Subtyping of Dengue Viruses using Return Time Distribution based Appproach

Dengue virus (DENV) is the causative agent of Dengue Hemorrhagic Fever and Dengue Shock Syndrome, and continues to represent a major public health hazard. DENVs are antigenically classified in four serotypes and each serotype is further divided into respective genotypes. The association between DENV subtypes and the kind & severity of disease caused by them is known. Experimental and computational approaches for subtyping are routinely used for the purpose of diagnosis and treatment of DENV, in addition to the study of phylodynamics. All virus-specific molecular subtyping tools make use of sequence alignments at backend. But as the volume of molecular data increases, alignment-dependent methods become computationally intensive. Hence, the need for alternative efficient approaches for subtyping of viruses becomes apparent. Recently, the concept of Return time distribution (RTD) was proposed and validated for alignment-free clustering and molecular phylogeny. The RTD-based approach is extended here for the subtyping of DENVs. 
Subtyping methodology involves compilation of curated genomic data of known subtypes, computing RTD of these sequences at different levels of k-mers, derivation a distance matrix and clustering. The subtype of the unknown is predicted based on its clustering with known subtypes.
Dataset consisting of 1359 DENV genomes with sequence identity (>92%) were clustered using the RTD based approach at k=5. Serotype specific clades, despite geographical and temporal variation in the dataset, were observed with 100% accuracy. The method was also found to be efficient in terms of time and implementation, apart from accuracy in the subtyping of DENV

Analysis of genotype diversity and evolution of Dengue virus serotype 2 using complete genomes

Background Dengue is one of the most common arboviral diseases prevalent worldwide and is caused by Dengue viruses (genus Flavivirus, family Flaviviridae). There are four serotypes of Dengue Virus (DENV-1 to DENV-4), each of which is further subdivided into distinct genotypes. DENV-2 is frequently associated with severe dengue infections and epidemics. DENV-2 consists of six genotypes such as Asian/American, Asian I, Asian II, Cosmopolitan, American and sylvatic. Comparative genomic study was carried out to infer population structure of DENV-2 and to analyze the role of evolutionary and spatiotemporal factors in emergence of diversifying lineages. Methods Complete genome sequences of 990 strains of DENV-2 were analyzed using Bayesian-based population genetics and phylogenetic approaches to infer genetically distinct lineages. The role of spatiotemporal factors, genetic recombination and selection pressure in the evolution of DENV-2 is examined using the sequence-based bioinformatics approaches. Results DENV-2 genetic structure is complex and consists of fifteen subpopulations/lineages. The Asian/American genotype is observed to be diversified into seven lineages. The Asian I, Cosmopolitan and sylvatic genotypes were found to be subdivided into two lineages, each. The populations of American and Asian II genotypes were observed to be homogeneous. Significant evidence of episodic positive selection was observed in all the genes, except NS4A. Positive selection operational on a few codons in envelope gene confers antigenic and lineage diversity in the American strains of Asian/American genotype. Selection on codons of non-structural genes was observed to impact diversification of lineages in Asian I, cosmopolitan and sylvatic genotypes. Evidence of intra/inter-genotype recombination was obtained and the uncertainty in classification of recombinant strains was resolved using the population genetics approach. Discussion Complete genome-based analysis revealed that the worldwide population of DENV-2 strains is subdivided into fifteen lineages. The population structure of DENV-2 is spatiotemporal and is shaped by episodic positive selection and recombination. Intra-genotype diversity was observed in four genotypes (Asian/American, Asian I, cosmopolitan and sylvatic). Episodic positive selection on envelope and non-structural genes translates into antigenic diversity and appears to be responsible for emergence of strains/lineages in DENV-2 genotypes. Understanding of the genotype diversity and emerging lineages will be useful to design strategies for epidemiological surveillance and vaccine design

RTD-based phylogenetic tree of <i>Rhinoviruses</i> using VP1 reference data set at <i>k</i> = 2.

