Genomic epidemiology of SARS-CoV-2 in the UAE reveals novel virus mutation, patterns of co-infection and tissue specific host 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 1067 nasopharyngeal swab samples collected between May 9th and Jun 29th, 2020 during the first peak of the local COVID-1...
Guardado en:
| Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Formato: | article |
| Lenguaje: | EN |
| Publicado: |
Nature Portfolio
2021
|
| Materias: | |
| Acceso en línea: | https://doaj.org/article/155c7dbdf7684b0188b0aa25c4d5b9e6 |
| Etiquetas: |
Agregar Etiqueta
Sin Etiquetas, Sea el primero en etiquetar este registro!
|
| id |
oai:doaj.org-article:155c7dbdf7684b0188b0aa25c4d5b9e6 |
|---|---|
| record_format |
dspace |
| spelling |
oai:doaj.org-article:155c7dbdf7684b0188b0aa25c4d5b9e62021-12-02T18:34:20ZGenomic epidemiology of SARS-CoV-2 in the UAE reveals novel virus mutation, patterns of co-infection and tissue specific host immune response10.1038/s41598-021-92851-32045-2322https://doaj.org/article/155c7dbdf7684b0188b0aa25c4d5b9e62021-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-92851-3https://doaj.org/toc/2045-2322Abstract 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.Rong LiuPei WuPauline OgrodzkiSally MahmoudKe LiangPengjuan LiuStephen S. FrancisHanif KhalakDenghui LiuJunhua LiTao MaFang ChenWeibin LiuXinyu HuangWenjun HeZhaorong YuanNan QiaoXin MengBudoor AlqarniJavier QuilezVinay KusumaLong LinXin JinChongguang YangXavier AntonAshish KoshyHuanming YangXun XuJian WangPeng XiaoNawal Al KaabiMohammed Saifuddin FasihuddinFrancis Amirtharaj SelvarajStefan WeberFarida Ismail Al HosaniSiyang LiuWalid Abbas ZaherNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-14 (2021) |
| institution |
DOAJ |
| collection |
DOAJ |
| language |
EN |
| topic |
Medicine R Science Q |
| spellingShingle |
Medicine R Science Q Rong Liu Pei Wu Pauline Ogrodzki Sally Mahmoud Ke Liang Pengjuan Liu Stephen S. Francis Hanif Khalak Denghui Liu Junhua Li Tao Ma Fang Chen Weibin Liu Xinyu Huang Wenjun He Zhaorong Yuan Nan Qiao Xin Meng Budoor Alqarni Javier Quilez Vinay Kusuma Long Lin Xin Jin Chongguang Yang Xavier Anton Ashish Koshy Huanming Yang Xun Xu Jian Wang Peng Xiao Nawal Al Kaabi Mohammed Saifuddin Fasihuddin Francis Amirtharaj Selvaraj Stefan Weber Farida Ismail Al Hosani Siyang Liu Walid Abbas Zaher Genomic epidemiology of SARS-CoV-2 in the UAE reveals novel virus mutation, patterns of co-infection and tissue specific host immune response |
| description |
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 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. |
| format |
article |
| author |
Rong Liu Pei Wu Pauline Ogrodzki Sally Mahmoud Ke Liang Pengjuan Liu Stephen S. Francis Hanif Khalak Denghui Liu Junhua Li Tao Ma Fang Chen Weibin Liu Xinyu Huang Wenjun He Zhaorong Yuan Nan Qiao Xin Meng Budoor Alqarni Javier Quilez Vinay Kusuma Long Lin Xin Jin Chongguang Yang Xavier Anton Ashish Koshy Huanming Yang Xun Xu Jian Wang Peng Xiao Nawal Al Kaabi Mohammed Saifuddin Fasihuddin Francis Amirtharaj Selvaraj Stefan Weber Farida Ismail Al Hosani Siyang Liu Walid Abbas Zaher |
| author_facet |
