Safety and efficacy profile of oral cyclosporine vs oral methotrexate vs oral acitretin in palmoplantar psoriasis: A hospital based prospective investigator blind randomized controlled comparative study.

Palmoplantar psoriasis (PPP) is a variant of psoriasis which affects only 5% body surface area, but has a devastating impact on affected individual's quality of life. There are few studies assessing efficacy of individual drugs, and few comparative studies of efficacy of two drugs in the literature, however randomized control trial comparing all three drugs against each other has not been done. A total of 75 patients of PPP were enrolled for study and randomly divided into three groups A, B, C of 25 each and assigned for treatment with cyclosporine (CSA) (2.5-5 mg/kg/d), methotrexate (MTX)(7.5-15 mg/week), and acitretin (ACT) (25-50 mg/d), respectively. Modified psoriasis area and severity index (PASI), psoriasis severity scale, visual analogue scale, physician global assessment, and PPQOL were used for monitoring response to therapy and improvement in quality of life up to end of study, and thereafter monthly follow-up was done to find duration of remission for next 90 days. Side effects if any were recorded. There was a statistically significant difference in modified PASI for CSA, MTX, and ACT. The mean modified PASI at baseline was 12.8 ± 4.8 for CSA, 12.57 ± 3.8 for MTX, and 11.92 ± 3.28 for ACT (P = .75). Mean modified PASI reduced to 2.91 ± 1.8 for CSA, 6.57 ± 2.2 for MTX, and 4.7 ± 2.2 for ACT at week 5 (P = <.01). Mean modified PASI further reduced to 0.095 ± 0.35 for CSA, 2.12 ± 1.4 for MTX, and 0.78 ± 0.97 for ACT at end of study (P = <.01). However, average duration of remission was 9 weeks for ACT group, followed by 6.47 and 3 weeks for CSA and MTX group, respectively. Adverse events were comparatively more in ACT group as compared to MTX and CSA groups. PPP affects quality of life tremendously and warrants systemic treatment for the same. CSA provides fastest resolution of lesions and have highest efficacy. MTX and ACT have similar efficacy, but ACT provides longer duration of remission.

Understanding evolution of SARS-CoV-2: A perspective from analysis of genetic diversity of RdRp gene.

Coronavirus disease 2019 emerged as the first example of "Disease X", a hypothetical disease of humans caused by an unknown infectious agent that was named as novel coronavirus and subsequently designated as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The origin of the outbreak at the animal market in Wuhan, China implies it as a case of zoonotic spillover. The study was designed to understand evolution of Betacoronaviruses and in particular diversification of SARS-CoV-2 using RNA dependent RNA polymerase (RdRp) gene, a stable genetic marker. Phylogenetic and population stratification analyses were carried out using maximum likelihood and Bayesian methods, respectively. Molecular phylogeny using RdRp showed that SARS-CoV-2 isolates cluster together. Bat-CoV isolate RaTG13 and Pangolin-CoVs are observed to branch off prior to SARS-CoV-2 cluster. While SARS-CoV form a single cluster, Bat-CoVs form multiple clusters. Population-based analyses revealed that both SARS-CoV-2 and SARS-CoV form separate clusters with no admixture. Bat-CoVs were found to have single and mixed ancestry and clustered as four sub-populations. Population-based analyses of Betacoronaviruses using RdRp revealed that SARS-CoV-2 is a homogeneous population. SARS-CoV-2 appears to have evolved from Bat-CoV isolate RaTG13, which diversified from a common ancestor from which Pangolin-CoVs have also evolved. The admixed Bat-CoV sub-populations indicate that bats serve as reservoirs harboring virus ensembles that are responsible for zoonotic spillovers such as SARS-CoV and SARS-CoV-2. The extent of admixed isolates of Bat-CoVs observed in population diversification studies underline the need for periodic surveillance of bats and other animal reservoirs for potential spillovers as a measure towards preparedness for emergence of zoonosis.

Population genomics of dengue virus serotype 4: insights into genetic structure and evolution.

