Submit to Special Issue Submit Abstract to Special Issue Review for Viruses Propose a Special Issue

Journal Browser

► Journal Browser

COVID-19 Diagnostics in Clinical Applications and Pandemic Controls 2024

Special Issue Editors
Special Issue Information
Keywords
Related Special Issues
Published Papers

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Coronaviruses".

Deadline for manuscript submissions: 31 October 2024 | Viewed by 4283

Share This Special Issue

Special Issue Editors

Dr. Luciana Jesus Costa

E-Mail Website
Guest Editor

Laboratory of Genetics and Immunology of Viral Infections, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
Interests: viral diseases
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Amilcar Tanuri

E-Mail Website
Guest Editor

Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
Interests: Zika virus; microcephaly; flaviviridae; phylogeny; HIV-1; RNA directed DNA polymerase inhibitor; cats; proviruses; felid herpesvirus 1
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Due to the unprecedented public health crises generated by the COVID-19 pandemic, researchers throughout the world have rushed to develop tools to detect both its etiological agent, SARS-CoV-2, and humans’ antibody response against it. The expedited development of sensitive and specific RT-qPCR to detect SARS-CoV-2 mRNA, in addition to the lateral flow rapid antigen and antibody tests, demonstrates the huge efforts as well as preparedness of research groups and biomedical companies to fight public health issues. After two years of the COVID-19 pandemic and the expressive amount of data generated in terms of SARS-CoV-2 diagnostics, full-genome molecular characterization, total antibody detection, and neutralizing antibodies, a comprehensive view of the usefulness and specific implementations of these tools, as well as how they changed the course of the pandemic, is needed.

Thus, to shed light on viral diagnostics in clinical applications, we welcome reviews and original research articles on the following themes:

SARS-CoV-2 nucleotide as well as antigen detection through the course of symptomatic and asymptomatic infection;
SARS-CoV-2 nucleotide as well as antigen detection and their relationship with the presence of infectious viruses in clinical samples;
SARS-CoV-2 and antibody detection in clinical samples as markers of acute infection;
Anti-SARS-CoV-2 neutralization antibodies and the course of infection;
Total as well as neutralizing antibodies and the persistence of SARS-CoV-2 in clinical samples.

Dr. Luciana Jesus Costa
Prof. Dr. Amilcar Tanuri
Guest Editors

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. Viruses is an international peer-reviewed open access monthly 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.

Keywords

humans’ antibody response to COVID-19 pandemic
RT-qPCR SARS-CoV-2 nucleotide antigen detection
anti-SARS-CoV-2 neutralization antibodies

Related Special Issues

COVID-19 Diagnostics in Clinical Applications and Pandemic Controls 2023 in Viruses (13 articles)
COVID-19 Diagnostics in Clinical Applications and Pandemic Control in Viruses (11 articles)

Published Papers (4 papers)

Download All Papers

Research

13 pages, 4145 KiB

Open AccessArticle

Characterizing Infections in Two Epidemic Waves of SARS-CoV-2 Omicron Variants: A Cohort Study in Guangzhou, China

by Lin Qu, Chunyan Xie, Ming Qiu, Lina Yi, Zhe Liu, Lirong Zou, Pei Hu, Huimin Jiang, Huimin Lian, Mingda Yang, Haiyi Yang, Huiling Zeng, Huimin Chen, Jianguo Zhao, Jianpeng Xiao, Jianfeng He, Ying Yang, Liang Chen, Baisheng Li, Jiufeng Sun and Jing Lu Show full author list Hide full author list

Viruses 2024, 16(4), 649; https://doi.org/10.3390/v16040649 - 22 Apr 2024

Viewed by 484

Abstract

Background: After the adjustment of COVID-19 epidemic policy, mainland China experienced two consecutive waves of Omicron variants within a seven-month period. In Guangzhou city, as one of the most populous regions, the viral infection characteristics, molecular epidemiology, and the dynamic of population immunity are still elusive. Methods: We launched a prospective cohort study in the Guangdong Provincial CDC from December 2022 to July 2023. Fifty participants who received the same vaccination regimen and had no previous infection were recruited. Results: 90% of individuals were infected with Omicron BA.5* variants within three weeks in the first wave. Thirteen cases (28.26%) experienced infection with XBB.1* variants, occurring from 14 weeks to 21 weeks after the first wave. BA.5* infections exhibited higher viral loads in nasopharyngeal sites compared to oropharyngeal sites. Compared to BA.5* infections, the XBB.1* infections had significantly milder clinical symptoms, lower viral loads, and shorter durations of virus positivity. The infection with the BA.5* variant elicited varying levels of neutralizing antibodies against XBB.1* among different individuals, even with similar levels of BA.5* antibodies. The level of neutralizing antibodies specific to XBB.1* determined the risk of reinfection. Conclusions: The rapid large-scale infections of the Omicron variants have quickly established herd immunity among the population in mainland China. In the future of the COVID-19 epidemic, a lower infection rate but a longer duration can be expected. Given the large population size and ongoing diversified herd immunity, it remains crucial to closely monitor the molecular epidemiology of SARS-CoV-2 for the emergence of new variants of concern in this region. Additionally, the timely evaluation of the immune status across different age groups is essential for informing future vaccination strategies and intervention policies. Full article

