Document text
Principal Investigator: Jessica Manning
Organization: NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES
Fiscal Year: 2020
Award: $615,967
Funding agency: National Institute of Allergy and Infectious Diseases
METAGENOMIC SEQUENCING OF EMERGING DISEASES
NIAID Cambodia ICER quickly repurposed an existing metagenomics pipeline, originally set up for vector-borne diseases, to genetically characterize index cases of COVID-19 in January 2020. At this early pre-pandemic timepoint, sequencing COVID-19 cases was critical given the SARS-CoV-2 genetic diversity in humans and animals was not completely known, and thus mutation rates and the consequences thereof were not understood. Further, non-specificity of tests combined with variable sample quality limited confidence in field diagnostics. Despite limited sequencing capacity in-country, ICER Cambodia successfully identified and sequenced the novel SARS-CoV-2 pathogen, after developing enrichment methods to overcome handicaps of low coverage of the genome. In a turn of reverse innovation, these methods are now being deployed and scaled up in hard-hit California to enable the sequencing of thousands of samples in a single run and to support virological data-driven public health response. In August 2020, an expanded program was submitted via protocol amendment NIH 19-I-N109 to include two additional sites in Phnom Penh for sequencing of emerging pathogens in clinical samples from febrile individuals in Cambodia.
CHARACTERIZING SARS-COV-2 AT-RISK POPULATIONS IN CAMBODIA
As the epidemic evolves in Southeast Asia, expanded testing may be hard to achieve given limited surveillance capacity and weak health infrastructure. Newly developed vaccines will likely not be deployed quickly or be widely available here. Important questions will be correspondingly difficult to answer, e.g. what proportion of the population remains non-immune to SARS-CoV-2? Considering the extent of human migration in the Greater Mekong Subregion, will the populations without herd immunity and therefore vulnerable to SARS-CoV-2 create another spike in transmission that may be difficult to control? How do case-fatality and infection-fatality ratios vary with age, and how do these ratios differ among populations due to ethnic backgrounds, natural factors affecting host susceptibility, and innate immune response? With these questions in mind, we have developed Protocol NIH 000083 which will launch by end of 2020 to measure antibody response to SARS-CoV-2 spike and RNP proteins.
Terms: <2019 novel coronavirus><2019-nCoV><Acute><Affect><Age><Age-Years><Amendment><Animals><Antibody Response><COVID-19><COVID-19 epidemic><COVID-19 pandemic><COVID19><COVID19 epidemic><COVID19 pandemic><California><Cambodia><Causality><City Hospitals><Clinical><Collaborations><Collection><Communities><Country><Cross Sectional Analysis><Cross-Sectional Analyses><Cross-Sectional Studies><Cross-Sectional Survey><Data><Detection><Diagnostic><Disease><Disease Frequency Surveys><Disorder><Early Diagnosis><Enrollment><Epidemic><Etiology><Fever><Functional Metagenomics><Genetic Alteration><Genetic Change><Genetic Diversity><Genetic Variation><Genetic defect><Genome><Health><Herd Immunity><Human><Human Migration / Distribution><Immune><Immunes><Individual><Infection><Infrastructure><Innate Immune Response><Inpatients><International><Kampuchea><Khmer Republic><Measures><Metagenomics><Methods><Metropolitan Hospitals><Mind><Modern Man><Mutation><NIAID><NIH><National Institute of Allergy and Infectious Disease><National Institutes of Health><Out-patients><Outpatients><Population><Populations at Risk><Predisposition><Proteins><Protocol><Protocols documentation><Public Health><Pyrexia><Recovery><Risk><Running><SARS-CoV-2><SARS-CoV2><SARS-associated coronavirus 2><SARS-coronavirus-2><SARS-related coronavirus 2><Sampling><Severe acute respiratory syndrome coronavirus 2><Site><Southeast Asia><Southeastern Asia><Susceptibility><Swab><Testing><Transmission><United States National Institutes of Health><Urban Hospitals><Vaccines><Vector-borne disease><Vector-borne infectious disease><Vector-transmitted disease><Vector-transmitted infectious disease><Vulnerable Populations><Wuhan coronavirus><aged><ages><base><causation><corona virus disease 2019><corona virus disease 2019 epidemic><corona virus disease 2019 pandemic><coronavirus disease 2019><coronavirus disease 2019 epidemic><coronavirus disease 2019 pandemic><disease causation><early detection><enroll><febrile><febris><genome mutation><human migration><i(19)><indexing><innovate><innovation><innovative><metagenome sequencing><metagenomic sequencing><novel><pandemic><pandemic disease><pathogen><peri-urban><periurban><programs><response><scale up><transmission process><vector-borne illness><vectorborne disease><vectorborne illness><vectorborne infectious disease><virology><vulnerable group>