Charles Chiu, MD, PhD

Professor

Charles Chiu, M.D./Ph.D. is a Professor of Laboratory Medicine and Medicine, Division of Infectious Diseases at University of California, San Francisco, Director of the UCSF-Abbott Viral Diagnostics and Discovery Center (VDDC), and Associate Director of the UCSF Clinical Microbiology Laboratory, He is a board-certified consulting infectious diseases physician at UCSF, and practices in both infectious diseases and clinical microbiology. Dr. Chiu obtained an MD and PhD in biophysics from UCLA and subsequently completed an internal medicine residency, infectious diseases fellowship, and postdoctoral research at UCSF. He heads a translational research laboratory engaged in clinical next-generation sequencing assay development for diagnosis of infectious diseases, pathogen discovery, bioinformatics software development, nanopore sequencing, and characterization of emerging infections (Lyme disease, enterovirus D68, and Zika virus). His work is supported by research grants from the NIH, Abbott Laboratories, Bay Area Lyme Disease Foundation, Global Lyme Alliance, USAID PREDICT program, UC Center for Accelerated Innovation, Sandler / Bowes Foundation, and California Initiative to Advance Precision Medicine. Dr. Chiu has authored more than 50 peer-reviewed publications, holds over 15 patents and patent applications, and serves on the scientific advisory board for Therabio, Karius, and Rubicon Genomics.
Education
M.D., 2001 - School of Medicine, University of California Los Angeles
Websites
Publications
  1. Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California.
  2. Clinical Outcomes and Serologic Response in Solid Organ Transplant Recipients with COVID-19: A Case Series from the United States.
  3. A SARS-CoV-2 serological assay to determine the presence of blocking antibodies that compete for human ACE2 binding.
  4. SARS-CoV-2 seroprevalence and neutralizing activity in donor and patient blood from the San Francisco Bay Area.
  5. Associations of Early COVID-19 Cases in San Francisco with Domestic and International Travel.
  6. Test performance evaluation of SARS-CoV-2 serological assays.
  7. Clinical features, diagnostics, and outcomes of patients presenting with acute respiratory illness: a comparison of patients with and without COVID-19.
  8. CRISPR-Cas12-based detection of SARS-CoV-2.
  9. Association of COVID-19 Infections in San Francisco in Early March 2020 with Travel to New York and Europe.
  10. Cryptic transmission of SARS-CoV-2 in Washington State.
  11. A Genomic Survey of SARS-CoV-2 Reveals Multiple Introductions into Northern California without a Predominant Lineage.
  12. Rapid Detection of 2019 Novel Coronavirus SARS-CoV-2 Using a CRISPR-based DETECTR Lateral Flow Assay.
  13. Author Correction: Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance.
  14. Human Tibroviruses: Commensals or Lethal Pathogens?
  15. Should we be performing metagenomic next-generation sequencing for infectious disease diagnosis in the clinical laboratory?
  16. Exploratory analysis of the potential for advanced diagnostic testing to reduce healthcare expenditures of patients hospitalized with meningitis or encephalitis.
  17. Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance.
  18. 236. The Comparative Utility Of Metagenomic Next-Generation Sequencing and Universal PCR for Pathogen Detection on Cerebrospinal Fluid: A Retrospective Analysis From a Tertiary Care Center.
  19. Pan-viral serology implicates enteroviruses in acute flaccid myelitis.
  20. Metagenomic Next-Generation Sequencing of the 2014 Ebola Virus Disease Outbreak in the Democratic Republic of the Congo.
  21. Acute Zika virus infection in an asymptomatic blood donor at the onset of the Puerto Rico epidemic.
  22. Gastroenteritis, Hepatitis, Encephalopathy, and Human Herpesvirus 6 Detection in an Immunocompetent Child: Benefits and Risks of Syndromic Multiplex Molecular Panel Testing.
  23. Clinical Metagenomic Sequencing for Diagnosis of Meningitis and Encephalitis.
  24. Clinical metagenomics.
  25. Human, Nonhuman Primate, and Bat Cells Are Broadly Susceptible to Tibrovirus Particle Cell Entry.
  26. Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid.
  27. Severe Epididymo-Orchitis and Encephalitis Complicating Anti-PD-1 Therapy.
  28. Whole blood human transcriptome and virome analysis of ME/CFS patients experiencing post-exertional malaise following cardiopulmonary exercise testing.
