Analytical and clinical performances of seven direct detection assays for SARS-CoV-2

Yasufumi Matsumura; Wataru Yamazaki; Taro Noguchi; Masaki Yamamoto; Miki Nagao

doi:10.1016/j.jcvp.2023.100138

Analytical and clinical performances of seven direct detection assays for SARS-CoV-2

J Clin Virol Plus. 2023 Feb;3(1):100138. doi: 10.1016/j.jcvp.2023.100138. Epub 2023 Jan 13.

Authors

Yasufumi Matsumura¹, Wataru Yamazaki², Taro Noguchi¹, Masaki Yamamoto¹, Miki Nagao¹

Affiliations

¹ Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, 54 Shogoin-kawaharacho, Sakyo-ku, Kyoto, 6068507, Japan.
² Center for Southeast Asian Studies, Kyoto University, 46 Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto, 6068501, Japan.

Abstract

Background: Direct detection tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that bypass complicated nucleic acid/antigen purification steps are promising tools for the rapid diagnosis of coronavirus disease 2019 (COVID-19).

Methods: To determine the analytical and clinical diagnostic performances of the direct detection assays, we compared 6 direct molecular detection assays, including two loop-mediated isothermal amplification (LAMP) assays and one lateral flow antigen assay, against the reference extraction-based RT-PCR assay using 183 respiratory samples (87 nasopharyngeal swabs, 51 saliva samples, and 45 sputum samples).

Results: Analytical sensitivity analysis showed that the direct RT-PCR assay of Toyobo exhibited the lowest LOD of 1,000 copies/mL. Compared with the 80 positive and 103 negative samples based on the reference assay, the Toyobo assay had the highest positive percent agreement (PPA) of 96.3%, followed by the two direct RT-PCR assays of Takara and Shimadzu and one LAMP assay of Eiken (86.3-87.5%). The Fujirebio antigen assay had the lowest PPA of 44.7% among the assays tested. The negative percent agreement of these direct detection assays was 100%, except for the Eiken assay (96.3%).

Conclusions: Large differences in PPA existed among the direct detection tests. Laboratories need to take these characteristics into consideration before implementing these assays.

Keywords: Direct detection; Lateral flow antigen assay; RT-PCR; SARS-CoV-2.