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 (BinaxNOWTM) and RT-PCR testing was performed. There were 296 (40.5%) positive tests by RT-PCR; 97% of a random sample 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 60-70%) for Ct threshold of < 30, < 35 and no threshold, respectively. A single BinaxNowTM rapid antigen test detected 95% of high viral load omicron cases from nasal specimens. As currently recommended, repeat testing should be done for high- risk persons with an initial negative antigen test result.

Congress of Neurological Surgeons Systematic Review and Evidence-based Guidelines Update on the Role of Neuropathology in the Management of Progressive Glioblastoma in Adults

Target population These recommendations apply to adult patients with progressive or recurrent glioblastoma (GBM).QuestionFor adult patients with progressive glioblastoma does testing for Isocitrate Dehydrogenase (IDH) 1 or 2 mutations provide new additional management or prognostic information beyond that derived from the tumor at initial presentation?RecommendationLevel III: Repeat IDH mutation testing is not necessary if the tumor is histologically similar to the primary tumor and the patient’s clinical course is as expected. Question For adult patients with progressive glioblastoma does repeat testing for MGMT promoter methylation provide new or additional management or prognostic information beyond that derived from the tumor at initial presentation and what methods of detection are optimal?Recommendation Level III: Repeat MGMT promoter methylation is not recommended. Question For adult patients with progressive glioblastoma does EGFR amplification or mutation testing provide management or prognostic information beyond that provided by histologic analysis and if performed on previous tissue samples, does it need to be repeated?RecommendationLevel III: In cases that are difficult to classify as glioblastoma on histologic features EGFR amplification testing may help in classification. If a previous EGFR amplification was detected, repeat testing is not necessary. Repeat EGFR amplification or mutational testing may be recommended in patients in which target therapy is being considered.Question For adult patients with progressive glioblastoma does whole genome or large panel sequencing provide management or prognostic information beyond that derived from histologic analysis?RecommendationLevel III: Primary or repeat whole genome or large panel sequencing may be considered in patients who are eligible or interested in molecularly guided therapy or clinical trials.QuestionFor adult patients with progressive glioblastoma should immune checkpoint biomarker testing be performed to provide management and prognostic information beyond that obtained from histologic analysis?RecommendationLevel III: The current evidence does not support making PD-L1 or mismatch repair (MMR) enzyme activity a component of standard testing.QuestionFor adult patients with progressive glioblastoma are there meaningful biomarkers for bevacizumab responsiveness and does their assessment provide additional information for tumor management and prognosis beyond that learned by standard histologic analysis?RecommendationLevel III: No established Bevacizumab biomarkers are currently available based upon the inclusion criteria of this guideline.

Duration of respiratory sample stability at -80ºC for SARS-CoV-2 PCR

Objective: To determine the stability of respiratory samples for SARS-CoV-2 PCR at standard laboratory ultra-freezer temperatures (-80°C). Methods: Five hundred and sixty-five archived, SARS-CoV-2 PCR positive patient specimens received at the Pathology Department of the Indus Hospital & Health Network between January 2021 and June 2021 were retested in June 2021. Samples had been stored at -70°C or below throughout this duration. Sample integrity following storage was assessed as the percentage of samples with reproducible results, and as consistency of cycle threshold (Ct) values between the original testing and the repeat testing. Results: Of the 565 samples evaluated in this study, 86% gave reproducible results upon retesting. However, there was no correlation between the duration of storage and result reproducibility, though the majority (69% for PCR Target-I and 78% for PCR Target-II respectively) of non-reproducible results had Ct values above 30. Similarly, there was a consistent increase of Ct values upon storage at ultra-freezer temperatures, though the effect again was more contingent upon freezing the sample in the ultra-freezer rather than the duration of storage. Conclusion: SARS-CoV-2 positive respiratory specimens for PCR can be stored for up to six months at -70°C or below without loss of sample integrity, though there is some loss of PCR-detected viral targets as evidenced by an immediate increased in the PCR-generated Ct values. In addition, samples with initial Ct values above 30 are more likely to give non-reproducible results. doi: https://doi.org/10.12669/pjms.38.ICON-2022.5777 How to cite this:Aijaz J, Naseer F, Dojki M, Jamal S. Duration of respiratory sample stability at -80ºC for SARS-CoV-2 PCR. Pak J Med Sci. 2022;38(2):393-398. doi: https://doi.org/10.12669/pjms.38.ICON-2022.5777 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Adherence to fecal immunochemical test screening among adults at average risk for colorectal cancer

Purpose This study examined adherence to screening for fecal immunochemical test (FIT). Methods Adults (≥ 50–75) with a FIT between 1/1/2014 and 6/30/2019 in MarketScan administrative claims were selected (index = earliest FIT). Patients were followed for 10 years pre- and 3 years post-index. Patients at increased risk for CRC or with prior screening were excluded. Year over year adherence was measured post-index. Results Of 10,253 patients, the proportion adherent to repeat testing at year 2 was 23.4% and 10.6% at year 3. Of 76.6% not adherent in year 2, 5.4% were adherent in year 3. Conclusion Results suggest adherence to FIT tests is poor, minimizing potential benefits. Future studies are needed to consider alternative test options and whether more choice will improve long-term adherence.

