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10, 2021;19 (5): 727-740.

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
Author Information
  1. Shuhui Song: 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. Cuiping Li: 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.
  3. Lu Kang: 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.
  4. Dongmei Tian: 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.
  5. Nazish Badar: Department of Virology and Immunology, National Institute of Health, Islamabad 45500, Pakistan.
  6. Wentai Ma: 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.
  7. Shilei Zhao: 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.
  8. Xuan Jiang: 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.
  9. Chun Wang: 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.
  10. Yongqiao Sun: China National Center for Bioinformation, Beijing 100101, China.
  11. Wenjie Li: China National Center for Bioinformation, Beijing 100101, China.
  12. Meng Lei: China National Center for Bioinformation, Beijing 100101, China.
  13. Shuangli Li: China National Center for Bioinformation, Beijing 100101, China.
  14. Qiuhui Qi: China National Center for Bioinformation, Beijing 100101, China.
  15. Aamer Ikram: Department of Virology and Immunology, National Institute of Health, Islamabad 45500, Pakistan.
  16. Muhammad Salman: Department of Virology and Immunology, National Institute of Health, Islamabad 45500, Pakistan.
  17. Massab Umair: Department of Virology and Immunology, National Institute of Health, Islamabad 45500, Pakistan.
  18. Huma Shireen: National Center for Bioinformatics, Programme of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan.
  19. Fatima Batool: National Center for Bioinformatics, Programme of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan.
  20. Bing Zhang: China National Center for Bioinformation, Beijing 100101, China.
  21. Hua Chen: 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.
  22. Yun-Gui Yang: 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.
  23. Amir Ali Abbasi: 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.
  24. Mingkun Li: 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.
  25. Yongbiao Xue: 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.
  26. Yiming Bao: 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.
PMID: 34695600 DOI: 10.1016/j.gpb.2021.08.007

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

References

  1. Euro Surveill. 2020 Jan;25(3): [PMID: 31992387]
  2. Biosaf Health. 2020 Dec;2(4):199-201 [PMID: 33235990]
  3. Genomics Proteomics Bioinformatics. 2021 Aug;19(4):584-589 [PMID: 34175476]
  4. BMC Public Health. 2014 Jul 04;14:681 [PMID: 24993370]
  5. Nucleic Acids Res. 2021 Jan 8;49(D1):D10-D17 [PMID: 33095870]
  6. Sci Bull (Beijing). 2021 Nov 30;66(22):2297-2311 [PMID: 33585048]
  7. JAMA. 2020 Jun 2;323(21):2191-2192 [PMID: 32338732]
  8. Glob Chall. 2017 Jan 10;1(1):33-46 [PMID: 31565258]
  9. Bioinformatics. 2009 Aug 15;25(16):2078-9 [PMID: 19505943]
  10. N Engl J Med. 2020 Dec 3;383(23):2291-2293 [PMID: 33176080]
  11. Bioinformatics. 2009 Jul 15;25(14):1754-60 [PMID: 19451168]
  12. Nature. 2021 Apr;592(7852):116-121 [PMID: 33106671]
  13. Asia Pac J Public Health. 2020 May;32(4):154-156 [PMID: 32429679]
  14. Natl Sci Rev. 2020 Feb;7(2):239-242 [PMID: 32288962]
  15. Genomics Proteomics Bioinformatics. 2020 Dec;18(6):640-647 [PMID: 32663617]
  16. Nucleic Acids Res. 2023 Jan 6;51(D1):D18-D28 [PMID: 36420893]
  17. Yi Chuan. 2020 Feb 20;42(2):212-221 [PMID: 32102777]
  18. Genome Biol. 2016 Jun 06;17(1):122 [PMID: 27268795]
  19. Genome Res. 2010 Sep;20(9):1297-303 [PMID: 20644199]
  20. Emerg Infect Dis. 2021 Jan;27(1): [PMID: 33075274]
  21. J Genet Genomics. 2020 Oct 20;47(10):610-617 [PMID: 33388272]
  22. Cell. 2020 Aug 20;182(4):812-827.e19 [PMID: 32697968]
  23. Clin Infect Dis. 2020 Jul 28;71(15):713-720 [PMID: 32129843]
  24. Proc Natl Acad Sci U S A. 2020 Dec 8;117(49):31519-31526 [PMID: 33203681]
  25. Arch Microbiol. 2021 Jan;203(1):59-66 [PMID: 32749662]
  26. Genomics Proteomics Bioinformatics. 2020 Dec;18(6):749-759 [PMID: 33704069]
  27. Euro Surveill. 2017 Mar 30;22(13): [PMID: 28382917]
  28. Mol Biol Evol. 2020 May 1;37(5):1530-1534 [PMID: 32011700]
  29. Natl Sci Rev. 2020 Jun;7(6):1012-1023 [PMID: 34676127]
  30. Nucleic Acids Res. 2019 Jul 2;47(W1):W636-W641 [PMID: 30976793]
  31. Mol Biol Evol. 2015 Jan;32(1):268-74 [PMID: 25371430]
  32. Genomics Proteomics Bioinformatics. 2021 Aug;19(4):578-583 [PMID: 34400360]
  33. Science. 2021 Feb 5;371(6529): [PMID: 33303686]
  34. Int J Environ Res Public Health. 2019 Apr 16;16(8): [PMID: 30995744]
  35. Nat Microbiol. 2020 Nov;5(11):1403-1407 [PMID: 32669681]
  36. Nature. 2020 Mar;579(7798):265-269 [PMID: 32015508]
  37. MMWR Morb Mortal Wkly Rep. 2020 May 22;69(20):632-635 [PMID: 32437338]
  38. Nat Rev Genet. 2008 Nov;9(11):855-67 [PMID: 18852697]

MeSH Term

COVID-19
Genome, Viral
Genomics
Humans
Pakistan
Phylogeny
SARS-CoV-2
Journal Article Research Support, Non-U.S. Gov't

Links to CNCB-NGDC Resources

BioProject: PRJCA003179 (Genome sequence evolutionary analysis of SARS-CoV-2)
GSA: CRA003122 (Genome sequence evolutionary analysis of SARS-CoV-2)

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