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IGI COVID-19 Initiative
Overview
In the early months of 2020, the global threat of COVID-19 united the scientific community. At the IGI, we created a pop-up coronavirus testing lab in our building on UC Berkeley campus over the course of three weeks. We tested patient samples from the UC Berkeley community, as well as first responders in the area, and vulnerable people without insurance or permanent housing. We developed new protocols for COVID testing, launched mobile testing for California farmworkers, and developed new rapid testing technology and clinical assays. Our scientists quickly formed rapid response research teams, working to better understand, detect, track, and treat the virus.
At the end of 2022, after processing over 650,000 tests, the IGI halted its COVID testing operations, but IGI investigators are still working on COVID-related research, and the IGI Clinical Laboratory is expanding its role in the institute as part of the Interventional Genomics Unit. Learn more and find resources below.
More COVID Resources
- Watch UC Berkeley Professor and IGI Investigator Britt Glaunsinger's molecular virology lecture, "Coronaviruses 101."
- Struggling through coronavirus literature? Try covidscholar.org, a COVID-19 research search portal.
- View our whiteboard video overview describing CRISPR-based diagnostic tools, which we and others are developing for rapid SARS-CoV-2 detection.
- Science@Cal has developed a great resource page with basic information about COVID-19.
- Read our Nature Biotechnology paper, Blueprint for a pop-up SARS-CoV-2 testing lab.
Related Publications
SARS-CoV-2 Spike triggers barrier dysfunction and vascular leak via integrins and TGF-β signaling
Biering SB, Gomes de Sousa FT, Tjang LV ... Näär AM, Baric RS, Stanley SA, Aguilar HC, Esko JD, Chiu CY, Pak JE, Beatty PR, Harris E. Nature Communications
(2022)Association of upper respiratory Streptococcus pneumoniae colonization with SARS-CoV-2 infection among adults
Parker AM, Jackson N, Awasthi S, Kim H, Alwan T, Wyllie AL, Baldwin AB, Brennick NB, Moehle EA, Giannikopoulos P, Kogut K, Holland N, Mora-Wyrobek A, Eskenazi B, Riley LW, and Lewnard JA. Clinical Infectious Diseases
(2022)Rapid detection of SARS-CoV-2 RNA in saliva via Cas13
Chandrasekaran SS, Agrawal S, Fanton A...Fletcher DA, Doudna JA, Savage DF and Hsu PD. Nature Biomedical Engineering
(2022)An intranasal ASO therapeutic targeting SARS-CoV-2
Zhu C, Lee JY, Woo JZ...Rouskin S and Näär AM. Nature Communications
(2022)Genome-wide bidirectional CRISPR screens identify mucins as host factors modulating SARS-CoV-2 infection
Biering SB, Sarnik SA, Wang E...Stanley SA, Harris E, Konermann S and Hsu PD. Nature Genetics
(2022)Omicron mutations enhance infectivity and reduce antibody neutralization of SARS-CoV-2 virus-like particles
Syed AM, Ciling A, Taha TY...Ott M, and Doudna JA. PNAS
(2022)Unlocking capacities of genomics for the COVID-19 response and future pandemics
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, and Mangul S. Nature Methods
(2022)Impact of COVID-19 pandemic on California farmworkers’ mental health and food security
Mora AM, Lewnard JA, Rauch S, Kogut K, Jewell N, Cuevas M, and Eskenazi B. Journal of Agromedicine
(2022)Neutralizing immunity in vaccine breakthrough infections from the SARS-CoV-2 Omicron and Delta variants
Servellita V, Syed AM, Morris MK, Brazer N, Saldhi P, Garcia-Knight M, Sreekumar B, Khalid MM, Ciling A, Chen PY, Kumar GR, Gliwa AS, Nguyen J, Sotomayor-Gonzalez A, Zhang Y, Frias E, Prostko J, Hackett Jr. J, Andino R, Wadford DA, Hanson C, Doudna JA, Ott M, and Chiu CY. Cell
(2022)Predominance of antibody-resistant SARS-CoV-2 variants in vaccine breakthrough cases from the San Francisco Bay Area, California