The spread of dengue disease has become a global public health concern. Dengue is caused by dengue virus, which is a mosquito-borne arbovirus of the genus Flavivirus, family Flaviviridae. There are four dengue virus serotypes (1-4), each of which is known to trigger mild to severe disease. Dengue virus serotype 4 (DENV-4) has four genotypes and is increasingly being reported to be re-emerging in various parts of the world. Therefore, the population structure and factors shaping the evolution of DENV-4 strains across the world were studied using genome-based population genetic, phylogenetic and selection pressure analysis methods. The population genomics study helped to reveal the spatiotemporal structure of the DENV-4 population and its primary division into two spatially distinct clusters: American and Asian. These spatial clusters show further time-dependent subdivisions within genotypes I and II. Thus, the DENV-4 population is observed to be stratified into eight genetically distinct lineages, two of which are formed by American strains and six of which are formed by Asian strains. Episodic positive selection was observed in the structural (E) and non-structural (NS2A and NS3) genes, which appears to be responsible for diversification of Asian lineages in general and that of modern lineages of genotype I and II in particular. In summary, the global DENV-4 population is stratified into eight genetically distinct lineages, in a spatiotemporal manner with limited recombination. The significant role of adaptive evolution in causing diversification of DENV-4 lineages is discussed. The evolution of DENV-4 appears to be governed by interplay between spatiotemporal distribution, episodic positive selection and intra/inter-genotype recombination.

Rapid evolution leads to extensive genetic diversification of cattle flu Influenza D virus.

Influenza D virus (IDV), the cattle flu virus, is a novel multi-host RNA virus, circulating silently worldwide, with widespread seropositivity among US cattle, reaching up to 80% in some areas raising a potential threat of cattle-to-human transmission. Currently, five genetic lineages of IDV have been described, but their evolutionary dynamics have not been studied. Although IDV was first identified in 2011, our comprehensive analysis of all known IDV genomes suggests that the earliest ancestors of IDV likely to have evolved towards the end of the 20th century and D/OK lineage appears to have emerged in 2005. We confirmed a significantly higher substitution rate in IDV than in Influenza C virus, which is consistent with their global distribution and multi-host tropism. We identified multiple sub-populations within the D/OK lineage, highlighting extensive diversification and dissemination. Other findings are evidence for potential reassortment among IDV strains in the USA and transboundary circulation of IDV in Europe with introductions into Danish cattle, some of which potentially originated from France. IDV, an emerging virus with a higher rate of evolution and uncontrolled circulation, could facilitate its adaptation to humans. Our findings underscore the importance of targeted surveillance for IDV in humans and at-risk animal populations.

IDV Typer: An Automated Tool for Lineage Typing of Influenza D Viruses Based on Return Time Distribution.

Influenza D virus (IDV) is the most recent addition to the Orthomyxoviridae family and cattle serve as the primary reservoir. IDV has been implicated in Bovine Respiratory Disease Complex (BRDC), and there is serological evidence of human infection of IDV. Evolutionary changes in the IDV genome have resulted in the expansion of genetic diversity and the emergence of multiple lineages that might expand the host tropism and potentially increase the pathogenicity to animals and humans. Therefore, there is an urgent need for automated, accurate and rapid typing tools for IDV lineage typing. Currently, IDV lineage typing is carried out using BLAST-based searches and alignment-based molecular phylogeny of the hemagglutinin-esterase fusion (HEF) gene sequences, and lineage is assigned to query sequences based on sequence similarity (BLAST search) and proximity to the reference lineages in the tree topology, respectively. To minimize human intervention and lineage typing time, we developed IDV Typer server, implementing alignment-free method based on return time distribution (RTD) of k-mers. Lineages are assigned using HEF gene sequences. The server performs with 100% sensitivity and specificity. The IDV Typer server is the first application of an RTD-based alignment-free method for typing animal viruses.

An Observational Study of Dermoscopic and Histopathological Correlation in Spongiotic Disorders - A Hospital Based Cross Sectional Study.

