Unique Variants of Avian Coronaviruses from Indigenous Chickens in Kenya

Henry M Kariithi; Jeremy D Volkening; Iryna V Goraichuk; Leonard O Ateya; Dawn Williams-Coplin; Tim L Olivier; Yatinder S Binepal; Claudio L Afonso; David L Suarez

doi:10.3390/v15020264

Unique Variants of Avian Coronaviruses from Indigenous Chickens in Kenya

Viruses. 2023 Jan 17;15(2):264. doi: 10.3390/v15020264.

Authors

Affiliations

¹ Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, USDA-ARS, 934 College Station Rd, Athens, GA 30605, USA.
² Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, Kaptagat Rd, Loresho, Nairobi P.O. Box 57811-00200, Kenya.
³ BASE2BIO, Oshkosh, WI 54904, USA.
⁴ National Scientific Center Institute of Experimental and Clinical Veterinary Medicine, 83 Pushkinska St., 61023 Kharkiv, Ukraine.

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.

Keywords: AvCoV; IBV lineage; NGS; TCoV; cloacal; gastroenteric; live bird market; recombinant.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Africa, Eastern
Animals
Chickens
Gammacoronavirus*
Humans
Infectious bronchitis virus* / genetics
Kenya / epidemiology

Grants and funding

This research was funded by The US Defense Threat Reduction Agency (DTRA; FRCALL12-6-2-0015), Agricultural Research Service (ARS), USDA CRIS (6040-32000-066-00-D), and by a postdoctoral appointment to the Oak Ridge Institute for Science and Education (ORISE). The mention of trade names or commercial products in this publication is solely to provide specific information and does not imply recommendation or endorsement by the USDA-ARS or ORISE/ORAU.