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Principal Investigator: RICHARD A GIBBS
Organization: BAYLOR COLLEGE OF MEDICINE
Fiscal Year: 2020
Award: $100,000
Funding agency: National Institute of Allergy and Infectious Diseases
OVERALL PROJECT SUMMARY
The novel coronavirus, SARS-CoV-2, that was first detected in China in December 2019 has now spread
globally. The Texas Medical Center in Houston, TX, the fourth largest city in the US, and among the top 10 in
racial diversity, mounted an aggressive early response to the pandemic, primarily focused on acute care. Within
Baylor College of Medicine, members of the TMC - Genomic Center for Infectious Disease (TMC-GCID) program
(https://gcid.research.bcm.edu/overview) are leveraging existing infrastructure, together with an active and
robust sample collection stream linked to both clinical and community testing, to characterize SARS-CoV-2
virulence and susceptibility across the region. This application requests supplemental funding to the TMC-GCID
to help support SARS-CoV-2 community-wide surveillance, complete viral genome sequencing, nasopharyngeal
microbiome profiling, and targeted host genetic analyses. The primary objective of this supplement will be
achieved through the collaborative efforts of a multidisciplinary, integrated team of basic and physician scientists
with a track-record of collaboration and who are already delivering on the primary goals of the TMC-GCID. The
overall goals of our GCID supplement is to study the biology of SARS-CoV-2 infection, the host and
microbial genetics associated with disease, and to address community needs, particularly in
underserved communities, through the following aims: i) expand an operational Emergency Use
Authorization- (EUA-) and IRB-compliant COVID-19 qPCR screening/surveillance program featuring
online enrollment and consent as well as HIPAA-compliant return of results, ii) sequence and analyze
full-length SARS-CoV-2 genomes from infected individuals collected from the TMC and surrounding
area, iii) identify microbial co-colonization/co-infections that predict COVID-19 disease severity and/or
outcome, iv) Characterize the host genetic variation with respect to viral titer, disease severity, and
outcome in patients positive for COVID-19, including polymorphisms in human leukocyte antigen (HLA),
angiotensin-converting enzyme 2 (ACE2), and natural killer cell immunoglobulin-like receptor (KIR)
regions. This supplement will leverage the cutting edge, high-throughput sequencing strategies and
technologies supplied by the TMC-GCID Sequencing Technology (ST) Core, in generating discoveries, data,
tools, and reagents that will be analyzed and disseminated to the infectious disease community through the
TMC-GCID Data Management Analysis and Resource Dissemination (DMARD) Core. The result will be a
comprehensive genetic profiling of hosts and microbes in SARS-CoV-2 infection that will reveal pathogen genetic
variants associated with individual host response phenotypes that will inform precision medicine-based
therapeutics and diagnostics, not just for SARS-CoV-2, but for other pandemic threats that we have already
observed to profoundly change the world around us.
Terms: <2019 novel coronavirus><2019-nCoV><Address><Age><Angiotensin Converting Enzyme><Angiotensin I-Converting Enzyme><Area><Authorization><Authorization documentation><Biology><CD143 Antigens><COVID-19><COVID19><Carboxycathepsin><China><Cities><Clinical><Clonal Expansion><CoV emergence><Code><Coding System><Collaborations><Collection><Communicable Diseases><Communities><Consent><Country><Cytotoxic cell><DNA Sequence><Data><Detection><Development><Diagnostic><Diathesis><Dipeptidyl Peptidase A><Disease><Disease susceptibility><Disorder><Emergencies><Emergency Situation><Enrollment><Ensure><Funding><Future><Gender><Gene variant><General Population><General Public><Genetic Diversity><Genetic Polymorphism><Genetic Variation><Genetic analyses><Genome><Genomic Centers for Infectious Diseases><Genomic approach><Goals><HIPAA><HL-A Antigens><HLA Antigens><Health Insurance Portability and Accountability Act><High-Throughput Nucleotide Sequencing><High-Throughput Sequencing><Human Leukocyte Antigens><IRB><IRBs><Immune Globulins><Immune response><Immunoglobulins><Immunological response><Individual><Infection><Infectious Disease Pathway><Infectious Diseases><Infectious Disorder><Infrastructure><Institutional Review Boards><K lymphocyte><Kennedy Kassebaum Act><Kininase A><Kininase II><Length><Leukocyte Antigens><Link><Mainland China><Medical center><Medicine><Metadata><Methods><Microbe><Microbial Genetics><NIH RFA><NK Cells><Natural Killer Cells><Outcome><PL 104-191><PL104-191><Pathogenesis><Patients><Peptidyl-Dipeptidase A><Permission><Phenotype><Physicians><Predisposition><Protocol><Protocols documentation><Public Law 104-191><RT-PCR><RTPCR><Reagent><Receptor Protein><Recombinant DNA><Recombinant DNA Molecular Biology><Request for Applications><Research><Research Resources><Research Specimen><Resources><Reverse Transcriptase Polymerase Chain Reaction><Role><SARS-CoV-2><SARS-CoV2><SARS-associated coronavirus 2><SARS-coronavirus-2><SARS-related coronavirus 2><SEQ-AN><Sampling><Scientist><Sequence Analyses><Sequence Analysis><Severe acute respiratory syndrome coronavirus 2><Severity of illness><Shotguns><Specimen><Speed><Stream><Surveillance Program><Susceptibility><Symptoms><Technology><Testing><Texas><Therapeutic><Time><United States><United States Health Insurance Portability and Accountability Act><Variant><Variation><Viral><Viral Genetics><Viral Genome><Virulence><Virus><Wuhan coronavirus><acute care><ages><allele variant><allelic variant><base><co-infection><co-morbid><co-morbidity><coinfection><college><collegiate><comorbidity><corona virus disease 2019><coronavirus disease 2019><coronavirus emergence><cost><data management><data tools><depository><developmental><disease severity><emergent CoV><emergent coronavirus><emerging CoV><emerging coronavirus><enroll><entire genome><experience><full genome><genetic analysis><genetic profiling><genetic variant><genome sequencing><genomic effort><genomic strategy><genomic variant><host response><immunoresponse><infection rate><innovate><innovation><innovative><liability to disease><member><meta data><metropolitan><microbial><microbiome><multidisciplinary><nCoV><new CoV><new coronavirus><new diagnostics><new drug treatments><new drugs><new therapeutics><new therapy><next generation diagnostics><next generation therapeutics><novel CoV><novel coronavirus><novel diagnostics><novel drug treatments><novel drugs><novel therapeutics><novel therapy><pandemic><pandemic disease><pathogen><polymorphism><precision medicine><precision-based medicine><programs><rDNA><racial diversity><racially diverse><rate of infection><receptor><reconstruction><repository><response><reverse transcriptase PCR><sample collection><screening><shot gun><social role><specimen collection><viral RNA><viral microbiome><virome><virus RNA><virus genetics><virus genome><whole genome>