Servellita V, Morris MK, Sotomayor-Gonzalez A, Gilwa AS, Torres E, Brazer N, Zhou A, Hernandez KT, Sankaran M, Wang B, Wong D, Wang C, Zhang Y, Reyes KR, Glasner D, Deng X, Streithorst J, Miller S, Frias E, Rodgers M, Cloherty G, Hackett Jr. J, Hanson C, Wadford D, Philip S, Topper S, Sachdev D, and Chiu CY. Nature Microbiology
(2022)Optimizing COVID-19 control with asymptomatic surveillance testing in a university environment
Brook CE, Northrup GR, Ehrenberg AJ, Doudna JA, and Boots M. Epidemics
(2021)Multiplexed SARS-CoV-2 detection in clinical swab and wastewater samples
Stahl EC, Gopez AR, Tsuchida CA, Fan VB, Moehle EA, Witkowsky LB, Hamilton JR, Lin-Shiao E, McElroy M, McDevitt SL, Ciling A, Tsui CK, Pestal K, Gildea HK, Keller A, Sylvain IA, Williams C, Hirsh A, Ehrenberg AJ, Kantor R, Metzger M, Nelson KL, Urnov FD, Ringeisen BR, Giannikopoulos P, Doudna JA, and the IGI Testing Consortium. PLoS One
(2021)Rapid assessment of SARS-CoV-2 evolved variants using virus-like particles
Syed AM, Taha TY, Tabata T, Chen IP, Ciling A, Khalid MM, Sreekumar B, Chen P, Hayashi JM, Soczek KM, Ott M, and Doudna JA. Science
(2021)The N-terminal domain of SARS-CoV-2 nsp1 plays key roles in suppression of cellular gene expression and preservation of viral gene expression
Mendez AS, Ly M, González-Sánchez AM, Hartenian E, Ingolia NT, Cate JH, and Glaunsinger BA. Cell Reports
(2021)Risk factors associated with SARS-CoV-2 infection among farmworkers in Monterey County, California
Mora AM, Lewnard JA, Kogut K, Rauch SA, Hernandez S, Wong MP, Huen K, Chang C, Jewell NP, Holland N, Harris E, Cuevas M, Eskenazi B, and the CHAMACOS-Project-19 Study Team. JAMA Network
(2021)A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa
Wilkinson E, Giovanetti M, Tegally H, et al. Science
(2021)Health inequities in SARS-CoV-2 infection, seroprevalence, and COVID-19 vaccination: Results from the East Bay COVID-19 study
Adams C, Horton M, Solomon O...Coloma J, Lewnard JA, Harris E, and Barcellos LF. PLOS Global Public Health
(2021)Robotic RNA extraction for SARS-CoV-2 surveillance using saliva samples
Hamilton JR, Stahl EC, Tsuchida CA, LinShiao E, Tsui CK, Pestal K, GildeaI HK, Witkowsky LB, Moehle EA, McDevitt SL, McElroy M, Keller A, Sylvain I, Hirsh A, Ciling A, Ehrenberg AJ, Ringeisen BR, Huberty G, Urnov FD, Giannikopoulos P, Doudna JA, and the IGI SARS-CoV-2 Consortium. PLoS One
(2021)Accelerated RNA detection using tandem CRISPR nucleases
Liu TY, Knott GJ, Smock DCJ, Desmarais JJ, Son S, Bhuiya A, Jakhanwal S, Prywes N, Agrawal S, Díaz de León Derby M, Switz NA, Armstrong M, Harris AR, Charles EJ, Thornton BW, Fozouni P, Shu J, Stephens SI, Kumar GR, Zhao C, Mok A, Iavarone AT, Escajeda AM, McIntosh R, Kim S, Dugan EJ, IGI Testing Consortium, Pollard KS, Tan MX, Ott M, Fletcher DA, Lareau LF, Hsu PD, Savage DF, and Doudna JA. Nature Chemical Biology
(2021)Reflections on conducting research from home during COVID-19
Coté LE. Project Muse
(2021)Screening a Library of FDA-Approved and Bioactive Compounds for Antiviral Activity against SARS-CoV-2
Biering SB, Van Dis E, Wehri E...Ott M, Murthy N, Nomura DK, Schaletzky J and Stanley SA. ACS Infectious Diseases
(2021)Extraction of Viral Nucleic Acids with Carbon Nanotubes Increases SARS-CoV‑2 Quantitative Reverse Transcription Polymerase Chain Reaction Detection Sensitivity
Jeong S, González-Grandío E, Navarro N, Pinals RL, Ledesma F, Yang D, and Landry MP. ACS Nano
(2021)Launching a saliva-based SARS-CoV-2 surveillance testing program on a university campus
Ehrenberg AJ, Moehle EA, Brook CE, Cate AHD, Witkowsky LB, Sachdeva R, Hirsh A, Barry K, Hamilton JR, Lin-Shiao E, McDevitt S, Valentin-Alvarado L, Letourneau KN, Hunter L, Keller A, Pestal K, Frankino PA, Murley A, Nandakumar D, Stahl EC, Tsuchida CA, Gildea HK, Murdock AG, Hochstrasser ML, O’Brien E, Ciling A, Tsitsiklis A, Worden K, Dugast-Darzacq C, Hays SG, Barber CC, McGarrigle R, Lam EK, Ensminger DC, Bardet L, Sherry C, Harte A, Nicolette G, Giannikopoulos P, Hockemeyer D, Petersen M, Urnov FD, Ringeisen BR, Boots M, and Doudna JA on behalf of the IGI SARS-CoV-2 Testing Consortium. PLoS One
