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Diagnostics
Special Issues
Molecular Detection and Typing of Viruses
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Molecular Detection and Typing of Viruses

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 (27 August 2021) | Viewed by 13010

Special Issue Editor

Dr. Ilka Engelmann

E-Mail Website
Guest Editor
Laboratoire de Virologie, CHU de Montpellier, Faculté de Médecine, Université de Montpellier, Montpellier, France
Interests: molecular diagnostics of viruses; markers of viral infection; viral infections in immunocompromised host; enterovirus; microRNAs in viral infections; viral persistance
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Molecular biology has revolutionized virology in several aspects. Due to the limitations of viral culture, antigen detection, and serology, the molecular detection of viral nucleic acids has become the method of choice for the diagnosis of viral infections in many circumstances. Molecular epidemiology of viruses has led to a better understanding of their phylogenetic relationships, which has led to changes in the taxonomy of several virus families. The recent development of rapid molecular techniques enhances the impact on viral diagnostics for patient management. Next generation sequencing is now entering clinical laboratories to permit the diagnosis of a previously unachieved large spectrum of viruses.

This Special Issue on "Molecular detection and typing of viruses" will include manuscripts on recent advancements in molecular biological techniques in the field of virology. Papers aiming to improve our understanding of epidemiology, diagnosis, and management of viral infections are welcome. Original research and reviews on these and related topics are invited.

You may choose our Joint Special Issue in IJMS.

Dr. Ilka Engelmann
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.

Keywords

  • PCR
  • molecular biology
  • typing
  • epidemiology
  • sequencing
  • molecular diagnostics

Published Papers (6 papers)

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Editorial

Jump to: Research

2 pages, 173 KiB  
Editorial
Special Issue “Molecular Detection and Typing of Viruses”
by Ilka Engelmann
Diagnostics 2021, 11(11), 2031; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics11112031 - 03 Nov 2021
Viewed by 956
Abstract
I thank all authors, reviewers and the editorial staff who contributed to this special issue [...] Full article
(This article belongs to the Special Issue Molecular Detection and Typing of Viruses)

