Self-collection: An appropriate alternative during the SARS-CoV-2 pandemic

The effect of sample site and collection procedure on identification of SARS-CoV-2 infection

BACKGROUND

Sample collection is a key driver of accuracy in the diagnosis of SARS-CoV-2 infection. Viral load may vary at different anatomical sampling sites and accuracy may be compromised by difficulties obtaining specimens and the expertise of the person taking the sample. It is important to optimise sampling accuracy within cost, safety and accessibility constraints.

OBJECTIVES

To compare the sensitivity of different sampling collection sites and methods for the detection of current SARS-CoV-2 infection with any molecular or antigen-based test.

SEARCH METHODS

Electronic searches of the Cochrane COVID-19 Study Register and the COVID-19 Living Evidence Database from the University of Bern (which includes daily updates from PubMed and Embase and preprints from medRxiv and bioRxiv) were undertaken on 22 February 2022. We included independent evaluations from national reference laboratories, FIND and the Diagnostics Global Health website. We did not apply language restrictions.

SELECTION CRITERIA

We included studies of symptomatic or asymptomatic people with suspected SARS-CoV-2 infection undergoing testing. We included studies of any design that compared results from different sample types (anatomical location, operator, collection device) collected from the same participant within a 24-hour period.

DATA COLLECTION AND ANALYSIS

Within a sample pair, we defined a reference sample and an index sample collected from the same participant within the same clinical encounter (within 24 hours). Where the sample comparison was different anatomical sites, the reference standard was defined as a nasopharyngeal or combined naso/oropharyngeal sample collected into the same sample container and the index sample as the alternative anatomical site. Where the sample comparison was concerned with differences in the sample collection method from the same site, we defined the reference sample as that closest to standard practice for that sample type. Where the sample pair comparison was concerned with differences in personnel collecting the sample, the more skilled or experienced operator was considered the reference sample. Two review authors independently assessed the risk of bias and applicability concerns using the QUADAS-2 and QUADAS-C checklists, tailored to this review. We present estimates of the difference in the sensitivity (reference sample (%) minus index sample sensitivity (%)) in a pair and as an average across studies for each index sampling method using forest plots and tables. We examined heterogeneity between studies according to population (age, symptom status) and index sample (time post-symptom onset, operator expertise, use of transport medium) characteristics.

MAIN RESULTS

This review includes 106 studies reporting 154 evaluations and 60,523 sample pair comparisons, of which 11,045 had SARS-CoV-2 infection. Ninety evaluations were of saliva samples, 37 nasal, seven oropharyngeal, six gargle, six oral and four combined nasal/oropharyngeal samples. Four evaluations were of the effect of operator expertise on the accuracy of three different sample types. The majority of included evaluations (146) used molecular tests, of which 140 used RT-PCR (reverse transcription polymerase chain reaction). Eight evaluations were of nasal samples used with Ag-RDTs (rapid antigen tests). The majority of studies were conducted in Europe (35/106, 33%) or the USA (27%) and conducted in dedicated COVID-19 testing clinics or in ambulatory hospital settings (53%). Targeted screening or contact tracing accounted for only 4% of evaluations. Where reported, the majority of evaluations were of adults (91/154, 59%), 28 (18%) were in mixed populations with only seven (4%) in children. The median prevalence of confirmed SARS-CoV-2 was 23% (interquartile (IQR) 13%-40%). Risk of bias and applicability assessment were hampered by poor reporting in 77% and 65% of included studies, respectively. Risk of bias was low across all domains in only 3% of evaluations due to inappropriate inclusion or exclusion criteria, unclear recruitment, lack of blinding, nonrandomised sampling order or differences in testing kit within a sample pair. Sixty-eight percent of evaluation cohorts were judged as being at high or unclear applicability concern either due to inflation of the prevalence of SARS-CoV-2 infection in study populations by selectively including individuals with confirmed PCR-positive samples or because there was insufficient detail to allow replication of sample collection. When used with RT-PCR • There was no evidence of a difference in sensitivity between gargle and nasopharyngeal samples (on average -1 percentage points, 95% CI -5 to +2, based on 6 evaluations, 2138 sample pairs, of which 389 had SARS-CoV-2). • There was no evidence of a difference in sensitivity between saliva collection from the deep throat and nasopharyngeal samples (on average +10 percentage points, 95% CI -1 to +21, based on 2192 sample pairs, of which 730 had SARS-CoV-2). • There was evidence that saliva collection using spitting, drooling or salivating was on average -12 percentage points less sensitive (95% CI -16 to -8, based on 27,253 sample pairs, of which 4636 had SARS-CoV-2) compared to nasopharyngeal samples. We did not find any evidence of a difference in the sensitivity of saliva collected using spitting, drooling or salivating (sensitivity difference: range from -13 percentage points (spit) to -21 percentage points (salivate)). • Nasal samples (anterior and mid-turbinate collection combined) were, on average, 12 percentage points less sensitive compared to nasopharyngeal samples (95% CI -17 to -7), based on 9291 sample pairs, of which 1485 had SARS-CoV-2. We did not find any evidence of a difference in sensitivity between nasal samples collected from the mid-turbinates (3942 sample pairs) or from the anterior nares (8272 sample pairs). • There was evidence that oropharyngeal samples were, on average, 17 percentage points less sensitive than nasopharyngeal samples (95% CI -29 to -5), based on seven evaluations, 2522 sample pairs, of which 511 had SARS-CoV-2. A much smaller volume of evidence was available for combined nasal/oropharyngeal samples and oral samples. Age, symptom status and use of transport media do not appear to affect the sensitivity of saliva samples and nasal samples. When used with Ag-RDTs • There was no evidence of a difference in sensitivity between nasal samples compared to nasopharyngeal samples (sensitivity, on average, 0 percentage points -0.2 to +0.2, based on 3688 sample pairs, of which 535 had SARS-CoV-2).

AUTHORS' CONCLUSIONS

When used with RT-PCR, there is no evidence for a difference in sensitivity of self-collected gargle or deep-throat saliva samples compared to nasopharyngeal samples collected by healthcare workers when used with RT-PCR. Use of these alternative, self-collected sample types has the potential to reduce cost and discomfort and improve the safety of sampling by reducing risk of transmission from aerosol spread which occurs as a result of coughing and gagging during the nasopharyngeal or oropharyngeal sample collection procedure. This may, in turn, improve access to and uptake of testing. Other types of saliva, nasal, oral and oropharyngeal samples are, on average, less sensitive compared to healthcare worker-collected nasopharyngeal samples, and it is unlikely that sensitivities of this magnitude would be acceptable for confirmation of SARS-CoV-2 infection with RT-PCR. When used with Ag-RDTs, there is no evidence of a difference in sensitivity between nasal samples and healthcare worker-collected nasopharyngeal samples for detecting SARS-CoV-2. The implications of this for self-testing are unclear as evaluations did not report whether nasal samples were self-collected or collected by healthcare workers. Further research is needed in asymptomatic individuals, children and in Ag-RDTs, and to investigate the effect of operator expertise on accuracy. Quality assessment of the evidence base underpinning these conclusions was restricted by poor reporting. There is a need for further high-quality studies, adhering to reporting standards for test accuracy studies.

Self-Collection for HPV Testing: Potential Issues Related to Performance Measures and Quality Improvement Among Federally Qualified Health Centers

CONTEXT

Most incident cases of cervical cancer in the United States are attributable to inadequate screening. Federally qualified health centers (FQHCs) serve a large proportion of women who are low-income, have no insurance, and are underserved-risk factors for insufficient cervical cancer screening. FQHCs must maintain quality measures to preserve their accreditation, address financial reimbursements, and provide quality care. Implementation of human papillomavirus (HPV) self-collection can improve cervical cancer screening coverage within FQHCs.

OBJECTIVES

To understand perspectives from clinical personnel on current cervical cancer screening rates at FQHCs in North Carolina and the impact of implementing HPV self-collection among underscreened patients on screening rates and performance measures.

DESIGN

The study used focus groups and key informant interviews. Coding-based thematic analysis was applied to both focus group and interview transcripts. Emergent themes regarding perspectives on self-collection implementation were mapped onto Consolidated Framework for Implementation Research (CFIR) constructs to identify future barriers and facilitators to implementation.

SETTING

Two FQHCs in North Carolina and a cloud-based videoconferencing platform.

PARTICIPANTS

Six FQHCs in North Carolina; 45 clinical and administrative staff from the 6 FQHCs; 1 chief executive officer (n = 6), 1 senior-level administrator (n = 6), 1 chief medical officer (n = 6), and 1 clinical data manager (n = 6) from each FQHC.

MAIN OUTCOME MEASURE

Achievement of clinical perspectives.

RESULTS

Societal-, practice-, and patient-level factors currently contribute to subpar cervical cancer screening rates. HPV self-collection was expected to improve screening uptake among underscreened women at FQHCs, and thus quality and performance measures, by offering an alternative screening approach for in-clinic or at-home use. Implementation barriers include financial uncertainties and HPV self-collection not yet a Food and Drug Administration-approved test.

CONCLUSION

HPV self-collection has potential to improve cervical cancer screening quality and performance measures of FQHCs. For a successful implementation, multilevel factors that are currently affecting low screening uptake need to be addressed. Furthermore, the financial implications of implementation and approval of HPV self-collection as a test for cervical cancer screening quality measures need to be resolved.

The Infectious Diseases Society of America Guidelines on the Diagnosis of COVID-19: Molecular Diagnostic Testing (December 2023)

Accurate molecular diagnostic tests are necessary for confirming a diagnosis of coronavirus disease 2019 (COVID-19) and for identifying asymptomatic carriage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The number of available SARS-CoV-2 nucleic acid detection tests continues to increase as does the COVID-19 diagnostic literature. Thus, the Infectious Diseases Society of America (IDSA) developed an evidence-based diagnostic guideline to assist clinicians, clinical laboratorians, patients, and policymakers in decisions related to the optimal use of SARS-CoV-2 nucleic acid amplification tests. In addition, we provide a conceptual framework for understanding molecular diagnostic test performance, discuss nuances of test result interpretation in a variety of practice settings, and highlight important unmet research needs related to COVID-19 diagnostic testing. IDSA convened a multidisciplinary panel of infectious diseases clinicians, clinical microbiologists, and experts in systematic literature review to identify and prioritize clinical questions and outcomes related to the use of SARS-CoV-2 molecular diagnostics. Grading of Recommendations Assessment, Development and Evaluation (GRADE) methodology was used to assess the certainty of evidence and make testing recommendations. The panel agreed on 12 diagnostic recommendations. Access to accurate SARS-CoV-2 nucleic acid testing is critical for patient care, hospital infection prevention, and the public health response to COVID-19 infection. Information on the clinical performance of available tests continues to grow, but the quality of evidence of the current literature to support this updated molecular diagnostic guideline remains moderate to very low. Recognizing these limitations, the IDSA panel weighed available diagnostic evidence and recommends nucleic acid testing for all symptomatic individuals suspected of having COVID-19. In addition, testing is suggested for asymptomatic individuals with known or suspected contact with a COVID-19 case when the results will impact isolation/quarantine/personal protective equipment (PPE) usage decisions. Evidence in support of rapid testing and testing of upper respiratory specimens other than nasopharyngeal swabs, which offer logistical advantages, is sufficient to warrant conditional recommendations in favor of these approaches.