Introduction: Spongiosis is defined as intercellular edema and vesicles in the epidermis. Histopathology is the gold standard for the diagnosis of spongiotic disorders. Clinical diagnosis of eczema is sometimes unclear and confused with other dermatoses; histopathology often shows spongiotic tissue reaction patterns; such conditions are called spongiotic disorders. It is challenging for a dermatologist to make the correct diagnosis noninvasively with a dermoscope and thus we have taken up the study to correlate the dermoscopic and histopathological findings in spongiotic disorders to set dermoscopic criteria for the diagnosis. Objective: To study the dermoscopic features of spongiotic disorders and correlate clinical, dermoscopic, and histopathological findings. Materials and Methods: Two hundred fifty two patients, with history and clinical presentation suggesting eczema were enrolled. They were classified as Acute (<6 weeks), Subacute (6 weeks to 3 months), and Chronic (>3 months) eczemas based on duration. Dermoscopy and skin biopsy were performed on representative lesions. Data were compiled and statistically analyzed using frequency distribution and Chi-square test. Results: We correlated the diagnosis based on acute, subacute, and chronic with three modalities, clinical examination, dermoscopy, and histopathology. On clinical examination, acute (27.4%), subacute (42.9%), and chronic (29.7%) dermatitis. On dermoscopy, acute (28.5%), subacute (40.4%), and chronic (31.1%) dermatitis. On histopathology, acute (29.5%), subacute (44.2%), and chronic (26.3%) spongiosis. A positive correlation of 99%, 96.2%, and 95% was observed on dermoscopy and histopathology, in acute, subacute, and chronic eczemas, respectively. Dermoscopy of acute eczemas showed linear vessels (100%) and red background (100%). White-Clods (98.9%) and excoriation marks (70.1%). Dermoscopy of subacute eczemas showed white scales (99.1%), irregular pigment network (98.3%), vascular changes with irregular dots (97.4%), a brown-white background (93.1%), and black/brown/grey dots (91.4%). Dermoscopy of chronic eczema showed brown-white background (100%), irregular pigment network (100%), and black/brown/grey blotches (100%). Conclusion: Definitive dermoscopic patterns are observed consistently with spongiotic diseases and these can be used additionally to set dermoscopic criteria and confirm the diagnosis. Also, dermoscopic findings are well correlated with the already established histopathological features.

Alignment-free distance measure based on return time distribution for sequence analysis: applications to clustering, molecular phylogeny and subtyping.

The data deluge in post-genomic era demands development of novel data mining tools. Existing molecular phylogeny analyses (MPAs) developed for individual gene/protein sequences are alignment-based. However, the size of genomic data and uncertainties associated with alignments, necessitate development of alignment-free methods for MPA. Derivation of distances between sequences is an important step in both, alignment-dependant and alignment-free methods. Various alignment-free distance measures based on oligo-nucleotide frequencies, information content, compression techniques, etc. have been proposed. However, these distance measures do not account for relative order of components viz. nucleotides or amino acids. A new distance measure, based on the concept of 'return time distribution' (RTD) of k-mers is proposed, which accounts for the sequence composition and their relative orders. Statistical parameters of RTDs are used to derive a distance function. The resultant distance matrix is used for clustering and phylogeny using Neighbor-joining. Its performance for MPA and subtyping was evaluated using simulated data generated by block-bootstrap, receiver operating characteristics and leave-one-out cross validation methods. The proposed method was successfully applied for MPA of family Flaviviridae and subtyping of Dengue viruses. It is observed that method retains resolution for classification and subtyping of viruses at varying levels of sequence similarity and taxonomic hierarchy.

Monotherapy of Biofiller for Atrophic Acne Scars: A Prospective Nonrandomized Study.

Background: Atrophic acne scarring is an unpleasant and often permanent complication and a therapeutic challenge for dermatologists. Platelet-poor plasma (PPP) gel injections are derived from the patient's own blood and used as a "biofiller" for skin rejuvenation. Objectives: The objective was to study the efficacy and safety profile of PPP gel in atrophic acne scars. Materials and Methods: Thirty patients with atrophic acne scars were included in the study. Topical anesthesia was applied on the area of interest 45 min prior to the procedure. 20 mL of blood was collected in eight sodium citrate bulbs and centrifuged to get PPP that is coagulated with heat to form gel. This gel (biofiller) was injected in the scarred areas monthly for 6 months. Patients were evaluated using Goodman and Baron Scar (GBS) scale (quantitative and qualitative), Physician Global Assessment, and Visual Analogue Scale (VAS) at each visit. The final visit was after 3 months of the last procedure. Results: The mean value of GBS at the first visit was 28, which reduced to 8.2 at the final visit. The analysis of variance test was applied to the quantitative scale from the baseline visit to the final visit. The F value was 462.55 with a P value < 0.0001. The paired t-test was applied for the GBS quantitative scale, which showed a value of 22.86 with a P value of <0.001. Transient local side effects were noted. Conclusion: Biofiller is efficacious in improving atrophic acne scars. It is a simple, minimally invasive, cost-effective procedure with no risk of immunogenic reaction.

Evaluation of Dermoscopic Patterns of Vesiculobullous Disorders.