<p>The branches are color coded as following, <i>Rhinovirus A</i> (red), <i>Rhinovirus B</i> (blue) and <i>Rhinovirus C</i> (green). The tip labels are divided in 4 parts by ‘|’ characters indicating species, serotype, serial number of that serotype and GenPept accession number respectively. Note: The RTD-based phylogenetic tree for the reference and the true positive sequences of RV types is provided as <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0149350#pone.0149350.s003" target="_blank">S3 Fig</a>.</p

The codons under episodic diversifying selection identified using MEME method are reported.

<p>The codons under episodic diversifying selection identified using MEME method are reported.</p

Sublevel clustering of HRV-A: The plot of <i>K</i> vs. <i>ΔK</i> obtained for HRV-A strains.

<p><i>ΔK</i> represents the rate of change of posterior probability given the number of clusters (<i>K</i>). <i>ΔK</i> is plotted against <i>K</i> to determine optimum number of clusters (<i>K_opt</i>) within <i>Rhinovirus A</i> population. A major peak at <i>K</i> = 2 and a minor peak at <i>K</i> = 13 is observed. It suggests that <i>Rhinovirus A</i> population primarily divides into two major groups. The minor peak at <i>K</i> = 13 indicates that <i>Rhinovirus A</i> population is further subdivided into 13 minor subpopulations.</p

Phylogenetic tree of <i>Rhinoviruses</i> obtained using Neighbor-joining method in MEGA 5.05.

<p>Complete genome sequence data with 1000 bootstrap replicates was used. The operational taxonomic unit (OTU) label consists of two parts divided by pipe (‘|’) character. The first part (before ‘|’) indicates species-serotype and second part constitute GenBank accession number of the associated entry. The branches in the tree are color coded as per the seven subpopulations obtained using STRUCTURE program [Subpopulation A: blue, A1: yellow, A2: red, A3: green, B: magenta, C1: orange, C2: cyan].</p

Evaluation of insecticidal activity of some benzofused heterocycles against different insect pests

754-762The twelve benzo-fused N,O,S-heterocyclic compounds have been investigated for biological activity against major pests of field crops, third instar larvae of Spodoptera litura (F.) and several stored product pests namely, Sitophilus zeamais (M.),<i style="mso-bidi-font-style: normal"> Tribolium castaneum (H.) and Callosobruchus chinensis (L.). Responses show variation with test compounds, insect species, doses and exposure times individually. All the reported benzothiazines and benzoxines heterocycles have been prepared by eco-friendly method and characterized by IR, 13C and 1H NMR. The bioassay has been investigated with oviposition deterrency, LC50, chi-square and randomized block design. These results suggest that most of the compounds demonstrate potent insecticidal activity by feeding method (mortality 77-97%) in comparison to the contact and larvicidal activity. </span

RV-Typer: A Web Server for Typing of <i>Rhinoviruses</i> Using Alignment-Free Approach

<div><p><i>Rhinoviruses</i> (RV) are increasingly being reported to cause mild to severe infections of respiratory tract in humans. RV are antigenically the most diverse species of the genus <i>Enterovirus</i> and family <i>Picornaviridae</i>. There are three species of RV (RV-A, -B and -C), with 80, 32 and 55 serotypes/types, respectively. Antigenic variation is the main limiting factor for development of a cross-protective vaccine against RV.Serotyping of <i>Rhinoviruses</i> is carried out using cross-neutralization assays in cell culture. However, these assays become laborious and time-consuming for the large number of strains. Alternatively, serotyping of RV is carried out by alignment-based phylogeny of both protein and nucleotide sequences of VP1. However, serotyping of RV based on alignment-based phylogeny is a multi-step process, which needs to be repeated every time a new isolate is sequenced. In view of the growing need for serotyping of RV, an alignment-free method based on “return time distribution” (RTD) of amino acid residues in VP1 protein has been developed and implemented in the form of a web server titled RV-Typer. RV-Typer accepts nucleotide or protein sequences as an input and computes return times of di-peptides (<i>k</i> = 2) to assign serotypes. The RV-Typer performs with 100% sensitivity and specificity. It is significantly faster than alignment-based methods. The web server is available at <a href="http://bioinfo.net.in/RV-Typer/home.html" target="_blank">http://bioinfo.net.in/RV-Typer/home.html</a>.</p></div