SARS-CoV-2 incidence, testing rates, and severe COVID-19 outcomes among people with and without HIV.

To assess SARS-CoV-2 outcomes, we matched a municipal COVID-19 registry and clinic rosters from a municipal primary care network containing a large HIV clinic and assessed clinical outcomes by HIV status. The risk of severe COVID-19 was higher among people with HIV (PWH, adjusted relative risk = 1.84, 95% confidence interval = 1.05-3.25), while SARS-CoV-2 incidence was lower despite higher testing rates. SARS-CoV-2 vaccination campaigns should prioritize PWH to prevent severe COVID-19 disease given potentially higher risk.

High Parental Vaccine Motivation at a Neighborhood-Based Vaccine and Testing Site Serving a Predominantly Latinx Community.

Purpose: To 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. Results: Among 1033 parents (75% Latinx), 92% would "definitely" or "probably" vaccinate their children. Vaccine concerns were higher for younger children and included side effects and impacts on fertility. Doctors and community organizations were noted as trusted sources of information, including among vaccine-concerned parents. Conclusion: Latinx parents accessing neighborhood-based COVID-19 testing/vaccination services are highly motivated to vaccinate their children for COVID-19.

Pragmatic randomized trial of a pre-visit intervention to improve the quality of telemedicine visits for vulnerable patients living with HIV.

INTRODUCTION: The COVID-19 pandemic has required a shift of many routine primary care visits to telemedicine, potentially widening disparities in care access among vulnerable populations. In a publicly-funded HIV clinic, we aimed to evaluate a pre-visit phone-based planning intervention to address anticipated barriers to telemedicine. METHODS: We conducted a pragmatic randomized controlled trial of patients scheduled for a phone-based HIV primary care visit at the Ward 86 HIV clinic in San Francisco from 15 April to 15 May 2020. Once reached by phone, patients were randomized to either have a structured pre-visit planning intervention to address barriers to an upcoming telemedicine visit versus a standard reminder call. The primary outcome was telemedicine visit attendance. RESULTS: Of 476 scheduled telemedicine visits, 280 patients were reached by a pre-visit call to offer enrollment. Patients were less likely to be reached if virally unsuppressed (odds ratio (OR) 0.11, 95% confidence intervals (CI) 0.03-0.48), CD4 < 200 (OR 0.24, 95% CI 0.07-0.85), or were homeless (OR 0.24, 95% CI 0.07-0.87). There was no difference between intervention and control in scheduled visit attendance (83% v. 78%, OR 1.38, 95% CI 0.67-2.81). CONCLUSIONS: A structured phone-based planning call to address barriers to telemedicine in a public HIV clinic was less likely to reach patients with poorly-controlled HIV and patients experiencing homelessness, suggesting additional interventions may be needed in this population to ensure access to telemedicine-based care. Among patients reachable by phone, telemedicine visit attendance was high and not improved with a structured pre-visit intervention, suggesting that standard reminders may be adequate in this population.

A 2-Gene Host Signature for Improved Accuracy of COVID-19 Diagnosis Agnostic to Viral Variants.

The continued emergence of SARS-CoV-2 variants is one of several factors that may cause false-negative viral PCR test results. Such tests are also susceptible to false-positive results due to trace contamination from high viral titer samples. Host immune response markers provide an orthogonal indication of infection that can mitigate these concerns when combined with direct viral detection. Here, we leverage nasopharyngeal swab RNA-seq data from patients with COVID-19, other viral acute respiratory illnesses, and nonviral conditions (n = 318) to develop support vector machine classifiers that rely on a parsimonious 2-gene host signature to diagnose COVID-19. We find that optimal classifiers include an interferon-stimulated gene that is strongly induced in COVID-19 compared with nonviral conditions, such as IFI6, and a second immune-response gene that is more strongly induced in other viral infections, such as GBP5. The IFI6+GBP5 classifier achieves an area under the receiver operating characteristic curve (AUC) greater than 0.9 when evaluated on an independent RNA-seq cohort (n = 553). We further provide proof-of-concept demonstration that the classifier can be implemented in a clinically relevant RT-qPCR assay. Finally, we show that its performance is robust across common SARS-CoV-2 variants and is unaffected by cross-contamination, demonstrating its utility for improved accuracy of COVID-19 diagnostics. IMPORTANCE In this work, we study upper respiratory tract gene expression to develop and validate a 2-gene host-based COVID-19 diagnostic classifier and then demonstrate its implementation in a clinically practical qPCR assay. We find that the host classifier has utility for mitigating false-negative results, for example due to SARS-CoV-2 variants harboring mutations at primer target sites, and for mitigating false-positive viral PCR results due to laboratory cross-contamination. Both types of error carry serious consequences of either unrecognized viral transmission or unnecessary isolation and contact tracing. This work is directly relevant to the ongoing COVID-19 pandemic given the continued emergence of viral variants and the continued challenges of false-positive PCR assays. It also suggests the feasibility of pan-respiratory virus host-based diagnostics that would have value in congregate settings, such as hospitals and nursing homes, where unrecognized respiratory viral transmission is of particular concern.

