Anatomical Site, Viral Ribonucleic Acid Abundance, and Time of Sampling Correlate With Molecular Detection of Severe Acute Respiratory Syndrome Coronavirus 2 During Infection
Author:
Lantry F Julian123, Epsi Nusrat J13, Pollett Simon D13, Simons Mark P1, Lindholm David A24, Colombo Rhonda E135, Fries Anthony C6, Maves Ryan C17, Ganesan Anuradha138, Utz Gregory C137, Lalani Tahaniyat139ORCID, Smith Alfred G9, Mody Rupal M10, Colombo Christopher J25, Chi Sharon W1311, Madar Cristian11, Huprikar Nikhil812, Larson Derek T12, Bazan Samantha13, Broder Christopher C2, Laing Eric D2, English Caroline13, Lanteri Charlotte1, Mende Katrin134, Tribble David R1, Agan Brian K13, Burgess Timothy H1, Richard Stephanie A13ORCID, Cowden J, Darling M, Merritt T, Wellington T, Rutt A, Chambers S, Robb-McGrath W, Berjohn C, Kirkland N, Broder C, Byrne C, Fritschlanski M, Hickey P, Laing E, Livezey J, Parmelee E, Rusiecki J, Scher A, Barton B, Hostler D, Hostler J, Lago K, Maldonado C, Wayman M, DeLeon S, Lindholm D, Markelz A, Mende K, Merritt S, Turner N, Darnall R, Bazan S, Love P K, Dimascio-Johnson N, Ewers E, Gallagher K, Larson D, Blair P, Chenoweth J, Clark D, Colombo C J, Colombo R, Conlon C, Everson K, Faestel P, Ferguson T, Gordon L, Grogan S, Lis S, Mount C, Musfeldt D, Odineal D, Perreault M, Sainato R, Schofield C, Skinner C, Stein M, Switzer M, Timlin M, Wood S, Banks S, Carpenter R, Kim L, Kronmann K, Lalani T, Lee T, Smith A, Smith R, Tant R, Warkentien T, Cammarata S, Maves R, Utz G, Chi S, Flanagan R, Jones M, Lucas C, Madar C, Miyasato K, Uyehara C, Agan B, Andronescu L, Austin A, Burgess T, Chung K, Davies J, English C, Epsi N, Fox C, Grother M, Hadley A, Lanteri C, Malloy A, Mohammed R, Morales C, Nwachukwu P, Olsen C, Pollett S, Richard S, Rozman J, Samuels E, Sanchez M, Simons M, Snow A, Telu K, Tribble D, Ulomi L, Chapleau R, Fries A, Harrington C, Huntsberger S, Purves S, Reynolds K, Rodriguez J, Starr C, Mehrer J, Hunter T, Mejia J, Mody R, Resendez R, Sandoval P, Barahona I, Baya A, Ganesan A, Huprikar N, Johnson B, Peel S,
Affiliation:
1. Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA 2. Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA 3. The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA 4. Brooke Army Medical Center, Joint Base San Antonio-Fort Sam Houston, Texas, USA 5. Madigan Army Medical Center, Joint Base Lewis-McChord, Washington, USA 6. US Air Force School of Aerospace Medicine, Wright-Patterson, Ohio, USA 7. Naval Medical Center San Diego, San Diego, California, USA 8. Walter Reed National Military Medical Center, Bethesda, Maryland, USA 9. Naval Medical Center Portsmouth, Portsmouth, Virginia, USA 10. William Beaumont Army Medical Center, El Paso, Texas, USA 11. Tripler Army Medical Center, Honolulu, Hawaii, USA 12. Fort Belvoir Community Hospital, Fort Belvoir, Virginia, USA 13. Carl R. Darnall Army Medical Center, Fort Hood, Texas, USA
Abstract
Abstract
Background
Nasopharyngeal (NP) swabs are the standard for SARS-CoV-2 diagnosis. If less invasive alternatives to NP swabs (eg, oropharyngeal [OP] or nasal swabs [NS]) are comparably sensitive, the use of these techniques may be preferable in terms of comfort, convenience, and safety.
Methods
This study compared the detection of SARS-CoV-2 in swab samples collected on the same day among participants with at least one positive PCR test.
Results
Overall, 755 participants had at least one set of paired swabs. Concordance between NP and other swab types was 75% (NS), 72% (OP), 54% (rectal swabs [RS]), and 78% (NS/OP combined). Kappa values were moderate for the NS, OP, and NS/OP comparisons (0.50, 0.45, and 0.54, respectively). Highest sensitivity relative to NP (0.87) was observed with a combination of NS/OP tests (positive if either NS or OP was positive). Sensitivity of the non-NP swab types was highest in the first week postsymptom onset and decreased thereafter. Similarly, virus RNA quantity was highest in the NP swabs as compared with NS, OP, and RS within two weeks postsymptom onset. OP and NS performance decreased as virus RNA quantity decreased. No differences were noted between NS specimens collected at home or in clinic.
Conclusions
NP swabs detected more SARS-CoV-2 cases than non-NP swabs, and the sensitivity of the non-NP swabs decreased with time postsymptom onset. While other swabs may be simpler to collect, NP swabs present the best chance of detecting SARS-CoV-2 RNA, which is essential for clinical care as well as genomic surveillance.
Funder
Defense Health Program National Institute of Allergy and Infectious Diseases National Institutes of Health
Publisher
Oxford University Press (OUP)
Subject
Infectious Diseases,Oncology
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