(This article belongs to the Special Issue COVID-19 Diagnostics in Clinical Applications and Pandemic Controls 2024)

► Show Figures

Figure 1

19 pages, 1905 KiB

Open AccessArticle

Performance of Three Anti-SARS-CoV-2 Anti-S and One Anti-N Immunoassays for the Monitoring of Immune Status and Vaccine Response

by Y. Victoria Zhang, Attila Kumanovics, Joesph Wiencek, Stacy E. F. Melanson, Tanzy Love, Alan H. B. Wu, Zhen Zhao, Qing H. Meng, David D. Koch, Fred S. Apple, Caitlin R. Ondracek and Robert H. Christenson

Viruses 2024, 16(2), 292; https://doi.org/10.3390/v16020292 - 14 Feb 2024

Viewed by 1225

Abstract

This study aimed to evaluate and compare the performance of three anti-S and one anti-N assays that were available to the project in detecting antibody levels after three commonly used SARS-CoV-2 vaccines (Pfizer, Moderna, and Johnson & Johnson). It also aimed to assess the association of age, sex, race, ethnicity, vaccine timing, and vaccine side effects on antibody levels in a cohort of 827 individuals. In September 2021, 698 vaccinated individuals donated blood samples as part of the Association for Diagnostics & Laboratory Medicine (ADLM) COVID-19 Immunity Study. These individuals also participated in a comprehensive survey covering demographic information, vaccination status, and associated side effects. Additionally, 305 age- and gender-matched samples were obtained from the ADLM 2015 sample bank as pre-COVID-19-negative samples. All these samples underwent antibody level analysis using three anti-S assays, namely Beckman Access SARS-CoV-2 IgG (Beckman assay), Ortho Clinical Diagnostics VITROS Anti-SARS-CoV-2 IgG (Ortho assay), Siemens ADVIA Centaur SARS-CoV-2 IgG (Siemens assay), and one anti-N antibody assay: Bio-Rad Platelia SARS-CoV-2 Total Ab assay (BioRad assay). A total of 827 samples (580 COVID-19 samples and 247 pre-COVID-19 samples) received results for all four assays and underwent further analysis. Beckman, Ortho, and Siemens anti-S assays showed an overall sensitivity of 99.5%, 97.6%, and 96.9%, and specificity of 90%, 100%, and 99.6%, respectively. All three assays indicated 100% sensitivity for individuals who received the Moderna vaccine and boosters, and over 99% sensitivity for the Pfizer vaccine. Sensitivities varied from 70.4% (Siemens), 81.5% (Ortho), and 96.3% (Beckman) for individuals who received the Johnson & Johnson vaccine. BioRad anti-N assays demonstrated 46.2% sensitivity and 99.25% specificity based on results from individuals with self-reported infection. The highest median anti-S antibody levels were measured in individuals who received the Moderna vaccine, followed by Pfizer and then Johnson & Johnson vaccines. Higher anti-S antibody levels were significantly associated with younger age and closer proximity to the last vaccine dose but were not associated with gender, race, or ethnicity. Participants with higher anti-S levels experienced significantly more side effects as well as more severe side effects (e.g., muscle pain, chills, fever, and moderate limitations) (p < 0.05). Anti-N antibody levels only indicated a significant correlation with headache. This study indicated performance variations among different anti-S assays, both among themselves and when analyzing individuals with different SARS-CoV-2 vaccines. Caution should be exercised when conducting large-scale studies to ensure that the same platform and/or assays are used for the most effective interpretation of the data. Full article

(This article belongs to the Special Issue COVID-19 Diagnostics in Clinical Applications and Pandemic Controls 2024)

► Show Figures

Figure 1

12 pages, 2216 KiB

Open AccessArticle

Epidemiological Insights into the Omicron Outbreak via MeltArray-Assisted Real-Time Tracking of SARS-CoV-2 Variants

by Ting Yan, Rongrong Zheng, Yinghui Li, Siyang Sun, Xiaohong Zeng, Zhijiao Yue, Yiqun Liao, Qinghua Hu, Ye Xu and Qingge Li

