Diagnostics

2024

Jump to: 2023, 2022, 2021, 2020

12 pages, 767 KiB

Open AccessArticle

Dengue Hemorrhagic Fever in Quang Nam Province (Vietnam) from 2020 to 2022—A Study on Serotypes Distribution and Immunology Factors

by Huong T. Pham, Thao N. T. Pham, Nhu H. T. Tran, Quang D. Ha, Duy K. Tran, Nam H. D. Nguyen, Van H. Pham and Son T. Pham

Diagnostics 2024, 14(16), 1772; https://doi.org/10.3390/diagnostics14161772 - 14 Aug 2024

Cited by 1 | Viewed by 1861

Abstract

Background: Dengue hemorrhagic fever (DHF) is the most prevalent and fastest-growing vector-borne disease globally, with symptoms ranging from mild to severe and, in some cases, fatal. Quang Nam province in Vietnam can serve as a model for dengue epidemiological study, as it is [...] Read more.

Background: Dengue hemorrhagic fever (DHF) is the most prevalent and fastest-growing vector-borne disease globally, with symptoms ranging from mild to severe and, in some cases, fatal. Quang Nam province in Vietnam can serve as a model for dengue epidemiological study, as it is an endemic region for DHF with a tropical climate, which significantly constrains the health system. However, there are very few epidemiological and microbiological reports on Dengue virus (DENV) serotypes in this region due to the limited availability of advanced surveillance infrastructure. Aims of the study: This study aims to (1) assess the PCR positivity rates among hospitalized patients with clinical Dengue presentation; (2) identify the circulating DENV serotypes; and (3) assess the impact of secondary DENV infections on outbreak severity by detecting the presence of DENV-specific IgG antibodies in the plasma of DENV-infected patients. Materials and methods: Blood samples from patients clinically diagnosed with DHF and admitted to Quang Nam General Hospital (2020–2022) were analyzed. RNA extraction was performed using the ^NKDNA/RNAprep MAGBEAD kit, followed by Multiplex Reverse Transcription real-time Polymerase Chain Reaction (MLP RT-rPCR) for DENV detection and serotype identification. Positive samples were further tested for DENV-specific IgG antibodies using an enzyme-linked immunosorbent assay (ELISA). Results: The PCR positivity rate among hospitalized patients was approximately 68% throughout the study period. A significant shift in DENV serotypes was observed, with DENV-2 initially dominant and later giving way to DENV-1. IgG was detected in nearly half of the MPL RT-rPCR-positive samples, indicating secondary DENV infections. Conclusions: Our study highlights persistent dengue prevalence and dynamic shifts in DENV serotypes in Quang Nam province, emphasizing the need for improved diagnostic strategies and timely sample collection. The significant serotype shifts and the presence of IgG in hospitalized patients suggest potential severe outcomes from recurrent DENV infections, possibly linked to antibody-dependent enhancement (ADE) effect, underscoring the importance of advanced surveillance, vector control, vaccination campaigns, and public education to predict and prevent future DHF epidemics. Full article

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11 pages, 469 KiB

Open AccessArticle

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 5 | Viewed by 2217

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

Open AccessArticle

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

Cited by 1 | Viewed by 1349

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

Open AccessArticle

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 1489

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

Open AccessArticle

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 5 | Viewed by 1888

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

Open AccessArticle

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 1997

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

Open AccessArticle

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 5 | Viewed by 2760

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

Open AccessArticle

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 29 | Viewed by 5499

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

Open AccessArticle

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 12 | Viewed by 3325

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

Open AccessArticle

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 14 | Viewed by 9555

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

Open AccessArticle

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 8 | Viewed by 4063

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

Open AccessArticle

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 26 | Viewed by 3853

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

Open AccessReview

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 40 | Viewed by 6487

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

Open AccessArticle

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 15 | Viewed by 4503

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

Open AccessArticle

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 5 | Viewed by 4107

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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