Genomics and pathogenesis of the avian coronavirus infectious bronchitis virus

Abstract

Infectious bronchitis virus (IBV) is a member of the family Coronaviridae, together with viruses such as SARS‐CoV, MERS‐CoV and SARS‐CoV‐2 (the causative agent of the COVID‐19 global pandemic). In this family of viruses, interspecies transmission has been reported, so understanding their pathobiology could lead to a better understanding of the emergence of new serotypes. IBV possesses a single‐stranded, non‐segmented RNA genome about 27.6 kb in length that encodes several non‐structural and structural proteins. Most functions of these proteins have been confirmed in IBV, but some other proposed functions have been based on research conducted on other members of the family Coronaviridae. IBV has variable tissue tropism depending on the strain, and can affect the respiratory, reproductive, or urinary tracts; however, IBV can also replicate in other organs. Additionally, the pathogenicity of IBV is also variable, with some strains causing only mild clinical signs, while infection with others results in high mortality rates in chickens. This paper extensively and comprehensibly reviews general aspects of coronaviruses and, more specifically, IBV, with emphasis on protein functions and pathogenesis. The pathogenicity of the Australian strains of IBV is also reviewed, describing the variability between the different groups of strains, from the classical to the novel and recombinant strains. Reverse genetic systems, cloning and cell culture growth techniques applicable to IBV are also reviewed.

Unique Variants of Avian Coronaviruses from Indigenous Chickens in Kenya

“…The S-protein coding sequence of isolate A376 appears to be of recombinant origin similar to but distinct from other sequenced TCoVs such as the Asian and North American TCoVs (at 85.9% and 79% nucleotide similarity, respectively), and only distantly related to other IBVs. This is a known phenomenon, in which the majority of TCoVs originate from a recombination of an IBV backbone with an S-gene fragment of often unknown origin [ 18 , 52 , 66 ]. The ability of AvCoVs to micro-evolve into novel variants via recombination of S1 sequence fragments from different backgrounds is consequential because they could confer on the variants the ability to infect new host tissues or naïve susceptible hosts (diversification of tissue tropism and host range), for instance, if the changes enhance the susceptibility of the S gene to proteolytic activation or increase affinity to receptor binding and efficiency to gain cellular entry (heightening of pathogenicity) [ 18 , 67 ].…”

“…This is a known phenomenon, in which the majority of TCoVs originate from a recombination of an IBV backbone with an S-gene fragment of often unknown origin [ 18 , 52 , 66 ]. The ability of AvCoVs to micro-evolve into novel variants via recombination of S1 sequence fragments from different backgrounds is consequential because they could confer on the variants the ability to infect new host tissues or naïve susceptible hosts (diversification of tissue tropism and host range), for instance, if the changes enhance the susceptibility of the S gene to proteolytic activation or increase affinity to receptor binding and efficiency to gain cellular entry (heightening of pathogenicity) [ 18 , 67 ]. Novel variants could also gain the ability for immune escape and unresponsiveness to vaccinations.…”

“…The IBV genome is generally organized as 5′UTR-[1ab-S-3a-3b-E-M-4b-4c-5a-5b-N-6b]-3′UTR. The S glycoprotein is the largest of the AvCoV proteins, and it defines tissue tropism and mediates binding and fusion of viral and host cellular membranes [ 17 , 18 ]. Its S1 subunit contains hypervariable regions (HVRs) and antigenic sites, and the complete S1 is currently used to classify IBV into six genotypes (GI to GVI) which comprise 32 distinct lineages (27 in genotypes GI-1 to GI-27, and one each in GII to GVI).…”

Sarbecoviruses of British Horseshoe Bats; Sequence Variation and Epidemiology

“…The sites sampled reflected the distribution of horseshoe bats in Great Britain, and infection was clearly common within and between populations of lesser horseshoe bats in this study, with no clear sex or age differences in likelihood of shedding. This high frequency of shedding and widespread distribution geographically and demographically, likely indicates either persistent infection and excretion, or frequent reinfection, of the gastrointestinal tract as has been reported for many other coronaviruses, such as those of cats, chickens and pigs (Quinteros, Noormohammadi et al 2022, Thayer, Gogolski et al 2022, Zhang, Chen et al 2022.…”

Sarbecoviruses of British horseshoe bats; sequence variation and epidemiology

“…The sites sampled reflected the distribution of horseshoe bats in Great Britain, and infection was clearly common within and between populations of lesser horseshoe bats in this study, with no clear sex or age differences in likelihood of shedding. This high frequency of shedding and widespread distribution geographically and demographically, likely indicates either persistent infection and excretion, or frequent reinfection, of the gastrointestinal tract as has been reported for many other coronaviruses, such as those of cats, chickens and pigs [67–69].…”