Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand.
Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand.
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DOI：
10.1038/s41467-020-20235-8
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发表时间：
2020-12-11
影响因子：
16.6
通讯作者：
de Ligt J
中科院分区：
文献类型：
--
作者：
Geoghegan JL;Ren X;Storey M;Hadfield J;Jelley L;Jefferies S;Sherwood J;Paine S;Huang S;Douglas J;Mendes FK;Sporle A;Baker MG;Murdoch DR;French N;Simpson CR;Welch D;Drummond AJ;Holmes EC;Duchêne S;de Ligt J
新西兰是一个地理位置偏远的太平洋岛国，边境容易封闭，为遏制COVID-19的传播，新西兰在全国范围内对所有非必要服务实施了“封锁”。在这里，我们从新西兰感染患者中产生了649个SARS-CoV-2基因组序列，这些样本是在“第一波”期间收集的，占这一时期所有确诊病例的56%。尽管地处偏远，但输入新西兰的病毒几乎代表了全球病毒种群测序的所有基因组多样性。这些数据有助于量化公共卫生干预措施的有效性。例如，新西兰最大集群的有效繁殖数Re在封锁的第一周内从7下降到0.2。同样，只有19%的病毒传入新西兰导致了一个以上的额外病例的持续传播。总的来说，这些结果证明了基因组病原体监测在为公共卫生和疾病缓解提供信息方面的实用性。新西兰在发现首例新冠肺炎病例后，很早就实施了严格的控制措施。在这里，作者对2020年5月22日之前采集的样本进行了全基因组测序，发现了高病毒多样性，表明有多个单独的引入和有限的社区传播。
New Zealand, a geographically remote Pacific island with easily sealable borders, implemented a nationwide ‘lockdown’ of all non-essential services to curb the spread of COVID-19. Here, we generate 649 SARS-CoV-2 genome sequences from infected patients in New Zealand with samples collected during the ‘first wave’, representing 56% of all confirmed cases in this time period. Despite its remoteness, the viruses imported into New Zealand represented nearly all of the genomic diversity sequenced from the global virus population. These data helped to quantify the effectiveness of public health interventions. For example, the effective reproductive number, Re of New Zealand’s largest cluster decreased from 7 to 0.2 within the first week of lockdown. Similarly, only 19% of virus introductions into New Zealand resulted in ongoing transmission of more than one additional case. Overall, these results demonstrate the utility of genomic pathogen surveillance to inform public health and disease mitigation. New Zealand implemented stringent COVID-19 control measures early after identification of its first case. Here, the authors perform whole genome sequencing of samples taken until 22 May 2020 and find high viral diversity indicative of multiple separate introductions and limited community transmission.
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