Molecular Detection of SARS-CoV-2 From Throat Swabs Performed With or Without Specimen Collection From the Tonsils: Protocol for a Multicenter Randomized Controlled Trial

BACKGROUND

Testing for SARS-CoV-2 is essential to provide early COVID-19 treatment for people at high risk of severe illness and to limit the spread of infection in society. Proper upper respiratory specimen collection is the most critical step in the diagnosis of the SARS-CoV-2 virus in public settings, and throat swabs were the preferred specimens used for mass testing in many countries during the COVID-19 pandemic. However, there is still a discussion about whether throat swabs have a high enough sensitivity for SARS-CoV-2 diagnostic testing, as previous studies have reported a large variability in the sensitivity from 52% to 100%. Many previous studies exploring the diagnostic accuracy of throat swabs lack a detailed description of the sampling technique, which makes it difficult to compare the different diagnostic accuracy results. Some studies perform a throat swab by only collecting specimens from the posterior oropharyngeal wall, while others also include a swab of the palatine tonsils for SARS-CoV-2 testing. However, studies suggest that the palatine tonsils could have a tissue tropism for SARS-CoV-2 that may improve the SARS-CoV-2 detection during sampling. This may explain the variation of sensitivity reported, but no clinical studies have yet explored the differences in sensitivity and patient discomfort whether the palatine tonsils are included during the throat swab or not.

OBJECTIVE

The objective of this study is to examine the sensitivity and patient discomfort of a throat swab including the palatine tonsils compared to only swabbing the posterior oropharyngeal wall in molecular testing for SARS-CoV-2.

METHODS

We will conduct a randomized controlled study to compare the molecular detection rate of SARS-CoV-2 by a throat swab performed from the posterior oropharyngeal wall and the palatine tonsils (intervention group) or the posterior oropharyngeal wall only (control group). Participants will be randomized in a 1:1 ratio. All participants fill out a baseline questionnaire upon enrollment in the trial, examining their reason for being tested, symptoms, and previous tonsillectomy. A follow-up questionnaire will be sent to participants to explore the development of symptoms after testing.

RESULTS

A total of 2315 participants were enrolled in this study between November 10, 2022, and December 22, 2022. The results from the follow-up questionnaire are expected to be completed at the beginning of 2024.

CONCLUSIONS

This randomized clinical trial will provide us with information about whether throat swabs including specimens from the palatine tonsils will improve the diagnostic sensitivity for SARS-CoV-2 molecular detection. These results can, therefore, be used to improve future testing recommendations and provide additional information about tissue tropism for SARS-CoV-2.

TRIAL REGISTRATION

ClinicalTrials.gov NCT05611203; https://clinicaltrials.gov/study/NCT05611203.

INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID)

DERR1-10.2196/47446.

At-home testing for respiratory viruses: a minireview of the current landscape

The landscape of at-home testing using over-the-counter (OTC) tests has been evolving over the last decade. The United States Food and Drug Administration Emergency Use Authorization rule has been in effect since the early 2000s, and it was widely employed during the severe acute respiratory syndrome coronavirus 2 pandemic to authorize antigen and nucleic acid detection tests for use in central laboratories as well as OTC. During the pandemic, the first at-home tests for respiratory viruses became available for consumer use, which opened the door for additional respiratory virus OTC tests. Concerns may exist regarding the public's ability to properly collect samples, perform testing, interpret results, and report results to public health authorities. However, favorable comparison studies between OTC testing and centralized laboratory test results suggest that OTC testing may have a place in healthcare, and it is likely here to stay. This mini-review of OTC tests for viral respiratory diseases will briefly cover the regulatory and reimbursement environment, current OTC test availability, as well as the advantages and limitations of OTC tests.

Diagnostic accuracy of direct reverse transcription-polymerase chain reaction using guanidine-based and guanidine-free inactivators for SARS-CoV-2 detection in saliva samples

This study aimed to evaluate diagnostic accuracy of SARS-CoV-2 RNA detection in saliva samples treated with a guanidine-based or guanidine-free inactivator, using nasopharyngeal swab samples (NPS) as referents. Based on the NPS reverse transcription-polymerase chain reaction (RT-PCR) results, participants were classified as with or without COVID-19. Fifty sets of samples comprising NPS, self-collected raw saliva, and saliva with a guanidine-based, and guanidine-free inactivator were collected from each group. In patients with COVID-19, the sensitivity of direct RT-PCR using raw saliva and saliva treated with a guanidine-based and guanidine-free inactivator was 100.0%, 65.9%, and 82.9%, respectively, with corresponding concordance rates of 94.3% (κ=88.5), 82.8% (κ=64.8), and 92.0% (κ=83.7). Among patients with a PCR Ct value of <30 in the NPS sample, the positive predictive value for the three samples was 100.0%, 80.0%, and 96.0%, respectively. The sensitivity of SARS-CoV-2 RNA detection was lower in inactivated saliva than in raw saliva and lower in samples treated with a guanidine-based than with a guanidine-free inactivator. However, in individuals contributing to infection spread, inactivated saliva showed adequate accuracy regardless of the inactivator used. Inactivators can be added to saliva samples collected for RT-PCR to reduce viral transmission risk while maintaining adequate diagnostic accuracy.

Estimating the incidence of COVID-19, influenza and respiratory syncytial virus infection in three regions of Queensland, Australia, winter 2022: findings from a novel longitudinal testing-based sentinel surveillance programme

OBJECTIVE

The 2022 Australian winter was the first time that COVID-19, influenza and respiratory syncytial virus (RSV) were circulating in the population together, after two winters of physical distancing, quarantine and borders closed to international travellers. We developed a novel surveillance system to estimate the incidence of COVID-19, influenza and RSV in three regions of Queensland, Australia.

DESIGN

We implemented a longitudinal testing-based sentinel surveillance programme. Participants were provided with self-collection nasal swabs to be dropped off at a safe location at their workplace each week. Swabs were tested for SARS-CoV-2 by PCR. Symptomatic participants attended COVID-19 respiratory clinics to be tested by multiplex PCR for SARS-CoV-2, influenza A and B and RSV. Rapid antigen test (RAT) results reported by participants were included in the analysis.

SETTING AND PARTICIPANTS

Between 4 April 2022 and 3 October 2022, 578 adults were recruited via their workplace. Due to rolling recruitment, withdrawals and completion due to positive COVID-19 results, the maximum number enrolled in any week was 423 people.

RESULTS

A total of 4290 tests were included. Participation rates varied across the period ranging from 25.9% to 72.1% of enrolled participants. The total positivity of COVID-19 was 3.3%, with few influenza or RSV cases detected. Widespread use of RAT may have resulted in few symptomatic participants attending respiratory clinics. The weekly positivity rate of SARS-CoV-2 detected during the programme correlated with the incidence of notified cases in the corresponding communities.

CONCLUSION

This testing-based surveillance programme could estimate disease trends and be a useful tool in settings where testing is less common or accessible. Difficulties with recruitment meant the study was underpowered. The frontline sentinel nature of workplaces meant participants were not representative of the general population but were high-risk groups providing early warning of disease.

Prospective, clinical comparison of self-collected throat-bilateral nares swabs and saline gargle compared to health care provider collected nasopharyngeal swabs among symptomatic outpatients with potential SARS-CoV-2 infection

Background

In British Columbia (BC), self-collected saline gargle (SG) is the only alternative to health care provider (HCP)-collected nasopharyngeal (NP) swabs to detect SARS-CoV-2 in an outpatient setting by polymerase chain reaction (PCR). However, some individuals cannot perform a SG. Our study aimed to assess combined throat-bilateral nares (TN) swabbing as a swab-based alternative.

Methods

Symptomatic individuals greater than 12 years of age seeking a COVID-19 PCR test at one of two COVID-19 collection centres in Metro Vancouver were asked to participate in this study. Participants provided a HCP-collected NP sample and a self-collected SG and TN sample for PCR testing, which were either HCP observed or unobserved.

Results

Three-hundred and eleven individuals underwent all three collections. Compared against HCP-NP, SG was 99% sensitive and 98% specific (kappa 0.97) and TN was 99% sensitive and 99% specific (kappa 0.98). Using the final clinical test interpretation as the reference standard, NP was 98% sensitive and 100% specific (kappa 0.98), and both SG and TN were 99% sensitive and 100% specific (both kappa 0.99). Mean cycle threshold values for each viral target were higher in SG specimens compared to the other sample types; however, this did not significantly impact the clinical performance, because the positivity rates were similar. The clinical performance of all specimen types was comparable within the first 7 days of symptom onset, regardless of the observation method. SG self-collections were rated the most acceptable, followed by TN.

Conclusions

TN provides another less invasive self-collection modality for symptomatic outpatient SARS-CoV-2 PCR testing.

Self-Collection for Primary HPV Testing: Perspectives on Implementation From Federally Qualified Health Centers

INTRODUCTION

Primary testing for high-risk human papillomavirus (HPV) by self-collection could result in higher rates of cervical cancer screening. Federally qualified health centers (FQHCs) in the US serve a large proportion of women who have low income and no health insurance and are medically underserved - risk factors for being insufficiently screened for cervical cancer. Although the implementation of self-collection for HPV testing is not yet widespread, health care entities need to prepare for its eventual approval by the US Food and Drug Administration. We conducted focus groups and interviews among clinical and administrative staff and leadership to gather data on key logistical concerns that must be addressed before implementing self-collection for HPV testing in FQHCs.

