Novel Lineage of Infectious Bronchitis Virus from Sub-Saharan Africa Identified by Random Amplification and Next-Generation Sequencing of Viral Genome

Avian infectious bronchitis (IB) is among the major viral respiratory and reproductive diseases of chickens caused by Avian coronavirus. In the African continent, IB was first described in countries located in the Mediterranean basin. In other parts of the continent, the epidemiological situation of IB remains unclear. In this study, the complete genome sequences of five IBV strains, originating from the sub-Saharan area were determined. Phylogenetic analysis based on the full-length S1 sequences identified three lineages (GI-14, GI-16, and GI-19) common in Africa and revealed that a strain, D2334/11/2/13/CI, isolated in Ivory Coast may represent a novel lineage within genotype GI. The maximum inter- and intragenotype sequence identities between this strain and other IBVs were 67.58% and 78.84% (nucleotide) and 64.44% and 78.6% (amino acid), respectively. The whole-genome nucleotide identity of the novel variant shared the highest values with a reference Belgian nephropathogenic strain (B1648, 92.4%) and with another study strain from Ivory Coast (D2334/12/2/13/CI, 94.6%). This study illustrates the importance of epidemiological monitoring of IBV in sub-Saharan Africa, as the area may serve as a focal point for newly emerging viral lineages.