Genomic Epidemiology of SARS-CoV-2 in Pakistan  

作　　者：Shuhui Song Cuiping Li Lu Kang Dongmei Tian Nazish Badar Wentai Ma Shilei Zhao Xuan Jiang Chun Wang Yongqiao Sun Wenjie Li Meng Lei Shuangli Li Qiuhui Qi Aamer Ikram Muhammad Salman Massab Umair Huma Shireen Fatima Batool Bing Zhang Hua Chen Yun-Gui Yang Amir Ali Abbasi Mingkun Li Yongbiao Xue Yiming Bao 

机构地区：[1]China National Center for Bioinformation,Beijing 100101,China [2]National Genomics Data Center,Beijing Institute of Genomics,Chinese Academy of Sciences,Beijing 100101,China [3]CAS Key Laboratory of Genome Sciences and Information,Beijing Institute of Genomics,Chinese Academy of Sciences,Beijing 100101,China [4]University of Chinese Academy of Sciences,Beijing 100049,China [5]CAS Key Laboratory of Genomic and Precision Medicine,Beijing Institute of Genomics,Chinese Academy of Sciences,Beijing 100101,China [6]Department of Virology and Immunology,National Institute of Health,Islamabad 45500,Pakistan [7]National Center for Bioinformatics,Programme of Comparative and Evolutionary Genomics,Faculty of Biological Sciences,Quaid-i-Azam University,Islamabad 45320,Pakistan [8]Center for Excellence in Animal Evolution and Genetics,Chinese Academy of Sciences,Kunming 650223,China [9]State Key Laboratory of Plant Cell and Chromosome Engineering,Institute of Genetics and Developmental Biology,The Innovation Academy of Seed Design,Chinese Academy of Sciences,Beijing 100101,China

出　　处：《Genomics, Proteomics & Bioinformatics》2021年第5期727-740,共14页基因组蛋白质组与生物信息学报（英文版）

基　　金：supported by grants from the National Key R&D Program of China(Grant Nos.2021YFC0863300,2020YFC0848900,and 2016YFE0206600);the National Natural Science Foundation of China(Grant No.82161148009);the Strategic Priority Research Program of Chinese Academy of Sciences,China(Grant Nos.XDA19090116 and XDB38060100);the Open Biodiversity and Health Big Data Programme of International Union of Biological Sciences,International Partnership Program of Chinese Academy of Sciences(Grant No.153F11KYSB20160008);the Professional Association of the Alliance of International Science Organizations(Grant No.ANSO-PA-2020-07);the Youth Innovation Promotion Association of Chinese Academy of Sciences(Grant No.2017141)。

摘　　要：COVID-19 has swept globally and Pakistan is no exception.To investigate the initial introductions and transmissions of the SARS-CoV-2 in Pakistan,we performed the largest genomic epidemiology study of COVID-19 in Pakistan and generated 150 complete SARS-CoV-2 genome sequences from samples collected from March 16 to June 1,2020.We identified a total of 347 mutated positions,31 of which were over-represented in Pakistan.Meanwhile,we found over 1000 intra-host single-nucleotide variants(iSNVs).Several of them occurred concurrently,indicating possible interactions among them or coevolution.Some of the high-frequency iSNVs in Pakistan were not observed in the global population,suggesting strong purifying selections.The genomic epidemiology revealed five distinctive spreading clusters.The largest cluster consisted of 74 viruses which were derived from different geographic locations of Pakistan and formed a deep hierarchical structure,indicating an extensive and persistent nation-wide transmission of the virus that was probably attributed to a signature mutation(G8371T in ORF1ab)of this cluster.Furthermore,28 putative international introductions were identified,several of which are consistent with the epidemiological investigations.In all,this study has inferred the possible pathways of introductions and transmissions of SARS-CoV-2 in Pakistan,which could aid ongoing and future viral surveillance and COVID-19 control.

关 键 词：SARS-CoV-2 VIRUS Molecular evolution Haplotype network Pakistan 

分 类 号：R563.1[医药卫生—呼吸系统] R181.3[医药卫生—内科学]