METHODS

We identified focus group and interview participants from 6 FQHCs in North Carolina. We conducted focus groups with clinical and administrative staff (N = 45) and semistructured interviews with chief executive officers, senior-level administrators, chief medical officers, and clinical data managers (N = 24). Transcripts were coded by using codebooks derived from research questions and notes taken during data collection. Themes emerged on implementation of self-collection for HPV testing. We applied the constructs from the Consolidated Framework for Implementation Research (CFIR) to themes to identify domains of potential barriers and facilitators to implementation.

RESULTS

Clinical personnel reported that offering self-collection for HPV testing is acceptable and feasible and can increase cervical cancer screening rates. Uncertainties emerged about accuracy of results, workflow disruptions, financial implications, and effects on clinic quality measures.

CONCLUSION

Implementing self-collection for HPV testing was considered feasible and acceptable by participants. However, important health service delivery considerations, including financial implications, must be addressed before integrating self-collection for HPV testing into the standard of care.

Dyadic Hair Cortisol Self-Collection Procedure

BACKGROUND

At-home self-collection of specimens has become more commonplace because of measures taken in response to the coronavirus pandemic. Self-collection of hair cortisol is important because chronic stress is present in many populations, such as older adults living with Alzheimer's disease and their family caregivers. For the evaluation of chronic stress, scalp hair can be used as a predictive biomarker because it examines the cumulative, retrospective stress from previous months.

OBJECTIVES

The aim of the paper is to provide a study procedure for at-home, scalp hair self-collection for cortisol concentration analysis from dyads consisting of a person living with Alzheimer's disease and their family caregiver.

METHODS

After informed electronic consent is obtained, a package containing the necessary tools for self-collection of hair samples from the dyad is mailed to the participant's home. Participants are provided detailed print and video multimedia guides outlining how to obtain the hair samples. Ideally, the hair samples are obtained during the virtual data collection meeting with research personnel. Participants mail back the hair sample in a prepaid package to the biomedical laboratory for analysis.

DISCUSSION

At-home, self-collection of hair provides potential advantages such as reduced participant burden, especially for vulnerable populations where transportation and different environments are challenging. At-home sample collection options may increase research participation and can be applied to multiple research foci. Research considerations for dyads, such as people living with Alzheimer's disease and their caregivers, are discussed.

Nasal swab as an alternative specimen for the detection of severe acute respiratory syndrome coronavirus 2

Background and Aims

The coronavirus disease 2019 (COVID-19) has brought serious threats to public health worldwide. Nasopharyngeal, nasal swabs, and saliva specimens are used to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, limited data are available on the performance of less invasive nasal swab for testing COVID-19. This study aimed to compare the diagnostic performance of nasal swabs with nasopharyngeal swabs using real-time reverse transcription polymerase chain reaction (RT-PCR) considering viral load, onset of symptoms, and disease severity.

Methods

A total of 449 suspected COVIDCOVID-19 individuals were recruited. Both nasopharyngeal and nasal swabs were collected from the same individual. Viral RNA was extracted and tested by real-time RT-PCR. Metadata were collected using structured questionnaire and analyzed by SPSS and MedCalc software.

Results

The overall sensitivity of the nasopharyngeal swab was 96.6%, and the nasal swab was 83.4%. The sensitivity of nasal swabs was more than 97.7% for low and moderate C t values. Moreover, the performance of nasal swab was very high (>87%) for hospitalized patients and at the later stage >7 days of onset of symptoms.

Conclusion

Less invasive nasal swab sampling with adequate sensitivity can be used as an alternative to nasopharyngeal swabs for the detection of SARS-CoV-2 by real-time RT-PCR.

Combined nasal- and oropharyngeal self-swab provides equivalent performance compared to professionally collected oropharyngeal swabs in detecting SARS-CoV-2 in a real-life setting

PURPOSE

To investigate the performance of a combined nasal midturbinate- and oropharyngeal (NAOP) self-swab compared to a deep oropharyngeal (OP) swab by health care workers (HCW) in detecting SARS-CoV-2 in a real-life setting.

METHODS

Paired swabs from 1119 participants were included. RT-PCR were used to detect SARS-CoV-2 in both swab samples.

RESULTS

330 participants tested positive. The sensitivity of the combined self-swab and OP swab was 96.9 % and 95.4 % respectively, whereas the Ct-values for self-swabs were significantly lower compared to OP swabs.

CONCLUSION

The combined NAOP self-swab outperformed the OP swab and thus, the NAOP self-swab may be an alternative sampling method under the given circumstances.

Accuracy of an antigen-detecting SARS-CoV-2 assay with self- and provider-collected specimens interpreted visually and with BD Veritor™ Plus analyzer

Background

SARS-CoV-2 rapid antigen tests (RATs) are in high demand for reducing the spread of SARS-CoV-2. Reduced involvement from health care professionals (HCPs) for collection and interpretation could significantly foster the wide-spread implementation of RATs, but data evaluating RATs, when used by lay people, is limited.

Objective

To valuate agreement between BD Veritor test results for self- and HCP-collected specimens, and visually- and analyzer-interpreted results.

Methods

Individuals with onset of COVID-19 symptoms within five days of enrollment had three nasal swabs collected; one self-collected and the other two HCP-collected. One HCP-collected swab was stored for future testing while the order of the other two (self and HCP) was randomized before testing. with the BD Veritor System for Rapid Detection of SARS-CoV-2. Results were first assessed visually, followed by interpretation with the analyzer.

Results

When self-collection was compared to HCP collection for SARS-CoV-2 detection, interpretation by analyzer resulted in positive percent agreement (PPA) of 94.7% (95% CI 82.7, 98.5) and negative percent agreement (NPA) of 99.0% (95% CI 97.5, 99.6). When visual interpretation was compared to analyzer-read results, collection by HCPs had a PPA of 97.4% (95% CI 86.5, 99.5) and NPA of 99.8% (95% CI 98.6, 100.0) while self-collection resulted in PPA of 94.9% (95% CI 83.1, 98.6) and NPA of 99.8% (95% CI 98.6, 100).

Conclusions

Similar PPA and NPA were observed for self- and HCP-collected specimens as well as visually- and analyzer-interpreted tests. The equivalence in performance supports the use of expanded collection and testing methods.

At-home blood self-sampling in rheumatology: a qualitative study with patients and health care professionals

BACKGROUND

The goal of the study was to investigate patients' with systemic rheumatic diseases and healthcare professionals' experiences and preferences regarding self-sampling of capillary blood in rheumatology care.

METHODS

Patients performed a supervised and consecutive unsupervised capillary blood self-collection using an upper arm based device. Subsequently, patients (n = 15) and their attending health care professionals (n = 5) participated in an explorative, qualitative study using problem-centered, telephone interviews. Interview data were analyzed using structured qualitative content analysis.

RESULTS

Interviewed patients reported easy application and high usability. Patients and health care professionals alike reported time and cost savings, increased independence and flexibility, improved monitoring and reduction of risk of infection during Covid-19 as benefits. Reported drawbacks include limited blood volume, limited usability in case of functional restrictions, and environmental concerns. Older, immobile patients with long journeys to traditional blood collection sites and young patients with little time to spare for traditional blood collection appointments could be user groups, likely to benefit from self-sampling services.

CONCLUSIONS

At-home blood self-sampling could effectively complement current rheumatology telehealth care. Appropriateness and value of this service needs to be carefully discussed with patients on an individual basis.

TRIAL REGISTRATION

WHO International Clinical Trials Registry: DRKS00024925. Registered on 15/04/2021.

Protocol for a winter sentinel surveillance program of notifiable respiratory viruses in Queensland

BACKGROUND

With the reduction in access to polymerase chain reaction (PCR) testing and changes in testing guidelines in Australia, a reduced number of people are seeking testing for coronavirus disease (COVID-19), limiting the opportunity to monitor disease transmission. Knowledge of community transmission of COVID-19 and other respiratory viruses is essential to better predict subsequent surges in cases during the pandemic to alert health services, protect vulnerable populations and enhance public health measures. We describe a methodology for a testing-based sentinel surveillance program to monitor disease in the community for early signal detection of SARS-CoV-2 and other respiratory viruses.

METHODS/DESIGN

A longitudinal active testing-based sentinel surveillance program for respiratory viruses (including SARS-CoV-2, influenza A, influenza B and Respiratory Syncytial Virus) will be implemented in some regions of Queensland. Adults will be eligible for enrolment if they are part of specific community groups at increased risk of exposure and have not had a COVID-19 infection in the last 13 weeks. Recruitment via workplaces will occur in-person, via email and through online advertisement. Asymptomatic participants will be tested via PCR for SARS-CoV-2 infection by weekly self-collected nasal swabs. In addition, symptomatic participants will be asked to seek SARS-CoV-2 and additional respiratory virus PCR testing at nominated COVID-19 testing sites. SARS-CoV-2 and respiratory virus prevalence data will be analysed weekly and at the end of the study period.

DISCUSSION

Once implemented, this surveillance program will determine the weekly prevalence of COVID-19 and other respiratory viruses in the broader community by testing a representative sample of adults, with an aim to detect early changes in the baseline positivity rate. This information is essential to define the epidemiology of SARS-CoV-2 in the community in near-real time to inform public health control measures and prepare health services and other stakeholders for a rise in service demand.

Viral load may impact the diagnostic performance of nasal swabs in nucleic acid amplification test and quantitative antigen test for SARS-CoV-2 detection

INTRODUCTION

Compared to nasopharyngeal swabs (NPS), there has been insufficient evaluation of the diagnostic performance of nasal swabs (NS) for the detection of severe acute respiratory coronavirus 2 (SARS-CoV-2) in the nucleic acid amplification test (NAAT) and quantitative SARS-CoV-2 antigen test (QAT).

METHODS

We prospectively compared healthcare worker-collected and flocked NS within nine days after symptom onset to paired NPS to detect SARS-CoV-2 in NAAT and QAT on the fully automated Lumipulse system. The agreement between sample types was evaluated, and cycle threshold (Ct) values and antigen levels were used as surrogate viral load measures.

RESULTS

Sixty sets of NPS and NS samples were collected from 40 patients with COVID-19. The overall agreements between NAAT and QAT samples were 76.7% and 65.0%, respectively. In NAAT, the Ct value of NS was significantly higher, 5.9, than that of NPS. Thirty-nine (95.1%) NS tested positive in 41 positive-paired NPS with Ct ≤ 30. The negative correlation was observed between antigen levels of NS in QAT and Ct values of NS in NAAT (r = -0.88). In QAT, the antigen level of NS was significantly lower than that of NPS. Thirty-six (90.0%) NS tested positive in 40 positive-paired NPS with antigen levels >100 pg/mL, which were collected significantly earlier than those with antigen levels ≤100 pg/mL.

