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Viruses
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Molecular Epidemiology, Evolution, and Dispersion of Flaviviruses (2nd Edition)
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Molecular Epidemiology, Evolution, and Dispersion of Flaviviruses (2nd Edition)

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Animal Viruses".

Deadline for manuscript submissions: 30 April 2026 | Viewed by 7065

Special Issue Editors

Dr. Marta Giovanetti

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Guest Editor
1. Department of Sciences and Technologies for Sustainable Development and One Health, Università Campus Bio-Medico di Roma, Rome, Italy
2. Instituto Rene Rachou Fundação Oswaldo Cruz, Belo Horizonte 30.190-009, Brazil
Interests: phylogenetic; phylodynamic; molecular evolution; genomic surveillance; WGS; emerging and re-emerging viral pathogens
Special Issues, Collections and Topics in MDPI journals
Dr. Fernanda De Bruycker Nogueira

E-Mail Website
Guest Editor
Laboratory of Flavivirus, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
Interests: arbovirus; flavivirus; phylogenetics; molecular screening
Special Issues, Collections and Topics in MDPI journals
Dr. Ana Maria Bispo De Filippis

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Guest Editor
Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil
Interests: arbovirus; flavivirus; surveillance; molecular screening
Special Issues, Collections and Topics in MDPI journals
Dr. Anne Paiva

E-Mail Website
Guest Editor
Fundação Oswaldo Cruz | FIOCRUZ · Departamento de Medicina Tropical (IOC), Rio de Janeiro, Brazil
Interests: flavivirus

Special Issue Information

Dear Colleagues,

The tremendous success and immense interest generated by the first volume of this Special Issue, titled "Molecular Epidemiology, Evolution and Dispersion of Flaviviruses", have paved the way for the initiation of an equally captivating second edition. Flaviviruses, with their captivating complexities, have continued to fascinate scientists and public health experts across the globe, from Africa to the Americas.

Building upon the foundations laid in the previous Special Issue, this second edition aims to delve deeper into the molecular intricacies, evolutionary dynamics, and global dispersal patterns of these formidable pathogens. Positive-strand RNA viruses belonging to the Flaviviridae family, which include the likes of West Nile virus, dengue virus, tick-borne encephalitis virus, yellow fever virus, and Zika virus, among others, have long posed a significant global health challenge.

The research presented in this Special Issue will showcase the latest advancements in our understanding of flaviviral behavior in natural conditions, shedding light on their multifaceted virulence mechanisms. Cutting-edge techniques in virus surveillance, genomic analysis, and phylogenetic reconstructions will be employed to unravel the complex relationships between flaviviral strains and their spread across geographical boundaries.

We invite researchers and experts from around the world to contribute their latest findings and insights on a wide range of topics, including virus genetics, epidemiology, virus–host interactions, pathogenesis, vaccine development, improvements in diagnostics, and vector entomology. Together, we aim to further our collective understanding of these important human pathogens and inform ongoing efforts to mitigate the global burden of flaviviral diseases.

Dr. Marta Giovanetti
Dr. Fernanda De Bruycker Nogueira
Dr. Ana Maria Bispo De Filippis
Dr. Anne Paiva
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. Viruses 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

  • flavivirus
  • evolution
  • genomic epidemiology
  • phylodynamics
  • transmission

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Related Special Issue

Published Papers (4 papers)

