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

Diagnostics ◽  
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).

scholarly journals Diagnosis of SARS-Cov-2 infection using specimens other than naso- and oropharyngeal swabs: a systematic review and meta-analysis

2021 ◽  
Author(s):  
Vânia M. Moreira ◽  
Paulo Mascarenhas ◽  
Vanessa Machado ◽  
João Botelho ◽  
José João Mendes ◽  
...  
Keyword(s):  
Systematic Review ◽  
Sensitivity And Specificity ◽  
Point Of Care ◽  
Meta Analysis ◽  
High Sensitivity ◽  
False Positives ◽  
Sample Collection ◽  
Oral Region ◽  
Free Sample ◽  
Alternative Specimen

SUMMARYBackgroundThe 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, yet, with some limitations. Several specimens that are easier to collect 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).MethodsIn 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. Methodological quality was assessed through the Quality Assessment of Diagnostic Accuracy Studies 2 (QUADAS 2).FindingsWe identified 3022 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). Remaining index specimens presented uncertainty given the lack of studies available.InterpretationOur meta-analysis shows that saliva samples from oral region provide a high sensitivity and specificity, being the best candidate as an alternative specimen to NPS/OPS for COVID-19 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 outbreak control spots (e.g. schools, airports, and nursing homes).FundingNothing to declare.Research in contextEvidence before this studyThe lack of systematized data on the accuracy performance of alternative specimens for the detection of SARS-CoV-2 (against the standard NPS/OPS). The ever-growing number of studies available, made this updated systematic review timely and of the utmost importanceAdded value of this studyOur meta-analysis shows that saliva samples from the oral region provide a high sensitivity and specificity, being the best candidate as an alternative specimen to NPS/OPS for COVID-19 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.Implications of all the available evidenceSaliva samples simply taken from the oral cavity are promising alternatives to the currently used nasal/throat swabs. Saliva specimens can be self-collected, mitigate the discomfort caused by sampling, reduce the transmission risk and increase testing capacity. Therefore, the validation of this alternative specimen will promote the implementation of truly deployable rapid tests for SARS-CoV-2 detection at the point-of-care or outbreak spots.

scholarly journals SARS-CoV-2 Detection in Different Respiratory Sites: A Systematic Review and Meta-Analysis

2020 ◽  
Author(s):  
Abbas Mohammadi ◽  
Elmira Esmaeilzadeh ◽  
Yijia Li ◽  
Ronald J Bosch ◽  
Jonathan Li
Keyword(s):  
Systematic Review ◽  
Symptom Onset ◽  
Meta Analysis ◽  
Nasopharyngeal Swab ◽  
Inclusion Criteria ◽  
Rna Detection ◽  
Timely Initiation ◽  
Detection Rates ◽  
Diverse Range ◽  
Oropharyngeal Swab

Background: The accurate detection of SARS-CoV-2 through respiratory sampling is critical for the prevention of further transmission and the timely initiation of treatment for COVID-19. There is a diverse range of SARS-CoV-2 detection rates in reported studies, with uncertainty as to the optimal sampling strategy for COVID-19 diagnosis and monitoring. Methods: We performed a systematic review and meta-analysis of studies comparing respiratory sampling strategies for the detection of SARS-CoV-2 RNA. The inclusion criteria were studies that assessed at least two respiratory sampling sites (oropharyngeal swab, nasopharyngeal swab, and sputum) in participants with COVID-19. The percentage positive tests were compared between sampling modalities by constructing a Z-test assuming independence and using the standard errors obtained from the random effects meta-analysis. Findings: From 1039 total studies, we identified 11 studies that met our inclusion criteria, with SARS-CoV-2 testing results from a total of 3442 respiratory tract specimens. Compared to nasopharyngeal swab sampling, sputum testing resulted in significantly higher rates of SARS-CoV-2 RNA detection while oropharyngeal swab testing had lower rates of viral RNA detection. Earlier sampling after symptom onset was associated with improved detection rates, but the differences in SARS-CoV-2 RNA detection by sampling method was consistent regardless of the duration of symptoms. Interpretation: The results support sputum sampling as a primary method of COVID-19 diagnosis and monitoring, and highlight the importance of early testing after symptom onset to increase the rates of COVID-19 diagnosis.

