Williams Gareth H, Llewelyn Alexander, Brandao Ruben, Chowdhary Kaiya, Hardisty Keeda-Marie, Loddo Marco
Oncologica UK Ltd. Suite 2, The Newnham Building, Chesterford Research Park, Cambridge CB10 1XL, United Kingdom.
EClinicalMedicine. 2021 Aug;38:101021. doi: 10.1016/j.eclinm.2021.101021. Epub 2021 Jul 14.
Mandatory Day 2 and Day 8 PCR testing and variant sequencing of international arrivals has been recently introduced by the UK Government to mitigate against cross-border transmission of high-risk SARS-CoV-2 variants.
SARS-CoV-2 testing and sequencing combines TaqPath CE-IVD COVID-19 RT-PCR with Ion AmpliSeq SARS-CoV-2 Next Generation Sequencing Assay. Retrospective analysis of test trending data was performed from initiation of testing on the 11th March through to the 14th April 2021.
During this time interval, 203,065 SARS-CoV-2 PCR tests were performed, with 3,855 samples testing positive, giving a prevalence of 1.9%. In total 1,913 SARS-CoV-2 genomes were sequenced from positive cases with Ct values < 30 and 1,635 (85.5%) sequences passed quality metrics for lineage analysis. A high diversity of 49 different SARS-CoV-2 variants were identified, including the VOCs B.1.1.7 (Kent; 80.6%), B.1.351 (South Africa; 4.2%), B.1.617.2 (India; 1.7%), P.1 (Brazil; 0.4%) and B.1.1.7 with E484K (Bristol; 0.2%). Vaccine effectiveness was age-related and dose-dependent, ranging from 5% in > 60 with a single dose to 83% in <60 with both doses of a vaccine. Viral load was variant dependent with the B.1.617.2 showing a 21 fold increase in viral copy number compared to the other variants.
The unexpectedly high prevalence of COVID-19 infection in UK arrivals is associated with a rich diversity of SARS-CoV-2 high risk variants entering the UK including the VOC B.1.617.2. Vaccination does not preclude infection and its effectiveness is significantly age-dependent and impacted by variant type. The rapid high-throughput test and sequence workflow we have adopted is particularly suited to the monitoring of cross border transmission and enables immediate public health interventions.
Data analysis conducted in this study was limited to secondary use of information previously collected in the course of normal care.
英国政府最近引入了对国际抵达者进行第2天和第8天的强制性PCR检测及变异株测序，以减轻高风险严重急性呼吸综合征冠状病毒2（SARS-CoV-2）变异株的跨境传播。
SARS-CoV-2检测和测序将TaqPath CE-IVD新冠病毒逆转录PCR与Ion AmpliSeq SARS-CoV-2下一代测序分析相结合。对2021年3月11日开始检测至4月14日的检测趋势数据进行回顾性分析。
在此时间间隔内，共进行了203,065次SARS-CoV-2 PCR检测，3,855份样本检测呈阳性，患病率为1.9%。共对Ct值<30的阳性病例中的1,913个SARS-CoV-2基因组进行了测序，其中1,635个（85.5%）序列通过了谱系分析的质量指标。鉴定出49种不同的SARS-CoV-2变异株，具有高度多样性，包括变异株B.1.1.7（肯特；80.6%）、B.1.351（南非；4.2%）、B.1.617.2（印度；1.7%）、P.1（巴西；0.4%）以及带有E484K的B.1.1.7（布里斯托尔；0.2%）。疫苗有效性与年龄相关且呈剂量依赖性，从60岁以上单剂接种的5%到60岁以下两剂接种的83%不等。病毒载量因变异株而异，与其他变异株相比，B.1.617.2的病毒拷贝数增加了21倍。
英国抵达者中新冠病毒感染的意外高患病率与进入英国的多种SARS-CoV-2高风险变异株有关，包括变异株B.1.617.2。接种疫苗并不能预防感染，其有效性明显取决于年龄且受变异株类型影响。我们采用的快速高通量检测和测序工作流程特别适合监测跨境传播，并能立即采取公共卫生干预措施。
本研究中的数据分析仅限于对先前在常规护理过程中收集的信息进行二次使用。