(2021)Transmission, infectivity, and neutralization of a spike L452R SARS-CoV-2 variant
Deng X, Garcia-Knight MA, Khalid MM, Servellita V, Wang C, Morris MK, Sotomayor-González A, Glasner DR, Reyes KR, Gliwa AS, Reddy NP, San Martin CS, Federman S, Cheng J, Balcerek J, Taylor J, Streithorst JA, Miller S, Sreekumar B, Chen PY, Schulze-Gahmen U, Taha TY, Hayashi J, Simoneau CR, Kumar GR, McMahon S, Lidsky PV, Xiao Y, Hemarajata P, Green NM, Espinosa A, Kath C, Haw M, Bell J, Hacker JK, Hanson C, Wadford DA, Anaya C, Ferguson D, Frankino PA, Shivram H, Lareau LF, Wyman SK, Ott M, Andino R, and Chiu CY. Cell
(2021)Sewage, salt, silica, and SARS-CoV-2 (4S): An economical kit-free method for direct capture of SARS-CoV-2 RNA from wastewater
Whitney ON, Kennedy LC, Fan VB, Hinkle A, Kantor R, Greenwald H, Crits-Christoph A, Al-Shayeb B, Chaplin M, Maurer AC, Tjian R, and Nelson KL. Environmental Science & Technology
(2021)Prevalence and Clinical Profile of Severe Acute Respiratory Syndrome Coronavirus 2 Infection among Farmworkers, California, USA, June–November 2020
Lewnard JA, Mora AM, Nkwocha O...Harris E, Cuevas M, Eskenazi B, and on behalf of the CHAMACOS-Project-19 Study Team. Emerging Infectious Diseases
(2021)Rapid SARS-CoV-2 spike protein detection by carbon nanotube-based near-infrared nanosensors.
Pinals RL, Ledesma F, Yang D, Navarro N, Jeong S, Pak JE, Kuo L, Chuang Y, Cheng Y, Sun H, and Landry MP. Nano Letters
(2021)Piloting an integrated SARS-CoV-2 testing and data system for outbreak containment among college students: A prospective cohort study.
Packel L, Reingold A, Hunter L, Facente S, Li Y, Harte A, Nicolette G, Urnov FD, Lu M, Peterson M, and the IGI Testing Consortium. PLoS One
(2021)Genome sequencing of sewage detects regionally prevalent SARS-CoV-2 variants.
Crits-Christoph A, Kantor RS, Olm MR, Whitney ON, Al-Shayeb B, Lou YC, Flamholz A, Kennedy LC, Greenwald H, Hinkle A, Hetzel J, Spitzer S, Koble J, Tan A, Hyde F, Schroth G, Kuersten S, Banfield JF, and Nelson KL. American Society for Microbiology
(2021)Genetic screens identify host factors for SARS-CoV-2 and common cold coronaviruses.
Wang R, Simoneau CR, Kulsuptrakul J, Bouhaddou M, Travisano KA, Hayashi JM, Carlson-Stevermer J, Zengel JR, Richards CM, Fozouni P, Oki J, Rodriguez L, Joehnk B, Walcott K, Holden K, Sil A, Carette JE, Krogan NJ, Ott M, and Puschnik AS. Cell
(2021)Identifying vaccine hesitant communities on twitter and their geolocations: A network approach
Ruiz JB, Featherstone JD, and Barnett GA. ScholarSpace
(2021)Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms.
Gordon DE, Hiatt J, Bouhaddou M...Rosenberg OS, Verba KA, Basler CF, Vignuzzi M, Peden AA, Beltrao P, and Krogan NJ. Science
(2020)Exploring childhood anti-vaccine and pro-vaccine communities on twitter – a perspective from influential users.
Featherstone JD, Barnett GA, Ruiz JB, Zhuang Y, and Millam BJ. ScienceDirect
(2020)Evaluation of SARS-CoV-2 serology assays reveals a range of test performance.
Whitman JD, Hiatt J, Mowery CT, Shy BR, Yu R, Yamamoto TN, Rathore U, Goldgof GM, Whitty C, Woo JM, Gallman AE, Miller TE, Levine AG, Nguyen DN, Bapat SP, Balcerek J, Bylsma SA, Lyons AM, Li S, Wong AW, Gillis-Buck EM, Steinhart ZB, Lee Y, Apathy R, Lipke MJ, Smith JA, Zheng T, Boothby IC, Isaza E, Chan J, Acenas II DD, Lee J, Macrae TA, Kyaw TS, Wu D, Ng DL, Gu W, York VA, Eskandarian HA, Callaway PC, Warrier L, Moreno ME, Levan J, Torres L, Farrington LA, Loudermilk RP, Koshal K, Zorn KC, Garcia-Beltran WF, Yang D, Astudillo MG, Bernstein BE, Gelfand JA, Ryan ET, Charles RC, Iafrate AJ, Lennerz JK, Miller S, Chiu CY, Stramer SL, Wilson MR, Manglik A, Ye CJ, Krogan NJ, Anderson MS, Cyster JG, Ernst JD, Wu AHB, Lynch KL, Bern C, Hsu PD, and Marson A. Nature Biotechnology
(2020)Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California.
