Development of the one-step qualitative RT-PCR assay to detect SARS-CoV-2 Omicron (B.1.1.529) variant in respiratory specimens

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/l. 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.

Evaluation of the Cepheid Xpert Xpress SARS-CoV-2 test for bronchoalveolar lavage

Accurate and rapid laboratory tests are essential for the prompt diagnosis of COVID-19, which is important to patients and infection control. The Xpert Xpress SARS-CoV-2 test is a real-time RT-PCR intended for the qualitative detection of nucleic acid from SARS-CoV-2 in upper respiratory specimens. In this study, we assessed the analytical and clinical performance characteristics of this rapid test for SARS-CoV-2 in 60 bronchoalveolar lavage (BAL) specimens. BAL is a specimen type that is not authorized under EUA for the Xpert Xpress SARS-CoV-2 test. The limit of detection of the Xpert Xpress SARS-CoV-2 test was 500 copies/ml. The overall agreement of the Xpert Xpress SARS-CoV-2 test was 100%. The Xpert Xpress SARS-CoV-2 test is sensitive and specific to aid in diagnosis of COVID-19 using bronchoalveolar lavage.

Evaluation of viral loads in patients with SARS-CoV-2 Delta variant infection: Higher loads do not translate into different testing scenarios

The Delta SARS-CoV-2 variant is very infectious, and it is spreading quickly during this pandemic. In the study, we compared viral loads in surging cases infected with the SARS-CoV-2 Delta variant in the fourth wave of COVID-19 with the three prior waves. The data comprised viral loads from positive cases detected within the UPMC health care system in Allegheny County, Pennsylvania. A total of 2,059 upper airway samples were collected and tested for SARS-CoV-2 positive by RT-PCR during March 2020-September 2021. We did not observe significant difference in viral load difference between the third (December 2020 - January 2021) and fourth (June 2021 - September 2021) waves; however, they had the higher viral load than the first (March 2020 - June 2020) and second waves (June 2020 - August 2020). We did find an age-related effect with the elderly presenting with lower viral loads, which was also seen in the earlier waves. However, the level of viral load in the fourth wave was not sufficient higher to qualitatively change our expected detected rates using various testing modalities.

Differences in detected viral loads guide use of SARS-CoV-2 antigen-detection assays towards symptomatic college students and children.

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.