ArVirInd—a database of arboviral antigenic proteins from the Indian subcontinent

Introduction

With the effects of climate change becoming more prominent, the enhanced propagation of arthropods has resulted in the emergence and re-emergence of Arthropod-borne viruses (arboviruses) worldwide (Ryan et al., 2017; Gould & Higgs, 2009; Mourya et al., 2016). The densely populated South Asian region, geographically known as the Indian subcontinent, with its unique monsoon-driven climate systems, is particularly vulnerable to arboviral diseases such as dengue, chikungunya, Japanese encephalitis, West Nile, Crimean-Congo hemorrhagic fever, Kyasanur Forest disease, etc. are on the rise (Nagpal et al., 2016; Dhiman et al., 2010; Shil, 2019; Mourya et al., 2016). In India, between 2015 and 2021, Dengue affected 913,817 individuals (1,490 deaths), Chikungunya affected 82,429 individuals (0 deaths), and Japanease Encephalitis affected 11,283 (1,414 deaths) (NVBDCP https://nvbdcp.gov.in/index.php). Apart from this, there were sporadic outbreaks of West Nile, and Zika. Dengue and Chikungunya are prevalent in all the countries of the Indian subcontinent (Bangladesh (Haider et al., 2021), Pakistan (Islam et al., 2022), Nepal (Rijal et al., 2021), etc.). In 2019 Nepal experienced huge epidemic of dengue covering 68 out of 77 districts (Adhikari & Subedi, 2020).

The re-emergence of these diseases is associated with complex factors such as viral recombination and mutation, leading to more virulent and adaptive strains (Tabachnick, 2016; Baylis, 2017). This necessitates analyses of genome and proteome information for tracing viral evolution and phylogenetics, identification of effects of mutations in newly emerging strains, and also the design and development of chimeric peptides for effective diagnostics and/or vaccines. All this research needs basic information about the nucleotide and protein sequence composition and characteristics from viral strains and in silico analyses using bioinformatics and immuno-informatics tools.

Since the last decade of the 20th-century emergence of bioinformatics tools, techniques and databases has revolutionized biological research. A huge amount of biological information generated from laboratory experiments is warehoused in databases, which are freely available through the internet. NCBI (https://www.ncbi.nlm.nih.gov/), Protein Information Resource (PIR) (https://proteininformationresource.org/), DDBJ (https://www.ddbj.nig.ac.jp/index-e.html), ExPASy (https://www.expasy.org/), Protein ligand interaction database (PLID) (https://ngdc.cncb.ac.cn/databasecommons/database/id/3794), TTRMDB (http://vit.ac.in/ttrmdb), and dbHDPLS (https://www.dlearningapp.com/web/dbDPLS/index.php) are a few examples of large and popular databases providing information on proteins, protein families and also provide users with online software tools for bioinformatics analyses (Reddy et al., 2008; Zhu et al., 2019; Srinivasan, Natarajan & Rajasekaran, 2020). Bioinformatics databases dedicated to viruses are available. Virus-Host DB is a database that provides users with information on various viral proteins (Virus-Host DB. URL: https://www.genome.jp/virushostdb/). The Virus Pathogen Database and Analyses resource (ViPR) is a valuable resource for viral proteins (https://www.viprbrc.org/). There also exists a database of flaviviruses, FLAVIdB (cvc.dfci.harvard.edu/flavi), which is of limited scope. The most recent dedicated database on dengue is DenvInt (Dey & Mukhopadhyay, 2017).

Bioinformatics plays important role in immunological studies and viral diagnostics like the design of ELISA based tests, chimeric peptides, antigen-antibody interactions, etc. (Gangwar et al., 2011; Gangwar et al., 2012; Shil, Chavan & Cherian, 2011a; Shil, Chavan & Cherian, 2011b; Pavitrakar et al., 2018; Pavitrakar et al., 2020) . Hence, quick and easy data retrieval from databases is essential. The practical difficulty faced while searching for Indian sequences is that none of the existing databases enlist entries by country of origin and date of sample collection or outbreak. Most databases enlist sequences by date of publication. So data mining from existing large databases is cumbersome as a large number of entries appears and each had to be read manually to identify the country of origin. Considering the huge burden of arboviral diseases in India and its immediate neighborhood, providing effective diagnostics and phylogenetic studies for tracing viral evolution are important aspects of virology research. Hence, there is a need to develop a database dedicated to arboviral antigenic proteins from strains isolated from the Indian subcontinent.

