Saliva or Nasopharyngeal Swab Specimens for Detection of SARS-CoV-2

Wyllie, Anne L.; Fournier, John; Casanovas‐Massana, Arnau; Campbell, Melissa; Tokuyama, Maria; Vijayakumar, Pavithra; Warren, Joshua L.; Geng, Bertie; Muenker, M. Catherine; Moore, Adam J.; Petrone, Mary E.; Ott, Isabel M.; Lu, Peiwen; Venkataraman, Arvind; Lu-Culligan, Alice; Klein, Jonathan; Earnest, Rebecca; Simonov, Michael; Datta, Rupak; Handoko, Ryan; Naushad, Nida; Sewanan, Lorenzo R.; Valdez, Jordan; White, Elizabeth B.; Lapidus, Sarah; Kalinich, Chaney C.; Jiang, Xiaodong; Kim, Daniel J.; Kudo, Eriko; Linehan, Melissa; Mao, Tianyang; Moriyama, Miyu; Oh, Ji Eun; Park, Annsea; Silva, Julio; Song, Eric; Takahashi, Takehiro; Taura, Manabu; Weizman, Orr-El; Wong, Patrick; Yang, Yexin; Bermejo, Santos; Odio, Camila D.; Omer, Saad B.; Cruz, Charles S. Dela; Farhadian, Shelli; Martinello, Richard A.; Iwasaki, Akiko; Grubaugh, Nathan D.; Ko, Albert Icksang

doi:10.1056/nejmc2016359

Cited by 895 publications

(1,099 citation statements)

References 21 publications

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“…2). [7][8][9]. In the present study, unexpectedly, a high number of samples with Ct values on the border of Ct < 40 and low sensitivity of our results for patients (53.4%) were observed.…”

Section: Resultscontrasting

confidence: 61%

“…An Italian study performed with 25 patients with COVID-19 concluded that saliva is a reliable medium for detecting SARS-CoV-2 [8]. A study performed with 70 inpatients with COVID-19 showed that saliva specimens and nasopharyngeal swabs have similar sensitivity during the course of hospitalization in the detection of SARS-CoV-2 using a primer set from the Centers for Disease Control and Prevention [9].…”

Section: Introductionmentioning

confidence: 99%

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SARS-CoV-2 Identification in Saliva: Are We Interpreting the Results Correctly?

Ramírez-Hinojosa

Rodríguez-Sánchez

Romero-Gonzalez

et al. 2020

Preprint

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BackgroundIn the present study, we obtained cycle threshold (Ct) values by qRT-PCR and compared them with clinical and laboratory data from saliva specimens of inpatients with COVID-19 and asymptomatic health workers (AHW).MethodsSaliva specimens from inpatients with COVID-19 and AHW were studied by qRT-PCR using three sets of primers for the N (N1, N2, and N3) gene of SARS-CoV-2. The Ct values obtained were compared with the clinical and laboratory data.ResultsData from 58 inpatients (37 critically ill patients and 21 patients with severe disease) and 105 AHW were analysed. In our system, the limit of viral detection corresponded to a Ct =46.5; therefore, our analysis focused on comparing the positivity rate obtained when using Ct <40 as the cut-off with that obtained using Ct <46 as the cut-off. The positivity rate was increased when the Ct cut-off of 46 was used as the criterion, yielding a sensitivity of 87.9% for patients and a sensitivity of 43% for AHW. The bivariate analysis revealed an association between Ct <40 for N2 and mechanical ventilation assistance among patients (p=0.013). In addition, the serological values of alanine transaminase (ALT), aspartate-transaminase (AST), lactate dehydrogenase (LDH), ferritin and creatine kinase–MB (CK-MB) showed significant correlations with the Ct values of N1 and N3.ConclusionDue to the intrinsic characteristics of the qRT-PCR process, obtaining amplification curves implies the presence of an active viral replication process, while Ct values may correlate with some clinical data. Our results support the claim that physicians should be informed of the Ct values obtained during the amplification of viral markers, as well as the Ct values that correspond to the limit of detection for viral RNA, which vary according to the characteristics of each system and amplification protocol used.

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“…2). [7][8][9]. In the present study, unexpectedly, a high number of samples with Ct values on the border of Ct < 40 and low sensitivity of our results for patients (53.4%) were observed.…”

Section: Resultscontrasting

confidence: 61%

Section: Introductionmentioning

confidence: 99%

SARS-CoV-2 Identification in Saliva: Are We Interpreting the Results Correctly?

