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

Knyazev, Sergey and Chhugani, Karishma and Sarwal, Varuni and Ayyala, Ram and Singh, Harman and Karthikeyan, Smruthi and Deshpande, Dhrithi and Comarova, Zoia and Lu, Angela and Porozov, Yuri and Wu, Aiping and Abedalthagafi, Malak S. and Nagaraj, Shivashankar H. and Smith, Adam L. and Skums, Pavel and Ladner, Jason and Lam, Tommy Tsan-Yuk and Wu, Nicholas C. and Zelikovsky, Alex and Knight, Rob and Crandall, Keith A. and Mangul, Serghei (2021) Unlocking capacities of viral genomics for the COVID-19 pandemic response. . (Unpublished)

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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.

Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription Paper CentralArticle
Knyazev, Sergey0000-0003-0385-1831
Chhugani, Karishma0000-0003-1328-5028
Sarwal, Varuni0000-0001-7563-9835
Ayyala, Ram0000-0001-7275-271X
Singh, Harman0000-0002-3970-6276
Karthikeyan, Smruthi0000-0001-6226-4536
Deshpande, Dhrithi0000-0003-3794-7364
Porozov, Yuri0000-0002-5450-3135
Abedalthagafi, Malak S.0000-0003-1786-3366
Skums, Pavel0000-0003-4007-5624
Ladner, Jason0000-0001-7751-4366
Lam, Tommy Tsan-Yuk0000-0002-9769-1527
Wu, Nicholas C.0000-0002-9078-6697
Zelikovsky, Alex0000-0003-4424-4691
Knight, Rob0000-0002-0975-9019
Crandall, Keith A.0000-0002-0836-3389
Mangul, Serghei0000-0003-4770-3443
Additional Information:We thank William M. Switzer and Ellsworth M. Campbell from the Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, 30333 GA, USA for useful discussions and suggestions. We also thank numerous anonymous reviewers who helped improve our manuscript by their valuable comments on the manuscript. S.M. was partially supported by National Science Foundation grants 2041984. Tommy Lam is supported by NSFC Excellent Young Scientists Fund (Hong Kong and Macau) (31922087) and Health and Medical Research Fund (COVID190223). Pavel Skums was supported by the National Institutes of Health grant 1R01EB025022. Malak Abedalthagafi MA a acknowledge King Abdulaziz City for Science and Technology and the Saudi Human Genome Project for technical and financial support ( Nicholas Wu: startup funds from the University of Illinois at Urbana-Champaign Adam Smith: acknowledge funding from NSF grant no. 2029025. Alex Zelikovsky: A.Z. has been partially supported by NSF Grant CCF-1619110 and NIH Grant 1R01EB025022-01. Sergey Knyazev S.K. has been partly supported by Molecular Basis of Disease at Georgia State University. Rob Knight: NSF project 2038509, RAPID: Improving QIIME 2 and UniFrac for Viruses to Respond to COVID-19. CDC project 30055281 with Scripps led by Kristian Andersen, Genomic sequencing of SARS-CoV-2 to investigate local and cross-border emergence and spread.
Funding AgencyGrant Number
National Natural Science Foundation of China31922087
Health and Medical Research Fund (China)COVID190223
King Abdulaziz City for Science and Technology (KACST)UNSPECIFIED
Saudi Human Genome ProjectUNSPECIFIED
University of Illinois Urbana-ChampaignUNSPECIFIED
Georgia State UniversityUNSPECIFIED
Centers for Disease Control and Prevention30055281
PubMed Central ID:PMC8095210
Record Number:CaltechAUTHORS:20221215-185439493
Persistent URL:
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:118342
Deposited By: George Porter
Deposited On:15 Dec 2022 22:31
Last Modified:15 Dec 2022 22:31

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