Field assessment of BinaxNOW antigen tests as COVID-19 treatment entry point at a community testing site in San Francisco during evolving omicron surges

BackgroundCOVID-19 oral treatments require initiation within 5 days of symptom onset. Although antigen tests are less sensitive than RT-PCR, rapid results could facilitate entry to treatment. As SARS-CoV-2 variants and host immunity evolve, it is important to characterize the use case for rapid antigen tests for treatment entry. MethodsWe collected anterior nasal swabs for BinaxNOW and RT-PCR testing and clinical data at a walk-up, community site in San Francisco, California between January and June 2022. SARS-CoV-2 genomic sequences were generated from positive samples and classified according to subtype and variant. Monte Carlo simulations were conducted to estimate the expected proportion of SARS-CoV-2 infected persons who would have been diagnosed within 5 days of symptom onset using RT-PCR versus BinaxNOW testing. ResultsAmong 25,309 persons tested with BinaxNOW, 2,952 had concomitant RT-PCR. 1321/2952 (44.7%) were SARS-CoV-2 RT-PCR positive. We identified waves of predominant omicron BA.1, BA.2, BA.2.12, BA.4, and BA.5 among 720 sequenced samples. Among 1,321 RT-PCR positive samples, 938/1321 (71%) were detected by BinaxNOW; 95% (774/817) of those with Ct value <30 were detected by BinaxNOW. BinaxNOW detection was consistent over lineages. In analyses to evaluate entry to treatment, BinaxNOW detected 82.7% (410/496, 95% CI: 79-86%) of persons with COVID-19 within 5 days of symptom onset. In comparison, RT-PCR (24-hour turnaround) detected 83.1% (412/496 95% CI: 79-86%) and RT-PCR (48-hour turnaround) detected 66.3% (329/496 95% CI: 62-70%) of persons with COVID-19 within 5 days of symptom onset. ConclusionsBinaxNOW detected high viral load from anterior nasal swabs consistently across omicron sublineages emerging between January and June of 2022. Simulations support BinaxNOW as an entry point for COVID-19 treatment in a community field setting.

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.

No Significant Difference in Viral Load Between Vaccinated and Unvaccinated, Asymptomatic and Symptomatic Groups Infected with SARS-CoV-2 Delta Variant

We found no significant difference in cycle threshold values between vaccinated and unvaccinated, asymptomatic and symptomatic groups infected with SARS-CoV-2 Delta. Given the substantial proportion of asymptomatic vaccine breakthrough cases with high viral levels, interventions, including masking and testing, should be considered for all in settings with elevated COVID-19 transmission.

Exposures to different SARS-CoV-2 spike variants elicit neutralizing antibody responses with differential specificity towards established and emerging strains

The wide spectrum of SARS-CoV-2 variants with phenotypes impacting transmission and antibody sensitivity necessitates investigation of the immune response to different spike protein versions. Here, we compare the neutralization of variants of concern, including B.1.617.2 (Delta) and B.1.1.529 (Omicron) in sera from individuals exposed to variant infection, vaccination, or both. We demonstrate that neutralizing antibody responses are strongest against variants sharing certain spike mutations with the immunizing exposure. We also observe that exposure to multiple spike variants increases the breadth of variant cross-neutralization. These findings contribute to understanding relationships between exposures and antibody responses and may inform booster vaccination strategies. SUMMARYThis study characterizes neutralization of eight different SARS-CoV-2 variants, including Delta and Omicron, with respect to nine different prior exposures, including vaccination, booster, and infections with Delta, Epsilon, and others. Different exposures were found to confer substantially differing neutralization specificity.

High parental vaccine motivation at a neighborhood-based vaccine and testing site serving a predominantly Latinx community

PurposeTo understand vaccine attitudes of Latinx parents highly impacted by COVID-19. Methods. In April 2021, we surveyed parents about their attitudes for COVID-19 vaccination of their children at a community-based outdoor testing/vaccination site serving predominantly low-income, Latinx persons in San Francisco. ResultsAmong 1,033 parents (75% Latinx), 92% would "definitely" or "probably" vaccinate their children. Vaccine hesitancy was higher for younger children; concerns included side effects and impacts on fertility. Doctors and community organizations were noted as trusted sources of information, including among vaccine-hesitant parents. ConclusionLatinx parents accessing neighborhood-based COVID-19 testing/vaccination services are highly motivated to vaccinate their children for COVID-19.