Deng X, Gu W, Federman S, Plessis LD, Pybus OG, Faria NR, Wang C, Yu G, Bushnell B, Pan CY, Guevara H, Sotomayor-Gonzalez A, Zorn K, Gopez A, Servellita V, Hsu E, Miller S, Bedford T, Greninger AL, Roychoudhury P, Starita LM, Famulare M, Chu HY, Shendure J, Jerome KR, Anderson C, Gangavarapu K, Zeller M, Spencer E, Andersen KG, MacCannell D, Paden CR, Li Y, Zhang J, Tong S, Armstrong G, Morrow S, Willis M, Matyas BT, Mase S, Kasirye O, Park M, Masinde G, Chan C, Yu AT, Chai SJ, Villarino Elsa, Bonin B, Wadford DA, and Chiu CY. Science
(2020)The global phosphorylation landscape of SARS-CoV-2 infection.
Bouhaddou M, Memon D, Meyer B, White KM, Rezelj VV, Marrero MC, Polacco BJ, Melnyk JE, Ulferts S, Kaake RM, Batra J, Richards AL, Stevenson E, Gordon DE, Rojc A, Obernier K, Fabius JM, Soucheray M, Miorin L, Moreno E, Koh C, Tran QD, Hardy A, Robinot R, Vallet T, Nilsson-Payant BE, Hernandez-Armenta C, Dunham A, Weigang S, Knerr J, Modak M, Quintero D, Zhou Y, Dugourd A, Valdeolivas A, Patil T, Li Q, Hüttenhain R, Cakir M, Muralidharan M, Kim M, Jang G, Tutuncuoglu B, Hiatt J, Guo JZ, Xu J, Bouhaddou S, Mathy CJP, Gaulton A, Manners EJ, Félix E, Shi Y, Goff M, Lim JK, McBride T, O'Neal MC, Cai Y, Chang JCJ, Broadhurst DJ, Klippsten S, De wit E, Leach AR, Kortemme T, Shoichet B, Ott M, Saez-Rodriguez J, tenOever BR, Mullins D, Fischer ER, Kochs G, Grosse R, García-Sastre A, Vignuzzi M, Johnson JR, Shokat KM, Swaney DL, Beltrao P, and Krogan NJ. Cell
(2020)Blueprint for a pop-up SARS-CoV-2 testing lab.
Amen AM, Barry KW, Boyle JM, Brook CE, Choo S, Cornmesser LT, Dilworth DJ, Doudna JA, Ehrenberg AJ, Fedrigo I, Friedline SE, Graham TGW, Green R, Hamilton JR, Hirsh A, Hochstrasser ML, Hockemeyer D, Krishnappa N, Lari A, Li H, Lin-Shiao E, Lu T, Lyons EF, Mark KG, Martell LA, Martins ARO, McDevitt SL, Mitchell PS, Moehle EA, Naca C, Nandakumar D, O'Brien E, Pappas DJ, Pestal K, Quach DL, Rubin BE, Sachdeva R, Stahl EC, Syed AM, Tan I, Tsuchida CA, Tollner A, Tsui CK, Turkalo TK, Urnov FD, Warf MB, Whitney ON, and Witkowsky LB. Nature Biotechnology
(2020)Building a COVID-19 pop-up testing lab.
Hamilton J. The CRISPR Journal
(2020)SARS-Cov2 clinical diagnostics: academic scientists take on the COVID-19 pandemic.
Urnov FD. Med
(2020)Selected Media Coverage
Articles:
- Why researchers hope to test high-risk groups in California — The New York Times
- Coronavirus is spreading under the radar in US homeless shelters — Nature News
- How a CRISPR Lab became a Pop-Up COVID testing center — WIRED
- Ivory Power: How genetic scientists at Berkeley raced to the labs and created a high-speed test for the coronavirus — Air Mail
TV News:
- Our New Reality: A Diane Sawyer Special — ABC News
- No nasal swab? UC Berkeley tries COVID spit test — Reuters
- East Bay pop-up laboratory to improve speed of COVID-19 test results — ABC7
- How CRISPR Can Be Used to Fight COVID-19 — Amanpour & Company
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