Deep mutational scanning identifies SARS-CoV-2 Nucleocapsid escape mutations of currently available rapid antigen tests.

The effects of mutations in continuously emerging variants of SARS-CoV-2 are a major concern for the performance of rapid antigen tests. To evaluate the impact of mutations on 17 antibodies used in 11 commercially available antigen tests with emergency use authorization, we measured antibody binding for all possible Nucleocapsid point mutations using a mammalian surface-display platform and deep mutational scanning. The results provide a complete map of the antibodies' epitopes and their susceptibility to mutational escape. Our data predict no vulnerabilities for detection of mutations found in variants of concern. We confirm this using the commercial tests and sequence-confirmed COVID-19 patient samples. The antibody escape mutational profiles generated here serve as a valuable resource for predicting the performance of rapid antigen tests against past, current, as well as any possible future variants of SARS-CoV-2, establishing the direct clinical and public health utility of our system.

Multisite Mpox Infection and Viral Dynamics Among Persons With HIV in Metro Atlanta.

The 2022 mpox outbreak primarily involved sexual transmission among men who have sex with men and disproportionately affected persons with human immunodeficiency virus (HIV). We examined viral dynamics and clinical features in a cohort evaluated for mpox infection at a comprehensive HIV clinic in Atlanta, Georgia. Viral DNA was found in 8 oropharyngeal and 5 anorectal specimens among 10 mpox cases confirmed by lesion swab polymerase chain reaction. Within-participant anatomic site of lowest cycle threshold (Ct) value varied, and lower Ct values were found in oropharyngeal and anorectal swabs when corresponding symptoms were present. This provides insight into mpox infection across multiple anatomic sites among people with HIV.

What's in a Name? Experimental Evidence of Gender Bias in Recommendation Letters Generated by ChatGPT.

BACKGROUND: Artificial intelligence chatbots such as ChatGPT (OpenAI) have garnered excitement about their potential for delegating writing tasks ordinarily performed by humans. Many of these tasks (eg, writing recommendation letters) have social and professional ramifications, making the potential social biases in ChatGPT's underlying language model a serious concern. OBJECTIVE: Three preregistered studies used the text analysis program Linguistic Inquiry and Word Count to investigate gender bias in recommendation letters written by ChatGPT in human-use sessions (N=1400 total letters). METHODS: We conducted analyses using 22 existing Linguistic Inquiry and Word Count dictionaries, as well as 6 newly created dictionaries based on systematic reviews of gender bias in recommendation letters, to compare recommendation letters generated for the 200 most historically popular "male" and "female" names in the United States. Study 1 used 3 different letter-writing prompts intended to accentuate professional accomplishments associated with male stereotypes, female stereotypes, or neither. Study 2 examined whether lengthening each of the 3 prompts while holding the between-prompt word count constant modified the extent of bias. Study 3 examined the variability within letters generated for the same name and prompts. We hypothesized that when prompted with gender-stereotyped professional accomplishments, ChatGPT would evidence gender-based language differences replicating those found in systematic reviews of human-written recommendation letters (eg, more affiliative, social, and communal language for female names; more agentic and skill-based language for male names). RESULTS: Significant differences in language between letters generated for female versus male names were observed across all prompts, including the prompt hypothesized to be neutral, and across nearly all language categories tested. Historically female names received significantly more social referents (5/6, 83% of prompts), communal or doubt-raising language (4/6, 67% of prompts), personal pronouns (4/6, 67% of prompts), and clout language (5/6, 83% of prompts). Contradicting the study hypotheses, some gender differences (eg, achievement language and agentic language) were significant in both the hypothesized and nonhypothesized directions, depending on the prompt. Heteroscedasticity between male and female names was observed in multiple linguistic categories, with greater variance for historically female names than for historically male names. CONCLUSIONS: ChatGPT reproduces many gender-based language biases that have been reliably identified in investigations of human-written reference letters, although these differences vary across prompts and language categories. Caution should be taken when using ChatGPT for tasks that have social consequences, such as reference letter writing. The methods developed in this study may be useful for ongoing bias testing among progressive generations of chatbots across a range of real-world scenarios. TRIAL REGISTRATION: OSF Registries osf.io/ztv96; https://osf.io/ztv96.