A multi-component, community-based strategy to facilitate COVID-19 vaccine uptake among Latinx populations: from theory to practice

BackgroundCOVID-19 vaccine coverage in the Latinx community depends on delivery systems that overcome barriers such as institutional distrust, misinformation, and access to care. We hypothesized that a community-centered vaccination strategy that included mobilization, vaccination, and "activation" components could successfully reach an underserved Latinx population, utilizing its social networks to boost vaccination coverage. Methods and FindingsOur community-academic-public health partnership, "Unidos en Salud," utilized a theory-informed approach to design our "Motivate, Vaccinate, and Activate" COVID-19 vaccination strategy. Our strategys design was guided by the PRECEDE Model and sought to address and overcome predisposing, enabling, and reinforcing barriers to COVID-19 vaccination faced by Latinx individuals in San Francisco. We evaluated our prototype outdoor, "neighborhood" vaccination program located in a central commercial and transport hub in the Mission District in San Francisco, using the Reach, Effectiveness, Adoption, Implementation and Maintenance (RE-AIM) framework during a 16-week period from February 1, 2021 to May 19, 2021. Programmatic data, city-wide COVID-19 surveillance data, and a survey conducted between May 2, 2021 and May 19, 2021 among 997 vaccinated clients [≥]16 years old were used in the evaluation. There were 20,792 COVID-19 vaccinations administered at the neighborhood site during the 16-week evaluation period. Vaccine recipients had a median age of 43 (IQR 32-56) years, 53.9% were male and 70.5% were Latinx, 14.1% white, 7.7% Asian, 2.4% Black, and 5.3% other. Latinx vaccinated clients were substantially more likely than non-Latinx clients to have an annual household income of less than $50,000 a year (76.1% vs. 33.5%), be a first-generation immigrant (60.2% vs. 30.1%), not have health insurance (47.3% vs. 16.0%), and not have access to primary care provider (62.4% vs. 36.2%). The most frequently reported reasons for choosing vaccination at the site were its neighborhood location (28.6%), easy and convenient scheduling (26.9%) and recommendation by someone they trusted (18.1%); approximately 99% reported having an overall positive experience, regardless of ethnicity. Notably, 58.3% of clients reported that they were able to get vaccinated earlier because of the neighborhood vaccination site, 98.4% of clients completed both vaccine doses, and 90.7% said that they were more likely to recommend COVID-19 vaccination to family and friends after their experience; these findings did not substantially differ according to ethnicity. There were 40.3% of vaccinated clients who said they still knew at least one unvaccinated person (64.6% knew [≥]3). Among clients who received both vaccine doses (n=729), 91.0% said that after their vaccination experience, they had personally reached out to at least one unvaccinated person they knew (61.6% reached out to [≥]3) to recommend getting vaccinated; 83.0% of clients reported that one or more friends, and/or family members got vaccinated as a result of their outreach, including 18.9% who reported 6 or more persons got vaccinated as a result of their influence. ConclusionsA multi-component, "Motivate, Vaccinate, and Activate" community-based strategy addressing barriers to COVID-19 vaccination for the Latinx population reached the intended population, and vaccinated individuals served as ambassadors to recruit other friends and family members to get vaccinated.

Estimation of secondary household attack rates for emergent SARS-CoV-2 variants detected by genomic surveillance at a community-based testing site in San Francisco

BackgroundSequencing of the SARS-CoV-2 viral genome from patient samples is an important epidemiological tool for monitoring and responding to the pandemic, including the emergence of new mutations in specific communities. MethodsSARS-CoV-2 genomic sequences were generated from positive samples collected, along with epidemiological metadata, at a walk-up, rapid testing site in the Mission District of San Francisco, California during November 22-December 2, 2020 and January 10-29, 2021. Secondary household attack rates and mean sample viral load were estimated and compared across observed variants. ResultsA total of 12,124 tests were performed yielding 1,099 positives. From these, 811 high quality genomes were generated. Certain viral lineages bearing spike mutations, defined in part by L452R, S13I, and W152C, comprised 54.9% of the total sequences from January, compared to 15.7% in November. Household contacts exposed to "West Coast" variants were at higher risk of infection compared to household contacts exposed to lineages lacking these variants (0.357 vs 0.294, RR=1.29; 95% CI:1.01-1.64). The reproductive number was estimated to be modestly higher than other lineages spreading in California during the second half of 2020. Viral loads were similar among persons infected with West Coast versus non-West Coast strains, as was the proportion of individuals with symptoms (60.9% vs 64.1%). ConclusionsThe increase in prevalence, relative household attack rates, and reproductive number are consistent with a modest transmissibility increase of the West Coast variants; however, additional laboratory and epidemiological studies are required to better understand differences between these variants. SummaryWe observed a growing prevalence and elevated attack rate for "West Coast" SARS-CoV-2 variants in a community testing setting in San Francisco during January 2021, suggesting its modestly higher transmissibility.

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%.