Novel genotype of infectious bronchitis virus isolated in China

Abstract

A B S T R A C T Recombination events are known to contribute to the emergence of novel infectious bronchitis virus (IBV) genotypes. In this study, we carried out detailed phylogenetic analysis and sequence comparisons based on 74 complete nucleotide sequences of the IBV S1 gene, including strain I0636/16 and 73 representative sequences from each genotype and lineage. The results showed that strain I0636/16 represented a novel genotype, designated as lineage 1 within genotype VII (GVII-1). Further comparative genomic analysis revealed at least two recombination sites that replaced the spike gene in a lineage 18 within genotype I (GI-18)-like virus with an asyet-unidentified sequence, likely derived from another IBV strain, resulting a novel serotype with a lower affinity to the respiratory tract in chickens. To the best of our knowledge, this provides the first evidence for recombination leading to replacement of the complete spike gene and the emergence of a novel genotype/serotype with a lower affinity to the respiratory tract in chickens comparing to one of its parental virus ck/CH/LGX/ 111119. These results emphasize the importance of limiting exposure to novel IBVs that may serve as a source of genetic material for emerging viruses, as well as the importance of IBV surveillance in chicken flocks.

Genetic, antigenic and pathogenic characterization of avian coronaviruses isolated from pheasants (Phasianus colchicus) in China

“…The S1 gene sequences of 213 reference AvCoV strains were used for phylogenetic analysis, together with those of the two new isolates I0623/17 and I0710/17. The 213 viruses included 199 reference IBV strains reported by Valastro et al (2016), three IBV GI-28 strains , three IBV GI-29 strains (Jiang et al, 2018), two IBV GVII-1 strains (Ma et al, 2019), two additional IBV GI-19 strains, ck/CH/LDL/091022 (LDL/091022) and ck/CH/LJL/140734 (LJL/140734) which were used the virus-neutralization (VN) test, three TCoVs and one guinea fowl CoV (Brown et al, 2016).…”

“…5A). Replication of the challenge viruses was also determined at 5 dpi in the tracheas, kidneys, lungs, proventriculus, and cecal tonsils from chickens and pheasants (Ma et al, 2019) (Fig. 5B).…”

Molecular and biological characteristics of the infectious bronchitis virus TC07-2/GVI-1 lineage isolated in China

“…Phylogenetic trees were constructed using a dataset, including our six IBV strains and 70 reference strains (including the TC07-2 strain) representing the established genotypes and lineages Jiang et al, 2017;Ma et al, 2019;Valastro et al, 2016) (Supplementary Table 1) using Mega version 6.0 software (http://www. megasoftware.net/).…”

“…Recently, a more definitive phylogeny-based classification system has been used and six genotypes which included 32 lineages were originally distinguished by Valastro et al (2016). Next new lineages GI-28 and GI-29 of GI genotype and even one new genotype (GVII) were recently added Jiang et al, 2017;Ma et al, 2019). This system provides reliable reference sequences and lineage prototypes to guide viral classification.…”

“…This system provides reliable reference sequences and lineage prototypes to guide viral classification. Based on the criteria used in this classification system, at least 16 lineages of IBV strains, including the GI-1 (Mass) (Liu et al, 2006), GI-3 (Valastro et al, 2016), GI-4 (Valastro et al, 2016), GI-5 (Valastro et al, 2016), GI-6 (Valastro et al, 2016), GI-7 (TW I and TW II) (Ma et al, 2012;Xu et al, 2016), GI-9 (Ark) , GI-13 (793/B, CR88, 4/91 or 1/96) (Han et al, 2011), GI-16 (ck/CH/LDL/97I or Q1) (Liu et al, 2007;Yu et al, 2001), GI-18 (Valastro et al, 2016), GI-19 (LX4 or QX) , GI-22 (ck/CH/LSC/99I) (Liu et al, 2006), GI-28 , GI-29 , GVI-1 (TC07-2) (Li et al, 2010), and GVII-1 (Ma et al, 2019), as well as a number of recombinants have been isolated in China . Although the majority of such variants cause only transitory problems, which subsequently resolve or remain confined within a specific geographical region, there are some variants that are able to persist and spread to new regions where they continue to cause disease (de Wit et al, 2011).…”