  29. Single-molecule sequencing detection of N6-methyladenine in microbial reference materials.
  30. Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults.
  31. 2291. A Real-Time Sequencing Approach for Simultaneous Metagenomic and Transcriptomic-Based Diagnosis of Infectious Diseases.
  32. 2563. Clinical Metagenomic Next-Generation Sequencing for Diagnosis of Meningitis and Encephalitis.
  33. 617. Characterization and Development of the Infant Gut Virome: A STORK Study.
  34. Publisher Correction: Experimental Zika Virus Infection in the Pregnant Common Marmoset Induces Spontaneous Fetal Loss and Neurodevelopmental Abnormalities.
  35. Clinical Metagenomic Next-Generation Sequencing for Pathogen Detection.
  36. Differentiation enhances Zika virus infection of neuronal brain cells.
  37. Identification of high-risk human papillomavirus and Rb/E2F pathway genomic alterations in mutually exclusive subsets of colorectal neuroendocrine carcinoma.
  38. Epidemiological and genomic characterization of community-acquired Clostridium difficile infections.
  39. Miscarriage and stillbirth following maternal Zika virus infection in nonhuman primates.
  40. Polyoma virus-associated carcinomas of the urologic tract: a clinicopathologic and molecular study.
  41. Metagenomic Sequencing Detects Respiratory Pathogens in Hematopoietic Cellular Transplant Patients.
  42. Metagenomic Next-Generation Sequencing for Pathogen Detection and Identification.
  43. Nanopore DNA Sequencing and Genome Assembly on the International Space Station.
  44. Experimental Zika Virus Inoculation in a New World Monkey Model Reproduces Key Features of the Human Infection.
  45. A composite of exhaled LTB4 , LXA4 , FeNO, and FEV1 as an "asthma classification ratio" characterizes childhood asthma.
  46. Neurobrucellosis: Unexpected Answer From Metagenomic Next-Generation Sequencing.
  47. Viral Surveillance in Serum Samples From Patients With Acute Liver Failure By Metagenomic Next-Generation Sequencing.
  48. Metagenomic-based Surveillance of Pacific Coast tick Dermacentor occidentalis Identifies Two Novel Bunyaviruses and an Emerging Human Ricksettsial Pathogen.
  49. Upregulation of Human Endogenous Retrovirus-K Is Linked to Immunity and Inflammation in Pulmonary Arterial Hypertension.
  50. Correction: Correction: A Novel Rhabdovirus Associated with Acute Hemorrhagic Fever in Central Africa.
  51. The eukaryotic gut virome in hematopoietic stem cell transplantation: new clues in enteric graft-versus-host disease.
  52. Hepatitis E Virus-Associated Meningoencephalitis in a Lung Transplant Recipient Diagnosed by Clinical Metagenomic Sequencing.
  53. Establishment and cryptic transmission of Zika virus in Brazil and the Americas.
  54. Establishment and characterization of an oral tongue squamous cell carcinoma cell line from a never-smoking patient.
  55. First Complete Genome Sequence of Corynebacterium riegelii.
  56. A hospital-wide screening programme to control an outbreak of vancomycin-resistant enterococci in a large tertiary hospital in Hong Kong.
  57. A mouse model of paralytic myelitis caused by enterovirus D68.
  58. RNA-Seq Analysis of Gene Expression, Viral Pathogen, and B-Cell/T-Cell Receptor Signatures in Complex Chronic Disease.
  59. Validation of Metagenomic Next-Generation Sequencing Tests for Universal Pathogen Detection.
  60. Beatrice Hill Virus Represents a Novel Species in the Genus Tibrovirus (Mononegavirales: Rhabdoviridae).
  61. First Draft Genome Sequences of Neisseria sp. Strain 83E34 and Neisseria sp. Strain 74A18, Previously Identified as CDC Eugonic Fermenter 4b Species.
  62. Longitudinal investigation of nasopharyngeal methicillin-resistant Staphylococcus aureus colonization in early infancy: The PATCH birth cohort study.
  63. Complete genome sequence of sequential Pandoraea apista isolates from the same cystic fibrosis patient supports a model of chronic colonization with in vivo strain evolution over time.
