A highly pathogenic GI-19 lineage infectious bronchitis virus originated from multiple recombination events with broad tissue tropism

Abstract

In the present study, an IBV strain I0305/19 was isolated from a diseased commercial broiler flock in 2019 in China with high morbidity and mortality. The isolate I0305/19 was clustered together with viruses in sublineage D of GI-19 lineage on the basis of the complete S1 sequence analysis. Isolate I0305/19 and other GI-19 viruses isolated in China have the amino acid sequence MIA at positions 110-112 in the S protein. Further analysis based on the complete genomic sequence showed that the isolate emerged through at least four recombination events between GI-19 ck/CH/LJS/120848-and GI-13 4/91-like strains, in which the S gene was found to be similar to that of the GI-19 ck/CH/LJS/120848-like strain. Pathological assessment showed the isolate was a nephropathogenic IBV strain that caused high morbidity of 100 % and mortality of 80 % in 1-day-old specificpathogen-free (SPF) chicks. The isolate I0305/19 exhibited broader tropisms in different tissues, including tracheas, lungs, bursa of Fabricius, spleen, liver, kidneys, proventriculus, small intestines, large intestines, cecum, and cecal tonsils. Furthermore, subpopulations of the virus were found in tissues of infected chickens; this finding is important in understanding how the virulent IBV strains can potentially replicate and evolve to cause disease. This information is also valuable for understanding the mechanisms of replication and evolution of other coronaviruses such as the newly emerged SARS-CoV-2.

The taxonomy, host range and pathogenicity of coronaviruses and other viruses in the Nidovirales order

“…Infectious bronchitis virus (IBV) is the prototype virus of Igacovirus subgenus, and various serotypes of IBV have been identified. IBV is the causal agent of infectious bronchitis that is prevalent worldwide and primarily infects the upper respiratory tract, but several IBV serotypes also infect kidney, digestive tract and reproductive system (Reddy et al 2015 ; Hou et al 2020 ). The genome of IBV contains at least 10 ORFs characterized by the following organization: 5’UTR-ORF1a/1b-S-3a-3b-E-M-5a-5b-N-3’UTR.…”

Detection and genetic characterization of novel infectious bronchitis viruses from recent outbreaks in broiler and layer chicken flocks in southern China, 2021

“…The emerging IBV strain HH09 in this study was found to be generated through a recombination events between CK/CH/SCDY2003-2 and I0305/19. Of note, I0305/19 has been reported to be a highly pathogenic strain and has broader tissue tropism, including both the respiratory tissues and digestive tract tissues ( Hou et al, 2020 ).…”

“…Therefore, the mutation and recombination of the S1 gene are crucial for the emergence of new IBV genotypes and serotypes. According to a classification scheme based on the S1 sequence, IBV strains have been classified into 36 lineages in 7 genotypes ( Valastro et al, 2016 ; Jiang et al, 2017 ; Ma et al, 2019 ; Hou et al, 2020 ; Molenaar et al, 2020 ). Due to this large number of serotypes and genotypes, IBV prevention remains to be a challenge.…”

Complete Genome Sequence of Infectious Bronchitis Virus Strain JP/KH/64, Isolated in Japan

“…1 ). Because the JP-I genotype has been reported in China, Taiwan, and Japan ( 12 , 13 ), this information about the JP/KH/64 strain might be important for the understanding of IBV evolution in Eastern Asian countries.…”