Research

Jump to: Editorial

10 pages, 3584 KiB  
Article
Rapid Automated Screening for SARS-CoV-2 B.1.617 Lineage Variants (Delta/Kappa) through a Versatile Toolset of qPCR-Based SNP Detection
by Dominik Nörz, Moritz Grunwald, Hui Ting Tang, Flaminia Olearo, Thomas Günther, Alexis Robitaille, Nicole Fischer, Adam Grundhoff, Martin Aepfelbacher, Susanne Pfefferle and Marc Lütgehetmann
Diagnostics 2021, 11(10), 1818; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics11101818 - 01 Oct 2021
Cited by 11 | Viewed by 2692
Abstract
Background: The recent emergence of distinct and highly successful SARS-CoV-2 lineages has substantial implications for individual patients and public health measures. While next-generation-sequencing is routinely performed for surveillance purposes, RT-qPCR can be used to rapidly rule-in or rule-out relevant variants, e.g., in outbreak [...] Read more.
Background: The recent emergence of distinct and highly successful SARS-CoV-2 lineages has substantial implications for individual patients and public health measures. While next-generation-sequencing is routinely performed for surveillance purposes, RT-qPCR can be used to rapidly rule-in or rule-out relevant variants, e.g., in outbreak scenarios. The objective of this study was to create an adaptable and comprehensive toolset for multiplexed Spike-gene SNP detection, which was applied to screen for SARS-CoV-2 B.1.617 lineage variants. Methods: We created a broad set of single nucleotide polymorphism (SNP)-assays including del-Y144/145, E484K, E484Q, P681H, P681R, L452R, and V1176F based on a highly specific multi-LNA (locked nucleic acid)-probe design to maximize mismatch discrimination. As proof-of-concept, a multiplex-test was compiled and validated (SCOV2-617VOC-UCT) including SNP-detection for L452R, P681R, E484K, and E484Q to provide rapid screening capabilities for the novel B.1.617 lineages. Results: For the multiplex-test (SCOV2-617VOC-UCT), the analytic lower limit of detection was determined as 182 IU/mL for L452R, 144 IU/mL for P681R, and 79 IU/mL for E484Q. A total of 233 clinical samples were tested with the assay, including various on-target and off-target sequences. All SNPs (179/179 positive) were correctly identified as determined by SARS-CoV-2 whole genome sequencing. Conclusion: The recurrence of SNP locations and flexibility of methodology presented in this study allows for rapid adaptation to current and future variants. Furthermore, the ability to multiplex various SNP-assays into screening panels improves speed and efficiency for variant testing. We show 100% concordance with whole genome sequencing for a B.1.617.2 screening assay on the cobas6800 high-throughput system. Full article
(This article belongs to the Special Issue Molecular Detection and Typing of Viruses)
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9 pages, 1608 KiB  
Article
Conserved Sequence Analysis of Influenza A Virus HA Segment and Its Application in Rapid Typing
by Qianyu Lin, Xiang Ji, Feng Wu and Lan Ma
Diagnostics 2021, 11(8), 1328; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics11081328 - 23 Jul 2021
Cited by 3 | Viewed by 2091
Abstract
The high mutation rate of the influenza A virus hemagglutinin segment poses great challenges to its long-term effective testing and subtyping. Our conserved sequence searching method achieves high-specificity conserved sequences on H1–H9 subtypes. In addition, PCR experiments show that primers based on conserved [...] Read more.
The high mutation rate of the influenza A virus hemagglutinin segment poses great challenges to its long-term effective testing and subtyping. Our conserved sequence searching method achieves high-specificity conserved sequences on H1–H9 subtypes. In addition, PCR experiments show that primers based on conserved sequences can be used in influenza A virus HA subtyping. Conserved sequence-based primers are expected to be long-term, effective subtyping tools for influenza A virus HA. Full article
(This article belongs to the Special Issue Molecular Detection and Typing of Viruses)
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13 pages, 587 KiB  
Article
A Versatile Processing Workflow to Enable Pathogen Detection in Clinical Samples from Organs Using VIDISCA
by Alba Folgueiras-González, Robin van den Braak, Martin Deijs, Lia van der Hoek and Ad de Groof
Diagnostics 2021, 11(5), 791; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics11050791 - 27 Apr 2021
Cited by 2 | Viewed by 1583
Abstract
In recent years, refined molecular methods coupled with powerful high throughput sequencing technologies have increased the potential of virus discovery in clinical samples. However, host genetic material remains a complicating factor that interferes with discovery of novel viruses in solid tissue samples as [...] Read more.
