Charles Chiu, MD, PhD

Director, UCSF-Abbott Viral Diagnostics and Discovery Center (VDDC)
Associate Director, UCSF Clinical Microbiology Laboratory
Professor
Department of Laboratory Medicine
Department of Medicine - Infectious Disease
Primary Thematic Area
Secondary Thematic Area
Research Summary
Metagenomics-Based Technologies for Virus Detection and Discovery
+1 415 514-8219

I am an infectious diseases physician and microbiologist and lead a translational research laboratory focusing on (i) metagenomic next-generation sequencing (mNGS) assay development for infectious disease diagnostics, (ii) discovery and characterization of emerging viral pathogens, and (iii) development of new bioinformatic tools and cutting-edge genomic technologies for clinical and public health applications. Current projects in my laboratory include (i) pathogen discovery in tickborne infections, acute febrile illness, and blood screening, (ii) investigating links between enterovirus infection and acute flaccid myelitis, and (iii) cell culture, human, and animal studies of Zika virus infection in acutely infected patients and pregnant women. We are also actively leveraging nanopore sequencing for diagnosis and surveillance of febrile illnesses in remote locations, including point-of-care outbreak settings and aboard the International Space Station, and developing bioinformatic pipelines for pathogen identification and host response characterization. Finally, we are investigating the use of machine-learning based methods for generation of models that can predict the cause of infection on the basis of RNA-Seq transcriptomic data.

Publications

Fungal meningitis in U.S. Patients who Received Epidural Anesthesia in Matamoros, Mexico.

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

Smith DJ, Misas E, Gold JAW, Evert N, Dang T, Prot E, Godwin S, Rivas J, Pearson J, Koenecke L, Bustamante ND, Marinissen MJ, Rodriquez GG, López-Martínez I, Lutfy C, Williams S, Vazquez Deida AA, Byrd KM, Villalba JA, Reagan-Steiner S, Parnell L, Gade L, Humphries RM, Wiederhold NP, Chiu CY, Lieberman JA, Litvintseva AP, Chiller T, Ostrosky-Zeichner L, Fungal Meningitis Response Team

Differential severity of SARS-CoV-2 variant infections in children and adults with COVID-19.

Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology

Brazer N, Servellita V, Jin C, Foresythe A, Oseguera M, Nguyen J, Sumimoto N, Huh HJ, Feder A, Bhattacharya S, Bhaskar S, Sotomayor-Gonzalez A, Saldhi P, Choi C, Li GX, Gopchandani K, Tippett A, Hsiao HM, Gonzalez MD, Gulick D, Kraft C, Kasinathan V, Wang YFW, Chen PY, Flores-Vazquez J, Patel K, Odom John AR, Spinler JK, Devaraj S, Annapragada AV, Luna RA, Gai X, Dien Bard J, Rostad CA, Planet PJ, Lazar AA, Chiu CY

Clinical translation of microbiome research.

Nature medicine

Gilbert JA, Azad MB, Bäckhed F, Blaser MJ, Byndloss M, Chiu CY, Chu H, Dugas LR, Elinav E, Gibbons SM, Gilbert KE, Henn MR, Ishaq SL, Ley RE, Lynch SV, Segal E, Spector TD, Strandwitz P, Suez J, Tropini C, Whiteson K, Knight R

Severe Non-Donor-Derived Lymphocytic Choriomeningitis Virus Infection in 2 Solid Organ Transplant Recipients.

Open forum infectious diseases

Sayyad LE, Smith KL, Sadigh KS, Cossaboom CM, Choi MJ, Whitmer S, Cannon D, Krapiunaya I, Morales-Betoulle M, Annambhotla P, Basavaraju SV, Ruberto I, Kretschmer M, Gutierrez N, Zabel K, Austin C, Sandoval E, Servellita V, Foresythe A, Sumimoto N, Aqel BA, Khamash HA, Jadlowiec CC, Grys TE, Jaramillo A, Grill MF, Montgomery JM, Shoemaker T, Klena JD, Chiu CY, Vikram HR

Plasma cell-free RNA signatures of inflammatory syndromes in children.

