Unique variants of avian coronaviruses from indigenous chickens in Kenya

Authors: KARIITHI, HENRY - Orise Fellow; VOLKENING, JEREMY - Base2bio; GORAICHUK, IRYNA - Orise Fellow; ATEYA, LEONARD - Kenya Agricultural And Livestock Research Organization; Williams Coplin, Tina; BINEPAL, YATINDER - Kenya Agricultural And Livestock Research Organization; Afonso, Claudio; Suarez, David

Submitted to: Viruses
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/15/2023
Publication Date: 1/17/2023
Citation: Kariithi, H.M., Volkening, J.D., Goraichuk, I.V., Ateya, L.O., Williams Coplin, T.D., Binepal, Y.S., Afonso, C.L., Suarez, D.L. 2023. Unique variants of avian coronaviruses from indigenous chickens in Kenya. Viruses. 15(2):264. https://doi.org/10.3390/v15020264.
DOI: https://doi.org/10.3390/v15020264

Interpretive Summary: The use of Next Generation Sequencing (NGS) techniques to identify pathogens in clinical samples continues to improve. Often full length viral genomes can be identified in samples and this sequence information can be used to not only identify what pathogens are in samples, but also determine the genotype, pathotype, or lineage of a virus. This information can be used to predict which viruses are likely to cause severe disease and can help guide the use of what vaccines should be used for control efforts. As part of a surveillance project in poultry in Kenya, samples were taken from chickens and pathogens were identified based on sequencing using an unbiased amplification approach and next generation sequencing. Multiple viruses were identified, and in two samples avian coronaviruses were identified. Sequence analysis showed one virus to be a unique infectious brochitis virus, and the second was found to be most closely related to turkey coronaviruses. It is unclear if these viruses cause clinical disease in poultry, but the identification of unique viruses should strengthen efforts to identify new variants in poultry. The use of next generation sequencing shows great promise in identifying both new and existing pathogens in cost efficient and timely manner.

Technical Abstract: The avian gamma-coronavirus infectious bronchitis virus (AvCoV, IBV; Coronaviridae family) causes upper respiratory disease associated with severe economic losses in the poultry industry worldwide. Here, we report for the first time in Kenya and the Eastern African region two novel AvCoVs, designated IBV/ck/KE/1920/A374/2017 (A374/17) and AvCoV/ck/KE/1922/A376/2017 (A376/17), inadvertently discovered using random nontargeted next-generation sequencing (NGS) of cloacal swabs collected from indigenous chickens. Despite having genome organization (5'UTR-[Rep1a/1ab-S-3a-3b-E-M-4b-4c-5a-5b-N-6b]-3'UTR), canonical conservation of essential genes and size (~27.6 kb) typical of IBVs, the Kenyan isolates do not phylogenetically cluster with any genotypes of the 37 IBV lineages and 26 unique variants (UVs). Excluding the spike gene, genome sequences of A374/17 and A376/17 are only 93.1% similar to each other and 86.7–91.4% identical to genomes of other AvCoVs. All five non-spike genes of the two isolates phylogenetically cluster together and distinctly from other IBVs and turkey coronaviruses (TCoVs), including the indigenous African GI-26 viruses, suggesting a common origin of the genome backbone of the Kenyan isolates. However, isolate A376/17 contains a TCoV-like spike (S) protein coding sequence and is most similar to Asian TCoVs (84.5–85.1%) compared to other TCoVs (75.6–78.5%), whereas isolate A374/17 contains an S1 gene sequence most similar to the globally distributed lineage GI-16 (78.4–79.5%) and the Middle Eastern lineage GI-23 (79.8–80.2%) viruses. Unanswered questions include the actual origin of the Kenyan AvCoVs, the potential pathobiological significance of their genetic variations, whether they have indeed established themselves as independent variants and subsequently spread within Kenya and to the neighboring east/central African countries that have porous live poultry trade borders, and whether the live-attenuated Mass-type (lineage GI-1)-based vaccines currently used in Kenya and most of the African countries provide protection against these genetically divergent field variants.