Navigating the complexities of mobile medical app development from idea to launch, a guide for clinicians and biomedical researchers.

With today's pace of rapid technological advancement, many patient issues in modern medicine are increasingly solvable by mobile app solutions, which also have the potential to transform how clinical research is conducted. However, many critical challenges in the app development process impede bringing these translational technologies to patients, caused in large part by the lack of knowledge among clinicians and biomedical researchers of "what it takes" to design, develop, and maintain a successful medical app. Indeed, problems requiring mobile app solutions are often nuanced, requiring more than just clinical expertise, and issues such as the cost and effort required to develop and maintain a well-designed, sustainable, and scalable mobile app are frequently underestimated. To bridge this skill set gap, we established an academic unit of designers, software engineers, and scientists that leverage human-centered design methodologies and multi-disciplinary collaboration to develop clinically viable smartphone apps. In this report, we discuss major misconceptions clinicians and biomedical researchers often hold regarding medical app development, the steps we took to establish this unit to address these issues and the best practices and lessons learned from successfully ideating, developing, and launching medical apps. Overall, this report will serve as a blueprint for clinicians and biomedical researchers looking to better benefit their patients or colleagues via medical mobile apps.

Sensitivity of rapid antigen tests against SARS-CoV-2 Omicron and Delta variants.

Rapid antigen tests (RATs) have become an invaluable tool for combating the COVID-19 pandemic. However, concerns have been raised regarding the ability of existing RATs to effectively detect emerging SARS-CoV-2 variants. We compared the performance of 10 commercially available, emergency use authorized RATs against the Delta and Omicron SARS-CoV-2 variants using both individual patient and serially diluted pooled clinical samples. The RATs exhibited lower sensitivity for Omicron samples when using PCR cycle threshold (CT) value (a rough proxy for RNA concentration) as the comparator. Interestingly, however, they exhibited similar sensitivity for Omicron and Delta samples when using quantitative antigen concentration as the comparator. We further found that the Omicron samples had lower ratios of antigen to RNA, which offers a potential explanation for the apparent lower sensitivity of RATs for that variant when using C T value as a reference. Our findings underscore the complexity in assessing RAT performance against emerging variants and highlight the need for ongoing evaluation in the face of changing population immunity and virus evolution.

Bridging the Divide: Unintended Consequences of the Shift to Home-Based Telemedicine.

OBJECTIVE: To evaluate the impact on health care access of the change in telemedicine delivery from a clinic-based model, in which patients connect with their healthcare provider from local telemedicine clinics, to a home-based model, in which patients independently connect from their homes. STUDY DESIGN: In this retrospective analysis, we compared relative uptake in telemedicine services in Period 1 (01/01/2019 to 03/15/2020, prepandemic, clinic-based model) vs Period 2 (03/16/2020 to 06/30/2022, home-based model) within a tertiary pediatric hospital system. Using multivariable logistic regression, we investigated the influence of telemedicine delivery model on patient sociodemographic characteristics of completed telemedicine visits. RESULTS: We analyzed 400 539 patients with 1 406 961 completed outpatient encounters (52% White, 35% Black), of which 62 920 (4.5%) were telemedicine. In the clinic-based model (Period 1), underserved populations had greater likelihoods of accessing telemedicine: Hispanic ethnicity (OR = 1.41, P = .028) vs reference group non-Hispanic, Medicaid (OR = 2.62, P < .001) vs private insurance, and low-income neighborhood (OR = 3.40, P < .001) vs medium-income. In aggregate, telemedicine utilization rapidly increased from Period 1 (1.5 encounters/day) to Period 2 (107.9 encounters/day). However, underserved populations saw less relative increase (Medicaid [OR = 0.28, P < .001], Hispanic [OR = 0.53, P < .001], low-income [OR = 0.23, P < .001]). CONCLUSIONS: We observe that the clinic-based model offers more equitable access, while the home-based model offers more absolute access, suggesting that a hybrid model that offers both home-based and clinic-based services may result in more absolute and equitable access to telemedicine.

