Diagnosis of Viral Respiratory Infections

A special issue of Diagnostics (ISSN 2075-4418). This special issue belongs to the section "Diagnostic Microbiology and Infectious Disease".

Deadline for manuscript submissions: closed (31 August 2023) | Viewed by 9228

Special Issue Editor

1. Department of Medicine and Surgery, University of Insubria, Varese, Italy
2. Clinical Microbiology Laboratory, Hospital of Circolo and Estabilshment Macchi, Varese, Italy
Interests: respiratory viruses; microbiology infection
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Respiratory tract infections (RTIs) are a major source of morbidity and mortality in humans. With about 3 million people dying from RTI-related causes each year, RTIs are one of the leading causes of death worldwide. A large fraction (50% to 90%) of RTIs are caused by respiratory viruses (RVs). RVs include human rhinovirus (HRV), influenza A and B virus (IAV and IBV), human respiratory syncytial virus (HRSV), human metapneumovirus (HMPV), the human coronaviruses (HCoVs), human parainfluenzavirus (HPIV), and human adenovirus (HAdV). The highest rates of morbidity and mortality from RTIs are found in infants, the elderly, and immunocompromised individuals; however, healthy individuals without underlying risk factors can also be affected. The recent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has increased awareness of the dramatic effect that respiratory infections can have on human and global health.

Before the SARS-CoV-2 pandemic, viral lower respiratory tract infections (LRTIs) and viral upper respiratory tract infections (URTIs) were underappreciated causes of critical illness in the population. As this pandemic has shown, options for prophylaxis and the treatment of viral RTIs are limited. Vaccines are available for some viruses, such as influenza virus or adenovirus; however, both efficacy and coverage are suboptimal.

This Special Issue welcomes submissions related to the monitoring of respiratory infections, the epidemiology of respiratory viruses, and the possible impacts of respiratory virus disease. In particular, we encourage submissions studying cases or clusters of viral variants in both small and large communities, and the detection of unusual epidemiological events.

Dr. Federica Novazzi
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Diagnostics is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Published Papers (7 papers)

Order results
Result details
Select all
Export citation of selected articles as:

Research

Jump to: Other

15 pages, 1275 KiB  
Article
Inflammation and Venous Thromboembolism in Hospitalized Patients with COVID-19
by Angelos Liontos, Dimitrios Biros, Rafail Matzaras, Konstantina-Helen Tsarapatsani, Nikolaos-Gavriel Kolios, Athina Zarachi, Konstantinos Tatsis, Christiana Pappa, Maria Nasiou, Eleni Pargana, Ilias Tsiakas, Diamantina Lymperatou, Sempastien Filippas-Ntekouan, Lazaros Athanasiou, Valentini Samanidou, Revekka Konstantopoulou, Ioannis Vagias, Aikaterini Panteli, Haralampos Milionis and Eirini Christaki
Diagnostics 2023, 13(22), 3477; https://doi.org/10.3390/diagnostics13223477 - 19 Nov 2023
Viewed by 785
Abstract
Background: A link between inflammation and venous thromboembolism (VTE) in COVID-19 disease has been suggested pathophysiologically and clinically. The aim of this study was to investigate the association between inflammation and disease outcomes in adult hospitalized COVID-19 patients with VTE. Methods: This was [...] Read more.
Background: A link between inflammation and venous thromboembolism (VTE) in COVID-19 disease has been suggested pathophysiologically and clinically. The aim of this study was to investigate the association between inflammation and disease outcomes in adult hospitalized COVID-19 patients with VTE. Methods: This was a retrospective observational study, including quantitative and qualitative data collected from COVID-19 patients hospitalized at the Infectious Diseases Unit (IDU) of the University Hospital of Ioannina, from 1 March 2020 to 31 May 2022. Venous thromboembolism was defined as a diagnosis of pulmonary embolism (PE) and/or vascular tree-in-bud in the lungs. The burden of disease, assessed by computed tomography of the lungs (CTBoD), was quantified as the percentage (%) of the affected lung parenchyma. The study outcomes were defined as death, intubation, and length of hospital stay (LoS). A chi-squared test and univariate logistic regression analyses were performed in IBM SPSS 28.0. Results: After propensity score matching, the final study cohort included 532 patients. VTE was found in 11.2% of the total population. In patients with VTE, we found that lymphocytopenia and a high neutrophil/lymphocyte ratio were associated with an increased risk of intubation and death, respectively. Similarly, CTBoD > 50% was associated with a higher risk of intubation and death in this group of patients. The triglyceride–glucose (TyG) index was also linked to worse outcomes. Conclusions: Inflammatory indices were associated with VTE. Lymphocytopenia and an increased neutrophil-to-lymphocyte ratio negatively impacted the disease’s prognosis and outcomes. Whether these indices unfavorably affect outcomes in COVID-19-associated VTE must be further evaluated. Full article
(This article belongs to the Special Issue Diagnosis of Viral Respiratory Infections)
Show Figures

