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

Knyazev, Sergey; Chhugani, Karishma; Sarwal, Varuni; Ayyala, Ram; Singh, Harman; Karthikeyan, Smruthi; Deshpande, Dhrithi; Icer Baykal, Pelin; Comarova, Zoia; Lu, Angela; Porozov, Yuri; Vasylyeva, Tetyana I.; Wertheim, Joel O.; Tierney, Braden T.; Chiu, Charles Y.; Sun, Ren; Wu, Aiping; Abedalthagafi, Malak S.; Pak, Victoria M.; Nagaraj, Shivashankar H.; Smith, Adam L.; Skums, Pavel; Pasaniuc, Bogdan; Komissarov, Andrey; Mason, Christopher E.; Bortz, Eric; Lemey, Philippe; Kondrashov, Fyodor; Beerenwinkel, Niko; Lam, Tommy Tsan-Yuk; Wu, Nicholas C.; Zelikovsky, Alex; Knight, Rob; Crandall, Keith A.; Mangul, Serghei

doi:10.1038/s41592-022-01444-z

Published April 2022 | Version public

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

1. University of California, Los Angeles
2. University of Southern California
3. Indian Institute of Technology Delhi
4. University of California, San Diego
5. ETH Zurich
6. Swiss Institute of Bioinformatics
7. Sechenov University
8. Sirius University of Science and Technology
9. Cornell University
10. University of California, San Francisco
11. University of Hong Kong
12. Chinese Academy of Medical Sciences & Peking Union Medical College
13. Suzhou Institute of Systems Medicine
14. King Abdulaziz City for Science and Technology
15. King Salman Center for Disability Research
16. Emory University
17. Queensland University of Technology
18. Translational Research Institute
19. Georgia State University
20. Research Institute of Influenza
21. University of Alaska Anchorage
22. Rega Institute for Medical Research
23. Institute of Science and Technology Austria
24. University of Illinois Urbana-Champaign
25. George Washington University

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.

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 (https://shgp.kacst.edu.sa) 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.

Additional details

PMCID: PMC9467803
Eprint ID: 118351
Resolver ID: CaltechAUTHORS:20221215-540336000.14

NSF
DBI-2041984
National Natural Science Foundation of China
31922087
Research Grants Council of Hong Kong
C7144-20GF
Research Grants Council of Hong Kong
R7021-20
Innovation and Technology Commission (Hong Kong)
D24H
Health and Medical Research Fund (China)
COVID190223
NIH
1R01EB025022
NSF
CCF-2047828
King Abdulaziz City for Science and Technology (KACST)
Saudi Human Genome Project
NIH
R00 AI139445
NIH
DP2 AT011966
NIH
R01 AI167910
NSF
CBET-2029025
NIH
1R01EB025022-01
NIH
1R21CA241044-01A1
Georgia State University
NIH
R01 HG009120
NIH
R01 MH115676
NIH
R01 AI153827
NIH
U01 HG011715
Chinese Academy of Medical Sciences
2021-I2M-1-061
NSF
DBI-2038509
Centers for Disease Control and Prevention
30055281
NIH
R01 AI135992
Branco Weiss Fellowship
Ministry of Science and Higher Education of the Russian Federation
N◦075-15-2020-926
NIH
P20GM103395
NIH
75N93019R00028
Testing for America
OpenCovidScreen Foundation
Igor Tulchinsky
WorldQuant Foundation
Pershing Square Foundation
Citadel Foundation
NIH
R01AI125416
NIH
R01AI151059
NIH
R21AI129851
NIH
U01DA053941
Alfred P. Sloan Foundation
G-2015-13964
Centers for Disease Control and Prevention
6NU50CK000539
California Department of Public Health
University of California, Berkeley
University of California, San Francisco
NIH
R33AI12945
Centers for Disease Control and Prevention
75D30121C10991
Russian Foundation for Basic Research
20-515-80017
European Research Council (ERC)
725422
Wellcome Trust
206298/Z/17/Z
NIH
R01 AI153044
NIH
U19 AI135995
NSF
DEB-2109688
European Research Council (ERC)
771209

Created: 2022-12-17

Created from EPrint's datestamp field
Updated: 2022-12-17

Created from EPrint's last_modified field

Caltech groups: COVID-19

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

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