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Molecular Assays for Mutation and Infectious Agent Detection
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Molecular Assays for Mutation and Infectious Agent Detection

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Technologies and Resources for Genetics".

Deadline for manuscript submissions: 10 October 2025 | Viewed by 775

Special Issue Editor

Dr. Gustavo Barra

E-Mail Website
Guest Editor
Sabin Laboratory, Brasilia, Brazil
Interests: molecular diagnostics; genetic mutations; pathogen detection; PCR; next-generation sequencing (NGS)

Special Issue Information

Dear Colleagues,

Molecular assays have revolutionized the detection of genetic mutations and infectious agents, providing rapid and precise diagnostic capabilities crucial for public health. This Special Issue focuses on advancements in molecular diagnostics, including PCR, digital PCR, next-generation sequencing and isothermal amplification, which enhance our ability to identify genetic mutations and detect pathogens efficiently. These technologies offer improved sensitivity, specificity and speed, facilitating the early diagnosis and targeted treatment of various diseases. We invite researchers to contribute original research and review articles that explore novel methodologies, comparative studies and practical applications of molecular assays in clinical and environmental settings. Our goal is to highlight the latest innovations and their impact on improving diagnostic accuracy and patient outcomes.

Dr. Gustavo Barra
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. Genes 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

  • molecular diagnostics
  • genetic mutations
  • pathogen detection
  • PCR
  • digital PCR
  • next-generation sequencing (NGS)
  • isothermal amplification
  • diagnostic technologies
  • clinical applications
  • public health

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Published Papers (2 papers)

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Research

13 pages, 1513 KiB  
Article
Development and Evaluation of a Molecular Test for Monkeypox Virus in the Federal District, Brazil
by Lucas Pereira da Silva, Fabián Andrés Hurtado, Aline Belmok, Rafael Correa, Claudia F. Sousa, Gislene P. Gil, Lara Velasco, Rafael H. Jácomo, Lídia F. Nery, Maria Tereza de Oliveira Rodrigues, Miguel S. Andrade and Rosângela Vieira de Andrade
Genes 2025, 16(7), 779; https://doi.org/10.3390/genes16070779 - 30 Jun 2025
Abstract
Background: Monkeypox virus, the etiological agent of Mpox, is a double-stranded DNA virus belonging to the Orthopoxvirus genus that has attracted increasing attention due to sporadic outbreaks in humans. In 2022, it was responsible for the largest Mpox outbreak outside the African continent, [...] Read more.
Background: Monkeypox virus, the etiological agent of Mpox, is a double-stranded DNA virus belonging to the Orthopoxvirus genus that has attracted increasing attention due to sporadic outbreaks in humans. In 2022, it was responsible for the largest Mpox outbreak outside the African continent, infecting over 117,000 individuals worldwide. In Brazil, since the first confirmed case in June 2022, more than 13,000 people have been diagnosed with the virus. Methods: In July 2022, we developed the first molecular test for the detection of monkeypox virus in the Midwest region of the country, allowing the diagnosis of the disease in various patients, mainly residents of the Federal District. Thus, in this work, we present the validation of a laboratory-developed qPCR test (LDT) for monkeypox virus detection, as well as a retrospective epidemiological analysis based on laboratory results. Results: The developed qPCR test demonstrated 100% accuracy, with a detection limit of 21.25 copies per reaction, and was validated for samples from swabbed pustule exudates and lesion crusts. To date, 295 tests have been conducted, with 88 (30%) returning positive. The positivity rate was 41.15% in male patients and 2.41% in female patients. A peak in positivity was observed in August 2022. From 2023 to 2024, there was a marked decline in test demand with occasional positive results. Conclusions: The rapid implementation of the test by our laboratory allowed for an immediate response to patients and provided important data for understanding the dynamics of monkeypox virus spread in Brazil, particularly in the Midwest region. Full article
(This article belongs to the Special Issue Molecular Assays for Mutation and Infectious Agent Detection)
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13 pages, 553 KiB  
Article
Evaluating the Diagnostic Utility of dd-cfDNA in Renal Allograft Surveillance: A Single-Center Perspective
by Aja Aravamudhan, Kira Krug, Michelle Stoffel and Penn Muluhngwi
Genes 2025, 16(7), 724; https://doi.org/10.3390/genes16070724 - 21 Jun 2025
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Abstract
Background: Donor-derived cell-free DNA (dd-cfDNA) testing offers a non-invasive approach for monitoring allograft health in transplant recipients. However, its diagnostic performance and clinical utility remain insufficiently characterized across diverse populations. Objectives: This study assesses concordance between dd-cfDNA, donor-specific antibody (DSA) testing, and biopsy, [...] Read more.
Background: Donor-derived cell-free DNA (dd-cfDNA) testing offers a non-invasive approach for monitoring allograft health in transplant recipients. However, its diagnostic performance and clinical utility remain insufficiently characterized across diverse populations. Objectives: This study assesses concordance between dd-cfDNA, donor-specific antibody (DSA) testing, and biopsy, while also comparing two commercial assays (AlloSure and Prospera) in kidney and pancreas transplant recipients. Methods: We retrospectively analyzed 271 transplant patient records from 2019 to 2024 at our institution, focusing on dd-cfDNA testing. Statistical analyses evaluated assay performance in relation to DSA and biopsy results. The impact of multi-organ transplantation (MOT) on dd-cfDNA levels was also assessed. Results: In our predominantly Caucasian cohort (61.5%) with a mean age of 53 years, increased levels of dd-cfDNA were significantly associated with DSA positivity, particularly within the Prospera group (p = 0.002), and were particularly higher in patients with HLA class II DSA. Both assays showed a limited correlation with biopsy-confirmed rejection. AlloSure had high specificity (80%) but low sensitivity (19%), whereas Prospera showed higher sensitivity (75%) with moderate specificity (60%). Dd-cfDNA levels were elevated in MOT recipients in a vendor-dependent manner. Conclusions: Our findings highlight the differing clinical strengths of dd-cfDNA assays: AlloSure demonstrates greater preference for ruling out rejection, whereas Prospera appears better suited for early detection. Dd-cfDNA interpretation in MOT recipients warrants cautious consideration. Overall, tailoring assay selection and optimizing diagnostic thresholds to clinical context may enhance transplant surveillance and patient management strategies. Full article
(This article belongs to the Special Issue Molecular Assays for Mutation and Infectious Agent Detection)
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