S1 gene-based phylogeny of infectious bronchitis virus: An attempt to harmonize virus classification

Abstract

Infectious bronchitis virus (IBV) is the causative agent of a highly contagious disease that results in severe economic losses to the global poultry industry. The virus exists in a wide variety of genetically distinct viral types, and both phylogenetic analysis and measures of pairwise similarity among nucleotide or amino acid sequences have been used to classify IBV strains. However, there is currently no consensus on the method by which IBV sequences should be compared, and heterogeneous genetic group designations that are inconsistent with phylogenetic history have been adopted, leading to the confusing coexistence of multiple genotyping schemes. Herein, we propose a simple and repeatable phylogeny-based classification system combined with an unambiguous and rationale lineage nomenclature for the assignment of IBV strains. By using complete nucleotide sequences of the S1 gene we determined the phylogenetic structure of IBV, which in turn allowed us to define 6 genotypes that together comprise 32 distinct viral lineages and a number of inter-lineage recombinants. Because of extensive rate variation among IBVs, we suggest that the inference of phylogenetic relationships alone represents a more appropriate criterion for sequence classification than pairwise sequence comparisons. The adoption of an internationally accepted viral nomenclature is crucial for future studies of IBV epidemiology and evolution, and the classification scheme presented here can be updated and revised novel S1 sequences should become available.

Phylogeny and S1 Gene Variation of Infectious Bronchitis Virus Detected in Broilers and Layers in Turkey

“…The reference sequence set for IBV classification obtained from Valastro and others (30) was used to reconstruct the topology of the S1 sequences generated in this study. The phylogenetic tree was inferred using the ML method available in PhyML 3.0 (10) incorporating a GTR model of nucleotide substitution with a gamma distribution of among-site rate variation (with four rate categories, C4) and a SPR branch-swapping search procedure.…”

“…Prior to phylogenetic analysis, all hypervariable and potentially poorly aligned regions were removed using the Gblocks program (http://molevol. cmima.csic.es/castresana/Gblocks.html) (5) as previously described by Valastro and others (30). Nodal supports in the PhyML analysis were assessed using Shimodaira-Hasegawa-like branch supports (10).…”

Phylogenetic analysis of avian infectious bronchitis virus isolates from Morocco: a retrospective study (1983 to 2014)

“…An ML phylogenetic tree was reconstructed, selecting as a substitution model that with the lowest Akaike information criterion: the Tamura 3-parameter model with gamma-distributed rates among sites. A reference sequence was selected for each known (sub)lineage of IBV as recently described (Valastro et al, 2016). Bootstrap values above 50 were labeled on major tree branches for reference to assign confidence levels to branches.…”

“…Valastro et al indeed recently recommended using the full S gene sequence to define IBV genotypes (Valastro et al, 2016), which, however, is not as straightforward to do in very resource-limited environments such as Moroccan laboratories. The heterogeneity between the numbers of samples per year is a bias in our retrospective study but is due to the small number of available archive strains in our laboratory.…”

Serotype, antigenicity, and pathogenicity of a naturally recombinant TW I genotype infectious bronchitis coronavirus in China

“…A large number of IBV genotypes and variants have been isolated in China in recent years (Han et al, 2011), among which two genotypes, the LX4 and ck/CH/LDL/97I types (also known as QX-and Q1-like, respectively), were first isolated in China and subsequently have become widespread worldwide (Valastro et al, 2016). Among these IBV genotypes, the TW1 type was first isolated in 1992 in Taiwan, and it was considered to have a different genotype than all of the other IBVs (Wang and Tsai, 1996).…”