Assessment of Sensitivity and Specificity of Patient-Collected Lower Nasal Specimens for Severe Acute Respiratory Syndrome Coronavirus 2 Testing

Altamirano, Jonathan; Govindarajan, Prasanthi; Blomkalns, Andra L.; Kushner, Lauren E.; Stevens, Bryan; Pinsky, Benjamin A.; Maldonado, Yvonne

doi:10.1001/jamanetworkopen.2020.12005

Cited by 59 publications

(68 citation statements)

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“…Our data support that self-sampling by OP swab is dependable, and thus provides an alternative method for unsupervised or remotely supervised sample acquisition outside of a healthcare setting. OP and other methods of self-sampling could enable sample processing by mail, which can greatly enhance testing coverage 28,29 . Another advantage of self-collection is that the person can control the swabbing and stop if they experience extreme discomfort.…”

Section: Discussionmentioning

confidence: 99%

CRISPR-based and RT-qPCR surveillance of SARS-CoV-2 in asymptomatic individuals uncovers a shift in viral prevalence among a university population

Rauch

Valois

Ponce-Rojas

et al. 2020

Preprint

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Background: The progress of the COVID-19 pandemic profoundly impacts the health of communities around the world, with unique impacts on colleges and universities. Transmission of SARS-CoV-2 by asymptomatic people is thought to be the underlying cause of a large proportion of new infections. However, the local prevalence of asymptomatic and pre-symptomatic carriers of SARS-CoV-2 is influenced by local public health restrictions and the community setting. Objectives: This study has three main objectives. First, we looked to establish the prevalence of asymptomatic SARS-CoV-2 infection on a university campus in California. Second, we sought to assess the changes in viral prevalence associated with the shifting community conditions related to non-pharmaceutical interventions (NPIs). Third, we aimed to compare the performance of CRISPR- and PCR-based assays for large-scale virus surveillance sampling in COVID-19 asymptomatic persons. Methods: We enrolled 1,808 asymptomatic persons for self-collection of oropharyngeal (OP) samples to undergo SARS-CoV-2 testing. We compared viral prevalence in samples obtained in two time periods: May 28th-June 11th; June 23rd-July 2nd. We detected viral genomes in these samples using two assays: CREST, a CRISPR-based method recently developed at UCSB, and the RT-qPCR test recommended by US Centers for Disease Control and Prevention (CDC). Results: Of the 1,808 participants, 1,805 were affiliates of the University of California, Santa Barbara, and 1,306 were students. None of the tests performed on the 732 samples collected between late May to early June were positive. In contrast, tests performed on the 1076 samples collected between late June to early July, revealed nine positive cases. This change in prevalence met statistical significance, p = 0.013. One sample was positive by RT-qPCR at the threshold of detection, but negative by both CREST and CLIA-confirmation testing. With this single exception, there was perfect concordance in both positive and negative results obtained by RT-qPCR and CREST. The estimated prevalence of the virus, calculated using the confirmed cases, was 0.74%. The average age of our sample population was 28.33 (18-75) years, and the average age of the positive cases was 21.7 years (19-30). Conclusions: Our study revealed that there were no COVID-19 cases in our study population in May/June. Using the same methods, we demonstrated a substantial shift in prevalence approximately one month later, which coincided with changes in community restrictions and public interactions. This increase in prevalence, in a young and asymptomatic population which would not have otherwise accessed COVID-19 testing, indicated the leading wave of a local outbreak, and coincided with rising case counts in the surrounding county and the state of California. Our results substantiate that large, population-level asymptomatic screening using self-collection may be a feasible and instructive aspect of the public health approach within large campus communities, and the almost perfect concordance between CRISPR- and PCR-based assays indicate expanded options for surveillance testing

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Section: Discussionmentioning

confidence: 99%

CRISPR-based and RT-qPCR surveillance of SARS-CoV-2 in asymptomatic individuals uncovers a shift in viral prevalence among a university population

Rauch

Valois

Ponce-Rojas

et al. 2020

Preprint

View full text Add to dashboard Cite

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“…A recent study showed that patient-collected foam nasal swabs were comparable to health care worker-collected NP swabs for collecting SARS-CoV-2 virus, providing a safer and less invasive sampling method [ 5 ]. Similarly, another independent study demonstrated that patient-collected nasal swabs were comparable to health care worker-collected oropharyngeal or nasal swabs [ 6 ]. These results validate findings for influenza testing [ 7 , 8 ].…”

Section: Introductionmentioning

confidence: 99%

A comparison of health care worker-collected foam and polyester nasal swabs in convalescent COVID-19 patients

