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

被引：29

作者：

Knyazev, Sergey ^{[1
]}

Chhugani, Karishma ^{[2
]}

Sarwal, Varuni ^{[3
]}

Ayyala, Ram ^{[4
]}

Singh, Harman ^{[5
]}

Karthikeyan, Smruthi ^{[6
]}

Deshpande, Dhrithi ^{[2
]}

Baykal, Pelin Icer ^{[7
,8
]}

Comarova, Zoia ^{[9
]}

Lu, Angela ^{[2
]}

Porozov, Yuri ^{[10
,11
]}

Vasylyeva, Tetyana, I ^{[12
]}

Wertheim, Joel O. ^{[12
]}

Tierney, Braden T. ^{[13
]}

Chiu, Charles Y. ^{[14
,15
,16
]}

Sun, Ren ^{[17
,18
]}

Wu, Aiping ^{[19
,20
]}

Abedalthagafi, Malak S. ^{[21
,22
,23
]}

Pak, Victoria M. ^{[24
,25
]}

Nagaraj, Shivashankar H. ^{[26
,27
]}

Smith, Adam L. ^{[9
]}

Skums, Pavel ^{[28
]}

Pasaniuc, Bogdan ^{[1
,29
,30
,31
,32
]}

Komissarov, Andrey ^{[33
]}

Mason, Christopher E. ^{[13
,34
,35
,36
]}

Bortz, Eric ^{[37
]}

Lemey, Philippe ^{[38
]}

Kondrashov, Fyodor ^{[39
]}

Beerenwinkel, Niko ^{[7
,8
]}

Lam, Tommy Tsan-Yuk ^{[40
,41
,42
]}

Wu, Nicholas C. ^{[43
,44
,45
,46
]}

Zelikovsky, Alex ^{[28
]}

Knight, Rob ^{[6
,47
,48
,49
]}

Crandall, Keith A. ^{[50
,51
]}

Mangul, Serghei ^{[52
]}

机构：

[1] Univ Calif Los Angeles, David Geffen Sch Med, Dept Pathol & Lab Med, Los Angeles, CA 90095 USA

[2] Univ Southern Calif, Sch Pharm, Dept Pharmacol & Pharmaceut Sci, Los Angeles, CA USA

[3] Univ Calif Los Angeles, Dept Comp Sci, Los Angeles, CA 90024 USA

[4] Univ Southern Calif, Dept Translat Biomed Informat, Los Angeles, CA USA

[5] Indian Inst Technol, Dept Elect Engn, New Delhi, India

[6] Univ Calif San Diego, Dept Pediat, La Jolla, CA USA

[7] Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland

[8] SIB Swiss Inst Bioinformat, Basel, Switzerland

[9] Univ Southern Calif, Astani Dept Civil & Environm Engn, Los Angeles, CA USA

[10] IM Sechenov First Moscow State Med Univ, World Class Res Ctr Digital Biodesign & Personali, Moscow, Russia

[11] Sirius Univ Sci & Technol, Dept Computat Biol, Soci, Russia

[12] Univ Calif San Diego, Dept Med, La Jolla, CA 92093 USA

[13] Weill Cornell Med, Dept Physiol & Biophys, New York, NY USA

[14] Univ Calif San Francisco, Dept Lab Med, San Francisco, CA USA

[15] Univ Calif San Francisco, Dept Med, Div Infect Dis, San Francisco, CA 94143 USA

[16] Univ Calif San Francisco, UCSF Abbott Viral Diagnost & Discovery Ctr, San Francisco, CA USA

[17] Univ Calif Los Angeles, Dept Mol & Med Pharmacol, Los Angeles, CA USA

[18] Univ Hong Kong, LKS Fac Med, Sch Biomed Sci, Hong Kong, Peoples R China

[19] Chinese Acad Med Sci & Peking Union Med Coll, Inst Syst Med, Beijing, Peoples R China

[20] Suzhou Inst Syst Med, Suzhou, Peoples R China

[21] King Fahad Med City, Genom Res Dept, Saudi Human Genome Project, Riyadh, Saudi Arabia

[22] King Abdulaziz City Sci & Technol, Riyadh, Saudi Arabia

[23] King Salman Ctr Disabil Res, Riyadh, Saudi Arabia

[24] Emory Univ, Sch Nursing, Atlanta, CA USA

[25] Emory Univ, Rollins Sch Publ Hlth, Dept Epidemiol, Atlanta, CA USA

[26] Queensland Univ Technol, Ctr Genom & Personalised Hlth, Brisbane, Qld, Australia

[27] Translat Res Inst, Brisbane, Qld, Australia

[28] Georgia State Univ, Coll Art & Sci, Dept Comp Sci, Atlanta, GA 30303 USA

[29] Univ Calif Los Angeles, Bioinformat Interdept Program, Los Angeles, CA USA

[30] Univ Calif Los Angeles, David Geffen Sch Med, Dept Human Genet, Los Angeles, CA 90095 USA

[31] Univ Calif Los Angeles, David Geffen Sch Med, Dept Computat Med, Los Angeles, CA 90095 USA

[32] Univ Calif Los Angeles, Inst Precis Hlth, Los Angeles, CA USA

[33] Smorodintsev Res Inst Influenza, St Petersburg, Russia

[34] Weill Cornell Med, HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsau, New York, NY USA

[35] Weill Cornell Med, WorldQuant Initiat Quantitat Predict, New York, NY USA

[36] Weill Cornell Med, Feil Family Brain & Mind Res Inst, New York, NY USA

[37] Univ Alaska, Dept Biol Sci, Anchorage, CA USA

[38] KU Leuven Univ Leuven, Rega Inst, Dept Microbiol Immunol & Transplantat, Leuven, Belgium

[39] IST Austria, Klosterneuburg, Austria

[40] Univ Hong Kong, Sch Publ Hlth, State Key Lab Emerging Infect Dis, Hong Kong, Peoples R China

[41] Lab Data Discovery Hlth Ltd, Hong Kong, Peoples R China

[42] Ctr Immunol & Infect Ltd, Hong Kong, Peoples R China

[43] Univ Illinois, Dept Biochem, Urbana, IL USA

[44] Univ Illinois, Carl R Woese Inst Genom Biol, Urbana, IL USA

[45] Univ Illinois, Ctr Biophys & Quantitat Biol, Urbana, IL USA

[46] Univ Illinois, Carle Illinois Coll Med, Urbana, IL USA

[47] Univ Calif San Diego, Dept Bioengn, La Jolla, CA 92093 USA

[48] Univ Calif San Diego, Dept Comp Sci & Engn, La Jolla, CA 92093 USA

[49] Univ Calif San Diego, Ctr Microbiome Innovat, La Jolla, CA 92093 USA

[50] George Washington Univ, Computat Biol Inst, Milken Inst Sch Publ Hlth, Washington, DC USA

来源：

NATURE METHODS | 2022年 / 19卷 / 04期

基金：

美国国家科学基金会; 美国国家卫生研究院; 欧洲研究理事会; 英国惠康基金;

关键词：

SARS-COV-2; EPIDEMIC; SURVEILLANCE; EMERGENCE; HEALTH;

D O I：

10.1038/s41592-022-01444-z

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：374 / 380

页数：7

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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
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