Navigating the Landscape: A Comprehensive Review of Current Virus Databases

Abstract

Viruses are abundant and diverse entities that have important roles in public health, ecology, and agriculture. The identification and surveillance of viruses rely on an understanding of their genome organization, sequences, and replication strategy. Despite technological advancements in sequencing methods, our current understanding of virus diversity remains incomplete, highlighting the need to explore undiscovered viruses. Virus databases play a crucial role in providing access to sequences, annotations and other metadata, and analysis tools for studying viruses. However, there has not been a comprehensive review of virus databases in the last five years. This study aimed to fill this gap by identifying 24 active virus databases and included an extensive evaluation of their content, functionality and compliance with the FAIR principles. In this study, we thoroughly assessed the search capabilities of five database catalogs, which serve as comprehensive repositories housing a diverse array of databases and offering essential metadata. Moreover, we conducted a comprehensive review of different types of errors, encompassing taxonomy, names, missing information, sequences, sequence orientation, and chimeric sequences, with the intention of empowering users to effectively tackle these challenges. We expect this review to aid users in selecting suitable virus databases and other resources, and to help databases in error management and improve their adherence to the FAIR principles. The databases listed here represent the current knowledge of viruses and will help aid users find databases of interest based on content, functionality, and scope. The use of virus databases is integral to gaining new insights into the biology, evolution, and transmission of viruses, and developing new strategies to manage virus outbreaks and preserve global health.

Open Science at PLOS Pathogens

“…The pathogens community has, and continues to, demonstrate its commitment to cooperative Open Science to improve and enhance science. One example would be the many community-curated virus databases used in pathogens research (see [ 17 ] for a review). A number of organizations, including the NIH HIV Reagent Program [ 18 ], the Biodefense & Emerging Infections Resources [ 19 ], the International Reagent Resource [ 20 ], the National Institute for Biological Standards and Control [ 21 ], and International Human Papillomavirus Reference Center [ 22 ], all freely provide reagents and standards that are vital to the pursuit of pathogen-focused research and have been provided by researchers in the field.…”