Proceedings of the National Academy of Sciences of the United States of America

Loy CJ, Servellita V, Sotomayor-Gonzalez A, Bliss A, Lenz JS, Belcher E, Suslovic W, Nguyen J, Williams ME, Oseguera M, Gardiner MA, P.E.M.K.D.R.G., C.H.A.R.M.S. the Study Group, Choi JH, Hsiao HM, Wang H, Kim J, Shimizu C, Tremoulet AH, Delaney M, DeBiasi RL, Rostad CA, Burns JC, Chiu CY, De Vlaminck I

Outcomes in solid organ transplant recipients receiving organs from a donor with Fusarium solani species complex meningitis.

Transplant infectious disease : an official journal of the Transplantation Society

Griffin IS, Smith DJ, Annambhotla P, Gold JAW, Ostrosky-Zeichner L, Kauffman CA, Gade L, Litvintseva A, Friedman DZ, Nishio Lucar AG, Parpia TC, Lieberman J, Bujan J, Corkrean J, Divatia MK, Grimes K, Lin J, Mobley C, Schwartz MR, Hannawi B, Malilay A, O'Boye A, Lysne J, Subramani MV, Heckmann H, Servellita V, Chiu C, Basavaraju SV

Plasma Cell-free RNA Signatures of Inflammatory Syndromes in Children.

medRxiv : the preprint server for health sciences

Loy CJ, Servellita V, Sotomayor-Gonzalez A, Bliss A, Lenz J, Belcher E, Suslovic W, Nguyen J, Williams ME, Oseguera M, Gardiner MA, Pediatric Emergency Medicine Kawasaki Disease Research Group (PEMKDRG), CHARMS Study Group, Choi JH, Hsiao HM, Wang H, Kim J, Shimizu C, Tremoulet A, Delaney M, DeBiasi RL, Rostad CA, Burns JC, Chiu CY, Vlaminck I

Previous exposure to Spike-providing parental strains confers neutralizing immunity to XBB lineage and other SARS-CoV-2 recombinants in the context of vaccination.

Emerging microbes & infections

Suryawanshi RK, Taha TY, McCavitt-Malvido M, Silva I, Khalid MM, Syed AM, Chen IP, Saldhi P, Sreekumar B, Montano M, Foresythe K, Tabata T, Kumar GR, Sotomayor-Gonzalez A, Servellita V, Gliwa A, Nguyen J, Kojima N, Arellanor T, Bussanich A, Hess V, Shacreaw M, Lopez L, Brobeck M, Turner F, Wang Y, Ghazarian S, Davis G, Rodriguez D, Doudna J, Spraggon L, Chiu CY, Ott M

Transmission of yellow fever vaccine virus through blood transfusion and organ transplantation in the USA in 2021: report of an investigation.

The Lancet. Microbe

Gould CV, Free RJ, Bhatnagar J, Soto RA, Royer TL, Maley WR, Moss S, Berk MA, Craig-Shapiro R, Kodiyanplakkal RPL, Westblade LF, Muthukumar T, Puius YA, Raina A, Hadi A, Gyure KA, Trief D, Pereira M, Kuehnert MJ, Ballen V, Kessler DA, Dailey K, Omura C, Doan T, Miller S, Wilson MR, Lehman JA, Ritter JM, Lee E, Silva-Flannery L, Reagan-Steiner S, Velez JO, Laven JJ, Fitzpatrick KA, Panella A, Davis EH, Hughes HR, Brault AC, St George K, Dean AB, Ackelsberg J, Basavaraju SV, Chiu CY, Staples JE, Yellow Fever Vaccine Virus Transplant and Transfusion Investigation Team

Association of culturable-virus detection and household transmission of SARS-CoV-2 - California and Tennessee, 2020-2022.

