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Unlocking capacities of genomics for the COVID-19 response and future pandemics

Knyazev, Sergey and Chhugani, Karishma and Sarwal, Varuni and Ayyala, Ram and Singh, Harman and Karthikeyan, Smruthi and Deshpande, Dhrithi and Icer Baykal, Pelin and Comarova, Zoia and Lu, Angela and Porozov, Yuri and Vasylyeva, Tetyana I. and Wertheim, Joel O. and Tierney, Braden T. and Chiu, Charles Y. and Sun, Ren and Wu, Aiping and Abedalthagafi, Malak S. and Pak, Victoria M. and Nagaraj, Shivashankar H. and Smith, Adam L. and Skums, Pavel and Pasaniuc, Bogdan and Komissarov, Andrey and Mason, Christopher E. and Bortz, Eric and Lemey, Philippe and Kondrashov, Fyodor and Beerenwinkel, Niko and Lam, Tommy Tsan-Yuk and Wu, Nicholas C. and Zelikovsky, Alex and Knight, Rob and Crandall, Keith A. and Mangul, Serghei (2022) Unlocking capacities of genomics for the COVID-19 response and future pandemics. Nature Methods, 19 (4). pp. 374-380. ISSN 1548-7091. PMCID PMC9467803. doi:10.1038/s41592-022-01444-z.

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During the COVID-19 pandemic, genomics and bioinformatics have emerged as essential public health tools. The genomic data acquired using these methods have supported the global health response, facilitated the development of testing methods and allowed the timely tracking of novel SARS-CoV-2 variants. Yet the virtually unlimited potential for rapid generation and analysis of genomic data is also coupled with unique technical, scientific and organizational challenges. Here, we discuss the application of genomic and computational methods for efficient data-driven COVID-19 response, the advantages of the democratization of viral sequencing around the world and the challenges associated with viral genome data collection and processing.

