Safety management of nasopharyngeal specimen collection from suspected cases of coronavirus disease 2019

Yan, Qingzhi; Zeng, Tieying; Wang, Hui; Xu, Min; Chen, Junhua; Hu, Na; Chen, Daiqi; Yu, Ling

doi:10.1016/j.ijnss.2020.03.012

Cited by 49 publications

(63 citation statements)

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“…We conservatively used the lower of the 25th percentile FPR values from the two EQA data sets to model the reliability of results. This FPR value (0.8%) is further conservative in that it doesn't include false positives produced during sampling, 22 and hasn't been adjusted for any expected increase in error rate stemming from the rapid expansion of SARS-CoV-2 testing and the use of novel diagnostic assays. 23 We used a false negative rate of 25%, based on published estimates that ranged from 0% to 52.2% (Supplemental Material-Version 3: Table S2).…”

Section: False Positives' Impact On the Reliability Of Positive Resultsmentioning

confidence: 99%

Diagnosing SARS-CoV-2 infection: the danger of over-reliance on positive test results

Cohen

Kessel

Milgroom

2020

Preprint

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Large-scale testing for SARS-CoV-2 by the reverse transcription polymerase chain reaction is a key part of the response to the COVID-19 pandemic, but little attention has been paid to the potential frequency and impacts of false positive results. In the absence of data on the clinical specificity of SARS-CoV-2 assays, we estimate a conservative false positive rate from external quality assessments of similar viral assays, and show that this rate may have large impacts on the reliability of positive test results. This has clinical and case management implications, affects an array of epidemiological statistics, and should inform the scale of testing and the allocation of testing resources. Measures to raise awareness of false positives, reduce their frequency, and mitigate their effects should be considered. outbreak of human coronavirus OC43 infection and serological crossreactivity with SARS coronavirus. Canadian Journal of Infectious Diseases and Medical Microbiology. 2006;17(6):330-6. 7 Koetz A, Nilsson P, Lindén MV, Van Der Hoek L, Ripa T. Detection of human coronavirus NL63, human metapneumovirus and respiratory syncytial virus in children with respiratory tract infections in south-west Sweden. Clinical microbiology and infection.

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Section: False Positives' Impact On the Reliability Of Positive Resultsmentioning

confidence: 99%

Diagnosing SARS-CoV-2 infection: the danger of over-reliance on positive test results

Cohen

Kessel

Milgroom

2020

Preprint

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“…18 Moreover, patients never find them in comfort zone during the NPS sample collection. 5,6 The current study has shown that saliva can be a good alternative diagnostic tool for the detection of SARS-CoV-2. Other possible sources like sputum and oropharyngeal secretions are recently suggested for the molecular diagnosis of COVID19.…”

Section: Discussionmentioning

confidence: 71%

“…Parallelly NPS collection technique is quite costly and time-consuming and often gives some uncomfortable complications like sneeze, cough or vomit to the sensitive patients. [5][6] If we consider these factors, NPS is quite complicated to be robustly used in a highly populated and economically developing countries. Throat swab sample are also being used for the detection of COVID-19 but sometimes it's treated as less sensitive method compared to NPS.…”

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confidence: 99%

Saliva as a potential clinical specimen for diagnosis of SARS-CoV-2

Bhattacharya

Parai

Rout

et al. 2020

Preprint

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Background It is almost nine months, still there is no sign to stop the spreading of the COVID-19 pandemic. Rapid and early detection of the virus is the master key to cease the rapid spread and break the human transmission chain. There are very few studies in search of an alternate and convenient diagnostic tool which can substitute nasopharyngeal swab (NPS) specimen for detection of SARS-CoV-2. We aimed to analyse the comparison and agreement between the feasibility of using the saliva in comparison to NPS for diagnosis of SARS-CoV-2. Methods A total number of 74 patients were enrolled for this study. We analysed and compared the NPS and saliva specimen collected within 48 h after the symptom onset. We used real time quantitative polymerase chain reaction (RT-qPCR), gene sequencing for the detection and determination SARS-CoV-2 specific genes. Phylogenetic tree was constructed to establish the isolation of viral RNA from saliva. We use Bland-Altman model to identify the agreement between two sampling methods. Findings This study shows a lower CT mean value for the detection of SARS-CoV-2 ORF1 gene (27.07; 95% CI, 25.62 to 28.52) in saliva methods than that of NPS (28.24; 95% CI, 26.62 to 29.85) sampling method. Bland-Altman analysis produces relatively smaller bias and high agreement between these specimen tools. Phylogenetic analysis with the RdRp and Spike gene confirmed the presence of SARS-CoV-2 in the saliva samples. Interpretation: In conclusion, our study highlights that saliva represents a promising tool in COVID-19 diagnosis and would reduce the exposure risk of frontline health workers which is one of biggest concern in primary healthcare settings.

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“…We obtained the highest extraction and recovery efficiency for type 3 (12.4 -38.9%) and the least extraction and recovery efficiency was obtained for type 1 (3.6 -24.7%) which shows a large part of the virus remained on the swab (Table 2). Although several specimen types are listed as acceptable for SARS-CoV-2 diagnosis by the CDC and WHO, the NP swabs are still the gold standard method of sampling (4,5,20). These swabs are minimally invasive but discomfort during sampling has been highlighted in some studies inciting bleeding, nausea and vomiting in patients probably caused by the swab surface properties (9,21,22).…”

Section: Swab Viral Capture Extraction and Recovery Efficiency Analysismentioning

confidence: 99%

Comparison of three nasopharyngeal swab types and the impact of physiochemical properties for optimal SARS-CoV-2 detection

Kahamba¹,

Noble²,

Stevens

et al. 2020

Preprint

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Adequate swab specimen collection, release and detection of nucleic acids by molecular diagnostic assays is largely attributed to the physical and chemical characteristics of different swab types. We investigated properties of three types of commercial nasopharyngeal swabs (nylon flocked: Type 1-Media Merge; Type 2- Kang Jian Medical Apparatus, China and Type 3- Wuxi NEST Biotechnology Co. Ltd, China) used in clinical diagnostics with the aim to establish if different swab designs and configurations had any effect on swab performance. Properties investigated included viral absorption, release, capture, extraction and recovery efficiency from each swab for the detection of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). All swab types (n=18) were inoculated with different amounts of SARS-CoV-2 live viral cultures (1:10, 1:100 and 1:1000 copies/ml) and eluted in sterile phosphate buffer saline. RNA was extracted from all swab eluates using a fully automated system (BD MAX System) and cycle threshold (Ct) values were compared. RNA stability was also investigated after dry storage of swabs at room temperature for 72 hours. Statistically significant differences (p<0.05) were observed in the absorption and release capabilities between Type 1 and 3 as well as between Type 2 and 3 swabs, however, no significant difference was observed between Type 1 and 2. Ct values and extraction efficiency amounts of SARS-CoV-2 varied amongst the swab types. We conclude that in order to facilitate accurate SARS-CoV-2 diagnosis, assessment of NP swab characteristics is of importance before implementation for specimen collection in the clinical setting.

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Safety management of nasopharyngeal specimen collection from suspected cases of coronavirus disease 2019

Cited by 49 publications

References 0 publications

Diagnosing SARS-CoV-2 infection: the danger of over-reliance on positive test results

Diagnosing SARS-CoV-2 infection: the danger of over-reliance on positive test results

Saliva as a potential clinical specimen for diagnosis of SARS-CoV-2

Comparison of three nasopharyngeal swab types and the impact of physiochemical properties for optimal SARS-CoV-2 detection

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