Genomic Epidemiology of SARS-CoV-2 in Pakistan

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

doi:10.1016/j.gpb.2021.08.007

Genomic Epidemiology of SARS-CoV-2 in Pakistan

Genomics Proteomics Bioinformatics. 2021 Oct;19(5):727-740. doi: 10.1016/j.gpb.2021.08.007. Epub 2021 Oct 23.

Authors

Shuhui Song¹, Cuiping Li¹, Lu Kang², Dongmei Tian¹, Nazish Badar³, Wentai Ma², Shilei Zhao², Xuan Jiang⁴, Chun Wang², Yongqiao Sun⁵, Wenjie Li⁵, Meng Lei⁵, Shuangli Li⁵, Qiuhui Qi⁵, Aamer Ikram³, Muhammad Salman³, Massab Umair³, Huma Shireen⁶, Fatima Batool⁶, Bing Zhang⁵, Hua Chen⁷, Yun-Gui Yang², Amir Ali Abbasi⁸, Mingkun Li⁹, Yongbiao Xue¹⁰, Yiming Bao¹¹

Affiliations

¹ China National Center for Bioinformation, Beijing 100101, China; National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
² China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
³ Department of Virology and Immunology, National Institute of Health, Islamabad 45500, Pakistan.
⁴ China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
⁵ China National Center for Bioinformation, Beijing 100101, China.
⁶ National Center for Bioinformatics, Programme of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan.
⁷ China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
⁸ National Center for Bioinformatics, Programme of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan. Electronic address: abbasiam@qau.edu.pk.
⁹ China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China. Electronic address: limk@big.ac.cn.
¹⁰ China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; 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. Electronic address: ybxue@big.ac.cn.
¹¹ China National Center for Bioinformation, Beijing 100101, China; National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address: baoym@big.ac.cn.

Abstract

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.

Keywords: Haplotype network; Molecular evolution; Pakistan; SARS-CoV-2; Virus.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

COVID-19* / epidemiology
Genome, Viral
Genomics
Humans
Pakistan / epidemiology
Phylogeny
SARS-CoV-2* / genetics