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

COVID-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. We 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. Among 25,309 persons tested with BinaxNOW, 2,799 had concomitant RT-PCR. 1137/2799 (40.6%) 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 1,137 RT-PCR positive samples, 788/1137 (69%) were detected by BinaxNOW; 94% (669/711) 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 81.7% (361/442, 95% CI: 77-85%) of persons with COVID-19 within 5 days of symptom onset. In comparison, RT-PCR (24-hour turnaround) detected 84.2% (372/442, 95% CI: 80-87%) and RT-PCR (48-hour turnaround) detected 67.0% (296/442, 95% CI: 62-71%) of persons with COVID-19 within 5 days of symptom onset. BinaxNOW 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.

Reproducibility and implementation of a rapid, community-based COVID-19 "test and respond" model in low-income, majority-Latino communities in Northern California.

OBJECTIVE: To evaluate implementation of a community-engaged approach to scale up COVID-19 mass testing in low-income, majority-Latino communities. METHODS: In January 2021, we formed a community-academic "Latino COVID-19 Collaborative" with residents, leaders, and community-based organizations (CBOs) from majority-Latinx, low-income communities in three California counties (Marin/Merced/San Francisco). The collaborative met monthly to discuss barriers/facilitators for COVID-19 testing, and plan mass testing events informed by San Francisco's Unidos en Salud "test and respond" model, offering community-based COVID-19 testing and post-test support in two US-census tracts: Canal (Marin) and Planada (Merced). We evaluated implementation using the RE-AIM framework. To further assess testing barriers, we surveyed a random sample of residents who did not attend the events. RESULTS: Fifty-five residents and CBO staff participated in the Latino collaborative. Leading facilitators identified to increase testing were extended hours of community-based testing and financial support during isolation. In March-April 2021, 1,217 people attended mass-testing events over 13 days: COVID-19 positivity was 3% and 1% in Canal and Planada, respectively. The RE-AIM evaluation found: census tract testing coverage of 4.2% and 6.3%, respectively; 90% of event attendees were Latino, 89% had household income <$50,000/year, and 44% first-time testers (reach), effectiveness in diagnosing symptomatic cases early (median isolation time: 7 days) and asymptomatic COVID-19 (41% at diagnosis), high adoption by CBOs in both counties, implementation of rapid testing (median: 17.5 minutes) and disclosure, and post-event maintenance of community-based testing. Among 265 non-attendees surveyed, 114 (43%) reported they were aware of the event: reasons for non-attendance among the 114 were insufficient time (32%), inability to leave work (24%), and perceptions that testing was unnecessary post-vaccination (24%) or when asymptomatic (25%). CONCLUSION: Community-engaged mass "test and respond" events offer a reproducible approach to rapidly increase COVID-19 testing access in low-income, Latinx communities.

COVID-19 Symptoms and Duration of Rapid Antigen Test Positivity at a Community Testing and Surveillance Site During Pre-Delta, Delta, and Omicron BA.1 Periods.

