key: cord-0724738-04gwxo4b authors: Pinninti, Swetha; Trieu, Connie; Pati, Sunil K; Latting, Misty; Cooper, Joshua; Seleme, Maria C; Boppana, Sushma; Arora, Nitin; Britt, William J; Boppana, Suresh B title: Comparing Nasopharyngeal and Mid-Turbinate Nasal Swab Testing for the Identification of SARS-CoV-2 date: 2020-06-29 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa882 sha: 5a5e4fde45c13908f448965f7380540da4a3c96f doc_id: 724738 cord_uid: 04gwxo4b Testing of paired mid-turbinate (MT) nasal and nasopharyngeal (NP) swabs, collected by trained personnel from 40 patients with COVID-19 showed more NP (76/95, 80%) than MT swabs tested positive (61/95, 64%; p=0.02). Among samples collected a week after study enrollment, fewer MT than NP samples were positive (45% vs 76%; p=0.001). A c c e p t e d M a n u s c r i p t 3 Initial reports of pneumonia caused by a novel coronavirus, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), and the infection referred to as COVID-19, were reported from Wuhan, China in December 2019 [1, 2] . COVID-19 has since been declared a pandemic and has been reported in almost all regions across the globe, contributing to significant mortality, morbidity, and economic losses. Use of nasopharyngeal samples for the detection of respiratory viruses is considered the standard of care. However, the Centers for Disease Control and Prevention (CDC) [3] and the Infectious Disease Society of America (IDSA) [4] currently recommend testing of NP, mid-turbinate nasal (MT), anterior nares, oropharyngeal and saliva swabs or washes from upper or lower respiratory tract for SARS-CoV-2 by reverse transcription (RT)-PCR based on limited data [5] [6] [7] . Moreover, MT swab testing is gaining wider acceptance due to the ease of sample collection, ability to self-collect and personal protective equipment may not be needed [8] . However, few studies have directly compared the reliability of NP and MT swabs for the detection of SARS-CoV-2 RNA [9] . The objective of this study is to determine whether MT swabs are comparable to NP swabs in detecting SARS-CoV-2 by RT-PCR in patients with confirmed COVID-19. Subjects and Specimens: All hospitalized patients with confirmed COVID-19 infection were eligible for participation in the study and 40 hospitalized patients with COVID-19 were enrolled in a prospective study between April 5 and May 16, 2020, from whom serial NP and MT nasal swabs were collected weekly and analyzed by RT-PCR. Both swabs were collected by the same medical provider from both nares. Demographic data and clinical characteristics for the study participants were collected from electronic medical records. The research A c c e p t e d M a n u s c r i p t 4 protocol was approved by the Institutional Review Board for Human Use and an informed consent was obtained from all study participants or their legally authorized representatives. Specimen collection and processing: Paired MT and NP swabs were collected at enrollment and weekly thereafter by trained bedside nursing staff, placed in transport media, and stored at -80 o C until processed. For the current study, paired samples collected at enrollment and a week after hospitalization were compared. RNA was extracted using commercial spin column kits (QAmp viral RNA mini kit, Qiagen, Inc., Valencia, CA), and stored at -80 o C. (Table S2 of the supplementary information) . The demographic and clinical characteristics are provided in Table S1 (supplementary information) Figure 1A ). While most initial NP (34/40, 85%) and the corresponding MT swabs (29/40, 73%) (sampling time point 1; Fig 1A) were positive (p=0.53), significantly fewer MT swabs were positive (24/29, 82% NP vs 13/29, 45% nasal; p=0.001) about a week later (sampling time point 2; Fig 1A) . The relationship between the CT value and the RT-PCR results of NP and MT swabs is shown in Figure 1B 0001; Fig 1C) . A modest correlation between NP and nasal swabs for SARS-CoV-2 RNA was observed only at CT values ≤30 (r=0.51) ( Figure 1C ). RNAse P PCR of discordant NP and MT samples showed similar amplification plots without significant differences in CT values (Table S2 ). Our study of paired NP and MT swabs from a cohort of hospitalized COVID-19 patients demonstrates that while both NP and MT swabs are reliable for diagnosis early during hospitalization, NP swabs are more reliable later in disease course (Figures 1B and 1C ). Both the CDC and the IDSA currently endorse testing of NP or MT samples for SARS-CoV-2 with limited data. By analyzing serial samples from 40 patients, we examined the reliability of MT swabs in the setting of varying SARS-CoV-2 viral load levels. Our findings suggest that patients whose NP swabs are PCR-positive but have a lower viral load as suggested by high CT values (>30), often test negative by MT swab. To date, only two peer reviewed publications have directly compared NP and MT swabs in patients with suspected COVID-19 [9, 10] . Péré et al. tested NP and MT swabs from 44 patients and found that NP and MT swabs were positive in 37 and 33 patients, respectively. We report similar findings but only for samples obtained earlier during hospitalization. Characteristics of and Important Lessons From the Coronavirus Disease 2019 (COVID-19) Outbreak in China: Summary of a Report of 72 314 Cases From the Chinese Center for Disease Control and Prevention A Novel Coronavirus from Patients with Pneumonia in China Interim Guidelines for Collecting, Handling, and Testing Clinical Specimens from Persons for Coronavirus Disease Infectious Diseases Society of America Guidelines on the Diagnosis of COVID-19 Detection of SARS-CoV-2 in Different Types of Clinical Specimens Evaluating the accuracy of different respiratory specimens in the laboratory diagnosis and monitoring the viral shedding of 2019-nCoV infections SARS-CoV-2 Viral Load in Upper Respiratory Specimens of Infected Patients Self-collection: An appropriate alternative during the SARS-CoV-2 pandemic Nasal swab sampling for SARS-CoV-2: A convenient alternative in time of nasopharyngeal swab shortage Swabs Collected by Patients or Health Care Workers for SARS-CoV-2 Testing Comparison of Commercially Available and Laboratory Developed Assays for Viral load dynamics and disease severity in patients infected with SARS-CoV-2 in Zhejiang province, China Acknowledgements: We thank the nursing staff for assistance with sample collection and the study participants and their families. 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