Secondary Logo

Journal Logo

Brief Reports

Nasal Swab as Preferred Clinical Specimen for COVID-19 Testing in Children

Palmas, Giordano MD; Moriondo, Maria MS, PhD; Trapani, Sandra MD, PhD; Ricci, Silvia MD; Calistri, Elisa MS, PhD; Pisano, Laura MS; Perferi, Giancarlo MS; Galli, Luisa MD; Venturini, Elisabetta MD, PhD; Indolfi, Giuseppe MD, PhD; Azzari, Chiara MD, PhD

Author Information
The Pediatric Infectious Disease Journal: September 2020 - Volume 39 - Issue 9 - p e267-e270
doi: 10.1097/INF.0000000000002812
  • Open


The coronavirus disease 2019 (COVID-19) outbreak has been declared a pandemic on March 11, 2020.1 Although exhaustive case finding represents the first step in the preventive strategy,2 the best type of clinical specimen for the initial diagnostic test remains controversial. As stated by the Center for Disease Prevention and Control, nasal (mid-turbinate), oropharyngeal (throat) and nasopharyngeal specimen collection are considered acceptable alternatives.3 Nasopharyngeal specimen collection is usually recommended,3–5 but its sensitivity has been questioned if compared with other clinical specimens,6 and it is not always feasible in young children, since specific swabs and containment measures are required to reach the pharynx through the small opening of the nostril.

The aim of this pediatric study is to compare the performance of nasal specimen testing and oropharyngeal specimen testing for severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) detection. Further potential benefits of nasal swabbing over the other upper respiratory sampling techniques are discussed.


Study Design and Participants

This prospective study included all children (age 0–18) with COVID-19 who were tested for detection of SARS-CoV-2 on both nasal and oropharyngeal specimens on admission to the Meyer Children’s University Hospital between March 12 and March 31, 2020. The Meyer Children’s University Hospital is a tertiary care referral pediatric hospital located in Florence, Italy. The screening consisted in collecting one of the recommended upper respiratory specimens (nasal, oropharyngeal or nasopharyngeal specimens)3 and testing for the presence of SARS-CoV-2.

If initial diagnostic testing resulted positive for COVID-19 and the patient required hospitalization, a simultaneous collection of nasal and oropharyngeal specimen was performed on admission and was repeated every 1–3 days during hospitalization. Paired results were considered in the statistical analysis, to compare the positivity rate of the 2 sampling techniques and to describe changes in the viral load.

On admission, parents signed an informed consent, including specific approval to anonymous research activity. The study protocol was approved by the institutional ethics board.

Specimen Collection and Testing

Nasal specimens were collected by mid-turbinate swabbing of both nares. Oropharyngeal specimens were collected swabbing the posterior pharynx, avoiding the tongue. A flocked swab (ESwab Copan, Brescia, Italy) was used for the collection of all clinical samples and handled as recommended in international guidelines.3

The presence of SAR-CoV-2 RNA in the samples was evaluated through quantitative reverse transcription-polymerase chain reaction (qRT-PCR), as described in international guidelines.7

The cycle threshold (CT) values of qRT-PCR are inversely related to the copy number of SARS-CoV-2 RNA and are commonly used as a proxy of viral loads. Therefore, CT values were used to compare viral loads in different clinical samples. If no increase in the intensity of the fluorescent signal was observed after 40 cycles, the sample was classified as negative.

Statistical Analysis

Data were processed with the SPSS release 24 statistical package. Results were expressed as means and SDs or as median and interquartile range (IQRs), as appropriate. The Student T test was used to assess group differences for continuous numerical variables, whereas the Fisher exact test and Kappa coefficient to assess group differences in categorical variables. P values <0.05 were considered statistically significant.


Eleven patients were identified as having laboratory-confirmed SARS-CoV-2 infection and were admitted for further evaluation. The median age was 4.5 (IQR 2–11) months. SARS-CoV-2 infected patients presented mild to moderate signs and symptoms, ranging from feeding difficulty to fever, rhinitis and cough.

A total of 52 paired clinical specimens (26 nasal swabs and 26 oropharyngeal swabs) were collected. The first paired samples were obtained on admission and, afterwards, up to 7 other paired samples per patient were obtained during hospitalization. Overall, 24 of 26 nasal specimens resulted positive, whereas 20 of 26 oropharyngeal specimens resulted positive. In particular, 20 nasal samples tested positive also on the 20 paired oropharyngeal samples; 4 nasal swabs resulted positive, but were paired to a negative oropharyngeal swab (Fig. 1A, patients A and B); the 2 remaining nasal swabs tested negative also on the 2 matched oropharyngeal swabs (Fisher exact test 0.046, Cohen K 0.43, confidence inteval 95% 0.014–0.855). The 2 patients with matched negative tests were tested 7 and 9 days after clinical onset, respectively (Fig. 1A, patients A and G).

Comparison of cycle threshold (CT) values of nasal samples and oropharyngeal samples; (A) repeated sampling during hospitalization; (B) first paired samples collected for each inpatient on admission; (C) all positive paired samples.

Analysis of viral load based on CT values was also performed. As shown in Figure 1B, CT values of the first simultaneous collected materials were always lower in nasal specimens than in the paired oropharyngeal ones. The mean difference in CT values (delta CT) was 7, which corresponds approximately to a 100-fold difference in the viral load. Moreover, when considering the 40 positive matched samples, the mean CT value on nasal samples was significantly lower, 21.6 (SD = 5.1), if compared with that of oropharyngeal swabs of 28.7 (SD = 5.3, P < 10−6), as represented in Figure 1C. A progressive increase in CT values on both nasal and oropharyngeal samples was recorded during hospitalization, indicating a progressive decrease in the viral load.