Importance: Characterizing the clinical symptoms and evolution of community-based SARS-CoV-2 infections may inform health practitioners and public health officials in a rapidly changing landscape of population immunity and viral variants. Objectives: To compare COVID-19 symptoms among people testing positive with a rapid antigen test (RAT) during the Omicron BA.1 variant period (December 1, 2021, to January 30, 2022) with the pre-Delta (January 10 to May 31, 2021) and Delta (June 1 to November 30, 2021) variant periods and to assess the duration of RAT positivity during the Omicron BA.1 surge. Design, Setting, and Participants: This cross-sectional study was conducted from January 10, 2021, to January 31, 2022, at a walk-up community COVID-19 testing site in San Francisco, California. Participants included children and adults seeking COVID-19 testing with an RAT, regardless of age, vaccine status, or symptoms. Main Outcomes and Measures: Fisher exact tests or χ2 tests were used to compare COVID-19 symptoms during the Omicron BA.1 period with the pre-Delta and Delta periods for vaccination status and age group. Among people returning for repeated testing during the Omicron period, the proportion with a positive RAT between 4 and 14 days from symptom onset or since first positive test if asymptomatic was estimated. Results: Among 63 277 persons tested (median [IQR] age, 32 [21-44] years, with 12.0% younger than 12 years; 52.0% women; and 68.5% Latinx), a total of 18 301 people (28.9%) reported symptoms, of whom 4565 (24.9%) tested positive for COVID-19. During the Omicron BA.1 period, 3032 of 7283 symptomatic participants (41.6%) tested positive, and the numbers of these reporting cough and sore throat were higher than during pre-Delta and Delta periods (cough: 2044 [67.4%] vs 546 [51.3%] of 1065 participants, P < .001 for pre-Delta, and 281 [60.0%] of 468 participants, P = .002, for Delta; sore throat: 1316 [43.4%] vs 315 [29.6%] of 1065 participants, P < .001 for pre-Delta, and 136 [29.1%] of 468 participants, P < .001, for Delta). Compared with the 1065 patients with positive test results in the pre-Delta period, congestion among the 3032 with positive results during the Omicron BA.1 period was more common (1177 [38.8%] vs 294 [27.6%] participants, P < .001), and loss of taste or smell (160 [5.3%] vs 183 [17.2%] participants, P < .001) and fever (921 [30.4%] vs 369 [34.7%] participants, P = .01) were less common. In addition, during the Omicron BA.1 period, fever was less common among the people with positive test results who had received a vaccine booster compared with those with positive test results who were unvaccinated (97 [22.5%] of 432 vs 42 [36.2%] of 116 participants, P = .003), and fever and myalgia were less common among participants who had received a booster compared with those with positive results who had received only a primary series (fever: 97 [22.5%] of 432 vs 559 [32.8%] of 1705 participants, P < .001; myalgia: 115 [26.6%] of 432 vs 580 [34.0%] of 1705 participants, P = .003). During the Omicron BA.1 period, 5 days after symptom onset, 507 of 1613 people (31.1%) with COVID-19 stated that their symptoms were similar, and 95 people (5.9%) reported worsening symptoms. Among people testing positive, 80.2% of participants who were symptomatic and retested remained positive 5 days after symptom onset. Conclusions and Relevance: In this cross-sectional study, COVID-19 upper respiratory tract symptoms were more commonly reported during the Omicron BA.1 period than during the pre-Delta and Delta periods, with differences by vaccination status. Rapid antigen test positivity remained high 5 days after symptom onset, supporting guidelines requiring a negative test to inform the length of the isolation period.

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Transmission Dynamics and Immune Responses in a Household of Vaccinated Persons.

While SARS-CoV-2 vaccines prevent severe disease effectively, postvaccination "breakthrough" COVID-19 infections and transmission among vaccinated individuals remain ongoing concerns. We present an in-depth characterization of transmission and immunity among vaccinated individuals in a household, revealing complex dynamics and unappreciated comorbidities, including autoimmunity to type 1 interferon in the presumptive index case.

A mid-level health manager intervention to promote uptake of isoniazid preventive therapy among people with HIV in Uganda: a cluster randomised trial.