BACKGROUND: Clinical diagnosis of vesiculobullous disorders (VBD) is not always straightforward. It is a challenge for a dermatologist to make the right diagnosis noninvasively in a short time. OBJECTIVE: To evaluate dermoscopic patterns associated with vesiculobullous disorders. METHODS: A total of 230 patients, irrespective of age and gender, with a history and clinical presentation suggestive of VBD (including primarily infectious, inflammatory, genetic, antibody-mediated, mechanical, environmental, metabolic, and drug-related) were recruited into the study. Patients with secondarily infected lesions were excluded. Dermoscopic examination along with Tzanck smear/skin biopsy smear test was performed on the most representative lesions. Data were compiled and statistically analyzed using SPSS version 21.0. RESULTS: Lesions with erythematous (vascular) and yellowish (serum) translucent background with regular margins were seen in most of the VBD studied. Chickenpox (CP) and herpes zoster (HZ) lesions evolved with the progress of their clinical stages. Follicular and eccrine openings were commonly seen, but the pigmentation around them was specific to pemphigus vulgaris. A distorted pigment network was noted in bullous pemphigoid. White rosettes (keratin blockage) were characteristic of epidermolysis bullosa, Wickham striae (orthokeratosis) of lichen planus, and crumpled fabric appearance (flaccidity) of Hailey-Hailey disease. Globules/dots (microvesicles) of different colors were also seen in various VBD. Blue/black color usually corresponded to retained melanin. CONCLUSION: Some dermoscopic patterns are observed consistently with certain diseases, and these can be used for their diagnosis, complementary to histopathological examination.

Circulation and Evolution of SARS-CoV-2 in India: Let the Data Speak.

The COVID-19 pandemic is a global challenge that impacted 200+ countries. India ranks in the second and third positions in terms of number of reported cases and deaths. Being a populous country with densely packed cities, SARS-CoV-2 spread exponentially. India sequenced ≈0.14% isolates from confirmed cases for pandemic surveillance and contributed ≈1.58% of complete genomes sequenced globally. This study was designed to map the circulating lineage diversity and to understand the evolution of SARS-CoV-2 in India using comparative genomics and population genetics approaches. Despite varied sequencing coverage across Indian States and Union Territories, isolates belonging to variants of concern (VoC) and variants of interest (VoI) circulated, persisted, and diversified during the first seventeen months of the pandemic. Delta and Kappa lineages emerged in India and spread globally. The phylogenetic tree shows lineage-wise monophyletic clusters of VoCs/VoIs and diversified tree topologies for non-VoC/VoI lineages designated as 'Others' in this study. Evolutionary dynamics analyses substantiate a lack of spatio-temporal clustering, which is indicative of multiple global and local introductions. Sites under positive selection and significant variations in spike protein corroborate with the constellation of mutations to be monitored for VoC/VoI as well as substitutions that are characteristic of functions with implications in virus-host interactions, differential glycosylation, immune evasion, and escape from neutralization.

Genetic and antigenic characterization of wild type rubella viruses isolated from India.

Rubella, is a contagious disease caused by Rubella virus (RuV) that manifests as fever with skin-rashes in children and adults along with complications in pregnant women. WHO-SEAR has set a target for Rubella elimination by 2023. This is the first report of antigenic characterization and genome sequencing of nine RuVs sampled during 1992, 2007-9, and 2015-17 from four Indian states. Comparative analysis of Indian RuVs (2B) with that of global isolates and vaccine strain RA 27/3 (1a) revealed that the observed mutations in structural proteins have no major impact on the 3D structure, function and antigenicity. Indian RuVs formed three major clusters (Pune-1992, Kannur-2009 and Chitradurg-2007) in genome-based phylogeny of global isolates. Neutralizing antibody titers in a panel of serum samples from measles negative cases were significantly higher to the vaccine strain compared to a wild-type 2B isolate (Kannur) with concordance of 91.9%, thereby substantiating the use of current vaccines.

Lichen Planus Severity Index: A new, valid scoring system to assess the severity of cutaneous lichen planus.

