Genomic epidemiology of SARS-CoV-2 in the United Arab Emirates reveals novel virus mutation, patterns of co-infection and tissue specific host innate immune response
Genomic epidemiology of SARS-CoV-2 in the United Arab Emirates reveals novel virus mutation, patterns of co-infection and tissue specific host innate immune response
Abstract 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 1,067 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 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.
Liu Rong、Wang Jian、Koshy Ashish、Yang Huanming、Xiao Peng、Al Kaabi Nawal Ahmed Mohamed、Selvaraj Francis Amirtharaj、Weber Stefan、Zaher Walid Abbas、Francis Stephen S.、Liu Denghui、Liu Weibin、Huang Xinyu、Qiao Nan、Meng Xin、Alqarni Budoor、Quilez Javier、Mahmoud Sally、Kusuma Vinay、Ma Tao、Liu Pengjuan、Li Junhua、Lin Long、Xu Xun、Liang Ke、He Wenjun、Al Hosani Farida Ismail、Jin Xin、Yuan Zhaorong、Ogrodzki Pauline、Chen Fang、Anton Xavier、Liu Siyang、Wu Pei、Fasihuddin Mohammed Saifuddin、Khalak Hanif、Yang Chongguang
Group42 Healthcare, Abu Dhabi||BGI-ShenzhenBGI-ShenzhenGroup42 Healthcare, Abu DhabiBGI-ShenzhenGroup42 Healthcare, Abu DhabiSEHA, Abu Dhabi Health Services Co, Abu DhabiSEHA, Abu Dhabi Health Services Co, Abu DhabiSEHA, Abu Dhabi Health Services Co, Abu DhabiGroup42 Healthcare, Abu DhabiDepartment of Neurological Surgery, University of California||Department of Epidemiology and Biostatistics, University of CaliforniaLaboratory of Health Intelligence, Huawei Technologies Co.BGI-ShenzhenMGI, BGI-ShenzhenLaboratory of Health Intelligence, Huawei Technologies Co.Laboratory of Health Intelligence, Huawei Technologies Co.Group42 Healthcare, Abu DhabiGroup42 Healthcare, Abu DhabiGroup42 Healthcare, Abu DhabiGroup42 Healthcare, Abu DhabiMGI, BGI-ShenzhenMGI, BGI-ShenzhenBGI-Shenzhen||Shenzhen Key Laboratory of Unknown Pathogen IdentificationBGI-ShenzhenBGI-ShenzhenMGI, BGI-ShenzhenLaboratory of Health Intelligence, Huawei Technologies Co.Department of Health, Abu DhabiBGI-ShenzhenLaboratory of Health Intelligence, Huawei Technologies Co.Group42 Healthcare, Abu DhabiMGI, BGI-ShenzhenGroup42 Healthcare, Abu DhabiBGI-ShenzhenGroup42 Healthcare, Abu Dhabi||BGI-ShenzhenSEHA, Abu Dhabi Health Services Co, Abu DhabiGroup42 Healthcare, Abu DhabiDepartment of Epidemiology of Microbial Diseases, Yale School of Public Health
基础医学分子生物学微生物学
SARS-CoV-2meta-transcriptomic sequencingphylogeneticshuman-to-human transmissionco-infectionmutation spectrumhost innate immune response
Liu Rong,Wang Jian,Koshy Ashish,Yang Huanming,Xiao Peng,Al Kaabi Nawal Ahmed Mohamed,Selvaraj Francis Amirtharaj,Weber Stefan,Zaher Walid Abbas,Francis Stephen S.,Liu Denghui,Liu Weibin,Huang Xinyu,Qiao Nan,Meng Xin,Alqarni Budoor,Quilez Javier,Mahmoud Sally,Kusuma Vinay,Ma Tao,Liu Pengjuan,Li Junhua,Lin Long,Xu Xun,Liang Ke,He Wenjun,Al Hosani Farida Ismail,Jin Xin,Yuan Zhaorong,Ogrodzki Pauline,Chen Fang,Anton Xavier,Liu Siyang,Wu Pei,Fasihuddin Mohammed Saifuddin,Khalak Hanif,Yang Chongguang.Genomic epidemiology of SARS-CoV-2 in the United Arab Emirates reveals novel virus mutation, patterns of co-infection and tissue specific host innate immune response[EB/OL].(2025-03-28)[2025-05-05].https://www.medrxiv.org/content/10.1101/2021.03.09.21252822.点此复制
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