Related Experiment Video

Updated: May 28, 2026

Bacterial Artificial Chromosomes: A Functional Genomics Tool for the Study of Positive-strand RNA Viruses
12:20

Bacterial Artificial Chromosomes: A Functional Genomics Tool for the Study of Positive-strand RNA Viruses

Published on: December 29, 2015

Recombination and positive selection identified in complete genome sequences of Japanese encephalitis virus

Jennifer Carney1, Janet M Daly, Ananda Nisalak

  • 1Brain Infections Group, Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool L69 3GA, UK.

Archives of Virology
|October 29, 2011
PubMed

Insights

Japanese encephalitis virus (JEV) causes severe encephalitis in humans but not pigs. Sequencing identified specific viral genetic sites potentially explaining JEV

Area of Science:

  • Virology
  • Genomics
  • Molecular Epidemiology

Background:

  • Japanese encephalitis virus (JEV) causes encephalitis in humans, with differing outcomes in pigs.
  • Understanding JEV virulence determinants is crucial for public health.
  • Previous studies have not fully elucidated the genetic basis for differential JEV pathogenicity.

Purpose of the Study:

  • To sequence complete JEV genomes from human, mosquito, and pig isolates from Thai outbreaks.
  • To identify genetic determinants of JEV virulence that explain differential outcomes in humans and pigs.
  • To investigate phylogenetic relationships and evolutionary patterns of JEV.

Main Methods:

  • Whole-genome sequencing of JEV isolates from human, mosquito, and pig sources.
  • Phylogenetic analysis to determine genetic relationships and genotypes.
  • Selection analysis to identify sites under positive selection.
  • Comparative genomic analysis to pinpoint specific amino acid substitutions.

Main Results:

  • Five Thai JEV isolates belonged to genotype I; one belonged to genotype III.
  • No recombination was detected among Thai isolates, but evidence suggested recombination in a Korean isolate.
  • Two sites (codons 996 and 2296) in the JEV genome were under positive selection.
  • A significant amino acid substitution at NS4B position 24 was observed in the human isolate compared to pig and mosquito isolates.

Conclusions:

  • Specific genetic sites under positive selection, particularly in NS1 and NS4B proteins, may influence JEV virulence.
  • The identified substitution at NS4B position 24 warrants further investigation for its role in JEV pathogenicity.
  • Further research into these genetic sites is essential for understanding JEV evolution and ecology.

More Related Videos

Detection of Polyfunctional T Cells in Children Vaccinated with Japanese Encephalitis Vaccine via the Flow Cytometry Technique09:37

Detection of Polyfunctional T Cells in Children Vaccinated with Japanese Encephalitis Vaccine via the Flow Cytometry Technique

Published on: September 23, 2022

Rapid, Seamless Generation of Recombinant Poxviruses using Host Range and Visual Selection09:25

Rapid, Seamless Generation of Recombinant Poxviruses using Host Range and Visual Selection

Published on: May 24, 2020

Related Concept Videos

Viral Recombination00:57

Viral Recombination

Cells are sometimes infected by more than one virus at once. When two viruses disassemble to expose their genomes for replication in the same cell, similar regions of their genomes can pair together and exchange sequences in a process called recombination. Alternatively, viruses with segmented genomes can swap segments in a process called reassortment.
Exon Recombination02:32

Exon Recombination

The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes. 
Exon shuffling follows “splice frame rules.” Each exon has three reading...
Conservative Site-specific Recombination and Phase Variation02:53

Conservative Site-specific Recombination and Phase Variation

Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...
Arboviral Encephalitis01:25

Arboviral Encephalitis

Arboviral encephalitis refers to brain inflammation caused by arthropod-borne viruses, particularly those transmitted through mosquito vectors. Among these, West Nile virus (WNV), a member of the Flaviviridae family, is a significant public health concern. WNV is an enveloped, positive-sense, single-stranded RNA virus. Human infection typically begins when an infected mosquito introduces the virus into the dermis during feeding. The primary transmission cycle involves birds as amplifying hosts...
Encephalitis ll: Pathophysiology01:26

Encephalitis ll: Pathophysiology

Encephalitis is inflammation of the brain parenchyma caused by direct viral invasion or immune-mediated mechanisms triggered by infections or tumors. Both processes lead to neuronal injury, disrupted neurotransmission, and diverse neurological symptoms, often with overlapping clinical and pathological features.Autoimmune EncephalitisIn autoimmune encephalitis, antibodies target neuronal antigens on cell surfaces, synapses, or within neurons. A key example is anti-NMDAR encephalitis, which can...
Viral Mutations00:36

Viral Mutations

A mutation is a change in the sequence of bases of DNA or RNA in a genome. Some mutations occur during replication of the genome due to errors made by the polymerase enzymes that replicate DNA or RNA. Unlike DNA polymerase, RNA polymerase is prone to errors because it is not capable of “proofreading” its work. Viruses with RNA-based genomes, like HIV, therefore accrue mutations faster than viruses with DNA-based genomes. Because mutation and recombination provide the raw material for adaptive...