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      Unlocking capacities of viral genomics for the COVID-19 pandemic response

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          Abstract

          More than any other infectious disease epidemic, the COVID-19 pandemic has been characterized by the generation of large volumes of viral genomic data at an incredible pace due to recent advances in high-throughput sequencing technologies, the rapid global spread of SARS-CoV-2, and its persistent threat to public health. However, distinguishing the most epidemiologically relevant information encoded in these vast amounts of data requires substantial effort across the research and public health communities. Studies of SARS-CoV-2 genomes have been critical in tracking the spread of variants and understanding its epidemic dynamics, and may prove crucial for controlling future epidemics and alleviating significant public health burdens. Together, genomic data and bioinformatics methods enable broad-scale investigations of the spread of SARS-CoV-2 at the local, national, and global scales and allow researchers the ability to efficiently track the emergence of novel variants, reconstruct epidemic dynamics, and provide important insights into drug and vaccine development and disease control. Here, we discuss the tremendous opportunities that genomics offers to unlock the effective use of SARS-CoV-2 genomic data for efficient public health surveillance and guiding timely responses to COVID-19.

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          Most cited references187

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          A Novel Coronavirus from Patients with Pneumonia in China, 2019

          Summary In December 2019, a cluster of patients with pneumonia of unknown cause was linked to a seafood wholesale market in Wuhan, China. A previously unknown betacoronavirus was discovered through the use of unbiased sequencing in samples from patients with pneumonia. Human airway epithelial cells were used to isolate a novel coronavirus, named 2019-nCoV, which formed a clade within the subgenus sarbecovirus, Orthocoronavirinae subfamily. Different from both MERS-CoV and SARS-CoV, 2019-nCoV is the seventh member of the family of coronaviruses that infect humans. Enhanced surveillance and further investigation are ongoing. (Funded by the National Key Research and Development Program of China and the National Major Project for Control and Prevention of Infectious Disease in China.)
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            Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus–Infected Pneumonia in Wuhan, China

            In December 2019, novel coronavirus (2019-nCoV)-infected pneumonia (NCIP) occurred in Wuhan, China. The number of cases has increased rapidly but information on the clinical characteristics of affected patients is limited.
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              A pneumonia outbreak associated with a new coronavirus of probable bat origin

              Since the outbreak of severe acute respiratory syndrome (SARS) 18 years ago, a large number of SARS-related coronaviruses (SARSr-CoVs) have been discovered in their natural reservoir host, bats 1–4 . Previous studies have shown that some bat SARSr-CoVs have the potential to infect humans 5–7 . Here we report the identification and characterization of a new coronavirus (2019-nCoV), which caused an epidemic of acute respiratory syndrome in humans in Wuhan, China. The epidemic, which started on 12 December 2019, had caused 2,794 laboratory-confirmed infections including 80 deaths by 26 January 2020. Full-length genome sequences were obtained from five patients at an early stage of the outbreak. The sequences are almost identical and share 79.6% sequence identity to SARS-CoV. Furthermore, we show that 2019-nCoV is 96% identical at the whole-genome level to a bat coronavirus. Pairwise protein sequence analysis of seven conserved non-structural proteins domains show that this virus belongs to the species of SARSr-CoV. In addition, 2019-nCoV virus isolated from the bronchoalveolar lavage fluid of a critically ill patient could be neutralized by sera from several patients. Notably, we confirmed that 2019-nCoV uses the same cell entry receptor—angiotensin converting enzyme II (ACE2)—as SARS-CoV.
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                Author and article information

                Contributors
                Journal
                ArXiv
                ArXiv
                arxiv
                ArXiv
                Cornell University
                2331-8422
                28 April 2021
                : arXiv:2104.14005v2
                Affiliations
                Department of Computer Science, College of Art and Science, Georgia State University, 1 Park Place, Room 618, Atlanta, GA 30303, USA
                Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, 30333 GA, USA
                Oak Ridge Institute for Science and Education, Oak Ridge, TN 37830, USA
                Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Room 713. Los Angeles, CA 90089, USA
                Department of Computer Science, University of California Los Angeles, 580 Portola Plaza, Los Angeles, CA 90095, USA
                Department of Neuroscience, College of Life Sciences, University of California Los Angeles, 580 Portola Plaza, Los Angeles, CA 90095, USA
                Department of Electrical Engineering, Indian Institute of Technology, Hauz Khas, New Delhi, 110016, India
                Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
                Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Room 713. Los Angeles, CA 90089, USA
                Paradigm Environmental, 3911 Old Lee Highway, Fairfax, VA 22030
                Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Room 713. Los Angeles, CA 90089-9121, USA
                World-Class Research Center “Digital biodesign and personalized healthcare”, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
                Department of Computational Biology, Sirius University of Science and Technology, Sochi, Russia
                Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
                Suzhou Institute of Systems Medicine, Suzhou, 215123, China
                Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
                Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, QLD 4059, Australia
                Translational Research Institute, Brisbane, Australia
                Astani Department of Civil and Environmental Engineering, University of Southern California, 3620 South Vermont Avenue, Los Angeles, CA 90089
                Department of Computer Science, College of Art and Science, Georgia State University, 1 Park Place, Floor 6, Atlanta, GA 30303, USA
                The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011
                State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong
                Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
                Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
                Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
                Department of Computer Science, College of Art and Science, Georgia State University, 1 Park Place, Floor 6, Atlanta, GA 30303, USA
                The Laboratory of Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, 119991, Russia
                Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
                Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
                Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA, USA
                Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
                Computational Biology Institute and Department of Biostatistics & Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC 20052
                Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, 1540 Alcazar Street, Los Angeles, CA 90033, USA
                Author notes
                Author information
                http://orcid.org/0000-0003-0385-1831
                http://orcid.org/0000-0003-1328-5028
                http://orcid.org/0000-0001-7563-9835
                http://orcid.org/0000-0001-7275-271X
                http://orcid.org/0000-0002-3970-6276
                http://orcid.org/0000-0003-3794-7364
                http://orcid.org/0000-0003-1786-3366
                http://orcid.org/0000-0002-9078-6697
                http://orcid.org/0000-0003-4424-4691
                http://orcid.org/0000-0003-4770-3443
                Article
                2104.14005
                8109901
                d1e6863e-8711-446e-97d3-9a41c2ce3b81

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