Identification and Dynamics of SARS-CoV-2 Sequence Variants in Idaho

摘要

ABSTRACT The first SARS-CoV-2 sequence published provided the foundation by which all currently approved detection methods and vaccines have been developed. However, variants of SARS-CoV-2 that carry multiple changes to their genome may enable the virus to evade detection and escape natural or vaccine-induced immunity, thwarting current abatement efforts. Additionally, variants that increase transmissibility, enhance disease severity, and improve resistance to therapeutic agents are also of significant concern in controlling the global COVID-19 pandemic. Thus, there remains a critical need for the rapid identification of SARS-CoV-2 variants among all populations, including those in underserved areas where surveillance efforts are lagging. One year after COVID-19 was declared a pandemic, fewer than 350 SARS-CoV-2 genomes originating from the state of Idaho have been sequenced, ranking among the bottom 6 IDeA states. To address this need, the Boise VA procured an Illumina NextSeq 500Dx sequencing platform to enable high capacity SARS-CoV-2 genome sequencing of local and statewide samples. With this existing technology, our Emerging and Reemerging Infectious Diseases COBRE investigators, in collaboration with the Idaho Bureau of Laboratories and the Boise VA Pathology and Laboratory Medicine Service are ideally positioned to address the following urgent priorities: (1) Are there different variants present in the study population, and how has the number of cases caused by different variants changed over time in the study population; (2) Are cases of infection by different variants associated with particular outbreak events, geographic locations, or specific times; (3) How are different variants distributed among different racial, ethnical, gender, and/or age groups; (4) Are specific variants associated with different levels of manifestation of COVID-19 symptoms; (5) For study populations undergoing vaccination, what percentage of the participants were SARS-CoV-2 positive prior to the first vaccine shot; and (6) Do vaccinated study participants still acquire the SARS-CoV-2 virus, and if so, what variants do they carry. With a large collaborative effort, we expect to sequence 5,000 SARS-CoV-2 viral genomes from samples collected throughout the state of Idaho, beginning in March of 2020 and collection will continue through the proposed study timeline. Resulting SARS-CoV-2 consensus sequence data will be deposited on NCBI GenBank, Nextstrain, and GISAID, while raw sequence data (FASTA) will be deposited on NCBI SRA, as permitted, and will be reported back to SARS-CoV-2 programs providing sample access. These efforts will vastly improve SARS-CoV-2 surveillance in Idaho, track circulating variants, and inform local and national health leaders to guide the pandemic response.