Genomic epidemiology of SARS-CoV-2 in the UAE reveals novel virus mutation, patterns of co-infection and tissue specific host immune response.
Genomic epidemiology of SARS-CoV-2 in the UAE reveals novel virus mutation, patterns of co-infection and tissue specific host immune response.
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阿联酋 SARS-CoV-2 的基因组流行病学揭示了新的病毒突变、共感染模式和组织特异性宿主免疫反应
DOI：
10.1038/s41598-021-92851-3
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发表时间：
2021-07-07
影响因子：
4.6
通讯作者：
Zaher WA
中科院分区：
文献类型：
--
作者：
Liu R;Wu P;Ogrodzki P;Mahmoud S;Liang K;Liu P;Francis SS;Khalak H;Liu D;Li J;Ma T;Chen F;Liu W;Huang X;He W;Yuan Z;Qiao N;Meng X;Alqarni B;Quilez J;Kusuma V;Lin L;Jin X;Yang C;Anton X;Koshy A;Yang H;Xu X;Wang J;Xiao P;Al Kaabi N;Fasihuddin MS;Selvaraj FA;Weber S;Al Hosani FI;Liu S;Zaher WA
为了揭示SARS-CoV-2的传入来源及其在阿拉伯联合酋长国的传播和演变模式，我们对2020年5月9日至6月29日在当地COVID-19疫情第一个高峰期间收集的1067份鼻咽拭子样本进行了元转录组测序。我们确定了全球分支分布和11个新的遗传变异，这些变异在世界其他地区几乎不存在，并定义了阿联酋病毒群体特有的5个亚分支。人与人之间的传播与当地的商业活动有关。也许令人惊讶的是，至少有5%的人群被同一宿主内的多个分支的SARS-CoV-2共感染。我们还发现从鼻咽收集的病毒群体中胞嘧啶到尿嘧啶突变的富集，这不同于先前在支气管肺泡灌洗液样品中报道的腺苷到肌苷的变化，以及先前未鉴定的感染患者鼻咽中APOBEC 4表达的上调，表明由阿达尔和APOBEC基因家族介导的先天免疫宿主应答可能是组织特异性的。本文的研究成果为SARS病毒的进化和传播提供了新的认识，并为宿主-病原体相互作用的研究指明了方向。
To unravel the source of SARS-CoV-2 introduction and the pattern of its spreading and evolution in the United Arab Emirates, we conducted meta-transcriptome sequencing of 1067 nasopharyngeal swab samples collected between May 9th and Jun 29th, 2020 during the first peak of the local COVID-19 epidemic. We identified global clade distribution and eleven novel genetic variants that were almost absent in the rest of the world and that defined five subclades specific to the UAE viral population. Cross-settlement human-to-human transmission was related to the local business activity. Perhaps surprisingly, at least 5% of the population were co-infected by SARS-CoV-2 of multiple clades within the same host. We also discovered an enrichment of cytosine-to-uracil mutation among the viral population collected from the nasopharynx, that is different from the adenosine-to-inosine change previously reported in the bronchoalveolar lavage fluid samples and a previously unidentified upregulation of APOBEC4 expression in nasopharynx among infected patients, indicating the innate immune host response mediated by ADAR and APOBEC gene families could be tissue-specific. The genomic epidemiological and molecular biological knowledge reported here provides new insights for the SARS-CoV-2 evolution and transmission and points out future direction on host–pathogen interaction investigation.
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