Genomic epidemiology of SARS-CoV-2 in the UAE reveals novel virus mutation, patterns of co-infection and tissue specific host immune response.

Autor:	Liu R; Group42 Healthcare, Abu Dhabi, United Arab Emirates.; BGI-Shenzhen, Shenzhen, 518083, Guangdong, China., Wu P; Group42 Healthcare, Abu Dhabi, United Arab Emirates.; BGI-Shenzhen, Shenzhen, 518083, Guangdong, China., Ogrodzki P; Group42 Healthcare, Abu Dhabi, United Arab Emirates., Mahmoud S; Group42 Healthcare, Abu Dhabi, United Arab Emirates., Liang K; MGI, BGI-Shenzhen, Shenzhen, 518083, Guangdong, China., Liu P; MGI, BGI-Shenzhen, Shenzhen, 518083, Guangdong, China., Francis SS; Department of Neurological Surgery, University of California, San Francisco, USA.; Department of Epidemiology and Biostatistics, University of California, San Francisco, USA., Khalak H; Group42 Healthcare, Abu Dhabi, United Arab Emirates., Liu D; Laboratory of Health Intelligence, Huawei Technologies Co., Ltd., Shenzhen, 518100, China., Li J; BGI-Shenzhen, Shenzhen, 518083, Guangdong, China.; Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, 518083, China., Ma T; MGI, BGI-Shenzhen, Shenzhen, 518083, Guangdong, China., Chen F; MGI, BGI-Shenzhen, Shenzhen, 518083, Guangdong, China., Liu W; BGI-Shenzhen, Shenzhen, 518083, Guangdong, China., Huang X; MGI, BGI-Shenzhen, Shenzhen, 518083, Guangdong, China., He W; Laboratory of Health Intelligence, Huawei Technologies Co., Ltd., Shenzhen, 518100, China., Yuan Z; Laboratory of Health Intelligence, Huawei Technologies Co., Ltd., Shenzhen, 518100, China., Qiao N; Laboratory of Health Intelligence, Huawei Technologies Co., Ltd., Shenzhen, 518100, China., Meng X; Laboratory of Health Intelligence, Huawei Technologies Co., Ltd., Shenzhen, 518100, China., Alqarni B; Group42 Healthcare, Abu Dhabi, United Arab Emirates., Quilez J; Group42 Healthcare, Abu Dhabi, United Arab Emirates., Kusuma V; Group42 Healthcare, Abu Dhabi, United Arab Emirates., Lin L; BGI-Shenzhen, Shenzhen, 518083, Guangdong, China., Jin X; BGI-Shenzhen, Shenzhen, 518083, Guangdong, China., Yang C; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, USA., Anton X; Group42 Healthcare, Abu Dhabi, United Arab Emirates., Koshy A; Group42 Healthcare, Abu Dhabi, United Arab Emirates., Yang H; BGI-Shenzhen, Shenzhen, 518083, Guangdong, China., Xu X; BGI-Shenzhen, Shenzhen, 518083, Guangdong, China., Wang J; BGI-Shenzhen, Shenzhen, 518083, Guangdong, China., Xiao P; Group42 Healthcare, Abu Dhabi, United Arab Emirates., Al Kaabi N; SEHA, Abu Dhabi Health Services Co., Sheikh Khalifa Medical City, Abu Dhabi, United Arab Emirates., Fasihuddin MS; SEHA, Abu Dhabi Health Services Co., Sheikh Khalifa Medical City, Abu Dhabi, United Arab Emirates., Selvaraj FA; SEHA, Abu Dhabi Health Services Co., Sheikh Khalifa Medical City, Abu Dhabi, United Arab Emirates., Weber S; SEHA, Abu Dhabi Health Services Co., Sheikh Khalifa Medical City, Abu Dhabi, United Arab Emirates., Al Hosani FI; Department of Health, Abu Dhabi, United Arab Emirates., Liu S; BGI-Shenzhen, Shenzhen, 518083, Guangdong, China. liusiyang@bgi.com.; School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, 510006, Guangdong, China. liusiyang@bgi.com., Zaher WA; Group42 Healthcare, Abu Dhabi, United Arab Emirates. Walid.Zaher@g42.ai.
Jazyk:	angličtina
Zdroj:	Scientific reports [Sci Rep] 2021 Jul 07; Vol. 11 (1), pp. 13971. Date of Electronic Publication: 2021 Jul 07.
DOI:	10.1038/s41598-021-92851-3
Abstrakt:	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.
Databáze:	MEDLINE
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