Genetic characterization of South American infectious bursal disease virus reveals the existence of a distinct worldwide-spread genetic lineage

Abstract

Infectious bursal disease virus (IBDV) is one of the most concerning health problems for world poultry production. IBDVs comprise four well-defined evolutionary lineages known as classic (c), classic attenuated (ca), variant (va) and very virulent (vv) strains. Here, we characterized IBDVs from South America by the genetic analysis of both segments of the viral genome. Viruses belonging to c, ca and vv strains were unambiguously classified by the presence of molecular markers and phylogenetic analysis of the hypervariable region of the vp2 gene. Notably, the majority of the characterized viruses (9 out of 15) could not be accurately assigned to any of the previously described strains and were then denoted as distinct (d) IBDVs. These dIBDVs constitute an independent evolutionary lineage that also comprises field IBDVs from America, Europe and Asia. The hypervariable VP2 sequence of dIBDVs has a unique and conserved molecular signature (272T, 289P, 290I and 296F) that is a diagnostic character for classification. A discriminant analysis of principal components (DAPC) also identified the dIBDVs as a cluster of genetically related viruses separated from the typical strains. DAPC and genetic distance estimation indicated that the dIBDVs are one of the most genetically divergent IBDV lineages. The vp1 gene of the dIBDVs has non-vvIBDV markers and unique nucleotide and amino acid features that support their divergence in both genomic segments. The present study suggests that the dIBDVs comprise a neglected, highly divergent lineage that has been circulating in world poultry production since the early time of IBDV emergence.

Development of an RT-qPCR assay for the specific detection of a distinct genetic lineage of the infectious bursal disease virus

“…Multiple sequence alignments were carried out with most of the hvVP2 sequences available in the GenBank database (n = 955) using the MUSCLE algorithm implemented in MEGA 5.0 (Tamura et al, 2011). The dIBDV sequences were identified by phylogenetic clustering and amino acid markers (T272, P289, I290 and F296) following Hernández et al (2015). Based on the nucleotide variants linked to the dIBDVs, specific primers and TaqMan-minor groove binding (TaqMan-MGB) probe were designed and synthesized by IDT DNA (Coralville, IA, USA) and Applied Biosystems (Foster City, CA, USA), respectively (Table 1).…”

“…Twenty Uruguayan dIBDV outbreaks were employed to test the clinical sensitivity of the developed RT-qPCR assay (Table 2). Molecular diagnosis of the strains were performed by quantitative PCR (Tomás et al, 2012), and assigned to the dIBDV lineage by hvVP2 sequence analysis (Hernández et al, 2015).…”

“…Recently, we described the existence of a worldwide spread genetic lineage denoted as distinct (d) IBDV (Hernández et al, 2015). This lineage is resolved in a well-supported clade and has a unique four-aminoacid signature (T272, P289, I290, F296).…”

“…Most isolates that are now classified as dIBDV were initially considered atypical classic or variant strains that harboured unique nucleotide and amino acid changes as a consequence of local differentiation (Kwon et al, 2000;Ikuta et al, 2001;Domanska et al, 2004;Remorini et al, 2006;Jackwood & Sommer-Wagner, 2007;Ojkic et al, 2007). Some dIBDV isolates have exhibited mild clinical signs and antigenic differences (Ikuta et al, 2001;Domanska et al, 2004;Vera et al, 2015) but further phenotypic studies are needed to understand the epidemiological and sanitary relevance of this lineage that contains part of the genetic variability of the virus (Hernández et al, 2015).…”

“…Global surveillance and research programmes require reliable assays for the diagnosis of IBDV variants to understand virus spreading and evolution, and to provide strain-specific treatments (Van den Berg et al, 2000). Strain classification can be performed by the phylogenetic analysis of the VP2 hypervariable region (hvVP2), which recovers all IBDV strains (cv, ca, va, vv and d) (Martin et al, 2007;Wu et al, 2007;Xia et al, 2008;Kim et al, 2010;Hernández et al, 2015). However, this methodology is time-consuming, expensive and requires trained staff, not being suitable to be widely applied in clinical settings.…”