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Research

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12 pages, 2139 KiB  
Article
Selection Pressure Profile Suggests Species Criteria among Tick-Borne Orthoflaviviruses
by Andrei A. Deviatkin, Yulia A. Aleshina, Galina G. Karganova and Alexander N. Lukashev
Viruses 2024, 16(10), 1554; https://doi.org/10.3390/v16101554 - 30 Sep 2024
Viewed by 1195
Abstract
Orthoflaviviruses are arthropod-borne viruses that are transmitted by mosquitoes or ticks and cause a range of significant human diseases. Among the most important tick-borne orthoflaviviruses (TBFVs) is tick-borne encephalitis virus (TBEV), which is endemic in Eurasia, and Powassan virus, which is endemic in [...] Read more.
Orthoflaviviruses are arthropod-borne viruses that are transmitted by mosquitoes or ticks and cause a range of significant human diseases. Among the most important tick-borne orthoflaviviruses (TBFVs) is tick-borne encephalitis virus (TBEV), which is endemic in Eurasia, and Powassan virus, which is endemic in Asia and North America. There is a significant controversy regarding species assignment in the tick-borne encephalitis virus complex due to the complex phylogenetic, serological, ecological, and pathogenetic properties of viruses. Comparing the rate of non-synonymous to synonymous substitutions (dN/dS) over the course of tick-borne orthoflavivirus diversification suggests that there is a very strong stabilizing selection (Nei-Gojobori dN/dS < 0.1) among tick-borne orthoflaviviruses that differ by less than 13.5% amino acid/21.4% nucleotide sequences, and discretely more rapid accumulation of non-synonymous substitutions (dN/dS > 0.13) among more divergent viruses that belong to distinct species. This pattern was similarly observed in genome regions encoding structural (E) and non-structural (NS3) proteins. Below this distance threshold, viruses appear fit and strongly tied to their ecological niche, whereas above the threshold, a greater degree of adaptation appears necessary. This species criterion suggests that all subtypes of TBEV, all related ovine/caprine encephalomyelitis viruses, and Omsk hemorrhagic fever virus (OHFV) together correspond to a single species. Within this species, viruses make up 11 subtypes that are reliably segregated by a 10% nucleotide distance cut-off suggested earlier for TBEV. The same 10% subtype cut-off suggests that Powassan virus includes two subtypes, Powassan and Deer Tick virus. Full article
(This article belongs to the Special Issue Molecular Epidemiology, Evolution, and Dispersion of Flaviviruses (2nd Edition))
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Review

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22 pages, 2267 KiB  
Review
Chasing Virus Replication and Infection: PAMP-PRR Interaction Drives Type I Interferon Production, Which in Turn Activates ISG Expression and ISGylation
by Imaan Muhammad, Kaia Contes, Moses T. Bility and Qiyi Tang
Viruses 2025, 17(4), 528; https://doi.org/10.3390/v17040528 - 4 Apr 2025
Viewed by 494
Abstract
The innate immune response, particularly the interferon-mediated pathway, serves as the first line of defense against viral infections. During virus infection, viral pathogen-associated molecular patterns (PAMPs) are recognized by host pattern recognition receptors (PRRs), triggering downstream signaling pathways. This leads to the activation [...] Read more.
The innate immune response, particularly the interferon-mediated pathway, serves as the first line of defense against viral infections. During virus infection, viral pathogen-associated molecular patterns (PAMPs) are recognized by host pattern recognition receptors (PRRs), triggering downstream signaling pathways. This leads to the activation of transcription factors like IRF3, IRF7, and NF-κB, which translocate to the nucleus and induce the production of type I interferons (IFN-α and IFN-β). Once secreted, type I interferons bind to their receptors (IFNARs) on the surfaces of infected and neighboring cells, activating the JAK-STAT pathway. This results in the formation of the ISGF3 complex (composed of STAT1, STAT2, and IRF9), which translocates to the nucleus and drives the expression of interferon-stimulated genes (ISGs). Some ISGs exert antiviral effects by directly or indirectly blocking infection and replication. Among these ISGs, ISG15 plays a crucial role in the ISGylation process, a ubiquitin-like modification that tags viral and host proteins, regulating immune responses and inhibiting viral replication. However, viruses have evolved counteractive strategies to evade ISG15-mediated immunity and ISGylation. This review first outlines the PAMP-PRR-induced pathways leading to the production of cytokines and ISGs, followed by a summary of ISGylation’s role in antiviral defense and viral evasion mechanisms targeting ISG15 and ISGYlation. Full article
(This article belongs to the Special Issue Molecular Epidemiology, Evolution, and Dispersion of Flaviviruses (2nd Edition))
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32 pages, 3920 KiB  
Review
Latin America’s Dengue Outbreak Poses a Global Health Threat
by Michelle Teixeira de Almeida, Davi Gabriel Salustiano Merighi, Aline Biazola Visnardi, Cauê Augusto Boneto Gonçalves, Vitor Martins de Freitas Amorim, Anielle Salviano de Almeida Ferrari, Anacleto Silva de Souza and Cristiane Rodrigues Guzzo
Viruses 2025, 17(1), 57; https://doi.org/10.3390/v17010057 - 1 Jan 2025
Cited by 2 | Viewed by 3104
Abstract
Dengue fever, caused by the dengue virus (DENV), poses a significant global health challenge, particularly in tropical and subtropical regions. Recent increases in indigenous DENV cases in Europe are concerning, reflecting rising incidence linked to climate change and the spread of Aedes albopictus [...] Read more.
Dengue fever, caused by the dengue virus (DENV), poses a significant global health challenge, particularly in tropical and subtropical regions. Recent increases in indigenous DENV cases in Europe are concerning, reflecting rising incidence linked to climate change and the spread of Aedes albopictus mosquitoes. These vectors thrive under environmental conditions like temperature and humidity, which are increasingly influenced by climate change. Additionally, global travel accelerates the cross-border spread of mosquito-borne diseases. DENV manifests clinically in a spectrum from asymptomatic cases to severe conditions like dengue hemorrhagic fever and dengue shock syndrome, influenced by viral serotype and host factors. In 2024, Brazil experienced a fourfold increase in dengue cases compared to 2023, accompanied by higher mortality. Conventional control measures, such as vector control, community engagement, and vaccination, proved insufficient as climate change exacerbated mosquito proliferation, challenging containment efforts. In this regard, our review analyzes prevention measures and therapeutic protocols during the outbreak while addressing DENV transmission dynamics, clinical presentations, and epidemiological shifts. It also evaluates diagnostic strategies combining clinical assessment with serological and molecular testing, providing information to improve diagnostic and preventive measures. The global expansion of dengue-endemic regions, including outbreaks in Europe, highlights the urgent need for enhanced surveillance, proactive interventions, and international collaboration to mitigate the growing threat of Dengue and other arboviruses like West Nile, Zika, Chikungunya, Oropouche, and Yellow Fever viruses. Full article
(This article belongs to the Special Issue Molecular Epidemiology, Evolution, and Dispersion of Flaviviruses (2nd Edition))
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Other