Figure 1

7 pages, 521 KiB  
Communication
SARS-CoV-2 Testing of Emergency Department Patients Using cobas® Liat® and eazyplex® Rapid Molecular Assays
by Renate Egerer, Birgit Edel, Franziska Hornung, Stefanie Deinhardt-Emmer, Michael Baier, Jan-Christoph Lewejohann, Wolfgang Pfister, Bettina Löffler and Jürgen Rödel
Diagnostics 2023, 13(13), 2245; https://doi.org/10.3390/diagnostics13132245 - 01 Jul 2023
Viewed by 1009
Abstract
Rapid testing for Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) of patients presenting to emergency departments (EDs) facilitates the decision for isolation on admission to hospital wards. Differences in the sensitivity of molecular assays have implications for diagnostic workflows. This study evaluated the performance [...] Read more.
Rapid testing for Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) of patients presenting to emergency departments (EDs) facilitates the decision for isolation on admission to hospital wards. Differences in the sensitivity of molecular assays have implications for diagnostic workflows. This study evaluated the performance of the cobas® Liat® RT-PCR, which is routinely used as the initial test for ED patients in our hospitals, compared with the eazyplex® RT-LAMP. A total of 378 oropharyngeal and nasal swabs with positive Liat® results were analysed. Residual sample aliquots were tested using NeuMoDx™, cobas® RT-PCR, and the eazyplex® assay. Patients were divided into asymptomatic (n = 157) and symptomatic (n = 221) groups according to the WHO case definition. Overall, 14% of positive Liat® results were not confirmed by RT-PCR. These samples were mainly attributed to 26.8% of asymptomatic patients, compared to 3.8% of the symptomatic group. Therefore, positive Liat® results were used to provisionally isolate patients in the ED until RT-PCR results were available. The eazyplex® assay identified 62% and 90.6% of RT-PCR-confirmed cases in asymptomatic and symptomatic patients, respectively. False-negative eazyplex® results were associated with RT-PCR Ct values > 30, and were more frequent in the asymptomatic group than in the symptomatic group (38.1% vs. 5.1%, respectively). Both the Liat® and eazyplex® assays are suitable for testing symptomatic patients. Their use in screening asymptomatic patients depends on the need to exclude any infection or identify those at high risk of transmission. Full article
(This article belongs to the Special Issue Diagnosis of Viral Respiratory Infections)
Show Figures

Figure 1

9 pages, 1059 KiB  
Article
Head-to-Head Comparison of Nasopharyngeal, Oropharyngeal and Nasal Swabs for SARS-CoV-2 Molecular Testing
by Kasper Daugaard Larsen, Mads Mose Jensen, Anne-Sophie Homøe, Elisabeth Arndal, Grethe Badsberg Samuelsen, Anders Koch, Xiaohui Chen Nielsen, Preben Homøe and Tobias Todsen
Diagnostics 2023, 13(2), 283; https://doi.org/10.3390/diagnostics13020283 - 12 Jan 2023
Cited by 2 | Viewed by 1443
Abstract
Nasopharyngeal swabs (NPS) are considered the gold standard for SARS-CoV-2 testing but are technically challenging to perform and associated with discomfort. Alternative specimens for viral testing, such as oropharyngeal swabs (OPS) and nasal swabs, may be preferable, but strong evidence regarding their diagnostic [...] Read more.
Nasopharyngeal swabs (NPS) are considered the gold standard for SARS-CoV-2 testing but are technically challenging to perform and associated with discomfort. Alternative specimens for viral testing, such as oropharyngeal swabs (OPS) and nasal swabs, may be preferable, but strong evidence regarding their diagnostic sensitivity for SARS-CoV-2 testing is still missing. We conducted a head-to-head prospective study to compare the sensitivity of NPS, OPS and nasal swabs specimens for SARS-CoV-2 molecular testing. Adults with an initial positive SARS-CoV-2 test were invited to participate. All participants had OPS, NPS and nasal swab performed by an otorhinolaryngologist. We included 51 confirmed SARS-CoV-2-positive participants in the study. The sensitivity was highest for OPS at 94.1% (95% CI, 87 to 100%) compared to NPS at 92.5% (95% CI, 85 to 99%) (p = 1.00) and lowest for nasal swabs at 82.4% (95% CI, 72 to 93%) (p = 0.07). Combined OPS/NPS was detected in 100% of cases, while the combined OPS/nasal swab increased the sensitivity significantly to 96.1% (95% CI, 90 to 100%) compared to that of the nasal swab alone (p = 0.03). The mean Ct value for NPS was 24.98 compared to 26.63 for OPS (p = 0.084) and 30.60 for nasal swab (p = 0.002). OPS achieved a sensitivity comparable to NPS and should be considered an equivalent alternative for SARS-CoV-2 testing. Full article
(This article belongs to the Special Issue Diagnosis of Viral Respiratory Infections)
Show Figures

