在贝叶斯系动力学中重建相对传播速率:在2021年12月期间,德国柏林的Omicron的传播优势增加了两倍

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Ariane Weber^1,2, Sanni Översti, Denise Kühnert^1,2,3

¹Transmission, Infection, Diversification & Evolution Group (tide), Max Planck Institute of Geoanthropology, Kahlaische Strasse 10, Jena, Thuringia 07745, Germany.

Virus evolution

|December 18, 2023

概括

我们开发了BDSKY,一种新的植物动力学工具,用于比较传染病变体传播率. 我们的研究表明,奥米克朗病毒在柏林的传播速度是德尔塔病毒的两倍.

科学领域:

流行病学流行病学
病毒进化是病毒的进化
计算生物学计算生物学

背景情况:

植物动力学方法对于追踪传染病传播至关重要.
在COVID-19大流行期间的基因组监测突显了对先进推断方法的需求.
新出现的SARS-CoV-2变种需要考虑不同传播速率的模型.

研究的目的:

为了引入和验证BDSKY,这是BEAST2出生死亡天际线模型的延伸.
为了能够对不同病毒系之间的相对传播率进行可靠的推断.
量化SARS-CoV-2变种的传播优势,例如Omicron与Delta相比.

主要方法:

开发了BDSKY[公式:参见文本],结合了联合推断树的传输速率缩放因子.
进行了广泛的模拟,以评估BDSKY在各种流行病情景中的稳定性.
应用BDSKY[公式:参见文本]到来自德国柏林的真实世界SARS-CoV-2基因组数据.

主要成果:

BDSKY在模拟中准确推断出相对传输速率.
与柏林的三角洲变种相比,Omicron变种的传播率增加了两倍.
在每个变体内的个别集群中观察到传染率的显著变化.

结论:

BDSKY有效量化了变种特定的传输优势.
考虑到谱系特定的传输差异对于准确的植物动力学推断至关重要.
这些发现为在现有干预期间的SARS-CoV-2变种动态提供了关键的见解.

关键词:

贝叶斯的植物动力学.这就是SARS-CoV-2病毒.出生的死亡的死亡.生殖号码生殖号码模拟器模拟器模拟器模拟器传输优势是传输优势.

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