Abstract
Studies on the epidemiology of viral diseases in aquaculture have for a long time depended on isolation of viruses from infected aquatic organisms. The role of aquatic environments in the epidemiology of viral diseases in aquaculture has not been extensively expounded mainly because of the lack of appropriate tools for environmental studies on aquatic viruses. However, the upcoming of metagenomics analyses opens great avenues in which environmental samples can be used to study the epidemiology of viral diseases outside their host species. Hence, in this review I have shown that epidemiological factors that influence the composition of viruses in different aquatic environments include ecological factors, anthropogenic activities and stocking densities of cultured organisms based on environmental metagenomics studies carried out this far. Ballast water transportation and global trade of aquatic organisms are the most common virus dispersal process identified this far. In terms of disease control for outdoor aquaculture systems, baseline data on viruses found in different environments intended for aquaculture use can be obtained to enable the design of effective disease control strategies. And as such, high-risk areas having a high specter of pathogenic viruses can be identified as an early warning system. As for the control of viral diseases for indoor recirculation aquaculture systems (RAS), the most effective disinfection methods able to eliminate pathogenic viruses from water used in RAS can be identified. Overall, the synopsis I have put forth in this review shows that environmental samples can be used to study the epidemiology of viral diseases in aquaculture using viral metagenomics analysis as an overture for the design of rational disease control strategies.
Highlights
Viruses are the most abundant biological agents on the planet with the majority being found in the freshwater and marine water environments (Fuhrman, 1999; Edwards and Rohwer, 2005)
Viral metagenomics is a culture independent sequencing tool able to identify a large number of viral genomes from the same sample at the same time without prior knowledge of genomic sequences of the viruses to be identified (Handelsman, 2004; Bibby, 2013). It has been used for the identification of viruses in water samples collected from different ecosystems (Suttle, 2005, 2007; Djikeng et al, 2009; Kim et al, 2015), which creates the basis for studying viral pathogens from environmental samples outside their hosts
Red sea bream iridovirus (RISV) was detected in ballast water discharged in the Los Angeles harbor in North America by viral metagenomics surveys (Kim et al, 2016) and yet outbreaks of RSIV have mostly been reported in Asia (Jung and Oh, 2000; Wang et al, 2002; Kim et al, 2005; Imajoh et al, 2007; Jeong et al, 2008; Shinmoto et al, 2009) further demonstrating that ballast water plays a vital role in the spread of viral diseases in aquaculture
Summary
Viruses are the most abundant biological agents on the planet with the majority being found in the freshwater and marine water environments (Fuhrman, 1999; Edwards and Rohwer, 2005). Viral metagenomics is a culture independent sequencing tool able to identify a large number of viral genomes from the same sample at the same time without prior knowledge of genomic sequences of the viruses to be identified (Handelsman, 2004; Bibby, 2013) Since its discovery, it has been used for the identification of viruses in water samples collected from different ecosystems (Suttle, 2005, 2007; Djikeng et al, 2009; Kim et al, 2015), which creates the basis for studying viral pathogens from environmental samples outside their hosts. It brings into perspective the different viral dispersal mechanisms identified this far and highlights the factors that influence the persistence of viruses in different aquatic environments It provides insight on the potential use of viral metagenomics analyses in the design of effective disease control strategies in aquaculture
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