Surveillance and Molecular Epidemiology of Viral Encephalitis Pathogens

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

Deadline for manuscript submissions: 31 May 2026 | Viewed by 1094

Special Issue Editor


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Guest Editor
National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing 102206, China
Interests: viral encephalitis pathogen surveillance and detection; technology and platform development; molecular epidemiology; molecular evolution; vaccine

Special Issue Information

Dear Colleagues,

Viral encephalitis remains a significant global threat to public health, causing severe neurological morbidity and mortality worldwide. The evolving landscape of pathogens and the challenges in rapid diagnosis and surveillance necessitate continued research efforts. This Special Issue focuses on the surveillance and molecular epidemiology of viral encephalitis pathogens, addressing a critical global public health need given the disease's significant impact on neurological health. It will feature cutting-edge research on the composition and regional/seasonal dynamics of viral encephalitis pathogen spectra, analyze epidemiological trends and transmission patterns, and explore molecular genetic traits (e.g., gene variation, evolutionary divergence) of key pathogens (e.g., enteroviruses, flaviviruses). The studies featured will contribute to optimizing surveillance systems, enhancing pathogen identification, and informing targeted prevention strategies, ultimately helping reduce the global burden of viral encephalitis.

Dr. Songtao Xu
Guest Editor

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Keywords

  • viral encephalitis
  • molecular epidemiology
  • pathogen spectrum
  • surveillance
  • molecular genetic characteristics
  • epidemiological trends
  • emerging viruses
  • global health

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Published Papers (1 paper)

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Research

16 pages, 4578 KB  
Article
The Emerging JEV Genotype 5 Exhibits Distinct Codon Usage Characteristics
by Xiaoyu Gu, Ruichen Wang, Yuhong Yang, Weijia Zhang, Qikai Yin, Kai Nie, Shihong Fu, Qianqian Cui, Fan Li, Huanyu Wang and Songtao Xu
Pathogens 2026, 15(1), 58; https://doi.org/10.3390/pathogens15010058 - 7 Jan 2026
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Abstract
This study investigates the codon usage characteristics of Japanese encephalitis virus (JEV) genotype 5 (G5). Based on 339 complete JEV genome sequences, we systematically compared the codon usage patterns of G5 with other genotypes (G1–G4) using a multi-faceted approach, including evolutionary analysis, nucleotide [...] Read more.
This study investigates the codon usage characteristics of Japanese encephalitis virus (JEV) genotype 5 (G5). Based on 339 complete JEV genome sequences, we systematically compared the codon usage patterns of G5 with other genotypes (G1–G4) using a multi-faceted approach, including evolutionary analysis, nucleotide composition, Relative Synonymous Codon Usage (RSCU), Principal Component Analysis (PCA), Effective Number of Codons Plot analysis (ENC-Plot), Parity Rule 2 analysis (PR2), Neutrality plot analysis, dinucleotide abundance analysis and Codon Adaptation Index analysis (CAI). The results indicate that G5 forms a distinct evolutionary branch, with both its overall GC content (50%) and GC content at the third codon position (GC3, 53%) being lower than those of other genotypes. RSCU analysis revealed a preferential use of A/U-ended codons in G5, indicating a trend towards reduced GC3 usage. ENC analysis demonstrated a stronger codon usage bias in G5 (mean ENC = 54.2). Furthermore, ENC-plot, PR2, and neutrality plot analyses collectively suggested that G5 is subject to stronger natural selection pressure. Analysis of dinucleotide abundance showed a significant increase in CA values in G5, while CAI analysis indicated higher translational efficiency in human hosts compared to Culex mosquito hosts. Our findings suggest that G5 JEV, potentially through reduced Cytosine-phosphate-Guanine (CpG) usage and optimized codon preference, may enhance its capabilities for immune evasion and host adaptation, and could possess the potential for efficient replication in humans or other mammalian hosts. This research provides crucial theoretical insights into the molecular evolutionary mechanisms of G5 JEV and informs related vaccine development. Full article
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