Analysis of new isolates reveals new genome organization and a hypervariable region in infectious myonecrosis virus (IMNV)

• Additional sequences revealed that IMNV genome has at least 8226 bp and not 7561 bp.
• These additional sequences affect the sizes predicted for 5′ UTR, 3′ UTR and ORF1.
• A polymorphism map based in the genome alignment of seven sequences reveals a hypervariable region in IMNV genome.
• The hypervariable region coincides with the region that encodes virion protrusions.

Infectious myonecrosis virus (IMNV) has been the cause of many losses in shrimp farming since 2002, when the first myonecrosis outbreak was reported at Brazilian's northeast coast. Two additional genomes of Brazilian IMNV isolates collected in 2009 and 2013 were sequenced and analyzed in the present study. The sequencing revealed extra 643 bp and 22 bp, at 5′ and 3′ ends of IMNV genome respectively, confirming that its actual size is at least 8226 bp long. Considering these additional sequences in genome extremities, ORF1 can starts at nt 470, encoding a 1708 aa polyprotein. Computational predictions reveal two stem loops and two pseudoknots in the 5′ end and a putative stem loop and a slippery motif located at 3′ end, indicating that these regions can be involved in the start and termination of translation. Through a careful phylogenetic analysis, a higher genetic variability among Brazilian isolates could be observed, comparing with Indonesian IMNV isolates. It was also observed that the most variable region of IMNV genome is located in the first half of ORF1, coinciding with a region which probably encodes the capsid protrusions. The results presented here are a starting point to elucidate the viral's translational regulation and the mechanisms involved in virulence.