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: 

Chagas Meningoencephalitis Diagnosed in Heart Transplant Patient Using Metagenomic Next-Generation Sequencing of Cerebrospinal Fluid.

The American journal of tropical medicine and hygiene

Teitelbaum J, Madan S, Patel S, Coyle C, Chiu CY, Thwe PM, Uehara M, Jermyn R, Hemmige V

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

The Regulatory Landscape for Clinical Metagenomic Testing.

JAMA neurology

Chiu CY, López-Labrador FX, Wilson MR, de Vries JJC

Metagenomic Identification of Fusarium solani Strain as Cause of US Fungal Meningitis Outbreak Associated with Surgical Procedures in Mexico, 2023.

Emerging infectious diseases

Chiu CY, Servellita V, de Lorenzi-Tognon M, Benoit P, Sumimoto N, Foresythe A, Cerqueira FM, Williams-Bouyer N, Ren P, Herrera LNS, Gaston DC, Sayyad L, Whitmer SL, Klena J, Vikram HR, Gold JAW, Gade L, Parnell L, Misas E, Chiller TM, Griffin IS, Basavaraju SV, Smith DJ, Litvintseva AP, Chow NA

Proposed research classification criteria for Lyme disease in infection associated chronic illness studies.

Frontiers in medicine

Fallon BA, Kuvaldina M, Zubcevik N, DeBiasi R, Mulkey SB, Chiu C, Chow F, Paolino K, Lai R, Putrino D, Proal A, Pavlicova M, Aucott J