A novel mobile health application to support cancer surveillance needs of patients and families with cancer predisposition syndromes.

BACKGROUND: At least 5%-10% of malignancies occur secondary to an underlying cancer predisposition syndrome (CPS). For these families, cancer surveillance is recommended with the goal of identifying malignancy earlier, in a presumably more curable form. Surveillance protocols, including imaging studies, bloodwork, and procedures, can be complex and differ based on age, gender, and syndrome, which adversely affect adherence. Mobile health (mHealth) applications (apps) have been utilized in oncology and could help to facilitate adherence to cancer surveillance protocols. METHODS: Applying a user-centered mobile app design approach, patients with a CPS and/or primary caregivers were interviewed to identify current methods for care management and barriers to compliance with recommended surveillance protocols. Broad themes from these interviews informed the design of the mobile app, HomeTown, which was subsequently evaluated by usability experts. The design was then converted into software code in phases, evaluated by patients and caregivers in an iterative fashion. User population growth and app usage data were assessed. RESULTS: Common themes identified included general distress surrounding surveillance protocol scheduling and results, difficulty remembering medical history, assembling a care team, and seeking resources for self-education. These themes were translated into specific functional app features, including push reminders, syndrome-specific surveillance recommendations, ability to annotate visits and results, storage of medical histories, and links to reliable educational resources. CONCLUSIONS: Families with CPS demonstrate a desire for mHealth tools to facilitate adherence to cancer surveillance protocols, reduce related distress, relay medical information, and provide educational resources. HomeTown may be a useful tool for engaging this patient population.

Engaging Cancer Care Physicians in Off-Label Drug Clinical Trials: Human-Centered Design Approach.

BACKGROUND: Using a human-centered design (HCD) approach can provide clinical trial design teams with a better understanding of the needs, preferences, and attitudes of clinical trial stakeholders. It can also be used to understand the challenges and barriers physician stakeholders face in initiating and completing clinical trials, especially for using off-label drugs (OLDs) to treat unmet clinical needs in cancer treatment. However, the HCD approach is not commonly taught in the context of clinical trial design, and few step-by-step guides similar to this study are available to demonstrate its application. OBJECTIVE: This study aims to demonstrate the feasibility and process of applying an HCD approach to creating clinical trial support resources for physician stakeholders to overcome barriers to pursuing clinical trials for OLDs to treat cancer. METHODS: An HCD approach was used to develop OLD clinical trial support concepts. In total, 45 cancer care physicians were contacted, of which 15 participated in semistructured interviews to identify barriers to prescribing OLDs or participating in cancer OLD clinical trials. Design research is qualitative-it seeks to answer "why" and "how" questions; thus, a sample size of 15 was sufficient to provide insight saturation to address the design problem. The team used affinity mapping and thematic analysis of qualitative data gathered from the interviews to inform subsequent web-based co-design sessions, which included creative matrix exercises and voting to refine and prioritize the ideas used in the final 3 recommended concepts. RESULTS: The findings demonstrate the potential of HCD methods to uncover important insights into the barriers physicians face in participating in OLD clinical trials or prescribing OLDs, such as recruitment challenges, low willingness to prescribe without clinical data, and stigma. Notably, only palliative care participants self-identified as "frequent prescribers" of OLDs, despite high national OLD prescription rates among patients with cancer. Participants found the HCD approach engaging, with 60% (9/15) completing this study; scheduling conflicts caused most of the dropouts. Over 150 ideas were generated in 3 co-design sessions, with the groups voting on 15 priority ideas that the design team then refined into 3 final recommendations, especially focused on increasing the participation of physicians in OLD clinical trials. CONCLUSIONS: Using participatory HCD methods, we delivered 3 concepts for clinical trial support resources to help physician stakeholders overcome barriers to pursuing clinical trials for OLDs to treat cancer. Overall, integrating the HCD approach can aid in identifying important stakeholders, such as prescribing physicians; facilitating their engagement; and incorporating their perspectives and needs into the solution design process. This paper highlights the process, methods, and potential of HCD to improve cancer clinical trial design. Future work is needed to train clinical trial designers in the HCD approach and encourage adoption in the field.

