Diagnostic Virology

A topical collection in Diagnostics (ISSN 2075-4418). This collection belongs to the section "Diagnostic Microbiology and Infectious Disease".

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Collection Editor
Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, 1649-003 Lisboa, Portugal
Interests: HIV; antivirals and vaccines; drug resistance; pathogenesis; antibody neutralization; virus evolution
Special Issues, Collections and Topics in MDPI journals

Topical Collection Information

Dear Colleagues,

In these troubled COVID-19 times we are living in, it has become more evident than ever that rapid, deployable, and highly sensitive, specific and precise diagnostic assays can save many lives. Together with the established qPCR-based and isothermal amplification-based methods, new technologies such as those based on CRISPR-Cas13 system and metagenomics are emerging and are enabling the rapid and sensitive detection and identification of multiple viruses at the same time with an unprecedented quality, both in the lab and outside the lab (PoC assays). These molecular methods of diagnostics rely on nucleic acid extraction methods whose performance characteristics may be very diverse and need a better assessment. High quality serologic assays are also paramount for the diagnosis and management of virus diseases, and for monitoring the response to vaccination. A better understanding of the advantages and limitations of currently available molecular and serologic assays for the diagnosis, treatment management, and cure assessment of each virus disease is needed. There is no better time for this Topical Collection in diagnostic virology. I would like to invite you to submit your best review or original work on all aspects of diagnostic virology mentioned above and others that I have missed to this topical collection issue. We are particularly seeking top level contributions on the development, validation, and implementation of molecular and serologic assays for the diagnosis, prognosis, and management of diseases caused by human viruses in all settings from the lab to the house and the bed of the patient.

Prof. Dr. Nuno Taveira
Collection Editor

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Keywords

  • Detecton and identification of viral pathogens
  • Development and validation of diagnostic tests (molecular, antigenic and serologic)
  • Implementation of diagnostic tests in different settings and geographies
  • Performance of nucleic acid extraction tests
  • Point of care assays
  • Multiplex assays
  • CRISPR diagnostics
  • Metagenomic diagnostics
  • Drug resistance assays
  • Diagnostic virology and public health

Published Papers (14 papers)

2024

Jump to: 2023, 2022, 2021, 2020

11 pages, 469 KiB  
Article
Assessment of the Diagnostic Performance of Fully Automated Hepatitis E Virus (HEV) Antibody Tests
by Anna Eichhorn, Franziska Neumann, Carina Bäumler, Imke Gutsmann, Olaf Grobe, Frieda Schlüter, Sina Müller and Andi Krumbholz
Diagnostics 2024, 14(6), 602; https://doi.org/10.3390/diagnostics14060602 - 12 Mar 2024
Cited by 1 | Viewed by 1133
Abstract
The detection of anti-hepatitis E virus (HEV) antibodies contributes to the diagnosis of hepatitis E. The diagnostic suitability of two automated chemiluminescence immunoassays (CLIAs, LIAISON® MUREX Anti-HEV IgG/Anti-HEV IgM test, DiaSorin) was assessed by comparison with the results of a combination of [...] Read more.
The detection of anti-hepatitis E virus (HEV) antibodies contributes to the diagnosis of hepatitis E. The diagnostic suitability of two automated chemiluminescence immunoassays (CLIAs, LIAISON® MUREX Anti-HEV IgG/Anti-HEV IgM test, DiaSorin) was assessed by comparison with the results of a combination of enzyme immunoassays and immunoblots (recomWell HEV IgG/IgM ELISA, recomLine HEV IgG/IgM, MIKROGEN). Samples with a deviating result were analyzed with the WANTAI ELISAs. Compared to the recomWell ELISAs, the Anti-HEV IgG CLIA had a percentage overall agreement (POA) of 100% (149/149; 95% CI: 97.5–100%) and the Anti-HEV IgM CLIA had a POA of 83.3% (85/102; 95% CI: 74.9–89.3%); considering the recomLine HEV IgM results, the POA was 71.7% (38/53; 95% CI: 58.4–82%). The WANTAI test confirmed 52.9% (9/17) of negative CLIA IgMs; HEV RNA was not detectable. Since acute infection with the Epstein–Barr virus (EBV) or human cytomegalovirus (CMV) may influence the results of other serological assays, HEV antibodies were examined in 17 EBV and 2 CMV patients: One had an isolated and probably unspecific HEV IgM in the CLIA, as HEV RNA was not detectable. Both CLIAs are well suited for HEV diagnostics, but isolated IgM should be confirmed. An acute EBV/CMV infection can influence HEV serodiagnostics. Full article
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2023

