When rare becomes common: N2 gene-positive, E gene-negative SARS-CoV-2 PCR results between 2021 and 2022

Frank Bernhard Kraus; Stefan Moritz; Könül Mamadova; Mario Popp; Marija Kocijancic; Beatrice Ludwig-Kraus

doi:10.1016/j.jcvp.2023.100152

When rare becomes common: N2 gene-positive, E gene-negative SARS-CoV-2 PCR results between 2021 and 2022

J Clin Virol Plus. 2023 Jun;3(2):100152. doi: 10.1016/j.jcvp.2023.100152. Epub 2023 May 12.

Authors

Frank Bernhard Kraus¹, Stefan Moritz², Könül Mamadova¹, Mario Popp², Marija Kocijancic¹, Beatrice Ludwig-Kraus¹

Affiliations

¹ Department for Laboratory Medicine, Central Laboratory, University Hospital Halle, Ernst Grube Str. 40, Halle Saale, Sachsen-Anhalt 06120, Germany.
² Section of Clinical Infectious Diseases, University Hospital Halle, Halle, Sachsen-Anhalt, Germany.

Abstract

Nucleocapsid gene-positive, envelope gene-negative (N2+/E-) SARS-CoV-2 PCR results obtained with the Cepheid Xpert Xpress SARS-CoV-2 assay are an infrequent phenomenon. We assessed the validity of the N2+/E- cases with an indirect approach by analyzing their occurrence in relation to overall positive PCR rates and absolute number of PCR tests (24,909 samples, collected June 2021 to July 2022). Additionally, 3022 samples were analyzed with the Xpert Xpress CoV-2-plus assay in August/September 2022. The incidence of monthly N2+/E- cases closely followed the overall frequency of positive tests (p < 0.001), while there was no correlation with the monthly number of PCR test. The observed distribution of N2+/E- cases implicates, that they are not merely artefacts, but rather represent samples with a very low viral load. This phenomenon will persist with the Xpert Xpress SARS-CoV-2 plus assay, which also produced more than 10% results where only one target gene replicated with a very high Ct value.

Keywords: COVID-19; N2 gene; RT-PCR; SARS-CoV-2; Xpert Xpress CoV-2 plus; Xpert Xpress SARS-CoV-2.