Comparing the accuracy of nasopharyngeal COVID-19 PCR alone versus combined nasopharyngeal and oropharyngeal COVID-19 PCR tests


  • Alan Saeed Department of Family Medicine, Primary Health Care Corporation, Doha City, Qatar
  • Anas Kalfah Department of Medical Education, Hamad Medical Corporation, Doha City, Qatar
  • Zhila Mohammed Department of Basic Science, College of Medicine, Qatar University, Doha City, Qatar



COVID-19, Inconclusive results, Nasopharyngeal swabs, Oropharyngeal swabs, PCR, SARS-CoV-2


Background: Efficient containment of the SARS-CoV-2 virus, responsible for the COVID-19 pandemic, is heavily reliant on precise diagnostic methodologies. Amidst prevalent use of nasopharyngeal (NP) and oropharyngeal (OP) swabs for detection, the superiority in sampling method effectiveness remains debated.

Methods: A retrospective study within Qatar's Primary Health Care Corporation (PHCC) contrasted the accuracy of combined NP/OP PCR tests versus NP-only tests, utilizing inconclusive test rates, primarily attributed to sampling adequacy, as a crucial accuracy measure. A total of 179,694 NP/OP and NP-only samples were analyzed across two phases: pre and post-16/01/2022, the latter marking a transition predominantly to NP-only swabs and increased reliance on rapid antigen testing. With a notable disparity in sample size between methods, a 1% simple random sample was extracted for analysis. Patients aged 18 years and below were excluded in this study.

Results: The dual NP and OP swab approach registered a 2% inconclusive rate pre-cut off, while a 5% inconclusive rate was observed with the NP-only technique post-cut off, presenting a statistically significant 3% differential (p<0.001). Subgroup analyses divulged a mere 1% inconclusive rate disparity between age groups and a 1% lower rate amidst symptomatic individuals, with chronic allergic rhinitis patients exhibiting a 2% elevation (p=0.086).

Conclusions: Combined NP/OP swabbing produced fewer inconclusive PCR results relative to NP-only swabbing, offering a 3% improvement in conclusive diagnostics. Notably, symptomatic presentation and chronic allergic rhinitis most significantly influenced accuracy, indicating potential avenues for further diagnostic refinement research, thus bolstering our current understanding and mitigation approaches towards COVID-19.


Van Damme W, Dahake R, Delamou A, Ingelbeen B, Wouters E, Vanham G, et al. The COVID-19 pandemic: diverse contexts; different epidemics-how and why?. BMJ Glob Heal. 2020;5(7):e003098.

Cucinotta, D. and M. Vanelli. WHO Declares COVID-19 a pandemic. Acta Biomed. 2020;91(1):157-60.

Wang MY, Zhao R, Gao LJ, Gao XF, Wang DP, Cao JM. SARS-CoV-2: structure, biology, and structure-based therapeutics development. Front Cellu Infect Microbiol. 2020;10:587269.

Zhang T, Wu Q, Zhang Z. Probable pangolin origin of SARS-CoV-2 Associated with the COVID-19 outbreak. Curr Biol. 2020;30(7):1346-51.e2.

Valencak TG, Csiszar A, Szalai G, Podlutsky A, Tarantini S, Fazekas-Pongor V, et al. Animal reservoirs of SARS-CoV-2: calculable COVID-19 risk for older adults from animal to human transmission. GeroSci. 2021;43(5):2305-20.

Mehraeen E, Salehi MA, Behnezhad F, Moghaddam HR, SeyedAlinaghi S. Transmission modes of COVID-19: a systematic review. Infect Dis-Drug Targets (Curr Drug Targ-Infect Dis). 2021;21(6):27-34.

Zhou L, Ayeh SK, Chidambaram V, Karakousis PC. Modes of transmission of SARS-CoV-2 and evidence for preventive behavioral interventions. BMC Infect Dis. 2021;21(1):1-9.

Johansson MA, Quandelacy TM, Kada S, Prasad PV, Steele M, Brooks JT, et al. SARS-CoV-2 transmission from people without COVID-19 symptoms. JAMA. 2021;4(1):e2035057.

Du RH, Liang LR, Yang CQ, Wang W, Cao TZ, Li M, et al. Predictors of mortality for patients with COVID-19 pneumonia caused by SARS-CoV-2: a prospective cohort study. Europ Respir J. 2020;55(5).

da Rosa Mesquita R, Francelino Silva Junior LC, Santos Santana FM, Farias de Oliveira T, Campos Alcântara R, Monteiro Arnozo G, et al. Clinical manifestations of COVID-19 in the general population: systematic review. Wie Klinis Wochensc. 2021;133(7-8):377-82.

Chen N, Zhou M, Dong X, Qu J, Gong F, Han Y, et al. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study. lancet. 2020;395(10223):507-13.

Huang C, Wang Y, Li X, Ren L, Zhao J, Hu Y, et al. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. lancet. 2020;395(10223):497-506.

Tang YW, Schmitz JE, Persing DH, Stratton CW. Laboratory diagnosis of COVID-19: current issues and challenges. J Clin Microbiol. 2020;58(6):10-128.

Shyu D, Dorroh J, Holtmeyer C, Ritter D, Upendran A, Kannan R, et al. Laboratory tests for COVID-19: a review of peer-reviewed publications and implications for clinical use. Missouri Medi. 2020;117(3):184.

Rao M, Rashid FA, Sabri FS, Jamil NN, Seradja V, Abdullah NA, et al. COVID‐19 screening test by using random oropharyngeal saliva. J Me Virol. 2021;93(4):2461-6.

