Center for Translational Pediatric Research (CTPR)

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.