"An app is just available at all times"-the process and outcomes of converting the Georgia Tuberculosis Reference Guide into a mobile application.

BACKGROUND: The physical, paper-based Georgia TB Reference Guide has served as the clinical reference handbook on tuberculosis (TB) diagnostic and treatment guidelines for the state of Georgia in the United States. Supported by the Georgia Department of Public Health, the production of the 112-page palm-sized booklet was previously led by a team of Georgia-based TB experts at Emory University and printed every three-five years with updates to clinical management guidelines and TB consult contact information. However, the costs associated with editorial printing combined with delays in updating a static printed booklet with revised guidance hampered the utility of the tool. Considering the barriers with paper-based production and based on the beneficial use of apps to support the dissemination of clinical management guidance in other settings, the booklet was converted into a mobile application. This paper describes the process of developing a mobile app version of the Georgia TB Reference Guide in an easy-to-update and readily available format. METHODS: We employed a user-centered design approach to develop the app, including a series of qualitative interviews and quantitative surveys. Participants included a mix of state officials and local TB experts. First, initial foundational interviews were conducted to conceptualize current utilization practices of both the paper and PDF versions of the tool. Second, the findings from the initial interviews were organized thematically and informed the design of the app, which was then beta tested by a round of previously unsampled TB experts as well as a re-sample from the initial interviews. Third, the designs were coded into developmental phases and beta tested among users of the current Georgia TB Reference Guide. Fourth, the app was published and downloaded by a pre-selected group of local users who provided answers to a follow-up survey after using the app for one month. Fifth, user growth, self-reported demographics, and app usage between February and July 2022 were recorded through automatic data metrics built into the app. RESULTS: The paper copy Georgia TB Reference Guide usage themes included commonly referenced content, navigation paths, and desired features and content. The themes were converted into features and designs such as prioritizing commonly reviewed topics and guide customization with bookmarks and notes. Iterations of the designs were driven by feedback from TB experts and included home page featured content, improving content readability, and improving the search feature. The follow-up survey revealed a 90% preference for the app over the paper version of the guide. In the six months following the app's release, the app was downloaded by 281 individuals in the United States. The majority of downloads were in Georgia and the app also expanded organically to 19 other states. CONCLUSION: The experience of converting the Georgia TB Reference Guide offers specific and effective steps to converting a medical reference guide into a mobile application tool that is readily available, easy to use, and easy to update. The organic dissemination of the app beyond the state of Georgia's borders within the first six months of app launch underscores desire among TB healthcare professionals for high-quality digital reference content outside the state. This experience offers clear outlines for replication in other contexts and demonstrates the utility of similar mobile medical reference tools.

Protocol for the creation and characterization of SARS-CoV-2 variant testing panels using remnant clinical samples for diagnostic assay testing.

The emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Alpha variant in 2020 demonstrated the need for reanalysis of diagnostic tests to ensure detection of emerging variants. Here, we present a protocol for creating and characterizing SARS-CoV-2 variant testing panels using remnant clinical samples for diagnostic assay testing. We describe steps for characterizing SARS-CoV-2 remnant clinical samples and preparing them into pools and their use in preparing varying quantities of virus. We then detail procedures for verifying variant detection using the resulting sample panel. For complete details on the use and execution of this protocol, please refer to Rao et al.1,2.

Incorporating Cardiovascular Risk Assessment into Adolescent Reproductive Health and Primary Care Visits.

