Sensitivity of midturbinate versus nasopharyngeal swabs for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)

To compare sensitivity of specimens for COVID-19 diagnosis, we tested 151 nasopharyngeal/midturbinate swab pairs from 117 COVID-19 inpatients using reverse-transcriptase polymerase chain reaction (RT-PCR). Sensitivity was 94% for nasopharyngeal and 75% for midturbinate swabs (P = .0001). In 88 nasopharyngeal/midturbinate pairs with matched saliva, sensitivity was 86% for nasopharyngeal swabs and 88% for combined midturbinate swabs/saliva.

(Received 20 August 2020; accepted 9 November 2020) Nasopharyngeal (NP) swabs are currently the preferred specimen collection method for coronavirus disease 2019 (COVID-19) diagnosis. However, there is increasing interest in midturbinate (MT) swabs because they cause less discomfort to patients, may be safer for healthcare workers to collect, and can be self-collected by adolescent and adult patients. 1,2 Two small studies have compared the sensitivity of NP and MT swabs for detecting severe acute respiratory coronavirus virus 2 (SARS-CoV-2) and found comparable sensitivity early in illness. 2,3 In our prospective cohort of inpatients with COVID-19 in Ontario, Canada, we compared the sensitivities of NP and saliva versus MT swabs.

Study population
The Toronto Invasive Bacterial Diseases Network (TIBDN) performs population-based surveillance for infectious diseases in Toronto and Peel (Ontario, Canada). The TIBDN clinical microbiology laboratories report specimens yielding SARS-CoV-2 to our study office. In this study, we enrolled consecutive inpatients with COVID-19 at 4 TIBDN hospitals from March 23 through May 22, 2020. The research ethics boards of all TIBDN hospitals approved this study.

Data collection
Demographic and clinical data were collected from charts and patient interviews. Study staff collected NP and MT swabs and saliva from consenting patients at enrollment and 6 days later if the patient was still hospitalized. Swabs were obtained using standard procedures 4,5 and placed in universal transport medium (UTM, COPAN Diagnostics, Murrietta, CA). Patients were asked to spit 1 teaspoon of saliva into a sterile container, then 2.5 mL phosphate-buffered saline was added. From April 14 through May 4, in a pilot test of alternative collection methods, saliva was provided by gargle and/or salivette; these specimens were excluded.

Laboratory methods
Specimens were aliquoted and frozen at −80°C on the day of collection until processing at the Sunnybrook Health Sciences research microbiology laboratory (Toronto, Canada). RNA extractions were performed using the QIAamp Viral RNA Mini Kit (Qiagen, Venlo, The Netherlands). Reverse transcriptase polymerase chain reaction (RT-PCR) using the Luna Universal Probe One- Step RT-qPCR Kit (New England BioLabs, Ipswich, MA) was performed to detect the 5' untranslated region and envelope (E) gene of SARS-CoV-2, with RNaseP as internal control. Cycle thresholds (Cts) were determined using Rotor-Gene Q software (Qiagen, Venlo, The Netherlands); results where all targets had Cts <40 were reported as positive.

Statistical methods
Sensitivities of specimen types were calculated using as the denominator samples with any 1 specimen in the pair or triplet testing positive for SARS-CoV-2. The McNemar test was used to assess differences in sensitivity between specimen types. The Wilcoxon rank-sum test was used to compare the Cts of NP swabs when the MT tested positive versus negative. Two-sided P values <.05 were considered statistically significant. Analyses were performed using SAS version 9.4M6 software (SAS Institute, Cary, NC).
For all analyses, results were similar when only the first or last pair or triplet for each patient was analyzed (Supplementary Material online).

Discussion
In this prospective cohort study of hospitalized patients with COVID-19, NP swabs were significantly more sensitive for SARS-CoV-2 detection than MT swabs. The difference in sensitivity between NP and MT swabs was greater later in illness. Saliva demonstrated intermediate sensitivity between MT and NP swabs.
We are aware of 2 studies comparing sensitivity of MT and NP swabs for SARS-CoV-2 detection. 2,3 Pinninti et al, 3 in inpatients similar to ours, reported NP swabs as more sensitive than MT swabs (80% vs 64% overall), with the difference in sensitivity increasing with time from illness onset. However, our difference in sensitivity between NP and MT swabs was statistically significant even in the first week of illness, whereas that of Pinninti et al was not. In an outpatient setting, Tu et al 2 found that NP swabs detected all 52 patients with either swab positive, while MT swabs detected 50.
Our previous analysis comparing saliva to NP swabs in this cohort using a different testing platform indicated that saliva was less sensitive than NP swabs, particularly later in illness. 6 The difference was not statistically significant in this sample, in which specimens were collected less frequently but over a longer period, likely due to sampling variability. More importantly, however, other studies have not found differences in sensitivities between NP swabs and saliva, particularly early in illness. 7,8 Saliva is an appealing alternative to NP swabs, especially during swab shortages or in settings requiring repeated COVID-19 screening.
The fact that MT swabs and saliva in combination have a similar sensitivity to NP swabs may simply be because a second specimen adds sensitivity; repeated testing is known to improve sensitivity among patients with COVID-19. 9 These data reinforce the concept that 1 specimen is not 100% sensitive and that patients with a high index of clinical suspicion for COVID-19 who test negative require repeated testing.
This study had several limitations. It included only hospitalized patients, with first study specimen at 1-27 days after diagnosis. Differences in sensitivity may be smaller at presentation. We only tested specimens on a single platform; results may vary between platforms, especially when Ct values are near the limit of detection. We did not perform sequencing or other validation of results in samples in which only 1 specimen yielded positive results, so some results may have been false positives.
In conclusion, this study of hospitalized patients found NP swabs to be 15% more sensitive than MT swabs for SARS-CoV-2 detection in the first week of COVID-19. Larger studies are needed, as are studies of specimens obtained for initial diagnosis and in milder illness. In the interim, we believe that the use of MT swabs for COVID-19 diagnosis should be approached with caution.