Table 1.
Genome annotation and protein attributes of Chandipura virus (isolate CIN0451, GenBank: NC_020805.1).
Fig 1.
Genome organization and structural protein annotation of Chandipura virus.
The schematic illustrates the genomic architecture of Chandipura virus (CHPV), a (–) sense single-stranded RNA genome of approximately 11.12 kb (RefSeq: NC_020805.1, isolate CIN 0451). The genome is depicted in the 3′ → 5′ orientation and annotated with the five canonical open reading frames corresponding to the nucleoprotein (N), phosphoprotein (P), matrix protein (M), glycoprotein (G), and RNA-dependent RNA polymerase (L).
Table 2.
Metadata of 23 Chandipura virus whole-genome sequences included in phylogenetic analysis.
Fig 2.
Global distribution of Chandipura virus (CHPV) human cases, vector isolations, and sandfly species occurrence.
The map illustrates confirmed human CHPV outbreaks across Indian states (with case numbers indicated by proportional symbols), regions in India and Africa where CHPV has been isolated from sandfly species (Sergentomyia spp. and Phlebotomus spp.), and the documented distribution of sandfly species in India. Data were compiled from published outbreak reports and entomological surveys. Base administrative boundaries (shapefile) obtained from Survey of India (Government of India) (https://onlinemaps.surveyofindia.gov.in/Digital_Product_Show.aspx); used with reproduction rights as per SoI copyright policy. https://surveyofindia.gov.in/pages/copyright-policy.
Fig 3.
Maximum-likelihood phylogenetic tree based on whole-genome nucleotide sequences of CHPV and other rhabdoviruses.
The tree was constructed under the Tamura–Nei model of nucleotide substitution. Bootstrap support values (1,000 replicates) are shown at the nodes. Included in the analysis are Vesicular stomatitis virus Indiana (VSVI), Vesicular stomatitis virus New Jersey (VSVNJ, bovine (Bo)), Isfahan virus (ISFV), Piry virus (PV), and Rabies virus (RABV) as reference rhabdoviruses. Tip labels indicate host species (Human [H], Sandfly [S], Hedgehog [HG]) and country of origin (e.g., India [IN], Kenya [KE], Senegal [SN], Nigeria [NG], Mexico [MX]), along with regional abbreviations (e.g., Gujarat [GJ], Vadodara [VD], Warangal [WR], Nagpur [NP], Karimnagar [KN], Andhra Pradesh [AP], Maharashtra [MH], Patan [PT], Turkana [TK], Baringo [BG], Kedougou [KD], Barkedji [BK]).
Fig 4.
Maximum-likelihood phylogenetic trees of CHPV coding sequences for individual genes.
Five phylogenetic trees were constructed from the coding sequences of the glycoprotein, matrix protein, nucleoprotein, phosphoprotein, and large RNA-dependent RNA polymerase labeled A to E. Trees were inferred using the Tamura-Nei model of nucleotide substitution, with bootstrap values from 1,000 replicates indicated at the nodes. The analysis includes CHPV sequences from India and West African countries, along with representative rhabdoviruses: Vesicular stomatitis virus Indiana (VSVI), Vesicular stomatitis virus New Jersey (VSVNJ, bovine [Bo]), Isfahan virus (ISFV), Piry virus (PV), and Rabies virus (RABV). Tip labels show host species (Human [H], Sandfly [S], Hedgehog [HG]) and country of origin (India [IN], Kenya [KE], Senegal [SN], Nigeria [NG], Mexico [MX]) with regional abbreviations (Gujarat [GJ], Vadodara [VD], Warangal [WR], Nagpur [NP], Karimnagar [KN], Andhra Pradesh [AP], Maharashtra [MH], Patan [PT], Turkana [TK], Baringo [BG], Kedougou [KD], Barkedji [BK]).
Fig 5.
Bayesian skyline plot of CHPV inferred from the whole genome dataset.
Bayesian skyline reconstruction of effective population size (Neτ) for CHPV based on the complete genome dataset (n = 23), inferred under an uncorrelated lognormal relaxed molecular clock model using BEAST 2.7.7. The solid line represents the median estimate, and the shaded region indicates the 95% highest posterior density (HPD) interval. The x-axis denotes time (years), and the y-axis represents scaled effective population size (Neτ).
Fig 6.
Heatmap representing pairwise nucleotide distances among 23 Chandipura virus (CHPV) isolates and five reference rhabdoviruses, based on full genome sequences.
Included reference viruses are Vesicular stomatitis virus Indiana (VSVI), Vesicular stomatitis virus New Jersey (VSVNJ, bovine), Isfahan virus (ISFV), Piry virus (PV), and Rabies virus (RABV).
Fig 7.
Structural mapping of episodic diversifying sites and predicted B-cell linear epitopes in CHPV structural proteins.
Surface representations of (A) glycoprotein, (B) matrix protein, and (C) nucleoprotein are shown with residues under episodic diversifying selection (MEME) colored red, predicted B-cell linear epitopes (IEDB BepiPred) highlighted in yellow, and residues overlapping both categories indicated in blue. Each panel includes a table listing the predicted B-cell epitopes alongside the corresponding protein sequence positions, facilitating correlation between structural features and immunologically relevant sites.