Jump to: 2024, 2022, 2021, 2020

11 pages, 864 KiB  
Article
Multiplexed RT-qPCR Coupled with Whole-Genome Sequencing to Monitor a SARS-CoV-2 Omicron Variant of Concern in a Hospital Laboratory Setting in Latvia
by Baiba Niedre-Otomere, Inara Kampenusa, Julija Trofimova, Jevgenijs Bodrenko, Reinis Vangravs, Girts Skenders, Sergejs Nikisins and Oksana Savicka
Diagnostics 2023, 13(22), 3467; https://doi.org/10.3390/diagnostics13223467 - 17 Nov 2023
Viewed by 779
Abstract
At the end of 2021, the SARS-CoV-2 Omicron variant of concern (VOC) displaced the previously dominant Delta VOC and enhanced diagnostic and therapeutic challenges worldwide. Respiratory specimens submitted to the Riga East University Hospital Laboratory Service by the central and regional hospitals of [...] Read more.
At the end of 2021, the SARS-CoV-2 Omicron variant of concern (VOC) displaced the previously dominant Delta VOC and enhanced diagnostic and therapeutic challenges worldwide. Respiratory specimens submitted to the Riga East University Hospital Laboratory Service by the central and regional hospitals of Latvia from January to March 2022 that were positive for SARS-CoV-2 RNA were tested by commercial multiplexed RT-qPCR targeting three of the Omicron VOC signature mutations: ΔH69/V70, E484A, and N501Y. Of the specimens tested and analyzed in parallel by whole-genome sequencing (WGS), 964 passed the internal quality criteria (genome coverage ≥90%, read depth ≥400×) and the Nextstrain’s quality threshold for “good”. We validated the detection accuracy of RT-qPCR for each target individually by using WGS as a control. The results were concordant with both approaches for 938 specimens, with the correct classification rate exceeding 96% for each target (CI 95%); however, the presumptive WHO label was misassigned for 21 specimens. The RT-qPCR genotyping provided an acceptable means to pre-monitor the prevalence of the two presumptive Omicron VOC sublineages, BA.1 and BA.2. Full article
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10 pages, 732 KiB  
Article
HCV RNA Quantification by a Domestic Commercial Assay: A Case Study among People Who Inject Drugs in Vietnam
by Quynh Bach Thi Nhu, Linh Le Thi Thuy, Hong Thi Nguyen, Binh Nguyen Thanh, Delphine Rapoud, Catherine Quillet, Hong Thi Tran, Roselyne Vallo, Thanh Nham Thi Tuyet, Laurent Michel, Laurence Weiss, Philippe Vande Perre, Vinh Vu Hai, Nicolas Nagot, Oanh Khuat Thi Hai, Don Des Jarlais, Huong Thi Duong, Khue Pham Minh, Didier Laureillard and Jean-Pierre Molès
Diagnostics 2023, 13(22), 3456; https://doi.org/10.3390/diagnostics13223456 - 16 Nov 2023
Viewed by 805
Abstract
The desired performance of nucleic acid testing (NAT) may vary if used for disease diagnosis or for the evaluation of the therapeutic efficacy of a treatment, although in most cases, the same assay is used. However, these tests may not be affordable in [...] Read more.
The desired performance of nucleic acid testing (NAT) may vary if used for disease diagnosis or for the evaluation of the therapeutic efficacy of a treatment, although in most cases, the same assay is used. However, these tests may not be affordable in many situations including in low/middle income countries that in response have developed domestic assays. Given the example of HCV NAT among people who inject drugs in Vietnam, we aimed at evaluating a domestic assay versus an FDA- and CE-approved assay. This cross-evaluation revealed that (i) the domestic assay had a poorer sensitivity with a threshold of detection above 104 IU/mL, and (ii) the FDA-approved assay had a percentage of false negative results close to 1%. Together, in the present study, the domestic assay had a performance compatible with diagnosis purposes (given that this population was 70% HCV seropositive) but not compatible with HCV treatment monitoring (given that treatment failures are rare and the observed viremia frequently below the threshold of detection). This study highlights the need for a proper evaluation of HCV RNA domestic assays in order to efficiently contribute to the WHO HCV elimination target by 2030. Full article
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11 pages, 2092 KiB  
Article
Evaluating the Efficiency of the Cobas 6800 System for BK Virus Detection in Plasma and Urine Samples
by Junhyup Song, Sinyoung Kim, Eunmin Kwak and Younhee Park
Diagnostics 2023, 13(17), 2860; https://doi.org/10.3390/diagnostics13172860 - 4 Sep 2023
Cited by 2 | Viewed by 1079
Abstract
We evaluated the overall performance of the Cobas 6800 BKV test in detecting BK virus (BKV). We examined the imprecision of the Cobas 6800 BKV test and compared the qualitative and quantitative results obtained from the Cobas 6800 BKV test and the Real-Q [...] Read more.
We evaluated the overall performance of the Cobas 6800 BKV test in detecting BK virus (BKV). We examined the imprecision of the Cobas 6800 BKV test and compared the qualitative and quantitative results obtained from the Cobas 6800 BKV test and the Real-Q BKV quantification assay. We assessed 88 plasma and 26 urine samples collected between September and November 2022 from patients with BKV infection using the Real-Q BKV quantitative assay. The lognormal coefficient of variation indicated that the inter-assay precision of the Cobas 6800 BKV test ranged from 13.86 to 33.83%. A strong correlation was observed between the quantitative results obtained using the Cobas 6800 BKV test and the Real-Q BKV quantification assay for plasma samples. The Spearman’s rank correlation coefficients (ρ) for plasma, polymerase chain reaction (PCR) media-stabilized urine, and raw urine samples were 0.939, 0.874, and 0.888, respectively. Our analyses suggest that the Cobas 6800 BKV test is suitable for clinical applications owing to the strong correlation between the results obtained using this test and the Real-Q BKV quantification assay in plasma and urine samples. Furthermore, utilizing fresh raw urine samples can be a viable approach for the Cobas 6800 BKV test as it is less labor- and time-intensive. Full article
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17 pages, 4053 KiB  
Article
Performance of T-Track® SARS-CoV-2, an Innovative Dual Marker RT-qPCR-Based Whole-Blood Assay for the Detection of SARS-CoV-2-Reactive T Cells
by Franziska M. Kanis, Johannes P. Meier, Harald Guldan, Hans-Helmut Niller, Michael Dahm, Alexander Dansard, Thomas Zander, Friedhelm Struck, Erwin Soutschek, Ludwig Deml, Selina Möbus and Sascha Barabas
Diagnostics 2023, 13(17), 2722; https://doi.org/10.3390/diagnostics13172722 - 22 Aug 2023
Viewed by 1318
Abstract
T-cell immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays a central role in the control of the virus. In this study, we evaluated the performance of T-Track® SARS-CoV-2, a novel CE-marked quantitative reverse transcription-polymerase chain reaction (RT-qPCR) assay, which relies [...] Read more.