CONCLUSIONS

In NAAT and QAT, NS had limited performance in detecting SARS-CoV-2 compared to NPS. However, NS may be helpful for patients with COVID-19 with high viral loads or those in the early stages of the illness.

Identifying SARS-CoV-2 Variants of Concern through Saliva-Based RT-qPCR by Targeting Recurrent Mutation Sites

SARS-CoV-2 variants of concern (VOCs) continue to pose a public health threat which necessitates a real-time monitoring strategy to complement whole genome sequencing. Thus, we investigated the efficacy of competitive probe RT-qPCR assays for six mutation sites identified in SARS-CoV-2 VOCs and, after validating the assays with synthetic RNA, performed these assays on positive saliva samples. When compared with whole genome sequence results, the SΔ69-70 and ORF1aΔ3675-3677 assays demonstrated 93.60 and 68.00% accuracy, respectively. The SNP assays (K417T, E484K, E484Q, L452R) demonstrated 99.20, 96.40, 99.60, and 96.80% accuracies, respectively. Lastly, we screened 345 positive saliva samples from 7 to 22 December 2021 using Omicron-specific mutation assays and were able to quickly identify rapid spread of Omicron in Upstate South Carolina. Our workflow demonstrates a novel approach for low-cost, real-time population screening of VOCs. IMPORTANCE SARS-CoV-2 variants of concern and their many sublineages can be characterized by mutations present within their genetic sequences. These mutations can provide selective advantages such as increased transmissibility and antibody evasion, which influences public health recommendations such as mask mandates, quarantine requirements, and treatment regimens. Our RT-qPCR workflow allows for strain identification of SARS-CoV-2 positive saliva samples by targeting common mutation sites shared between variants of concern and detecting single nucleotides present at the targeted location. This differential diagnostic system can quickly and effectively identify a wide array of SARS-CoV-2 strains, which can provide more informed public health surveillance strategies in the future.

Perceptions of COVID-19 self-testing and recommendations for implementation and scale-up among Black/African Americans: implications for the COVID-19 STEP project

BACKGROUND

COVID-19 self-testing (ST) is an innovative strategy with the potential to increase the access and uptake of testing and ultimately to limit the spread of the virus. To maximize the uptake and reach of this promising strategy and inform intervention development and scale up, research is needed to understand the acceptability of and willingness to use this tool. This is vital to ensure that Black/African Americans are reached by the Biden-Harris Administration's free national COVID-19 ST program. This study aimed to explore the acceptability and recommendations to promote and scale-up the uptake of COVID-19 ST among Black/African Americans.

METHODS

We conducted a cross-sectional qualitative study using a semi-structured questionnaire to assess barriers and facilitators to the uptake of COVID-19 ST among a convenience sample of 28 self-identified Black/African Americans from schools, community centers, and faith-based institutions in Ohio and Maryland. Inductive content analysis was conducted to identify categories and subcategories related to acceptability and recommendations for implementing and scaling up COVID-19 ST in communities.

RESULTS

Participants perceived COVID-19 self-testing as an acceptable tool that is beneficial to prevent transmission and address some of the barriers associated with health facility testing, such as transportation cost and human contact at the health facility. However, concerns were raised regarding the accurate use of the kits and costs. Recommendations for implementing and scaling up COVID-19 ST included engagement of community stakeholders to disseminate information about COVID-19 self-testing and creating culturally appropriate education tools to promote knowledge of and clear instructions about how to properly use COVID-19 ST kits. Based on these recommendations, the COVID-19 STEP (Self-Testing Education and Promotion) Project is being developed and will involve engaging community partners such as barbers, church leaders, and other community-based organizations to increase the uptake and use of free COVID-19 ST kits among Black/African Americans.

CONCLUSION

Findings showed that most participants considered COVID-19 ST valuable for encouraging COVID-19 testing. However, cost and accuracy concerns may pose barriers. Future work should consider implementing interventions that leverage the benefits of COVID-19 ST and further assess the extent to which these identified facilitators and barriers may influence COVID-19 ST uptake.

Detection of SARS-CoV-2 RNA by Reverse Transcription-Polymerase Chain Reaction (RT-PCR) on Self-Collected Nasal Swab Compared With Professionally Collected Nasopharyngeal Swab

Background: Self-collection of nasal swabs for the detection of SARS-CoV-2 RNA by reverse transcription-polymerase chain reaction (RT-PCR) would considerably increase the testing capability and decrease the risk of transmission among healthcare workers (HCW) and the use of personal protective equipment (PPE).

Objectives: This study aimed to evaluate the performance of self-collected nasal swabs compared with professionally collected nasopharyngeal (NP) swabs for detection of SARS-CoV-2 RNA by RT-PCR.

Materials and methods: We performed a cross-sectional study where the suspected cases of coronavirus disease 2019 (COVID-19) were instructed about the self-collection of nasal swabs from their mid-turbinate. The results were compared to a nasopharyngeal swab collected by a trained healthcare worker in the same patient at the same sitting.

Results: We enrolled 100 participants, of which, 69 (69%) were male and 31 (31%) were female. The median age of the study participant was 36 years. Of the participants, 58 (58%) were symptomatic, and the commonest clinical presentation was cough, which was present in 42 (42%) participants. Out of 100 samples, 31 (31%) professionally collected nasopharyngeal swabs and 28 (28%) self-collected nasal swabs were positive for SARS-CoV-2 by RT-PCR. Out of 31 professionally collected positive samples, three samples were negative in self-collection. Out of 28 self-collected positive samples, no sample was negative in the professional collection. The sensitivity and specificity of self-collected nasal swabs compared to professionally collected nasopharyngeal swabs were 90.32% and 100.00%, respectively. The sensitivity of self-collected nasal was 100% when the cycle threshold (Ct) value of the professionally collected NP swab was less than 30.

Conclusion: Our study showed that self-collected nasal swabs' sensitivities were similar to professionally collected NP swabs with a high viral load (low Ct value). Hence, this method could be used when the patient is symptomatic and come to the health providers in the early stage of COVID-19 illness.

K–8 Classroom Self-Collection Using XpressCollect Nasal Swab: A Usability and Efficacy Study

This study demonstrates that students in kindergarten through eighth grade can use the XpressCollect nasal swab to self-collect a specimen under the guidance of a teacher. This phased study was conducted with parents, teachers, and students. Phases 1 and 2 were conducted as interviews with teachers and parents to assess the suitability of the XpressCollect for children in kindergarten through eighth grade. Additionally, teacher and parent feedback was obtained to develop and optimize the instructional materials for subsequent phases. In Phases 3 and 4, teachers guided small groups and full classes of students through the sample collection process with XpressCollect. The samples collected by the students were sent to a laboratory to analyze the effectiveness of specimen self-collection based on the presence of ribonuclease P (RNase P) on each nasal swab. The presence of RNase P enables disease determination; thus, student samples were analyzed for adequate or inadequate sampling. All students in kindergarten through eighth grade are capable of self-collecting an anterior nares specimen with XpressCollect, as the laboratory results identified acceptable RNase P Ct values for the samples collected in a classroom setting.

Implementation of a Rural Community Diagnostic Testing Strategy for SARS-CoV-2 in Upstate South Carolina

By developing a partnership amongst a public university lab, local city government officials and community healthcare providers, we established a drive-through COVID-19 testing site aiming to improve access to SARS-CoV-2 testing in rural Upstate South Carolina. We collected information on symptoms and known exposures of individuals seeking testing to determine the number of pre- or asymptomatic individuals. We completed 71,102 SARS-CoV-2 tests in the community between December 2020-December 2021 and reported 91.49% of results within 24 h. We successfully identified 5,244 positive tests; 73.36% of these tests originated from individuals who did not report symptoms. Finally, we identified high transmission levels during two major surges and compared test positivity rates of the local and regional communities. Importantly, the local community had significantly lower test positivity rates than the regional community throughout 2021 (p < 0.001). While both communities reached peak case load and test positivity near the same time, the local community returned to moderate transmission as indicated by positivity 4 weeks before the regional community. Our university lab facilitated easy testing with fast turnaround times, which encouraged voluntary testing and helped identify a large number of non-symptomatic cases. Finding the balance of simplicity, accessibility, and community trust was vital to the success of our widespread community testing program for SARS-CoV-2.

SARS-CoV-2 Diagnostics Based on Nucleic Acids Amplification: From Fundamental Concepts to Applications and Beyond

COVID-19 pandemic ignited the development of countless molecular methods for the diagnosis of SARS-CoV-2 based either on nucleic acid, or protein analysis, with the first establishing as the most used for routine diagnosis. The methods trusted for day to day analysis of nucleic acids rely on amplification, in order to enable specific SARS-CoV-2 RNA detection. This review aims to compile the state-of-the-art in the field of nucleic acid amplification tests (NAATs) used for SARS-CoV-2 detection, either at the clinic level, or at the Point-Of-Care (POC), thus focusing on isothermal and non-isothermal amplification-based diagnostics, while looking carefully at the concerning virology aspects, steps and instruments a test can involve. Following a theme contextualization in introduction, topics about fundamental knowledge on underlying virology aspects, collection and processing of clinical samples pave the way for a detailed assessment of the amplification and detection technologies. In order to address such themes, nucleic acid amplification methods, the different types of molecular reactions used for DNA detection, as well as the instruments requested for executing such routes of analysis are discussed in the subsequent sections. The benchmark of paradigmatic commercial tests further contributes toward discussion, building on technical aspects addressed in the previous sections and other additional information supplied in that part. The last lines are reserved for looking ahead to the future of NAATs and its importance in tackling this pandemic and other identical upcoming challenges.