Ramírez-Hinojosa

Rodríguez-Sánchez

Romero-Gonzalez

et al. 2020

Preprint

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“…Viral RNA measurement SARS-CoV-2 RNA concentrations were measured from nasopharyngeal samples and saliva samples by RT-PCR as previously described 18,19 . In short, total nucleic acid was extracted from 300 μl of viral transport media from the nasopharyngeal swab or 300 μl of whole saliva using the MagMAX Viral/Pathogen Nucleic Acid Isolation kit (ThermoFisher Scientific) using a modified protocol and eluted into 75 μl of elution buffer 19 . For SARS-CoV-2 RNA detection, 5 μl of RNA template was tested as previously described 18 , using the US CDC real-time RT-PCR primer/ probe sets for 2019-nCoV_N1, 2019-nCoV_N2, and the human RNase P (RP) as an extraction control.…”

Section: Patients and Hcwsmentioning

confidence: 99%

Sex differences in immune responses that underlie COVID-19 disease outcomes

Takahashi

Ellingson

Wong

et al. 2020

Nature

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CLIA-certified laboratories were enrolled through the IMPACT biorepository study 15. In the IMPACT study, biospecimens including blood, nasopharyngeal swabs, saliva, urine and stool samples were collected at study enrolment (baseline denotes the first time point) and longitudinally on average every 3 to 7 days (serial time points). The detailed demographics and clinical characteristics of these 98 participants are shown in Extended Data Table 1. Plasma and peripheral blood mononuclear cells (PBMCs) were isolated from whole blood, and plasma was used for titre measurements of SARS-CoV-2 spike S1 protein-specific IgG and IgM antibodies (anti-S1-IgG and-IgM) and cytokine or chemokine measurements. Freshly isolated PBMCs were stained and analysed by flow cytometry 15. We obtained longitudinal serial time-point samples from a subset of these 98 study participants (n = 48; information in Extended Data Table 1). To compare the immune phenotypes between sexes, two sets of data analyses were performed in parallel-baseline and longitudinal, as described below. As a control group, healthcare workers (HCWs) from Yale-New Haven Hospital were enrolled who were uninfected with COVID-19. Demographics and background information for the HCW group and the demographics of HCWs for cytokine assays and flow cytometry assays for the primary analyses are in Extended Data Table 1. Demographic data, time-point information of the samples defined by the days from the symptom onset (DFSO) in each patient, treatment information, and raw data used to generate figures and tables is in Supplementary Table 1. Baseline analysis The baseline analysis was performed on samples from the first time point of patients who met the following criteria: not in intensive care unit (ICU), had not received tocilizumab, and had not received high doses of corticosteroids (prednisone equivalent of more than 40 mg) before the first sample collection date. This patient group, cohort A, consisted of 39 patients (17 male and 22 female) (Extended Data Tables 1, 2). Intersex and transgender individuals were not represented in this study. Figures 1-4 represent analyses of baseline raw values obtained from patients in cohort A. In cohort A patients, male and female patients were matched in terms of age, body mass index (BMI), and DFSO at the first time point sample collection (Extended Data Fig. 1a). However, there were significant differences in age and BMI between HCW controls and patients (patients had higher age and BMI values) (Extended Data Table 1), and therefore an age-and BMI-adjusted difference-indifferences analysis was also performed in parallel (Extended Data Table 3). Longitudinal analysis As parallel secondary analyses, we performed longitudinal analysis on a total patient cohort (cohort B) to evaluate the difference in immune response over the course of the disease between male and female patients. Cohort B included all patient samples from cohort A (including several time-point samples from the cohort A patients) as well as an additional 59 patients who d...

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“…Of the individuals included in the study, 27 of the 46 with active infections and 40 of the 68 overall were from staff and vendors. The median number of tests administered to each of the 68 individuals was 41 (IQR [14,51]; Range [5,70]). The median number of positive Ct values recorded for each person was 3 (IQR [2,4]; Range [1,9]).…”

Section: Main Textmentioning

confidence: 99%

Viral dynamics of acute SARS-CoV-2 infection

Kissler

Fauver

Mack

et al. 2020

Preprint

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SARS-CoV-2 diagnostics that report viral RNA concentrations can be used to determine a patient's stage of infection, but this potential has not yet been realized due to a lack of prospective longitudinal data to calibrate such inferences. Here, we report the viral RNA trajectories for 68 individuals using quantitative PCR testing. On average, symptomatic and asymptomatic individuals reached similar peak viral RNA concentrations (22.2 Ct, 95% credible interval [19.1, 25.1] vs. 22.4 Ct [20.2, 24.5]) within similar amounts of time (2.9 days [0.7, 4.7] vs. 3.0 days [1.3, 4.3]), but acute shedding lasted longer for symptomatic individuals (10.5 days [6.5, 14.0] vs. 6.7 days [3.2, 9.2]). A second test within 2 days after an initial positive PCR result reliably indicated whether viral RNA concentration was increasing, decreasing, or in a low-level persistent phase. Quantitative viral RNA assessment, informed by viral trajectory, can improve algorithms for clinical and public health management.

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Saliva or Nasopharyngeal Swab Specimens for Detection of SARS-CoV-2

Cited by 895 publications

References 21 publications

SARS-CoV-2 Identification in Saliva: Are We Interpreting the Results Correctly?

SARS-CoV-2 Identification in Saliva: Are We Interpreting the Results Correctly?

Sex differences in immune responses that underlie COVID-19 disease outcomes

Viral dynamics of acute SARS-CoV-2 infection

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