384. SARS-CoV-2 Surveillance Testing Patterns among Hospitalized Pediatric Patients in a Single Academic Medical Center

Background Children infected with SARS-CoV-2 often have mild or no symptoms, making symptom screening an ineffective tool for determining isolation precautions. As an infection control measure, universal pre-procedural and admission SARS-CoV-2 testing for pediatric patients was implemented in April and August 2020, respectively. Limited data exist on the utility screening programs in the pediatric population. Methods We performed a retrospective cohort study of pediatric patients (birth to 18 years) admitted to a tertiary care academic medical center from April 2020 to May 2021 that had one or more SARS-CoV-2 point-of-care or polymerase chain reaction tests performed. We describe demographic data, positivity rates and repeat testing trends observed in our cohort. Results A total of 2,579 SARS-CoV-2 tests were performed among 1,027 pediatric inpatients. Of these, 51 tests (2%) from 45 patients (4.3%) resulted positive. Community infection rates ranged from 4.5-60 cases/100,000 persons/day during the study period. Hispanic patients comprised 16% of the total children tested, but were disproportionately overrepresented (40%) among those testing positive (Figure1). Of 654 children with repeated tests, 7 (0.1%) converted to positive from a prior negative result. Median days between repeat tests was 12 (IQR 6-45), not necessarily performed during the same hospital stay. Five of these 7 patients had tests repeated &lt; 3 days from a negative result, of which only 2 had no history of recent infection by testing performed at an outside facility. Pre-procedural tests accounted for 35% of repeat testing, of which 0.9% were positive. Repeated tests were most frequently ordered for patients in hematology/oncology (35%) and solid organ transplant/surgical (33%) wards, each with &lt; 3% positive conversion rate. Notably, no hematopoietic stem cell transplant patients tested positive for SARS-CoV-2 during the study period. Pediatric SARS-CoV-2 Testing Distributed by Race/Ethnicity Conclusion The positivity rate of universal pre-procedural and admission SARS-CoV-2 testing in pediatric patients was low in our inpatient cohort. Tests repeated &lt; 3 days from a negative result were especially low yield, suggesting limited utility of this practice. Diagnostic testing stewardship in certain populations may be useful, especially as community infection rates decline. Disclosures Michael J. Smith, MD, M.S.C.E, Merck (Grant/Research Support)Pfizer (Grant/Research Support) Rebekah W. Moehring, MD, MPH, UpToDate, Inc. (Other Financial or Material Support, Author Royalties)

491. Persistence of SARS-CoV-2 Iinfection in Immunocompromised Children

Background The temporal dynamics of SARS-CoV-2 infectivity in immunocompromised children (IC) are unknown but may have important infection control implications. We evaluated SARS-CoV-2 viral persistence and assessed factors associated with viral persistence and cycle threshold (CT) values as a surrogate of viral load for IC. Methods We conducted a retrospective cohort study of SARS-CoV-2-positive IC at a large quaternary pediatric hospital from March 2020-2021. Immunocompromised status was defined as primary or secondary/acquired immunodeficiencies due to comorbidities or immunosuppressive treatment. The primary outcome was time to first-of-two consecutively negative SARS-CoV-2 PCR tests ≥ 24 hours apart. Polymerase chain reaction (PCR) testing of sequential patient samples was conducted using the Centers for Disease Control 2019-nCoV Real-Time RT-PCR Diagnostic Panel (CDC assay). Chi-square, Fisher exact, and Wilcoxon tests were used to compare demographic and clinical characteristics. Kaplan-Meier curve median event times and log-rank tests were used to compare outcomes. Subjects without 2 consecutive negative tests censored at the last test. Analyses were conducted using SAS v 9.4. Results Ninety-one children met inclusion criteria, and 67 children had more than 1 test (Figure 1). Median age was 15.5 years (IQR 8-18 yrs), 64% were male, 58% of children were white, and 43% were Latinx. Most (67%) were tested in outpatient settings, and 58% of children were asymptomatic. The median time to two negative tests was 42 days (IQR 25.0,55.0), with no difference in duration of positivity with specific diagnoses, degree of lymphopenia, or symptomatic vs asymptomatic illness. Five of 7 (71%) children with samples available for repeat testing had initial CT values &lt; 30, indicating a moderate to high viral load, and of these, 4 (57%) had repeat testing 21 to 30 days later with CT values &lt; 30 (Figure 2), suggesting persistence of moderate to high viral loads. Figure 1. Plot of immunocompromised children in cohort with positive SARS CoV2 PCR and subsequent testing (n = 67). Timelines of immunocompromised children in cohort with positive SARS CoV2 PCR and subsequent testing, grouped by immunocompromising condition. Each line represents an individual patient. Positive results are shown in light grey, negative results are shown in black. Figure 2. Plot of CT values from SARS-CoV-2 PCR testing over time among children with sequential samples available for retesting (n = 7) Plot of CT values (y axis) from SARS-CoV-2 PCR testing on the CDC assay over time (x axis) in days from initial positive test. Repeated testing which yielded a negative result on the CDC assay or intermittent negative results on clinical testing represented as CT value of 40. Each line represents a unique patient. Conclusion The median duration of viral persistence among IC with SARS-CoV-2 infection was 6 weeks, with no significant difference in immunocompromised diagnoses or clinical presentation, with over half of children with testing on the same platform having moderate to high viral loads after 3 weeks, suggesting potential transmission risk. Disclosures Samuel R. Dominguez, MD, PhD, BioFire Diagnostics (Consultant, Research Grant or Support)DiaSorin Molecular (Consultant)Pfizer (Grant/Research Support) Samuel R. Dominguez, MD, PhD, BioFire (Individual(s) Involved: Self): Consultant, Research Grant or Support; DiaSorin Molecular (Individual(s) Involved: Self): Consultant; Pfizer (Individual(s) Involved: Self): Grant/Research Support Suchitra Rao, MBBS, MSCS, BioFire (Research Grant or Support)

