Biology subjects

Swain, S. K.

Publications and source records attributed to Swain, S. K..

3 recordsLinked to original sources

bioRxiv2023

First complete genome characterization of an Indian pigeon pox virus directly from a clinical sample

Avian pox disease is a highly contagious infection caused by pox virus and has serious consequences on avian species with regards to economic and conservation aspects. This viral genus named as Avipox virus (APV) that infects nearly 300 bird species and lack of enough complete genome information creates hindrance to infer this virus biology. Thus in this study, we have revealed the first complete genome of an Indian pigeon pox virus that belongs to the genus APV followed by comparative genomics analysis. The entire genome of present isolate (PPV/Pur-Od-4b/01/Ind) having 280058 bp nucleotide sequences with the GC content 29.51%. The unique feature of this complete genome revealed the presence of 270 open reading frames (ORFs) circumscribed by inverted terminal repeats (ITRs) of 4,689 bp at each end and lack of recombination events. The concatenated amino acid phylogenetic tree deciphered the present isolate closely related with Feral Pigeon pox virus derived from Africa. The molecular markers, such as microsatellites were ubiquitously distributed throughout the genome and more prevalent within the functional genes.

evolutionary biology↗

bioRxiv2023

Inferring B-cell derived T-cell receptor induced multi epitope-based vaccine candidate against enterovirus 71 (EV 71): A reverse vaccinology approach.

In addition to Coxsackie virus (CV), another pathogen that causes Hand-foot and mouth disease (HFMD), Enterovirus 71 (EV 71) is currently regarded as an increasing neurotropic virus in Asia and can cause severe complications in paediatric patients with blister like sores or rashes on the hand, feet and mouth. Not withstanding the significant burden of the disease, few treatments are currently available, and there is no authorised vaccine available for the disease prevention. Several vaccinations based on attenuated and inactivated vaccines have previously been identified, however they become worthless over time owing to changes in the viral genome. As a result, the goal of the study is to create an immunoinformatics and reverse vaccinology pipeline for predicting a multi epitope vaccine. A novel vaccine construct using B-cell derived T-cell epitopes from the virulent polyprotein and found the induction of possible immune response, in order to boost the immune system, aBeta-defensin 1 preproprotein adjuvant with EAAAK linker was added at the N-terminal end of the vaccine sequence. The immunogenicity of the designed, refined, and verified prospective 3D- structure of multi-epitope vaccine was found to be quite high with non-allergen, and antigenic property. The vaccine candidates bound to the TLR-3 in a molecular docking analysis and the efficacy of the potential vaccine to generate a strong immune response was assessed by means of an in silico immunological simulation. Computational analysis has shown that the proposed multi epitope vaccine possibility safe for use in humans and elicit an immune response, making it a promising tool against HFMD viral genome.

immunology↗

bioRxiv2023

Genome-wide mining and comparative analysis of microsatellite markers from Orientia tsutsugamushi genomes

Microsatellite markers, otherwise known as the simple sequence repeats (SSRs), are being used for molecular identification and characterization as well as estimation of evolution pattern of the organism due to their high polymorphic nature. These are tandemly repeated sequences observed almost all organisms and differentially distributed across the genome. Although the primary genome information of Orientia tsutsugamushi (OT) suggested the repeats hold the 40% entire of its genome, but lack of characteristic of this repeats increase our interest to study more about it. Thus we investigated a genome-wide presence of microsatellites within nine complete genomes within OT and analyzed their distribution pattern, composition and complexity. The in-silico study revealed the genome of OT enrich with microsatellites having a total of 126187 SSR and 10374 cSSR throughout the genome from which 70% and 30% represented within the coding and non coding region respectively. The relative density (RD) and relative abundance (RA) of SSRs were 42-44.43/kb and 6.25-6.59/kb while for cSSRs this value ranged from 7.06-8.1/kb and 0.50-0.55/kb respectively. However, RA and RD were weakly correlate with genome size and incidence microsatellites. The mononucleotide repeats (54.55%) were prevalent over di- (33.22%), tri- (11.88%), tetra- (0.27%), penta- (0.02%), hexanucleotide (0.04%) repeats, with poly (A/T) richness over poly (G/C). Motif composition of cSSRs revealed that maximum cSSRs were made up of two microsatellites having unique duplication pattern such as AT-x-AT, CG-x-CG. More numbers microsatellites represented within the coding region provides an insight into the genome plasticity that may interfere for gene regulation to mitigate with host-pathogen interaction and evolution of the species.

genomics↗