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RNA based mNGS approach identifies a novel human coronavirus from two individual pneumonia cases in 2019 Wuhan outbreak.
Emerging Microbes & Infections ( IF 8.4 ) Pub Date : 2020-02-05 , DOI: 10.1080/22221751.2020.1725399
Liangjun Chen 1, 2 , Weiyong Liu 3 , Qi Zhang 1 , Ke Xu 1 , Guangming Ye 2 , Weichen Wu 4 , Ziyong Sun 3 , Fang Liu 1 , Kailang Wu 1 , Bo Zhong 1 , Yi Mei 1 , Wenxia Zhang 1 , Yu Chen 1 , Yirong Li 2 , Mang Shi 4 , Ke Lan 1 , Yingle Liu 1
Affiliation  

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.

中文翻译:

基于RNA的mNGS方法从2019年武汉爆发的两例肺炎病例中鉴定出一种新型人冠状病毒。

从2019年12月开始,武汉市爆发了不寻常的肺炎疫情,许多病例与出售海鲜以及活体外来动物的华南海鲜市场有关。我们调查了与该市场独立接触史后出现急性呼吸综合征的两名患者。两名患者具有共同的临床特征,包括发烧,咳嗽以及双侧肺野中有片状浸润的多个毛玻璃样混浊。在这里,我们重点介绍了对从支气管肺泡灌洗液(BALF)提取的RNA的低输入宏基因组学下一代测序(mNGS)方法的使用。它迅速鉴定出一种新型冠状病毒(根据世界卫生组织的公告命名为2019-nCoV),它是样品中唯一的病原体,具有很高的丰度水平(测序总RNA的1.5%和0.62%)。整个病毒基因组的长度为29,881 nt(GenBank MN988668和MN988669,Sequence Read Archive数据库Bioproject登录号PRJNA601736),并被分类为β冠状病毒属。系统发育分析表明,2019-nCoV与在犀牛(Horseshoe bats)中循环的冠状病毒(CoVs)接近,例如与蝙蝠冠状病毒BtCoV / 4991(GenBank KP876546,370nt的RdRp序列)的部分RdRp基因具有98.7%的核苷酸同一性蝙蝠冠状病毒菌株bat-SL-CoVZC45和bat-SL-CoVZXC21具有87.9%的核苷酸同一性。基于ORF1a / 1b,S和N基因的进化分析还表明,2019-nCoV更有可能是一种从动物独立引入人类的新型CoV。序列读取存档数据库Bioproject登录号PRJNA601736),并分为β-冠状病毒属。系统发育分析表明,2019-nCoV与在犀牛(Horseshoe bats)中循环的冠状病毒(CoVs)接近,例如与蝙蝠冠状病毒BtCoV / 4991(GenBank KP876546,370nt的RdRp序列)的部分RdRp基因具有98.7%的核苷酸同一性蝙蝠冠状病毒菌株bat-SL-CoVZC45和bat-SL-CoVZXC21具有87.9%的核苷酸同一性。基于ORF1a / 1b,S和N基因的进化分析还表明,2019-nCoV更有可能是一种从动物独立引入人类的新型CoV。序列读取存档数据库Bioproject登录号PRJNA601736),并分为β-冠状病毒属。系统发育分析表明,2019-nCoV与在犀牛(Horseshoe bats)中循环的冠状病毒(CoVs)接近,例如与蝙蝠冠状病毒BtCoV / 4991(GenBank KP876546,370nt的RdRp序列)的部分RdRp基因具有98.7%的核苷酸同一性蝙蝠冠状病毒菌株bat-SL-CoVZC45和bat-SL-CoVZXC21具有87.9%的核苷酸同一性。基于ORF1a / 1b,S和N基因的进化分析还表明,2019-nCoV更有可能是一种从动物独立引入人类的新型CoV。与蝙蝠冠状病毒株BtCoV / 4991(GenBank KP876546,RdRp的370 nt序列,缺少其他基因组序列)的部分RdRp基因具有7%的核苷酸同一性,与蝙蝠冠状病毒株bat-SL-CoVZC45和bat-SL- CoVZXC21。基于ORF1a / 1b,S和N基因的进化分析还表明,2019-nCoV更有可能是一种从动物独立引入人类的新型CoV。与蝙蝠冠状病毒株BtCoV / 4991(GenBank KP876546,RdRp的370 nt序列,缺少其他基因组序列)的部分RdRp基因具有7%的核苷酸同一性,与蝙蝠冠状病毒株bat-SL-CoVZC45和bat-SL- CoVZXC21。基于ORF1a / 1b,S和N基因的进化分析还表明,2019-nCoV更有可能是一种从动物独立引入人类的新型CoV。
更新日期:2020-02-05
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