Arimide Dawit Assefa, Esquivel-Gómez Luis Roger, Kebede Yenew, Sasinovich Sviataslau, Balcha Taye, Björkman Per, Kühnert Denise, Medstrand Patrik
Department of Translational Medicine, Lund University, Malmo, Sweden.
TB/HIV Department, Ethiopian Public Health Institute, Addis Ababa, Ethiopia.
Front Microbiol. 2022 Feb 25;13:821006. doi: 10.3389/fmicb.2022.821006. eCollection 2022.
Ethiopia is one of the sub-Saharan countries hit hard by the HIV epidemic. Previous studies have shown that subtype C dominates the Ethiopian HIV-1 epidemic, but the evolutionary and temporal dynamics of HIV-1 in Ethiopia have not been closely scrutinized. Understanding the evolutionary and epidemiological pattern of HIV is vital to monitor the spread, evaluate and implement HIV prevention strategies.
We analyzed 1,276 Ethiopian HIV-1 subtype C polymerase ( sequences), including 144 newly generated sequences, collected from different parts of the country from 1986 to 2017. We employed state-of-art maximum likelihood and Bayesian phylodynamic analyses to comprehensively describe the evolutionary dynamics of the HIV-1 epidemic in Ethiopia. We used Bayesian phylodynamic models to estimate the dynamics of the effective population size (N) and reproductive numbers (R) through time for the HIV epidemic in Ethiopia.
Our analysis revealed that the Ethiopian HIV-1 epidemic originated from two independent introductions at the beginning of the 1970s and 1980s from eastern and southern African countries, respectively, followed by epidemic growth reaching its maximum in the early 1990s. We identified three large clusters with a majority of Ethiopian sequences. Phylodynamic analyses revealed that all three clusters were characterized by high transmission rates during the early epidemic, followed by a decline in HIV-1 transmissions after 1990. R was high (4-6) during the earlier time of the epidemic but dropped significantly and remained low (R < 1) after the mid-1990. Similarly, with an expected shift in time, the effective population size (N) steadily increased until the beginning of 2000, followed by a decline and stabilization until recent years. The phylodynamic analyses corroborated the modeled UNAIDS incidence and prevalence estimates.
The rapid decline in the HIV epidemic took place a decade before introducing antiretroviral therapy in Ethiopia and coincided with early behavioral, preventive, and awareness interventions implemented in the country. Our findings highlight the importance of behavioral interventions and antiretroviral therapy scale-up to halt and maintain HIV transmissions at low levels (R < 1). The phylodynamic analyses provide epidemiological insights not directly available using standard surveillance and may inform the adjustment of public health strategies in HIV prevention in Ethiopia.
埃塞俄比亚是受艾滋病病毒流行影响严重的撒哈拉以南国家之一。先前的研究表明，C亚型在埃塞俄比亚的艾滋病病毒1型流行中占主导地位，但埃塞俄比亚艾滋病病毒1型的进化和时间动态尚未得到密切审视。了解艾滋病病毒的进化和流行病学模式对于监测其传播、评估和实施艾滋病预防策略至关重要。
我们分析了1276份埃塞俄比亚艾滋病病毒1型C亚型聚合酶序列，其中包括144条新生成的序列，这些序列于1986年至2017年从该国不同地区收集。我们采用了最先进的最大似然法和贝叶斯系统发育动力学分析来全面描述埃塞俄比亚艾滋病病毒1型流行的进化动态。我们使用贝叶斯系统发育动力学模型来估计埃塞俄比亚艾滋病流行随时间变化的有效种群大小（N）和繁殖数（R）的动态。
我们的分析表明，埃塞俄比亚艾滋病病毒1型流行分别起源于20世纪70年代初和80年代初来自东部和南部非洲国家的两次独立传入，随后疫情在20世纪90年代初达到顶峰。我们确定了三个包含大多数埃塞俄比亚序列的大簇。系统发育动力学分析表明，所有三个簇在疫情早期的特征都是高传播率，随后1990年后艾滋病病毒1型传播有所下降。在疫情早期，R值较高（4 - 6），但在1990年中期后显著下降并一直保持在较低水平（R < 1）。同样，随着时间的预期变化，有效种群大小（N）在2000年初之前稳步增加，随后下降并趋于稳定直至近年来。系统发育动力学分析证实了联合国艾滋病规划署模拟的发病率和流行率估计。
埃塞俄比亚艾滋病流行的快速下降发生在该国引入抗逆转录病毒治疗的十年前，并且与该国早期实施的行为、预防和宣传干预措施相吻合。我们的研究结果强调了行为干预和扩大抗逆转录病毒治疗以阻止并将艾滋病病毒传播维持在低水平（R < 1）的重要性。系统发育动力学分析提供了使用标准监测无法直接获得的流行病学见解，并可能为埃塞俄比亚艾滋病预防公共卫生策略的调整提供参考。
