A needle in the haystack? Assessing the significance of envelope (E) gene-negative, nucleocapsid (N2) gene-positive SARS-CoV-2 detection by the Cepheid Xpert Xpress SARS-COV-2 assay

•Controversy exists surrounding the clinical significance of high Crossing threshold (Ct) detections of SARS-CoV-2.•Single target detection of SARS-CoV-2 (E-target-negative, N2-target positive) by the Cepheid Xpert Xpress SARS-Cov-2 accounted for 3.9 % of positive detections during a period of high COVID-19 activity (15.4 % overall positivity).•Most patients with E-target-negative, N2-target-positive results were asymptomatic, but 25 % of those who underwent chest radiographic imaging had findings concerning for viral pneumonia suggesting subclinical infection.•E-target-negative, N2-target-positive results were present in 8 symptomatic patients with a new diagnosis of COVID-19.•Our findings suggest that the maximal PCR sensitivity is essential in hospital settings and that E-negative, N2-positive results can be significant. The clinical significance of high crossing threshold (Ct) detection of SARS-CoV-2 by RT-PCR is inadequately defined. In the course of universal admission screening with the Cepheid Xpert Xpress SARS-CoV-2 assay at our institution, we observed that 3.9 % (44/1123) of SARS-CoV-2 positive results were negative for the envelope (E) gene target but positive for the nucleocapsid (N2) target. The overall SARS-CoV-2 positivity rate during the three-month study period was 15.4 % (1123/7285), spanning April-June 2020. The majority of patients with E-negative, N2-positive results were asymptomatic, with 29.5 % of patients symptomatic for COVID-19 at the time of presentation. Asymptomatic patients with E-negative, N2-positive results were significantly younger than symptomatic patients with the same results (average 37.6 vs. 58.4, p = 0.003). Similar proportions of prior SARS-CoV-2 positivity were noted among symptomatic and asymptomatic individuals (38.5 % vs. 33.3 %, p = 0.82). Among the 16 asymptomatic patients with radiographic imaging performed, four (25 %) had chest radiographic findings concerning for viral pneumonia. Interestingly, we observed an E-negative, N2-positive result in one patient with a previous SARS-CoV-2 by the Xpert Xpress that occurred 71 days prior. Critically, E-negative, N2-positive results were observed in 8 symptomatic patients with a new diagnosis of COVID-19. Thus, though concerns remain about extended SARS-CoV-2 RT-PCR positivity in some patients, the ability of clinical laboratories to detect patients with high Ct values (including E-negative, N2-positive results) is vital for retaining maximal sensitivity for diagn