Background Antigen testing offers rapid and inexpensive testing for SARS-CoV-2 but concerns regarding performance, especially sensitivity, remain. Limited data exists for use of antigen testing in asymptomatic patients; thus, performance and reliability of antigen testing remains unclear. Methods 148 symptomatic and 144 asymptomatic adults were included. A nasal swab was collected for testing by Quidel Sofia SARS IFA (Sofia) as point of care. A nasopharyngeal swab was also collected and transported to the laboratory for testing by Cepheid Xpert Xpress SARS-CoV-2/Flu/RSV RT-PCR (Cepheid). Results Overall, Sofia had good agreement with Cepheid (> 95%) in adults, however was less sensitive. Sofia had a sensitivity of 87.8% and 33.3% for symptomatic and asymptomatic patients, respectively. Among symptomatic patients, testing > 5 days post symptom onset resulted in lower sensitivity (82%) when compared with testing within 5 days of symptom onset (90%). Of the four Sofia false-negative results in the asymptomatic cohort, 50% went on to develop COVID-19 disease within 5 days of testing. Specificity in both symptomatic and asymptomatic cohorts was 100%. Conclusions Sofia has acceptable performance in symptomatic adults when tested < 5 days of symptom onset. Caution should be taken when testing patients with ≥ 5 days of symptoms. The combination of low prevalence and reduced sensitivity results in relatively poor performance of in asymptomatic patients. NAAT-based diagnostic assays should be considered in when antigen testing is unreliable, particularly in symptomatic patients with > 5 days of symptom onset and asymptomatic patients.

At the time of writing, the world continues to witness the extraordinarily rapid evolution and selection of SARS-CoV-2, with the Omicron variants comprising five lineages known as BA.1, BA.2, BA.3, BA.4, and BA.5. 1 The Omicron variant shows a large number of mutations leading to amino-acid changes, which are widely distributed on many structural and nonstructural regions of SARS-CoV-2. 2 The spike protein of the Omicron variant is characterized by at least 32 amino acid substitutions, some small deletions, and insertions. 2 From the beginning of the COVID-19 pandemics, a large number of SARS-CoV-2 whole-genome sequences have been generated from all around the world and shared, mostly through GISAID (https://www.gisaid.org/). 3 Pyrosequencing has played an important role to discover and track the spread of SARS-CoV-2 variants having a large number of mutations nearly in real-time by worldwide genome sequencing efforts. 3,4 Unsurprisingly, given the vaccine-and prior infection-driven selection pressures, many of the changes are located in the receptor-binding domain of the spike protein that are important for virus-host cell interaction mediated by ACE-2 receptor. 5 In the virus-host cell interaction, the nucleocapsid protein binds directly to host mRNAs in cells and suppresses the physiological stress response of host cells. 6 Of note, these mutations are associated with more efficient cell entry, immune escape, and increased infectivity of the Omicron variant. 7 BA.1 was first found in southern Africa in November 2021 during the investigation of an unexplained burst in positive case numbers. 8 BA.1 was reported to be associated with an Sgene target failure or SGTF (also called S-gene dropout) on the Thermo Fisher TaqPath COVID-19 RT-PCR assay because of the small deletion at the positions 69 and 70 in the spike gene. 7 After the initial discovery, BA.1 had spread rapidly and WHO estimated that this variant was already in most countries. 9 The United Kingdom reported the first death associated with BA.1 infection. 10 In the United States, BA.1 displaced Delta to become the predominant variant, accounting for more than 98% by the end of January 2022 (https://covid.cdc.gov/covid-datatracker/#variant-proportions). Chen et al. 11 reported low neutralizing antibodies against the Omicron variant, even at 3-to 5-week postvaccination. 11 | 4053 BA.5 have the del69-70 in the spike gene (https://cov-lineages.org/ lineage_list.html). Therefore, BA.3 through BA.5 are positive for del69-70 and negative for ins214EPE tested by the RT-PCR BA.1 assay. It is obvious that the "del69-70 negative/ins214EPE negative" result or the "del69-70 positive/ins214EPE negative" result can be used as a rapid proxy to flag potential BA.2 or BA.3 through BA.5 cases, respectively. Omicron BA.4 and BA.5 are new variants, which were first discovered in Botswana and South Africa (https://www.afro.who.int/ news/botswana-south-africa-deepen-probe-new-omicron-sub-variants). According to the World Health Organization, BA.4 and BA.5 are circulating at lo...

The first case of the new SARS-CoV-2 Omicron Variant of Concern (VOC) from South Africa was reported to WHO on November 24, 2021.…

A new SARS-CoV-2 Omicron (B.1.1.529) Variant of Concern has been emerging worldwide. We are seeing an unprecedented surge in patients due to Omicron in this COVID-19 pandemic. A rapid and accurate molecular test that effectively differentiates Omicron from other SARS-CoV-2 variants would be important for both epidemiologic value and for directing variant-specific therapies such as monoclonal antibody infusions. In this study, we developed a real-time RT-PCR assay for the qualitative detection of Omicron from routine clinical specimens sampling the upper respiratory tract. The limit of detection of the SARS-CoV-2 Omicron variant RT-PCR assay was 2 copies/μl. Notably, the assay did not show any cross-reactivity with other SARS-CoV-2 variants including Delta (B.1.617.2). This SARS-CoV-2 Omicron variant RT-PCR laboratory-developed assay is sensitive and specific to detect Omicron in nasopharyngeal and nasal swab specimens.

Limitations in timely testing for SARS-CoV-2 drive the need for new approaches in suspected COVID-19 disease. We queried whether viral load (VL) in the upper airways at presentation could improve the management and diagnosis of patients. This study was conducted in a 9 hospital system in Allegheny County, Pennsylvania between March 1-August 31 2020. Viral load was determined by PCR assays for patients presenting to the Emergency Departments (ED), community pediatrics practices and college health service. We found that for the ED patients, VL did not vary substantially between those admitted and not. VL was relatively equivalent across ages, except for the under 25 age groups that tended to present with higher loads. To determine if rapid antigen testing (RAT) could aid diagnosis in certain populations, we compared BD Veritor and Quidel Sofia to SOC PCR-based tests. The antigen assay provided a disease-detection sensitivity of >90% in a selection of 32 positive students and was modeled to have an 80% sensitivity in all positive students. In the outpatient pediatric population, the antigen assay detected 70% of PCR-positives. Extrapolating these findings to viral loads in older hospitalized patients, a minority would be detected by RAT (40%). Higher loads did correlate with death, though the prognostic value was marginal (ROC AUC of only 0.66). VL did not distinguish between those needing mechanical ventilation and routine inpatients. We conclude that VL in upper airways, while not prognostic for disease management, may aid in selecting proper testing methodologies for certain patient populations.