The Journal of infectious diseases

Deyoe JE, Kelly JD, Grijalva CG, Bonenfant G, Lu S, Anglin K, Garcia-Knight M, Pineda-Ramirez J, Briggs Hagen M, Saydah S, Abedi GR, Goldberg SA, Tassetto M, Zhang A, Donohue KC, Davidson MC, Diaz Sanchez R, Djomaleu M, Mathur S, Shak JR, Deeks SG, Peluso MJ, Chiu CY, Zhu Y, Halasa NB, Chappell JD, Mellis A, Reed C, Andino R, Martin JN, Zhou B, Talbot HK, Midgley CM, Rolfes MA

Adeno-associated virus type 2 in US children with acute severe hepatitis.

Nature

Servellita V, Gonzalez AS, Lamson DM, Foresythe A, Huh HJ, Bazinet AL, Bergman NH, Bull RL, Garcia KY, Goodrich JS, Lovett SP, Parker K, Radune D, Hatada A, Pan CY, Rizzo K, Bertumen JB, Morales C, Oluniyi PE, Nguyen J, Tan J, Stryke D, Jaber R, Leslie MT, Lyons Z, Hedman HD, Parashar U, Sullivan M, Wroblewski K, Oberste MS, Tate JE, Baker JM, Sugerman D, Potts C, Lu X, Chhabra P, Pediatric Hepatitis of Unknown Etiology Working Group, Ingram LA, Shiau H, Britt W, Sanchez LHG, Ciric C, Rostad CA, Vinj? J, Kirking HL, Wadford DA, Raborn RT, St George K, Chiu CY

Transfusion-Transmitted Cache Valley Virus Infection in a Kidney Transplant Recipient with Meningoencephalitis.

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

Al-Heeti O, Wu EL, Ison MG, Saluja RK, Ramsey G, Matkovic E, Ha K, Hall S, Banach B, Wilson MR, Miller S, Chiu CY, McCabe M, Bari C, Zimler RA, Babiker H, Freeman D, Popovitch J, Annambhotla P, Lehman JA, Fitzpatrick K, Velez JO, Davis EH, Hughes HR, Panella A, Brault A, Erin Staples J, Gould CV, Tanna S

Magnitude and determinants of SARS-CoV-2 household transmission: a longitudinal cohort study.

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

Daniel Kelly J, Lu S, Anglin K, Garcia-Knight M, Pineda-Ramirez J, Goldberg SA, Tassetto M, Zhang A, Donohue K, Davidson MC, Romero M, Sanchez RD, Djomaleu M, Mathur S, Chen JY, Forman CA, Servellita V, Montejano RD, Shak JR, Rutherford GW, Deeks SG, Abedi GR, Rolfes MA, Saydah S, Briggs-Hagen M, Peluso MJ, Chiu C, Midgley CM, Andino R, Martin JN

Infectious viral shedding of SARS-CoV-2 Delta following vaccination: A longitudinal cohort study.

PLoS pathogens

Garcia-Knight M, Anglin K, Tassetto M, Lu S, Zhang A, Goldberg SA, Catching A, Davidson MC, Shak JR, Romero M, Pineda-Ramirez J, Diaz-Sanchez R, Rugart P, Donohue K, Massachi J, Sans HM, Djomaleu M, Mathur S, Servellita V, McIlwain D, Gaudiliere B, Chen J, Martinez EO, Tavs JM, Bronstone G, Weiss J, Watson JT, Briggs-Hagen M, Abedi GR, Rutherford GW, Deeks SG, Chiu C, Saydah S, Peluso MJ, Midgley CM, Martin JN, Andino R, Kelly JD

An intranasal ASO therapeutic targeting SARS-CoV-2.

Nature communications

Zhu C, Lee JY, Woo JZ, Xu L, Nguyenla X, Yamashiro LH, Ji F, Biering SB, Van Dis E, Gonzalez F, Fox D, Wehri E, Rustagi A, Pinsky BA, Schaletzky J, Blish CA, Chiu C, Harris E, Sadreyev RI, Stanley S, Kauppinen S, Rouskin S, N??r AM

Limited cross-variant immunity from SARS-CoV-2 Omicron without vaccination.

