Contribution of Next-Generation Sequencing to Aquatic and Fish Virology

Abstract

The recent technological advances in nucleic acid sequencing, called next-generation sequencing (NGS), have revolutionized the field of genomics and have also influenced viral research. Aquatic viruses, and especially those infecting fish, have also greatly benefited from NGS technologies, which provide a huge amount of molecular information at a low cost in a relatively short period of time. Here, we review the use of the current high-throughput sequencing platforms with a special focus on the associated challenges (regarding sample preparation and bioinformatics) in their applications to the field of aquatic virology, especially for: (i) discovering novel viruses that may be associated with fish mortalities, (ii) elucidating the mechanisms of pathogenesis, and finally (iii) studying the molecular epidemiology of these pathogens.

Viral Detection: Past, Present, and Future

“…[120,121] In 2000, a company named Massively Parallel Signature Sequencing Lynx Therapeutics (later bought by Illumina) launched the first real NGS technology, but it was in 2004 that the Roche/454 sequencing technology, followed by Illumina/ Solexa and ABI/SOLiD, led to "second-generation sequencing (2G)." [122,126,127] Since new technologies are rapidly developing, a fifthgeneration sequencing will probably make its appearance making the numbering of generations difficult to follow. Fragmented DNA or cDNA was attached to linker/ adapter sequences to construct template libraries, which were then amplified on solid surfaces or beads and isolated in arrays or chip.…”

“…Fragmented DNA or cDNA was attached to linker/ adapter sequences to construct template libraries, which were then amplified on solid surfaces or beads and isolated in arrays or chip. [126,129] In order to identify viruses in a sample at present different approaches are used: 1) sequencing of small RNAs and 2) sequencing of long RNAs. Sequences of millions of short reads were generated without the need for an electrophoresis step, but with the requirement of bioinformatics software for the analysis.…”

“…[124,125] Both SMRT and the ONT apparatus are fast but with higher error rates at present than the 2G technology, making them less attractive. [122,126,127] Since new technologies are rapidly developing, a fifthgeneration sequencing will probably make its appearance making the numbering of generations difficult to follow. Thus, the more accurate term of HTS has emerged in the last couple of years.…”

“…[128] Since then a significant number of viruses have been identified. [126,129] In order to identify viruses in a sample at present different approaches are used: 1) sequencing of small RNAs and 2) sequencing of long RNAs. In the first case, total small RNAs, including viral ones, are sequenced.…”

A transcriptomic approach to study the effect of long-term starvation and diet composition on the expression of mitochondrial oxidative phosphorylation genes in gilthead sea bream (Sparus aurata)

“…A major advantage of next-generation sequencing (NGS) technology is the ability to provide a huge amount of gene expression data due to its high throughput [1–3]. Among NGS approaches, massive 454 sequencing has become a feasible method for increasing sequencing depth and coverage.…”