Rong Liu Pei Wu Pauline Ogrodzki Sally Mahmoud Ke Liang Pengjuan Liu Stephen S. Francis Hanif Khalak Denghui Liu Junhua Li Tao Ma Fang Chen Weibin Liu Xinyu Huang Wenjun He Zhaorong Yuan Nan Qiao Xin Meng Budoor Alqarni Javier Quilez Vinay Kusuma Long Lin Xin Jin Chongguang Yang Xavier Anton Ashish Koshy Huanming Yang Xun Xu Jian Wang Peng Xiao Nawal Al Kaabi Mohammed Saifuddin Fasihuddin Francis Amirtharaj Selvaraj Stefan Weber Farida Ismail Al Hosani Siyang Liu Walid Abbas Zaher |
| author_sort |
Rong Liu |
| title |
Genomic epidemiology of SARS-CoV-2 in the UAE reveals novel virus mutation, patterns of co-infection and tissue specific host immune response |
| title_short |
Genomic epidemiology of SARS-CoV-2 in the UAE reveals novel virus mutation, patterns of co-infection and tissue specific host immune response |
| title_full |
Genomic epidemiology of SARS-CoV-2 in the UAE reveals novel virus mutation, patterns of co-infection and tissue specific host immune response |
| title_fullStr |
Genomic epidemiology of SARS-CoV-2 in the UAE reveals novel virus mutation, patterns of co-infection and tissue specific host immune response |
| title_full_unstemmed |
Genomic epidemiology of SARS-CoV-2 in the UAE reveals novel virus mutation, patterns of co-infection and tissue specific host immune response |
| title_sort |
genomic epidemiology of sars-cov-2 in the uae reveals novel virus mutation, patterns of co-infection and tissue specific host immune response |
| publisher |
Nature Portfolio |
| publishDate |
2021 |
| url |
https://doaj.org/article/155c7dbdf7684b0188b0aa25c4d5b9e6 |
| work_keys_str_mv |
AT rongliu genomicepidemiologyofsarscov2intheuaerevealsnovelvirusmutationpatternsofcoinfectionandtissuespecifichostimmuneresponse AT peiwu genomicepidemiologyofsarscov2intheuaerevealsnovelvirusmutationpatternsofcoinfectionandtissuespecifichostimmuneresponse AT paulineogrodzki genomicepidemiologyofsarscov2intheuaerevealsnovelvirusmutationpatternsofcoinfectionandtissuespecifichostimmuneresponse AT sallymahmoud genomicepidemiologyofsarscov2intheuaerevealsnovelvirusmutationpatternsofcoinfectionandtissuespecifichostimmuneresponse AT keliang genomicepidemiologyofsarscov2intheuaerevealsnovelvirusmutationpatternsofcoinfectionandtissuespecifichostimmuneresponse AT pengjuanliu genomicepidemiologyofsarscov2intheuaerevealsnovelvirusmutationpatternsofcoinfectionandtissuespecifichostimmuneresponse AT stephensfrancis genomicepidemiologyofsarscov2intheuaerevealsnovelvirusmutationpatternsofcoinfectionandtissuespecifichostimmuneresponse AT hanifkhalak genomicepidemiologyofsarscov2intheuaerevealsnovelvirusmutationpatternsofcoinfectionandtissuespecifichostimmuneresponse AT denghuiliu genomicepidemiologyofsarscov2intheuaerevealsnovelvirusmutationpatternsofcoinfectionandtissuespecifichostimmuneresponse AT junhuali genomicepidemiologyofsarscov2intheuaerevealsnovelvirusmutationpatternsofcoinfectionandtissuespecifichostimmuneresponse AT taoma genomicepidemiologyofsarscov2intheuaerevealsnovelvirusmutationpatternsofcoinfectionandtissuespecifichostimmuneresponse AT fangchen genomicepidemiologyofsarscov2intheuaerevealsnovelvirusmutationpatternsofcoinfectionandtissuespecifichostimmuneresponse AT weibinliu genomicepidemiologyofsarscov2intheuaerevealsnovelvirusmutationpatternsofcoinfectionandtissuespecifichostimmuneresponse AT xinyuhuang