Abolnik C, Olivier A J, Grewar J, Gers S, Romito M
Agricultural Research Council--Onderstepoort Veterinary Institute, Private Bag X5, Onderstepoort, 0110, South Africa.
Avian Dis. 2012 Dec;56(4 Suppl):865-79. doi: 10.1637/10171-041012-Reg.1.
The third outbreak of highly pathogenic avian influenza (HPAI) H5N2 in less than seven years affected ostriches of South Africa's Western Cape during 2011. Twenty farms tested PCR positive for the presence of HPAI H5N2 between March and November 2011. Three HPAI H5N2 (AI2114, AI2214, AI2512) and 1 H1N2 (AI2887) viruses were isolated during this period, but H6N2 and H1N2 infections of ostriches were also confirmed by PCR. HPAI H5N2 isolate AI2114 produced an intravenous pathogenicity index (IVPI) score of 1.37 in chickens whereas isolate AI2214 produced an IVPI score of 0.8. The former virus had an additional, predicted N-linked glycosylation site at position 88 of the hemagglutinin protein as well as an E627K mutation in the PB2 protein that was lacking from AI2214. Four variations at HA0 were detected in the PCR-positive cases. Phylogenetically, the branching order of outbreak strains indicated a lack of reassortment between outbreak strains that implied a single outbreak source and a wild duck origin for the progenitor outbreak strain. The 2011 outbreak strains had no genetic relationships to the previous 2004 and 2006 HPAI H5N2 outbreak viruses. Molecular clock analysis based on the N2 neuraminidase genes estimated a recent common ancestor for the outbreak tentatively dated at September 2010. Deep sequencing results of 16 clinical PCR-positive samples yielded data in the range of 573 to 12,590 base pairs (bp), with an average of 4468 bp of total genomic sequence recovered per sample. This data was used to confirm the lack ofreassortment and to assign samples into one of two epidemiologic groups to support epidemiologic tracing of the spread of the outbreak. One farm (no. 142), thought to have played a major epidemiologic role in the outbreak, was confirmed by deep sequencing to contain a mix of both epidemiologic virus groups.
2011年，不到七年时间里的第三次高致病性禽流感（HPAI）H5N2疫情影响了南非西开普省的鸵鸟。2011年3月至11月期间，20个养殖场的HPAI H5N2检测呈PCR阳性。在此期间分离出3株HPAI H5N2病毒（AI2114、AI2214、AI2512）和1株H1N2病毒（AI2887），但鸵鸟的H6N2和H1N2感染也通过PCR得到确认。HPAI H5N2分离株AI2114在鸡中产生的静脉内致病性指数（IVPI）评分为1.37，而分离株AI2214的IVPI评分为0.8。前一种病毒在血凝素蛋白的88位有一个额外的预测N - 连接糖基化位点，以及PB2蛋白中的E627K突变，而AI2214缺乏该突变。在PCR阳性病例中检测到HA0的四个变异。从系统发育来看，疫情毒株的分支顺序表明疫情毒株之间缺乏重配，这意味着单一的疫情源头以及始祖疫情毒株的野鸭起源。2011年的疫情毒株与之前2004年和2006年的HPAI H5N2疫情病毒没有遗传关系。基于N2神经氨酸酶基因的分子钟分析估计，此次疫情的最近共同祖先初步定于2010年9月。16份临床PCR阳性样本的深度测序结果产生的数据范围为573至12590碱基对（bp），每个样本平均回收4468 bp的总基因组序列。这些数据用于确认缺乏重配，并将样本分为两个流行病学组之一，以支持对疫情传播的流行病学追踪。一个被认为在疫情中起主要流行病学作用的养殖场（142号），通过深度测序证实含有两种流行病学病毒组的混合。
