Genetic diversity and evolution of infectious bronchitis virus (IBV) in South African poultry and that of some neighbouring countries during the 2011-2020

Infectious bronchitis virus (IBV) (family <em>Gammacoronavirus)</em> considered to be the most significant diseases that has major economic losses within the poultry industry worldwide. 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.

传染性支气管炎病毒（IBV，属γ冠状病毒科）被认为是全球家禽业中造成重大经济损失的最严重疾病之一。本研究分析了2011-2020年间从博茨瓦纳、埃斯瓦蒂尼、纳米比亚以及南非的东开普省、自由州省、豪登省、夸祖鲁-纳塔尔省、林波波省、普马兰加省、西北省和西开普省商品鸡群中采集的385株田间分离株，这些分离株均在Deltamune (Pty)实验室的SPF鸡胚中培养。研究对刺突蛋白基因（spike protein gene）的745 bp片段进行了扩增和测序，并开展系统发育分析（phylogenetic analysis）。其中24份（6.2%）样本含有病毒共感染（viral coinfections）产生的混合序列，未进行进一步分析。在剩余364株分离株中，鉴定出7个遗传谱系（genetic lineages）：184株（50.5%）为GI-19（QX）株，78株（21.4%）为GI-1（Mass/H120）株；39株（10.7%）属于2011-2019年间检测到的GI-13（4/91）谱系，29株（8.0%）属于2010-2020年间检测到的GVI-1（TC07-2）谱系，19株（5.2%）属于GI-23（Var II）谱系（2019-2020年为主，2010和2015年各有1株），13株（3.6%）属于2011-2020年间检测到的GI-11（UFMG/G - Brazil）谱系；2株（0.5%）病毒与GIV-1（DE/072/92）谱系密切相关，但仅在2011和2013年分离得到。GI-1和GI-13谱系中的3株病毒可能为重组体（recombinant），但需进一步分析证实。