T-cell immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays a central role in the control of the virus. In this study, we evaluated the performance of T-Track® SARS-CoV-2, a novel CE-marked quantitative reverse transcription-polymerase chain reaction (RT-qPCR) assay, which relies on the combined evaluation of IFNG and CXCL10 mRNA levels in response to the S1 and NP SARS-CoV-2 antigens, in 335 participants with or without a history of SARS-CoV-2 infection and vaccination, respectively. Of the 62 convalescent donors, 100% responded to S1 and 88.7% to NP antigens. In comparison, of the 68 naïve donors, 4.4% were reactive to S1 and 19.1% to NP. Convalescent donors <50 and ≥50 years of age demonstrated a 100% S1 reactivity and an 89.1% and 87.5% NP reactivity, respectively. T-cell responses by T-Track® SARS-CoV-2 and IgG serology by recomLine SARS-CoV-2 IgG according to the time from the last immunisation (by vaccination or viral infection) were comparable. Both assays showed a persistent cellular and humoral response for at least 36 weeks post immunisation in vaccinated and convalescent donors. Our results demonstrate the very good performance of the T-Track® SARS-CoV-2 molecular assay and suggest that it might be suitable to monitor the SARS-CoV-2-specific T-cell response in COVID-19 vaccinations trials and cross-reactivity studies. Full article
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13 pages, 1784 KiB  
Article
Use of Envelope Domain III Protein for the Detection of IgG Type Antibodies Specific to Zika Virus by Indirect ELISA
by Oumar Ndiaye, Cheikh Tidiane Diagne, Ahmed Abd El Wahed, Fatou Dia, Moussa Dia, Adama Faye, Silvania Da Veiga Leal, Menilita dos Santos, Maria da Luz de Lima Mendonça, Carolina Cardoso da Silva Leite, Cheikh Saad Bouh Boye, Juliet E. Bryant, Philippe Desprès, Ousmane Faye, Amadou Alpha Sall and Oumar Faye
Diagnostics 2023, 13(3), 462; https://doi.org/10.3390/diagnostics13030462 - 26 Jan 2023
Cited by 4 | Viewed by 1879
Abstract
Zika virus (ZIKV) diagnostics are crucial for proper antenatal and postnatal care and also for surveillance and serosurvey studies. Since the viremia during ZIKV infection is fleeting, serological testing is highly valuable to inform diagnosis. However, current serology tests using whole virus antigens [...] Read more.
Zika virus (ZIKV) diagnostics are crucial for proper antenatal and postnatal care and also for surveillance and serosurvey studies. Since the viremia during ZIKV infection is fleeting, serological testing is highly valuable to inform diagnosis. However, current serology tests using whole virus antigens frequently suffer from cross reactivity issues, delays, and technical complexity, especially in low and middle income countries (LMICs) and endemic countries. Here, we describe an indirect ELISA to detect specific IgG antibodies using the ZIKV envelope domain III (EDIII) protein expressed in Drosophila S2 cells as an immunogen. Using a total of 367 clinical samples, we showed that the EDIII-ELISA was able to detect IgG antibodies against ZIKV with high sensitivity of 100.0% and specificity of 94.7% when compared to plaque reduction neutralization tests (PRNTs) as the gold standard and using 0.208 as the cut-off OD value. These results show the usefulness of the recombinant envelope domain III as an alternative to standard whole virus proteins for ZIKV diagnostics as it improves the sensitivity and specificity of IgG ELISA assay when used as an immunogen. This method should, therefore, be extended to serological diagnostic techniques for other members of the flavivirus genus and for use in IgM diagnostic testing. Full article
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2022

