Potential biomarkers in Japanese encephalitis from different hosts and geographical locations

Abstract

Japanese encephalitis (JE) is a single-stranded, mosquito-borne, positive-sense RNA flavivirus that causes one of the most severe encephalitides. There are treatments available for those who contact this illness; however, there are no known cures. This disease has a 30% fatality rate, and of the people who survive, 30-50% develops neurologic and psychiatric sequelae. The JE virus genome size is 10.98 kb and contains two coding DNA sequences (CDS), two genes, and 15 mature peptides; the CDS polyprotein is 10.3 kb. In this study, we used 29 genomics sequences of the JE virus reported from different countries and infecting different animals and analysed vast dimensions of the genomic annotation of JE comparatively to understand its evolutionary aspects. The extensive SNPs analysis revealed that KF907505.1, reported from Taiwan, has only three SNPs, similar to sequences reported from India. Repeat and polymorphism analyses revealed that the genome tends to be similar in most JE sequences.

Keywords: Japanese encephalitis virus; Single Nucleotide Polymorphism (SNPs); phobos; phylogenomics; transcription factors.

Figure 1

Global reporting of Japanese encephalitis, year-wise reporting from worldwide in PubMed. The highest number of publications was reported in 2013.

Figure 2

Comparative graphical representation for 29 sequences collected from NCBI, filtered based o different geographical locations, year of reporting, and most importantly, from the different hosts for comparative analytics and plotted with referencing to Accession number and sequence length.

Figure 3

Graphical representation of count of whole-genome annotations, data includes the count of 3' UTR in the red-orange bar, 5' in the grey bar, CDS in the copper colour bar, a mature peptide in the ultramarine bar, ORF in the green bar, repeat region in the red colour line graph, a signal peptide in a carmine line graph, restriction site in a yellow line graph, transcriptional factors in the purple bar graph and % of GC in the blue colour bar.

Figure 4

Untranslated Region of genomes is categorised and extracted based on their direction in the genome; 11 strains have 3'UTRs while only 3 strains show 5'UTRs. Data were plotted proportionately based on length and direction to the accession number and differentiated by colour.

Figure 5

The extracted short sequence repeats from all Japanese encephalitis virus, plotted concerning SSR direction and differentiated with repeat colour. Each SSRs took as the sum of its repeat in particular JE strains.

Figure 6

Extracted mature peptides were found in 8 strains plotted in different opacity ranges with an accession number-extracted data plotted with the sum of the length for each mature peptide broken down by accession numbers. Data have been labelled on each proportionally plotted mature peptide and accessions.

Figure 7

Single nucleotide polymorphism, HM596272.1, taken as reference. Y represents C is replaced by T (blue), M represents A replaced by C (green), W represents A replace by T (orange), K represents G replace by T (indigo), R represents A replace by G (yellow), S represents C replace by G (grey), N represents the deletion (red).

Figure 8

Comparative Distance plot among all organisms; Data were aligned using MAFFT aligner and calculated the distance in 2D matrices by taking HM596272.1 as a reference and calculating the exact amount of similarity with other species.

Figure 9

Phylogenetic trees for all Japanese encephalitis taken under study. The green colour shows species reported from India, the violet colour shows species reported from Japan, the sky-blue colour is those strains reported from China, and the red shows reference species reported from Malaysia. The further distance among all species is labelled for understanding the evolutionary aspects.