Figure 1

11 pages, 617 KiB  
Article
Clinical Performance Evaluation of the NeuMoDx Flu A-B/RSV/SARS-CoV-2 Vantage Assay
by Georgios Meletis, Areti Tychala, Ioanna Gkeka, Athanasia Gkotzia, Aikaterini Triantafyllou, Styliani Pappa, Maria Exindari, Georgia Gioula, Anna Papa and Lemonia Skoura
Diagnostics 2022, 12(12), 3201; https://doi.org/10.3390/diagnostics12123201 - 16 Dec 2022
Cited by 1 | Viewed by 1591
Abstract
SARS-CoV-2 infections may present with various symptoms that are similar to those of other respiratory diseases. For this reason, the need for simultaneous detection of at least RSV and influenza viruses together with SARS-CoV-2 was evident from the early stages of the pandemic. [...] Read more.
SARS-CoV-2 infections may present with various symptoms that are similar to those of other respiratory diseases. For this reason, the need for simultaneous detection of at least RSV and influenza viruses together with SARS-CoV-2 was evident from the early stages of the pandemic. In the present study, we evaluated the clinical performance of the NeuMoDx™ Flu A-B/RSV/SARS-CoV-2 Vantage Assay against the conventional low-plex PCR utilized to detect influenza A-B, RSV, and SARS-CoV-2. There were 115 known positive clinical samples and 35 negative controls obtained from asymptomatic health-care workers included in the study; 25 samples were positive for influenza viruses, 46 for RSV, and 44 for SARS-CoV-2. The sensitivity, specificity, positive predictive value, and negative predictive value of the evaluated method for influenza and SARS-CoV-2 were 100%. The Spearman correlation coefficient was 0.586 (p < 0.05) for influenza and 0.893 (p < 0.05) for SARS-CoV-2. The sensitivity of the aforementioned assay for RSV was 93.47%; the specificity and the positive predictive value were 100%, and the negative predictive value was 92.10%, while the Spearman correlation coefficient was not applicable for the RSV. Overall, the assay under evaluation was shown to be a reliable alternative for the simultaneous detection of influenza viruses, RSV and SARS-CoV-2. Full article
(This article belongs to the Special Issue Diagnosis of Viral Respiratory Infections)
Show Figures

Figure 1

Other

Jump to: Research

9 pages, 417 KiB  
Brief Report
Interest of Absolute Eosinopenia as a Marker of Influenza in Outpatients during the Fall-Winter Seasons 2016–2018 in the Greater Paris Area: The SUPERFLUOUS Study
by Benjamin Davido, Benoit Lemarie, Elyanne Gault, Jennifer Dumoulin, Emma D’anglejan, Sebastien Beaune and Pierre De Truchis
Diagnostics 2023, 13(12), 2115; https://doi.org/10.3390/diagnostics13122115 - 19 Jun 2023
Viewed by 799
Abstract
Introduction: Prior to the emergence of COVID-19, when influenza was the predominant cause of viral respiratory tract infections (VRTIs), this study aimed to analyze the distinct biological abnormalities associated with influenza in outpatient settings. Methods: A multicenter retrospective study was conducted among outpatients, [...] Read more.
Introduction: Prior to the emergence of COVID-19, when influenza was the predominant cause of viral respiratory tract infections (VRTIs), this study aimed to analyze the distinct biological abnormalities associated with influenza in outpatient settings. Methods: A multicenter retrospective study was conducted among outpatients, with the majority seeking consultation at the emergency department, who tested positive for VRTIs using RT-PCR between 2016 and 2018. Patient characteristics were compared between influenza (A and B types) and non-influenza viruses, and predictors of influenza were identified using two different models focusing on absolute eosinopenia (0/mm3) and lymphocyte count <800/mm3. Results: Among 590 VRTIs, 116 (19.7%) were identified as outpatients, including 88 cases of influenza. Multivariable logistic regression analysis revealed the following predictors of influenza: in the first model, winter season (adjusted odds ratio [aOR] 7.1, 95% confidence interval [CI] 1.12–45.08) and absolute eosinopenia (aOR 6.16, 95% CI 1.14–33.24); in the second model, winter season (aOR 9.08, 95% CI 1.49–55.40) and lymphocyte count <800/mm3 (aOR 7.37, 95% CI 1.86–29.20). Absolute eosinopenia exhibited the highest specificity and positive predictive value (92% and 92.3%, respectively). Conclusion: During the winter season, specific biological abnormalities can aid physicians in identifying influenza cases and guide the appropriate use of antiviral therapy when rapid molecular tests are not readily available. Full article
(This article belongs to the Special Issue Diagnosis of Viral Respiratory Infections)
Show Figures