STUDY OBJECTIVE: This study aimed to evaluate the usability and feasibility of incorporating a cardiovascular risk assessment tool into adolescent reproductive health and primary care visits. DESIGN, SETTING, AND PARTICIPANTS: We recruited 60 young women ages 13-21 years to complete the HerHeart web-tool in 2 adolescent clinics in Atlanta, GA. MAIN OUTCOME MEASURES: Participants rated the tool's usability via the Website Analysis and Measurement Inventory (WAMMI, range 0-95) and their perceived 10-year and lifetime risk of cardiovascular disease (CVD) on a visual analog scale (range 0-10). Participants' perceived risk, blood pressure, and body mass index were measured at baseline and 3 months after enrollment. Health care providers (HCP, n = 5) completed the WAMMI to determine the usability and feasibility of incorporating the HerHeart tool into clinical practice. RESULTS: Adolescent participants and HCPs rated the tool's usability highly on the WAMMI with a median of 79 (interquartile range [IQR] 65, 84) and 76 (IQR 71, 84). At the baseline visit, participants' median perceived 10-year risk of a heart attack was 1 (IQR 0, 3), and perceived lifetime risk was 2 (IQR 0, 4). Immediately after engaging with the tool, participants' median perceived 10-year risk was 2 (IQR 1, 4.3), and perceived lifetime risk was 3 (IQR 1.8, 6). Thirty-one participants chose to set a behavior change goal, and 12 participants returned for follow-up. Clinical metrics were similar at the baseline and follow-up visits. CONCLUSION: HerHeart is acceptable to young women and demonstrates potential for changing risk perception and improving health habits to reduce risk of CVD. Future research should focus on improving retention in studies to promote cardiovascular health within reproductive health clinics.

Performance of the Xpert™ Mpox PCR assay with oropharyngeal, anorectal, and cutaneous lesion swab specimens.

Anorectal and oropharyngeal exposures are implicated in sexual transmission of mpox, but authorized assays in the United States are only validated with cutaneous lesion swabs. Diagnostic assays for anorectal and oropharyngeal swabs are needed to address potential future outbreaks. The Cepheid Xpert® Mpox is the first point-of-care assay to receive FDA emergency use authorization in the United States and would be a valuable tool for evaluating these sample types. Our exploratory study demonstrates 100 % positive agreement with our in-house PCR assay for natural positive anorectal and oropharyngeal specimens and 92 % sensitivity with low-positive spiked specimens. The Xpert® assay detected viral DNA in specimens not detected by our reference PCR assay from four participants with mpox DNA at other sites, suggesting it may be more sensitive at low viral loads. In conclusion, the validation of the Xpert® for oropharyngeal and anorectal sample types can be rapidly achieved if clinical need returns and prospective samples become available.

Comparison of RT-PCR and antigen test sensitivity across nasopharyngeal, nares, and oropharyngeal swab, and saliva sample types during the SARS-CoV-2 omicron variant.

Limited data highlight the need to understand differences in SARS-CoV-2 omicron (B.1.1.529) variant viral load between the gold standard nasopharyngeal (NP) swab, mid-turbinate (MT)/anterior nasal swabs, oropharyngeal (OP) swabs, and saliva. MT, OP, and saliva samples from symptomatic individuals in Atlanta, GA, in January 2022 and longitudinal samples from a small familial cohort were tested by both RT-PCR and ultrasensitive antigen assays. Higher concentrations in the nares were observed in the familial cohort, but a dominant sample type was not found among 39 cases in the cross-sectional cohort. The composite of positive MT or OP assay for both RT-PCR and antigen assay trended toward higher diagnostic yield but did not achieve significant difference. Our data did not identify a singular preferred sample type for SARS-CoV-2 testing, but higher levels of saliva nucleocapsid, a trend toward higher yield of composite OP/MT result, and association of apparent MT or OP predominance with symptoms warrant further study.

A Web-Based Intervention to Address Risk Factors for Maternal Morbidity and Mortality (MAMA LOVE): Development and Evaluation Study.

Background: Maternal mortality in the United States is a public health crisis and national emergency. Missed or delayed recognition of preventable life-threatening symptoms and untimely treatment of preventable high-risk medical conditions have been cited as key contributors to the nation's worsening mortality rates. Effective strategies are urgently needed to address this maternal health crisis, particularly for Black birthing populations. Morbidity and Mortality Assessment: Lifting Outcomes Via Education (MAMA LOVE) is a web-based platform that focuses on the identification of maternal morbidity and mortality risk factors. Objective: The purpose of this paper is to present the conceptualization, development, heuristics, and utility evaluation of the web-based maternal mortality risk assessment and educational tool MAMA LOVE. Methods: A user-centered design approach was used to gain feedback from clinical experts and potential end users to ensure that the tool would be effective among groups most at risk for maternal morbidity and mortality. A heuristic evaluation was conducted to evaluate usability and need within the current market. Algorithms describing key clinical, mental health, and social conditions were designed using digital canvas software (Miro) and incorporated into the final wireframes of the revised prototype. The completed version of MAMA LOVE was designed in Figma and built with the SurveyJS platform. Results: The creation of the MAMA LOVE tool followed three distinct phases: (1) the content development and creation of an initial prototype; (2) the feedback gathering and usability assessment of the prototype; and (3) the design, development, and testing of the final tool. The tool determines the corresponding course of action using the algorithm developed by the authors. A total of 38 issues were found in the heuristic evaluation of the web tool's initial prototype. Conclusions: Maternal morbidity and mortality is a public health crisis needing immediate effective interventions. In the current market, there are few digital resources available that focus specifically on the identification of dangerous symptoms and risk factors. MAMA LOVE is a tool that can address that need by increasing knowledge and providing resources and information that can be shared with health care professionals.