Jump to: 2024, 2023, 2021, 2020

11 pages, 2097 KiB  
Article
Highly Specific and Rapid Detection of Hepatitis C Virus Using RT-LAMP-Coupled CRISPR–Cas12 Assay
by Nang Kham-Kjing, Nicole Ngo-Giang-Huong, Khajornsak Tragoolpua, Woottichai Khamduang and Sayamon Hongjaisee
Diagnostics 2022, 12(7), 1524; https://doi.org/10.3390/diagnostics12071524 - 23 Jun 2022
Cited by 20 | Viewed by 3943
Abstract
Hepatitis C virus (HCV) infection can be cured with pan-genotypic direct-acting antiviral agents. However, identifying individuals with current hepatitis C remains a major challenge, especially in resource-limited settings where access to or availability of molecular tests is still limited. The goal of this [...] Read more.
Hepatitis C virus (HCV) infection can be cured with pan-genotypic direct-acting antiviral agents. However, identifying individuals with current hepatitis C remains a major challenge, especially in resource-limited settings where access to or availability of molecular tests is still limited. The goal of this study was to develop and validate a molecular assay for the rapid detection of HCV RNA in resource-limited settings. It is based on a combination of reverse transcription loop-mediated isothermal amplification (RT-LAMP) with the clustered regularly interspaced short palindromic repeats–CRISPR-associated protein 12a (CRISPR–Cas12a) cleavage assay that allows the recognition of specific HCV nucleic acid sequences. Amplified products after the cleavage reactions can be visualized on lateral flow strips or measured with a fluorescence detector. When tested on clinical samples from individuals infected with HCV, HIV, or HBV, or from healthy donors, the RT-LAMP-coupled CRISPR–Cas12 assay yielded 96% sensitivity, 100% specificity, and 97% agreement as compared to the reference method (Roche COBAS AmpliPrep/COBAS TaqMan HCV Test). This assay could detect HCV RNA concentrations as low as 10 ng/µL (an estimated 2.38 Log10 IU/mL). Therefore, this sensitive and specific assay may represent an affordable and reliable point-of-care test for the identification of individuals with active hepatitis C in low-resource settings. Full article
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9 pages, 1552 KiB  
Article
Unusual N Gene Dropout and Ct Value Shift in Commercial Multiplex PCR Assays Caused by Mutated SARS-CoV-2 Strain
by Petros Bozidis, Eleni T. Tsaousi, Charilaos Kostoulas, Prodromos Sakaloglou, Athanasia Gouni, Despoina Koumpouli, Hercules Sakkas, Ioannis Georgiou and Konstantina Gartzonika
Diagnostics 2022, 12(4), 973; https://doi.org/10.3390/diagnostics12040973 - 13 Apr 2022
Cited by 10 | Viewed by 2473
Abstract
Several SARS-CoV-2 variants have emerged and early detection for monitoring their prevalence is crucial. Many identification strategies have been implemented in cases where sequencing data for confirmation is pending or not available. The presence of B.1.1.318 among prevalent variants was indicated by an [...] Read more.
Several SARS-CoV-2 variants have emerged and early detection for monitoring their prevalence is crucial. Many identification strategies have been implemented in cases where sequencing data for confirmation is pending or not available. The presence of B.1.1.318 among prevalent variants was indicated by an unusual amplification pattern in various RT-qPCR commercial assays. Positive samples for SARS-CoV-2, as determined using the Allplex SARS-CoV-2 Assay, the Viasure SARS-CoV-2 Real Time Detection Kit and the GeneFinder COVID-19 Plus RealAmp Kit, presented a delay or failure in the amplification of the N gene, which was further investigated. Whole-genome sequencing was used for variant characterization. The differences between the mean Ct values for amplification of the N gene vs. other genes were calculated for each detection system and found to be at least 14 cycles. Sequencing by WGS revealed that all the N gene dropout samples contained the B.1.1.318 variant. All the isolates harbored three non-synonymous mutations in the N gene, which resulted in four amino acid changes (R203K, G204R, A208G, Met234I). Although caution should be taken when the identification of SARS-CoV-2 variants is based on viral gene amplification failure, such patterns could serve as a basis for rapid and cost-effective screening, functioning as indicators of community circulation of specific variants, requiring subsequent verification via sequencing. Full article
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2021

