Daily SARS-CoV-2 Nasal Antigen Tests Miss Infected and Presumably Infectious People Due to Viral Load Differences among Specimen Types

Creators: Winnett, Alexander Viloria; Akana, Reid; Shelby, Natasha; Davich, Hannah; Caldera, Saharai; Yamada, Taikun; Reyna, John Raymond B.; Romano, Anna E.; Carter, Alyssa M.; Kim, Mi Kyung; Thomson, Matt; Tognazzini, Colten; Feaster, Matthew; Goh, Ying-Ying; Chew, Yap Ching; Ismagilov, Rustem F.¹

1. California Institute of Technology

Abstract

In a recent household transmission study of SARS-CoV-2, we found extreme differences in SARS-CoV-2 viral loads among paired saliva, anterior nares swab (ANS), and oropharyngeal swab specimens collected from the same time point. We hypothesized these differences may hinder low-analytical-sensitivity assays (including antigen rapid diagnostic tests [Ag-RDTs]) by using a single specimen type (e.g., ANS) from reliably detecting infected and infectious individuals. We evaluated daily at-home ANS Ag-RDTs (Quidel QuickVue) in a cross-sectional analysis of 228 individuals and a longitudinal analysis (throughout infection) of 17 individuals enrolled early in the course of infection. Ag-RDT results were compared to reverse transcription-quantitative PCR (RT-qPCR) results and high, presumably infectious viral loads (in each, or any, specimen type). The ANS Ag-RDT correctly detected only 44% of time points from infected individuals on cross-sectional analysis, and this population had an inferred limit of detection of 7.6 × 10⁶ copies/mL. From the longitudinal cohort, daily Ag-RDT clinical sensitivity was very low (<3%) during the early, preinfectious period of the infection. Further, the Ag-RDT detected ≤63% of presumably infectious time points. The poor observed clinical sensitivity of the Ag-RDT was similar to what was predicted based on quantitative ANS viral loads and the inferred limit of detection of the ANS Ag-RDT being evaluated, indicating high-quality self-sampling. Nasal Ag-RDTs, even when used daily, can miss individuals infected with the Omicron variant and even those presumably infectious. Evaluations of Ag-RDTs for detection of infected or infectious individuals should be compared with a composite (multispecimen) infection status to correctly assess performance. Importance: We reveal three findings from a longitudinal study of daily nasal antigen rapid diagnostic test (Ag-RDT) evaluated against SARS-CoV-2 viral load quantification in three specimen types (saliva, nasal swab, and throat swab) in participants enrolled at the incidence of infection. First, the evaluated Ag-RDT showed low (44%) clinical sensitivity for detecting infected persons at all infection stages. Second, the Ag-RDT poorly detected (≤63%) time points that participants had high and presumably infectious viral loads in at least one specimen type. This poor clinical sensitivity to detect infectious individuals is inconsistent with the commonly held view that daily Ag-RDTs have near-perfect detection of infectious individuals. Third, use of a combination nasal-throat specimen type was inferred by viral loads to significantly improve Ag-RDT performance to detect infectious individuals.

Additional Information

© 2023 Viloria Winnett et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. We sincerely thank the study participants for making this work possible. We thank Lauriane Quenee, Grace Fisher-Adams, Junie Hildebrandt, Megan Hayashi, RuthAnne Bevier, Chantal D'Apuzzo, Ralph Adolphs, Victor Rivera, Steve Chapman, Gary Waters, Leonard Edwards, Gaylene Ursua, Cynthia Ramos, and Shannon Yamashita for their assistance and advice on study implementation and/or administration. We thank Jessica Leong, Ojas Pradhan, Si Hyung Jin, Emily Savela, Bridget Yang, Ekta Patel, Hsiuchen Chen, Paresh Samantaray, Zeynep Turan, Cindy Kim, Trinity Lee, Vanessa Mechan, Katherine Stiefel, Rosie Zedan, Rahulijeet Chadha, Minkyo Lee, and Jenny Ji for volunteering their time to help with this study. We thank Prabhu Gounder, Tony Chang, Jennifer Howes, and Nari Shin for their support with recruitment. Finally, we thank all the case investigators and contact tracers at the Pasadena Public Health Department and Caltech Student Wellness Services for their efforts in study recruitment and their work in the pandemic response. R.F.I. is a cofounder, consultant, and director and has stock ownership of Talis Biomedical Corp. All other authors declare that they have no competing interests. Conceptualization, M.F., Y.-Y.G., R.F.I., N.S., and A.V.W. Methodology, R.A., N.S., and A.V.W. Investigation, R.A., A.M.C., Y.C.C., S.C., H.D., M.K.K., J.R.B.R., A.E.R., N.S., A.V.W., and T.Y. Visualization, R.A., N.S., and A.V.W. Funding acquisition, R.F.I. and A.V.W. Project administration, R.F.I. and N.S. Supervision, Y.C.C. and R.F.I. Writing – original draft, R.A., N.S., and A.V.W. Writing – review & editing, R.A., A.M.C., R.F.I., A.E.R., N.S., and A.V.W. Detailed author contributions are given in the supplemental material. This work was supported in part by a grant from the Ronald and Maxine Linde Center for New Initiatives at the California Institute of Technology (to R.F.I.) and the Jacobs Institute for Molecular Engineering for Medicine at the California Institute of Technology (to R.F.I.). A.V.W. is supported by a UCLA DGSOM Geffen Fellowship.

Files

spectrum.01295-23-s0001.pdf

Files (7.0 MB)

Name	Size	Download all
spectrum.01295-23-s0001.pdf md5:8133925cfcecffc61e9d0b97caa8fb03	1.7 MB	Preview Download
spectrum.01295-23.pdf md5:d7c0be3552e614479b67e374e7051229	5.3 MB	Preview Download

Additional details

	All versions	This version
Views	0	0
Downloads	0	0
Data volume	0 Bytes	0 Bytes