Item Type:Article
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URLURL TypeDescription CentralArticle ReadCube access
Knyazev, Sergey0000-0003-0385-1831
Chhugani, Karishma0000-0001-8764-9352
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
Icer Baykal, Pelin0000-0002-9542-5292
Porozov, Yuri0000-0002-5450-3135
Vasylyeva, Tetyana I.0000-0002-9736-7022
Wertheim, Joel O.0000-0003-4882-5856
Chiu, Charles Y.0000-0003-2915-2094
Abedalthagafi, Malak S.0000-0003-1786-3366
Skums, Pavel0000-0003-4007-5624
Mason, Christopher E.0000-0002-1850-1642
Bortz, Eric0000-0002-1376-0012
Lemey, Philippe0000-0003-2826-5353
Beerenwinkel, Niko0000-0002-0573-6119
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:Our paper is dedicated to all freedom-loving people around the world, and to the people of Ukraine who fight for our freedom. We thank William M. Switzer and Ellsworth M. Campbell from the Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA, for discussions and suggestions. We thank Jason Ladner from the Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, for providing suggestions and feedback. S.M. was partially supported by National Science Foundation grants 2041984. T.L. is supported by the NSFC Excellent Young Scientists Fund (Hong Kong and Macau; 31922087), Research Grants Council (RGC) Collaborative Research Fund (C7144-20GF), RGC Research Impact Fund (R7021-20), Innovation and Technology Commission’s InnoHK funding (D24H) and Health and Medical Research Fund (COVID190223). P.S. was supported by US National Institutes of Health (NIH) grant 1R01EB025022 and National Science Foundation (NSF) grant 2047828. M.A. acknowledges King Abdulaziz City for Science and Technology and the Saudi Human Genome Project for technical and financial support ( N.W. was supported by US NIH grants R00 AI139445, DP2 AT011966 and R01 AI167910. A.S. acknowledge funding from NSF grant no. 2029025. A.Z. has been partially supported by NIH grants 1R01EB025022-01 and 1R21CA241044-01A1. S. Knyazev has been partly supported by Molecular Basis of Disease at Georgia State University and NIH awards R01 HG009120, R01 MH115676, R01 AI153827 and U01 HG011715. A.W. has been supported by the CAMS Innovation Fund for Medical Sciences (2021-I2M-1-061). R.K. was supported by 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. J.O.W. was supported by NIH–National Institute of Allergy and Infectious Diseases (NIAID) R01 AI135992 and receives funding from the CDC unrelated to this work. T.I.V. is supported by the Branco Weiss Fellowship. Y.P. was supported by the Ministry of Science and Higher Education of the Russian Federation within the framework of state support for the creation and development of World-Class Research Centers “Digital biodesign and personalized healthcare” N◦075-15-2020-926. E.B. was supported by a US National Institute of General Medical Sciences IDeA Alaska INBRE (P20GM103395) and NIAID CEIRR (75N93019R00028). C.E.M. thanks Testing for America (501c3), OpenCovidScreen Foundation, Igor Tulchinsky and the WorldQuant Foundation, Bill Ackman and Olivia Flatto and the Pershing Square Foundation, Ken Griffin and Citadel, the US National Institutes of Health (R01AI125416, R01AI151059, R21AI129851, U01DA053941), and the Alfred P. Sloan Foundation (G-2015-13964). C.Y.C. is supported by US CDC Epidemiology and Laboratory Capacity (ELC) for Infectious Diseases grant 6NU50CK000539 to the California Department of Public Health, the Innovative Genomics Institute (IGI) at the University of California, Berkeley, and University of California, San Francisco, NIH grant R33AI12945 and US CDC contract 75D30121C10991. A.K. was partly supported by RFBR grant 20-515-80017. P.L. acknowledges support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. ~725422 - ReservoirDOCS), the Wellcome Trust through project 206298/Z/17/Z (Artic Network) and NIH grants R01 AI153044 and U19 AI135995. K.C. acknowledges support from the US NSF award EEID-IOS-2109688. F.K.’s work was supported by an ERC Consolidator grant to F.K. (771209–CharFL). These authors contributed equally: Sergey Knyazev, Karishma Chhugani. Contributions. S.M. conceived of the idea presented and supervised the project. S.M., S. Knyazev and K.C. led the project. S.M., S. Knyazev, K.C., S. Karthikeyan, D.D., P.I.B., Z.C., A.L., Y.P., T.I.V., J.O.W., B.T.T., C.Y.C., R.S., A.W., M.S.A., V.M.P., S.H.N, A.L.S., P.S., A.K., B.P., C.E.M., E.B., F.K., N.C.W., N.B., P.L., S.K.N., T.T.-Y.L., A.Z., R.K. and K.A.C. contributed to the writing of the manuscript. V.S. produced figures in the main text. V.S. and H.S. produced supplementary figures. H.S. and R.A. created supplementary tables. All authors discussed the text and commented on the manuscript. All authors read and approved the final manuscript. These authors contributed equally: Sergey Knyazev and Karishma Chhugani (joint first co-authors). These authors contributed equally: Varuni Sarwal, Ram Ayyala and Harman Singh (joint second co-authors). The authors declare no competing interests.
Funding AgencyGrant Number
National Natural Science Foundation of China31922087
Research Grants Council of Hong KongC7144-20GF
Research Grants Council of Hong KongR7021-20
Innovation and Technology Commission (Hong Kong)D24H
Health and Medical Research Fund (China)COVID190223
King Abdulaziz City for Science and Technology (KACST)UNSPECIFIED
Saudi Human Genome ProjectUNSPECIFIED
NIHR00 AI139445
NIHDP2 AT011966
NIHR01 AI167910
Georgia State UniversityUNSPECIFIED
NIHR01 HG009120
NIHR01 MH115676
NIHR01 AI153827
NIHU01 HG011715
Chinese Academy of Medical Sciences2021-I2M-1-061
Centers for Disease Control and Prevention30055281
NIHR01 AI135992
Branco Weiss FellowshipUNSPECIFIED
Ministry of Science and Higher Education of the Russian FederationN◦075-15-2020-926
Testing for AmericaUNSPECIFIED
OpenCovidScreen FoundationUNSPECIFIED
Igor TulchinskyUNSPECIFIED
WorldQuant FoundationUNSPECIFIED
Pershing Square FoundationUNSPECIFIED
Citadel FoundationUNSPECIFIED
Alfred P. Sloan FoundationG-2015-13964
Centers for Disease Control and Prevention6NU50CK000539
California Department of Public HealthUNSPECIFIED
University of California, BerkeleyUNSPECIFIED
University of California, San FranciscoUNSPECIFIED
Centers for Disease Control and Prevention75D30121C10991
Russian Foundation for Basic Research20-515-80017
European Research Council (ERC)725422
Wellcome Trust206298/Z/17/Z
NIHR01 AI153044
NIHU19 AI135995
European Research Council (ERC)771209
Issue or Number:4
PubMed Central ID:PMC9467803
Record Number:CaltechAUTHORS:20221215-540336000.14
Persistent URL:
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:118351
Deposited By: George Porter
Deposited On:17 Dec 2022 00:12
Last Modified:17 Dec 2022 00:12

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