Nature

Suryawanshi RK, Chen IP, Ma T, Syed AM, Brazer N, Saldhi P, Simoneau CR, Ciling A, Khalid MM, Sreekumar B, Chen PY, Kumar GR, Montano M, Gascon R, Tsou CL, Garcia-Knight MA, Sotomayor-Gonzalez A, Servellita V, Gliwa A, Nguyen J, Silva I, Milbes B, Kojima N, Hess V, Shacreaw M, Lopez L, Brobeck M, Turner F, Soveg FW, George AF, Fang X, Maishan M, Matthay M, Morris MK, Wadford D, Hanson C, Greene WC, Andino R, Spraggon L, Roan NR, Chiu CY, Doudna JA, Ott M

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

Nature methods

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, Wu NC, Zelikovsky A, Knight R, Crandall KA, Mangul S

Limited cross-variant immunity after infection with the SARS-CoV-2 Omicron variant without vaccination.

medRxiv : the preprint server for health sciences

Suryawanshi RK, Chen IP, Ma T, Syed AM, Simoneau CR, Ciling A, Khalid MM, Sreekumar B, Chen PY, George AF, Kumar GR, Montano M, Garcia-Knight MA, Brazer N, Saldhi P, Sotomayor-Gonzalez A, Servellita V, Gliwa A, Nguyen J, Silva I, Milbes B, Kojima N, Hess V, Shacreaw M, Lopez L, Brobeck M, Turner F, Soveg FW, Fang X, Maishan M, Matthay M, Morris MK, Wadford D, Hanson C, Greene WC, Andino R, Spraggon L, Roan NR, Chiu CY, Doudna J, Ott M

Detection of SARS-CoV-2 variants by Abbott molecular, antigen, and serological tests.

Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology

Rodgers MA, Olivo A, Harris BJ, Lark C, Luo X, Berg MG, Meyer TV, Mohaimani A, Orf GS, Goldstein Y, Fox AS, Hirschhorn J, Glen WB, Nolte F, Landay A, Jennings C, Moy J, Servellita V, Chiu C, Batra R, Snell LB, Nebbia G, Douthwaite S, Tanuri A, Singh L, de Oliveira T, Ahouidi A, Mboup S, Cloherty GA

Author Correction: Pan-viral serology implicates enteroviruses in acute flaccid myelitis.

Nature medicine

Schubert RD, Hawes IA, Ramachandran PS, Ramesh A, Crawford ED, Pak JE, Wu W, Cheung CK, O'Donovan BD, Tato CM, Lyden A, Tan M, Sit R, Sowa GM, Sample HA, Zorn KC, Banerji D, Khan LM, Bove R, Hauser SL, Gelfand AA, Johnson-Kerner BL, Nash K, Krishnamoorthy KS, Chitnis T, Ding JZ, McMillan HJ, Chiu CY, Briggs B, Glaser CA, Yen C, Chu V, Wadford DA, Dominguez SR, Ng TFF, Marine RL, Lopez AS, Nix WA, Soldatos A, Gorman MP, Benson L, Messacar K, Konopka-Anstadt JL, Oberste MS, DeRisi JL, Wilson MR

SARS-CoV-2 Community Transmission disproportionately affects Latinx population during Shelter-in-Place in San Francisco.

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

Chamie G, Marquez C, Crawford E, Peng J, Petersen M, Schwab D, Schwab J, Martinez J, Es DJ, Black D, Gandhi M, Kerkhoff AD, Jain V, Sergi F, Jacobo J, Rojas S, Tulier-Laiwa V, Gallardo-Brown T, Appa A, Chiu C, Rodgers M, Hackett J, Kistler A, Hao S, Kamm J, Dynerman D, Batson J, Greenhouse B, DeRisi J, Havlir DV

SARS-CoV-2 antibody magnitude and detectability are driven by disease severity, timing, and assay.

