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 I 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

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 I Vasylyeva, Joel O Wertheim, Braden T Tierney, Charles Y Chiu, Ren Sun, Aiping Wu, Malak S Abedalthagafi, Victoria M Pak, Shivashankar H NagarajAdam 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

Research output: Contribution to journal › Article › peer-review

Abstract

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.

Original language	English (US)
Pages (from-to)	374-380
Number of pages	7
Journal	Nature Methods
Volume	19
Issue number	4
DOIs	https://doi.org/10.1038/s41592-022-01444-z
State	Published - Apr 2022

Keywords

COVID-19
Genomics
Humans
Pandemics
SARS-CoV-2/genetics

Online availability

10.1038/s41592-022-01444-z

Library availability

Discover UIUC Full Text

Cite this

Knyazev, S., Chhugani, K., Sarwal, V., Ayyala, R., Singh, H., Karthikeyan, S., Deshpande, D., Baykal, P. I., Comarova, Z., Lu, A., Porozov, Y., Vasylyeva, T. I., Wertheim, J. O., Tierney, B. T., Chiu, C. Y., Sun, R., Wu, A., Abedalthagafi, M. S., Pak, V. M., ... Mangul, S. (2022). Unlocking capacities of genomics for the COVID-19 response and future pandemics. Nature Methods, 19(4), 374-380. https://doi.org/10.1038/s41592-022-01444-z

Knyazev, S, Chhugani, K, Sarwal, V, Ayyala, R, Singh, H, Karthikeyan, S, Deshpande, D, Baykal, PI, Comarova, Z, Lu, A, Porozov, Y, Vasylyeva, TI, Wertheim, JO, Tierney, BT, Chiu, CY, Sun, R, Wu, A, Abedalthagafi, MS, Pak, VM, Nagaraj, SH, Smith, AL, Skums, P, Pasaniuc, B, Komissarov, A, Mason, CE, Bortz, E, Lemey, P, Kondrashov, F, Beerenwinkel, N, Lam, TT-Y, Wu, NC, Zelikovsky, A, Knight, R, Crandall, KA & Mangul, S 2022, 'Unlocking capacities of genomics for the COVID-19 response and future pandemics', Nature Methods, vol. 19, no. 4, pp. 374-380. https://doi.org/10.1038/s41592-022-01444-z

@article{dc2f076663424c68813ca71d5fa77bc8,

title = "Unlocking capacities of genomics for the COVID-19 response and future pandemics",

abstract = "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.",

keywords = "COVID-19, Genomics, Humans, Pandemics, SARS-CoV-2/genetics",

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

note = "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{\textquoteright}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{\textquoteright}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.{\textquoteright}s work was supported by an ERC Consolidator grant to F.K. (771209–CharFL).",

year = "2022",

month = apr,

doi = "10.1038/s41592-022-01444-z",

language = "English (US)",

volume = "19",

pages = "374--380",

journal = "Nature Methods",

issn = "1543-8384",

publisher = "American Chemical Society",

number = "4",

}

TY - JOUR

T1 - Unlocking capacities of genomics for the COVID-19 response and future pandemics

AU - Knyazev, Sergey

AU - Chhugani, Karishma

AU - Sarwal, Varuni

AU - Ayyala, Ram

AU - Singh, Harman

AU - Karthikeyan, Smruthi

AU - Deshpande, Dhrithi

AU - Baykal, Pelin Icer

AU - Comarova, Zoia

AU - Lu, Angela

AU - Porozov, Yuri

AU - Vasylyeva, Tetyana I

AU - Wertheim, Joel O

AU - Tierney, Braden T

AU - Chiu, Charles Y

AU - Sun, Ren

AU - Wu, Aiping

AU - Abedalthagafi, Malak S

AU - Pak, Victoria M

AU - Nagaraj, Shivashankar H

AU - Smith, Adam L

AU - Skums, Pavel

AU - Pasaniuc, Bogdan

AU - Komissarov, Andrey

AU - Mason, Christopher E

AU - Bortz, Eric

AU - Lemey, Philippe

AU - Kondrashov, Fyodor

AU - Beerenwinkel, Niko

AU - Lam, Tommy Tsan-Yuk

AU - Wu, Nicholas C

AU - Zelikovsky, Alex

AU - Knight, Rob

AU - Crandall, Keith A

AU - Mangul, Serghei

N1 - 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).

PY - 2022/4

Y1 - 2022/4

N2 - 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.

AB - 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.

KW - COVID-19

KW - Genomics

KW - Humans

KW - Pandemics

KW - SARS-CoV-2/genetics

U2 - 10.1038/s41592-022-01444-z

DO - 10.1038/s41592-022-01444-z

M3 - Article

C2 - 35396471

SN - 1543-8384

VL - 19

SP - 374

EP - 380

JO - Nature Methods

JF - Nature Methods

IS - 4

ER -

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

Abstract

Keywords

Online availability

Library availability

Fingerprint

Cite this