Pivot, persevere, or perish: how Ellume Health overcame development and regulatory obstacles to become the first authorized over-the-counter COVID-19 test in the United States.

The Ellume COVID-19 home test from Ellume Health (Brisbane, Aus) became the first COVID-19 diagnostic tool authorized for home use by the United States FDA in December 2020. This early pandemic success was built on over ten years of work on the Ellume influenza home test. Ellume overcame critical technology challenges during the development of their influenza test. In addition, it faced a recall of its COVID-19 home test in 2021 due to false positive results. While Ellume initially persevered through the recall and restarted sales in the United States, the combination of the recall and the wide availability of competitors' low-cost over the counter tests in the United States led to Ellume entering voluntary administration in September 2022. This paper traces the history of Ellume and how 10 years of experience with a home influenza test allowed the company to quickly develop the Ellume COVID-19 home test. We will also provide to diagnostic developers the key strategies employed by Ellume to succeed while highlighting the pitfalls that have challenged the company's business success.

SARS-CoV-2 molecular testing and whole genome sequencing following RNA recovery from used BinaxNOW COVID-19 Antigen Self Tests.

Widespread use of over-the-counter rapid diagnostic tests for SARS-CoV-2 has led to a decrease in availability of clinical samples for viral genomic surveillance. As an alternative sample source, we evaluated RNA isolated from BinaxNOW swabs stored at ambient temperature for SARS-CoV-2 rRT-PCR and full viral genome sequencing. 81 of 103 samples (78.6%) yielded detectable RNA, and 46 of 57 samples (80.7 %) yielded complete genome sequences. Our results illustrate that SARS-CoV-2 RNA extracted from used Binax test swabs provides an important opportunity for improving SARS-CoV-2 genomic surveillance, evaluating transmission clusters, and monitoring within-patient evolution.

Effect of swab pooling on the Accula point-of-care RT-PCR for SARS-CoV-2 detection.

Introduction: Swab pooling may allow for more efficient use of point-of-care assays for SARS-CoV-2 detection in settings where widespread testing is warranted, but the effects of pooling on assay performance are not well described. Methods: We tested the Thermo-Fisher Accula rapid point-of-care RT-PCR platform with contrived pooled nasal swab specimens. Results: We observed a higher limit of detection of 3,750 copies/swab in pooled specimens compared to 2,250 copies/swab in individual specimens. Assay performance appeared worse in a specimen with visible nasal mucous and debris, although performance was improved when using a standard laboratory mechanical pipette compared to the transfer pipette included in the assay kit. Conclusion: Clinicians and public health officials overseeing mass testing efforts must understand limitations and benefits of swab or sample pooling, including reduced assay performance from pooled specimens. We conclude that the Accula RT-PCR platform remains an attractive candidate assay for pooling strategies owing to the superior analytical sensitivity compared to most home use and point-of-care tests despite the inhibitory effects of pooled specimens we characterized.

SARS-CoV-2 molecular testing and whole genome sequencing following RNA recovery from used BinaxNOW COVID-19 antigen self tests.

