Abstract
Hepatitis D virus (HDV) is a unique pathogen with significant global health implications, especially among individuals coinfected with Hepatitis B virus (HBV). HDV infection has pro-found clinical consequences, manifesting either as coinfection with HBV, resulting in acute hep-atitis and potential liver failure, or as superinfection in chronic HBV cases, substantially increasing the risk of cirrhosis and hepatocellular carcinoma. Given the complex dynamics of HDV infection and the urgent need for advanced research tools, this article introduces vHDvDB 2.0, a compre-hensive HDV full length sequence database. This innovative platform integrates data prepro-cessing, secondary structure prediction, and epidemiological research tools. The primary goal of vHDvDB 2.0 is to consolidate HDV sequence data into a user-friendly repository, thereby facili-tating access for researchers and enhancing the broader scientific understanding of HDV. The significance of this database lies in its potential to streamline HDV research by providing a cen-tralized resource for analyzing viral sequences and exploring genotype-specific characteristics. It will also enable more in-depth research within the HDV sequence domains.
| Genotype | Count |
|---|---|
| HDV-1 | 496 |
| HDV-2A | 28 |
| HDV-2B | 3 |
| HDV-3 | 59 |
| HDV-4A | 17 |
| HDV-4B | 25 |
| HDV-5 | 22 |
| HDV-6 | 17 |
| HDV-7 | 45 |
| HDV-8 | 9 |
| Recombinant HDV genotype I and II | 1 |
| NO Data | 6 |
| Total | 728 |
Database Summary
General rules for extracting Large Antigen
The relevant nucleotides were extracted from the Antigenome of the full-length sequence.
In the Antigenome, all start codons are point A; the RNA editing position is point B; the stop codon is point C. The position of
point A cannot exceed B and the position of point B cannot exceed C. The lengths of AB and BC must be divisible by 3. The position
of point A cannot be greater than 90, and the length of AC must be between 600 and 660.
Finally, use the ORF tool provided by Biopython to calculate its protein. The first amino acid of the protein sequence must be M,
the fourth amino acid at the end must be C, and the length must be greater than 200.
vHDvDB system architecture
Provided from GenBank based on AccessionID through PHP programAPI to download relevant files, and then use a series of PHP and Python programs to prepare the dataProcessed, the data is stored on the server in file form. The front-end PHP web program extracts data from various corresponding filesThe program reads the information and provides various functions based on JavaScript, jQuery and other tools.
User Adjust HDV RNA
The length of the sequence uploaded by the user must be between 1650 and 1700. Taking the starting position of M21012 as an indicator, the starting position of the sequence uploaded by the user is presented relative to the corresponding position of M21012. Press Align +1 site to align the starting positions of the user uploaded sequence and the M21012 sequence. Users can download the aligned sequences, including GBK FASTA CDS Translation and other files for users to choose.
