Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany.
Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany.
Nat Commun. 2024 Jun 20;15(1):5267. doi: 10.1038/s41467-024-48641-2.
During the early stages of the SARS-CoV-2 pandemic, before vaccines were available, nonpharmaceutical interventions (NPIs) such as reducing contacts or antigenic testing were used to control viral spread. Quantifying their success is therefore key for future pandemic preparedness. Using 1.8 million SARS-CoV-2 genomes from systematic surveillance, we study viral lineage importations into Germany for the third pandemic wave from late 2020 to early 2021, using large-scale Bayesian phylogenetic and phylogeographic analysis with a longitudinal assessment of lineage importation dynamics over multiple sampling strategies. All major nationwide NPIs were followed by fewer importations, with the strongest decreases seen for free rapid tests, the strengthening of regulations on mask-wearing in public transport and stores, as well as on internal movements and gatherings. Most SARS-CoV-2 lineages first appeared in the three most populous states with most cases, and spread from there within the country. Importations rose before and peaked shortly after the Christmas holidays. The substantial effects of free rapid tests and obligatory medical/surgical mask-wearing suggests these as key for pandemic preparedness, given their relatively few negative socioeconomic effects. The approach relates environmental factors at the host population level to viral lineage dissemination, facilitating similar analyses of rapidly evolving pathogens in the future.
在 SARS-CoV-2 大流行的早期，在疫苗可用之前，非药物干预（NPIs），如减少接触或抗原检测，被用于控制病毒传播。因此，量化它们的成功对于未来的大流行准备至关重要。利用来自系统监测的 180 万份 SARS-CoV-2 基因组，我们使用大规模贝叶斯系统发育和系统地理学分析，并对多种采样策略下的谱系输入动力学进行纵向评估，研究了 2020 年底至 2021 年初第三波大流行期间德国的病毒谱系输入情况。所有主要的全国性非药物干预措施之后，输入的病例都减少了，其中快速免费检测、加强公共交通和商店戴口罩的规定，以及内部流动和集会的限制，效果最为显著。大多数 SARS-CoV-2 谱系首先出现在病例最多的三个人口最多的州，并从那里在国内传播。输入病例在圣诞节假期前后增加，并在假期后不久达到峰值。免费快速检测和强制佩戴医用/外科口罩的显著效果表明，这些措施对于大流行的准备至关重要，因为它们对社会经济的负面影响相对较少。该方法将宿主人群层面的环境因素与病毒谱系传播联系起来，为未来快速进化病原体的类似分析提供了便利。