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

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.

scholarly journals Vertical Transmission of Severe Acute Respiratory Syndrome Coronavirus 2: A Systematic Review

2020 ◽  
Vol 37 (10) ◽  
pp. 1055-1060 ◽  
Author(s):  
Ziyi Yang ◽  
Yi Liu
Keyword(s):  
Systematic Review ◽  
Severe Acute Respiratory Syndrome ◽  
Amniotic Fluid ◽  
Cord Blood ◽  
Vertical Transmission ◽  
Meta Analysis ◽  
Nasopharyngeal Swab ◽  
Rt Pcr ◽  
Serum Samples ◽  
Virus Specific Antibody

Objective The aim of this study is to summarize currently available evidence on vertical transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Study Design A systematic review was conducted following the guidelines of the Preferred Reporting Items for Systematic Reviews and Meta-analysis Statement. Results A total of 22 studies comprising 83 neonates born to mothers diagnosed with coronavirus disease 2019 were included in the present systematic review. Among these neonates, three were confirmed with SARS-CoV-2 infection at 16, 36, and 72 hours after birth, respectively, by nasopharyngeal swab real-time polymerase chain reaction (RT-PCR) tests; another six had elevated virus-specific antibody levels in serum samples collected after birth, but negative RT-PCR test results. However, without positive RT-PCR tests of amniotic fluid, placenta, or cord blood, there is a lack of virologic evidence for intrauterine vertical transmission. Conclusion There is currently no direct evidence to support intrauterine vertical transmission of SARS-CoV-2. Additional RT-PCR tests on amniotic fluid, placenta, and cord blood are needed to ascertain the possibility of intrauterine vertical transmission. For pregnant women infected during their first and second trimesters, further studies focusing on long-term outcomes are needed. Key Points

scholarly journals Point-of-Care Diagnostic Tests for Detecting SARS-CoV-2 Antibodies: A Systematic Review and Meta-Analysis of Real-World Data

2020 ◽  
Vol 9 (5) ◽  
pp. 1515 ◽  
Author(s):  
Matteo Riccò ◽  
Pietro Ferraro ◽  
Giovanni Gualerzi ◽  
Silvia Ranzieri ◽  
Brandon Michael Henry ◽  
...  
Keyword(s):  
Systematic Review ◽  
Diagnostic Tests ◽  
Large Scale ◽  
Point Of Care ◽  
Meta Analysis ◽  
Rapid Diagnostic Tests ◽  
Diagnostic Methods ◽  
Rt Pcr ◽  
Real World Data ◽  
Healthcare Facilities

SARS-CoV-2 is responsible for a highly contagious infection, known as COVID-19. SARS-CoV-2 was discovered in late December 2019 and, since then, has become a global pandemic. Timely and accurate COVID-19 laboratory testing is an essential step in the management of the COVID-19 outbreak. To date, assays based on the reverse-transcription polymerase chain reaction (RT-PCR) in respiratory samples are the gold standard for COVID-19 diagnosis. Unfortunately, RT-PCR has several practical limitations. Consequently, alternative diagnostic methods are urgently required, both for alleviating the pressure on laboratories and healthcare facilities and for expanding testing capacity to enable large-scale screening and ensure a timely therapeutic intervention. To date, few studies have been conducted concerning the potential utilization of rapid testing for COVID-19, with some conflicting results. Therefore, the present systematic review and meta-analysis was undertaken to explore the feasibility of rapid diagnostic tests in the management of the COVID-19 outbreak. Based on ten studies, we computed a pooled sensitivity of 64.8% (95%CI 54.5–74.0), and specificity of 98.0% (95%CI 95.8–99.0), with high heterogeneity and risk of reporting bias. We can conclude that: (1) rapid diagnostic tests for COVID-19 are necessary, but should be adequately sensitive and specific; (2) few studies have been carried out to date; (3) the studies included are characterized by low numbers and low sample power, and (4) in light of these results, the use of available tests is currently questionable for clinical purposes and cannot substitute other more reliable molecular tests, such as assays based on RT-PCR.

scholarly journals Screening for SARS-CoV-2 by RT-PCR: Saliva or Nasopharyngeal Swab? Systematic Review and Meta-Analysis

2021 ◽  
Author(s):  
Nusaïbah Ibrahimi ◽  
Agnès Delaunay-Moisan ◽  
Catherine Hill ◽  
Gwénaël Le Teuff ◽  
Jean-François Rupprecht ◽  
...  
Keyword(s):  
Systematic Review ◽  
Meta Analysis ◽  
Nasopharyngeal Swab ◽  
Rt Pcr

scholarly journals Evaluation of the clinical performance of a magnetic force-assisted electrochemical immunoassay for the detection of SARS-CoV-2 antigens

PLoS ONE ◽  
2021 ◽  
Vol 16 (10) ◽  
pp. e0258394
Author(s):  
Sung Jin Jo ◽  
Sang-hyun Shin ◽  
Jungrok Kim ◽  
Seungok Lee ◽  
Jehoon Lee
Keyword(s):  
Magnetic Force ◽  
Limit Of Detection ◽  
Clinical Performance ◽  
Point Of Care ◽  
Electrical Current ◽  
Republic Of Korea ◽  
Nasopharyngeal Swab ◽  
Electrochemical Immunoassay ◽  
Rt Pcr ◽  
Viral Culture