Jump to: 2024, 2023, 2022, 2020

12 pages, 12390 KiB  
Article
A Reliable Indirect ELISA Protocol for Detection of Human Antibodies Directed to SARS-CoV-2 NP Protein
by Arwa A. Faizo, Thamir A. Alandijany, Ayman T. Abbas, Sayed S. Sohrab, Sherif A. El-Kafrawy, Ahmed M. Tolah, Ahmed M. Hassan and Esam I. Azhar
Diagnostics 2021, 11(5), 825; https://doi.org/10.3390/diagnostics11050825 - 2 May 2021
Cited by 12 | Viewed by 7383
Abstract
A few months ago, the availability of a reliable and cost-effective testing capacity for COVID-19 was a concern for many countries. With the emergence and circulation of new SARS-CoV-2 variants, another layer of challenge can be added for COVID-19 testing at both molecular [...] Read more.
A few months ago, the availability of a reliable and cost-effective testing capacity for COVID-19 was a concern for many countries. With the emergence and circulation of new SARS-CoV-2 variants, another layer of challenge can be added for COVID-19 testing at both molecular and serological levels. This is particularly important for the available tests principally designed to target the S gene/protein where multiple mutations have been reported. Herein, the SARS-CoV-2 NP recombinant protein was utilized to develop a simple and reliable COVID-19 NP human IgG ELISA. The optimized protocol was validated against a micro-neutralization (MN) assay, in-house S-based ELISA, and commercial chemiluminescence immunoassay (CLIA). The developed assay provides 100% sensitivity, 98.9% specificity, 98.9% agreement, and high overall accuracy with an area under curve equal to 0.9998 ± 0.0002 with a 95% confidence interval of 0.99 to 1.00. The optical density values of positive samples significantly correlated with their corresponding MN titers. The assay specifically detects IgG antibodies to the SARS-CoV-2 NP protein and does not cross-detect IgG to the viral S protein. Moreover, it does not cross-react with antibodies related to other coronaviruses (e.g., the Middle East respiratory syndrome coronavirus or human coronavirus HKU1). The availability of this reliable COVID-19 NP IgG ELISA protocol is highly valuable for its diagnostic and epidemiological applications. Full article
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11 pages, 1676 KiB  
Article
Detection and Differentiation of SARS-CoV-2, Influenza, and Respiratory Syncytial Viruses by CRISPR
by Huifen Zhou, Jen-Hui Tsou, Molangur Chinthalapally, Hongjie Liu and Feng Jiang
Diagnostics 2021, 11(5), 823; https://doi.org/10.3390/diagnostics11050823 - 1 May 2021
Cited by 6 | Viewed by 3224
Abstract
SARS-CoV-2, influenza, and respiratory syncytial viruses (RSVs) cause acute respiratory infections with similar symptoms. Since the treatments and outcomes of these infections are different, the early detection and accurate differentiation of the viruses are clinically important for the prevention and treatment of the [...] Read more.
SARS-CoV-2, influenza, and respiratory syncytial viruses (RSVs) cause acute respiratory infections with similar symptoms. Since the treatments and outcomes of these infections are different, the early detection and accurate differentiation of the viruses are clinically important for the prevention and treatment of the diseases. We previously demonstrated that clustered regularly interspaced short palindromic repeats (CRISPR) could rapidly and precisely detect SARS-CoV-2. The objective of this study was to develop CRISPR as a test for simultaneously detecting and accurately distinguishing the viruses. The CRISPR assay with an RNA guide against each virus was performed in the reference standards of SARS-CoV-2, influenza A and B, and RSV. The CRISPR assay had a limit of detection of 1–100 copies/µL for specifically detecting SARS-CoV-2, influenza A and B, and RSV without cross-reaction with other respiratory viruses. The validation of the test in nasopharyngeal specimens showed that it had a 90–100% sensitivity and 100% specificity for the detection of SARS-CoV-2, influenza A and B, and RSV. The CRISPR assay could potentially be used for sensitive detection and specific differentiation of the respiratory viruses. Full article
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12 pages, 4006 KiB  
Article
Risk Score for Predicting In-Hospital Mortality in COVID-19 (RIM Score)
by Alejandro López-Escobar, Rodrigo Madurga, José María Castellano, Sara Velázquez, Rafael Suárez del Villar, Justo Menéndez, Alejandro Peixoto, Sara Jimeno, Paula Sol Ventura and Santiago Ruiz de Aguiar
