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Special Issue "Molecular Detection and Characterisation of Viral Pathogens"

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

Deadline for manuscript submissions: 31 July 2023 | Viewed by 5070

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Special Issue Editors

Prof. Dr. Armanda Bastos

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Guest Editor

Department of Zoology & Entomology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
Interests: veterinary virology; transboundary animal diseases; vector-borne and zoonotic diseases; wildlife infectious diseases; molecular diagnostics; molecular epidemiology; wildlife conservation; one health
Special Issues, Collections and Topics in MDPI journals

Dr. David P. Tchouassi
E-Mail Website
Guest Editor

International Centre of Insect Physiology and Ecology (ICIPE), Nairobi, Kenya
Interests: arboviral diseases; vector ecology

Special Issue Information

Dear Colleagues,

Viruses are highly diverse entities capable of infecting all life forms. Whilst their genomes, modes of transmission and pathogenicity are highly variable, all viruses require the machinery of the infected host cell to replicate, and as such are subject to selective processes within the host environment. It is both this dependency and diversity that binds viruses together, and which continue to challenge virus detection, classification and control efforts and, at the most fundamental level, the determination of virus evolutionary origin. In light of these challenges and the undeniable impact that these “organisms at the edge of life” have on plant, animal and human health, this Special Issue seeks to explore how our own dependency on diverse molecular detection and characterization approaches can be leveraged to effectively deal with these impacts. Whilst virus isolation remains the gold standard, the sheer diversity and associated constraint of suitable culturing options means that molecular biology approaches remain central to virus discovery, diagnostics, epidemiology, vaccinology and, ultimately, disease control. In this Special Issue we invite you to submit manuscripts that report on components of virus ecology, epidemiology and control that hinge on molecular detection and characterization, including virus discovery, diagnosis, co-infection, virulence, evolution/co-evolution, epidemiology, transmission dynamics, vaccine strain selection and host–pathogen interactions. We welcome contributions in the form of original research papers or reviews.

We look forward to receiving your contributions.

Prof. Dr. Armanda Bastos
Dr. David P. Tchouassi
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. 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 2200 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

diversity
evolution
genomics
molecular diagnostics
molecular epidemiology
vaccines
vector-borne
virulence
zoonotic

Published Papers (5 papers)

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Open AccessArticle

Divergent Hantavirus in Somali Shrews (Crocidura somalica) in the Semi-Arid North Rift, Kenya

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Pathogens 2023, 12(5), 685; https://doi.org/10.3390/pathogens12050685 - 07 May 2023

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Abstract

Hantaviruses are zoonotic rodent-borne viruses that are known to infect humans and cause various symptoms of disease, including hemorrhagic fever with renal and cardiopulmonary syndromes. They have a segmented single-stranded, enveloped, negative-sense RNA genome and are widely distributed. This study aimed to investigate the circulation of rodent-borne hantaviruses in peridomestic rodents and shrews in two semi-arid ecologies within the Kenyan Rift Valley. The small mammals were trapped using baited folding Sherman traps set within and around houses, then they were sedated and euthanatized through cervical dislocation before collecting blood and tissue samples (liver, kidney, spleen, and lungs). Tissue samples were screened with pan-hantavirus PCR primers, targeting the large genome segment (L) encoding the RNA-dependent RNA polymerase (RdRp). Eleven of the small mammals captured were shrews (11/489, 2.5%) and 478 (97.5%) were rodents. A cytochrome b gene-based genetic assay for shrew identification confirmed the eleven shrews sampled to be Crocidura somalica. Hantavirus RNA was detected in three (3/11, 27%) shrews from Baringo County. The sequences showed 93–97% nucleotide and 96–99% amino acid identities among each other, as well as 74–76% nucleotide and 79–83% amino acid identities to other shrew-borne hantaviruses, such as Tanganya virus (TNGV). The detected viruses formed a monophyletic clade with shrew-borne hantaviruses from other parts of Africa. To our knowledge, this constitutes the first report published on the circulation of hantaviruses in shrews in Kenya. Full article

(This article belongs to the Special Issue Molecular Detection and Characterisation of Viral Pathogens)

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Open AccessArticle

MultiSero: An Open-Source Multiplex-ELISA Platform for Measuring Antibody Responses to Infection

Pathogens 2023, 12(5), 671; https://doi.org/10.3390/pathogens12050671 - 02 May 2023

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Abstract

A multiplexed enzyme-linked immunosorbent assay (ELISA) that simultaneously measures antibody binding to multiple antigens can extend the impact of serosurveillance studies, particularly if the assay approaches the simplicity, robustness, and accuracy of a conventional single-antigen ELISA. Here, we report on the development of multiSero, an open-source multiplex ELISA platform for measuring antibody responses to viral infection. Our assay consists of three parts: (1) an ELISA against an array of proteins in a 96-well format; (2) automated imaging of each well of the ELISA array using an open-source plate reader; and (3) automated measurement of optical densities for each protein within the array using an open-source analysis pipeline. We validated the platform by comparing antibody binding to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) antigens in 217 human sera samples, showing high sensitivity (0.978), specificity (0.977), positive predictive value (0.978), and negative predictive value (0.977) for classifying seropositivity, a high correlation of multiSero determined antibody titers with commercially available SARS-CoV-2 antibody tests, and antigen-specific changes in antibody titer dynamics upon vaccination. The open-source format and accessibility of our multiSero platform can contribute to the adoption of multiplexed ELISA arrays for serosurveillance studies, for SARS-CoV-2 and other pathogens of significance. Full article

(This article belongs to the Special Issue Molecular Detection and Characterisation of Viral Pathogens)