INTRODUCTION: Lichen planus is a chronic autoimmune inflammatory disorder. At present, there is a lack of any specific scoring system to judge the severity of cutaneous lichen planus. Hence, a study was undertaken to establish and validate a system to define the severity of cutaneous lichen planus, i.e. Lichen Planus Severity Index. MATERIALS AND METHODS: SETTING: Skin outpatient department, Krishna Institute of Medical Sciences, Karad. MODEL: The formulation model was Psoriasis Area Severity Index (PASI) and the validation model was Onychomycosis Severity Index (OSI). PARTICIPANTS: The consensus group included two dermatologists and two dermatology residents with special interest in lichen planus and a statistician. Results of the consensus group were compared with a preliminary reproducibility group of two dermatologists and four dermatology residents. Later, reliability assessment was carried out by two groups: 1. Twenty-one dermatologists scored 20 photographs of four patients of lichen planus after being trained to use Lichen Planus Severity Index. 2. Six doctors (three experts and three randomly selected physicians) evaluated ten real-world patients of lichen planus in skin outpatient department. The physicians were blind to the scores assigned by experts. STEPS TO CALCULATE SCORE: There are five morphological types of lesions seen in lichen planus, namely, erythematous papule, violaceous papule, violaceous plaque, hyperpigmented hypertrophic papule and plaque and postinflammatory hyperpigmentation. Total involved body surface area is determined and a body surface area factor is assigned. Area involvement factor for each of these morphological lesions is calculated and multiplied with the respective multiplication factor. Sum of all the products gives the lesion severity score. Product of lesion severity score with the body surface area factor gives the final Lichen Planus Severity Score. RESULTS: There was no significant difference between the scores of consensus group and preliminary reproducibility group. Both assessment groups showed high reliability. (Group 1: Cronbach alpha = 0.92, ICC = 0.85; Group 2: Cronbach's alpha = 0.99, ICC = 0.92). The correlation between Lichen Planus Severity Index and the standard Physician Global Assessment score was found to be positive (correlation coefficient = 0.73). LIMITATIONS: : The system is tedious and requires a steep learning curve. Possible uses of Lichen Planus Severity Index are yet to be explored and validated. CONCLUSION: Lichen Planus Severity Index is a new reproducible tool to grade the severity of lichen planus.

Characterization of diversity of measles viruses in India: Genomic sequencing and comparative genomics studies.

OBJECTIVE: To map genomic diversity of Measles virus (MeV) isolates collected during 2009-2017 from ten states of India. METHODS: Genome sequencing of Indian isolates and comparative genomics with global MeV using phylogeny, population stratification and selection pressure approaches were performed. RESULTS: The first report of complete genome sequences of forty-three Indian MeV isolates belonging to genotypes D4 (eight) and D8 (thirty-five). Three Indian isolates mapped to named strains D4-Enfield, D8-Villupuram and D8-Victoria. Indian D4 isolates deviate from standard genome length due to indels in M-F intergenic region. Estimated nucleotide substitution rates of Indian MeV derived using genome and individual genes are lower than that of global isolates. Phylogeny revealed genotype-based temporal clustering, suggesting existence of two lineages of D4 and three lineages of D8 in India. Absence of spatial clustering suggests role of cross-border travel in MeV transmission. CONCLUSIONS: Evolutionary analyses suggest the need for surveillance of MeV in India, particularly in view of diversified trajectories of D4 and D8 isolates. This study contributes to global measles epidemiology and indicates no major impact on antigenicity in Indian isolates, thereby substantiating the use of current vaccines to meet measles elimination target of 2023 set by World Health Organization for South-East Asia Region.

Efficacy of 800 nm Diode Laser to Treat Trichostasis Spinulosa in Asian Patients.

CONTEXT: Trichostasis spinulosa (TS) is a common but underdiagnosed follicular disorder involving retention of successive telogen hair in the hair follicle. Laser hair removal is a newer treatment modality for TS with promising results. AIMS: This study aims to evaluate the efficacy of 800 nm diode laser to treat TS in Asian patients. SUBJECTS AND METHODS: We treated 50 Indian subjects (Fitzpatrick skin phototype IV-V) with untreated trichostasis spinulosa on the nose with 800 nm diode laser at fluence ranging from 22 to 30 J/cm2 and pulse width of 30 ms. The patients were given two sittings at 8 week intervals. The evaluation was done by blinded assessment of photographs by independent dermatologists. RESULTS: Totally 45 (90%) patients had complete clearance of the lesions at the end of treatment. Five (10%) subjects needed one-third sitting for complete clearance. 45 patients had complete resolution and no recurrence even at 2 years follow-up visit. 5 patients had partial recurrence after 8-9 months and needed an extra laser session. CONCLUSIONS: Laser hair reduction in patients with TS targets and removes the hair follicles which are responsible for the plugged appearance. Due to permanent ablation of the hair bulb and bulge, the recurrence which is often seen with other modalities of treatment for TS is not observed here.