BACKGROUND: Despite longstanding guidelines endorsing isoniazid preventive therapy (IPT) for people with HIV, uptake is low across sub-Saharan Africa. Mid-level health managers oversee IPT programmes nationally; interventions aimed at this group have not been tested. We aimed to establish whether providing structured leadership and management training and facilitating subregional collaboration and routine data feedback to mid-level managers could increase IPT initiation among people with HIV compared with standard practice. METHODS: We conducted a cluster randomised trial in Uganda among district-level health managers. We randomly assigned clusters of between four and seven managers in a 1:1 ratio to intervention or control groups. Our intervention convened managers into mini-collaboratives facilitated by Ugandan experts in tuberculosis and HIV, and provided business leadership and management training, SMS platform access, and data feedback. The control was standard practice. Participants were not masked to trial group, but study statisticians were masked until trial completion. The primary outcome was IPT initiation rates among adults with HIV in facilities overseen by participants over a period of 2 years (2019-21). We conducted prespecified analyses that excluded the third quarter of 2019 (Q3-2019) to understand intervention effects independent of a national 100-day IPT push tied to a financial contingency during Q3-2019. This trial is registered with ClinicalTrials.gov (NCT03315962), and is ongoing. FINDINGS: Between Nov 15, 2017, and March 14, 2018, managers from 82 of 82 eligible districts (61% of Uganda's 135 districts) were enrolled and randomised: 43 districts to intervention, 39 to control. Intervention delivery took place between Dec 6, 2017, and Feb 2, 2022. Over 2 years, IPT initiation rates were 0·74 versus 0·65 starts per person-year in intervention versus control groups (incidence rate ratio [IRR] 1·14, 95% CI 0·88-1·46; p=0·16). Excluding Q3-2019, IPT initiation was higher in the intervention group versus the control group: 0·32 versus 0·25 starts per person-year (IRR 1·27, 95% CI 1·00-1·61; p=0·026). INTERPRETATION: Following an intervention targeting managers in more than 60% of Uganda's districts, IPT initiation rates were not significantly higher in intervention than control groups. After accounting for large increases in IPT from a 100-day push in both groups, the intervention led to significantly increased IPT rates, sustained after the push and during the COVID-19 pandemic. Our findings suggest that interventions centred on mid-level health managers can improve IPT implementation on a large, subnational scale, and merit further exploration to address key public health challenges for which strong evidence exists but implementation remains suboptimal. FUNDING: National Institute of Allergy and Infectious Diseases.

Brief Report: Heterogeneous Preferences for Care Engagement Among People With HIV Experiencing Homelessness or Unstable Housing During the COVID-19 Pandemic.

BACKGROUND/SETTING: In San Francisco, HIV viral suppression is 71% among housed individuals but only 20% among unhoused individuals. We conducted a discrete choice experiment at a San Francisco public HIV clinic to evaluate care preferences among people living with HIV (PLH) experiencing homelessness/unstable housing during the COVID-19 pandemic. METHODS: From July to November 2020, we conducted a discrete choice experiment among PLH experiencing homelessness/unstable housing who accessed care through (1) an incentivized, drop-in program (POP-UP) or (2) traditional primary care. We investigated 5 program features: single provider vs team of providers; visit incentives ($0, $10, and $20); location (current site vs current + additional site); drop-in vs scheduled visits; in-person only vs optional telehealth visits; and navigator assistance. We estimated relative preferences using mixed-effects logistic regression and conducted latent class analysis to evaluate preference heterogeneity. RESULTS: We enrolled 115 PLH experiencing homelessness/unstable housing, 40% of whom lived outdoors. The strongest preferences were for the same provider (ß = 0.94, 95% CI: 0.48 to 1.41), visit incentives (ß = 0.56 per $5; 95% CI: 0.47 to 0.66), and drop-in visits (ß = 0.47, 95% CI: 0.12 to 0.82). Telehealth was not preferred. Latent class analysis revealed 2 distinct groups: 78 (68%) preferred a flexible care model, whereas 37 (32%) preferred a single provider. CONCLUSIONS: We identified heterogeneous care preferences among PLH experiencing homelessness/unstable housing during the COVID-19 pandemic, with two-thirds preferring greater flexibility and one-third preferring provider continuity. Telehealth was not preferred, even with navigator facilitation. Including patient choice in service delivery design can improve care engagement, particularly for marginalized populations, and is an essential tool for ending the HIV epidemic.

Integrating Rapid Diabetes Screening Into a Latinx Focused Community-Based Low-Barrier COVID-19 Testing Program.

