Salivary molecular testing for SARS-CoV-2: simplifying the diagnosis without losing accuracy

Background Quantitative RT-PCR on NasoPharyngeal Swab (NPS) is still considered the standard for the diagnosis of SARS-CoV-2 infection, even if saliva has been evaluated in several studies as a possible alternative. The use of point of care (POC) platforms, providing highly specific results performed on saliva could simplify the diagnosis of COVID-19 and contribute to contain the spreading of SARS-CoV-2. Methods We assess the sensitivity and specificity of molecular testing performed on saliva in comparison to NPS using two different POC platforms (DiaSorin Simplexa ™ and Cepheid Xpert ®). NPS and saliva were collected prospectically from asymptomatic health care workers and mildly symptomatic patients. Moreover, the stability of saliva samples after storage at -80 C ° for up to 45 days was tested. Results The obtained results in comparison to NPS demonstrated for both DiaSorin Simplexa ™ and Xpert ® Xpress a specificity of 100% and a sensitivity of 90.24%. The overall agreement between the tests performed on saliva was 98%. A positive correlation in Ct values detected on saliva and on NPS was identified for all the targets shared by the tests in analysis (Orf1ab, E and N2). Both S Ct values and Orf1ab Ct values were not significantly different before and after the freezing in the tested saliva samples. Conclusion The obtained results demonstrated an overall performance of saliva comparable to NPS, confirming that RT-PCR performed using POCs on saliva could represent a valid public health solution for controlling SARS-CoV-2 pandemic.

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Clinical performance of the point-of-care cobas Liat for detection of SARS-CoV-2 in 20 minutes: A multicenter study

Journal of Clinical Microbiology ◽

10.1128/jcm.02811-20 ◽

2020 ◽

Author(s):

Glen Hansen ◽

Jamie Marino ◽

Zi-Xuan Wang ◽

Kathleen G. Beavis ◽

John Rodrigo ◽

...

Keyword(s):

Influenza A ◽

Clinical Performance ◽

Point Of Care ◽

Nasopharyngeal Swab ◽

Molecular Testing ◽

Rt Pcr ◽

Percent Agreement ◽

Individual Care ◽

Pcr Technology ◽

Acid Test

Background: Highly accurate testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the point of care (POC) is an unmet diagnostic need in emergency care and time-sensitive outpatient care settings. Reverse transcription-polymerase chain reaction (RT-PCR) technology is the gold-standard for SARS-CoV-2 diagnostics. Methods: We performed a multi-site United States (US) study comparing the clinical performance of the first US Food and Drug Administration (FDA) authorized POC RT-PCR test for detection of SARS-CoV-2 in 20 minutes, the cobas® Liat SARS-CoV-2 & Influenza A/B nucleic acid test, to the most widely used RT-PCR laboratory test, the cobas® 68/8800 SARS-CoV-2 test. Results: Clinical nasopharyngeal swab specimens from 444 patients with 357 evaluable specimens at five US clinical laboratories were enrolled from September 21, 2020 to October 23, 2020. The overall agreement between the Liat and 68/8800 systems for SARS-CoV-2 diagnostics was 98.6% (352/357). Using Liat, positive percent agreement for SARS-CoV-2 was 100% (162/162) and the negative percent agreement was 97.4% (190/195). Conclusion: The Liat is an RT-PCR POC test that provides highly accurate SARS-CoV-2 results in 20 minutes with equivalent performance to high-throughput laboratory molecular testing. Rapid RT-PCR testing at the POC can enable more timely infection control and individual care decisions for Coronavirus Disease 2019.

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Effectiveness of Preventive Measures in Keeping Low Prevalence of SARS-CoV-2 Infection in Health Care Workers in a Referral Children’s Hospital in Southern Italy

Pediatric Reports ◽

10.3390/pediatric13010017 ◽

2021 ◽

Vol 13 (1) ◽

pp. 118-124

Author(s):

Désirée Caselli ◽

Daniela Loconsole ◽

Rita Dario ◽

Maria Chironna ◽

Maurizio Aricò

Keyword(s):