In this article, we describe the development of a bioinformatics database, ArVirInd, dedicated to arboviral antigenic proteins covering strains reported from India and its neighboring countries. The database is being developed as a knowledge base and envisages providing information on antigenic characteristics apart from the sequence composition.

Materials & Methods

Database formulation and architecture

ArVirInd has a relational database structure setup using MySQL which facilitates storage, query, and visualization of information. Hyper Text Markup Language (HTML) and Cascading Style Sheet (CSS) have been used for the web-interface design. Annotated sequences data is stored in tables. The application layer between the backend tables and the web interface has been implemented by using PHP. Figure 1 explains the overall architecture of the ArVirInd knowledgebase.

Results

Database availability and search

The ArVirInd database is open access, annotated, and curated collection of publicly available arboviral antigenic proteins from India and its neighboring countries in the subcontinent. The ArVirInd knowledgebase is available at: http://www.arvirind.co.in.

ArVirInd homepage provides the user the following ways to search: (a) search by “Virus Name”, (b) search by “Country of Origin”, (c) search by “Year of Origin” or a combination of these options. This is a unique feature of the database. A query returns a tabular output which gives the list of all entries in the searched category. From this table user can choose any particular entry by clicking on the respective “ArVirInd ID”. The record for each entry can be printed or downloaded in PDF format. The display of the ArVirInd homepage is shown in Fig. 2A.

ArVirInd also allows the user to search (Fig. 2B) the database by submitting a query peptide (or epitope) through the “Search Your Peptide” search box (Fig. 2C). AJAX scripting is implemented to search option, which facilitates auto-search and auto-suggest query for the user.

Database dashboard

An interactive dashboard for the ArVirInd database is also available at http://arvirind.co.in/dashboard/. These summaries of the country-wise, virus-wise, and protein-wise records count information about the database (Fig. 5).

Discussion

ArVirInd is a first-of-its-kind knowledge base dedicated to antigenic proteins from arboviral strains isolated from India and neighboring countries (the Indian subcontinent). This database enlists sequences by year of collection/isolation which coincided with the year of the outbreak. ArVirInd knowledgebase allows users to search sequences by the year of collection/isolation and country of origin, which is a unique feature. We have carried out exhaustive literature reviews to trace the year of origin for each strain. For each sequence entry, we have carried out in silico antigenic characterization using bioinformatics tools. The summary of the findings is available in the database records for each entry. The user can also search by peptide against a record of 8,398 epitopes covering more than 400 amino acid sequences.

The online database also provides the user with an analyses tool. The EpiMapAr tool helps the user in understanding the epitope conservancy between strains (virus-wise) included in the database. This gives the user the choice of “virus” and “antigenic protein”. As an output, it displays all the available sequences in the database for the selected category as below:

• Yellow highlighted sequence pattern represent Predicted B-cell Epitope (Kolaskar method)

• Green highlighted sequence pattern represent Confirmed Epitope (experimentally known).

• Purple highlighted sequence pattern represent Variability (sequence with mutation/s).

The dashboard provides the user with a summary of the datasets. Users can also submit sequences to the database through the “SeqKosh” sequence submission tool.

Dedicated databases exist for epitopes like the Bcipep, AbDb (Ferdous & Martin, 2018; Dunbar et al., 2014) and viruses such as the Ebola virus database (Swetha et al., 2016), or VIPR (Pickett et al., 2012). However, these databases provide specific information about epitopes (known) or pathogens, but none are the repository of strains belonging to specific geographical regions. Finding sequences by country of origin or year of outbreak/isolation from other databases remains an uphill task. We tried to overcome this by creating a database that will enlist sequence information from arboviral strains isolated in the Indian subcontinent region. ArVirInd is user-friendly and enables the user to search for arboviral antigenic proteins by country of origin and year of outbreak/strain isolation. This is a unique feature of ArVirInd. In the future, we will expand the database by including tick-borne viruses such as Kyasanur Forest Disease and Crimean-Congo hemorrhagic fever (CCHF) viruses as well.

Conclusions

This article presents the formulation of a database of antigenic proteins from arbovirus strains from the countries of the Indian subcontinent. We anticipate that this database will be maintained and constantly expanded with information added for new and emerging strains of arboviruses. We believe that the ArVirInd knowledge base will benefit researchers working in immuno-informatics, arboviral diagnostics, and vaccinology. ArVirInd has the potential to become an important source of information on arboviral proteins for researchers working in India as well as countries like Bhutan, Nepal, Maldives, Bangladesh, Sri Lanka, and Pakistan. The database will be updated and expanded periodically.

Supplemental Information