Molecular characteristic and pathogenicity analysis of a virulent recombinant avain infectious bronchitis virus isolated in China

Abstract

A virulent infectious bronchitis virus (IBV), designated as CK/CH/GD/QY16 (referred as QY16), was isolated from a diseased chicken farm in Guangdong province, China, in 2016. The complete genome of the strain was sequenced and analyzed. The results show that the genome of QY16 consists of 27,670 nucleotides, excluding poly (A) tail, and that its genome organization is 5' UTR-1a-1b-S-3a-3b-E-M-4b-4c-5a-5b-N-6b-3' UTR-poly (A) tail. Sequence comparison among QY16 and other IBV strains was conducted and its results demonstrate that the S1 gene of QY16 has the highest nucleotide sequence identity with that of 4/91, and the other part of its genome is highly similar to that of YX10. The results of the phylogenic analysis show that the entire genome of QY16 and most of the QY16 genes are located in the same cluster as those of YX10, except for the S1 gene which is located in the same cluster with that of 4/91. It has been further confirmed by the RDP and SimPlot analysis that QY16 is a recombinant strain deriving from YX10 (as the major parental sequence) and 4/91 (as the minor parental sequence), and that the recombination occurs in a region which includes the 3'-terminal 1b sequence (85 nt) and the 5'-terminal S1 protein gene sequence (1,466 nt). The results of the vaccination-challenge test suggest that QY16 is a nephropathogenic strain of IBV and that the vaccine strains-H120 and 4/91-cannot provide effective protection against it. These results indicate that the continuing evolution of IBV strains by genetic drift and genetic recombination may lead to IBV outbreaks even among the vaccinated chickens in China.

Genetic and biological characteristics of four novel recombinant avian infectious bronchitis viruses isolated in China

“…It has been reported that the side effects of the 4/91 vaccine might provide the basis for recombination with other strains. This phenomenon has been shown by several studies which have traced the emergence of many novel IBV strains to recombination events between the 4/91 vaccine and field strains (Feng et al, 2018;Han et al, 2017;Jiang et al, 2017Jiang et al, , 2018Liu et al, 2013;Mo et al, 2013;Ovchinnikova et al, 2011;Zhang et al, 2015Zhang et al, , 2016Zhou et al, 2017) in cases where the 4/91 vaccine strain could not provide effective protection against the field strains , leading to coinfection of the vaccine and field strains in the same chickens and ultimately resulting in recombination. In this study, we performed complete genome sequence analysis of strains I0718/17, I0722/17, I0724/17, and I0737/17 and confirmed the occurrence of recombination events at the 5′ ends of the S1 gene between a 4/91-like virus (GI-13 lineage) and a YX10-like virus (GI-19) (Xu et al, 2018), which contributed to the emergence of the IBV strains.…”

A novel low virulent respiratory infectious bronchitis virus originating from the recombination of QX, TW and 4/91 genotype strains in China

“…By sequence comparison, phylogenetic analysis, and recombination analysis, JX17 was shown to derive from QX strain, TW strain and 4/91 strain. JX17 has the highest nucleotide identity of 95.94% with YX10 strain, which was isolated in Zhejiang province, China, in 2010 (Feng et al, 2015) and reported to be involved in recombinant variants in recent years, such as SAIBK2 Jiang et al, 2017;Wu et al, 2016) and QY16 (Feng et al, 2018). TW and 4/91 strains are the minor parent strains of JX17.…”

“…In recent years, the recombinant strains of QX and 4/91 genotype emerged. One typical strain referred as CK/CH/GD/QY16 was isolated in 2016, and then appeared with high frequency (Feng et al, 2018). Additionally, the recombinant viruses involving widespread TW type strains, such as the recombinant of QX and TW I genotype, also began to accumulate .…”

The coronavirus proofreading exoribonuclease mediates extensive viral recombination

“…Coronaviruses (CoVs) are a family of positive-sense, single-stranded RNA viruses with 41 genomes ranging in size between 26 and 32 kb ( Figure 1A and 3A). CoV recombination 42 has been reported to be associated with increased spread, severe disease, and vaccine 43 failure in livestock CoV epidemics (Chen et al, 2017;Feng et al, 2018) and proposed 44 to be important in the emergence of human CoVs including the beta-CoVs (b-CoVs) 45 severe acute respiratory syndrome coronavirus (SARS-CoV) (Anthony et al, 2017;46 are subsequently translated into structural and accessory proteins (Dufour et al, 2011;70 Kirchdoerfer and Ward, 2019; Subissi et al, 2014;Weiss et al, 1994). CoV replication 71 also generates defective viral genomes (DVGs) that contain multiple deletions of 72 genomic sequence.…”