Health Care ◽

Health Care Workers ◽

Southern Italy ◽

Hospital Setting ◽

Nasopharyngeal Swab ◽

Rt Pcr ◽

Children's Hospital ◽

Care Workers ◽

Children’S Hospital ◽

Second Wave

The coronavirus disease 2019 (COVID-19) pandemic now represents a major threat to public health. Health care workers (HCW) are exposed to biological risk. Little is currently known about the risk of HCW operating in pediatric wards for SARS-CoV-2 infection. The aim is to assess the prevalence of SARS-CoV-2 infection in HCW in a third-level children’s hospital in Southern Italy. An observational cohort study of all asymptomatic HCW (physician, technicians, nurses, and logistic and support operators) was conducted. HCW were screened, on a voluntary basis, for SARS-CoV-2 by RT-PCR on nasopharyngeal swab performed during the first wave of COVID-19. The study was then repeated, with the same modalities, at a 7-month interval, during the “second wave” of the COVID-19 pandemic. At the initial screening between 7 and 24 April 2020, 525 HCW were tested. None of them tested positive. At the repeated screening, conducted between 9 and 20 November 2020, 627 HCW were tested, including 61 additional ones resulting from COVID-emergency recruitment. At this second screening, eight subjects (1.3%) tested positive, thus being diagnosed as asymptomatic carriers of SARS-CoV-2. They were one physician, five nurses, and two HCW from the logistic/support services. They were employed in eight different wards/services. In all cases, the epidemiological investigation showed convincing evidence that the infection was acquired through social contacts. The study revealed a very low circulation of SARS-CoV-2 infection in HCW tested with RT-PCR. All the infections documented in the second wave of epidemic of SARS-CoV-2 were acquired outside of the workplace, confirming that in a pediatric hospital setting, HCW education, correct use of personal protective equipment, and separation of the COVID-patient pathway and staff flow may minimize the risk derived from occupational exposure.

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Impact of Full Vaccination with mRNA BNT162b2 on SARS-CoV-2 Infection: Genomic and Subgenomic Viral RNAs Detection in Nasopharyngeal Swab and Saliva of Health Care Workers

Microorganisms ◽

10.3390/microorganisms9081738 ◽

2021 ◽

Vol 9 (8) ◽

pp. 1738

Author(s):

Michela Deiana ◽

Antonio Mori ◽

Chiara Piubelli ◽

Francesca Perandin ◽

Davide Treggiari ◽

...

Keyword(s):

Health Care ◽

Real Time ◽

Health Care Workers ◽

Low Frequency ◽

Nasopharyngeal Swab ◽

Rt Pcr ◽

Subgenomic Rna ◽

Viral Rnas ◽

Social Settings ◽

Care Workers

SARS-CoV-2 infection was monitored in 1898 health care workers (HCWs) after receiving full vaccination with BNT162b2. Untill 30 June 2021, 10 HCWs tested positive for SARS-CoV-2 using real time RT-PCR, resulting in a 4-month cumulative incidence of 0.005%. The infection was mildly symptomatic in six (60%) and asymptomatic in four (40%) individuals. Among the infected HCWs, eight consenting individuals provided paired NPS and saliva during the course of infection, for the purpose of the analysis performed in the present study. Genomic and subgenomic viral RNAs were investigated using real-time RT-PCR in both biological specimens. The temporal profile of viral load was measured using ddPCR. Viral mutations were also analysed. Subgenomic viral RNA was detected in 8/8 (100%) NPS and in 6/8 (75%) saliva specimens at the baseline. The expression of subgenomic RNA was observed for up to 7 days in 3/8 (38%) symptomatic cases. Moreover, concordance was observed between NPS and saliva in the detection of viral mutations, and both N501Y and 69/70del (associated with the B.1.1.7 variant) were detected in the majority 6/8 (75%) of subjects, while the K417T mutation (associated with the P.1-type variants) was detected in 2/8 (25%) individuals. Overall, our findings report a low frequency of infected HCWs after full vaccination. It is, therefore, important to monitor the vaccinees in order to identify asymptomatic infected individuals. Saliva can be a surrogate for SARS-CoV-2 surveillance, particularly in social settings such as hospitals.

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Mobile Swab Collection Vehicle; a Blend of Necessity, Innovation, and Technology in a Resource-poor Country

Journal of Nepal Health Research Council ◽

10.33314/jnhrc.v18i4.3230 ◽

2021 ◽

Vol 18 (4) ◽

pp. 785-788

Author(s):

Arun Kumar Neopane ◽

Sailendra Kumar Duwal Shrestha ◽

Suman Raj Dangol ◽

Bikal Shrestha ◽

Ashis Dutta ◽

...

