Current Advances on Virus Discovery and Diagnostic Role of Viral Metagenomics in Aquatic Organisms

Abstract

The global expansion of the aquaculture industry has brought with it a corresponding increase of novel viruses infecting different aquatic organisms. These emerging viral pathogens have proved to be a challenge to the use of traditional cell-cultures and immunoassays for identification of new viruses especially in situations where the novel viruses are unculturable and no antibodies exist for their identification. Viral metagenomics has the potential to identify novel viruses without prior knowledge of their genomic sequence data and may provide a solution for the study of unculturable viruses. This review provides a synopsis on the contribution of viral metagenomics to the discovery of viruses infecting different aquatic organisms as well as its potential role in viral diagnostics. High throughput Next Generation sequencing (NGS) and library construction used in metagenomic projects have simplified the task of generating complete viral genomes unlike the challenge faced in traditional methods that use multiple primers targeted at different segments and VPs to generate the entire genome of a novel virus. In terms of diagnostics, studies carried out this far show that viral metagenomics has the potential to serve as a multifaceted tool able to study and identify etiological agents of single infections, co-infections, tissue tropism, profiling viral infections of different aquatic organisms, epidemiological monitoring of disease prevalence, evolutionary phylogenetic analyses, and the study of genomic diversity in quasispecies viruses. With sequencing technologies and bioinformatics analytical tools becoming cheaper and easier, we anticipate that metagenomics will soon become a routine tool for the discovery, study, and identification of novel pathogens including viruses to enable timely disease control for emerging diseases in aquaculture.

Viruses in the Built Environment (VIBE) meeting report

“…However, the infectivity of a virus in a well-defined laboratory assay setting may not correlate to dynamic real-world settings with fluctuating environmental conditions, chemical microenvironments, and host sensitivities. Furthermore, the appropriate host of the virus may not be known, and some viruses have proven to be unculturable or difficult to culture even in cases where the host is known [100][101][102]. As a result of these challenges, several culture-independent methods for evaluating viral infectivity have been proposed, typically using a measure of the integrity of one or more parts of the virus as a proxy for the infectivity of the virus as a whole [103][104][105].…”

Identification of a piscine reovirus-related pathogen in proliferative darkening syndrome (PDS) infected brown trout (Salmo trutta fario) using a next-generation technology detection pipeline

“…As a certain proportion of sequences generated by NGS approaches remain uncharacterized because no similar sequences are available from gene banks, possible causatives can be overlooked. The verification of a relation between found pathogen and a specific disease can also be a difficult challenge, however the application of next-generation sequencing combined with bioinformatics approaches unraveled a large number of previously unknown pathogens of aquatic organisms and have significantly accelerated the ability to identify novel viruses of fish [ 46 ].…”

Current Advances in Functional Genomics in Aquaculture

“…In ish, viruses discovered using metagenomics include circoviruses from common bream [34] and European eel [35], posavirus [36] and seadornavirus [37] from freshwater carp and totivirus from golden shiner. As shown in our recent study [9], more than 20 novel ish pathogenic viruses have been identiied using metagenomics in the last 4 years, which is more than the number identiied using traditional diagnostic tools in the last 5 decades, clearly showing the rapid rate at which metagenomics has accelerated our ability to identify novel pathogens compared with traditional diagnostic methods.…”

“…Metagenomics analyses have the capacity to sequence all nucleic acids present in a sample at once thereby generating a vast array of data that requires computational analyses for interpretation [20,21]. As pointed out in our previous studies [9,10], it has the advantage of identifying co-infections and in the case of viral pathogens, it has the capacity to generate all variable proteins that form complete virions thereby permiting comparative phylogenetic analyses with other viruses present in public databases. Moreover, it is a proactive diagnostic tool able to identify novel pathogens before they cause outbreaks unlike the reactive traditional diagnostic tools in which etiological agents are only identiied after causing disease outbreaks reaching epidemic proportions [21].…”

“…These omics technologies have not only accelerated whole genome sequencing projects of diferent aquatic organisms [7,8], but they also have the capacity to unravel the sequences of entire genomes without prior knowledge of the genes to be sequenced thereby enhancing the discovery and annotation of novel genes in non-model species. And as shown from recent studies, their applications in aquaculture have accelerated our ability to identify emerging pathogens [9], monitor the microbiomes of diferent aquatic environments [10], develop nutritional diets with less side efects [11,12] and understand the cellular networks that regulate diferent biological processes in aquatic organisms [13][14][15]. It is evident from studies carried out this far that an integrated use of different omics technologies is bound to improve our production systems in aquaculture [10,12,[16][17][18].…”