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Open AccessArticle

The Evolution of Post-Vaccine G8P[4] Group a Rotavirus Strains in Rwanda; Notable Variance at the Neutralization Epitope Sites

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Pathogens 2023, 12(5), 658; https://doi.org/10.3390/pathogens12050658 - 28 Apr 2023

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Abstract

Africa has a high level of genetic diversity of rotavirus strains, which is suggested to be a possible reason contributing to the suboptimal effectiveness of rotavirus vaccines in this region. One strain that contributes to this rotavirus diversity in Africa is the G8P[4]. This study aimed to elucidate the entire genome and evolution of Rwandan G8P[4] strains. Illumina sequencing was performed for twenty-one Rwandan G8P[4] rotavirus strains. Twenty of the Rwandan G8P[4] strains had a pure DS-1-like genotype constellation, and one strain had a reassortant genotype constellation. Notable radical amino acid differences were observed at the neutralization sites when compared with cognate regions in vaccine strains potentially playing a role in neutralization escape. Phylogenetic analysis revealed that the closest relationship was with East African human group A rotavirus (RVA) strains for five of the genome segments. Two genome sequences of the NSP4 genome segment were closely related to bovine members of the DS-1-like family. Fourteen VP1 and eleven VP3 sequences had the closest relationships with the RotaTeq™ vaccine WC3 bovine genes. These findings suggest that the evolution of VP1 and VP3 might have resulted from reassortment events with RotaTeq™ vaccine WC3 bovine genes. The close phylogenetic relationship with East African G8P[4] strains from Kenya and Uganda suggests co-circulation in these countries. These findings highlight the need for continued whole-genomic surveillance to elucidate the evolution of G8P[4] strains, especially after the introduction of rotavirus vaccination. Full article

(This article belongs to the Special Issue Molecular Detection and Characterisation of Viral Pathogens)

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Open AccessArticle

Molecular Characterization of the First African Swine Fever Virus Genotype II Strains Identified from Mainland Italy, 2022

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Pathogens 2023, 12(3), 372; https://doi.org/10.3390/pathogens12030372 - 24 Feb 2023

Cited by 2 | Viewed by 1699

Abstract

African swine fever (ASF) is responsible for important socio-economic effects in the global pig industry, especially for countries with large-scale piggery sectors. In January 2022, the African swine fever virus (ASFV) genotype II was identified in a wild boar population in mainland Italy (Piedmont region). This study describes the molecular characterization, by Sanger and next-generation sequencing (NGS), of the first index case 632/AL/2022 and of another isolate (2802/AL/2022) reported in the same month, in close proximity to the first, following multiple ASF outbreaks. Phylogenetic analysis based on the B646L gene and NGS clustered the isolates 632/AL/2022 and 2802/AL/2022 within the wide and most homogeneous p72 genotype II that includes viruses from European and Asian countries. The consensus sequence obtained from the ASFV 2802/AL/2022 isolate was 190,598 nucleotides in length and had a mean GC content of 38.38%. At the whole-genome level, ASF isolate 2802/AL/2022 showed a close genetic correlation with the other representative ASFV genotype II strains isolated between April 2007 and January 2022 from wild and domestic pigs in Eastern/Central European (EU) and Asian countries. CVR subtyping clustered the two Italian ASFV strains within the major CVR variant circulating since the first virus introduction in Georgia in 2007. Intergenic region I73R-I329L subtyping placed the Italian ASFV isolates within the variant identical to the strains frequently identified among wild boars and domestic pigs. Presently, given the high sequence similarity, it is impossible to trace the precise geographic origin of the virus at a country level. Moreover, the full-length sequences available in the NCBI are not completely representative of all affected territories. Full article

(This article belongs to the Special Issue Molecular Detection and Characterisation of Viral Pathogens)

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Open AccessBrief Report

Rapid Identification of ASFV, CSFV and FMDV from Mongolian Outbreaks with MinION Short Amplicon Sequencing

Dashzeveg Bold

Jayme A. Souza-Neto

Delgerzul Gombo-Ochir

Natasha N. Gaudreault

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Pathogens 2023, 12(4), 533; https://doi.org/10.3390/pathogens12040533 - 29 Mar 2023

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Abstract

African swine fever virus (ASFV), classical swine fever virus (CSFV), and foot-and-mouth disease virus (FMDV) cause important transboundary animal diseases (TADs) that have a significant economic impact. The rapid and unequivocal identification of these pathogens and distinction from other animal diseases based on clinical symptoms in the field is difficult. Nevertheless, early pathogen detection is critical in limiting their spread and impact as is the availability of a reliable, rapid, and cost-effective diagnostic test. The purpose of this study was to evaluate the feasibility to identify ASFV, CSFV, and FMDV in field samples using next generation sequencing of short PCR products as a point-of-care diagnostic. We isolated nucleic acids from tissue samples of animals in Mongolia that were infected with ASFV (2019), CSFV (2015), or FMDV (2018), and performed conventional (RT-) PCR using primers recommended by the Terrestrial Animal Health Code of the World Organization for Animal Health (WOAH). The (RT-) PCR products were then sequenced in Mongolia using the MinION nanopore portable sequencer. The resulting sequencing reads successfully identified the respective pathogens that exhibited 91–100% nucleic acid similarity to the reference strains. Phylogenetic analyses suggest that the Mongolian virus isolates are closely related to other isolates circulating in the same geographic region. Based on our results, sequencing short fragments derived by conventional (RT-) PCR is a reliable approach for rapid point-of-care diagnostics for ASFV, CSFV, and FMDV even in low-resource countries. Full article

(This article belongs to the Special Issue Molecular Detection and Characterisation of Viral Pathogens)

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