Analytical sensitivity and efficiency comparisons of SARS-COV-2 qRT-PCR primer-probe sets

Vogels, Chantal B.F.; Brito, Anderson F.; Wyllie, Anne Louise; Fauver, Joseph R; Ott, Isabel M.; Kalinich, Chaney C.; Petrone, Mary E.; Casanovas-Massana, Arnau; Muenker, M. Catherine; Moore, Adam J.; Klein, Jonathan; Lu, Peiwen; Lu-Culligan, Alice; Jiang, Xiaodong; Kim, Daniel J.; Kudo, Eriko; Mao, Tianyang; Moriyama, Miyu; Oh, Ji Eun; Park, Annsea; Silva, Julio; Song, Eric; Takehashi, Takehiro; Taura, Manabu; Tokuyama, Maria; Venkataraman, Arvind; Weizman, Orr-El; Wong, Patrick; Yang, Yexin; Cheemarla, Nagarjuna R.; White, Elizabeth; Lapidus, Sarah; Earnest, Rebecca; Geng, Bertie; Vijayakumar, Pavithra; Odio, Camila; Fournier, John; Bermejo, Santos; Farhadian, Shelli; Dela Cruz, Charles; Iwasaki, Akiko; Ko, Albert I.; Landry, Marie-Louise; Foxman, Ellen F.; Grubaugh, Nathan D.

The recent spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exemplifies the critical need for accurate and rapid diagnostic assays to prompt clinical and public health interventions. Currently, several quantitative reverse-transcription polymerase chain reaction (qRT-PCR) assays are being used by clinical, research, and public health laboratories. However, it is currently unclear if results from different tests are comparable. Our goal was to evaluate the primer-probe sets used in four common diagnostic assays available on the World Health Organization (WHO) website. To facilitate this effort, we generated RNA transcripts to be used as assay standards and distributed them to other laboratories for internal validation. We then used (1) RNA transcript standards, (2) full-length SARS-CoV-2 RNA, (3) pre-COVID-19 nasopharyngeal swabs, and (4) clinical samples from COVID-19 patients to determine analytical efficiency and sensitivity of the qRT-PCR primer-probe sets. We show that all primer-probe sets can be used to detect SARS-CoV-2 at 500 virus copies per reaction, except for the RdRp-SARSr (Charite) confirmatory primer-probe set which has low sensitivity. Our findings characterize the limitations of currently used primer-probe sets and can assist other laboratories in selecting appropriate assays for the detection of SARS-CoV-2.