  64. Coinfections of Zika and Chikungunya Viruses in Bahia, Brazil, Identified by Metagenomic Next-Generation Sequencing.
  65. Antibodies to the Novel Human Pegivirus 2 Are Associated with Active and Resolved Infections.
  66. Two human immunodeficiency virus Type 2 cases in US blood donors including serologic, molecular, and genomic characterization of an epidemiologically unusual case.
  67. Correction: A Novel Rhabdovirus Associated with Acute Hemorrhagic Fever in Central Africa.
  68. Whole-Genome Sequencing of Methicillin-Resistant Staphylococcus aureus Resistant to Fifth-Generation Cephalosporins Reveals Potential Non-mecA Mechanisms of Resistance.
  69. Longitudinal Transcriptome Analysis Reveals a Sustained Differential Gene Expression Signature in Patients Treated for Acute Lyme Disease.
  70. Erratum to: Clinical metagenomic identification of Balamuthia mandrillaris encephalitis and assembly of the draft genome: the continuing case for reference genome sequencing.
  71. Discovery of a Novel Human Pegivirus in Blood Associated with Hepatitis C Virus Co-Infection.
  72. Balamuthia Mandrillaris Encephalitis Detected by Next Generation Sequencing of Cerebrospinal Fluid.
  73. Acute Flaccid Myelitis of Unknown Etiology in California, 2012-2015.
  74. Clinical metagenomic identification of Balamuthia mandrillaris encephalitis and assembly of the draft genome: the continuing case for reference genome sequencing.
  75. Utility of Metagenomic Next-Generation Sequencing for Characterization of HIV and Human Pegivirus Diversity.
  76. Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis.
  77. Draft Genome Sequence of Mycobacterium heckeshornense Strain RLE.
  78. Genomic Assays for Identification of Chikungunya Virus in Blood Donors, Puerto Rico, 2014.
  79. Draft Genome Sequence of Mycobacterium heraklionense Strain Davo.
  80. Draft Genome Sequence of Mycobacterium elephantis Strain Lipa.
  81. Draft Genome Sequence of Mycobacterium arupense Strain GUC1.
  82. Draft Genome Sequence of Mycobacterium obuense Strain UC1, Isolated from Patient Sputum.
  83. Two Rapidly Growing Mycobacterial Species Isolated from a Brain Abscess: First Whole-Genome Sequences of Mycobacterium immunogenum and Mycobacterium llatzerense.
  84. Idiopathic pneumonia syndrome after hematopoietic cell transplantation: evidence of occult infectious etiologies.
  85. No viral association found in a set of differentiated vulvar intraepithelial neoplasia cases by human papillomavirus and pan-viral microarray testing.
  86. Advances in testing technology to ensure transfusion safety – NAT and beyond.
  87. A novel outbreak enterovirus D68 strain associated with acute flaccid myelitis cases in the USA (2012-14): a retrospective cohort study.
  88. Genome Sequence of Bivens Arm Virus, a Tibrovirus Belonging to the Species Tibrogargan virus (Mononegavirales: Rhabdoviridae).
  89. An ensemble strategy that significantly improves de novo assembly of microbial genomes from metagenomic next-generation sequencing data.
  90. Diagnosis of neuroinvasive astrovirus infection in an immunocompromised adult with encephalitis by unbiased next-generation sequencing.
  91. DNA microarray for detection of gastrointestinal viruses.
  92. A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples.
  93. Actionable diagnosis of neuroleptospirosis by next-generation sequencing.
  94. Multiplexed immunoglobulin E sensitization in relation to exhaled nitric oxide in a population sample of children.
  95. Concerns over the origin of NIH-CQV, a novel virus discovered in Chinese patients with seronegative hepatitis.
  96. Chapter 2 Bas-Congo Virus A Novel Rhabdovirus Associated with Acute Hemorrhagic Fever.
  97. The perils of pathogen discovery: origin of a novel parvovirus-like hybrid genome traced to nucleic acid extraction spin columns.
  98. Rosavirus: the prototype of a proposed new genus of the Picornaviridae family.
  99. Experimental cross-species infection of common marmosets by titi monkey adenovirus.
  100. Characterization of the Bas-Congo virus glycoprotein and its function in pseudotyped viruses.
  101. Viral pathogen discovery.
  102. The genome sequence of Lone Star virus, a highly divergent bunyavirus found in the Amblyomma americanum tick.
  103. The hidden threat of unidentified agents of disease in human and veterinary biologicals.
  104. A novel adenovirus species associated with an acute respiratory outbreak in a baboon colony and evidence of coincident human infection.
