Image: Darryl Leja, NHGRI

New method developed for sequencing the complete genome of ISAV

A team of scientists has created an amplicon-based sequencing protocol that enables rapid study in cases of infectious salmon anaemia outbreaks


In a new published study, researchers from the Norwegian Veterinary Institute and the Faroe Islands Veterinary and Food Authority developed an amplicon-based sequencing protocol that sequenced the entire genome of the infectious salmon anaemia (ISA) virus.

This new methodology allows for more precise and detailed sequencing of the virus genome, which facilitates the identification of specific variants and the monitoring of the evolution of the pathogen in salmon populations.

The method consists of 80 ISAV-specific primers covering 92% of the virus genome and was designed for use on an Illumina MiSeq platform. Sequencing accuracy was analyzed by comparing this method with previously published Sanger sequences.

“The sequences obtained were almost identical to those obtained through Sanger sequencing, which demonstrates that the sequences produced through this amplicon sequencing protocol had acceptable precision,” the experts detailed.

Helps identify mutations

In addition to offering greater resolution compared to traditional techniques, according to the authors this new approach not only allows a better understanding of the genetic structure of ISAV, but also helps scientists identify mutations that could affect the virulence of the virus and the effectiveness of vaccines.

The technique was tested for the sequencing of the genome of 12 different virus isolates obtained from an outbreak in northern Norway, finding that during the outbreak a rearrangement of segments occurred among some of the isolates.

According to what the scientists stated, complete genome sequencing allows all segments of the ISAV to be analyzed, making virus tracking more robust to rearrangements of a single segment and offers the possibility of evaluating the agreement of the information obtained for each segment individually.

“The comparisons in this study demonstrate that the ISAV whole genome sequencing method can be an important contribution to the characterisation of the outbreak and the epidemiological dynamics of this virus,” the experts concluded.

Read the full study titled “Development and application of a whole genome amplicon sequencing method for infectious salmon anemia virus (ISAV),” here.