Genomics

  1. Sequencing SARS-CoV-2 in a Malaria Research Laboratory in Mali, West Africa: The Road to Sequencing the First SARS-CoV-2 Genome in Mali

    1. Antoine Dara
    2. Bourema Kouriba
    3. Amadou Daou
    4. Abdoul Karim Sangare
    5. Djibril Kassogue
    6. Charles Dara
    7. Abdoulaye A. Djimde

    Reviewed by ScreenIT

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  2. Multifractal Analysis of SARS-CoV-2 Coronavirus genomes using the wavelet transform

    1. Sid-Ali Ouadfeul

    Reviewed by ScreenIT

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  3. A repurposed, blood gene signature is associated with poor outcomes in SARS-CoV-2

    1. Brenda M. Juan-Guardela
    2. Jiehuan Sun
    3. Tong Zhang
    4. Bing Xu
    5. Gaetane Michaud
    6. Jose D. Herazo-Maya

    Reviewed by ScreenIT

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  4. Patterns of within-host genetic diversity in SARS-CoV-2

    1. Gerry Tonkin-Hill
    2. Inigo Martincorena
    3. Roberto Amato
    4. Andrew RJ Lawson
    5. Moritz Gerstung
    6. Ian Johnston
    7. David K Jackson
    8. Naomi Park
    9. Stefanie V Lensing
    10. Michael A Quail
    11. Sónia Gonçalves
    12. Cristina Ariani
    13. Michael Spencer Chapman
    14. William L Hamilton
    15. Luke W Meredith
    16. Grant Hall
    17. Aminu S Jahun
    18. Yasmin Chaudhry
    19. Myra Hosmillo
    20. Malte L Pinckert
    21. Iliana Georgana
    22. Anna Yakovleva
    23. Laura G Caller
    24. Sarah L Caddy
    25. Theresa Feltwell
    26. Fahad A Khokhar
    27. Charlotte J Houldcroft
    28. Martin D Curran
    29. Surendra Parmar
    30. The COVID-19 Genomics UK (COG-UK) Consortium
    31. Alex Alderton
    32. Rachel Nelson
    33. Ewan M Harrison
    34. John Sillitoe
    35. Stephen D Bentley
    36. Jeffrey C Barrett
    37. M Estee Torok
    38. Ian G Goodfellow
    39. Cordelia Langford
    40. Dominic Kwiatkowski
    41. Wellcome Sanger Institute COVID-19 Surveillance Team

    • Curated by eLife

      Evaluation Summary:

      Tonkin-Hill and colleagues present a large set of deep sequencing data from acute SARS-CoV-2 infections with each sample sequenced in duplicate. They use these data to characterize the within-host mutational patterns and diversity and relate them to SARS-CoV-2 diversity in consensus sequences sampled around the globe. It further allows understanding how this variation can or cannot be used to understand transmission dynamics and other applications in genomic epidemiology.

      (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #3 agreed to share their names with the authors.)

    Reviewed by eLife, ScreenIT

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  5. Emerging SARS-CoV-2 Diversity Revealed by Rapid Whole-Genome Sequence Typing

    1. Ahmed M Moustafa
    2. Paul J Planet

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  6. Single-nucleotide conservation state annotation of the SARS-CoV-2 genome

    1. Soo Bin Kwon
    2. Jason Ernst

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  7. Two mutations in the SARS-CoV-2 spike protein and RNA polymerase complex are associated with COVID-19 mortality risk

    1. Georg Hahn
    2. Chloe M. Wu
    3. Sanghun Lee
    4. Julian Hecker
    5. Sharon M. Lutz
    6. Sebastien Haneuse
    7. Dandi Qiao
    8. Dawn DeMeo
    9. Manish C. Choudhary
    10. Behzad Etemad
    11. Abbas Mohammadi
    12. Elmira Esmaeilzadeh
    13. Michael H. Cho
    14. Rudolph E. Tanzi
    15. Jonathan Z. Li
    16. Adrienne G. Randolph
    17. Nan M. Laird
    18. Scott T. Weiss
    19. Edwin K. Silverman
    20. Katharina Ribbeck
    21. Christoph Lange

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  8. Large-scale single-cell analysis reveals critical immune characteristics of COVID-19 patients

    1. Xianwen Ren
    2. Wen Wen
    3. Xiaoying Fan
    4. Wenhong Hou
    5. Bin Su
    6. Pengfei Cai
    7. Jiesheng Li
    8. Yang Liu
    9. Fei Tang
    10. Fan Zhang
    11. Yu Yang
    12. Jiangping He
    13. Wenji Ma
    14. Jingjing He
    15. Pingping Wang
    16. Qiqi Cao
    17. Fangjin Chen
    18. Yuqing Chen
    19. Xuelian Cheng
    20. Guohong Deng
    21. Xilong Deng
    22. Wenyu Ding
    23. Yingmei Feng
    24. Rui Gan
    25. Chuang Guo
    26. Weiqiang Guo
    27. Shuai He
    28. Chen Jiang
    29. Juanran Liang
    30. Yi-min Li
    31. Jun Lin
    32. Yun Ling
    33. Haofei Liu
    34. Jianwei Liu
    35. Nianping Liu
    36. Yang Liu
    37. Meng Luo
    38. Qiang Ma
    39. Qibing Song
    40. Wujianan Sun
    41. GaoXiang Wang
    42. Feng Wang
    43. Ying Wang
    44. Xiaofeng Wen
    45. Qian Wu
    46. Gang Xu
    47. Xiaowei Xie
    48. Xinxin Xiong
    49. Xudong Xing
    50. Hao Xu
    51. Chonghai Yin
    52. Dongdong Yu
    53. Kezhuo Yu
    54. Jin Yuan
    55. Biao Zhang
    56. Tong Zhang
    57. Jincun Zhao
    58. Peidong Zhao
    59. Jianfeng Zhou
    60. Wei Zhou
    61. Sujuan Zhong
    62. Xiaosong Zhong
    63. Shuye Zhang
    64. Lin Zhu
    65. Ping Zhu
    66. Bin Zou
    67. Jiahua Zou
    68. Zengtao Zuo
    69. Fan Bai
    70. Xi Huang
    71. Xiuwu Bian
    72. Penghui Zhou
    73. Qinghua Jiang
    74. Zhiwei Huang
    75. Jin-Xin Bei
    76. Lai Wei
    77. Xindong Liu
    78. Tao Cheng
    79. Xiangpan Li
    80. Pingsen Zhao
    81. Fu-Sheng Wang
    82. Hongyang Wang
    83. Bing Su
    84. Zheng Zhang
    85. Kun Qu
    86. Xiaoqun Wang
    87. Jiekai Chen
    88. Ronghua Jin
    89. Zemin Zhang

    Reviewed by ScreenIT

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  9. Host transcriptional responses and SARS-CoV-2 isolates from the nasopharyngeal samples of Bangladeshi COVID-19 patients

    1. Abul Bashar Mir Md. Khademul Islam
    2. Md. Abdullah-Al-Kamran Khan
    3. Rasel Ahmed
    4. Md. Sabbir Hossain
    5. Shah Md. Tamim Kabir
    6. Md. Shahidul Islam
    7. A.M.A.M. Zonaed Siddiki

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  10. Phylogenomics reveals multiple introductions and early spread of SARS-CoV-2 into Peru

    1. Eduardo Juscamayta-López
    2. David Tarazona
    3. Faviola Valdivia
    4. Nancy Rojas
    5. Dennis Carhuaricra
    6. Lenin Maturrano
    7. Ronnie Gavilán

    Reviewed by ScreenIT

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