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

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

doi:10.1038/s41592-022-01444-z

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

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

Sergey Knyazev, Karishma Chhugani, Varuni Sarwal, Ram Ayyala, Harman Singh, Smruthi Karthikeyan, Dhrithi Deshpande, Pelin Icer Baykal, Zoia Comarova, Angela Lu, …

Nature methods, Vol.19(4), pp.374-380

01/04/2022

DOI: https://doi.org/10.1038/s41592-022-01444-z

PMID: 35396471

Abstract

Biochemical Research Methods

Biochemistry & Molecular Biology

Life Sciences & Biomedicine

Science & Technology

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.

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Title: Unlocking capacities of genomics for the COVID-19 response and future pandemics
Creators - without role: Sergey Knyazev - University of California, Los Angeles
Karishma Chhugani - University of Southern California
Varuni Sarwal - University of California, Los Angeles
Ram Ayyala - University of Southern California
Harman Singh - Indian Institute of Technology Delhi
Smruthi Karthikeyan - University of California, San Diego
Dhrithi Deshpande - University of Southern California
Pelin Icer Baykal - ETH Zurich
Zoia Comarova - University of Southern California
Angela Lu - University of Southern California
Yuri Porozov - Sechenov University
Tetyana Vasylyeva - University of California, San Diego
Joel O. Wertheim - University of California, San Diego
Braden T. Tierney - Cornell College
Charles Y. Chiu - University of California, San Francisco
Ren Sun - University of California, Los Angeles
Aiping Wu - Chinese Academy of Medical Sciences & Peking Union Medical College
Malak S. Abedalthagafi - King Abdulaziz City for Science and Technology
Victoria M. Pak - Emory University
Shivashankar H. Nagaraj - Queensland University of Technology
Adam L. Smith - University of Southern California
Pavel Skums - Georgia State University
Bogdan Pasaniuc - University of California, Los Angeles
Andrey Komissarov - Research Institute of Influenza
Christopher E. Mason - Cornell College
Eric Bortz - University of Alaska Anchorage
Philippe Lemey - Rega Institute for Medical Research
Fyodor Kondrashov - Institute of Science and Technology Austria
Niko Beerenwinkel - ETH Zurich
Tommy Tsan-Yuk Lam - Laboratory of Data Discovery for Health
Nicholas C. Wu - University of Illinois Urbana-Champaign
Alex Zelikovsky - Georgia State University
Rob Knight - University of California, San Diego
Keith A. Crandall - Milken Institute
Serghei Mangul - University of Southern California
Publication Details: Nature methods, Vol.19(4), pp.374-380
Publisher: NATURE PORTFOLIO
Number of pages: 7
Grant note: OpenCovidScreen Foundation Branco Weiss Fellowship P20GM103395 / US National Institute of General Medical Sciences IDeA Alaska INBRE 2041984 / National Science Foundation; National Science Foundation (NSF) Igor Tulchinsky R7021-20 / RGC Research Impact Fund 2047828 / National Science Foundation (NSF) R01AI125416; R01AI151059; R21AI129851; U01DA053941 / US National Institutes of Health; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA WorldQuant Foundation D24H / Innovation and Technology Commission's InnoHK 1R01EB025022 / US National Institutes of Health (NIH); United States Department of Health & Human Services; National Institutes of Health (NIH) - USA 75N93019R00028 / NIAID CEIRR 1R01EB025022-01; 1R21CA241044-01A1; R01 HG009120; R01 MH115676; R01 AI153827; U01 HG011715; R33AI12945; R01 AI153044; U19 AI135995 / NIH; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA R01 AI135992 / NIH-National Institute of Allergy and Infectious Diseases (NIAID); United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of Allergy & Infectious Diseases (NIAID) R00 AI139445; DP2 AT011966; R01 AI167910 / US NIH; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA 31922087 / NSFC Excellent Young Scientists Fund (Hong Kong and Macau) similar to725422 / European Research Council (ERC) under the European Union; European Research Council (ERC) King Abdulaziz City for Science and Technology 206298/Z/17/Z / Wellcome Trust G-2015-13964 / Alfred P. Sloan Foundation 501c3 / Testing for America 2021-I2M-1-061 / CAMS Innovation Fund for Medical Sciences Molecular Basis of Disease at Georgia State University 20-515-80017 / RFBR; Russian Foundation for Basic Research (RFBR) 075-15-2020-926 / Ministry of Science and Higher Education of the Russian Federation 6NU50CK000539 / US CDC Epidemiology and Laboratory Capacity (ELC) Ken Griffin and Citadel 771209 / ERC; European Research Council (ERC); European Commission 2029025; 2038509 / NSF; National Science Foundation (NSF) Pershing Square Foundation 30055281 / CDC; United States Department of Health & Human Services; Centers for Disease Control & Prevention - USA Saudi Human Genome Project COVID190223 / Health and Medical Research Fund C7144-20GF / Research Grants Council (RGC) Collaborative Research Fund 75D30121C10991 / US CDC; United States Department of Health & Human Services; Centers for Disease Control & Prevention - USA EEID-IOS-2109688 / US NSF; National Science Foundation (NSF)
Identifiers: 9918783408331
Academic Unit: King Abdulaziz City for Science & Technology
Language: English
Resource Type: Journal article