Science advances

Peluso MJ, Takahashi S, Hakim J, Kelly JD, Torres L, Iyer NS, Turcios K, Janson O, Munter SE, Thanh C, Donatelli J, Nixon CC, Hoh R, Tai V, Fehrman EA, Hernandez Y, Spinelli MA, Gandhi M, Palafox MA, Vallari A, Rodgers MA, Prostko J, Hackett J, Trinh L, Wrin T, Petropoulos CJ, Chiu CY, Norris PJ, DiGermanio C, Stone M, Busch MP, Elledge SK, Zhou XX, Wells JA, Shu A, Kurtz TW, Pak JE, Wu W, Burbelo PD, Cohen JI, Rutishauser RL, Martin JN, Deeks SG, Henrich TJ, Rodriguez-Barraquer I, Greenhouse B

In vivo monoclonal antibody efficacy against SARS-CoV-2 variant strains.

Nature

Chen RE, Winkler ES, Case JB, Aziati ID, Bricker TL, Joshi A, Darling TL, Ying B, Errico JM, Shrihari S, VanBlargan LA, Xie X, Gilchuk P, Zost SJ, Droit L, Liu Z, Stumpf S, Wang D, Handley SA, Stine WB, Shi PY, Davis-Gardner ME, Suthar MS, Knight MG, Andino R, Chiu CY, Ellebedy AH, Fremont DH, Whelan SPJ, Crowe JE, Purcell L, Corti D, Boon ACM, Diamond MS

In vivo monoclonal antibody efficacy against SARS-CoV-2 variant strains.

Research square

Diamond M, Chen R, Winkler E, Case J, Aziati I, Bricker T, Joshi A, Darling T, Ying B, Errico J, Shrihari S, VanBlargan L, Xie X, Gilchuk P, Zost S, Droit L, Liu Z, Stumpf S, Wang D, Handley S, Stine W, Shi PY, Garcia-Knight M, Andino R, Chiu C, Ellebedy A, Fremont D, Whelan S, Crowe J, Purcell L, Corti D, Boon A

Transmission, infectivity, and neutralization of a spike L452R SARS-CoV-2 variant.

Cell

Deng X, Garcia-Knight MA, Khalid MM, Servellita V, Wang C, Morris MK, Sotomayor-González A, Glasner DR, Reyes KR, Gliwa AS, Reddy NP, Sanchez San Martin C, Federman S, Cheng J, Balcerek J, Taylor J, Streithorst JA, Miller S, Sreekumar B, Chen PY, Schulze-Gahmen U, Taha TY, Hayashi JM, 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, Chiu CY

Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation.

medRxiv : the preprint server for health sciences

Deng X, Garcia-Knight MA, Khalid MM, Servellita V, Wang C, Morris MK, Sotomayor-González A, Glasner DR, Reyes KR, Gliwa AS, Reddy NP, Sanchez San Martin C, Federman S, Cheng J, Balcerek J, Taylor J, Streithorst JA, Miller S, Kumar GR, Sreekumar B, Chen PY, Schulze-Gahmen U, Taha TY, Hayashi J, Simoneau CR, 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, Lareau LF, Frankino PA, Shivram H, Wyman SK, Ott M, Andino R, Chiu CY

SARS-CoV-2 antibody magnitude and detectability are driven by disease severity, timing, and assay.

medRxiv : the preprint server for health sciences

Peluso MJ, Takahashi S, Hakim J, Kelly JD, Torres L, Iyer NS, Turcios K, Janson O, Munter SE, Thanh C, Nixon CC, Hoh R, Tai V, Fehrman EA, Hernandez Y, Spinelli MA, Gandhi M, Palafox MA, Vallari A, Rodgers MA, Prostko J, Hackett J, Trinh L, Wrin T, Petroplolous CJ, Chiu CY, Norris PJ, DiGermanio C, Stone M, Busch MP, Elledge SK, Zhou XX, Wells JA, Shu A, Kurtz TW, Pak JE, Wu W, Burbelo PD, Cohen JI, Rutishauser RL, Martin JN, Deeks SG, Henrich TJ, Rodriguez-Barraquer I, Greenhouse B

Timely Intervention and Control of a Novel Coronavirus (COVID-19) Outbreak at a Large Skilled Nursing Facility - San Francisco, California, 2020.

