Emerging Viruses: Detection, Genomic Analysis and Antiviral Activities

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Virology".

Deadline for manuscript submissions: closed (30 April 2026) | Viewed by 2870

Special Issue Editors


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Guest Editor
Pathogen-Vector Interaction Insectarium, Scientific Development Center, Butantan Institute, São Paulo 05503-900, Brazil
Interests: arboviruses; vector competence; genomic surveillance; mosquito–virus interactions; entomological surveillance; antiviral natural products; vector control strategies; qRT-PCR; diagnosis; dengue; chikungunya; detection of new viruses

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Guest Editor
Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro 21941-909, Brazil
Interests: insect vector chitin metabolism (Rhodnius prolixus, Aedes aegypti); ABC transporters characterization; P-glycoprotein and insecticide resistance; entomological and epidemiological control of dengue and Zika; evaluation of larvicidal and adulticidal compounds; Aedes aegypti; iRNA; arbovirus; vector control; entomological control
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Special Issue Information

Dear Colleagues,

Emerging and re-emerging viruses represent a growing global health concern due to their remarkable ability to evolve and adapt to new ecological niches. Arboviruses are particularly relevant within this group because of their intrinsic capacity to cross species barriers during transmission cycles. The intense and recurrent circulation of arboviruses such as dengue, chikungunya, Zika, yellow fever, Rift Valley fever, Japanese encephalitis, West Nile, Mayaro, and St. Louis encephalitis viruses in tropical and subtropical regions greatly increases the likelihood of novel viral variants or species arising. Developing effective strategies for surveillance, early detection, prediction, and control remains a major challenge, as these infections often present with overlapping clinical symptoms, which complicates differential diagnosis. Moreover, genetic and proteomic similarities among closely related viral species may hinder accurate molecular detection and genomic characterization.

This Special Issue welcomes contributions focusing on emerging and re-emerging viruses, with particular emphasis on arboviruses. We encourage submissions addressing viral detection in vectors, novel diagnostic methodologies, genomic and evolutionary analyses, and antiviral strategies. Reports describing the emergence or re-emergence of arboviruses in new geographic regions, as well as studies on sustainable vector control programs, are of special interest. Overall, this collection aims to provide an updated overview of innovative approaches to detect, analyze, and combat emerging viral threats.

  • Biotechnological uses of vector control;
  • Characterization of new arboviruses and their mechanisms;
  • Molecular and evolutionary aspects of arboviruses;
  • Interactions between insects and arboviruses;
  • Medical entomology and zoonoses;
  • Epidemiology and public health;
  • Neglected diseases;
  • Vector-borne diseases;
  • Discovery of antivirals.

Dr. Tiago Souza Salles
Dr. Monica Ferreira Moreira
Guest Editors

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Keywords

  • arbovirus
  • dengue
  • chikungunya
  • Zika
  • yellow fever
  • Ilheus fever
  • St. Louis encephalitis
  • West Nile fever
  • genomics
  • transcriptomics
  • vector–virus interactions
  • vector control
  • insecticides and insecticide resistance
  • discovery of antivirals from natural products

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Published Papers (3 papers)

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Research

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8 pages, 1661 KB  
Article
The Genomic Characteristics of a Novel Partitivirus Infecting Industrial Hemp in Yunnan, China
by Yuying Liu, Yanpin Xu, Xiaoxia Su, Fang Guan, Kuanyu Zheng and Xuan Chen
Microorganisms 2025, 13(12), 2682; https://doi.org/10.3390/microorganisms13122682 - 25 Nov 2025
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Abstract
In this study, we identified a novel partitivirus infecting industrial hemp (Cannabis sativa L.), named as industrial hemp cryptic virus (IHCV). The complete genome sequence of IHCV comprises two RNA segments: dsRNA1 (1683 nt) encoding an RNA-dependent RNA polymerase (RdRp, 481 aa), [...] Read more.
In this study, we identified a novel partitivirus infecting industrial hemp (Cannabis sativa L.), named as industrial hemp cryptic virus (IHCV). The complete genome sequence of IHCV comprises two RNA segments: dsRNA1 (1683 nt) encoding an RNA-dependent RNA polymerase (RdRp, 481 aa), and dsRNA2 (1669 nt) encoding a coat protein (CP, 417 aa). Comparative sequence analyses revealed that RdRp shares 68.10% amino acid similarity with the Citrullus lanatus cryptic virus (CiLCV), while the CP exhibits 35.80% similarity with the vitis cryptic virus (VCV). Moreover, phylogenetic analysis showed that both the RdRp and CP proteins of IHCV clustered together with the pepper cryptic virus 1 (PCV1), which belongs to the genus Deltapartitivirus. Seeds detection assays revealed seed infection rates ranging from 20% to 90% among different industrial hemp cultivars. This is the first report of a novel partitivirus virus infecting industrial hemp. Full article
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Review