genomicepidemiologyofsarscov2intheuaerevealsnovelvirusmutationpatternsofcoinfectionandtissuespecifichostimmuneresponse AT wenjunhe genomicepidemiologyofsarscov2intheuaerevealsnovelvirusmutationpatternsofcoinfectionandtissuespecifichostimmuneresponse AT zhaorongyuan genomicepidemiologyofsarscov2intheuaerevealsnovelvirusmutationpatternsofcoinfectionandtissuespecifichostimmuneresponse AT nanqiao genomicepidemiologyofsarscov2intheuaerevealsnovelvirusmutationpatternsofcoinfectionandtissuespecifichostimmuneresponse AT xinmeng genomicepidemiologyofsarscov2intheuaerevealsnovelvirusmutationpatternsofcoinfectionandtissuespecifichostimmuneresponse AT budooralqarni genomicepidemiologyofsarscov2intheuaerevealsnovelvirusmutationpatternsofcoinfectionandtissuespecifichostimmuneresponse AT javierquilez genomicepidemiologyofsarscov2intheuaerevealsnovelvirusmutationpatternsofcoinfectionandtissuespecifichostimmuneresponse AT vinaykusuma genomicepidemiologyofsarscov2intheuaerevealsnovelvirusmutationpatternsofcoinfectionandtissuespecifichostimmuneresponse AT longlin genomicepidemiologyofsarscov2intheuaerevealsnovelvirusmutationpatternsofcoinfectionandtissuespecifichostimmuneresponse AT xinjin genomicepidemiologyofsarscov2intheuaerevealsnovelvirusmutationpatternsofcoinfectionandtissuespecifichostimmuneresponse AT chongguangyang genomicepidemiologyofsarscov2intheuaerevealsnovelvirusmutationpatternsofcoinfectionandtissuespecifichostimmuneresponse AT xavieranton genomicepidemiologyofsarscov2intheuaerevealsnovelvirusmutationpatternsofcoinfectionandtissuespecifichostimmuneresponse AT ashishkoshy genomicepidemiologyofsarscov2intheuaerevealsnovelvirusmutationpatternsofcoinfectionandtissuespecifichostimmuneresponse AT huanmingyang genomicepidemiologyofsarscov2intheuaerevealsnovelvirusmutationpatternsofcoinfectionandtissuespecifichostimmuneresponse AT xunxu genomicepidemiologyofsarscov2intheuaerevealsnovelvirusmutationpatternsofcoinfectionandtissuespecifichostimmuneresponse AT jianwang genomicepidemiologyofsarscov2intheuaerevealsnovelvirusmutationpatternsofcoinfectionandtissuespecifichostimmuneresponse AT pengxiao genomicepidemiologyofsarscov2intheuaerevealsnovelvirusmutationpatternsofcoinfectionandtissuespecifichostimmuneresponse AT nawalalkaabi genomicepidemiologyofsarscov2intheuaerevealsnovelvirusmutationpatternsofcoinfectionandtissuespecifichostimmuneresponse AT mohammedsaifuddinfasihuddin genomicepidemiologyofsarscov2intheuaerevealsnovelvirusmutationpatternsofcoinfectionandtissuespecifichostimmuneresponse AT francisamirtharajselvaraj genomicepidemiologyofsarscov2intheuaerevealsnovelvirusmutationpatternsofcoinfectionandtissuespecifichostimmuneresponse AT stefanweber genomicepidemiologyofsarscov2intheuaerevealsnovelvirusmutationpatternsofcoinfectionandtissuespecifichostimmuneresponse AT faridaismailalhosani genomicepidemiologyofsarscov2intheuaerevealsnovelvirusmutationpatternsofcoinfectionandtissuespecifichostimmuneresponse AT siyangliu genomicepidemiologyofsarscov2intheuaerevealsnovelvirusmutationpatternsofcoinfectionandtissuespecifichostimmuneresponse AT walidabbaszaher genomicepidemiologyofsarscov2intheuaerevealsnovelvirusmutationpatternsofcoinfectionandtissuespecifichostimmuneresponse |
| _version_ |
1718377844848984064 |