Phylodynamic inference suggests introductions as main driver of Mpox Clade II outbreak in 2022 in Slovenia.

IF 2.2 4区 医学 Q3 INFECTIOUS DISEASES
Bastiaan Van der Roest, Egil A J Fischer, Don Klinkenberg, Martin C J Bootsma, Mojca Maticic, Katarina Resman-Rus, Miša Korva, Tatjana Avsic-Zupanc, Mirjam Kretzschmar
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Abstract

In 2022, an Mpox clade II outbreak affected many countries. To optimize control, knowledge on the number of new introductions (human cases infected from outside the study population) versus local transmission is important. We extracted sequences of all 48 Mpox cases in Slovenia in 2022 from the NCBI database, of which 42 passed quality control. We estimated the number of introductions using the phylodynamic model phybreak by integrating genomic and epidemiological data and inferred transmission events. By repeating this analysis with weekly cumulative case data, we assessed if introductions could have been reliably inferred in real time. The number of introductions, estimated after the outbreak ended, was 19 (95% CI: 13-29), and two larger transmission clusters existed. As these introductions occurred throughout the outbreak, we conclude that the Slovenian Mpox outbreak was mainly driven by new introductions. Analysing the data 'in real time' would have only slightly overestimated the number of introductions per week, capturing the trend of introductions as main driver of the outbreak. This makes it useful for guiding control policy during outbreaks, prioritizing the rapid identification of cases among travellers, and with that preventing emergence of new transmission chains.

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系统动力学推断表明,引入是2022年斯洛文尼亚II型天花暴发的主要驱动因素。
2022年,II型麻疹疫情影响了许多国家。为了优化控制,了解新引入病例(来自研究人群以外的人类感染病例)与本地传播的数量非常重要。我们从NCBI数据库中提取了2022年斯洛文尼亚所有48例Mpox病例的序列,其中42例通过了质量控制。我们通过整合基因组和流行病学数据以及推断的传播事件,使用系统动力学模型phybreak来估计引入的数量。通过对每周累积病例数据重复这一分析,我们评估了引入是否可以实时可靠地推断出来。疫情结束后估计的传入病例数为19例(95% CI: 13-29),存在两个较大的传播聚集群。由于这些引种发生在整个疫情期间,我们得出结论,斯洛文尼亚麻疹疫情主要是由新的引种引起的。“实时”分析数据只会略微高估每周的引进数量,捕捉到作为疫情主要驱动因素的引进趋势。这有助于在疫情期间指导控制政策,优先迅速查明旅行者中的病例,从而防止出现新的传播链。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
Epidemiology and Infection
Epidemiology and Infection 医学-传染病学
CiteScore
4.10
自引率
2.40%
发文量
366
审稿时长
3-6 weeks
期刊介绍: Epidemiology & Infection publishes original reports and reviews on all aspects of infection in humans and animals. Particular emphasis is given to the epidemiology, prevention and control of infectious diseases. The scope covers the zoonoses, outbreaks, food hygiene, vaccine studies, statistics and the clinical, social and public-health aspects of infectious disease, as well as some tropical infections. It has become the key international periodical in which to find the latest reports on recently discovered infections and new technology. For those concerned with policy and planning for the control of infections, the papers on mathematical modelling of epidemics caused by historical, current and emergent infections are of particular value.
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