Complete genome sequence analysis of Japanese encephalitis virus isolated from a horse in India.

The research article provides a detailed analysis of the full genome sequence of a Japanese encephalitis virus (JEV) strain named H225, which was isolated from an infected horse in India. This is the first time a comprehensive genome sequencing of a genotype III JEV has been done from an equine source.

Genome Structure

• The researchers were able to map the complete genome of the JEV strain which is referred to as H225. The genome is composed of 10,977 nucleotides.
• The genome includes one open reading frame (ORF) which is 10,299-nucleotides long. ORFs are parts of the genome which potentially have the ability to code for proteins.
• They also identified a 5’-untranslated region (UTR) of 95 nucleotides and a 3′-UTR of 582 nucleotides. These UTRs are segments included in RNA molecules which do not code for protein sequences but play a role in regulating gene expression.

Sequence Comparison and Phylogenetic Analysis

• The researchers compared the H225 genome with 47 completely sequenced JEV genomes that were previously published. They found high levels of sequence identity ranging from 99.3% to 75.5% for nucleotides and 99.2% to 91.5% for amino acid sequences.
• On assessing the phylogenetic relationships based on this full-length sequence, the researchers determined that the H225 strain belongs to genotype III and is closely related to the Indian JEV strain Vellore P20778.

Evaluation of Virulence

• The amino acids associated with neurovirulence, in both the E proteins and non-structural proteins, of known virulent and attenuated JEV strains were compared with H225 strain.
• From these comparisons, the H225 strain appeared to be a highly virulent strain. Neurovirulence refers to the ability of the microorganism to cause disease in the nervous system. Therefore, this particular strain can potentially lead to serious health complications.

Significance of the Research

• This research is the first to report on the whole-genome sequencing of a genotype III JEV genome isolated from equines.
• This identification broadens our understanding of the genetic spectrum of JEV, which can be pivotal in formulating vaccination plans or antiviral drugs against the disease.