Importance: Community-based COVID-19 testing and vaccination programs play a crucial role in mitigating racial and ethnic disparities in COVID-19 service delivery. They also represent a platform that can be leveraged to expand access to testing for chronic diseases, including diabetes, that disproportionately affect the Latinx community and other marginalized communities. Objective: To evaluate outcomes associated with a diabetes testing strategy designed to reach low-income Latinx persons by leveraging COVID-19 testing infrastructure and community trust developed during the COVID-19 pandemic. Design, Setting, and Participants: This health care improvement study was conducted from August 1 to October 5, 2021, at an outdoor, community-based COVID-19 testing site at a transport hub in the Mission Neighborhood in San Francisco, California. Because the program was designed to expand access to diabetes screening to the local community, all individuals presenting for on-site testing were eligible. Data were analyzed in November 2021. Interventions: Integration of rapid, point-of-care hemoglobin A1c screening as a testing option in an existing low-barrier COVID-19 testing program. Main Outcomes and Measures: Evaluation was guided by the Reach, Effectiveness, Adoption, Implementation and Maintenance (RE-AIM) framework and utilized programmatic data and structured surveys among clients and staff. Results: Of 6631 individuals tested (median [IQR] age 39.3 [29.7-51.3] years; 3417 [52.3%] female, 4348 [65.6%] Latinx), 923 (13.9%) underwent hemoglobin A1c testing with or without COVID-19 testing and 5708 (86.1%) underwent COVID-19 testing only. Individuals tested for diabetes were more likely to be Latinx (763 of 923 individuals [82.7%] who underwent testing were Latinx vs 3585 of 5708 [62.8%] not undergoing testing), have an annual household income of less than $50 000 (450 individuals [81.2%] vs 2409 individuals [66.0%]), and not have health insurance (381 individuals [47.2%] vs 1858 individuals [39.9%]), and 206 (48.0%) had never tested for diabetes before. Overall, 313 (33.9%) and 113 (12.2%) individuals had prediabetes and diabetes, respectively; only 141 of 354 of these individuals (39.8%) had a primary care clinician whom they had seen in the prior 12 months, which was lower among Latinx individuals (113 of 307 individuals [36.8%] vs 28 of 47 [59.6%]). Acceptability of the rapid testing program was high-98% were satisfied with their visit and 96% said they would return for future services; key factors underpinning acceptability included friendly staff, efficiency, and a convenient location. Conclusions and Relevance: In this health care improvement study conducted within an existing community-based COVID-19 testing program, integrating rapid testing for diabetes was feasible, reached low-income Latinx individuals, and identified many persons with prediabetes and diabetes, most of whom lacked access to services in formal health care settings. Leveraging pandemic-related public health responses represents an important opportunity for engaging socioeconomically disadvantaged populations into care for diabetes.

Viral Load Among Vaccinated and Unvaccinated, Asymptomatic and Symptomatic Persons Infected With the SARS-CoV-2 Delta Variant.

We found no significant difference in cycle threshold values between vaccinated and unvaccinated persons infected with severe acute respiratory syndrome coronavirus 2 Delta, overall or stratified by symptoms. Given the substantial proportion of asymptomatic vaccine breakthrough cases with high viral levels, interventions, including masking and testing, should be considered in settings with elevated coronavirus disease 2019 transmission.

Impact of Multicomponent Support Strategies on Human Immunodeficiency Virus Virologic Suppression Rates During Coronavirus Disease 2019: An Interrupted Time Series Analysis.

BACKGROUND: After coronavirus disease 2019 (COVID-19) shelter-in-place (SIP) orders, viral suppression (VS) rates initially decreased within a safety-net human immunodeficiency virus (HIV) clinic in San Francisco, particularly among people living with HIV (PLWH) who are experiencing homelessness. We sought to determine if proactive outreach to provide social services, scaling up of in-person visits, and expansion of housing programs could reverse this decline. METHODS: We assessed VS 24 months before and 13 months after SIP using mixed-effects logistic regression followed by interrupted time series (ITS) analysis to examine changes in the rate of VS per month. Loss to follow-up (LTFU) was assessed via active clinic tracing. RESULTS: Data from 1816 patients were included; the median age was 51 years, 12% were female, and 14% were experiencing unstable housing/homelessness. The adjusted odds of VS increased 1.34 fold following institution of the multicomponent strategies (95% confidence interval [CI], 1.21-1.46). In the ITS analysis, the odds of VS continuously increased 1.05 fold per month over the post-intervention period (95% CI, 1.01-1.08). Among PLWH who previously experienced homelessness and successfully received housing support, the odds of VS were 1.94-fold higher (95% CI, 1.05-3.59). The 1-year LTFU rate was 2.8 per 100 person-years (95% CI, 2.2-3.5). CONCLUSIONS: The VS rate increased following institution of the multicomponent strategies, with a lower LFTU rate compared with prior years. Maintaining in-person care for underserved patients, with flexible telemedicine options, along with provision of social services and permanent expansion of housing programs, will be needed to support VS among underserved populations during the COVID-19 pandemic.