Keyword(s):

Health Care Workers ◽

Poor Country ◽

Nasopharyngeal Swab ◽

Rt Pcr ◽

Virus Diseases ◽

Resource Poor Country ◽

Care Workers ◽

Resource Poor ◽

Innovation And Technology ◽

Polymerase Chain

Mobile Swab Collection Vehicle is a concept that has been innovated by a team of medical and non-medical personals based upon the dire need to perform throat or nasopharyngeal swab collections to do reverse transcription polymerase chain reaction ‘RT-PCR’ quickly, safely, and comfortably during this Corona Virus Diseases 2019, ‘COVID-19’ pandemic in a resource-poor country like Nepal. Inputs from the health care workers, beneficiaries, and engineers have been taken to construct this vehicle-mounted booth for swab collection. This vehicle is the ‘first of its kind’ in Nepal. Keywords: COVID-19; Nepal; swab collection vehicle

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Less Exposure for Health Care Workers, More Comfort for Patients During COVID-19 Swab Testing

Workplace Health & Safety ◽

10.1177/21650799211045309 ◽

2021 ◽

pp. 216507992110453

Author(s):

Adeviyye Karaca ◽

Mehmet Akçimen ◽

Hatice Özen

Keyword(s):

Health Care ◽

Health Care Workers ◽

Tertiary Care ◽

Care Hospital ◽

Test Results ◽

Rt Pcr ◽

Exposure Risk ◽

Care Workers ◽

Before And After ◽

Pcr Test

Background Nasopharyngeal (NP) and oropharyngeal (OP) swab sampling for coronavirus disease 2019 (COVID-19) diagnosis may lead to droplet and/or airborne particle transmission and increase the exposure risk for health care workers (HCWs). However, there is limited evidence for effective methods to reduce occupational exposure from NP and OP swab sampling. This study aimed to reduce droplet-forming responses (DFRs) and the related exposure risk of NP and OP swab sampling by administering 10% lidocaine spray (LS) to the NP and OP areas prior to conducting swab tests. Methods This quasi-experimental study was conducted with 100 patients who presented to our tertiary care hospital with symptoms of COVID-19 between December 1 and 15, 2020. First, NP and OP swabbings were performed on each patient. Thereafter, LS was applied to the OP and NP regions, and the swab samples were taken once again. Frequency of DFRs and real-time polymerase chain reaction (RT-PCR) test results before and after LS application were recorded for comparison. In addition, the cycle threshold (Ct) was used as a proxy indicator for SARS-CoV-2 viral load in COVID-19 positive cases. Findings Significant differences in OP DFR frequencies before and after LS intervention were found (37% and 9%, respectively), as well as before and after NP DFR (31% and 18%, respectively). The mean Ct values for the positive samples did not differ before and after applying LS. Conclusion Our results suggest that applying LS to the OP and NP area prior to swab testing reduces DFR frequencies without affecting (RT-PCR) test results for SARS-CoV-2 and may increase patient and practitioner comfort.

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Screening, Diagnostic and Prognostic Tests for COVID-19: A Comprehensive Review

Life ◽

10.3390/life11060561 ◽

2021 ◽

Vol 11 (6) ◽

pp. 561

Author(s):

Mariana Ulinici ◽

Serghei Covantev ◽

James Wingfield-Digby ◽

Apostolos Beloukas ◽

Alexander G. Mathioudakis ◽

...

Keyword(s):

Point Of Care ◽

Standard Test ◽

Current Evidence ◽

Molecular Testing ◽

Rt Pcr ◽

Diagnostic Screening ◽

Comprehensive Review ◽

Prognostic Tests ◽

Polymerase Chain ◽

Antigen Testing

While molecular testing with real-time polymerase chain reaction (RT-PCR) remains the gold-standard test for COVID-19 diagnosis and screening, more rapid or affordable molecular and antigen testing options have been developed. More affordable, point-of-care antigen testing, despite being less sensitive compared to molecular assays, might be preferable for wider screening initiatives. Simple laboratory, imaging and clinical parameters could facilitate prognostication and triage. This comprehensive review summarises current evidence on the diagnostic, screening and prognostic tests for COVID-19.