Genetic diversity and evolution of dengue virus serotype 3: A comparative genomics study.

Dengue virus serotype 3 (DENV-3), one of the four serotypes of Dengue viruses, is geographically diverse. There are five distinct genotypes (I-V) of DENV-3. Emerging strains and lineages of DENV-3 are increasingly being reported. Availability of genomic data for DENV-3 strains provides opportunity to study its population structure. Complete genome sequences are available for 860 strains of four genotypes (I, II, III and V) isolated worldwide and were analyzed using population genetics and evolutionary approaches to map landscape of genomic diversity. DENV-3 population is observed to be stratified into five major subpopulations. Genotype I and II formed independent subpopulations while genotype III is subdivided into three subpopulations (GIII-a, GIII-b and GIII-c) and is therefore heterogeneous. Genotypes I, II and GIII-a subpopulations comprise of Asian strains whereas GIII-c comprises of American strains. GIII-b subpopulation includes mainly of American strains along with a few strains from Sri Lanka. Genetic admixture is predominantly observed in Sri Lankan strains of genotype III and all strains of genotype V. Inter-genotype recombination was observed to occur in non-structural region of several Asian strains whereas extent of recombination was limited in American strains. Significant positive selection was found to be operational on all genes and observed to be the main driving force of genetic diversity. Positive selection was strongly operational on the branches leading to Asian genotypes and helped to delineate the genetic differences between Asian and American lineages. Thus, inter-genotype recombination, migration and adaptive evolution are the major determinants of evolution of DENV-3.

Characterization of bacterial community associated with phytoplankton bloom in a eutrophic lake in South Norway using 16S rRNA gene amplicon sequence analysis.

Interactions between different phytoplankton taxa and heterotrophic bacterial communities within aquatic environments can differentially support growth of various heterotrophic bacterial species. In this study, phytoplankton diversity was studied using traditional microscopic techniques and the bacterial communities associated with phytoplankton bloom were studied using High Throughput Sequencing (HTS) analysis of 16S rRNA gene amplicons from the V1-V3 and V3-V4 hypervariable regions. Samples were collected from Lake Akersvannet, a eutrophic lake in South Norway, during the growth season from June to August 2013. Microscopic examination revealed that the phytoplankton community was mostly represented by Cyanobacteria and the dinoflagellate Ceratium hirundinella. The HTS results revealed that Proteobacteria (Alpha, Beta, and Gamma), Bacteriodetes, Cyanobacteria, Actinobacteria and Verrucomicrobia dominated the bacterial community, with varying relative abundances throughout the sampling season. Species level identification of Cyanobacteria showed a mixed population of Aphanizomenon flos-aquae, Microcystis aeruginosa and Woronichinia naegeliana. A significant proportion of the microbial community was composed of unclassified taxa which might represent locally adapted freshwater bacterial groups. Comparison of cyanobacterial species composition from HTS and microscopy revealed quantitative discrepancies, indicating a need for cross validation of results. To our knowledge, this is the first study that uses HTS methods for studying the bacterial community associated with phytoplankton blooms in a Norwegian lake. The study demonstrates the value of considering results from multiple methods when studying bacterial communities.

RV-Typer: A Web Server for Typing of Rhinoviruses Using Alignment-Free Approach.

Rhinoviruses (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 Enterovirus and family Picornaviridae. 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 Rhinoviruses 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 (k = 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 http://bioinfo.net.in/RV-Typer/home.html.

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.

WNV Typer: a server for genotyping of West Nile viruses using an alignment-free method based on a return time distribution.

West Nile virus (WNV), genus Flavivirus, family Flaviviridae, is a major cause of viral encephalitis with broad host range and global spread. The virus has undergone a series of evolutionary changes with emergence of various genotypic lineages that are known to differ in type and severity of the diseases caused. Currently, genotyping is carried out using molecular phylogeny of complete coding sequences and genotype is assigned based on proximity to reference genotypes in tree topology. Efficient epidemiological surveillance of WNVs demands development of objective criteria for typing. An alignment-free approach based on return time distribution (RTD) of k-mers has been validated for genotyping of WNVs. The RTDs of complete genome sequences at k=7 were found to be optimum for classification of the known lineages of WNVs as well as for genotyping. It provides time and computationally efficient alternative for genome based annotation of WNV lineages. The development of a WNV Typer server based on RTD is described (http://bioinfo.net.in/wnv/homepage.html). Both the method and the server have 100% sensitivity and specificity.