Abstract
Objectives: Emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant strains can be associated with increased transmissibility, more severe disease, and reduced effectiveness of treatments. To improve the availability of regional variant surveillance, we describe a variant genotyping system that is rapid, accurate, adaptable, and able to detect new low-level variants built with existing hospital infrastructure.
Methods: We used a tiered high-throughput SARS-CoV-2 screening program to characterize variants in a supraregional health system over 76 days. Combining targeted reverse transcription-polymerase chain reaction (RT-PCR) and selective sequencing, we screened SARS-CoV-2 reactive samples from all hospitals within our health care system for genotyping dominant and emerging variants.
Results: The median turnaround for genotyping was 2 days using the high-throughput RT-PCR-based screen, allowing us to rapidly characterize the emerging Delta variant. In our population, the Delta variant is associated with a lower cycle threshold value, lower age at infection, and increased vaccine-breakthrough cases. Detection of low-level and potentially emerging variants highlights the utility of a tiered approach.
Conclusions: These findings underscore the need for fast, low-cost, high-throughput monitoring of regional viral sequences as the pandemic unfolds and the emergence of SARS-CoV-2 variants increases. Combining RT-PCR-based screening with selective sequencing allows for rapid genotyping of variants and dynamic system improvement.
Keywords: Delta variant; E484K; SARS-CoV-2; Targeted testing; Variant identification; Variant of concern; Variant screening.
【저자키워드】 SARS-CoV-2, delta variant, variant of concern, E484K, Targeted testing, Variant identification, Variant screening., 【초록키워드】 coronavirus, pandemic, Health care, hospital, Sequencing, variant, SARS-CoV-2 variant, Infection, Delta, detection, severe acute respiratory syndrome Coronavirus, delta variant, RT-PCR, variants, polymerase chain reaction, Health, Transmissibility, Surveillance, SARS-CoV-2 variants, Effectiveness, E484K, age, health system, utility, Health care system, genotyping, Care, Cycle threshold value, strain, severe disease, Chain Reaction, screening program, acute respiratory syndrome, acute respiratory syndrome coronavirus, acute respiratory syndrome coronavirus 2, Increases, selective, dominant, approach, reactive, highlight, Dynamic system, IMPROVE, detect, viral sequence, reduced, screened, median, 【제목키워드】 Screening, Rapid, identification, Regional,