Hart

Jennings

et al. 2020

PLoS ONE

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Both polyester and foam nasal swabs were collected from convalescent COVID-19 patients at a single visit and stored in viral transport media (VTM), saline or dry. Sensitivity of each swab material and media combination were estimated, three by three tables were constructed to measure polyester and foam concordance, and cycle threshold (Ct) values were compared. 126 visits had polyester and foam swabs stored in viral transport media (VTM), 51 had swabs stored in saline, and 63 had a foam swab in VTM and a polyester swab stored in a dry tube. Polyester and foam swabs had an estimated sensitivity of 87.3% and 94.5% respectively in VTM, 87.5% and 93.8% respectively in saline, and 75.0% and 90.6% respectively for dry polyester and foam VTM. Polyester and foam Ct values were correlated, but polyester showed decreased performance for cases with a viral load near the detection threshold and higher Ct values on average.

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“…This is consistent with results in the U.S. population and in MN specifically during the period these samples were collected. The sensitivity of our screening tests might have been low due to the use self-collected NPS, although recent studies report self-collection protocols to have acceptable sensitivity 9,10 . Tests among symptom-free individuals could also have reduced sensitivity, however, prior studies in asymptomatic pregnant women 11,12 and residents of long-term care facilities 13 Our results suggest that while the healthcare worker force is very likely to be at increased relative risk for infection compared to the general population 8 , the point prevalence of SARS-CoV-2 infection was low in symptom-free Minnesota healthcare workers.…”

Section: Discussionmentioning

confidence: 99%

SARS-CoV-2 Screening Among Symptom-Free Healthcare Workers

Demmer

Ulrich

Wiggen

et al. 2020

Preprint

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Importance: Current evidence suggests that transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is possible among symptom-free individuals but limited data are available on this topic in healthcare workers (HCW). The quality and acceptability of self-collected nasopharyngeal swabs (NPS) is unknown. Objective: To estimate the prevalence of SARS-CoV-2 infection and to assess the acceptability of self-collected NPS among HCW. Design: Cross-sectional convenience sample enrolled between April 20th and June 24th, 2020. We had >95% power to detect at least one positive test if the true underlying prevalence of SARS-CoV2 was > 1%. Setting: The metropolitan area surrounding Minneapolis and St. Paul, Minnesota. Participants: HCW free of self-reported upper respiratory symptoms were recruited. Exposures: Participants completed questionnaires regarding demographics, household characteristics, personal protective equipment (PPE) utilization and comorbidities. Outcomes: A participant self-collected nasopharyngeal swab (NPS) was obtained. SARS-CoV-2 infection was assessed via polymerase chain reaction. NPS discomfort was assessed on a scale of 1 (no discomfort) - 10 (extreme discomfort). NPS duration and depth into the nasopharynx, and willingness to perform future self-collections were assessed. Results: Among n=489 participants 80% were female and mean age+/-SD was 41+/-11. Participants reported being physicians (14%), nurse practitioners (8%), physicians assistants (4%), nurses (51%), medics (3%), or other which predominantly included laboratory technicians and administrative roles (22%). Exposure to a known/suspected COVID-19 case in the 14 days prior to enrollment was reported in 40% of participants. SARS-CoV-2 was not detected in any participant. The mean+/-SD discomfort level of the NPS was 4.5+/-2.0. 95% of participants reported that their self-swab was longer than or equal to the duration of patient swabs they had previously performed, and 89% reported the depth to be deeper than or equal to the depth of previous patient swabs. Over 95% of participants reported a willingness to repeat a self-collected NP swab in the future. Conclusions and Relevance: The point prevalence of SARS-CoV-2 infection was likely very low in symptom-free Minnesota healthcare workers from April 20th and June 24th, 2020. Self-collected NP swabs are well-tolerated and a viable alternative to provider-collected swabs to preserve PPE.

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Assessment of Sensitivity and Specificity of Patient-Collected Lower Nasal Specimens for Severe Acute Respiratory Syndrome Coronavirus 2 Testing

Abstract: Participant 27 was asymptomatic but had been exposed to sudden acute respiratory syndrome coronavirus 2 by close contact 4 days before the study swab was obtained.

Cited by 59 publications

References 1 publication

CRISPR-based and RT-qPCR surveillance of SARS-CoV-2 in asymptomatic individuals uncovers a shift in viral prevalence among a university population

CRISPR-based and RT-qPCR surveillance of SARS-CoV-2 in asymptomatic individuals uncovers a shift in viral prevalence among a university population

A comparison of health care worker-collected foam and polyester nasal swabs in convalescent COVID-19 patients

SARS-CoV-2 Screening Among Symptom-Free Healthcare Workers

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