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34 pages, 4203 KB  
Review
Insights into Monkeypox Virus: Host Immunity, Viral Immune Evasion, Recent Advances in Vaccines, Therapeutic Development, and Future Perspectives
by Mingzhuo Chen, Weigang Ren, Xin Wu, Jamal Muhammad Khan, Humera Nazir, Shafeeq Ur Rehman, Faizan Ali and Junwei Li
Microorganisms 2026, 14(2), 317; https://doi.org/10.3390/microorganisms14020317 - 29 Jan 2026
Cited by 1 | Viewed by 1678
Abstract
Monkeypox (Mpox), a zoonotic viral disease caused by the Monkeypox Virus (MPXV), has gained significant attention in recent years due to its increasing incidence and the grave threat it poses to global health. MPXV has spread at a rapid pace during the COVID-19 [...] Read more.
Monkeypox (Mpox), a zoonotic viral disease caused by the Monkeypox Virus (MPXV), has gained significant attention in recent years due to its increasing incidence and the grave threat it poses to global health. MPXV has spread at a rapid pace during the COVID-19 pandemic, causing 10,000+ confirmed cases and ~300 fatalities in 122 countries. This virus comprises two major clades, Clade I (Central African), which is evidently more virulent, and Clade II (West African), which has caused the recent outbreaks across the world and caused fewer deaths. Clinically, Mpox presents as a milder form with fever, lymphadenopathy, and vesiculopustular rash similar to smallpox. Diagnostic measures such as polymerase chain reaction (PCR) are the main diagnostic confirmatory tools. Advanced diagnostics involve electronic microscopy, serology, and immunohistochemistry. Alternative drugs like tecovirimat and brincidofovir have demonstrated potential for treating smallpox, but there is scanty evidence on their efficacy against MPXV. Most recent advancements in the study of vaccines have resulted in the creation and introduction of MVA-BN (JYNNEOS/Imvanex/Imvamune) and ACAM2000 vaccines, which conferred cross-protection against MPXV. MVA-BN is suggested to perform better than other types due to its enhanced safety and immunogenicity. Researchers are also developing DNA and protein subunit vaccines against Mpox to induce specific immune responses by presenting viral proteins. The discovery of novel vaccine candidates and antiviral treatments will be needed to prevent future outbreaks and reduce the global health burden of Mpox. This review focuses on the characterization of MPXV, summarizing current knowledge on its genomic structure, pathogenesis, replication, potential targets of anti-MPXV drugs, clinical features, and epidemiological patterns, along with recent advances in vaccine development. Full article
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Other

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12 pages, 2136 KB  
Case Report
Intra-Omicron Reinfection with JN.1.16 and NB.1.8.1 in a Preterm Infant: First NB.1.8.1 Detection in Tunisia—A Case Report
by Zaineb Hamzaoui, Sana Ferjani, Ameni Sallemi, Salma Abid, Amal Miraoui, Ichrak Landolsi, Latifa Charaa, Khaled Menif, Lamia Kanzari and Ilhem Boutiba-Ben Boubaker
Microorganisms 2026, 14(5), 1009; https://doi.org/10.3390/microorganisms14051009 - 30 Apr 2026
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Abstract
Highly mutated Omicron sub-lineages JN.1 and NB.1.8.1 harbor extensive spike changes, but their impact in preterm infants is poorly documented. We report a preterm male infant with three hospitalizations in seven weeks: severe SARS-CoV-2 ARDS at 40 days of life (DOL 40) requiring [...] Read more.
Highly mutated Omicron sub-lineages JN.1 and NB.1.8.1 harbor extensive spike changes, but their impact in preterm infants is poorly documented. We report a preterm male infant with three hospitalizations in seven weeks: severe SARS-CoV-2 ARDS at 40 days of life (DOL 40) requiring ventilation caused by JN.1.16, HCoV-OC43 infection at DOL 65, and a mild SARS-CoV-2 reinfection at DOL 87 due to NB.1.8.1, the first detection of this variant in Tunisia. Spike analysis showed a shared JN.1 backbone but distinct N-terminal and receptor-binding domain changes, supporting intra-Omicron reinfection driven by antigenic divergence and immature immunity and underscoring the value of pediatric genomic surveillance, including phylogenetic placement of case genomes within local Omicron diversity. Full article
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