Figure 1

11 pages, 629 KiB  
Brief Report
SARS-CoV-2 Variants of Concern: Presumptive Identification via Sanger Sequencing Analysis of the Receptor Binding Domain (RBD) Region of the S Gene
by Grazielle Motta Rodrigues, Fabiana Caroline Zempulski Volpato, Priscila Lamb Wink, Rodrigo Minuto Paiva, Afonso Luís Barth and Fernanda de-Paris
Diagnostics 2023, 13(7), 1256; https://doi.org/10.3390/diagnostics13071256 - 27 Mar 2023
Viewed by 1198
Abstract
Variants of concern (VOCs) of SARS-CoV-2 are viral strains that have mutations associated with increased transmissibility and/or increased virulence, and their main mutations are in the receptor binding domain (RBD) region of the viral spike. This study aimed to characterize SARS-CoV-2 VOCs via [...] Read more.
Variants of concern (VOCs) of SARS-CoV-2 are viral strains that have mutations associated with increased transmissibility and/or increased virulence, and their main mutations are in the receptor binding domain (RBD) region of the viral spike. This study aimed to characterize SARS-CoV-2 VOCs via Sanger sequencing of the RBD region and compare the results with data obtained via whole genome sequencing (WGS). Clinical samples (oro/nasopharyngeal) with positive RT-qPCR results for SARS-CoV-2 were used in this study. The viral RNA from SARS-CoV-2 was extracted and a PCR fragment of 1006 base pairs was submitted for Sanger sequencing. The results of the Sanger sequencing were compared to the lineage assigned by WGS using next-generation sequencing (NGS) techniques. A total of 37 specimens were sequenced via WGS, and classified as: VOC gamma (8); delta (7); omicron (10), with 3 omicron specimens classified as the BQ.1 subvariant and 12 specimens classified as non-VOC variants. The results of the partial Sanger sequencing presented as 100% in agreement with the WGS. The Sanger protocol made it possible to characterize the main SARS-CoV-2 VOCs currently circulating in Brazil through partial Sanger sequencing of the RBD region of the viral spike. Therefore, the sequencing of the RBD region is a fast and cost-effective laboratory tool for clinical and epidemiological use in the genomic surveillance of SARS-CoV-2. Full article
(This article belongs to the Special Issue Diagnosis of Viral Respiratory Infections)
Show Figures

Figure 1

15 pages, 3337 KiB  
Systematic Review
Potential Use of Exhaled Breath Condensate for Diagnosis of SARS-CoV-2 Infections: A Systematic Review and Meta-Analysis
by Matteo Riccò, Alessandro Zaniboni, Elia Satta, Silvia Ranzieri and Federico Marchesi
Diagnostics 2022, 12(9), 2245; https://doi.org/10.3390/diagnostics12092245 - 17 Sep 2022
Cited by 5 | Viewed by 1785
Abstract
Background. Reverse-transcriptase polymerase chain reaction (RT-qPCR) assays performed on respiratory samples collected through nasal swabs still represent the gold standard for COVID-19 diagnosis. Alternative methods to this invasive and time-consuming options are still being inquired, including the collection of airways lining fluids through [...] Read more.
Background. Reverse-transcriptase polymerase chain reaction (RT-qPCR) assays performed on respiratory samples collected through nasal swabs still represent the gold standard for COVID-19 diagnosis. Alternative methods to this invasive and time-consuming options are still being inquired, including the collection of airways lining fluids through exhaled breath condensate (EBC). Materials and Methods. We performed a systematic review and meta-analysis in order to explore the reliability of EBC as a way to collect respiratory specimens for RT-qPCR for diagnosis of COVID-19. Results. A total of 4 studies (205 specimens), were ultimately collected, with a pooled sensitivity of 69.5% (95%CI 26.8–93.4), and a pooled specificity of 98.3% (95%CI 87.8–99.8), associated with high heterogeneity and scarce diagnostic agreement with the gold standard represented by nasal swabs (Cohen’s kappa = 0.585). Discussion. Even though non-invasive options for diagnosis of COVID-19 are still necessary, EBC-based RT-qPCR showed scarce diagnostic performances, ultimately impairing its implementation in real-world settings. However, as few studies have been carried out to date, and the studies included in the present review are characterized by low numbers and low sample power, further research are requested to fully characterize the actual reliability of EBC-based RT-qPCR in the diagnosis of COVID-19. Full article
(This article belongs to the Special Issue Diagnosis of Viral Respiratory Infections)
Show Figures

Figure 1

Back to TopTop