Whole-genome characterization of Uruguayan strains of avian infectious bronchitis virus reveals extensive recombination between the two major South American lineages

Abstract

Infectious bronchitis virus (Gammacoronavirus, Coronaviridae) is a genetically variable RNA virus that causes one of the most persistent respiratory diseases in poultry. The virus is classified in genotypes and lineages with different epidemiological relevance. Two lineages of the GI genotype (11 and 16) have been widely circulating for decades in South America. GI-11 is an exclusive South American lineage while the GI-16 lineage is distributed in Asia, Europe and South America. Here, we obtained the whole genome of two Uruguayan strains of the GI-11 and GI-16 lineages using Illumina high-throughput sequencing. The strains here sequenced are the first obtained in South America for the infectious bronchitis virus and provide new insights into the origin, spreading and evolution of viral variants. The complete genome of the GI-11 and GI-16 strains have 27,621 and 27,638 nucleotides, respectively, and possess the same genomic organization. Phylogenetic incongruence analysis reveals that both strains have a mosaic genome that arose by recombination between Euro Asiatic strains of the GI-16 lineage and ancestral South American GI-11 viruses. The recombination occurred in South America and produced two viral variants that have retained the full-length S1 sequences of the parental lineages but are extremely similar in the rest of their genomes. These recombinant virus have been extraordinary successful, persisting in the continent for several years with a notorious wide geographic distribution. Our findings reveal a singular viral dynamics and emphasize the importance of complete genomic characterization to understand the emergence and evolutionary history of viral variants.

Molecular characterization of whole genome sequence of infectious bronchitis virus 624I genotype confirms the close relationship with Q1 genotype

“…For easiness of representation, strain reported in the present study and closely related strains, are marked in red. (b) Expanded phylogenetic tree based on Maximum Likelihood method with Kimura-2 model constructed using S1 complete sequences closely related to gammaCoV/AvCov/Ck/Italy/IP14425/96 [Colour figure can be viewed at wileyonlinelibrary.com] accessory genes 4b, 4c, and 6b already reported for TCoV and other IBVs (Abolnik, 2015;Hewson, Ignjatovic, Browning, Devlin, & Noormohammadi, 2011 (Marandino et al, 2017) did not support the presence of ORF 6b in contrast to the results presented here. On the contrary, a recent study confirmed the expression of the 4b protein after M41 IBV infection in vitro (Bentley, Keep, Armesto, & Britton, 2013).…”

Synanthropic rodents as virus reservoirs and transmitters

“…Betacoronaviruses are found mainly in mammals, such as humans, dogs, cats, pigs, bats, mice, rats, horses, and cattle 114,[118][119][120][121][122][123] , while Gama and Deltacoronaviruses infect mainly birds, with exceptions such as the white whale Gamacoronavirus (Delphinapterus leucas) 124 and the porcine Deltacoronavirus 125 .…”

GI-16 lineage (624/I or Q1), there and back again: The history of one of the major threats for poultry farming of our era

“…However, from the 1990s, its detection and reporting became sporadic or absent. At the same time, in 1996, a new IBV strain (later renamed Q1) was identified in animals affected by proventriculitis [13] in China and thereafter in other Asian [14,15], Middle Eastern [16,17], South American [18,19] and European countries [7,20–22]. Remarkably, not recognizing the relationship between these strains, a new spread from Asia was supposed, similarly what was proven for the GI-19 lineage (QX genotype) [23].…”