  105. A novel bocavirus in canine liver.
  106. Bas-Congo virus: another deadly virus?
  107. The mitochondrial genome and a 60-kb nuclear DNA segment from Naegleria fowleri, the causative agent of primary amoebic meningoencephalitis.
  108. Discovery of a novel polyomavirus in acute diarrheal samples from children.
  109. Toward an understanding of changes in diversity associated with fecal microbiome transplantation based on 16S rRNA gene deep sequencing.
  110. A novel rhabdovirus associated with acute hemorrhagic fever in central Africa.
  111. In-depth investigation of archival and prospectively collected samples reveals no evidence for XMRV infection in prostate cancer.
  112. Cross-species transmission of a novel adenovirus associated with a fulminant pneumonia outbreak in a new world monkey colony.
  113. Using a pan-viral microarray assay (Virochip) to screen clinical samples for viral pathogens.
  114. Viral infection in acute exacerbation of idiopathic pulmonary fibrosis.
  115. Pandemic (H1N1) 2009 infection in patients with hematologic malignancy.
  116. A metagenomic analysis of pandemic influenza A (2009 H1N1) infection in patients from North America.
  117. Identification of two novel missense mutations in the KAL1 gene in Han Chinese subjects with Kallmann Syndrome.
  118. Cultivation and serological characterization of a human Theiler's-like cardiovirus associated with diarrheal disease.
  119. Metagenomics for the discovery of novel human viruses.
  120. Thoracic CT findings of novel influenza A (H1N1) infection in immunocompromised patients.
  121. Differential bacterial dynamics promote emergent community robustness to lake mixing: an epilimnion to hypolimnion transplant experiment.
  122. Bacteriologic features of surgical site infections following breast surgery.
  123. The complete genome of klassevirus - a novel picornavirus in pediatric stool.
  124. The long march: a sample preparation technique that enhances contig length and coverage by high-throughput short-read sequencing.
  125. Identification of cardioviruses related to Theiler's murine encephalomyelitis virus in human infections.
  126. Recovery of divergent avian bornaviruses from cases of proventricular dilatation disease: identification of a candidate etiologic agent.
  127. Utility of DNA microarrays for detection of viruses in acute respiratory tract infections in children.
  128. Streptococcus suis meningitis, United States.
  129. Availability and immobilization of 137Cs in subtropical high mountain forest and grassland soils.
  130. Diagnosis of a critical respiratory illness caused by human metapneumovirus by use of a pan-virus microarray.
  131. Microarray detection of human parainfluenzavirus 4 infection associated with respiratory failure in an immunocompetent adult.
  132. E-Predict: a computational strategy for species identification based on observed DNA microarray hybridization patterns.
  133. Structural analysis of a fiber-pseudotyped adenovirus with ocular tropism suggests differential modes of cell receptor interactions.
  134. Uterine artery embolisation for treatment of fibroids: experience in Chinese women.
  135. Digitally collected cryo-electron micrographs for single particle reconstruction.
  136. Review: resolution issues in single-particle reconstruction.
  137. Structure of adenovirus complexed with its internalization receptor, alphavbeta5 integrin.
  138. A helper-independent adenovirus vector with E1, E3, and fiber deleted: structure and infectivity of fiberless particles.
  139. Cryo-EM imaging of the catalytic subunit of the DNA-dependent protein kinase.
  140. Modification of a receptor-binding surface of epidermal growth factor (EGF): analogs with enhanced receptor affinity at low pH or at neutrality.
  141. Oligonucleotide N3'-->P5' phosphoramidates as antisense agents.
  142. Enhanced antibody responses in infants given different sequences of heterogeneous Haemophilus influenzae type b conjugate vaccines.
  143. Comparison of naturally acquired and vaccine-induced antibodies to Haemophilus influenzae type b capsular polysaccharide.
  144. Effects of age, breast feeding, and household structure on Haemophilus influenzae type b disease risk and antibody acquisition in Alaskan Eskimos.
  145. Developmental and metabolic regulation of the Drosophila melanogaster 3-hydroxy-3-methylglutaryl coenzyme A reductase.