Clinical Virology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland.
Transplantation and Clinical Virology, Department of Biomedicine, University of Basel, Basel, Switzerland.
J Infect Dis. 2020 Sep 14;222(8):1270-1279. doi: 10.1093/infdis/jiaa464.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in China as the cause of coronavirus disease 2019 in December 2019 and reached Europe by late January 2020, when community-acquired respiratory viruses (CARVs) are at their annual peak. We validated the World Health Organization (WHO)-recommended SARS-CoV-2 assay and analyzed the epidemiology of SARS-CoV-2 and CARVs.
Nasopharyngeal/oropharyngeal swabs (NOPS) from 7663 patients were prospectively tested by the Basel S-gene and WHO-based E-gene (Roche) assays in parallel using the Basel N-gene assay for confirmation. CARVs were prospectively tested in 2394 NOPS by multiplex nucleic acid testing, including 1816 (75%) simultaneously for SARS-CoV-2.
The Basel S-gene and Roche E-gene assays were concordant in 7475 cases (97.5%) including 825 (11%) SARS-CoV-2 positives. In 188 (2.5%) discordant cases, SARS-CoV-2 loads were significantly lower than in concordant positive ones and confirmed in 105 (1.4%). Adults were more frequently SARS-CoV-2 positive, whereas children tested more frequently CARV positive. CARV coinfections with SARS-CoV-2 occurred in 1.8%. SARS-CoV-2 replaced CARVs within 3 weeks, reaching 48% of all detected respiratory viruses followed by rhinovirus/enterovirus (13%), influenza virus (12%), coronavirus (9%), respiratory syncytial virus (6%), and metapneumovirus (6%).
Winter CARVs were dominant during the early SARS-CoV-2 pandemic, impacting infection control and treatment decisions, but were rapidly replaced, suggesting competitive infection. We hypothesize that preexisting immune memory and innate immune interference contribute to the different SARS-CoV-2 epidemiology among adults and children.
严重急性呼吸综合征冠状病毒 2（SARS-CoV-2）于 2019 年 12 月在中国引发 2019 年冠状病毒病（COVID-19），并于 2020 年 1 月底传播至欧洲，此时社区获得性呼吸道病毒（CARVs）正处于每年的高峰。我们对世界卫生组织（WHO）推荐的 SARS-CoV-2 检测方法进行了验证，并分析了 SARS-CoV-2 和 CARVs 的流行病学。
前瞻性收集 7663 例患者的鼻咽/口咽拭子（NOPS），采用 Basel S 基因和基于 WHO 的 E 基因（罗氏）检测方法进行平行检测，同时采用 Basel N 基因检测方法进行确证。前瞻性对 2394 例 NOPS 进行 CARVs 检测，采用多重核酸检测方法，包括同时对 1816 例（75%）进行 SARS-CoV-2 检测。
在 7475 例病例中，Basel S 基因和罗氏 E 基因检测方法一致（97.5%），包括 825 例（11%）SARS-CoV-2 阳性病例。在 188 例（2.5%）不一致的病例中，SARS-CoV-2 载量明显低于一致阳性病例，经确认其中 105 例（1.4%）为阳性。成年人 SARS-CoV-2 阳性率更高，而儿童 CARV 阳性率更高。SARS-CoV-2 与 CARV 合并感染率为 1.8%。3 周内 SARS-CoV-2 取代了 CARVs，成为所有检测到的呼吸道病毒的 48%，随后是鼻病毒/肠道病毒（13%）、流感病毒（12%）、冠状病毒（9%）、呼吸道合胞病毒（6%）和副流感病毒（6%）。
在 SARS-CoV-2 大流行的早期，冬季 CARVs 占主导地位，影响感染控制和治疗决策，但很快被取代，提示存在竞争感染。我们假设，成人和儿童中 SARS-CoV-2 不同的流行病学特点与先天免疫记忆和先天免疫干扰有关。