Diagnostics 2021, 11(4), 596; https://doi.org/10.3390/diagnostics11040596 - 26 Mar 2021
Cited by 24 | Viewed by 3274
Abstract
Infection by SARS-CoV2 has devastating consequences on health care systems. It is a global health priority to identify patients at risk of fatal outcomes. 1955 patients admitted to HM-Hospitales from 1 March to 10 June 2020 due to COVID-19, were were divided into [...] Read more.
Infection by SARS-CoV2 has devastating consequences on health care systems. It is a global health priority to identify patients at risk of fatal outcomes. 1955 patients admitted to HM-Hospitales from 1 March to 10 June 2020 due to COVID-19, were were divided into two groups, 1310 belonged to the training cohort and 645 to validation cohort. Four different models were generated to predict in-hospital mortality. Following variables were included: age, sex, oxygen saturation, level of C-reactive-protein, neutrophil-to-platelet-ratio (NPR), neutrophil-to-lymphocyte-ratio (NLR) and the rate of changes of both hemogram ratios (VNLR and VNPR) during the first week after admission. The accuracy of the models in predicting in-hospital mortality were evaluated using the area under the receiver-operator-characteristic curve (AUC). AUC for models including NLR and NPR performed similarly in both cohorts: NLR 0.873 (95% CI: 0.849–0.898), NPR 0.875 (95% CI: 0.851–0.899) in training cohort and NLR 0.856 (95% CI: 0.818–0.895), NPR 0.863 (95% CI: 0.826–0.901) in validation cohort. AUC was 0.885 (95% CI: 0.885–0.919) for VNLR and 0.891 (95% CI: 0.861–0.922) for VNPR in the validation cohort. According to our results, models are useful in predicting in-hospital mortality risk due to COVID-19. The RIM Score proposed is a simple, widely available tool that can help identify patients at risk of fatal outcomes. Full article
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24 pages, 3090 KiB  
Review
Diagnosis of SARS-Cov-2 Infection by RT-PCR Using Specimens Other Than Naso- and Oropharyngeal Swabs: A Systematic Review and Meta-Analysis
by Vânia M. Moreira, Paulo Mascarenhas, Vanessa Machado, João Botelho, José João Mendes, Nuno Taveira and M. Gabriela Almeida
Diagnostics 2021, 11(2), 363; https://doi.org/10.3390/diagnostics11020363 - 21 Feb 2021
Cited by 38 | Viewed by 5074
Abstract
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 [...] Read more.
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). Full article
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7 pages, 1351 KiB  
Article
Multicenter Evaluation of the Cepheid Xpert® HBV Viral Load Test
by Fabbio Marcuccilli, Stephane Chevaliez, Thomas Muller, Luna Colagrossi, Giulia Abbondanza, Kurt Beyser, Mélanie Wlassow, Valérie Ortonne, Carlo Federico Perno and Marco Ciotti
Diagnostics 2021, 11(2), 297; https://doi.org/10.3390/diagnostics11020297 - 12 Feb 2021
Cited by 12 | Viewed by 3422
Abstract
Accurate measurement of the hepatitis B virus (HBV) DNA is important for the management of patients with chronic HBV infection. Here, the performance of the Xpert® HBV Viral Load test (Xpert HBV Viral Load) versus the Roche COBAS® Ampliprep/COBAS® TaqMan [...] Read more.
Accurate measurement of the hepatitis B virus (HBV) DNA is important for the management of patients with chronic HBV infection. Here, the performance of the Xpert® HBV Viral Load test (Xpert HBV Viral Load) versus the Roche COBAS® Ampliprep/COBAS® TaqMan® system (CAP/CTM HBV) HBV test v2.0 was evaluated. From September 2017 to December 2017, a total of 876 prospectively collected or archived serum or EDTA plasma specimens from subjects chronically infected with HBV were tested using the Xpert HBV Viral Load and the CAP/CTM HBV v2.0 assays. Of the 876 specimens tested, 560 were within the quantitative range of both assays. The agreement between the two methods was 90.0%. No difference in plasma or serum samples was observed. Deming regression analysis showed a good correlation of the Xpert HBV Viral Load assay with the CAP/CTM HBV v2.0 assay. The Bland–Altman analysis showed a good agreement between the results of the Xpert HBV Viral Load assay and the CAP/CTM HBV assay, with a mean difference (±1.96 standard deviation) of 0.0091 ± 0.3852 Log IU/mL. Comparing the two assays, only nineteen specimens (2.1%) had a difference greater than 1.96 times the standard deviation. The Xpert® HBV Viral Load test is suitable for monitoring patients with HBV infection and is useful in diagnostic settings. Full article
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2020

