Molecular epidemiology of infectious bronchitis coronavirus in southern African poultry from 2011 to 2020

Abstract

Infectious bronchitis virus (IBV) (family Gammacoronavirus) is an ever-evolving avian pathogen that causes major economic losses within the poultry industry worldwide. Antigenic variations allow the virus to evade vaccine induced immunity and produce new variants at an alarming rate. Epidemiological studies of IBV are imperative to selection of vaccines. Field isolates (n=385) grown in SPF embryonated chicken eggs at Deltamune (Pty) Laboratory, that originated in commercial flocks were collected from Botswana, Eswatini, Namibia and South Africa’s Eastern Cape, Free State, Gauteng, KwaZulu-Natal, Limpopo, Mpumalanga, North West, and Western Cape provinces from 2011-2020, were analysed in this study. A 745 bp region of the spike protein gene was amplified and sequenced, and phylogenetic analysis was performed. Twenty-four (6,2 %) samples contained mixed sequences from viral coinfections and were not evaluated further. In the remaining 364 isolates, 7 genetic lineages were identified. 184 (50,5%) viruses were identified as GI-19 (QX) strains and 78 (21,4%) as the GI-1 (Mass/H120) strain. 39 (10,7%) samples were identified as the GI-13 (4/91) lineage detected between 2011 and 2019, 29 (8,0%) as the GVI-1 (TC07-2) lineage detected from 2010-2020, 19 (5,2%) as the GI-23 (Var II) lineage from 2019-2020 with single isolates in 2010 and 2015, and 13 (3,6%) as the GI-11 (UFMG/G - Brazil) lineage detected from 2011-2020. Two (0.5%) viruses were closely related to GIV-1 (DE/072/92) lineages but were only isolated in 2011 and 2013. Three viruses from GI-1 and GI-13 may have been recombinants, but further analysis is required to confirm this. Overall, this study reveals the co-circulation of diverse IBV field and vaccine-derived genotypes in southern African poultry flocks for the first time.