Molecular tracing of aquatic viruses: where epidemiology needs to meet genomics

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Background

Aquatic viruses constitute major threats for sustainable aquaculture production of both fish and shellfish worldwide. Thus, considerable resources are constantly invested in controlling the spread of viral pathogens in aquaculture. These control strategies have been primarily designed according to general biosecurity rules, mainly because disease-specific transmission patterns are still poorly understood. This leads to compromised efficiency of preventive interventions. A variety of pathways for the spread of pathogens between aquaculture stocks have been suggested, e.g. horizontal and vertical transmission, passive drift in the water, or commercial trade of live animals. These different routes of propagation are prone to facilitate the quick mix of isolates from different geographic origins, which subsequently co-occur within populations. In this particular context, analysis of outbreaks requires typing methods that offer a high level of strain discrimination. Among these, whole genome sequencing not only enables to resolve micro-evolutionary distances, but it also has the power to discover new and rare variations, including polymorphisms that arise during an outbreak or that evolve in vivo during an infection. Whole genome sequencing may as well allow identification of areas of increased divergence (i.e. subjected to selective pressures and/or to faster evolution), which in turn may prove valuable for more accurate molecular epidemiological investigations. Therefore, comprehensive studies integrating epidemiological, phylogenetic and genomic analyses should be encouraged in order to gain new knowledge on the viral spreading strategies within aquatic environments. This, however, requires access to high quality data on representative isolates, including whole genome sequences together with reliable spatiotemporal epidemiological data.
In this context, all contributions describing new methods for the acquisition of such high-quality data and their application to identify important factors affecting the spread of viruses in aquatic environments, to construct scenario simulation models in view of assessing the effects of different control strategies, or to study the factors (from the environment, the host and the virus) that drive the evolution of viruses in aquatic environments, are relevant to this Frontiers topic. The purpose of this Frontiers topic is to gather up-to-date information on the recently developed molecular, genetic or computer tools that contribute to these goals. Studies and/or reviews comparing different virus models are particularly welcome.

Important note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.

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