Predicting the evolutionary and epidemiological dynamics of SARS-CoV-2 in South Africa

Since the outbreak of coronavirus disease 2019 (COVID-19), the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continuously mutated and evolved, causing several waves of infection. Predicting the evolutionary and epidemiological dynamics of SARS-CoV-2 remains a challenge. This study combines the epidemic data of different variants of SARS-CoV-2 in South Africa to predict their evolutionary and epidemiological dynamics. Based on the susceptible-infectious-recovered-susceptible (SIRS) transmission dynamics, we consider the transmission rate as an evolutionary trait and the disease-deduced mortality and recovery rates as trade-off functions of the trait. Using the adaptive dynamics method, combined with the epidemic data of the five most recent variants in South Africa, we find that South Africa will be continuously invaded and infected by the new mutant strain with a higher transmission rate. In addition, we find that changing the recovery rate by enhancing treatment, for example, will alter the trade-off function and thereby affect the evolutionary dynamics of SARS-CoV-2, which may evolve into a continuously stable strategy. This study is the first to use evolutionary dynamics theory to predict the future evolutionary and epidemiological dynamics of SARS-CoV-2, which is helpful for the government to predict the epidemic dynamics of COVID-19 and to take effective measures in advance, and it is proposed that advancing treatment time and improving treatment efficiency will contribute to disease control.

自2019冠状病毒病（COVID-19）暴发以来，严重急性呼吸综合征冠状病毒2型（SARS-CoV-2）持续发生突变与演化，引发多轮感染浪潮。精准预测新冠病毒的演化与流行病学动态仍是一项学界挑战。本研究整合南非境内不同新冠病毒变异株的流行数据，以预测其演化与流行病学动态。基于易感-感染-恢复-易感（SIRS）传播动力学模型，本研究将传播速率视作演化性状，并将疾病导致的死亡率与恢复速率定义为该性状的权衡函数。通过采用适应性演化动力学方法，结合南非境内近期出现的五种变异株的流行数据，研究发现南非将持续被传播速率更高的新型突变株入侵并引发感染。此外，研究表明，通过强化治疗等手段调整恢复速率，可改变上述权衡函数，进而影响新冠病毒的演化动态，使其演化成为持续稳定策略。本研究首次运用演化动力学理论预测新冠病毒未来的演化与流行病学动态，可为政府预判新冠疫情流行态势、提前制定有效防控措施提供科学参考；同时提出，尽早开展治疗、提升治疗效率将有助于新冠疫情的防控工作。