Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA.
Am J Clin Pathol. 2022 Jun 7;157(6):927-935. doi: 10.1093/ajcp/aqab212.
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.
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.
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.
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.
新出现的严重急性呼吸综合征冠状病毒 2（SARS-CoV-2）变异株可能与传染性增加、疾病更严重以及治疗效果降低有关。为了提高区域变异监测的可用性，我们描述了一种快速、准确、适应性强且能够利用现有医院基础设施检测新的低水平变异的变异基因分型系统。
我们使用分层高通量 SARS-CoV-2 筛选计划在 76 天内对超区域卫生系统中的变异进行了特征描述。我们结合靶向逆转录-聚合酶链反应（RT-PCR）和选择性测序，对我们医疗保健系统内所有医院的 SARS-CoV-2 反应性样本进行了基因分型，以确定主要和新兴变异。
使用基于高通量 RT-PCR 的筛选，基因分型的中位周转时间为 2 天，使我们能够快速描述新出现的 Delta 变异。在我们的人群中，Delta 变异与较低的循环阈值、感染时较低的年龄以及增加的疫苗突破性病例相关。低水平和潜在新兴变异的检测突出了分层方法的实用性。
这些发现强调了随着大流行的发展和 SARS-CoV-2 变异的出现，需要快速、低成本、高通量监测区域病毒序列。将基于 RT-PCR 的筛选与选择性测序相结合，可实现快速的变异基因分型和系统的动态改进。
