Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, MD, United States.
National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, United States.
Front Cell Infect Microbiol. 2022 Apr 11;12:809407. doi: 10.3389/fcimb.2022.809407. eCollection 2022.
Large-scale SARS-CoV-2 molecular testing coupled with whole genome sequencing in the diagnostic laboratories is instrumental for real-time genomic surveillance. The extensive genomic, laboratory, and clinical data provide a valuable resource for understanding cases of reinfection versus prolonged RNA shedding and protracted infections. In this study, data from a total of 22,292 clinical specimens, positive by SARS-CoV-2 molecular diagnosis at Johns Hopkins clinical virology laboratory between March 11 2020 to September 23 2021, were used to identify patients with two or more positive results. A total of 3,650 samples collected from 1,529 patients who had between 2 and 20 positive results were identified in a time frame that extended up to 403 days from the first positive. Cycle threshold values (Ct) were available for 1,622 samples, the median of which was over 30 by 11 days after the first positive. Extended recovery of infectious virus on cell culture was notable for up to 70 days after the first positive in immunocompromised patients. Whole genome sequencing data generated as a part of our SARS-CoV-2 genomic surveillance was available for 1,027 samples from patients that had multiple positive tests. Positive samples collected more than 10 days after initial positive with high quality sequences (coverage >90% and mean depth >100), were more likely to be from unvaccinated, or immunosuppressed patients. Reinfections with viral variants of concern were found in 3 patients more than 130 days from prior infections with a different viral clade. In 75 patients that had 2 or more high quality sequences, the acquisition of more substitutions or deletions was associated with lack of vaccination and longer time between the recovered viruses. Our study highlights the value of integrating genomic, laboratory, and clinical data for understanding the biology of SARS-CoV-2 as well as for setting a precedent for future epidemics and pandemics.
大规模的 SARS-CoV-2 分子检测与全基因组测序在诊断实验室中对于实时基因组监测至关重要。广泛的基因组、实验室和临床数据为理解再感染与延长 RNA 脱落和持续感染病例提供了有价值的资源。在这项研究中，使用了约翰霍普金斯临床病毒学实验室 2020 年 3 月 11 日至 2021 年 9 月 23 日期间通过 SARS-CoV-2 分子诊断呈阳性的 22292 份临床标本的总数据，以识别有两个或更多阳性结果的患者。从 1529 名患者中收集了 3650 个样本，这些患者的阳性结果在从第一次阳性开始长达 403 天的时间内有 2 到 20 个。有 1622 个样本可获得循环阈值（Ct）值，其中中位数在第一次阳性后 11 天超过 30。在免疫功能低下的患者中，细胞培养中传染性病毒的延长恢复时间长达第一次阳性后 70 天。作为我们 SARS-CoV-2 基因组监测的一部分生成的全基因组测序数据可用于有多个阳性测试的 1027 名患者。从首次阳性后 10 天以上收集的高质量序列（覆盖度> 90%且平均深度> 100）的阳性样本更可能来自未接种疫苗或免疫抑制的患者。在距先前不同病毒分支感染超过 130 天的 3 名患者中发现了具有关切性病毒变异的再感染。在有 2 个或更多高质量序列的 75 名患者中，获得更多的替换或缺失与未接种疫苗和恢复病毒之间的时间延长有关。我们的研究强调了整合基因组、实验室和临床数据的价值，用于了解 SARS-CoV-2 的生物学以及为未来的传染病和大流行树立先例。