Li Q, Guan X, Wu P, Wang X, Zhou L, Tong Y, et al. Early transmission dynamics in Wuhan, China, of novel coronavirus–infected pneumonia. N Eng J Medi. 2020;382(13):1199-207.

Patel MR, Carroll D, Ussery E, Whitham H, Elkins CA, Noble-Wang J, et al. Performance of oropharyngeal swab testing compared with nasopharyngeal swab testing for diagnosis of coronavirus disease 2019-United States, January 2020–February 2020. Clin Infect Dis. 2021;72(3):482-5.

Singh A, Gupta P, Mathuria YP, Kalita D, Prasad A, Panda PK, et al. Comparative evaluation of nasopharyngeal and oropharyngeal swab based rapid SARS-CoV-2 antigen detection and real-time RT-PCR for diagnosis of COVID-19 in tertiary care hospital. Cureus. 2021;13(7).

Prendki V, Huttner B, Marti C, Mamin A, Fubini PE, Meynet MP, et al. Accuracy of comprehensive PCR analysis of nasopharyngeal and oropharyngeal swabs for CT-scan-confirmed pneumonia in elderly patients: a prospective cohort study. Clin Microbiol Infect. 2019;25(9):1114-9.

Li L, Chen QY, Li YY, Wang YF, Yang ZF, Zhong NS. Comparison among nasopharyngeal swab, nasal wash, and oropharyngeal swab for respiratory virus detection in adults with acute pharyngitis. BMC Infect Dis. 2013;13(1):1-5.

Pondaven-Letourmy S, Alvin F, Boumghit Y, Simon F. How to perform a nasopharyngeal swab in adults and children in the COVID-19 era. Europ Ann Otorhinolaryngol Head Neck Dis. 2020;137(4):325-7.

Kim D, Moon JW, Chae SW. Complications of nasopharyngeal swabs and safe procedures for COVID-19 testing based on anatomical knowledge. Jo Kor Med Sci. 2022;37(11).

Fazekas B, Fazekas B, Darraj E, Jayakumar D. Preseptal cellulitis and infraorbital abscess as a complication of a routine COVID-19 swab. BMJ Case Reports CP. 2021;14(5):e241963.

Wang H, Liu Q, Hu J, Zhou M, Yu MQ, Li KY, et al. Nasopharyngeal swabs are more sensitive than oropharyngeal swabs for COVID-19 diagnosis and monitoring the SARS-CoV-2 load. Fronti Med. 2020;7:334.

Thomas HM, Mullane MJ, Ang S, Barrow T, Leahy A, Whelan A, et al. Acceptability of OP/Na swabbing for SARS-CoV-2: a prospective observational cohort surveillance study in Western Australian schools. BMJ open. 2022;12(1):e055217.

Todsen T, Kirkby N, Benfield T. Is oropharyngeal sampling a reliable test to detect SARS-CoV-2? Lancet Infect Dis. 2021;21(10):1348.

Petruzzi G, De Virgilio A, Pichi B, Mazzola F, Zocchi J, Mercante G, et al. COVID‐19: nasal and oropharyngeal swab. Head Neck. 2020;42(6):1303-4.

Desmet T, Paepe PD, Boelens J, Coorevits L, Padalko E, Vandendriessche S, et al. Combined oropharyngeal/nasal swab is equivalent to nasopharyngeal sampling for SARS-CoV-2 diagnostic PCR. BMC Microbiol. 2021;21:1-4.

Böger B, Fachi MM, Vilhena RO, Cobre AF, Tonin FS, Pontarolo R. Systematic review with meta-analysis of the accuracy of diagnostic tests for COVID-19. Ame J Infect Contr. 2021;49(1):21-9.

Hellewell J, Russell TW, Beale R, Kelly G, Houlihan C, Nastouli E, Kucharski AJ. Estimating the effectiveness of routine asymptomatic PCR testing at different frequencies for the detection of SARS-CoV-2 infections. BMC medicine. 2021;19(1):1-0.

Braunstein GD, Schwartz L, Hymel P, Fielding J. False positive results with SARS-CoV-2 RT-PCR tests and how to evaluate a RT-PCR-positive test for the possibility of a false positive result. J Occupat Environm Medi. 2021;63(3):e159.

Wang X, Tan L, Wang X, Liu W, Lu Y, Cheng L, Sun Z. Comparison of nasopharyngeal and oropharyngeal swabs for SARS-CoV-2 detection in 353 patients received tests with both specimens simultaneously. Inter J Inf Dis. 2020;94:107-9.

Callahan C, Lee RA, Lee GR, Zulauf K, Kirby JE, Arnaout R. Nasal swab performance by collection timing, procedure, and method of transport for patients with SARS-CoV-2. J Clin Microbiol. 2021;59(9):10-128.

Stoykova Z, Kostadinova T, Todorova T, Niyazi D, Bozhkova M, Bizheva S, et al. Dealing with inconclusive SARS-CoV-2 PCR samples-Our experience. PLoS One. 2022;17(5):e0268187.

La Jeon Y, Lee SG, Lee EH, Song S, Go UY, Chun GY. Different interpretations of inconclusive results of SARS-CoV-2 real-time RT PCR. Diagn Microbiol Infect Dis. 2023;106(2):115888.




How to Cite

Saeed, A., Kalfah, A., & Mohammed, Z. (2023). Comparing the accuracy of nasopharyngeal COVID-19 PCR alone versus combined nasopharyngeal and oropharyngeal COVID-19 PCR tests. International Journal of Research in Medical Sciences, 11(11), 3969–3975.



Original Research Articles