Infection control and hospital epidemiology

Karmarkar E, Blanco I, Amornkul P, DuBois A, Deng X, Moonan PK, Rubenstein BL, Miller DA, Kennedy I, Yu J, Dauterman J, Ongpin M, Hathaway W, Hoo L, Trammell S, Ememu E, Yu G, Khwaja Z, Lu W, Talai N, Jain S, Louie J, Philip S, Federman S, Masinde G, Wadford DA, Bobba N, Stoltey J, Smith A, Epson E, Chiu C, Bennett A, Vasquez AM, Williams T

Rapid deployment of SARS-CoV-2 testing: The CLIAHUB.

PLoS pathogens

Crawford ED, Acosta I, Ahyong V, Anderson EC, Arevalo S, Asarnow D, Axelrod S, Ayscue P, Azimi CS, Azumaya CM, Bachl S, Bachmutsky I, Bhaduri A, Brown JB, Batson J, Behnert A, Boileau RM, Bollam SR, Bonny AR, Booth D, Borja MJB, Brown D, Buie B, Burnett CE, Byrnes LE, Cabral KA, Cabrera JP, Caldera S, Canales G, Castañeda GR, Chan AP, Chang CR, Charles-Orszag A, Cheung C, Chio U, Chow ED, Citron YR, Cohen A, Cohn LB, Chiu C, Cole MA, Conrad DN, Constantino A, Cote A, Crayton-Hall T, Darmanis S, Detweiler AM, Dial RL, Dong S, Duarte EM, Dynerman D, Egger R, Fanton A, Frumm SM, Fu BXH, Garcia VE, Garcia J, Gladkova C, Goldman M, Gomez-Sjoberg R, Gordon MG, Grove JCR, Gupta S, Haddjeri-Hopkins A, Hadley P, Haliburton J, Hao SL, Hartoularos G, Herrera N, Hilberg M, Ho KYE, Hoppe N, Hosseinzadeh S, Howard CJ, Hussmann JA, Hwang E, Ingebrigtsen D, Jackson JR, Jowhar ZM, Kain D, Kim JYS, Kistler A, Kreutzfeld O, Kulsuptrakul J, Kung AF, Langelier C, Laurie MT, Lee L, Leng K, Leon KE, Leonetti MD, Levan SR, Li S, Li AW, Liu J, Lubin HS, Lyden A, Mann J, Mann S, Margulis G, Marquez DM, Marsh BP, Martyn C, McCarthy EE, McGeever A, Merriman AF, Meyer LK, Miller S, Moore MK, Mowery CT, Mukhtar T, Mwakibete LL, Narez N, Neff NF, Osso LA, Oviedo D, Peng S, Phelps M, Phong K, Picard P, Pieper LM, Pincha N, Pisco AO, Pogson A, Pourmal S, Puccinelli RR, Puschnik AS, Rackaityte E, Raghavan P, Raghavan M, Reese J, Replogle JM, Retallack H, Reyes H, Rose D, Rosenberg MF, Sanchez-Guerrero E, Sattler SM, Savy L, See SK, Sellers KK, Serpa PH, Sheehy M, Sheu J, Silas S, Streithorst JA, Strickland J, Stryke D, Sunshine S, Suslow P, Sutanto R, Tamura S, Tan M, Tan J, Tang A, Tato CM, Taylor JC, Tenvooren I, Thompson EM, Thornborrow EC, Tse E, Tung T, Turner ML, Turner VS, Turnham RE, Turocy MJ, Vaidyanathan TV, Vainchtein ID, Vanaerschot M, Vazquez SE, Wandler AM, Wapniarski A, Webber JT, Weinberg ZY, Westbrook A, Wong AW, Wong E, Worthington G, Xie F, Xu A, Yamamoto T, Yang Y, Yarza F, Zaltsman Y, Zheng T, DeRisi JL

SARS-CoV-2 seroprevalence and neutralizing activity in donor and patient blood.