Perceptions of COVID-19 Self-Testing and Recommendations for Implementation and Scale up Among Black/African Americans: Implications for the COVID-19 STEP Project

Background COVID-19 self-testing (ST) is an innovative strategy with the potential to increase the access and uptake of testing and ultimately to limit the spread of the virus. To maximize the uptake and reach of this promising strategy and inform intervention development and scale up, research is needed to understand the acceptability of and willingness to use this tool. This is vital to ensure that Black/African Americans are reached by the Biden-Harris Administration’s free national COVID-19 ST program. This study aimed to explore the acceptability and recommendations to promote and scale up the uptake of COVID-19 ST among Black/African Americans. Methods We conducted a cross-sectional qualitative study using a semi-structured survey to assess barriers and facilitators to the uptake of COVID-19 ST among a convenience sample of 28 self-identified Black/African Americans from schools, community centers, and faith-based institutions in Ohio and Maryland. Inductive content analysis was conducted to identify categories and subcategories related to acceptability and recommendations for implementing and scaling up COVID-19 ST in communities. Results Participants perceived COVID-19 self-testing as an acceptable tool that is beneficial to prevent transmission and address some of the barriers associated with health facility testing, such as transportation cost and human contact at the health facility. However, concerns were raised regarding the accurate use of the kits and costs. Recommendations for implementing and scaling up COVID-19 ST included engagement of community stakeholders to disseminate information about COVID-19 self-testing and creating culturally appropriate education tools to promote knowledge of and clear instructions about how to properly use COVID-19 ST kits. Based on these recommendations, the COVID-19 STEP (Self-Testing Education and Promotion) Project is being developed and will involve engaging community partners such as barbers, church leaders, and other community-based organizations to increase the uptake and use of free COVID-19 ST kits among Black/African Americans. Conclusion Findings showed that most participants considered COVID-19 ST valuable for encouraging COVID-19 testing. However, cost and accuracy concerns may pose barriers. Future work should consider implementing interventions that leverage the benefits of COVID-19 ST and further assess the extent to which these identified facilitators and barriers may influence COVID-19 ST uptake.

Efficient SARS-CoV-2 Quantitative Reverse Transcriptase PCR Saliva Diagnostic Strategy utilizing Open-Source Pipetting Robots

The emergence of the recent SARS-CoV-2 global health crisis introduced key challenges for epidemiological research and clinical testing. Characterized by a high rate of transmission and low mortality, the COVID-19 pandemic necessitated accurate and efficient diagnostic testing, particularly in closed populations such as residential universities. Initial availability of nucleic acid testing, like nasopharyngeal swabs, was limited due to supply chain pressure which also delayed reporting of test results. Saliva-based reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) testing has shown to be comparable in sensitivity and specificity to other testing methods, and saliva collection is less physically invasive to participants. Consequently, we developed a multiplex RT-qPCR diagnostic assay for population surveillance of Clemson University and the surrounding community. The assay utilized open-source liquid handling robots and thermocyclers instead of complex clinical automation systems to optimize workflow and system flexibility. Automation of saliva-based RT-qPCR enables rapid and accurate detection of a wide range of viral RNA concentrations for both large- and small-scale testing demands. The average turnaround for the automated system was < 9 h for 95% of samples and < 24 h for 99% of samples. The cost for a single test was $2.80 when all reagents were purchased in bulk quantities.

Acceptability of OP/Na swabbing for SARS-CoV-2: a prospective observational cohort surveillance study in Western Australian schools

OBJECTIVES

When the COVID-19 pandemic was declared, Governments responded with lockdown and isolation measures to combat viral spread, including the closure of many schools. More than a year later, widespread screening for SARS-CoV-2 is critical to allow schools and other institutions to remain open. Here, we describe the acceptability of a minimally invasive COVID-19 screening protocol trialled by the Western Australian Government to mitigate the risks of and boost public confidence in schools remaining open. To minimise discomfort, and optimise recruitment and tolerability in unaccompanied children, a combined throat and nasal (OP/Na) swab was chosen over the nasopharyngeal swab commonly used, despite slightly reduced test performance.

DESIGN, SETTING AND PARTICIPANTS

Trialling of OP/Na swabbing took place as part of a prospective observational cohort surveillance study in 79 schools across Western Australia. Swabs were collected from 5903 asymptomatic students and 1036 asymptomatic staff in 40 schools monthly between June and September 2020.

OUTCOME MEASURES

PCR testing was performed with a two-step diagnostic and independent confirmatory PCR for any diagnostic PCR positives. Concurrent surveys, collected online through the REDCap platform, evaluated participant experiences of in-school swabbing.

RESULTS

13 988 swabs were collected from students and staff. There were zero positive test results for SARS-CoV-2, including no false positives. Participants reported high acceptability: 71% of students reported no or minimal discomfort and most were willing to be reswabbed (4% refusal rate).

CONCLUSIONS

OP/Na swabbing is acceptable and repeatable in schoolchildren as young as 4 years old and may combat noncompliance rates by significantly increasing the acceptability of testing. This kind of minimally-invasive testing will be key to the success of ongoing, voluntary mass screening as society adjusts to a new 'normal' in the face of COVID-19.

TRIAL REGISTRATION NUMBER

Australian New Zealand Clinical Trials Registry-ACTRN12620000922976.

Side-by-side comparison of parent vs. technician-collected respiratory swabs in low-income, multilingual, urban communities in the United States

Background

Home-based swabbing has not been widely used. The objective of this analysis was to compare respiratory swabs collected by mothers of 7–12-year-olds living in low-income, multilingual communities in the United States with technician collected swabs.

Methods

Retrospective data analysis of respiratory samples collected at home by mothers compared to technicians. Anterior nasal and throat specimens collected using flocked swabs were combined in dry tubes. Test was done using TaqMan array cards for viral and bacterial pathogens. Cycle threshold (Ct) values of ribonuclease P (RNP) gene were used to assess specimen quality. Ct < 40 was interpreted as a positive result. Concordance of pathogen yield from mother versus technician collected swabs were analyzed using Cohen’s Kappa coefficients. Correlation analysis, paired t-test, and Wilcoxon signed-rank test for paired samples were used for RNP Ct values.

Results

We enrolled 36 households in Cincinnati (African American) and 44 (predominately Chinese or Latino) in Boston. In Cincinnati, eight of 32 (25%) mothers did not finish high school, and 11 (34%) had finished high school only. In Boston, 13 of 44 (30%) mothers had less than a high school diploma, 23 (52%) had finished high school only. Mother versus technician paired swabs (n = 62) had similar pathogen yield (paired t-test and Wilcoxon signed rank test p-values = 0.62 and 0.63, respectively; 95% confidence interval of the difference between the two measurements = − 0.45–0.75). Median Ct value for RNP was 22.6 (interquartile range, IQR = 2.04) for mother-collected and 22.4 (IQR = 2.39) for technician-collected swabs (p = 0.62). Agreement on pathogen yield between samples collected by mothers vs. technicians was higher for viruses than for bacterial pathogens, with high concordance for rhinovirus/enterovirus, human metapneumovirus, and adenovirus (Cohen’s kappa coefficients ≥80%, p < 0.0001). For bacterial pathogens, concordance was lower to moderate, except for Chlamydia pneumoniae, for which kappa coefficient indicated perfect agreement.

Conclusion

Mothers with a range of education levels from low-income communities were able to swab their children equally well as technicians. Home-swabbing using dry tubes, and less invasive collection procedures, could enhance respiratory disease surveillance.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12889-022-12523-3.

A Telemedicine-Guided Self-Collection Approach for PCR-Based SARS-CoV-2 Testing: Comparative Study

Background

Large-scale, polymerase chain reaction (PCR)-based SARS-CoV-2 testing is expensive, resource intensive, and time consuming. A self-collection approach is a probable alternative; however, its feasibility, cost, and ability to prevent infections need to be evaluated.

Objective

This study aims to compare an innovative self-collection approach with a regular SARS-CoV-2 testing strategy in a large European industrial manufacturing site.

Methods

The feasibility of a telemedicine-guided PCR-based self-collection approach was assessed for 150 employees (intervention group) and compared with a regular SARS-CoV-2 testing approach used for 143 employees (control group). Acceptance, ergonomics, and efficacy were evaluated using a software application. A simulation model was implemented to evaluate the effectiveness. An interactive R shiny app was created to enable customized simulations.

Results

The test results were successfully communicated to and interpreted without uncertainty by 76% (114/150) and 76.9% (110/143) of the participants in the intervention and control groups, respectively (P=.96). The ratings for acceptability, ergonomics, and efficacy among intervention group participants were noninferior when compared to those among control group participants (acceptability: 71.6% vs 37.6%; ergonomics: 88.1% vs 74.5%; efficacy: 86.4% vs 77.5%). The self-collection approach was found to be less time consuming (23 min vs 38 min; P<.001). The simulation model indicated that both testing approaches reduce the risk of infection, and the self-collection approach tends to be slightly less effective owing to its lower sensitivity.

Conclusions

The self-collection approach for SARS-CoV-2 diagnosis was found to be technically feasible and well rated in terms of acceptance, ergonomics, and efficacy. The simulation model facilitates the evaluation of test effectiveness; nonetheless, considering context specificity, appropriate adaptation by companies is required.

Evaluation of the Practicability of Biosynex Antigen Self-Test COVID-19 AG+ for the Detection of SARS-CoV-2 Nucleocapsid Protein from Self-Collected Nasal Mid-Turbinate Secretions in the General Public in France

Due to their ease-of-use, lateral flow assay SARS-CoV-2 antigen-detecting rapid diagnostic tests could be suitable candidates for antigen-detecting rapid diagnostic self-test (Ag-RDST). We evaluated the practicability of the Ag-RDST BIOSYNEX Antigen Self-Test COVID-19 Ag+ (Biosynex Swiss SA, Freiburg, Switzerland), using self-collected nasal secretions from the turbinate medium (NMT), in 106 prospectively included adult volunteers living in Paris, France. The majority of the participants correctly understood the instructions for use (94.4%; 95% confidence interval (CI): 88.3-97.4), showing a great ability to perform the entire self-test procedure to obtain a valid and interpretable result (100%; 95% CI: 96.5-100), and demonstrated the ability to correctly interpret test results (96.2%; 95% CI: 94.2-97.5) with a high level of general satisfaction. About one in eight participants (# 15%) needed verbal help to perform or interpret the test, and only 3.8% of test results were misinterpreted. By reference to multiplex real-time RT-PCR, the Ag-RDST showed 90.9% and 100% sensitivity and specificity, respectively, and high agreement (98.1%), reliability (0.94), and accuracy (90.9%) to detect SARS-CoV-2 antigen. Taken together, our study demonstrates the high usability and accuracy of BIOSYNEX Antigen Self-Test COVID-19 Ag+ for supervised self-collected NMT sampling in an unselected adult population living in France.