POC Programs: A Brief Survey on Critical Value Thresholds, Instrumentation, Repeat Testing, and Training Documentation

Introduction/Objective Across the United States, Point of Care (POC) programs oversee glucometer testing and are often expected to enforce thresholds for critical values, as well as provide guidance on repeat testing. Additionally, POC must track training and ongoing competency assessments of glucometer operators. Our aim was to survey POC across North America to capture the current state of variation in these POC functions, and identify opportunities for standardization. Methods/Case Report In July of 2021, an online survey was created on www.surveymonkey.com and distributed via the POC listserv of the American Association for Clinical Chemistry (AACC). The survey listed nine questions regarding instrumentation, threshold levels for critical-high and critical-low, policies on repeat testing, and practices around documentation and record retention. Results (if a Case Study enter NA) Of the 63 responses received, almost all (95.2%, n=60) indicated that their institution defines glucometer critical value thresholds. Of these, the most common threshold for critical-high was 400 mg/dL (44.4%, n=28) and for critical-low was 50 mg/dL (39.7%, n=25). A majority (55.5%, n=35) of programs require repeat testing of results that exceeded critical limits. The most popular POC result management software (50.8%, n=32) was RALS (Abbott Diagnostics, Chicago, IL) and the most popular glucometer (56%, n=23) was Roche Accu- Chek Inform II (Roche Diagnostics, Basel, Switzerland). Regarding institutions that disclosed training and competency documentation practices (93.7%, n=59), a majority (57.6%, n=34) used online-only storage, followed by hybrid online- paper storage (32.2%, n=19), and paper-only storage (10.2%, n=6). Conclusion Our brief survey has uncovered variations and insights that should raise queries on the feasibility of standardized critical value thresholds, as well as uniform recommendations for retesting critical values. We observed widespread adoption of middleware, as well as online record-keeping. We hope that our findings will trigger further discussions and follow-up studies by other researchers in the POC field.

Evaluation of indeterminate SARS-CoV-2 results with repeat testing on an alternative platform

Introduction/Objective Accurate SARS-CoV-2 results are crucial for patient management and infection prevention. Result confidence decreases with low viral load because near the assay’s limit of detection (LOD), test results may alternate between positive and negative, as characterized by Poisson distribution for target analytes at low density. Low positive results may indicate past infection, early infection, a vaccinated individual with low level viral shed, or a false-positive result. EUA methods provide guidance on test interpretation, but laboratories should assess clinical accuracy. The purpose of this study was to assess clinical accuracy of specimens with low positive results. Methods/Case Report Respiratory specimens were tested by Cepheid Xpert® Xpress SARS-CoV-2 assay with positive results up to a Ct of 45. A low positive (defined as Ct ≥35), which could not be confirmed by Hologic Aptima® SARS-CoV-2 assay was reported as indeterminate and repeat testing recommended. Repeat testing occurred by Cepheid, Hologic, BioFire, Roche, or Quest assays. Retrospectively, final results were extracted from the LIS (Epic Beaker, Madison, WI, version May 2020) for 5-months (12/1/2020 to 5/31/2021), and chart review performed. Results (if a Case Study enter NA) A total of 19,969 tests were performed; 10.4% (n=2,083) were positive, 89% (n=17,728) negative, and 0.79% (n=158) indeterminate. Previous infection (up to 3 months prior) was documented in 18% (n=28) of indeterminate results and defined as true positive. Of remaining indeterminate results, 43% (n=68) had repeat testing as recommended by laboratory; 26% (n=18) were positive and 74% (n=50) were negative. The average number of days between indeterminate and negative result was 7.25 (range 1-38). Conclusion Result discordance occurred in &lt; 1% of all samples, excellent agreement. For low positive samples, discordance was higher, as expected. It’s impossible to determine if negative results from the 50 repeat samples were false-positive by Cepheid or false-negative by other methods. In summary, 32% (50/158) of indeterminant samples did not repeat as positive. Overall concordance was high and results fluctuate when low virus is present. In absence of symptoms, we conclude repeat testing is not routinely recommended. Laboratories must recognize that normal variability occurs near assay LOD and must critically assess performance against other methods with similar LODs to fully assess performance of EUA methods.