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
+1 415 514-8219
Research Overview: 

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.

Primary Thematic Area: 
Virology & Microbial Pathogenesis
Secondary Thematic Area: 
Immunology
Research Summary: 
Metagenomics-Based Technologies for Virus Detection and Discovery

Websites

Publications: 

Two sides of a coin: a Zika virus mutation selected in pregnant rhesus macaques promotes fetal infection in mice but at a cost of reduced fitness in nonpregnant macaques and diminished transmissibility by vectors.

Journal of virology

Lemos D, Stuart JB, Louie W, Singapuri A, Ramírez AL, Watanabe J, Usachenko J, Keesler RI, Martin CS, Li T, Martyn C, Oliveira G, Saraf S, Grubaugh ND, Andersen KG, Thissen J, Allen J, Borucki M, Tsetsarkin KA, Pletnev AG, Chiu CY, Van Rompay KKA, Coffey LL

ReScan, a Multiplex Diagnostic Pipeline, Pans Human Sera for SARS-CoV-2 Antigens.

Cell reports. Medicine

Zamecnik CR, Rajan JV, Yamauchi KA, Mann SA, Loudermilk RP, Sowa GM, Zorn KC, Alvarenga BD, Gaebler C, Caskey M, Stone M, Norris PJ, Gu W, Chiu CY, Ng D, Byrnes JR, Zhou XX, Wells JA, Robbiani DF, Nussenzweig MC, DeRisi JL, Wilson MR

Metagenomic sequencing of stool samples in Bangladeshi infants: virome association with poliovirus shedding after oral poliovirus vaccination.

Scientific reports

Tan SK, Granados AC, Bouquet J, Hoy-Schulz YE, Green L, Federman S, Stryke D, Haggerty TD, Ley C, Yeh MT, Jannat K, Maldonado YA, Andino R, Parsonnet J, Chiu CY

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

Competitive SARS-CoV-2 Serology Reveals Most Antibodies Targeting the Spike Receptor-Binding Domain Compete for ACE2 Binding.

mSphere

Byrnes JR, Zhou XX, Lui I, Elledge SK, Glasgow JE, Lim SA, Loudermilk RP, Chiu CY, Wang TT, Wilson MR, Leung KK, Wells JA