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Comparative Study
. 2012;7(1):e30315.
doi: 10.1371/journal.pone.0030315. Epub 2012 Jan 17.

Whole genomes of Chandipura virus isolates and comparative analysis with other rhabdoviruses

Sarah S Cherian  1 , Rashmi S Gunjikar, Arpita Banerjee, Satyendra Kumar, Vidya A Arankalle
Affiliations
Comparative Study

Whole genomes of Chandipura virus isolates and comparative analysis with other rhabdoviruses

Sarah S Cherian et al. PLoS One. 2012.

Abstract

The Chandipura virus (CHPV) belonging to the Vesiculovirus genus and Rhabdoviridae family, has recently been associated with a number of encephalitis epidemics, with high mortality in children, in different parts of India. No full length genome sequences of CHPV isolates were available in GenBank and little is known about the molecular markers for pathogenesis. In the present study, we provide the complete genomic sequences of four isolates from epidemics during 2003-2007. These sequences along with the deduced sequence of the prototype isolate of 1965 were analysed using phylogeny, motif search, homology modeling and epitope prediction methods. Comparison with other rhaboviruses was also done for functional extrapolations. All CHPV isolates clustered with the Isfahan virus and maintained several functional motifs of other rhabdoviruses. A notable difference with the prototype vesiculovirus, Vesicular Stomatitis Virus was in the L-domain flanking sequences of the M protein that are known to be crucial for interaction with host proteins. With respect to the prototype isolate, significant additional mutations were acquired in the 2003-2007 isolates. Several mutations in G mapped onto probable antigenic sites. A mutation in N mapped onto regions crucial for N-N interaction and a putative T-cell epitope. A mutation in the Casein kinase II phosphorylation site in P may attribute to increased rates of phosphorylation. Gene junction comparison revealed changes in the M-G junction of all the epidemic isolates that may have implications on read-through and gene transcription levels. The study can form the basis for further experimental verification and provide additional insights into the virulence determinants of the CHPV.

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Figures

Figure 1
Figure 1. Phylogenetic tree of the whole genomes of the CHPV isolates and other rhabdoviruses using the Maximum likelihood method as implemented in MEGA. v.5.05.
Bootstrap values greater than 60% are indicated at the appropriate nodes. Scale bar indicates number of nucleotide substitutions per site. Abbreviations: CHPV (Chandipura virus; acc nos. GU212856.1-58.1 [CIN0327, CIN0451, CIN0751], GU190711.1 [CIN0728], CIN6514 [deduced 1965 CHPV sequence]); ISFV (Isfahan virus; acc. no. AJ810084.2); VSV (vesicular stomatitis virus; acc. no. NC_001560.1); PFRV (pike fry rhabdovirus; acc. no. FJ872827.1); SVCV (spring viraemia of carp virus; acc. no. DQ097384.2); SMRV (Scopthalmus maximus rhabdovirus; acc. no. HQ003891.1); BEFV (Bovine Ephemeral fever virus; acc. no. AF234533.1); MOKV (Mokola virus; acc. no. NC_006429.1); EBLV-1 (European bat lyssavirus-1; acc. no. EU293112.1); IRKV (Irkut virus; acc. no. EF614260.1); ABLV (Australian bat lyssavirus; acc. no. AF418014.1); RABV (rabies virus; acc. no. GQ918139); ARAV (Aravan virus; acc. no. EF614259.1); EBLV-2 (European bat lyssavirus-2; acc. no. NC_009528.1); KHUV (Khujand virus; acc. no. EF614261.1).
Figure 2
Figure 2. Profile alignment of N protein of representative CHPV isolates (shown in bold) with other representative rhabdoviruses.
Residues known to be critical for VSV N protein function are highlighted in grey to indicate conservation. Putative CK II phosphorylation sites are underlined while putative CAMP phosphorylation sites are italicized and underlined. The two-headed arrow delineates the T cell epitope of lyssaviruses. Mutations in CHPV isolates are indicated by downward arrows.
Figure 3
Figure 3. Homology models of CHPV proteins and mapping of significant functional residues.
All observed CHPV mutations (residue numbering as per the location in the sequence) in cyan. (A) Nucleoprotein: RNA binding residues shown in orange, residues part of RNA binding groove in blue and loop Ser340-Val375 in yellow. (B) Matrix (C) Glycoprotein: BEFV antigenic site G3 shown in shades of grey.
Figure 4
Figure 4. Alignment of P protein of representative CHPV isolates (indicated in bold) with closely related vesiculoviruses VSV and ISFV.
All putative phosphorylation sites are underlined. The different domains defined for the P protein of VSV are indicated by two-headed dashed overhead arrows. The mutations within the CHPV isolates are indicated by downward arrows.
Figure 5
Figure 5. Profile alignment of M protein (res: 1 – 117) of representative CHPV isolates (indicated in bold) with other representative rhabdoviruses.
The conserved PPxY and Px[TS]AP motifs are highlighted in grey. Putative glycosylation sites are underlined. The mutations within the CHPV isolates are indicated by downward arrows.
Figure 6
Figure 6. Alignment of G protein of representative CHPV whole genome isolates (in bold) with other representative rhabdoviruses.
BEFV antigenic sites and RABV antigenic sites are indicated by arrows above the sequence. Functionally important motifs are highlighted in grey and putative glycosylation sites are underlined. The signal peptide is indicated by dashed arrow. Highly conserved cysteine residues are highlighted in faint grey. Mutations within CHPV isolates are indicated by downward arrows.
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