Laboratory of Advanced Biotechnology & State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, China.
Medical College of Guizhou University, Guiyang, 550025, China.
BMC Infect Dis. 2024 Mar 14;24(1):314. doi: 10.1186/s12879-024-09200-8.
Lassa fever is a hemorrhagic disease caused by Lassa virus (LASV), which has been classified by the World Health Organization as one of the top infectious diseases requiring prioritized research. Previous studies have provided insights into the classification and geographic characteristics of LASV lineages. However, the factor of the distribution and evolution characteristics and phylodynamics of the virus was still limited.
To enhance comprehensive understanding of LASV, we employed phylogenetic analysis, reassortment and recombination detection, and variation evaluation utilizing publicly available viral genome sequences.
The results showed the estimated the root of time of the most recent common ancestor (TMRCA) for large (L) segment was approximately 634 (95% HPD: [385879]), whereas the TMRCA for small (S) segment was around 1224 (95% HPD: [10301401]). LASV primarily spread from east to west in West Africa through two routes, and in route 2, the virus independently spread to surrounding countries through Liberia, resulting in a wider spread of LASV. From 1969 to 2018, the effective population size experienced two significant increased, indicating the enhanced genetic diversity of LASV. We also found the evolution rate of L segment was faster than S segment, further results showed zinc-binding protein had the fastest evolution rate. Reassortment events were detected in multiple lineages including sub-lineage IIg, while recombination events were observed within lineage V. Significant amino acid changes in the glycoprotein precursor of LASV were identified, demonstrating sequence diversity among lineages in LASV.
This study comprehensively elucidated the transmission and evolution of LASV in West Africa, providing detailed insights into reassortment events, recombination events, and amino acid variations.
拉沙热是由拉沙病毒（LASV）引起的出血性疾病，世界卫生组织已将其列为需要优先研究的传染病之一。先前的研究提供了有关 LASV 谱系分类和地理特征的见解。然而，病毒的分布、进化特征和系统发育动力学的因素仍有限。
为了增强对 LASV 的全面了解，我们利用已公开的病毒基因组序列进行了系统发育分析、重配和重组检测以及变异评估。
结果表明，大（L）节段最近共同祖先（TMRCA）的估计时间约为 634（95%HPD：[385879]），而小（S）节段的 TMRCA 约为 1224（95%HPD：[10301401]）。LASV 主要通过两条路线从东向西在西非传播，在第二条路线中，病毒通过利比里亚独立传播到周边国家，导致 LASV 传播范围更广。从 1969 年到 2018 年，有效种群大小经历了两次显著增加，表明 LASV 的遗传多样性增强。我们还发现 L 节段的进化率快于 S 节段，进一步的结果表明锌结合蛋白的进化率最快。在包括亚谱系 IIg 在内的多个谱系中检测到重配事件，而在谱系 V 中观察到重组事件。在 LASV 的糖蛋白前体中发现了显著的氨基酸变化，表明 LASV 谱系之间存在序列多样性。
本研究全面阐明了 LASV 在西非的传播和进化，详细了解了重配事件、重组事件和氨基酸变异。