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460. Point-of-Care, In-Home SARS-CoV-2 IgG Antibody Testing to Assess Seroprevalence in At-Risk Health Care Workers

Open Forum Infectious Diseases ◽

10.1093/ofid/ofaa439.653 ◽

2020 ◽

Vol 7 (Supplement_1) ◽

pp. S297-S297

Author(s):

Eric G Meissner ◽

Christine Litwin ◽

Tricia Crocker ◽

Elizabeth Mack ◽

Lauren Card

Keyword(s):

Health Care ◽

At Risk ◽

Health Care Workers ◽

Medical Center ◽

Point Of Care ◽

Academic Medical Center ◽

Significant Risk ◽

Documented Infection ◽

Inconclusive Result ◽

Care Workers

Abstract Background Health care workers are at significant risk for infection with the novel coronavirus SARS-CoV-2. Methods We utilized a point-of-care, lateral flow SARS-CoV-2 IgG immunoassay (RayBiotech) to conduct a seroprevalence study in a cohort of at-risk health care workers (n=339) and normal-risk controls (n=100) employed at an academic medical center. To minimize exposure risk while conducting the study, consents were performed electronically, tests were mailed and then self-administered at home using finger stick blood, and subjects uploaded a picture of the test result while answering an electronic questionnaire. We also validated the assay using de-identified serum samples from patients with PCR-proven SARS-CoV-2 infection. Results Between April 14th and May 6th 2020, 439 subjects were enrolled. Subjects were 68% female, 93% white, and most were physicians (38%) and nurses (27%). In addition, 37% had at least 1 respiratory symptom in the prior month, 34% had cared for a patient with known SARS-CoV-2 infection, 57% and 23% were worried about exposure at work or in the community, respectively, and 5 reported prior documented SARS-CoV-2 infection. On initial testing, 3 subjects had a positive IgG test, 336 had a negative test, and 87 had an inconclusive result. Of those with an inconclusive result who conducted a repeat test (85%), 96% had a negative result. All 3 positive IgG tests were in subjects reporting prior documented infection. Laboratory validation showed that of those with PCR-proven infection more than 13 days prior, 23/30 were IgG positive (76% sensitivity), whereas 1/26 with a negative prior PCR test were seropositive (95% specificity). Repeat longitudinal serologic testing every 30 days for up to 4 times is currently in progress. Conclusion We conducted a contact-free study in the setting of a pandemic to assess SARS-CoV-2 seroprevalence in an at-risk group of health care workers. The only subjects found to be IgG positive were those with prior documented infection, even though a substantial proportion of subjects reported significant potential occupational or community exposure and symptoms that were potentially compatible with SARS-COV-2 infection. Disclosures All Authors: No reported disclosures

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Diagnosis of SARS-Cov-2 Infection by RT-PCR Using Specimens Other Than Naso- and Oropharyngeal Swabs: A Systematic Review and Meta-Analysis

Diagnostics ◽

10.3390/diagnostics11020363 ◽

2021 ◽

Vol 11 (2) ◽

pp. 363

Author(s):

Vânia M. Moreira ◽

Paulo Mascarenhas ◽

Vanessa Machado ◽

João Botelho ◽

José João Mendes ◽

...

Keyword(s):

