Phylogenetic relationships of aquatic birnaviruses based on deduced amino acid sequences of genome segment A cDNA

Abstract

Aquatic birnaviruses, such as infectious pancreatic necrosis virus (IPNV), cause serious diseases in a variety of fish species used worldwide in aquaculture and have also been isolated from a variety of healthy fish and shellfish species. These viruses exhibit a high degree of antigenic heterogeneity and variation in biological properties such as pathogenicity, host range, and temperature of replication. To better understand genetic and biological diversity among these viruses, the nucleotide and deduced amino acid sequences were determined from cDNA of the large open reading frame (ORF) of genome segment A of the 9 type strains of Serogroup A and 4 other representative strains of Serotype A1, the predominant serotype in the United States. In addition, nucleotide and deduced amino acid sequences were determined for the VP2 coding region of a variety of isolates representing 5 of the 9 serotypes. VP2 is the major outer capsid protein of aquatic birnaviruses. RT-PCR was used to amplify a 2904 bp cDNA fragment including all but a few bp of the large ORF of genome segment A or a 1611 bp fragment representing the entire VP2 coding region. Nucleotide and deduced amino acid sequences were determined from the PCR products. Pairwise comparisons were made among our data and 2 other aquatic birnavirus sequences previously published. Several hypervariable regions were identified within the large ORF. The most divergent pair of viruses exhibited a similarity of 80.1% in the deduced amino acid sequence encoded by the large ORF. Genomic relationships revealed in a phylogenetic tree constructed from comparison of the deduced amino acid sequences of the large ORF demonstrated that these viruses were clustered into several genogroups. Phylogenetic comparison of the deduced amino acid sequences of the VP2 coding region of 28 aquatic birnavirus isolates, including the type strains of all 9 serotypes, demonstrated 6 genogroups, some of which were comprised of several genotypes. The most divergent pair of viruses exhibited a similarity of 81.2% in the deduced amino acid sequence from the VP2 coding region. In contrast to previous studies of much shorter genomic sequences within the C-terminus-pVP2/NS junction coding region, these genogroups based on the entire large ORF or the VP2 coding region generally correlated with geographical origin and serological classification. Isolates from the major Canadian serotypes were more closely related to the European isolates than to isolates from the United States. KEY WORDS: Aquatic birnavirus · Infectious pancreatic necrosis virus · Genogroups · Phylogenetic relationships Resale or republication not permitted without written consent of the publisherDis Aquat Org 45: [89][90][91][92][93][94][95][96][97][98][99][100][101][102] 2001 implicated as the etiologic agents of disease in a variety of fish species important in fish farming and aquaculture worldwide. Different strains of aquatic birnaviruses infect different species of fish and cause different diseases, such as infectious pan...

Genotipificacion y relacion hospedador especifica del virus de la necrosis pancreatica infecciosa en Chile

“…La primera clasificación filogenética fue propuesta por Blake et al (2001), donde se describió la presencia de 6 genogrupos, compuestos por diferentes cepas de origen europeo, americano y asiático. Posteriormente, Nishizawa et al (2005) revelaron la existencia de un séptimo genogrupo integrado únicamente por cepas japonesas, y recientemente en Australia se aisló un nuevo Aquabirnavirus desde trucha arcoíris, que fue clasificado en un octavo genogrupo (McCowan et al, 2015;Mohr et al, 2015).…”

“…Las secuencias obtenidas se compararon y clasificaron en base a cepas de referencia de birnavirus acuáticos chilenos y extranjeros disponibles en Genbank y reportadas en publicaciones científicas (i.e., Blake et al, 2001;Eissler et al, 2011;Mutoloki & Evensen, 2011;Calleja et al, 2012;Ruane et al, 2015;Jorquera et al, 2016). Además se incluyen algunas muestras utilizadas también en el trabajo realizado por Tapia et al (2015) (ver Tabla 1).…”

“…En la Figura 1 se observan dos subgrupos dentro del Genogrupo 5, el 5A que incluyó los virus reportados para Chile, en este y otros trabajos anteriores y el 5B que agrupó cepas de origen australiano. En el Genogrupo 1 se distinguen a su vez tres subgrupos, uno correspondiente a los genotipos 1-3 del análisis filogenético mostrado por Blake et al (2001), otro solamente compuesto por el genotipo 4 y un último compuesto únicamente por los virus chilenos de este estudio y los reportados en trabajos previos. Este subgrupo también fue reportado por Tapia et al (2015), por lo que sugerimos que este clúster sea considerado como un genotipo chileno dentro del Genogrupo 1.…”

Aquabirnavirus polyploidy: a new strategy to modulate virulence?

“…The larger ORF encodes a polyprotein that, through co-translational proteolytic processing, yields pVP2 (the precursor of the VP2 capsid polypeptide), VP3 and VP4 polypeptides. VP2, the capsid protein, is related to virulence (Heppell et al, 1995;Blake et al, 2001;Santi et al, 2004). VP3 is a modular, self-oligomerizing protein that interacts with dsRNA and VP1, thus suggesting its involvement in RNA replication and genome packaging.…”

Detection and Genetic Analysis of Aquabirnaviruses in Subclinically Infected Aquarium Fish

“…2 The nested RT-PCR-positive samples were detected from 3 different clinically healthy marine fish species imported from Japan. The fact that virus was not isolated from nested RT-PCR-positive fish samples may be due to the presence of a low virus titer in the carrier fish.…”