Prospective Study of the Performance of Parent-Collected Nasal and Saliva Swab Samples, Compared with Nurse-Collected Swab Samples, for the Molecular Detection of Respiratory Microorganisms

Respiratory tract infections (RTIs) are ubiquitous among children in the community. A prospective observational study was performed to evaluate the diagnostic performance and quality of at-home parent-collected (PC) nasal and saliva swab samples, compared to nurse-collected (NC) swab samples, from children with RTI symptoms. Children with RTI symptoms were swabbed at home on the same day by a parent and a nurse. We compared the performance of PC swab samples as the test with NC swab samples as the reference for the detection of respiratory pathogen gene targets by reverse transcriptase PCR, with quality assessment using a human gene. PC and NC paired nasal and saliva swab samples were collected from 91 and 92 children, respectively. Performance and interrater agreement (Cohen's κ) of PC versus NC nasal swab samples for viruses combined showed sensitivity of 91.6% (95% confidence interval [CI], 85.47 to 95.73%) and κ of 0.84 (95% CI, 0.79 to 0.88), respectively; the respective values for bacteria combined were 91.4% (95% CI, 86.85 to 94.87%) and κ of 0.85 (95% CI, 0.80 to 0.89). In saliva samples, viral and bacterial sensitivities were lower at 69.0% (95% CI, 57.47 to 79.76%) and 78.1% (95% CI, 71.60 to 83.76%), as were κ values at 0.64 (95% CI, 0.53 to 0.72) and 0.70 (95% CI, 0.65 to 0.76), respectively. Quality assessment for human biological material (18S rRNA) indicated perfect interrater agreement. At-home PC nasal swab samples performed comparably to NC swab samples, whereas PC saliva swab samples lacked sensitivity for the detection of respiratory microbes. IMPORTANCE RTIs are ubiquitous among children. Diagnosis involves a swab sample being taken by a health professional, which places a considerable burden on community health care systems, given the number of cases involved. The coronavirus disease 2019 (COVID-19) pandemic has seen an increase in the at-home self-collection of upper respiratory tract swab samples without the involvement of health professionals. It is advised that parents conduct or supervise swabbing of children. Surprisingly, few studies have addressed the quality of PC swab samples for subsequent identification of respiratory pathogens. We compared NC and PC nasal and saliva swab samples taken from the same child with RTI symptoms, for detection of respiratory pathogens. The PC nasal swab samples performed comparably to NC samples, whereas saliva swab samples lacked sensitivity for the detection of respiratory microbes. Collection of swab samples by parents would greatly reduce the burden on community nurses without reducing the effectiveness of diagnoses.

Usability of an At-Home Anterior Nares SARS-CoV-2 RT-PCR Sample Collection Kit: Human Factors Feasibility Study

Background

Readily available testing for SARS-CoV-2 is necessary to mitigate COVID-19 disease outbreaks. At-home collection kits, in which samples are self-collected without requiring a laboratory or clinic visit and sent to an external laboratory for testing, can provide convenient testing to those with barriers to access. They can prevent unnecessary exposure between patient and clinical staff, increase access for patients with disabilities or remote workers, and decrease burdens on health care resources, such as provider time and personal protective equipment. Exact Sciences developed an at-home collection kit for samples to be tested to detect SARS-CoV-2 that includes an Instructions for Use (IFU) document, which guides people without prior experience on collecting a nasal swab sample. Demonstrating successful sample collection and usability is critical to ensure that these samples meet the same high-quality sample collection standards as samples collected in clinics.

Objective

The aim of this study was to determine the usability of a SARS-CoV-2 at-home nasal swab sample collection kit.

Methods

A human factors usability study was conducted with 30 subjects without prior medical, laboratory, or health care training and without COVID-19 sample self-collection experience. Subjects were observed while they followed the IFU for the at-home sample collection portion of the SARS-CoV-2 test in a setting that simulated a home environment. IFU usability was further evaluated by requiring the subjects to complete a survey, answer comprehension questions, provide written feedback, and respond to questions from the observer about problems during use.

Results

All 30 subjects successfully completed the sample collection process, and all 30 samples were determined by reverse transcription–polymerase chain reaction (RT-PCR) testing to meet quality standards for SARS-CoV-2 testing. The subjects’ written feedback and comments revealed several recommendations to improve the IFU.

Conclusions

The study demonstrated the overall usability of an at-home SARS-CoV-2 collection kit. Various feedback mechanisms provided opportunities to improve the wording and graphics for some critical tasks, including placing the label correctly on the tube. A modified IFU was prepared based on study outcomes.

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

Nasopharyngeal swabbing (NPS) coupled with RT-PCR is the current gold standard for detecting SARS-CoV-2 infections. However, numerous studies have recently demonstrated the advantages of alternative nasal specimen collection approaches over NPS specifically for COVID-19 diagnosis. The present review was conducted according to PRISMA guidelines and summarises the current literature to give a clear overview of nasal specimen collection methods for SARS-CoV-2 detection. Publications investigating NPS and at least one other form of nasal specimen collection in combination with RT-PCR for viral detection in the context of COVID-19 were assessed. We identified 425 articles and ultimately included 18 studies in this systematic review. The suitable publications evaluated different forms of nasal specimen collection, with anterior nasal swabbing (ANS) and midturbinate swabbing (MTS) being the most frequently examined techniques. The analysed studies report sensitivity and specificity results (67.5-96.2% and 97.9-100.0%, respectively) similar to those achieved via NPS, especially in the early stages of disease or when paired with an oropharyngeal swab. Results from these studies suggest that ANS and MTS are suitable alternatives to NPS for COVID-19 testing. Due to their ease of collection, ANS and MTS collection techniques may facilitate broader testing strategies and allow for economization of medical staff.

Accuracy and Acceptance of a Self-Collection Model for Respiratory Tract Infection Diagnostics: A Concise Clinical Literature Review

Background

Nurses are the primary clinicians who collect specimens for respiratory tract infection testing. The specimen collection procedure is time and resource-consuming, but more importantly, it places nurses at risk for potential infection. The practice of allowing patients to self-collect their diagnostic specimens may provide an alternative testing model for the current COVID-19 outbreaks. The objective of this paper was to evaluate the accuracy and patient perception of self-collected specimens for respiratory tract infection diagnostics.

Methods

A concise clinical review of the recently published literature was conducted.

Results

A total of 11 articles were included the review synthesis. The concept of self-collected specimens has a high patient acceptance rate of 83-99%. Self-collected nasal-swab specimens demonstrated strong diagnostic fidelity for respiratory tract infections with a sensitivity between 80-100%, this is higher than the 76% sensitivity observed with self-collected throat specimens. In a comparative study evaluating a professionally collected to a self-collected specimen for COVID-19 testing, a high degree of agreement (k = 0.89) was observed between the two methods.

Conclusion

As we continue to explore for testing models to combat the COVID-19 pandemic, self-collected specimens is a practical alternative to nurse specimen collection.

Self-collection and pooling of samples as resources-saving strategies for RT-PCR-based SARS-CoV-2 surveillance, the example of travelers in French Polynesia

In French Polynesia, the first case of SARS-CoV-2 infection was detected on March 10^th, 2020, in a resident returning from France. Between March 28^th and July 14^th, international air traffic was interrupted and local transmission of SARS-CoV-2 was brought under control, with only 62 cases recorded. The main challenge for reopening the air border without requiring travelers to quarantine on arrival was to limit the risk of re-introducing SARS-CoV-2. Specific measures were implemented, including the obligation for all travelers to have a negative RT-PCR test for SARS-CoV-2 carried out within 3 days before departure, and to perform another RT-PCR testing 4 days after arrival. Because of limitation in available medical staff, travelers were provided a kit allowing self-collection of oral and nasal swabs. In addition to increase our testing capacity, self-collected samples from up to 10 travelers were pooled before RNA extraction and RT-PCR testing. When a pool tested positive, RNA extraction and RT-PCR were performed on each individual sample. We report here the results of COVID-19 surveillance (COV-CHECK PORINETIA) conducted between July 15^th, 2020, and February 15^th, 2021, in travelers using self-collection and pooling approaches. We tested 5,982 pools comprising 59,490 individual samples, and detected 273 (0.46%) travelers positive for SARS-CoV-2. A mean difference of 1.17 Ct (CI 95% 0.93–1.41) was found between positive individual samples and pools (N = 50), probably related to the volume of samples used for RNA extraction (200 μL versus 50 μL, respectively). Retrospective testing of positive samples self-collected from October 20^th, 2020, using variants-specific amplification kit and spike gene sequencing, found at least 6 residents infected by the Alpha variant. Self-collection and pooling approaches allowed large-scale screening for SARS-CoV-2 using less human, material and financial resources. Moreover, this strategy allowed detecting the introduction of SARS-CoV-2 variants of concern in French Polynesia.

Reliable detection of SARS-CoV-2 with patient-collected swabs and saline gargles: A three-headed comparison on multiple molecular platforms

With increasing demands for SARS-CoV-2 testing, as well as the shortages for testing supplies, collection devices, and trained healthcare workers (HCWs) to collect specimens, self-collection is an attractive prospect to reduce the need for HCWs and expenditure of personal protective equipment. Apart from the traditional nasopharyngeal swab used for SARS-CoV-2 detection, alternative specimens have been validated such as a combined swabs of the oropharynx and anterior nares (OP/N), or throat samples using saline gargles. Both the alternative specimen types are amenable to self-collection. Objectives. This study aimed to compare the sensitivity of HCW-collected (OP/N) swabs, self-collected OP/N swabs, and self-collected saline gargles. Among 38 individuals previously testing positive for SARS-CoV-2 (or their close contacts), two self-collected specimen types (OP/N and saline gargles) were compared to HCW-collected OP/N swabs. SARS-CoV-2 testing was performed on three molecular assays: a laboratory-developed test (LDT), and two commercial assays on automated platforms: Cobas 6800 (Roche Diagnostics) and Panther (Hologic). The sensitivity of self-collected OP/N swabs was equivalent to healthcare worker (HCW)-collected OP/N swabs at 100.0 % [92.6%-100.0%] for all three molecular tests. The sensitivity of saline gargles was not significantly different than HCW-collected OP/N swabs, but varied slightly between instruments at 93.8 % [85.9%-93.8%] for the LDT, 96.8 % [88.6%-96.8%] for the Cobas assay, and 96.7 % [89.2%-96.9%] for the Panther assay. Overall, self-collection using OP/N swabs or saline gargles are reasonable alternatives to HCW-based collections for SARS-CoV-2 detection, and could facilitate broader surveillance strategies.

