Infectious hypodermal and hematopoietic necrosis virus from Brazil: Sequencing, comparative analysis and PCR detection

• Published in: Virus research 2014-08, Vol.189, p.136-146
• Main Authors: Silva, Douglas C.D., Nunes, Allan R.D., Teixeira, Dárlio I.A., Lima, João Paulo M.S., Lanza, Daniel C.F.
• Format: Article
• Language: English
• Subjects: 3' Untranslated Regions; 5' Untranslated Regions; Amino Acid Sequence; Animals; Base Sequence; Brazil; Brevidensovirus; Cluster Analysis; Densovirinae - classification; Densovirinae - genetics; Densovirinae - isolation & purification; DNA, Viral - chemistry; DNA, Viral - genetics; Gene Order; Genome, Viral; Infectious hypodermal and hematopoietic necrosis virus; Molecular Sequence Data; Nucleic Acid Conformation; Penaeus stitlirostris densovirus; Phylogeny; Sequence Analysis, DNA; Sequence Homology; Shrimp nanism; Viral Proteins - genetics; White Spot Syndrome
• ISSN: 0168-1702; 1872-7492
• DOI: 10.1016/j.virusres.2014.05.008

•A 3739 nucleotide fragment of a Brazilian IHHNV detected in Litopenaeus vannamei was sequenced.•Brazilian IHHNV is very similar to Hawaii isolate, and belongs to a group of viruses that produce infection.•Polymorphic sites and conserved regions in IHHNV genome were identified.•Untranslated regions of IHHNV can form hairpins that would be involved in mechanisms of virus replication.•A semi-nested PCR using primers that anneal in sites that show low polymorphism is proposed to IHHNV detection. A 3739 nucleotide fragment of Infectious hypodermal and hematopoietic necrosis virus (IHHNV) from Brazil was amplified and sequenced. This fragment contains the entire coding sequences of viral proteins, the full 3′ untranslated region (3′UTR) and a partial sequence of 5′ untranslated region (5′UTR). The genome organization of IHHNV revealed the three typical major coding domains: a left ORF1 of 2001bp that codes NS1, a left ORF2 (NS2) of 1091bp that codes NS2 and a right ORF3 of 990bp that codes VP. Nucleotide and amino acid sequences of the three viral proteins were compared with putative amino acid sequences of viruses reported from different regions. Comparisons among genomes from different geographic locations reveal 31 nucleotide regions that are 100% similar, distributed throughout the genome. An analysis of secondary structure of UTR regions, revealed regions with high probability to form hairpins, that may be involved in mechanisms of viral replication. Additionally, a maximum likelihood analysis indicates that Brazilian IHHNV belongs to lineage III, in the infectious IHHNV group, and is clustered with IHHNV isolates from Hawaii, China, Taiwan, Vietnam and South Korea. A new nested PCR targeting conserved nucleotide regions is proposed to detect IHHNV.