Acta Laser Biology Sinica, Volume. 30, Issue 4, 305(2021)

Genome Sequencing and Variation Analysis of 12 overseas Chinese SARS-CoV-2 Infected Patients

ZENG Yong1, CHEN Jianwei2, CUI Enhai3, HU Guohai4, WANG Xiaoguang5, JI Qiaoying5, CONG Ying1, YANG Yang6, and YANG Weibin6、*
Author Affiliations
  • 1[in Chinese]
  • 2[in Chinese]
  • 3[in Chinese]
  • 4[in Chinese]
  • 5[in Chinese]
  • 6[in Chinese]
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    References(20)

    [1] [1] LI Q, GUAN X H, WU P, et al. Early transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia[J]. The New England Journal of Medicine, 2020, 382(13): 1199-1207.

    [2] [2] WAN Y L, LI J, SHEN L H, et al. Enteric involvement in hospitalised patients with COVID-19 outside Wuhan[J]. The Lancet Gastroenterology & Hepatology, 2020, 5(6): 534-535.

    [3] [3] ZHU N, ZHANG D Y, WANG W L, et al. A novel coronavirus from patients with pneumonia in China, 2019[J]. The New England Journal of Medicine, 2020, 382(8): 727-733.

    [4] [4] LU R J, ZHAO X, LI J, et al. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding[J]. Lancet, 2020, 395(10224): 565-574.

    [5] [5] World Health Organization. Coronavirus disease (COVID-2019) situation report-188[R]. World Health Organization, 2020. https://reliefweb.int/report/world/coronavirus-disease-covid-19-situation-report-188-26-july-2020.

    [6] [6] WU A P, NIU P H, WANG L L, et al. Mutations, recombination and insertion in the evolution of 2019-nCoV[J/OL]. BioRxiv, 2020 (2020-03-02) [2020-11-10]. https://pubmed.ncbi.nlm.nih.gov/32511312/. DOI: 10.1101/2020.02.29.971101.

    [7] [7] PLANTE J A, LIU Y, LIU J Y, et al. Spike mutation D614G alters SARS-CoV-2 fitness[J]. Nature, 2021, 592(7852): 116-121.

    [8] [8] ZHANG L Z, JACKSON C B, MOU H H, et al. The D614G mutation in the SARS-CoV-2 spike protein reduces S1 shedding and increases infectivity[J/OL]. BioRxiv, 2020 (2020-06-12) [2020-11-10]. https://pubmed.ncbi.nlm.nih.gov/32587973/. DOI: 10.1101/2020.06.12.148726.

    [9] [9] METSKY H C, MATRANGA C B, WOHL S, et al. Zika virus evolution and spread in the Americas[J]. Nature, 2017, 546(7658): 411-415.

    [10] [10] XIAO M F, LIU X Q, JI J K, et al. Multiple approaches for massively parallel sequencing of SARS-CoV-2 genomes directly from clinical samples[J]. Genome Medicine, 2020, 12(1): 57.

    [15] [15] WOOD D E, SALZBERG S L. Kraken: ultrafast metagenomic sequence classification using exact alignments[J]. Genome Biology, 2014, 15(3): R46.

    [16] [16] WU F, ZHAO S, YU B, et al. A new coronavirus associated with human respiratory disease in China[J]. Nature, 2020, 579(7798): 265-269.

    [17] [17] BANKEVICH A, NURK S, ANTIPOV D, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing[J]. Journal of Computational Biology, 2012, 19(5): 455-477.

    [18] [18] PENG Y, LEUNG H C M, YIU S M, et al. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth[J]. Bioinformatics, 2012, 28(11): 1420-1428.

    [19] [19] GARRISON E, MARTH G. Haplotype-based variant detection from short-read sequencing[J/OL]. ArXiv, 2012 (2012-07-20)[2020-10-20]. https://arxiv.org/abs/1207.3907.

    [20] [20] CINGOLANI P, PLATTS A, WANG L L, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3[J]. Fly, 2012, 6(2): 80-92.

    [21] [21] WALKER B J, ABEEL T, SHEA T, et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement[J]. PLoS One, 2014, 9(11): e112963.

    [22] [22] NI M, CHEN C, QIAN J, et al. Intra-host dynamics of Ebola virus during 2014[J]. Nature Microbiology, 2016, 1(11): 16151.

    [23] [23] KORBER B, FISCHER W M, GNANAKARAN S, et al. Tracking changes in SARS-CoV-2 spike: evidence that D614G increases infectivity of the COVID-19 virus[J]. Cell, 2020, 182(4): 812-827.

    [24] [24] GRUBAUGH N D, HANAGE W P, RASMUSSEN A L. Making sense of mutation: what D614G means for the COVID-19 pandemic remains unclear[J]. Cell, 2020, 182(4): 794-795.

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    ZENG Yong, CHEN Jianwei, CUI Enhai, HU Guohai, WANG Xiaoguang, JI Qiaoying, CONG Ying, YANG Yang, YANG Weibin. Genome Sequencing and Variation Analysis of 12 overseas Chinese SARS-CoV-2 Infected Patients[J]. Acta Laser Biology Sinica, 2021, 30(4): 305

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    Paper Information

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    Received: Nov. 10, 2020

    Accepted: --

    Published Online: Sep. 12, 2021

    The Author Email: Weibin YANG (153407547@qq.com)

    DOI:10.3969/j.issn.1007-7146.2021.04.003

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