Rapid antigen (Ag) tests for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) provide quick results, do not require specialized technical skills or infrastructure, and can be used as a point-of-care method to prevent the spread of coronavirus disease (COVID-19). The performance of a magnetic force-assisted electrochemical immunoassay-based test, namely the MARK-B COVID-19 Ag test (BBB, Sungnam, Republic of Korea), was evaluated using 170 nasopharyngeal swab specimens and compared to that of RT-PCR and commercial rapid Ag test (STANDARD Q COVID-19 Ag Test, SD Biosensor, Suwon-si, Republic of Korea). The overall sensitivity and specificity of the MARK-B test were 90.0% (95% CI 79.4%–96.2%) and 99.0% (95% CI 95.0%–99.9%), respectively, with a kappa coefficient of 0.908. The correlations between the electrical current values of MARK-B and the Ct values of RT-PCR were −0.898 (E gene, 95% CI −0.938 to −0.834) and −0.914 (RdRp gene, 95% CI −0.948 to −0.860), respectively. The limit of detection of the MARK-B was measured using the viral culture reference samples and found to be 1 x 102 pfu/mL. The magnetic force-assisted electrochemical immunoassay-based Ag test can be used to rapidly detect SARS-CoV-2 infections, and the corresponding fully automated portable device can provide easy readability and semi-quantitative results.

Effective optimization of SARS-CoV-2 laboratory testing variables in an era of supply chain constraints

2020 ◽  
Vol 15 (15) ◽  
pp. 1483-1487
Author(s):  
Nikhil S Sahajpal ◽  
Ashis K Mondal ◽  
Allan Njau ◽  
Sudha Ananth ◽  
Kimya Jones ◽  
...  
Keyword(s):  
Supply Chain ◽  
Rna Extraction ◽  
Nasopharyngeal Swab ◽  
Sample Collection ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Short Supply ◽  
Viral Transport ◽  
3D Printed ◽  
Bridging Studies

RT-PCR-based assays for the detection of SARS-CoV-2 have played an essential role in the current COVID-19 pandemic. However, the sample collection and test reagents are in short supply, primarily due to supply chain issues. Thus, to eliminate testing constraints, we have optimized three key process variables: RNA extraction and RT-PCR reactions, different sample types and media to facilitate SARS-CoV-2 testing. By performing various validation and bridging studies, we have shown that various sample types such as nasopharyngeal swab, bronchioalveolar lavage and saliva, collected using conventional nasopharyngeal swabs, ESwab or 3D-printed swabs and, preserved in viral transport media, universal transport media, 0.9% sodium chloride or Amies media are compatible with RT-PCR assay for COVID-19. Besides, the reduction of PCR reagents by up to fourfold also produces reliable results.

scholarly journals The management of surgical patients in the emergency setting during COVID-19 pandemic: the WSES position paper

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Belinda De Simone ◽  
Elie Chouillard ◽  
Massimo Sartelli ◽  
Walter L. Biffl ◽  
Salomone Di Saverio ◽  
...  
Keyword(s):  
Systematic Review ◽  
Emergency Surgery ◽  
Healthcare Workers ◽  
Mass Casualty ◽  
Position Paper ◽  
Surgical Patients ◽  
Nasopharyngeal Swab ◽  
Emergency Setting ◽  
Open Approach ◽  
Rt Pcr

Abstract Background Since the COVID-19 pandemic has occurred, nations showed their unpreparedness to deal with a mass casualty incident of this proportion and severity, which resulted in a tremendous number of deaths even among healthcare workers. The World Society of Emergency Surgery conceived this position paper with the purpose of providing evidence-based recommendations for the management of emergency surgical patients under COVID-19 pandemic for the safety of the patient and healthcare workers. Method A systematic review was conducted in accordance with the Preferred Reporting Items for Systematic Review and Meta-analysis Protocols (PRISMA-P) through the MEDLINE (PubMed), Embase and SCOPUS databases. Synthesis of evidence, statements and recommendations were developed in accordance with the GRADE methodology. Results Given the limitation of the evidence, the current document represents an effort to join selected high-quality articles and experts’ opinion. Conclusions The aim of this position paper is to provide an exhaustive guidelines to perform emergency surgery in a safe and protected environment for surgical patients and for healthcare workers under COVID-19 and to offer the best management of COVID-19 patients needing for an emergency surgical treatment. We recommend screening for COVID-19 infection at the emergency department all acute surgical patients who are waiting for hospital admission and urgent surgery. The screening work-up provides a RT-PCR nasopharyngeal swab test and a baseline (non-contrast) chest CT or a chest X-ray or a lungs US, depending on skills and availability. If the COVID-19 screening is not completed we recommend keeping the patient in isolation until RT-PCR swab test result is not available, and to manage him/she such as an overt COVID patient. The management of COVID-19 surgical patients is multidisciplinary. If an immediate surgical procedure is mandatory, whether laparoscopic or via open approach, we recommend doing every effort to protect the operating room staff for the safety of the patient.

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