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Pathogens
Special Issues
New Insights into Molecular Epidemiology and Diagnostics of Human Pathogens
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New Insights into Molecular Epidemiology and Diagnostics of Human Pathogens

A special issue of Pathogens (ISSN 2076-0817). This special issue belongs to the section "Epidemiology of Infectious Diseases".

Deadline for manuscript submissions: 30 June 2024 | Viewed by 4326

Special Issue Editor

Dr. Alban Ramette

E-Mail Website
Guest Editor
Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
Interests: microbiology; epidemiology; biostatistics; microbial ecology; bioinformatics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Recent scientific advancements have revolutionized our understanding of human pathogens, transmission dynamics, and their impact on public health. By combining pathogen molecular data with clinical and contextual information, researchers can now trace infection sources, identify transmission routes, and assess the influence of pathogen evolution on disease severity and outcomes. Wet laboratory innovations, including sequencing technologies and diagnostic assays, have played a crucial role in these advancements. However, to fully unlock the potential of these innovations, it is essential to integrate them with innovations in bioinformatics, data analysis, and data interpretation.

In this context, we are excited to announce an open call for submissions of both original articles and review papers on the topic of "New Insights into Molecular Epidemiology and Diagnostics of Human Pathogens".

This call aims to assemble a diverse range of perspectives and expertise in wet laboratory innovations, bioinformatics, and data interpretation. Potential topics of interest include novel laboratory techniques for studying human pathogens, applications of sequencing technologies in molecular epidemiology, innovative diagnostic assays for rapid pathogen detection, advances in bioinformatics for processing large-scale genomic data, statistical approaches for interpreting genetic variations and inferring transmission dynamics, and challenges and solutions in data interpretation for public health interventions. We encourage early submissions to secure your opportunity to contribute to this crucial series.

Dr. Alban Ramette
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. Pathogens 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 2700 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

  • human pathogens
  • molecular epidemiology
  • diagnostics
  • genetic diversity
  • next-generation sequencing (NGS)
  • transmission routes
  • novel diagnostic methods
  • nucleic acid amplification
  • gene expression profiling
  • early detection
  • disease management
  • data integration
  • outbreaks
  • control measures
  • public health

Published Papers (4 papers)