Nasal Swab Performance by Collection Timing, Procedure, and Method of Transport for Patients with SARS-CoV-2

The urgent need for large-scale diagnostic testing for SARS-CoV-2 has prompted interest in sample collection methods of sufficient sensitivity to replace nasopharynx (NP) sampling. Nasal swab samples are an attractive alternative; however, previous studies have disagreed over how nasal sampling performs relative to NP sampling. Here, we compared nasal versus NP specimens collected by health care workers in a cohort of individuals clinically suspected of COVID-19 as well as SARS-CoV-2 reverse transcription (RT)-PCR-positive outpatients undergoing follow-up. We compared subjects being seen for initial evaluation versus follow-up, two different nasal swab collection protocols, and three different transport conditions, including traditional viral transport media (VTM) and dry swabs, on 307 total study participants. We compared categorical results and viral loads to those from standard NP swabs collected at the same time from the same patients. All testing was performed by RT-PCR on the Abbott SARS-CoV-2 RealTime emergency use authorization (EUA) (limit of detection [LoD], 100 copies viral genomic RNA/ml transport medium). We found low concordance overall, with Cohen's kappa (κ) of 0.49, with high concordance only for subjects with very high viral loads. We found medium concordance for testing at initial presentation (κ = 0.68) and very low concordance for follow-up testing (κ = 0.27). Finally, we show that previous reports of high concordance may have resulted from measurement using assays with sensitivity of ≥1,000 copies/ml. These findings suggest nasal-swab testing be used for situations in which viral load is expected to be high, as we demonstrate that nasal swab testing is likely to miss patients with low viral loads.

Self-collected oral, nasal and saliva samples yield sensitivity comparable to professionally collected oro-nasopharyngeal swabs in SARS-CoV-2 diagnosis among symptomatic outpatients

Introduction

Containing COVID-19 requires broad-scale testing. However, sample collection requires qualified personnel and protective equipment and may cause transmission. We assessed the sensitivity of SARS-CoV-2-rtPCR applying three self-sampling techniques as compared to professionally collected oro-nasopharyngeal samples (cOP/NP).

Methods

From 62 COVID-19 outpatients, we obtained: (i) multi-swab, MS; (ii) saliva sponge combined with nasal vestibula, SN; (iii) gargled water, GW; (iv) professionally collected cOP/NP (standard). We compared ct-values for E-gene and ORF1ab and analysed variables reducing sensitivity of self-collecting procedures.

Results

The median ct-values for E-gene and ORF1ab obtained in cOP/NP samples were 20.7 and 20.2, in MS samples 22.6 and 21.8, in SN samples 23.3 and 22.3, and in GW samples 30.3 and 29.8, respectively. MS and SN samples showed sensitivities of 95.2% (95%CI, 86.5-99.0) and GW samples of 88.7% (78.1-95.3). Sensitivity was inversely correlated with ct-values, and became <90% for samples obtained more than 8 days after symptom onset. For MS and SN samples, false negativity was associated with language problems, sampling errors, and symptom duration.

Conclusion

Conclusions from this study are limited to the sensitivity of self-sampling in mildly to moderately symptomatic patients. Still, self-collected oral/nasal/saliva samples can facilitate up-scaling of testing in early symptomatic COVID-19 patients if operational errors are minimized.

Detection of Severe Acute Respiratory Syndrome Coronavirus 2 on Self-Collected Saliva or Anterior Nasal Specimens Compared With Healthcare Personnel-Collected Nasopharyngeal Specimens

BACKGROUND

Nasopharyngeal specimens (NPS) are commonly used for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing but can be uncomfortable for patients. Self-collected saliva specimens (SS) or anterior nasal specimens (ANS) for SARS-CoV-2 detection are less invasive, but the sensitivity of these specimen types has not been thoroughly evaluated.

METHODS

During September-November 2020, 730 adults undergoing SARS-CoV-2 testing at community testing events and homeless shelters in Denver provided self-collected SS and ANS before NPS collection and answered a short survey about symptoms and specimen preference. Specimens were tested for SARS-CoV-2 by means of real-time reverse-transcription polymerase chain reaction (rRT-PCR); viral culture was performed on a subset of specimens positive by rRT-PCR. The sensitivity of SS and ANS for SARS-CoV-2 detection by rRT-PCR was measured against that of NPS. Subgroup analyses included test outcomes by symptom status and culture results.

RESULTS

Sensitivity for SARS-CoV-2 detection by rRT-PCR appeared higher for SS than for ANS (85% vs 80%) and higher among symptomatic participants than among those without symptoms (94% vs 29% for SS; 87% vs 50% for ANS). Among participants with culture-positive SARS-CoV-2 by any specimen type, the sensitivities of SS and ANS by rRT-PCR were 94% and 100%, respectively. SS and ANS were equally preferred by participants; most would undergo NPS collection again despite this method's being the least preferred.

CONCLUSIONS

SS were slightly more sensitive than ANS for SARS-CoV-2 detection with rRT-PCR. With both SS and ANS, SARS-CoV-2 was reliably detected among participants with symptoms. Self-collected SS and ANS offer practical advantages, are preferred by patients, and might be most useful for testing people with coronavirus disease 2019 symptoms.

Take-home kits to detect respiratory viruses among healthcare personnel: Lessons learned from a cluster randomized clinical trial

BACKGROUND

Health care personnel (HCP) working in outpatient settings routinely interact with patients with acute respiratory illnesses. Absenteeism following symptom development and lack of staff trained to obtain samples limit efforts to identify pathogens among infected HCP.

METHODS

The Respiratory Protection Effectiveness Clinical Trial assessed respiratory infection incidence among HCP between 2011 and 2015. Research assistants obtained anterior nasal and oropharyngeal swabs from HCP in the workplace following development of respiratory illness symptoms and randomly while asymptomatic. Participants received take-home kits to self-collect swabs when absent from work. Samples mailed to a central laboratory were tested for respiratory viruses by reverse transcription polymerase chain reaction.

RESULTS

Among 2,862 participants, 3,467 swabs were obtained from symptomatic participants. Among symptomatic HCP, respiratory virus was detected in 904 of 3,467 (26.1%) samples. Self-collected samples by symptomatic HCP at home had higher rates of viral detection (40.3%) compared to 24% obtained by trained research assistants in the workplace (P < .001).

CONCLUSIONS

In this randomized clinical trial, take-home kits were an easily implemented, effective method to self-collect samples by HCP. Other studies have previously shown relative equivalence of self-collected samples to those obtained by trained healthcare workers. Take-home kit self-collection could diminish workforce exposures and decrease the demand for personnel protective equipment worn to protect workers who collect respiratory samples.

A Systematic Review and Meta-analysis of Upper Airway Swab Collection for Detection of Viral and Bacterial Pathogens by Individuals or Caregivers Compared to Health Care Workers

Self- or caregiver collection of upper airway swabs reduces infectious exposures of health care workers (HCWs) and the need to redeploy clinical staff to testing roles. We aimed to determine whether self- or caregiver collection has adequate diagnostic performance for detection of viral and bacterial upper airway pathogens. We did a systematic review and meta-analysis of studies comparing diagnostic accuracy of self- or caregiver-collected upper airway swabs collected by patients or caregivers compared to HCWs. All study types except case reports and series were included if sufficient data were presented to calculate sensitivity, specificity, and Cohen's kappa. Studies published from 1946 to 17 August 2020 were included in the search. We did a meta-analysis to assess pooled sensitivity and specificity. Twenty studies were included in the systematic review and 15 in the meta-analysis. The overall sensitivity of swabs collected by patients or caregivers compared to HCWs was 91% (95% confidence interval [CI], 87 to 94), and specificity was 98% (95% CI, 96 to 99). Sensitivity ranged from 65% to 100% and specificity from 73% to 100% across the studies. All but one study concluded that self- or caregiver-collected swabs were acceptable for detection of upper airway pathogens. Self- and caregiver collection of upper airway swabs had reassuring diagnostic performance for multiple pathogens. There are numerous potential benefits of self- and caregiver-collected swabs for patients, families, researchers, and health systems. Further research to optimize implementation of sample collection by patients and caregivers is warranted.

Self-sampling versus health care professional-guided swab collection for SARS-CoV-2 testing

Purpose

To evaluate the diagnostic reliability and practicability of self-collected oropharyngeal swab samples for the detection of SARS-CoV-2 infection as self-sampling could enable broader testing availability and reduce both personal protective equipment and potential exposure.

Methods

Hospitalized SARS-CoV-2-infected patients were asked to collect two oropharyngeal swabs (SC-OPS1/2), and an additional oropharyngeal swab was collected by a health care professional (HCP-OPS). SARS-CoV-2 PCR testing for samples from 58 participants was performed, with a 48-h delay in half of the self-collected samples (SC-OPS2). The sensitivity, probability of concordance, and interrater reliability were calculated. Univariate and multivariate analyses were performed to assess predictive factors. Practicability was evaluated through a questionnaire.

Results

The test sensitivity for HCP-OPS, SC-OPS1, and SC-OPS2 was 88%, 78%, and 77%, respectively. Combining both SC-OPS results increased the estimated sensitivity to 88%. The concordance probability between HCP-OPS and SC-OPS1 was 77.6% and 82.5% between SC-OPS1 and SC-OPS2, respectively. Of the participants, 69% affirmed performing future self-sampling at home, and 34% preferred self-sampling over HCP-guided testing. Participants with both positive HCP-OPS1 and SC-OPS1 indicating no challenges during self-sampling had more differences in viral load levels between HCP-OPS1 and SC-OPS1 than those who indicated challenges. Increasing disease duration and the presence of anti-SARS-CoV-2-IgG correlated with negative test results in self-collected samples of previously confirmed SARS-CoV-2 positive individuals.

Conclusion

Oropharyngeal self-sampling is an applicable testing approach for SARS-CoV-2 diagnostics. Self-sampling tends to be more effective in early versus late infection and symptom onset, and the collection of two distinct samples is recommended to maintain high test sensitivity.

Supplementary Information

The online version contains supplementary material available at 10.1007/s15010-021-01614-9.

