Self-collection: An appropriate alternative during the SARS-CoV-2 pandemic.
Author(s): Wehrhahn MC, Robson J, Brown S, Bursle E, Byrne S, New D, Chong S, Newcombe JP, Siversten T, Hadlow N
Publication: J Clin Virol, 2020, Vol. 128, Page 104417
PubMed ID: 32403007 PubMed Review Paper? No
Purpose of Paper
This paper compared detection of SARS-CoV-2, the virus that causes the novel 2019 coronavirus disease (COVID, COVID-19, COVID19), and other respiratory viruses between self-collected throat and nasal swabs and healthcare worker-collected swabs.
Conclusion of Paper
Diagnoses were 89% concordant between self-collected and healthcare worker-collected swabs. The sensitivity of self-collected and healthcare worker-collected swabs were 100% and 96%, respectively, for SARS-CoV-2 and 94% and 91%, respectively, for other respiratory viruses. In general, the CT values for detection of SARS-CoV-2 E-gene, SARS-CoV-2 N-gene, rhinovirus, and parainfluenza were lower in healthcare worker-collected swabs (combination of nasal and throat) than self-collected throat or nasal swabs but the significance depended on the collection location and the virus.
Studies
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Study Purpose
This study compared detection of SARS-CoV-2 and other respiratory viruses between self-collected throat and nasal swabs and healthcare worker-collected swabs. A total of 212 patients (59 at Site 1 and 153 at Site 2) undergoing screening for SARS-CoV-2 and 24 patients recently diagnosed with SARS-CoV-2 (11 at Site 1 and 13 at Site 2) self-collected specimens from the throat and nose using open-cell polyurethane foam swabs and placed in Amies medium. Nasal swabs were collected by insertion of the swab as far into the nostril as comfortable (≥ 2-3 cm) and rotating five times. Following self-collection, throat and nasal swabs were obtained by healthcare workers from all patients undergoing screening using open-cell polyurethane foam swabs at Site 1 and flocked NP swabs for nasal collection and the open-cell polyurethane foam swabs for the throat collection at Site 2. RNA was extracted from the specimens using the MagNA Pure 96 System and SARS-CoV-2 was detected using the real-time RT-PCR based Allplex 2019-nCoV Assay at Site 1 and an in-house real-time RT-PCR assay targeting the E gene with N-gene amplification performed on the positives. The real-time RT-PCR based Seegene RV Essential Assay was used to screen for other respiratory viruses including influenza A, influenza B, parainfluenza, Respiratory Syncytial Virus (RSV), human metapneumovirus (HMPV), adenovirus, and rhinovirus. Results for healthcare worker-collected swabs were not separated based on collection location.
Summary of Findings:
Overall, diagnoses were 89% concordant between self-collected and healthcare worker-collected swabs (92.9% at Site 1 and 86.3% at Site 2). Overall, the sensitivity of self-collected and healthcare worker-collected swabs were 100% and 96%, respectively, for SARS-CoV-2 and 94% and 91%, respectively, for other respiratory viruses. For specimens collected at Site 1, the detection of SARS-CoV-2 did not differ between self-collected and healthcare worker-collected swabs but detection of non-SARS-CoV-2 viruses was 6% higher in self-collected swabs. In four or five cases of discordance at Site 1, the self-collected swab was positive for non-coronavirus respiratory viruses (two cases of parainfluenza, one case of rhinovirus, and one case with coinfection of rhinovirus and influenza A) while the healthcare worker-collected swabs were negative for all viruses. In the fifth case, co-infection of rhinovirus and RSV was found in the healthcare collected swab, but no viruses were detected in the self-collected swab. At Site 2, SARS-CoV-2 infection was only detected in the self-collected nasal swab of one of the confirmed SARS-CoV-2 patients and not in the healthcare worker-collected specimen. Additionally, there was one more case each of rhinovirus and parainfluenza and one fewer cases of adenovirus among healthcare worker-collected specimens than in self-collected swabs.
When detected, the CT value for the SARS-CoV-2 E-gene was comparable in the self-collected nasal swab specimen and the healthcare worker-collected swab (combined locations) specimens but was higher in the self-collected throat swabs specimen then the healthcare worker-collected specimen (P<0.001). However, the CT value for the SARS-CoV-2 N-gene was higher in self-collected throat and nasal swab specimens than the healthcare worker-collected specimens (P<0.001 and P=0.006, respectively). Similarly, the CT value for rhinovirus was higher in self-collected throat and nasal swab specimens than the healthcare worker-collected specimens (P<0.001 and P=0.002, respectively). In patients with parainfluenza, the CT values were higher in self-collected than healthcare worker-collected nasal swabs (P=0.014) but did not differ between self-collected and healthcare worker-collected throat specimens.
Biospecimens
Preservative Types
- None (Fresh)
Diagnoses:
- Pneumonia/Respiratory Infection
Platform:
Analyte Technology Platform RNA Real-time qRT-PCR Pre-analytical Factors:
Classification Pre-analytical Factor Value(s) Biospecimen Acquisition Biospecimen location Nostril
Throat/Tonsil
Real-time qRT-PCR Specific Targeted nucleic acid SARS-CoV-2 E gene
SARS-CoV-2 N gene
Biospecimen Acquisition Method of cell acquisition Healthcare worker collected
Self collected