This is the first pediatric study comparing nasal swabbing to other upper respiratory sampling methods. Results support the superiority of nasal over oropharyngeal swab collection, determined by a significantly higher positivity rate and a significantly higher mean viral load on nasal samples. In fact, the difference in CT suggests a 100-fold higher viral load in nasal specimens when compared with the oropharyngeal ones. This finding was recorded not only on the first combined analysis of infected inpatients but also on the repeated testing during hospitalization.

The clinical impact of our statistical analysis is most evident in patient A, which resulted positive on the repeated testing of nasal specimens, but never on oropharyngeal specimens. In fact, a diagnostic approach based on the evaluation of only oropharyngeal samples would have missed this SARS-CoV-2 infected patient (Fig. 1A).

The dynamic changes in CT following the initial detection support the above-mentioned data and show that the viral load progressively decreased over time for both clinical specimens. The same result has already been described and confirmed for other clinical specimens,8 strengthening the representativeness of our sample.

Interestingly, nasal specimens tested positive for a longer time span. The virus was still detectable on nasal samples collected during the recovery phase of 2 patients, when the simultaneous oropharyngeal swab tested negative for the presence of the virus. Since our knowledge on the interruption of viral shedding is limited and relies on negative tests,9 the above-mentioned findings would confer a preferential role to nasal sampling not only as a screening tool but also as a confirmatory sampling technique to end quarantine.

For the initial diagnostic testing of COVID-19, most international organizations indicate also nasopharyngeal swabbing as a possible alternative.3–5 Although our study does not compare directly the performance of nasal swab with the nasopharyngeal one, we highlight several limitations to this approach, at least in the pediatric setting. In fact, it might be reasonable that sensitivity does not change between the two tests, considering the apparent higher viral load of the virus in nasal mid-turbinate samples as compared with oropharyngeal ones.6 Furthermore, when dealing with the smaller upper airway diameter of neonates and infants, specific swabs are required, which are not currently available worldwide.5 For this reason, many pediatric centers perform oropharyngeal swabbing instead of nasopharyngeal one. In addition, the sampling technique requires a deep and repeated insertion of the swab, which is not comfortable: less compliant patients, such as infants and young children, might oppose and cough during the collection, thus exposing the healthcare worker to a higher risk of viral transmission.5 In fact, according to the European Centers for Disease Control and Prevention, pharyngeal sampling (nasopharyngeal and oropharyngeal) has to be considered an aerosol-generating procedure.5

The strength of this work is the simultaneous collection of both nasal and oropharyngeal specimens and the peculiarity of the selected population accounting many infants. The results are consistent with those on adult SARS-CoV-2 infection.6,8 There are two main limitations: first, the small sample size, due to the low number of pediatric patients with known infection;2 second, the single-swab-based screening of patients, due to shortages of specific materials in the first phase of the outbreak.


In conclusion, this study highlights the superiority of nasal specimen over oropharyngeal specimen collection in detecting SARS-CoV-2 in children, mainly due to a significantly higher positivity rate and a significantly higher mean viral load on nasal samples. Although larger studies are required to strengthen our conclusions, these results are of great importance, especially among the youngest, where the most recommended nasopharyngeal swabbing method is not always feasible. The benefits described might also extend to a lower collection-related exposure risk for healthcare workers.

We suggest nasal swabbing as the preferred clinical specimen for COVID-19 initial diagnostic testing and discontinuation of isolation strategy in children, as we are doing in the clinical practice of our pediatric hospital.


On behalf of the Tuscany Pediatric Network for Molecular Surveillance of Infectious Disease: Agostiniani R, Pistoia; Astorino V, Firenze; Citera F, Firenze; Contimiglia M, Firenze; Mangoni G, Firenze; Nieddu F, Firenze; Pezzati M, Firenze; Valleriani C, Firenze; Vasarri P, Prato.


1. World Health Organization. Coronavirus disease 2019 (COVID-19), situation report - 78.Available at: Accessed May 5, 2020.
2. World Health Organization. WHO report of the WHO-China joint mission on coronavirus disease 2019 (COVID-19).Available at: Accessed February, 2020.
3. Centers for Disease Control and Prevention. Interim guidelines for collecting, handling, and testing clinical specimens from persons for coronavirus disease 2019 (COVID-19).Available at: Accessed May 5, 2020.
4. World Health Organization. Laboratory testing strategy recommendations for COVID-19: interim guidance. World Health Organization.Available at: Accessed March 22, 2020.
5. European Centre for Disease Prevention and Control. Coronavirus Disease 2019 (COVID-19) Pandemic: Increased Transmission in the EU/EEA and the UK – Seventh Update, 25 March 2020. 2020.Stockholm: ECDC.
6. Wang W, Xu Y, Gao R, et al. Detection of SARS-CoV-2 in different types of clinical specimens. JAMA. 2020;323:1843–1844.
7. Centers for Disease Control and Prevention. Research use only real-time RT-PCR protocol for identification of 2019-nCoV. Centers for Disease Control and Prevention (2020). Available at: Accessed February 12, 2020.
8. Zou L, Ruan F, Huang M, et al. SARS-CoV-2 viral load in upper respiratory specimens of infected patients. N Engl J Med. 2020;382:1177–1179.
9. European Centre for Disease Prevention and Control. Technical Report – Discharge Criteria for Confirmed COVID-19 Cases. 2020Stockholm: ECDC; Available at: Accessed May 5, 2020.

swab; coronavirus disease 2019; severe acute respiratory syndrome corona virus 2; pediatric; child

Copyright © 2020 The Author(s). Published by Wolters Kluwer Health, Inc.