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Principal Investigator: Alan Tackett
Organization: ARKANSAS CHILDREN'S HOSPITAL RES INST
Fiscal Year: 2021
Award: $770,000
Funding agency: National Institute of General Medical Sciences
PROJECT SUMMARY
The continuing emergence and subsequent circulation of SARS-CoV-2 variants across the world is of concern
for the global effort of controlling the Coronavirus Disease (COVID)-19 pandemic. Despite a high-burden of
disease overall, Arkansas has been slow to sequence viruses associated with infections in the state. For this
proposal, our Center for Translational Pediatric Research (CTPR) Center of Biomedical Research Excellence
(COBRE) and Arkansas IDeA Network of Biomedical Research Excellence (INBRE) have partnered together to
deliver sustainable SARS CoV-2 genomic surveillance data and analyses for the State of Arkansas. At the core
of this proposal, we have built a powerful collaboration named the Arkansas Sequencing (ArkSeq) Consortium
which includes the University of Arkansas for Medical Sciences (UAMS), Arkansas Children’s Hospital (ACH),
including Arkansas Children’s Northwest and UAMS Northwest extensions, Baptist Health (BH) in Little Rock,
drive-through centers across the State run by the Arkansas Department of Health (ADH), and Arkansas
Children’s Research Institute (ACRI). This consortium provides remnant viral transport media (VTM) that have
been identified as positive for SARS-CoV-2. Our objective is to continuously monitor these samples for SARS-
CoV-2 sequence diversity and viral phylodynamics and to provide actionable data back to the ADH and CDC
regarding variants. Aim 1 of this proposal is to provide genomic surveillance for Arkansas. To fulfill this aim, we
will use Illumina-based platforms to sequence at least 12288 samples from our ArkSeq Consortium for variants
of concern (VoCs) over the next year with a goal to scale to all patients. We will obtain clinical information on
these samples, including the subject’s demographics (age, sex, race, ethnicity, county of residence, and zip
code), date of collection, symptoms at the time of sampling, other respiratory viruses present at the time of
positive result, and vaccination status (vaccine type and date of vaccination). This approach will allow us to
answer the research questions: “What are the relative levels of the different variants in Arkansas?”; “How does
this change over time?” and “How are different Arkansas variants distributed across different geographical
regions, as well among racial, ethnic, gender, and/or age groups?” In collaboration with the ADH and the CDC,
we will integrate VoCs and other lineages from Arkansas into national databases. We plan to provide actionable
sequencing information on current strains of SARS-CoV-2 that are circulating within Arkansas. To meet this
goal, we are currently participating in the weekly SPHERES calls with CDC, and we are partnering with ADH
and ArkSeq partners to have monthly meetings regarding identified variants. Upon successful completion of this
proposal, we will have provided ~21 times more sequences from Arkansas to the databases than are currently
available from our State, with many other samples maintained for future evaluation.
