Longitudinal assessment of diagnostic test performance over the course of acute SARS-CoV-2 infection

Smith, Rebecca L; Gibson, Laura L; Martinez, Pamela P; Ke, Ruian; Mirza, Agha; Conte, Madison; Gallagher, Nicholas; Conte, Abigail; Wang, Leyi; Fredrickson, Richard; Edmonson, Darci C; Baughman, Melinda E; Chiu, Karen K; Choi, Hannah; Jensen, Tor W; Scardina, Kevin R; Bradley, Shannon; Gloss, Stacy L; Reinhart, Crystal; Yedetore, Jagadeesh; Owens, Alyssa N; Broach, John; Barton, Bruce; Lazar, Peter; Henness, Darcy; Young, Todd; Dunnett, Alastair; Robinson, Matthew L; Mostafa, Heba H; Pekosz, Andrew; Manabe, Yukari C; Heetderks, William J; McManus, David D; Brooke, Christopher B

BACKGROUND: Serial screening is critical for restricting spread of SARS-CoV-2 by facilitating the timely identification of infected individuals to interrupt transmission chains. The variation in sensitivity of different diagnostic tests at different stages of infection has not been well documented. METHODS: This is a longitudinal study of 43 adults newly infected with SARS-CoV-2. All participants provided daily samples for saliva and nasal swab RTqPCR, Quidel SARS Sofia antigen FIA, and live virus culture. RESULTS: We show that both RTqPCR and the Quidel SARS Sofia antigen FIA peak in sensitivity during the period in which live virus is detected in nasal swabs, but the sensitivity of RTqPCR tests rises more rapidly prior to this period. We also estimate the sensitivities of RTqPCR and antigen tests as a function of testing frequency. CONCLUSIONS: RTqPCR tests are more effective than antigen tests at identifying infected individuals prior to or early during the infectious period and thus for minimizing forward transmission (given timely results reporting). All tests showed >98% sensitivity for identifying infected individuals if used at least every three days. Daily screening using antigen tests can achieve ~90% sensitivity for identifying infected individuals while they are viral culture positive.