Alkhamis Moh A, Fountain-Jones Nicholas M, Khajah Mohammad M, Alghounaim Mohammad, Al-Sabah Salman K
Department of Epidemiology and Biostatistics, Faculty of Public Health, Health Sciences Centre, Kuwait University, Street 109, Jabriya Campus, Safat, Kuwait City 13110, Kuwait.
School of Natural Sciences, University of Tasmania, Hobart, Dynnyrne, TAS 7000, Australia.
Virus Evol. 2022 May 18;8(1):veac040. doi: 10.1093/ve/veac040. eCollection 2022.
Emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants continue to be responsible for an unprecedented worldwide public health and economic catastrophe. Accurate understanding and comparison of global and regional evolutionary epidemiology of novel SARS-CoV-2 variants are critical to guide current and future interventions. Here, we utilized a Bayesian phylodynamic pipeline to trace and compare the evolutionary dynamics, spatiotemporal origins, and spread of five variants (Alpha, Beta, Delta, Kappa, and Eta) across the Arabian Peninsula. We found variant-specific signatures of evolution and spread that are likely linked to air travel and disease control interventions in the region. Alpha, Beta, and Delta variants went through sequential periods of growth and decline, whereas we inferred inconclusive population growth patterns for the Kappa and Eta variants due to their sporadic introductions in the region. Non-pharmaceutical interventions imposed between mid-2020 and early 2021 likely played a role in reducing the epidemic progression of the Beta and the Alpha variants. In comparison, the combination of the non-pharmaceutical interventions and the rapid rollout of vaccination might have shaped Delta variant dynamics. We found that the Alpha and Beta variants were frequently introduced into the Arab peninsula between mid-2020 and early 2021 from Europe and Africa, respectively, whereas the Delta variant was frequently introduced between early 2021 and mid-2021 from East Asia. For these three variants, we also revealed significant and intense dispersal routes between the Arab region and Africa, Europe, Asia, and Oceania. In contrast, the restricted spread and stable effective population size of the Kappa and the Eta variants suggest that they no longer need to be targeted in genomic surveillance activities in the region. In contrast, the evolutionary characteristics of the Alpha, Beta, and Delta variants confirm the dominance of these variants in the recent outbreaks. Our study highlights the urgent need to establish regional molecular surveillance programs to ensure effective decision making related to the allocation of intervention activities targeted toward the most relevant variants.
新型严重急性呼吸综合征冠状病毒2（SARS-CoV-2）变种持续引发一场史无前例的全球公共卫生和经济灾难。准确理解和比较新型SARS-CoV-2变种的全球及区域进化流行病学，对于指导当前和未来的干预措施至关重要。在此，我们利用贝叶斯系统发育动力学流程，追踪并比较了阿拉伯半岛上五个变种（阿尔法、贝塔、德尔塔、卡帕和埃塔）的进化动态、时空起源及传播情况。我们发现了变种特异性的进化和传播特征，这些特征可能与该地区的航空旅行及疾病控制干预措施有关。阿尔法、贝塔和德尔塔变种经历了相继的增长期和衰退期，而由于卡帕和埃塔变种在该地区的零星引入，我们推断它们的种群增长模式尚无定论。2020年年中至2021年初实施的非药物干预措施可能在减缓贝塔和阿尔法变种的疫情发展方面发挥了作用。相比之下，非药物干预措施与疫苗接种的迅速推广相结合，可能塑造了德尔塔变种的动态变化。我们发现，阿尔法和贝塔变种分别于2020年年中至2021年初频繁从欧洲和非洲传入阿拉伯半岛，而德尔塔变种则于2021年初至2021年年中频繁从东亚传入。对于这三个变种，我们还揭示了阿拉伯地区与非洲、欧洲、亚洲及大洋洲之间重要且密集的传播路径。相比之下，卡帕和埃塔变种传播受限且有效种群规模稳定，这表明在该地区的基因组监测活动中，不再需要将它们作为重点关注对象。相比之下，阿尔法、贝塔和德尔塔变种的进化特征证实了这些变种在近期疫情爆发中的主导地位。我们的研究凸显了迫切需要建立区域分子监测项目，以确保在针对最相关变种分配干预活动方面做出有效决策。
