Abstract
The rapid spread of the COVID-19 pandemic has led to a major public health crisis. Accurate screening methods for COVID-19 infection is essential and crucial for case detection, isolation, prevention and control of the current pandemic. At present, nasopharyngeal and oropharyngeal swabs are typically used as the method of choice for the diagnosis of SARS-CoV-2 infection. We carried out a review on the accuracy of the two different sampling sites, the nasopharyngeal and oropharyngeal swab sampling, focusing on the viral load, detection of positive cases and sensitivity in real-time polymerase chain reaction (RT-PCR) assay in diagnosing COVID-19. A total of 25 articles related to the topic were selected out of 5221 articles searched online using Scopus, PubMed and Medline, Embase, Web of Science, and Google scholar with the keywords COVID-19, SARS-CoV-2, nasopharyngeal swab, oropharyngeal swab, nasal swab and throat swab. All full text original articles were obtained and reviewed. Nasopharyngeal swab had significantly higher SARS-CoV-2 load than oropharyngeal swab (mean Ct value ranging from 24.3-37.8, higher detection of positive rate (highest rate 62.5%) and sensitivity (highest sensitivity 98.3%, P<0.05) in RT-PCR assay compared to oropharyngeal swab. Based on the scientific literature review, both nasopharyngeal and oropharyngeal swabs were reported to have 30% probability of yielding false negative results; thus clinically suspicious patients with negative results should be viewed with concern. In conclusion, although several methods of COVID-19 screening and type of specimen are available, nasopharyngeal swab is the best option for large scale screening as it yields significantly higher viral load, higher detection of positive rate among cases and higher sensitivity in RT-PCR assay compared to oropharyngeal swab in detecting SARS-CoV-2.
Highlights
The first case of Coronavirus disease 2019 (COVID-19) was identified in Wuhan, China in December 2019
The recent study reported by Zou et al among 18 patients infected by SARS-CoV-2 suggested that NP swab yielded a higher viral load than OP swab (Zou et al, 2020)
This study showed that the lower the cycle threshold (Ct) value, the higher the viral load but contrary to this finding, the result of a study by Yu et al, (2020) showed that the OP swab had significantly higher viral load than NP swab (2552 copies/test [ SD=1965], p < 0.001) and (651 copies/test [SD= 501], p < 0.001) respectively
Summary
The first case of Coronavirus disease 2019 (COVID-19) was identified in Wuhan, China in December 2019. The agent causing the unusual pneumonia was from the Coronaviridae family and was formerly named 2019 novel coronavirus (2019-nCoV) (WHO, 2020). Epidemiological reports of the viral transmission involved the population who lived in or had visited Wuhan and it was suggestive of human-to-human transmission. The World Health Organization (WHO) declared COVID-19 as a pandemic on 11 March 2020 (WHO, 2020). In Malaysia, the first cases of COVID-19 were reported on 25 January 2020, among visitors from China who entered the country via Singapore. The number of COVID-19 cases have rapidly increased in numbers with appearance of new clusters leading to the implementation of the Movement Control Order (MCO) on 18 March 2020 (Reuters, 2020)
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