Systematic Review ◽

Clinical Performance ◽

Point Of Care ◽

Meta Analysis ◽

High Sensitivity ◽

Nasopharyngeal Swab ◽

Sample Collection ◽

Rt Pcr ◽

Oropharyngeal Swab ◽

Nucleic Acid Assays

The rapid and accurate testing of SARS-CoV-2 infection is still crucial to mitigate, and eventually halt, the spread of this disease. Currently, nasopharyngeal swab (NPS) and oropharyngeal swab (OPS) are the recommended standard sampling techniques, yet, these have some limitations such as the complexity of collection. Hence, several other types of specimens that are easier to obtain are being tested as alternatives to nasal/throat swabs in nucleic acid assays for SARS-CoV-2 detection. This study aims to critically appraise and compare the clinical performance of RT-PCR tests using oral saliva, deep-throat saliva/posterior oropharyngeal saliva (DTS/POS), sputum, urine, feces, and tears/conjunctival swab (CS) against standard specimens (NPS, OPS, or a combination of both). In this systematic review and meta-analysis, five databases (PubMed, Scopus, Web of Science, ClinicalTrial.gov and NIPH Clinical Trial) were searched up to the 30th of December, 2020. Case-control and cohort studies on the detection of SARS-CoV-2 were included. The methodological quality was assessed using the Quality Assessment of Diagnostic Accuracy Studies 2 (QUADAS 2). We identified 1560 entries, 33 of which (1.1%) met all required criteria and were included for the quantitative data analysis. Saliva presented the higher accuracy, 92.1% (95% CI: 70.0–98.3), with an estimated sensitivity of 83.9% (95% CI: 77.4–88.8) and specificity of 96.4% (95% CI: 89.5–98.8). DTS/POS samples had an overall accuracy of 79.7% (95% CI: 43.3–95.3), with an estimated sensitivity of 90.1% (95% CI: 83.3–96.9) and specificity of 63.1% (95% CI: 36.8–89.3). The remaining index specimens could not be adequately assessed given the lack of studies available. Our meta-analysis shows that saliva samples from the oral region provide a high sensitivity and specificity; therefore, these appear to be the best candidates for alternative specimens to NPS/OPS in SARS-CoV-2 detection, with suitable protocols for swab-free sample collection to be determined and validated in the future. The distinction between oral and extra-oral salivary samples will be crucial, since DTS/POS samples may induce a higher rate of false positives. Urine, feces, tears/CS and sputum seem unreliable for diagnosis. Saliva testing may increase testing capacity, ultimately promoting the implementation of truly deployable COVID-19 tests, which could either work at the point-of-care (e.g. hospitals, clinics) or at outbreak control spots (e.g., schools, airports, and nursing homes).

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COVID – 19 related knowledge and preventive practices early in the outbreak among health care workers in selected public health facilities of Illu aba Bor and Buno Bedelle zones, Southwest Ethiopia

BMC Infectious Diseases ◽

10.1186/s12879-021-06218-0 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Dereje Tsegaye ◽

Muluneh Shuremu ◽

Dereje Oljira ◽

Sileshi Dubale ◽

Getachew Befekadu ◽

...

Keyword(s):

Public Health ◽

Health Care ◽

Health Care Workers ◽

Personal Protective Equipment ◽

Infection Prevention ◽

Health Facilities ◽

Protective Equipment ◽

Southwest Ethiopia ◽

Preventive Practices ◽

Care Workers

Abstract Background Novel-coronavirus 2019 (COVID-19) disease is currently a worldwide health risk and public health emergency concern. The virus is transmitted from an infected person to another person through close contact and droplets. Frontline health care workers are the most at risk of infection, and so a WHO interim guidance document was issued by the World Health Organization (WHO) which underscores the importance of proper sanitation and waste management practices for COVID- 19 in health-care settings. This study aimed at assessing knowledge and preventive practices towards Covid-19 among health care providers in selected health facilities of Illu Aba Bor and Buno Bedele zones, Southwest Ethiopia. Methods An institution-based cross-sectional study was conducted from April to May 2020 among 330 health workers in selected health facilities of Illu Aba Bor and Buno-Bedelle Zones, Southwest Ethiopia. Data were collected using a self-administered structured questionnaire. The collected data were entered into Epidata version 3.1 and exported to SPSS version 23 for analysis. Bivariate and multivariable logistic regression analysis was used to identify independent predictors of preventive practices towards Covid-19. Statistical significance was declared at a p-value of < 0.05. Result The majority of respondents (93.3%) demonstrated good knowledge of COVID-19, and the mean (SD) knowledge score was 9.04 ± 1.06. Nearly two-thirds (64.2%) of the study participants had good infection prevention practices. Being male (AOR = 3.65, 95% CI: (1.96, 6.80)), education level (AOR = 1.82, 95% CI (1.02, 3.22)), profession (AOR = 3.17, 95% CI (1.08, 9.33)), service year (5–10 years) (AOR = 2.00 (1.02, 3.92)) and more than 10 years (AOR = 3.14 (1.51, 6.52)), availability of personal protective equipment (AOR = 1.96 (1.06, 3.61)) and Knowledge level (AOR = 2.61 (1.48, 4.62)) were independent predictors of COVID-19 preventive practices. Conclusion The overall level of knowledge of HCWs was good. However, the practice was relatively low. Gender, educational status, profession, year of service, knowledge towards COVID-19, and availability of personal protective equipment were independent predictors of good infection prevention practices. Optimizing the infection prevention and control loop of the health facilities is recommended.

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