Jump to: 2024, 2023, 2022, 2021

13 pages, 478 KiB  
Article
Accuracy of the Zika IgM Antibody Capture Enzyme-Linked Immunosorbent Assay from the Centers for Disease Control and Prevention (CDC Zika MAC-ELISA) for Diagnosis of Zika Virus Infection
by Moyra Machado Portilho, Laise de Moraes, Mariana Kikuti, Leile Camila Jacob Nascimento, Mitermayer Galvão Reis, Viviane Sampaio Boaventura, Ricardo Khouri and Guilherme Sousa Ribeiro
Diagnostics 2020, 10(10), 835; https://doi.org/10.3390/diagnostics10100835 - 18 Oct 2020
Cited by 3 | Viewed by 3344
Abstract
Serological diagnosis of Zika virus (ZIKV) infection is challenging because of antigenic cross-reactivity with dengue virus (DENV). This study evaluated the accuracy of the Zika IgM antibody capture enzyme-linked immunosorbent assay (CDC Zika IgM MAC-ELISA) in differentiating between ZIKV and DENV infections. To [...] Read more.
Serological diagnosis of Zika virus (ZIKV) infection is challenging because of antigenic cross-reactivity with dengue virus (DENV). This study evaluated the accuracy of the Zika IgM antibody capture enzyme-linked immunosorbent assay (CDC Zika IgM MAC-ELISA) in differentiating between ZIKV and DENV infections. To determine sensitivity, we used acute- and convalescent-phase sera from 21 patients with RT-PCR-confirmed ZIKV infection. To determine specificity, we used acute- and convalescent-phase sera from 60 RT-PCR-confirmed dengue cases and sera from 23 blood donors. During the acute-phase of the illness, the assay presented a sensitivity of 12.5% (2/16) for samples collected 0–4 days post symptoms onset (DPSO), and of 75.0% (3/4) for samples collected 5–9 DPSO. During the convalescent-phase of the illness, the test sensitivity was 90.9% (10/11), 100% (2/2), and 0% (0/2) for samples obtained 12–102, 258–260, and 722–727 DPSO, respectively. Specificity for acute- and convalescent-phase samples from RT-PCR-confirmed dengue cases was 100% and 93.2%, respectively. Specificity for blood donor samples was 100%. The assay is an accurate method for Zika serological diagnosis and proved to be reliable for use during surveillance and outbreak investigations in settings where ZIKV and DENV cocirculate. Full article
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