Excellent option for mass testing during the SARS-CoV-2 pandemic: painless self-collection and direct RT-qPCR

The early identification of asymptomatic yet infectious cases is vital to curb the 2019 coronavirus (COVID-19) pandemic and to control the disease in the post-pandemic era. In this paper, we propose a fast, inexpensive and high-throughput approach using painless nasal-swab self-collection followed by direct RT-qPCR for the sensitive PCR detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This approach was validated in a large prospective cohort study of 1038 subjects, analysed simultaneously using (1) nasopharyngeal swabs obtained with the assistance of healthcare personnel and analysed by classic two-step RT-qPCR on RNA isolates and (2) nasal swabs obtained by self-collection and analysed with direct RT-qPCR. Of these subjects, 28.6% tested positive for SARS-CoV-2 using nasopharyngeal swab sampling. Our direct RT-qPCR approach for self-collected nasal swabs performed well with results similar to those of the two-step RT-qPCR on RNA isolates, achieving 0.99 positive and 0.98 negative predictive values (cycle threshold [Ct] < 37). Our research also reports on grey-zone viraemia, including samples with near-cut-off Ct values (Ct ≥ 37). In all investigated subjects (n = 20) with grey-zone viraemia, the ultra-small viral load disappeared within hours or days with no symptoms. Overall, this study underscores the importance of painless nasal-swab self-collection and direct RT-qPCR for mass testing during the SARS-CoV-2 pandemic and in the post-pandemic era.

Performance of Saliva, Oropharyngeal Swabs, and Nasal Swabs for SARS-CoV-2 Molecular Detection: a Systematic Review and Meta-analysis

Nasopharyngeal (NP) swabs are considered the highest-yield sample for diagnostic testing for respiratory viruses, including SARS-CoV-2. The need to increase capacity for SARS-CoV-2 testing in a variety of settings, combined with shortages of sample collection supplies, have motivated a search for alternative sample types with high sensitivity. We systematically reviewed the literature to understand the performance of alternative sample types compared to NP swabs. We systematically searched PubMed, Google Scholar, medRxiv, and bioRxiv (last retrieval 1 October 2020) for comparative studies of alternative specimen types (saliva, oropharyngeal [OP], and nasal [NS] swabs) versus NP swabs for SARS-CoV-2 diagnosis using nucleic acid amplification testing (NAAT). A logistic-normal random-effects meta-analysis was performed to calculate % positive alternative-specimen, % positive NP, and % dual positives overall and in subgroups. The QUADAS 2 tool was used to assess bias. From 1,253 unique citations, we identified 25 saliva, 11 NS, 6 OP, and 4 OP/NS studies meeting inclusion criteria. Three specimen types captured lower % positives (NS [82%, 95% CI: 73 to 90%], OP [84%, 95% CI: 57 to 100%], and saliva [88%, 95% CI: 81 to 93%]) than NP swabs, while combined OP/NS matched NP performance (97%, 95% CI: 90 to 100%). Absence of RNA extraction (saliva) and utilization of a more sensitive NAAT (NS) substantially decreased alternative-specimen yield of positive samples. NP swabs remain the gold standard for diagnosis of SARS-CoV-2, although alternative specimens are promising. Much remains unknown about the impact of variations in specimen collection, processing protocols, and population (pediatric versus adult, late versus early in disease course), such that head-to head studies of sampling strategies are urgently needed.

Evaluating Specimen Quality and Results from a Community-Wide, Home-Based Respiratory Surveillance Study

While influenza and other respiratory pathogens cause significant morbidity and mortality, the community-based burden of these infections remains incompletely understood. The development of novel methods to detect respiratory infections is essential for mitigating epidemics and developing pandemic-preparedness infrastructure.

While influenza and other respiratory pathogens cause significant morbidity and mortality, the community-based burden of these infections remains incompletely understood. The development of novel methods to detect respiratory infections is essential for mitigating epidemics and developing pandemic-preparedness infrastructure. From October 2019 to March 2020, we conducted a home-based cross-sectional study in the greater Seattle, WA, area, utilizing electronic consent and data collection instruments. Participants received nasal swab collection kits via rapid delivery within 24 hours of self-reporting respiratory symptoms. Samples were returned to the laboratory and were screened for 26 respiratory pathogens and a housekeeping gene. Participant data were recorded via online survey at the time of sample collection and 1 week later. Of the 4,572 consented participants, 4,359 (95.3%) received a home swab kit and 3,648 (83.7%) returned a nasal specimen for respiratory pathogen screening. The 3,638 testable samples had a mean RNase P relative cycle threshold (C_rt) value of 19.0 (SD, 3.4), and 1,232 (33.9%) samples had positive results for one or more pathogens, including 645 (17.7%) influenza-positive specimens. Among the testable samples, the median time between shipment of the home swab kit and completion of laboratory testing was 8.0 days (interquartile range [IQR], 7.0 to 14.0). A single adverse event occurred and did not cause long-term effects or require medical attention. Home-based surveillance using online participant enrollment and specimen self-collection is a safe and feasible method for community-level monitoring of influenza and other respiratory pathogens, which can readily be adapted for use during pandemics.

Performance of Saliva, Oropharyngeal Swabs, and Nasal Swabs for SARS-CoV-2 Molecular Detection: a Systematic Review and Meta-analysis

Nasopharyngeal (NP) swabs are considered the highest-yield sample for diagnostic testing for respiratory viruses, including SARS-CoV-2. The need to increase capacity for SARS-CoV-2 testing in a variety of settings, combined with shortages of sample collection supplies, have motivated a search for alternative sample types with high sensitivity. We systematically reviewed the literature to understand the performance of alternative sample types compared to NP swabs. We systematically searched PubMed, Google Scholar, medRxiv, and bioRxiv (last retrieval 1 October 2020) for comparative studies of alternative specimen types (saliva, oropharyngeal [OP], and nasal [NS] swabs) versus NP swabs for SARS-CoV-2 diagnosis using nucleic acid amplification testing (NAAT). A logistic-normal random-effects meta-analysis was performed to calculate % positive alternative-specimen, % positive NP, and % dual positives overall and in subgroups. The QUADAS 2 tool was used to assess bias. From 1,253 unique citations, we identified 25 saliva, 11 NS, 6 OP, and 4 OP/NS studies meeting inclusion criteria. Three specimen types captured lower % positives (NS [82%, 95% CI: 73 to 90%], OP [84%, 95% CI: 57 to 100%], and saliva [88%, 95% CI: 81 to 93%]) than NP swabs, while combined OP/NS matched NP performance (97%, 95% CI: 90 to 100%). Absence of RNA extraction (saliva) and utilization of a more sensitive NAAT (NS) substantially decreased alternative-specimen yield of positive samples. NP swabs remain the gold standard for diagnosis of SARS-CoV-2, although alternative specimens are promising. Much remains unknown about the impact of variations in specimen collection, processing protocols, and population (pediatric versus adult, late versus early in disease course), such that head-to head studies of sampling strategies are urgently needed.

Comparing Nasopharyngeal and Midturbinate Nasal Swab Testing for the Identification of Severe Acute Respiratory Syndrome Coronavirus 2

Testing of paired mid-turbinate (MT) nasal and nasopharyngeal (NP) swabs, collected by trained personnel from 40 patients with COVID-19 showed more NP (76/95, 80%) than MT swabs tested positive (61/95, 64%; p=0.02). Among samples collected a week after study enrollment, fewer MT than NP samples were positive (45% vs 76%; p=0.001).

Diagnostic accuracy of nasopharyngeal swab, nasal swab and saliva swab samples for the detection of SARS-CoV-2 using RT-PCR

Background

The current gold standard in coronavirus disease (COVID-19) diagnostics is the real-time reverse transcription–polymerase chain reaction (RT-PCR) assay for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in nasopharyngeal swab (NPS) samples. Alternatively, nasal swab (NS) or saliva swab (SS) specimens are used, although available data on test accuracy are limited. We examined the diagnostic accuracy of NPS/NS/SS samples for this purpose.

Methods

Ten patients were included after being tested positive for SARS-CoV-2 RT-PCR in NPS samples according to the National Institute of Infectious Disease guidelines. In comparison with this conventional diagnostic method, NPS/NS/SS samples were tested using the cobas 6800 systems RT-PCR device. To investigate the usefulness of the cobas method and the difference among sample types, the agreement and sensitivity were calculated. Five to six samples were collected over a total period of 5–6 d from each patient.

Results

Fifty-seven sets of NPS/NS/SS samples were collected, of which 40 tested positive for COVID-19 by the conventional method. Overall, the concordance rates using the conventional method were 86.0%/70.2%/54.4% for NPS/NS/SS samples (cobas); however, for samples collected up to and including on Day 9 after disease onset (22 negative and one positive specimens), the corresponding rates were 95.7%/87.0%/65.2%. The overall sensitivity estimates were 100.0%/67.5%/37.5% for NPS/NS/SS samples (cobas). For samples up to 9 d after onset, the corresponding values were 100.0%/86.4%/63.6%.

Conclusions

NS samples are more reliable than SS samples and can be an alternative to NPS samples. They can be a useful diagnostic method in the future.

Investigation of structural, treatment and clinical characteristics of COVID-19 along with the challenges caused by its prevalence

In the late 2019, a report from China was published stating a disease with unknown cause. After that,the outbreak of the COVID-19 caused a pandemic in the world. On March 11, 2020, the outbreak of this virus was reported in 100 countries. The virus is currently spreading rapidly around the world.In the past, coronaviruses caused life-threatening diseases such as SARS and MERSsome areas.Although there is still a debate about the origin of this new coronavirus, it is most likely linked with some animals including bats, civet and pangolin. In this review, we try to simply describe the features of the new coronavirusas well as the recent diagnostic and therapeutic findings.

How home anterior self-collected nasal swab simplifies SARS-CoV-2 testing: new surveillance horizons in public health and beyond

The sample collection procedure for SARS-CoV-2 has a strong impact on diagnostic capability, contact tracing approach, ultimately affecting the infection containment performance. This study demonstrates that self-collected nasal-swab has shown to be a valid and well tolerated procedure to SARS-CoV-2 surveillance in a healthcare system. More significantly, no performance adequacy difference was detected in self-administered swabs between healthcare worker (HCW) and non-HCW which allows to speculate that this procedure could be successfully extended to the entire population for mass screening.

Considerations for diagnostic COVID-19 tests

During the early phase of the coronavirus disease 2019 (COVID-19) pandemic, design, development, validation, verification and implementation of diagnostic tests were actively addressed by a large number of diagnostic test manufacturers. Hundreds of molecular tests and immunoassays were rapidly developed, albeit many still await clinical validation and formal approval. In this Review, we summarize the crucial role of diagnostic tests during the first global wave of COVID-19. We explore the technical and implementation problems encountered during this early phase in the pandemic, and try to define future directions for the progressive and better use of (syndromic) diagnostics during a possible resurgence of COVID-19 in future global waves or regional outbreaks. Continuous global improvement in diagnostic test preparedness is essential for more rapid detection of patients, possibly at the point of care, and for optimized prevention and treatment, in both industrialized countries and low-resource settings.