Nasopharyngeal versus nasal swabs for detection of SARS-CoV-2: a systematic review

There is a need for more precise models to assess the determinants of health crises like COVID-19

The COVID-19 pandemic has had a significant impact on global mortality. While the causal relationship between SARS-CoV-2 and the anomalous increase in deaths is established, more precise and complex models are needed to determine the exact weight of epidemiological factors involved. Indeed, COVID-19 behavior is influenced by a wide range of variables, including demographic characteristics, population habits and behavior, healthcare performance, and environmental and seasonal risk factors. The bidirectional causality between impacted and impacting aspects, as well as confounding variables, complicates efforts to draw clear, generalizable conclusions regarding the effectiveness and cost-benefit ratio of non-pharmaceutical health countermeasures. Thus, it is imperative that the scientific community and health authorities worldwide develop comprehensive models not only for the current pandemic but also for future health crises. These models should be implemented locally to account for micro-differences in epidemiological characteristics that may have relevant effects. It is important to note that the lack of a universal model does not imply that local decisions have been unjustified, and the request to decrease scientific uncertainty does not mean denying the evidence of the effectiveness of the countermeasures adopted. Therefore, this paper must not be exploited to denigrate either the scientific community or the health authorities.

Performance Analysis of Self-Collected Nasal and Oral Swabs for Detection of SARS-CoV-2

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the third highly pathogenic human coronavirus and is rapidly transmitted by infected individuals regardless of their symptoms. During the COVID-19 pandemic, owing to the dearth of skilled healthcare workers (HCWs) to collect samples for early diagnosis, self-collection emerged as a viable alternative. To evaluate the reliability of self-collection, we compared the virus detection rate using 3990 self-collected swabs and HCW-collected swabs, procured from the same individuals and collected immediately after the self-collection. The results of multiplex reverse-transcription quantitative polymerase chain reaction revealed that the viral load in the HCW-collected swabs was marginally (18.4–28.8 times) higher than that in self-collected swabs. Self-collection showed no significant difference in sensitivity and specificity from HCW-collection (κ = 0.87, McNemar’s test; p = 0.19), indicating a comparable performance. These findings suggest that self-collected swabs are acceptable substitutes for HCW-collected swabs, and that their use improved the specimen screening efficiency and reduced the risk of SARS-CoV-2 infection among HCWs during and after the COVID-19 pandemic.

Comparison of the SARS-CoV-2 BD Veritor Nasal Antigen Test with Nasopharyngeal Reverse Transcription-PCR in Symptomatic Patients

This study evaluated the BD Veritor system for rapid detection of SARS-CoV-2, an immunochromatographic point-of-care test, by comparing it with a standard reverse transcription-PCR (RT-PCR) methodology using samples from symptomatic patients. Samples from 146 symptomatic and 2 asymptomatic patients between the 1st and the 40th day of infection were evaluated. The nasopharyngeal and/or oropharyngeal swabs were inserted in a tube containing 0.9% saline solution and stored at refrigerator temperature until the moment of use. The samples were first tested with the Xpert Xpress SARS-CoV-2 (GeneXpert) kit (RT-PCR method), and the cycle thresholds (C_Ts) for the E and N2 genes encoding the SARS-CoV-2 envelope and nucleoprotein, respectively, were established. Subsequently, the same samples were tested using the Veritor rapid test. We analyzed the C_Ts of the N2 gene, which is detected in both methodologies, and observed sensitivities of 100%, 98.8%, 89.6%, and 82.7% for the C_Ts of <25, <27, and <30 and all the C_Ts, respectively. The greatest sensitivity was observed when we performed the test on patients within 5 days of symptom onset. The BD Veritor system’s workflow is simple and fast, taking approximately 16 min from sample preparation to obtaining the test result. In addition to its satisfactory sensitivity, with results that correlate with those of the RT-PCR, the BD Veritor analyzer instrument reduces the subjectivity of unaided visual readings and consequent potential variation in result interpretation. Therefore, our results showed that the BD Veritor diagnostic test can provide a rapid and accurate diagnosis for SARS-CoV-2.

IMPORTANCE This study provides important and useful information, especially for diagnostic laboratories, since the results show that the BD Veritor system can provide a fast and safe point-of-care antigen diagnostic test for rapid detection of COVID-19 that has high sensitivity, reproducibility, and accuracy.

Very High Negative Concordance Rate of RT-PCR for SARS-CoV-2 in Nasopharyngeal Swab and Tracheo-Bronchial Aspirate in Children

Reliable testing methods for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in children are essential to allow normal activities. Diagnosis of SARS-CoV-2 infection is currently based on real-time reverse transcriptase-polymerase chain reaction (RT-PCR) performed on nasopharyngeal (NP) swabs; concerns have been raised regarding NP swab accuracy in children to detect the virus because of potential lack of cooperation of the patients or due to general uncertainties about concordance between high and low respiratory tract specimens in children. The aim of the study (IRB approval: ST/2020/405) is to prospectively compare RT-PCR results on NP and tracheo-bronchial aspirate (TA) in children admitted to the hospital for surgery or admitted to the Pediatric Intensive Care Unit (PICU) of a tertiary children hospital in Milano, Italy, during a peak of COVID-19 infections in the city. A total of 385 patients were enrolled in the study: 364 from surgical theater and 21 from PICU. Two patients (0.5%) tested positive on TA and were negative on NP; both cases occurred in November 2020, during a peak of infection in the city. Specificity of NP swab was.995 (95% CI: 0.980-0.999). Two patients with positive NP swabs tested negative on TA.

CONCLUSION

Our study shows that the specificity of SARS-CoV-2 RT-PCR on TA swab, compared to results of SARS-CoV-2 RT-PCR on NP, was very high for negative cases in our pediatric cohort during a period of high epidemiological pressure.