Prosperi Mattia, Rife Brittany, Marini Simone, Salemi Marco
Department of Epidemiology, College of Public Health and Health Professions, University of Florida Gainesville, Fl, USA.
Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida Gainesville, Fl, USA.
IEEE Int Conf Bioinform Biomed Workshops. 2022 Dec;2022:2940-2944. doi: 10.1109/bibm55620.2022.9995364. Epub 2023 Jan 2.
The SARS-CoV-2 pandemic has been presenting in periodic waves and multiple variants, of which some dominated over time with increased transmissibility. SARS-CoV-2 is still adapting in the human population, thus it is crucial to understand its evolutionary patterns and dynamics ahead of time. In this work, we analyzed transmission clusters and topology of SARS-CoV-2 phylogenies at the global, regional (North America) and clade-specific (Delta and Omicron) epidemic scales. We used the Nextstrain's nCov open global all-time phylogeny (September 2022, 2,698 strains, 2,243 for North America, 499 for Delta21A, and 543 for Omicron20M), with Nextstrain's clade annotation and Pango lineages. Transmission clusters were identified using Phylopart, DYNAMITE, and several tree imbalance measures were calculated, including staircase-ness, Sackin and Colless index. We found that the phylogenetic clustering profiles of the global epidemic have highest diversification at a distance threshold of 3% (divergence of 10, where the tree sampled median is 49). Phylopart and DYNAMITE clusters moderately-to-highly agree with the Pango nomenclature and the Nextstrain's clade. At the regional and clade-specific scale, transmission clustering profiles tend to flatten and similar clusters are found at distance thresholds between 0.05% and 25%. All the considered phylogenies exhibit high tree imbalance with respect to what expected in random phylogenies, suggesting short infection times and antigenic drift, perhaps due to progressive transition from innate to adaptive immunity in the population.
严重急性呼吸综合征冠状病毒2（SARS-CoV-2）大流行呈周期性浪潮且出现多种变体，其中一些随着时间推移因传播性增加而占据主导。SARS-CoV-2仍在人类群体中不断演变，因此提前了解其进化模式和动态至关重要。在这项研究中，我们分析了SARS-CoV-2系统发育的传播簇和拓扑结构，涵盖全球、区域（北美）以及特定分支（德尔塔和奥密克戎）的流行规模。我们使用了Nextstrain的nCov开放全球全时系统发育树（2022年9月，2698个毒株，北美2243个，德尔塔21A分支499个，奥密克戎20M分支543个），以及Nextstrain的分支注释和Pango谱系。使用Phylopart、DYNAMITE识别传播簇，并计算了几种树不平衡度量，包括阶梯度、萨克林指数和科利斯指数。我们发现，全球流行的系统发育聚类概况在距离阈值为3%（分歧度为10，树采样中位数为49）时具有最高的多样性。Phylopart和DYNAMITE聚类与Pango命名法和Nextstrain的分支中度到高度一致。在区域和特定分支尺度上，传播聚类概况趋于平缓，在0.05%至25%的距离阈值之间发现了相似的聚类。所有考虑的系统发育树相对于随机系统发育树的预期而言都表现出高度的树不平衡，这表明感染时间较短且存在抗原漂移，这可能是由于人群中从先天免疫到适应性免疫的逐渐转变所致。
