Comparison of RT-PCR and antigen test sensitivity across nasopharyngeal, nares, and oropharyngeal swab, and saliva sample types during the SARS-CoV-2 omicron variant

Gregory L Damhorst; Jessica Lin; Jennifer K Frediani; Julie A Sullivan; Adrianna Westbrook; Kaleb McLendon; Tyler J Baugh; William H O'Sick; John D Roback; Anne L Piantadosi; Jesse J Waggoner; Leda Bassit; Anuradha Rao; Morgan Greenleaf; Jared W O'Neal; Seegar Swanson; Nira R Pollock; Greg S Martin; Wilbur A Lam; Joshua M Levy

doi:10.1016/j.heliyon.2024.e27188

Comparison of RT-PCR and antigen test sensitivity across nasopharyngeal, nares, and oropharyngeal swab, and saliva sample types during the SARS-CoV-2 omicron variant

Heliyon. 2024 Feb 29;10(6):e27188. doi: 10.1016/j.heliyon.2024.e27188. eCollection 2024 Mar 30.

Authors

Gregory L Damhorst^{1

2}, Jessica Lin^{1

3}, Jennifer K Frediani^{1

4}, Julie A Sullivan^{1

5}, Adrianna Westbrook^{1

6}, Kaleb McLendon^{1

7}, Tyler J Baugh^{1

7}, William H O'Sick^{1

7}, John D Roback^{1

7}, Anne L Piantadosi^{1

2

7}, Jesse J Waggoner^{1

2}, Leda Bassit^{1

8}, Anuradha Rao^{1

5}, Morgan Greenleaf¹, Jared W O'Neal^{1

9}, Seegar Swanson¹, Nira R Pollock^{1

10}, Greg S Martin^{1

9}, Wilbur A Lam^{1

3

5

11}, Joshua M Levy^{1

12

13}

Affiliations

¹ Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Emory University, USA.
² Division of Infectious Diseases, Emory University School of Medicine, USA.
³ Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, USA.
⁴ Nell Hodgson Woodruff School of Nursing, Emory University, USA.
⁵ Department of Pediatrics, Emory University School of Medicine, USA.
⁶ Pediatric Biostatistics Core, Department of Pediatrics, Emory University School of Medicine, USA.
⁷ Department of Pathology and Laboratory Medicine, Emory University School of Medicine, USA.
⁸ Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, USA.
⁹ Emory University School of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, USA.
¹⁰ Department of Laboratory Medicine, Boston Children's Hospital, USA.
¹¹ Aflac Cancer and Blood Disorders Center of Children's Healthcare of Atlanta, USA.
¹² Emory University School of Medicine, Department of Otolaryngology-Head and Neck Surgery, USA.
¹³ Sinonasal and Olfaction Program, National Institute on Deafness and Other Communication Disorders, NIDCD/NIH.

Abstract

Limited data highlight the need to understand differences in SARS-CoV-2 omicron (B.1.1.529) variant viral load between the gold standard nasopharyngeal (NP) swab, mid-turbinate (MT)/anterior nasal swabs, oropharyngeal (OP) swabs, and saliva. MT, OP, and saliva samples from symptomatic individuals in Atlanta, GA, in January 2022 and longitudinal samples from a small familial cohort were tested by both RT-PCR and ultrasensitive antigen assays. Higher concentrations in the nares were observed in the familial cohort, but a dominant sample type was not found among 39 cases in the cross-sectional cohort. The composite of positive MT or OP assay for both RT-PCR and antigen assay trended toward higher diagnostic yield but did not achieve significant difference. Our data did not identify a singular preferred sample type for SARS-CoV-2 testing, but higher levels of saliva nucleocapsid, a trend toward higher yield of composite OP/MT result, and association of apparent MT or OP predominance with symptoms warrant further study.

Keywords: COVID-19 testing; Point of care testing; SARS-CoV-2; SARS-CoV-2 variants.

Grants and funding

UL1 TR002378/TR/NCATS NIH HHS/United States