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Genes
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Molecular Epidemiology, Genome and Evolution of Viruses
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Molecular Epidemiology, Genome and Evolution of Viruses

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

Deadline for manuscript submissions: closed (1 February 2025) | Viewed by 3722

Special Issue Editor

Dr. Marta Giovanetti

E-Mail Website
Guest Editor
1. Department of Sciences and Technologies for Sustainable Development and One Health, Universita Campus Bio-Medico di Roma, Rome, Italy
2. Oswaldo Cruz Foundation, Belo Horizonte, Brazil
Interests: mosquito-borne pathogens; genomic surveillance; public health; epidemic pandemic prepardness
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

We introduce the Special Issue "Molecular Epidemiology, Genome and Evolution of Viruses". Viruses, as constantly evolving global health threats, demand a profound understanding of their molecular epidemiology, genomics, and evolution. This Special Issue offers a comprehensive platform for researchers to explore intricate viral relationships with hosts and the environment.

Molecular epidemiology reveals insights into viral transmission dynamics, host adaptation, and geographic spread. Advances in sequencing and bioinformatics facilitate outbreak tracing and strain monitoring, uncovering genetic diversity, origins, and transmission routes that fuel viral epidemics.

Genomic analysis is crucial for deciphering viral genetics, identifying virulence factors, and guiding targeted therapeutics. This Special Issue focuses on characterizing viral genomes, studying structural variations, and understanding genetic mutations' functional consequences to counter potential viral threats.

Evolutionary dynamics govern viral adaptation within hosts over time. This Special Issue delves into the evolutionary processes shaping viral populations, exploring mechanisms of antigenic variation, immune evasion, and drug resistance emergence. These insights inform strategies against viral diseases and future challenges.

In conclusion, the "Molecular Epidemiology, Genome and Evolution of Viruses" Special Issue is a vital resource for researchers, clinicians, and policymakers, advancing our understanding of viruses and their behavior. Bridging molecular biology, epidemiology, and evolutionary science, it contributes to public health protection and enhances viral disease knowledge.

Sincerely,

Dr. Marta Giovanetti
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

  • viral pathogens
  • genomic monitoring
  • viral evolution

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Published Papers (2 papers)

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Research

10 pages, 538 KiB  
Article
Impact of Hepatitis Delta Virus Infection on the Selection of Hepatitis B Surface Antigen Mutations
by Kabo Baruti, Wonderful T. Choga, Bonolo B. Phinius, Basetsana Phakedi, Lynnette Bhebhe, Gorata G. A. Mpebe, Patience C. Motshosi, Tsholofelo Ratsoma, Sikhulile Moyo, Mosimanegape Jongman, Motswedi Anderson and Simani Gaseitsiwe
Genes 2024, 15(8), 982; https://doi.org/10.3390/genes15080982 - 25 Jul 2024
Cited by 1 | Viewed by 1520
Abstract
The interaction of multiple viruses in one host is thought to enhance the development of mutations. However, the impact of hepatitis D virus (HDV) positivity on the development of unique hepatitis B virus (HBV) mutations among people living with human immunodeficiency virus (HIV) [...] Read more.
The interaction of multiple viruses in one host is thought to enhance the development of mutations. However, the impact of hepatitis D virus (HDV) positivity on the development of unique hepatitis B virus (HBV) mutations among people living with human immunodeficiency virus (HIV) (PLWH) remains poorly understood in African countries, including Botswana. We used HBV sequences generated from the Botswana Combination Prevention Project (BCPP), which is the largest pair-matched cluster-randomized HIV trial in Botswana. Only participants with available HBV sequences (n = 55) were included in our study ([HIV/HBV-positive (n = 50) and HIV/HBV/HDV-positive (n = 5)]. Geno2pheno was used to determine HBV genotypes, and HBV surface region sequences (all subgenotype A1) were aligned in AliView for mutational analysis, while the impact of mutations was assessed using Phyre2. Our results identified 182 common mutations between the two groups. In the HIV/HBV/HDV cohort, only three mutations (L95W, W156Q, C221Y) were classified as deleterious, with only L95W being the most frequent. In the HIV/HBV cohort, four mutations (W199R, C221A, C221S, W223G) were also classified as deleterious. Our results demonstrate the presence of unique HBV mutations among the HIV/HBV/HDV-positive cohort. Functional characterization of these mutations is recommended to determine their effect on HDV. Full article
(This article belongs to the Special Issue Molecular Epidemiology, Genome and Evolution of Viruses)
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12 pages, 2107 KiB  
Article
Exploring Microorganisms Associated to Acute Febrile Illness and Severe Neurological Disorders of Unknown Origin: A Nanopore Metagenomics Approach
by Keldenn Melo Farias Moreno, Virgínia Antunes de Andrade, Felipe Campos de Melo Iani, Vagner Fonseca, Maurício Teixeira Lima, Emerson de Castro Barbosa, Luiz Marcelo Ribeiro Tomé, Natália Rocha Guimarães, Hegger Machado Fritsch, Talita Adelino, Tatiana Oliveira Fereguetti, Maíra Cardoso Aspahan, Tereza Gamarano Barros, Luiz Carlos Junior Alcantara and Marta Giovanetti
Genes 2024, 15(7), 922; https://doi.org/10.3390/genes15070922 - 15 Jul 2024
Cited by 1 | Viewed by 1725
Abstract
Acute febrile illness (AFI) and severe neurological disorders (SNDs) often present diagnostic challenges due to their potential origins from a wide range of infectious agents. Nanopore metagenomics is emerging as a powerful tool for identifying the microorganisms potentially responsible for these undiagnosed clinical [...] Read more.
Acute febrile illness (AFI) and severe neurological disorders (SNDs) often present diagnostic challenges due to their potential origins from a wide range of infectious agents. Nanopore metagenomics is emerging as a powerful tool for identifying the microorganisms potentially responsible for these undiagnosed clinical cases. In this study, we aim to shed light on the etiological agents underlying AFI and SND cases that conventional diagnostic methods have not been able to fully elucidate. Our approach involved analyzing samples from fourteen hospitalized patients using a comprehensive nanopore metagenomic approach. This process included RNA extraction and enrichment using the SMART-9N protocol, followed by nanopore sequencing. Subsequent steps involved quality control, host DNA/cDNA removal, de novo genome assembly, and taxonomic classification. Our findings in AFI cases revealed a spectrum of disease-associated microbes, including Escherichia coli, Streptococcus sp., Human Immunodeficiency Virus 1 (Subtype B), and Human Pegivirus. Similarly, SND cases revealed the presence of pathogens such as Escherichia coli, Clostridium sp., and Dengue virus type 2 (Genotype-II lineage). This study employed a metagenomic analysis method, demonstrating its efficiency and adaptability in pathogen identification. Our investigation successfully identified pathogens likely associated with AFI and SNDs, underscoring the feasibility of retrieving near-complete genomes from RNA viruses. These findings offer promising prospects for advancing our understanding and control of infectious diseases, by facilitating detailed genomic analysis which is critical for developing targeted interventions and therapeutic strategies. Full article
(This article belongs to the Special Issue Molecular Epidemiology, Genome and Evolution of Viruses)
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