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8 pages, 588 KiB  
Case Report
Exploring Dengue Infection in a Vaccinated Individual: Preliminary Molecular Diagnosis and Sequencing Insights
by Talita Émile Ribeiro Adelino, Sílvia Helena Sousa Pietra Pedroso, Maurício Lima, Luiz Marcelo Ribeiro Tomé, Natália Rocha Guimarães, Vagner Fonseca, Paulo Eduardo de Souza da Silva, Keldenn Melo Farias Moreno, Ana Cândida Araújo e Silva, Náthale Rodrigues Pinheiro, Carolina Senra Alves de Souza, Luiz Carlos Junior Alcantara, Marta Giovanetti and Felipe Campos de Melo Iani
Viruses 2024, 16(10), 1603; https://doi.org/10.3390/v16101603 - 12 Oct 2024
Cited by 2 | Viewed by 1683
Abstract
This study examines a case involving a 7-year-old child who developed dengue symptoms following Qdenga vaccination. Despite initial negative diagnostic results, molecular analysis confirmed an infection with DENV4. Next-generation sequencing detected viral RNA from both DENV2 and DENV4 serotypes, which were identified as [...] Read more.
This study examines a case involving a 7-year-old child who developed dengue symptoms following Qdenga vaccination. Despite initial negative diagnostic results, molecular analysis confirmed an infection with DENV4. Next-generation sequencing detected viral RNA from both DENV2 and DENV4 serotypes, which were identified as vaccine-derived strains using specific primers. Phylogenetic analysis further confirmed that these sequences belonged to the Qdenga vaccine rather than circulating wild-type viruses. This case underscores the critical need for precise diagnostic interpretation in vaccinated individuals to avoid misdiagnosis and to strengthen public health surveillance. A comprehensive understanding of vaccine-induced viremia is essential for refining dengue surveillance, improving diagnostic accuracy, and informing public health strategies in endemic regions. Full article
(This article belongs to the Special Issue Molecular Epidemiology, Evolution, and Dispersion of Flaviviruses (2nd Edition))
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