ZikaVR is an integrative multi-omics platform dedicated to the Zika virus genomic and proteomic analysis along with comparative genomics and therapeutic knowledge.
It is classified in different sections represent individual components i.e. genomic annotation, phylogenomics, therapeutics, molecular diagnostics, comparative genomic analysis and tools.
It also includes graphical genome browser for the collective representation of annotation and regulatory information.
Q2- What type of data ZikaVR address ?
It is comprises of whole genome sequences, their respective functional information regarding proteins, genes, and structural content.
Additionally, it also delivers sophisticated analysis such as whole-genome alignments, conservation and variation, CpG islands, GC content, codon usage bias, codon context, synteny and phylogenetic inferences at whole genome; gene and protein level with user-friendly visual environment.
It offers highly interactive genomic browser (Zika Browser) to explore genomic and regulatory components powered by JBrowse. Resource also provides primers and related knowledge for molecular diagnostics applications.
Furthermore, ZikaVR also deals with therapeutically imperative constituents i.e. siRNAs, miRNAs, sgRNAs, epitopes, and pathway or network information. Epitope knowledge critical in vaccine development supported using Epitope Map.
It also provides useful analysis tools like a local Zblast server, Align viewer, Blockcon, Genoplotter, Str3D and Physicoprop.
Q3- What are the unique features of ZikaVR virus resource ?
Upto now, there is no resoruce available for Zika virus study, We have analyzed and compiled complete genomic, proteomic and structural data along with therapeutically potential candidates. It is the first of its kind and very important since it addresses overall landscape of Zika virus. It also facilitate useful analysis tools.
Q4- ZikaVR virus resource is free ?
This integrated resource is freely available to facilitate research on zika virus, All curated and annotated genomic data can also be downloaded to perform in-house analysis.
Blood or serum samples are normally used for detection of Zika virus. Also, urine samples have been shown to give positive results even after the virus has been depleted from the serum samples. Zika virus strains have also been detected in breast milk and nasopharyngeal swabs.
Q6- What are the diagnostic techniques used for detection of Zika virus infection ?
Diagnosis of Zika infection is not easy, as the symptoms are similar to other febrile illnesses. The primary mode of detection is IgM and IgG ELISA or EIA, mostly followed by virus neutralization tests like PRNT for conclusive detection. Also, haemagglutination, and Complement fixation tests have been used in the past. Recently, RT-PCR has proven to be the most definitive detection technique for this virus, as it is highly conclusive as there is no cross reactivity as in case of serological tests.
Q7- Are there any ZIKV specific primers available ?
Yes, six pairs of ZIKV specific primers have been used in several studies. These are ZIKENVF, ZIKENVR, ZIKAf, ZIKAr, ZIKVF9027, ZIKVR9197c, ZIKV 835, ZIKV 911c, ZIKV 1086, ZIKV 1162c, and one unnamed pair
[AA(A,G)TACACATACCA(A,G)AACAAAGTGGT and TCC(A,G)CTCCC(C,T)CT(C,T)TGGTCTTG]
Q8- What are the universal primers available for identification of ZIKV infections ?
Universal flaviviridae primers that can also detect ZIKV among others are: VD8, EMF1, Flav100F, Flav200R, FU1, cFD3, PF1S5, PF2R-bis, Unifor, Unirev, Mounifor2, Mounirev.
Q9- What is the incubation period of zika virus ?
It is reported to range from 3 to 14 days, as in other flaviviruses such as West Nile virus and dengue virus. Specifically, in one study it was reported to be 3-7 days [25294619] and < 9 days in another [21529401].
Q10- What are epitopes and how they serve as potential vaccine candidates?
Epitopes refer to the antigenic region i.e. specifically recognized by the immune system via B-cells, T-cells and other antibodies. These epitopes can be conformational or linear depending on the structure and type of interactions. Epitopes are believed to possess high credentials for directing effectual vaccine design. The epitope-driven vaccine development approach has proved advantageous against several infections and recently an epitope-based vaccine called RTS,S has effectively moved to phase-III trials utilizing an engineered T-cell epitope of the causative protozoan parasite. Once, it successfully passes all the trials it will potentially be the first commercial vaccine against malaria. The epiotpe-based vaccines are also considered safer than conventional vaccine development approaches as they expose body to a nominal activating unit, i.e. epitopes which are small enough; wherein the complete antigen has deleterious impact on the host.
Q11- How are the drug targets and drugs against zika proposed in the resource?
Since, there is no available drug till date for treating zika infection and the drug development process being tedious and an expensive task, computational methods provide valuable perceptions in steering therapeutic strategies. For the identification of drug targets and potential drugs against zika, the ZIKV genome was subjected to repositioning for testified drugs in DrugBank that perhaps have approved toxicity and other safety regulations against closely related viruses. This approach of therapeutic switching reveals crucial findings and are judicious processes as these reduce the encountered costs during clinical trials. This analysis indicate that well-characterized drugs for related infections could probably be tested for fighting zika as well. Thus, reducing complexity for determining effective drugs and rendering drug discovery process simpler.
Q12- What are cell penetrating peptides? How they have been provided in ZikaVR?
Cell penetrating peptides are small peptides that facilitate transport of molecules ranging from nano scale to large DNA fragments into the cell. Thus, they have ability to effciently deliver targeted vaccine or drugs. Due to their therapeutic advantages, these peptides were also identified from zika genome by classifying the genome into 10mer sequences. These 10mer peptides were then analyzed using CellPPD method by choosing SVM based model. This information on peptides can ultimately help researchers in determining key candidates for therapeutic purposes.