Terms: <0-11 years old><2019 novel corona virus><2019 novel coronavirus><2019-nCoV><2019-nCoV variant><2019-nCoV variant forms><2019-nCoV variant strains><21+ years old><Adult><Adult Human><Age><Arkansas><B.1.1.7><Back><Baptist Church><Baptists><Bio-Informatics><Bioinformatics><Biomedical Research><Blood Circulation><Bloodstream><CDC><COBRE><COVID><COVID-19 genome><COVID-19 monitoring><COVID-19 positive><COVID-19 positivity><COVID-19 surveillance><COVID-19 variant><COVID-19 variant forms><COVID-19 variant strains><COVID-19 virus><COVID-19 virus genome><COVID19 genome><COVID19 monitoring><COVID19 positive><COVID19 positivity><COVID19 surveillance><COVID19 virus><COVID19 virus genome><Categories><Center of Biomedical Research Excellence><Centers for Disease Control><Centers for Disease Control and Prevention><Centers for Disease Control and Prevention (U.S.)><Centers of Research Excellence><Child><Child Youth><Children (0-21)><Children's Hospital><Circulation><Clinical><CoV disease><CoV-2><CoV2><Code><Coding System><Collaborations><Collection><County><Data><Data Analyses><Data Analysis><Data Bases><Databases><Deposit><Deposition><Diagnostic><Disease><Disorder><Dorsum><Environment><Ethnic Origin><Ethnicity><Evaluation><Future><Gender><Genome><Genomics><Geographic Area><Geographic Locations><Geographic Region><Geographical Location><Goals><Grant><Health><Health Policy><Infection><Infrastructure><Interdisciplinary Research><Interdisciplinary Study><Measures><Medical><Monitor><Multidisciplinary Collaboration><Multidisciplinary Research><Names><Patients><Pediatric Hospitals><Pediatric Research><Population><Position><Positioning Attribute><Public Health><R-Series Research Projects><R01 Mechanism><R01 Program><Race><Racial Group><Racial Stocks><Reporting><Research><Research Grants><Research Institute><Research Project Grants><Research Projects><Running><Rural><SARS corona virus 2><SARS-CoV-2><SARS-CoV-2 B.1.1.7><SARS-CoV-2 genome><SARS-CoV-2 monitoring><SARS-CoV-2 positive><SARS-CoV-2 positivity><SARS-CoV-2 surveillance><SARS-CoV-2 variant><SARS-CoV-2 variant forms><SARS-CoV-2 variant strains><SARS-CoV2><SARS-CoV2 genome><SARS-associated corona virus 2><SARS-associated coronavirus 2><SARS-coronavirus-2><SARS-related corona virus 2><SARS-related coronavirus 2><SARSCoV2><Sampling><Science><Scientist><Secure><Severe Acute Respiratory Distress Syndrome CoV 2><Severe Acute Respiratory Distress Syndrome Corona Virus 2><Severe Acute Respiratory Distress Syndrome Coronavirus 2><Severe Acute Respiratory Syndrome CoV 2><Severe Acute Respiratory Syndrome-associated coronavirus 2><Severe Acute Respiratory Syndrome-related coronavirus 2><Severe acute respiratory syndrome associated corona virus 2><Severe acute respiratory syndrome corona virus 2><Severe acute respiratory syndrome coronavirus 2><Severe acute respiratory syndrome coronavirus 2 positive><Severe acute respiratory syndrome coronavirus 2 positivity><Severe acute respiratory syndrome related corona virus 2><Symptoms><Systems Biology><Techniques><Technology><Testing><Time><Translational Research><Translational Science><U.K. variant><UK variant><United Kingdom variant><United States Centers for Disease Control><United States Centers for Disease Control and Prevention><Universities><Vaccination><Vaccines><Variant><Variation><Viral><Virus><Writing><Wuhan coronavirus><adulthood><age group><ages><base><biobank><biorepository><burden of disease><burden of illness><corona virus disease><coronavirus disease><coronavirus disease 2019 genome><coronavirus disease 2019 monitoring><coronavirus disease 2019 positive><coronavirus disease 2019 positivity><coronavirus disease 2019 surveillance><coronavirus disease 2019 variant><coronavirus disease 2019 variant forms><coronavirus disease 2019 variant strains><coronavirus disease 2019 virus><coronavirus disease 2019 virus genome><data base><data dissemination><data interpretation><demographics><disease burden><ethnoracial><feasibility testing><geographic site><hCoV19><health care policy><healthcare policy><meetings><multiomics><multiple omics><nCoV2><pandemic><pandemic disease><parent grant><racial and ethnic><residence><residential building><residential site><respiratory virus><severe acute respiratory syndrome coronavirus 2 B.1.1.7><severe acute respiratory syndrome coronavirus 2 genome><severe acute respiratory syndrome coronavirus 2 monitoring><severe acute respiratory syndrome coronavirus 2 surveillance><severe acute respiratory syndrome coronavirus 2 variant><severe acute respiratory syndrome coronavirus 2 variant forms><severe acute respiratory syndrome coronavirus 2 variant strains><sex><study population><success><surveillance data><translation research><variants of concern><years of life lost to disability><years of life lost to disease><youngster>