Background

The rise of new SARS-CoV-2 variants worldwide requires global molecular surveillance strategies to support public health control. Early detection and evaluation of their associated risk of spreading within the population are pivotal.

Methods

Between April 2020 and February 2021, the UK Lighthouse Labs Network at Alderley Park tested more than eight million nose and throat swab samples for the presence of SARS-CoV-2, via PCR. The assay targeted three genomic regions of the virus: N, Orf1ab and S. Whole-genome next-generation sequencing was used to confirm positive PCR results. Positive results were mapped using the postal district origin of samples to allow real-time tracking of the spread of a new variant through the UK.

Findings

In mid-November 2020, the assay identified an increasing number of S gene negative, N and Orf1ab positive samples. Whole-genome sequencing demonstrated that the loss of S gene detection was due to the appearance of a SARS-CoV-2 lineage (B.1.1.7) designated as Variant of concern (VOC) 202012/01. By the beginning of January 2021, the new SARS-CoV-2 VOC comprised 70% of daily positive samples tested at Alderley Park and ∼98% by the end of February 2021.

Interpretation

The timeline view identified the rapid spread of the new SARS-CoV-2 variant across England during the first three weeks of December. Coupling high-throughput diagnostics and molecular surveillance was pivotal to the early detection of the spread of this variant. The availability of real-time tracking of an emerging variant is an important new tool to inform decision-making authorities for risk mitigation. In a respiratory pandemic, a tool for the timely response to the emergence and spread of a novel variant is vital, even more so when a variant is associated with the enhanced transmission, as has occurred with VOC 202012/01.

中文翻译：

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SARS-CoV-2 相关变异的高通量诊断和动态风险评估

背景

全球范围内新的 SARS-CoV-2 变体的兴起需要全球分子监测策略来支持公共卫生控制。早期检测和评估其在人群中传播的相关风险至关重要。

方法

2020 年 4 月至 2021 年 2 月期间，位于奥尔德利公园的英国灯塔实验室网络通过 PCR 检测了超过 800 万份鼻和咽拭子样本中是否存在 SARS-CoV-2。该法针对的病毒三种基因组区域：ñ，Orf1ab和小号。全基因组二代测序用于确认阳性 PCR 结果。使用样本的邮政区来源绘制了阳性结果，以便实时跟踪新变种在英国的传播。

发现

2020 年 11 月中旬，该测定确定了越来越多的S基因阴性、N和 Orf1ab 阳性样本。全基因组测序表明，S基因检测的丢失是由于 SARS-CoV-2 谱系 (B.1.1.7) 的出现，该谱系被指定为关注变体 (VOC) 202012/01。到 2021 年 1 月初，新的 SARS-CoV-2 VOC 占奥尔德利公园每日检测的阳性样本的 70%，到 2021 年 2 月底约为 98%。

解释

时间线视图确定了新的 SARS-CoV-2 变体在 12 月的前三周在英格兰迅速传播。结合高通量诊断和分子监测对于早期检测这种变体的传播至关重要。实时跟踪新出现的变体是一种重要的新工具，可以通知决策当局以减轻风险。在呼吸道大流行中，及时应对新型变异的出现和传播的工具至关重要，尤其是当变异与增强传播相关时，如 VOC 202012/01 所发生的情况。