Widespread use of over-the-counter rapid diagnostic tests for SARS-CoV-2 has led to a decrease in availability of clinical samples for viral genomic surveillance. As an alternative sample source, we evaluated RNA isolated from BinaxNOW swabs stored at ambient temperature for SARS-CoV-2 rRT-PCR and full viral genome sequencing. 81 of 103 samples (78.6%) yielded detectable RNA, and 46 of 57 samples (80.7 %) yielded complete genome sequences. Our results illustrate that SARS-CoV-2 RNA extracted from used Binax test swabs provides an important opportunity for improving SARS-CoV-2 genomic surveillance, evaluating transmission clusters, and monitoring within-patient evolution.

Standardization and Comparison of Emergency Use Authorized COVID-19 Assays and Testing Laboratories.

Motivation: The motivation for this work was the need to establish a predefined cutoff based on genome copies per ml (GE/ml) rather than Ct, which can vary depending on the laboratory and assay used. A GE/ml-based threshold was necessary to define what constituted 'low positives" for samples that were included in data sets submitted to the FDA for emergency use approval for SARS-CoV-2 antigen tests. Summary: SARS-CoV-2, the causal agent of the global COVID-19 pandemic, made its appearance at the end of 2019 and is still circulating in the population. The pandemic led to an urgent need for fast, reliable, and widely available testing. After December 2020, the emergence of new variants of SARS-CoV-2 led to additional challenges since new and existing tests had to detect variants to the same extent as the original Wuhan strain. When an antigen-based test is submitted to the Food and Drug Administration (FDA) for Emergency Use Authorization (EUA) consideration it is benchmarked against PCR comparator assays, which yield cycle threshold (CT) data as an indirect indicator of viral load - the lower the CT, the higher the viral load of the sample and the higher the CT, the lower the viral load. The FDA mandates that 10-20% of clinical samples used to evaluate the antigen test have to be low positive. Low positive, as defined by the FDA, are clinical samples in which the CT of the SARS-CoV-2 target gene is within 3 CT of the mean CT value of the approved comparator test's Limit of Detection (LOD). While all comparator tests are PCR-based, the results from different PCR assays used are not uniform. Results vary depending on assay platform, target gene, LOD and laboratory methodology. The emergence and dominance of the Omicron variant further challenged this approach as the fraction of low positive clinical samples dramatically increased as compared to earlier SARS-CoV-2 variants. This led to 20-40% of clinical samples having high CT values and therefore assays vying for an EUA were failing to achieve the 80% Percent Positive Agreement (PPA) threshold required. Here we describe the methods and statistical analyses used to establish a predefined cutoff, based on genome copies per ml (GE/ml) to classify samples as low positive (less than the cutoff GE/ml) or high positive (greater than the cutoff GE/mL). CT 30 for the E gene target using Cobas® SARS-CoV-2-FluA/B platform performed at TriCore Reference Laboratories, and this low positive cutoff value was used for two EUA authorizations. Using droplet digital PCR and methods described here, a value 49,447.72 was determined as the GE/ml equivalent for the low positive cutoff. The CT cutoff corresponding to 49447.72 GE/ml was determined across other platforms and laboratories. The methodology and statistical analysis described here can now be used for standardization of all comparators used for FDA submissions with a goal towards establishing uniform criteria for EUA authorization.

Sensitivity of Rapid Antigen Tests Against SARS-CoV-2 Omicron and Delta Variants.

Rapid Antigen Tests (RAT) have become an invaluable tool for combating the COVID-19 pandemic. However, concerns have been raised regarding the ability of existing RATs to effectively detect emerging SARS-CoV-2 variants. We compared the performance of eight commercially available, emergency use authorized RATs against the Delta and Omicron SARS-CoV-2 variants using individual patient and serially diluted pooled clinical samples. The RATs exhibited lower sensitivity for Omicron samples when using PCR Cycle threshold (C T ) value (a proxy for RNA concentration) as the comparator. Interestingly, however, they exhibited similar sensitivity for Omicron and Delta samples when using quantitative antigen concentration as the comparator. We further found that the Omicron samples had lower ratios of antigen to RNA, which offers a potential explanation for the apparent lower sensitivity of RATs for that variant when using C T value as a reference. Our findings underscore the complexity in assessing RAT performance against emerging variants and highlight the need for ongoing evaluation in the face of changing population immunity and virus evolution.