Viruses 2023, 15(12), 2397; https://doi.org/10.3390/v15122397 - 08 Dec 2023

Cited by 1 | Viewed by 987

Abstract

The prolonged course of the COVID-19 pandemic necessitates sustained surveillance of emerging variants. This study aimed to develop a multiplex real-time polymerase chain reaction (rt-PCR) suitable for the real-time tracking of Omicron subvariants in clinical and wastewater samples. Plasmids containing variant-specific mutations were used to develop a MeltArray assay. After a comprehensive evaluation of both analytical and clinical performance, the established assay was used to detect Omicron variants in clinical and wastewater samples, and the results were compared with those of next-generation sequencing (NGS) and droplet digital PCR (ddPCR). The MeltArray assay identified 14 variant-specific mutations, enabling the detection of five Omicron sublineages (BA.2*, BA.5.2*, BA.2.75*, BQ.1*, and XBB.1*) and eight subvariants (BF.7, BN.1, BR.2, BQ.1.1, XBB.1.5, XBB.1.16, XBB.1.9, and BA.4.6). The limit of detection (LOD) of the assay was 50 copies/reaction, and no cross-reactivity was observed with 15 other respiratory viruses. Using NGS as the reference method, the clinical evaluation of 232 swab samples exhibited a clinical sensitivity of > 95.12% (95% CI 89.77–97.75%) and a specificity of > 95.21% (95% CI, 91.15–97.46%). When used to evaluate the Omicron outbreak from late 2022 to early 2023, the MeltArray assay performed on 1408 samples revealed that the epidemic was driven by BA.5.2* (883, 62.71%) and BF.7 (525, 37.29%). Additionally, the MeltArray assay demonstrated potential for estimating variant abundance in wastewater samples. The MeltArray assay is a rapid and scalable method for identifying SARS-CoV-2 variants. Integrating this approach with NGS and ddPCR will improve variant surveillance capabilities and ensure preparedness for future variants. Full article

(This article belongs to the Special Issue COVID-19 Diagnostics in Clinical Applications and Pandemic Controls 2024)

► Show Figures

Figure 1

13 pages, 2306 KiB

Open AccessArticle

Longitudinal Analysis of Antibody Response Following SARS-CoV-2 Infection Depending on Disease Severity: A Prospective Cohort Study

by Christina Zirou, Sentiljana Gumeni, Ioannis Bellos, Ioannis Ntanasis-Stathopoulos, Aimilia D. Sklirou, Tina Bagratuni, Eleni Korompoki, Filia Apostolakou, Ioannis Papassotiriou, Ioannis P. Trougakos and Evangelos Terpos

Viruses 2023, 15(11), 2250; https://doi.org/10.3390/v15112250 - 13 Nov 2023

Viewed by 1007

Abstract

Objective: Severe coronavirus disease 19 (COVID-19) is characterized by a dysregulated inflammatory response, with humoral immunity playing a central role in the disease course. The objective of this study was to assess the immune response and the effects of vaccination in recovered individuals with variable disease severity up to one year following natural infection. Methods: A prospective cohort study was conducted including patients with laboratory-confirmed COVID-19. Disease severity was classified as mild, moderate, and severe based on clinical presentation and outcomes. Anti-RBD (receptor binding domain) and neutralizing antibodies were evaluated at multiple timepoints during the first year after COVID-19 diagnosis. Results: A total of 106 patients were included; of them, 28 were diagnosed with mild, 38 with moderate, and 40 with severe disease. At least one vaccine dose was administered in 58 individuals during the follow-up. Participants with mild disease presented significantly lower anti-RBD and neutralizing antibodies compared to those with moderate and severe disease up to the 3rd and 6th months after the infection, respectively. After adjusting for covariates, in the third month, severe COVID-19 was associated with significantly higher anti-RBD (β: 563.09; 95% confidence intervals (CI): 257.02 to 869.17) and neutralizing (β: 21.47; 95% CI: 12.04 to 30.90) antibodies. Among vaccinated individuals, at the 12th month, a history of moderate disease was associated with significantly higher anti-RBD levels (β: 5615.19; 95% CI: 657.92 to 10,572.46). Conclusions: Severe COVID-19 is associated with higher anti-RBD and neutralizing antibodies up to 6 months after the infection. Vaccination of recovered patients is associated with a remarkable augmentation of antibody titers up to one year after COVID-19 diagnosis, regardless of disease severity. Full article

(This article belongs to the Special Issue COVID-19 Diagnostics in Clinical Applications and Pandemic Controls 2024)

► Show Figures