A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance.

More than one year into a global pandemic, SARS-CoV-2 is now defined by a variety of rapidly evolving variant lineages. Several FDA authorized molecular diagnostic tests have been impacted by viral variation, while no reports of viral variation affecting antigen test performance have occurred to date. While determining the analytical sensitivity of the Quidel Sofia SARS Antigen FIA test (Sofia 2), we uncovered a high viral load specimen that repeatedly tested negative by this antigen test. Whole genome sequencing of the specimen uncovered two mutations, T205I and D399N, present in the nucleocapsid protein of the isolate. All six SARS-CoV-2 positive clinical specimens available in our laboratory with a D399N nucleocapsid mutation and CT < 31 were not detected by the Sofia 2 but detected by the Abbott BinaxNOW COVID-19 Ag Card, while clinical specimens with the T205I mutation were detected by both assays. Testing of recombinant SARS-CoV-2 nucleocapsid with these variants demonstrated an approximate 1000-fold loss in sensitivity for the Quidel Sofia SARS Antigen FIA test associated with the D399N mutation, while the BinaxNOW and Quidel Quickvue SARS Antigen tests were unaffected by the mutation. The D399N nucleocapsid mutation has been relatively uncommon to date, appearing in only 0.02% of genomes worldwide at time of writing. Our results demonstrate how routine pathogen genomics can be integrated into the clinical microbiology laboratory to investigate diagnostic edge cases, as well as the importance of profiling antigenic diversity outside of the spike protein for SARS-CoV-2 diagnostics.

Low Prevalence of Severe Acute Respiratory Syndrome Coronavirus 2 Among Pregnant and Postpartum Patients With Universal Screening in Seattle, Washington.

We found low prevalence of SARS-CoV-2 (2.7% [5/188]) among pregnant and postpartum patients with universal testing. Prevalence among symptomatic patients was similar under initial targeted screening (22.2% [4/18]) and universal approaches (19.1% [8/42]). Among 170 asymptomatic patients, 2 were positive or inconclusive, respectively; repeat testing at 24 hours was negative.

Coping With COVID-19.

OBJECTIVES: The first coronavirus disease 2019 (COVID-19) case in the United States was reported in Washington State. The pandemic caused drastic disruptions to medical institutions, including medical education. The Department of Laboratory Medicine at the University of Washington responded by rapidly implementing substantial changes to medical student clerkships. METHODS: In real time, we converted one ongoing case- and didactic-based course, LabM 685, to remote learning. RESULTS: Fifteen of 17 scheduled sessions proceeded as planned, including two sessions for student presentations. Two didactics were canceled as the functions of the teleconferencing platform were not sufficient to proceed. One grand rounds speaker canceled due to COVID-19 precautions. Elements of an immersive clinical laboratory clerkship, LabM 680, were repurposed to accommodate 40 medical students per class via remote learning, highlighting clinical laboratory activities that continue throughout the outbreak. A new remote clerkship, MedSci 585C, was developed incorporating distance learning and guided small-group sessions. This coincided with parallel efforts to make resident and fellow service work, conferences, and didactics available remotely to comply with social distancing. CONCLUSIONS: The changes in medical education described reflect the dynamic interplay of current events affecting the world of clinical pathology. Throughout this, technology-while with some limitations-has provided the platform for innovative learning.

Laboratory Perspective on Racial Disparities in Sexually Transmitted Infections.

BACKGROUND: Rates of sexually transmitted infections (STI) have risen steadily in recent years, and racial and ethnic minorities have borne the disproportionate burden of STI increases in the United States. Historical inequities and social determinants of health are significant contributors to observed disparities and affect access to diagnostic testing for STI. CONTENT: Public health systems rely heavily on laboratory medicine professionals for diagnosis and reporting of STI. Therefore, it is imperative that clinicians and laboratory professionals be familiar with issues underlying disparities in STI incidence and barriers to reliable diagnostic testing. In this mini-review, we will summarize contributors to racial/ethnic disparity in STI, highlight current epidemiologic trends for gonorrhea, chlamydia, and syphilis, discuss policy issues that affect laboratory and public health funding, and identify specific analytic challenges for diagnostic laboratories. SUMMARY: Racial and ethnic disparities in STI in the US are striking and are due to complex interactions of myriad social determinants of health. Budgetary cuts for laboratory and public health services and competition for resources during the COVID-19 pandemic are major challenges. Laboratory professionals must be aware of these underlying issues and work to maximize efforts to ensure equitable access to diagnostic STI testing for all persons, particularly those most disproportionately burdened by STI.