In recent years, refined molecular methods coupled with powerful high throughput sequencing technologies have increased the potential of virus discovery in clinical samples. However, host genetic material remains a complicating factor that interferes with discovery of novel viruses in solid tissue samples as the relative abundance of the virus material is low. Physical enrichment processing methods, although usually complicated, labor-intensive, and costly, have proven to be successful for improving sensitivity of virus detection in complex samples. In order to further increase detectability, we studied the application of fast and simple high-throughput virus enrichment methods on tissue homogenates. Probe sonication in high EDTA concentrations, organic extraction with Vertrel™ XF, or a combination of both, were applied prior to chromatography-like enrichment using Capto™ Core 700 resin, after which effects on virus detection sensitivity by the VIDISCA method were determined. Sonication in the presence of high concentrations of EDTA showed the best performance with an increased proportion of viral reads, up to 9.4 times, yet minimal effect on the host background signal. When this sonication procedure in high EDTA concentrations was followed by organic extraction with Vertrel™ XF and two rounds of core bead chromatography enrichment, an increase up to 10.5 times in the proportion of viral reads in the processed samples was achieved, with reduction of host background sequencing. We present a simple and semi-high-throughput method that can be used to enrich homogenized tissue samples for viral reads. Full article
(This article belongs to the Special Issue Molecular Detection and Typing of Viruses)
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11 pages, 1469 KiB  
Article
Spatial and Temporal Virus Load Dynamics of SARS-CoV-2: A Single-Center Cohort Study
by Enagnon Kazali Alidjinou, Julien Poissy, Mahdi Ouafi, Morgan Caplan, Ilyes Benhalima, Julien Goutay, Claire Tinez, Karine Faure, Marie-Charlotte Chopin, Cécile Yelnik, Marc Lambert, Didier Hober, Sébastien Preau, The Lille COVID Research Network (LICORNE), Saad Nseir and Ilka Engelmann
Diagnostics 2021, 11(3), 427; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics11030427 - 03 Mar 2021
Cited by 10 | Viewed by 2154
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused an ongoing pandemic. Reverse transcription polymerase chain reaction (RT-PCR) is the gold standard for the detection of SARS-CoV-2 and has been applied to different specimen types. Understanding the virus load and virus detection [...] Read more.
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused an ongoing pandemic. Reverse transcription polymerase chain reaction (RT-PCR) is the gold standard for the detection of SARS-CoV-2 and has been applied to different specimen types. Understanding the virus load and virus detection frequency in different specimen types is important to improve diagnosis and estimate the duration of potential infectivity. We conducted a retrospective single-center cohort study on hospitalized and outpatients with SARS-CoV-2 infection. We analyzed the frequency of virus detection, virus load, and duration of the virus excretion in upper and lower respiratory specimens as well as stool and plasma. We found that the frequency of SARS-CoV-2 detection, the virus load, and duration of virus excretion was higher in lower respiratory tract (LRT) than in upper respiratory tract (URT) specimens. The duration of virus excretion was longer in patients requiring intensive care unit (ICU) admission. In conclusion, LRT specimens are the most appropriate specimen type for the detection and follow-up of SARS-CoV-2 infection. Duration of virus excretion is longer in severe cases of SARS-CoV-2 infection. Full article
(This article belongs to the Special Issue Molecular Detection and Typing of Viruses)
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15 pages, 1718 KiB  
Article
Time and Mode of Epidemic HCV-2 Subtypes Spreading in Europe: Phylodynamics in Italy and Albania
by Erika Ebranati, Alessandro Mancon, Martina Airoldi, Silvia Renica, Renata Shkjezi, Pranvera Dragusha, Carla Della Ventura, Anna Rita Ciccaglione, Massimo Ciccozzi, Silvia Bino, Elisabetta Tanzi, Valeria Micheli, Elisabetta Riva, Massimo Galli and Gianguglielmo Zehender
Diagnostics 2021, 11(2), 327; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics11020327 - 17 Feb 2021
Cited by 1 | Viewed by 2485
Abstract
Hepatitis C virus (HCV) genotype 2 causes about 10% of global infections and has the most variable circulation profile in Europe. The history of “endemic” HCV-2 subtypes has been satisfactorily reconstructed, instead there is little information about the recent spread of the “epidemic” [...] Read more.
Hepatitis C virus (HCV) genotype 2 causes about 10% of global infections and has the most variable circulation profile in Europe. The history of “endemic” HCV-2 subtypes has been satisfactorily reconstructed, instead there is little information about the recent spread of the “epidemic” subtypes, including HCV-2c. To investigate the origin and dispersion pathways of HCV-2c, 245 newly characterized Italian and Albanian HCV-2 NS5B sequences were aligned with 247 publicly available sequences and included in phylogeographic and phylodynamic analyses using the Bayesian framework. Our findings show that HCV-2c was the most prevalent subtype in Italy and Albania. The phylogeographic analysis suggested an African origin of HCV-2c before it reached Italy about in the 1940s. Phylodynamic analysis revealed an exponential increase in the effective number of infections and Re in Italy between the 1940s and 1960s, and in Albania between the 1990s and the early 2000s. It seems very likely that HCV-2c reached Italy from Africa at the time of the second Italian colonization but did not reach Albania until the period of dramatic migration to Italy in the 1990s. This study contributes to reconstructing the history of the spread of epidemic HCV-2 subtypes to Europe. Full article
(This article belongs to the Special Issue Molecular Detection and Typing of Viruses)
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