Viral Load Among Vaccinated and Unvaccinated, Asymptomatic and Symptomatic Persons Infected with the SARS-CoV-2 Delta Variant

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

Comparison of SARS-CoV-2 Reverse Transcriptase Polymerase Chain Reaction and BinaxNOW Rapid Antigen Tests at a Community Site During an Omicron Surge : A Cross-Sectional Study.

BACKGROUND: SARS-CoV-2 rapid antigen tests are an important public health tool. OBJECTIVE: To evaluate field performance of the BinaxNOW rapid antigen test (Abbott) compared with reverse transcriptase polymerase chain reaction (RT-PCR) for detecting infection with the Omicron variant of SARS-CoV-2. DESIGN: Cross-sectional surveillance study. SETTING: Free, walk-up, outdoor, urban community testing and vaccine site led by Unidos en Salud, serving a predominantly Latinx community highly impacted by COVID-19. PARTICIPANTS: Persons seeking COVID-19 testing in January 2022. MEASUREMENTS: Simultaneous BinaxNOW and RT-PCR from nasal, cheek, and throat swabs, including cycle threshold (Ct) measures; a lower Ct value is a surrogate for higher amounts of virus. RESULTS: Among 731 persons tested with nasal swabs, there were 296 (40.5%) positive results on RT-PCR; 98.9% were the Omicron variant. BinaxNOW detected 95.2% (95% CI, 91% to 98%) of persons who tested positive on RT-PCR with a Ct value below 30, 82.1% (CI, 77% to 87%) of those who tested positive on RT-PCR with a Ct value below 35, and 65.2% (CI, 60% to 71%) of all who were positive on RT-PCR. Among 75 persons with simultaneous nasal and cheek swabs, BinaxNOW using a cheek swab failed to detect 91% (20 of 22) of specimens that were positive on BinaxNOW with a nasal swab. Among persons with simultaneous nasal and throat swabs who were positive on RT-PCR with a Ct value below 30, 42 of 49 (85.7%) were detected by nasal BinaxNOW, 23 of 49 (46.9%) by throat BinaxNOW, and 44 of 49 (89.8%) by either. LIMITATION: Participants were a cross-sectional sample from a community-based sentinel surveillance site, precluding study of viral or symptom dynamics. CONCLUSION: BinaxNOW detected persons with high SARS-CoV-2 levels during the Omicron surge, enabling rapid responses to positive test results. Cheek or throat swabs should not replace nasal swabs. As currently recommended, high-risk persons with an initial negative BinaxNOW result should have repeated testing. PRIMARY FUNDING SOURCE: University of California, San Francisco.

Field Performance and Public Health Response Using the BinaxNOWTM Rapid Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Antigen Detection Assay During Community-Based Testing.

Among 3302 persons tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by BinaxNOWTM and reverse transcription polymerase chain reaction (RT-PCR) in a community setting, rapid assay sensitivity was 100%/98.5%/89% using RT-PCR cycle thresholds of 30, 35, and no threshold. The specificity was 99.9%. Performance was high across ages and those with and without symptoms. Rapid resulting permitted immediate public health action.

Estimation of Secondary Household Attack Rates for Emergent Spike L452R Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants Detected by Genomic Surveillance at a Community-Based Testing Site in San Francisco.

BACKGROUND: Sequencing of the severe acute respiratory syndrome coronavirus 2 (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. METHODS: SARS-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 22 November to 1 December, 2020, and 10-29 January 2021. Secondary household attack rates and mean sample viral load were estimated and compared across observed variants. RESULTS: A total of 12 124 tests were performed yielding 1099 positives. From these, 928 high-quality genomes were generated. Certain viral lineages bearing spike mutations, defined in part by L452R, S13I, and W152C, comprised 54.4% of the total sequences from January, compared to 15.7% in November. Household contacts exposed to the "California" or "West Coast" variants (B.1.427 and B.1.429) were at higher risk of infection compared to household contacts exposed to lineages lacking these variants (0.36 vs 0.29, risk ratio [RR] = 1.28; 95% confidence interval [CI]: 1.00-1.64). 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 64.3%). CONCLUSIONS: The increase in prevalence, relative household attack rates, and reproductive number are consistent with a modest transmissibility increase of the West Coast variants. Summary: We observed a growing prevalence and modestly elevated attack rate for "West Coast" severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants in a community testing setting in San Francisco during January 2021, suggesting its modestly higher transmissibility.