RNA based mNGS approach identifies a novel human coronavirus from two individual pneumonia cases in 2019 Wuhan outbreak
RNA based mNGS approach identifies a novel human coronavirus from two individual pneumonia cases in 2019 Wuhan outbreak
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基于 RNA 的 mNGS 方法从 2019 年武汉爆发的两例肺炎病例中识别出一种新型人类冠状病毒
DOI：
10.1080/22221751.2020.1725399
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发表时间：
2020-01-01
影响因子：
13.2
通讯作者：
Liu, Yingle
中科院分区：
文献类型：
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作者：
Chen, Liangjun;Liu, Weiyong;Liu, Yingle
摘要从2019年12月起，武汉报告了一起罕见肺炎的爆发，许多病例与华南海鲜市场有关，该市场出售海鲜和活的外来动物。我们调查了两名患者，他们在与这个市场独立接触后出现了急性呼吸综合征。这两名患者都有共同的临床特征，包括发热、咳嗽和双侧肺野多发磨玻璃样阴影，并伴有斑片状浸润性病变。在这里，我们强调使用低输入的元基因组下一代测序(MNGS)方法对从支气管肺泡灌洗液(BALF)中提取的RNA进行分析。它迅速鉴定出一种新的冠状病毒(根据世界卫生组织宣布命名为2019-nCoV)，这是样本中唯一的病原体，丰度水平非常高(分别占总RNA测序的1.5%和0.62%)。病毒基因组全长29,881个 核苷酸(GenBank MN988668和MN988669，序列读取档案数据库BioProject登录号PRJNA601736)，被归类为β冠状病毒属。系统进化分析表明，2019-nCoV与蝙蝠冠状病毒BtCoV/4991株RdRp基因部分核苷酸同源性为98.7%(GenBank KP876546,370 的RdRp核苷酸序列，缺少其他基因组序列)，与蝙蝠冠状病毒BAT-SL-CoVZC45和BAT-SL-CoVZXC21的核苷酸同源性为87.9%。基于ORF1a/1b、S和N基因的进化分析也表明，2019-nCoV更有可能是一种从动物独立引入人类的新型冠状病毒。
ABSTRACT From December 2019, an outbreak of unusual pneumonia was reported in Wuhan with many cases linked to Huanan Seafood Market that sells seafood as well as live exotic animals. We investigated two patients who developed acute respiratory syndromes after independent contact history with this market. The two patients shared common clinical features including fever, cough, and multiple ground-glass opacities in the bilateral lung field with patchy infiltration. Here, we highlight the use of a low-input metagenomic next-generation sequencing (mNGS) approach on RNA extracted from bronchoalveolar lavage fluid (BALF). It rapidly identified a novel coronavirus (named 2019-nCoV according to World Health Organization announcement) which was the sole pathogens in the sample with very high abundance level (1.5% and 0.62% of total RNA sequenced). The entire viral genome is 29,881 nt in length (GenBank MN988668 and MN988669, Sequence Read Archive database Bioproject accession PRJNA601736) and is classified into β-coronavirus genus. Phylogenetic analysis indicates that 2019-nCoV is close to coronaviruses (CoVs) circulating in Rhinolophus (Horseshoe bats), such as 98.7% nucleotide identity to partial RdRp gene of bat coronavirus strain BtCoV/4991 (GenBank KP876546, 370 nt sequence of RdRp and lack of other genome sequence) and 87.9% nucleotide identity to bat coronavirus strain bat-SL-CoVZC45 and bat-SL-CoVZXC21. Evolutionary analysis based on ORF1a/1b, S, and N genes also suggests 2019-nCoV is more likely a novel CoV independently introduced from animals to humans.