Nature communications

Ng DL, Goldgof GM, Shy BR, Levine AG, Balcerek J, Bapat SP, Prostko J, Rodgers M, Coller K, Pearce S, Franz S, Du L, Stone M, Pillai SK, Sotomayor-Gonzalez A, Servellita V, Martin CSS, Granados A, Glasner DR, Han LM, Truong K, Akagi N, Nguyen DN, Neumann NM, Qazi D, Hsu E, Gu W, Santos YA, Custer B, Green V, Williamson P, Hills NK, Lu CM, Whitman JD, Stramer SL, Wang C, Reyes K, Hakim JMC, Sujishi K, Alazzeh F, Pham L, Thornborrow E, Oon CY, Miller S, Kurtz T, Simmons G, Hackett J, Busch MP, Chiu CY

Cryptic transmission of SARS-CoV-2 in Washington state.

Science (New York, N.Y.)

Bedford T, Greninger AL, Roychoudhury P, Starita LM, Famulare M, Huang ML, Nalla A, Pepper G, Reinhardt A, Xie H, Shrestha L, Nguyen TN, Adler A, Brandstetter E, Cho S, Giroux D, Han PD, Fay K, Frazar CD, Ilcisin M, Lacombe K, Lee J, Kiavand A, Richardson M, Sibley TR, Truong M, Wolf CR, Nickerson DA, Rieder MJ, Englund JA, Hadfield J, Hodcroft EB, Huddleston J, Moncla LH, Müller NF, Neher RA, Deng X, Gu W, Federman S, Chiu C, Duchin JS, Gautom R, Melly G, Hiatt B, Dykema P, Lindquist S, Queen K, Tao Y, Uehara A, Tong S, MacCannell D, Armstrong GL, Baird GS, Chu HY, Shendure J, Jerome KR

Evaluation of SARS-CoV-2 serology assays reveals a range of test performance.

Nature biotechnology

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 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, Marson A

SARS-CoV-2 Community Transmission During Shelter-in-Place in San Francisco.

medRxiv

Gabriel Chamie, Carina Marquez, Emily Crawford, James Peng, Maya Petersen, Daniel Schwab, Joshua Schwab, Jackie Martinez, Diane Jones, Douglas Black, Monica Gandhi, Andrew D. Kerkhoff, Vivek Jain, Francesco Sergi, Jon Jacobo, Susana Rojas, Valerie Tulier-Laiwa, Tracy Gallardo-Brown, Ayesha Appa, Charles Y Chiu, Mary Rodgers, John Hackett, Amy Kistler, Samantha Hao, Jack Kamm, David Dynerman, Joshua Batson, Bryan Greenhouse, Joe DeRisi, Diane V. Havlir

Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California.

Science (New York, N.Y.)

Deng X, Gu W, Federman S, du Plessis L, Pybus OG, Faria N, 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 E, Bonin B, Wadford DA, Chiu CY

SARS-CoV-2 seroprevalence and neutralizing activity in donor and patient blood from the San Francisco Bay Area.

medRxiv : the preprint server for health sciences

Ng D, Goldgof G, Shy B, Levine A, Balcerek J, Bapat SP, Prostko J, Rodgers M, Coller K, Pearce S, Franz S, Du L, Stone M, Pillai S, Sotomayor-Gonzalez A, Servellita V, Sanchez-San Martin C, Granados A, Glasner DR, Han LM, Truong K, Akagi N, Nguyen DN, Neumann N, Qazi D, Hsu E, Gu W, Santos YA, Custer B, Green V, Williamson P, Hills NK, Lu CM, Whitman JD, Stramer S, Wang C, Reyes K, Hakim J, Sujishi K, Alazzeh F, Pharm L, Oon CY, Miller S, Kurtz T, Hackett J, Simmons G, Busch MP, Chiu CY

Test performance evaluation of SARS-CoV-2 serological assays.

medRxiv : the preprint server for health sciences

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medRxiv : the preprint server for health sciences

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medRxiv : the preprint server for health sciences

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medRxiv : the preprint server for health sciences

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Nature microbiology

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Nature microbiology

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Nature medicine

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The New England journal of medicine

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Nature medicine

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Nature

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