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Research

13 pages, 2418 KiB  
Article
Retrospective Genotyping of Enteroviruses Using a Diagnostic Nanopore Sequencing Workflow
by Vanessa van Ackeren, Stefan Schmutz, Ian Pichler, Gabriela Ziltener, Maryam Zaheri, Verena Kufner and Michael Huber
Pathogens 2024, 13(5), 390; https://doi.org/10.3390/pathogens13050390 - 8 May 2024
Viewed by 212
Abstract
Enteroviruses are among the most common viruses pathogenic to humans. They are associated with various forms of disease, ranging from mild respiratory illness to severe neurological diseases. In recent years, an increasing number of isolated cases of children developing meningitis or encephalitis as [...] Read more.
Enteroviruses are among the most common viruses pathogenic to humans. They are associated with various forms of disease, ranging from mild respiratory illness to severe neurological diseases. In recent years, an increasing number of isolated cases of children developing meningitis or encephalitis as a result of enterovirus infection have been reported, as well as discrete enterovirus D68 outbreaks in North America in 2014 and 2016. We developed an assay to rapidly genotype enteroviruses by sequencing a region within the VP1 gene using nanopore Flongles. We retrospectively analyzed enterovirus-/rhinovirus-positive clinical samples from the Zurich, Switzerland area mainly collected during two seasons in 2019/2020 and 2021/2022. Respiratory, cerebrospinal fluid, and stool samples were analyzed. Whole-genome sequencing was performed on samples with ambiguous genotyping results and enterovirus D68-positive samples. Out of 255 isolates, a total of 95 different genotypes were found. A difference in the prevalence of enterovirus and rhinovirus infections was observed for both sample type and age group. In particular, children aged 0–4 years showed a higher frequency of enterovirus infections. Comparing the respiratory seasons, a higher prevalence was found, especially for enterovirus A and rhinovirus A after the SARS-CoV-2 pandemic. The enterovirus genotyping workflow provides a rapid diagnostic tool for individual analysis and continuous enterovirus surveillance. Full article
(This article belongs to the Special Issue New Insights into Molecular Epidemiology and Diagnostics of Human Pathogens)
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11 pages, 1266 KiB  
Article
Echovirus 30 in Bulgaria during the European Upsurge of the Virus, 2017–2018
by Irina Georgieva, Asya Stoyanova, Savina Stoitsova and Lubomira Nikolaeva-Glomb
Pathogens 2024, 13(2), 143; https://doi.org/10.3390/pathogens13020143 - 5 Feb 2024
Viewed by 702
Abstract
In 2018, an increase in echovirus 30 (E30) detections was reported in some European countries. To assess the circulation and phylogenetic relationships of E30 in Bulgaria, E30 samples identified at the National Reference Laboratory for Enteroviruses, National Centre of Infectious and Parasitic Diseases, [...] Read more.
In 2018, an increase in echovirus 30 (E30) detections was reported in some European countries. To assess the circulation and phylogenetic relationships of E30 in Bulgaria, E30 samples identified at the National Reference Laboratory for Enteroviruses, National Centre of Infectious and Parasitic Diseases, Bulgaria (NRL for Enteroviruses) in 2017 and 2018 were subjected to sequencing and phylogenetic analysis. The present study revealed that sample positivity did not significantly increase in Bulgaria during the European upsurge. E30 was identified in six patients, two of whom were epidemiologically linked. The maximum-likelihood phylogenetic tree showed that sequences from five patients belonged to the G1 lineage (clades G1a and G1b). The sequence from one patient belonged to the G2 lineage and was grouped closer to sequences from the last E30 outbreak in Bulgaria in 2012. No recombination events were detected. The European E30 upsurge in 2018 was caused by two clades, and one of them was G1. The fact that the majority of the Bulgarian samples belonged to G1 indicated that the virus was present in the country but did not cause a local upsurge. Phylogenetic and epidemiological data indicated sporadic E30 cases and a possible shift towards G1 lineage in 2017 and 2018. Full article
(This article belongs to the Special Issue New Insights into Molecular Epidemiology and Diagnostics of Human Pathogens)
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14 pages, 1444 KiB  
Article
NASCarD (Nanopore Adaptive Sampling with Carrier DNA): A Rapid, PCR-Free Method for SARS-CoV-2 Whole-Genome Sequencing in Clinical Samples
by Miguel A. Terrazos Miani, Loïc Borcard, Sonja Gempeler, Christian Baumann, Pascal Bittel, Stephen L. Leib, Stefan Neuenschwander and Alban Ramette
Pathogens 2024, 13(1), 61; https://doi.org/10.3390/pathogens13010061 - 9 Jan 2024
Cited by 1 | Viewed by 1689
Abstract
Whole-genome sequencing (WGS) represents the main technology for SARS-CoV-2 lineage characterization in diagnostic laboratories worldwide. The rapid, near-full-length sequencing of the viral genome is commonly enabled by high-throughput sequencing of PCR amplicons derived from cDNA molecules. Here, we present a new approach called [...] Read more.
Whole-genome sequencing (WGS) represents the main technology for SARS-CoV-2 lineage characterization in diagnostic laboratories worldwide. The rapid, near-full-length sequencing of the viral genome is commonly enabled by high-throughput sequencing of PCR amplicons derived from cDNA molecules. Here, we present a new approach called NASCarD (Nanopore Adaptive Sampling with Carrier DNA), which allows a low amount of nucleic acids to be sequenced while selectively enriching for sequences of interest, hence limiting the production of non-target sequences. Using COVID-19 positive samples available during the omicron wave, we demonstrate how the method may lead to >99% genome completeness of the SARS-CoV-2 genome sequences within 7 h of sequencing at a competitive cost. The new approach may have applications beyond SARS-CoV-2 sequencing for other DNA or RNA pathogens in clinical samples. Full article
(This article belongs to the Special Issue New Insights into Molecular Epidemiology and Diagnostics of Human Pathogens)
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10 pages, 2418 KiB  
Communication
SARS-CoV-2 Nucleocapsid Protein Mutations Found in Switzerland Disrupt N-Gene Amplification in Commonly Used Multiplex RT-PCR Assay
by Dominique Hilti, Faina Wehrli, Anna Roditscheff, Martin Risch, Lorenz Risch, Adrian Egli, Thomas Bodmer and Nadia Wohlwend
Pathogens 2023, 12(12), 1383; https://doi.org/10.3390/pathogens12121383 - 24 Nov 2023
Cited by 2 | Viewed by 1062
Abstract
At the end of 2021, we observed an increase in N-gene target failures (NGTF) with the TaqPathTM COVID-19 CE-IVD RT-PCR Kit from Thermo Fisher Scientific (TaqPath). We subsequently used whole-genome sequencing (Oxford Nanopore Technology) to identify potential issues with N-gene PCR efficacy. Among [...] Read more.
At the end of 2021, we observed an increase in N-gene target failures (NGTF) with the TaqPathTM COVID-19 CE-IVD RT-PCR Kit from Thermo Fisher Scientific (TaqPath). We subsequently used whole-genome sequencing (Oxford Nanopore Technology) to identify potential issues with N-gene PCR efficacy. Among 168,101 positive samples with a cycle threshold (CT) value <30 from August 2021 to May 2022, 194 specimens without N-gene amplification by PCR were identified (0.12%). Most NGTF samples originated from a wave of infection attributable to the Delta variant (B.1.617.2) and its sublineages. Sequencing revealed the nucleotide substitution G28922T (A217S) in 151 samples (88.8%). The substitution G215C, a hallmark mutation for Delta lineages, was concurrently present in all of these samples. Ten samples (5.9%) carried the deletion 28,913–28,918 (del214/215), eight samples (4.7%) the deletion 28,913–28,915 (del214) and one sample (0.6%) the deletion 28,892–28,930 (del207–219). Samples showing intact N-gene amplification by PCR lacked these specific mutations, but delayed-type amplification (i.e., partial or pNGTF) was attributable to the exclusive presence of A217S. As the N gene is a common target in many RT-PCR methods for SARS-CoV-2, an in-depth analysis of single-target failures using a combination with viral whole genome sequencing may allow for the identification of diagnostic flaws and eventual new variants. Full article
(This article belongs to the Special Issue New Insights into Molecular Epidemiology and Diagnostics of Human Pathogens)
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