test collection. No virus was detected by RT-PCR; seven participants had antibodies. Observed adherence to stated camp mitigation policies for masking, physical distancing, and stable cohorting was generally high. ConclusionsSupervised, self-collected serial anterior nasal and saliva-based SARS-CoV-2 testing was acceptable, with successful repeated participation by children ages 5-14. This strategy for testing and the observed infection mitigation practices comprise potential core components for safe school reopening.

Identification of a polymorphism in the N gene of SARS-CoV-2 that adversely impacts detection by a widely-used RT-PCR assay

We identify a mutation in the N gene of SARS-CoV-2 that adversely affects annealing of a commonly used RT-PCR primer; epidemiologic evidence suggests the virus retains pathogenicity and competence for spread. This reinforces the importance of using multiple targets, preferably in at least 2 genes, for robust SARS-CoV-2 detection. Article Summary LineA SARS-CoV-2 variant that occurs worldwide and has spread in California significantly affects diagnostic sensitivity of an N gene assay, highlighting the need to employ multiple viral targets for detection.

Universal PCR and antibody testing demonstrate little to no transmission of SARS-CoV-2 in a rural community

BackgroundThe absence of systematic surveillance for SARS-CoV-2 has curtailed accurate appraisal of transmission intensity. Our objective was to perform case detection of an entire rural community to quantify SARS-CoV-2 transmission using PCR and antibody testing. MethodsWe conducted a cross-sectional survey of the prevalence and cumulative incidence of SARSCoV-2 infection in the rural town of Bolinas, California (population 1,620), four weeks following shelter-in-place orders. Residents and county essential workers were tested between April 20th - 24th, 2020. Prevalence by PCR and seroprevalence combining data from two forms of antibody testing were performed in parallel (Abbott ARCHITECT IgG to nucleocapsid protein and in-house IgG ELISA to the receptor binding domain). ResultsOf 1,891 participants, 1,312 were confirmed Bolinas residents (>80% community ascertainment). Zero participants were PCR positive. Assuming 80% sensitivity, it would have been unlikely to observe these results (p< 0.05) if there were > 3 active infections in the community. Based on antibody results, estimated prevalence of prior infection was 0.16% (95% CrI: 0.02%, 0.46%). Seroprevalence estimates using only one of the two tests would have been higher, with greater uncertainty. The positive predictive value (PPV) of a positive result on both tests was 99.11% (95% CrI: 95.75%, 99.94%), compared to PPV 44.19%-63.32% (95% CrI range 3.25%-98.64%) if only one test was utilized. ConclusionsFour weeks following shelter-in-place, active and prior SARS-CoV-2 infection in a rural Northern California community was extremely rare. In this low prevalence setting, use of two antibody tests increased the PPV and precision of seroprevalence estimates.

SARS-CoV-2 PCR and antibody testing for an entire rural community: methods and feasibility of high-throughput testing procedures

High-volume, community-wide ascertainment of SARS-CoV-2 prevalence by PCR and antibody testing was successfully performed using a community-led, drive-through model with strong operational support, well-trained testing units, and an effective technical platform

Clinical features, diagnostics, and outcomes of patients presenting with acute respiratory illness: a comparison of patients with and without COVID-19

BackgroundEmerging data on the clinical presentation, diagnostics, and outcomes of patients with COVID-19 have largely been presented as case series. Few studies have compared these clinical features and outcomes of COVID-19 to other acute respiratory illnesses. MethodsWe examined all patients presenting to an emergency department in San Francisco, California between February 3 and March 31, 2020 with an acute respiratory illness who were tested for SARS-CoV-2. We determined COVID-19 status by PCR and metagenomic next generation sequencing (mNGS). We compared demographics, comorbidities, symptoms, vital signs, and laboratory results including viral diagnostics using PCR and mNGS. Among those hospitalized, we determined differences in treatment (antibiotics, antivirals, respiratory support) and outcomes (ICU admission, ICU interventions, acute respiratory distress syndrome, cardiac injury). FindingsIn a cohort of 316 patients, 33 (10%) tested positive for SARS-CoV-2; 31 patients, all without COVID-19, tested positive for another respiratory virus (16%). Among patients with additional viral testing, no co-infections with SARS-CoV-2 were identified by PCR or mNGS. Patients with COVID-19 reported longer symptoms duration (median 7 vs. 3 days) and were more likely to report fever (82% vs. 44%) fatigue (85% vs. 50%) and myalgias (61% vs 27%); p<0.001 for all comparisons. Lymphopenia (55% vs 34%, p=0.018) and bilateral opacities on initial chest radiograph (55% vs. 24%, p=0.001) were more common in patients with COVID-19. Patients with COVID-19 were more often hospitalized (79% vs. 56%, p=0.014). Of 186 hospitalized patients, patients with COVID-19 had longer hospitalizations (median 10.7d vs. 4.7d, p<0.001) and were more likely to develop ARDS (23% vs. 3%, p<0.001). Most comorbidities, home medications, signs and symptoms, vital signs, laboratory results, treatment, and outcomes did not differ by COVID-19 status. InterpretationWhile we found differences in clinical features of COVID-19 compared to other acute respiratory illnesses, there was significant overlap in presentation and comorbidities. Patients with COVID-19 were more likely to be admitted to the hospital, have longer hospitalizations and develop ARDS, and were unlikely to have co-existent viral infections. These findings enhance understanding of the clinical characteristics of COVID-19 in comparison to other acute respiratory illnesses.