Data from: Phenotypic evolution of SARS-CoV-2: A statistical inference approach

Since its emergence in late 2019, the SARS-CoV-2 virus has spread
globally, causing the ongoing COVID-19 pandemic. In the fall of 2020, the
Alpha variant (lineage B.1.1.7) was detected in England and spread
rapidly, outcompeting the previous lineage. Yet, very little is known
about the underlying modifications of the infection process that can
explain this selective advantage. Here, we try to quantify how the Alpha
variant differed from its predecessor on two phenotypic traits: the
transmission rate and the duration of infectiousness. To this end, we
analysed the joint epidemiological and evolutionary dynamics as a function
of the Stringency Index, a measure of the amount of Non-Pharmaceutical
Interventions. Assuming that these control measures reduce contact rates
and transmission, we developed a two-step approach based on SEIR models
and the analysis of a combination of epidemiological and evolutionary
information. First, we quantify the link between the Stringency Index and
the reduction in viral transmission. Secondly, based on a novel
theoretical derivation of the selection gradient in an SEIR model, we
infer the phenotype of the Alpha variant from its frequency changes. We
show that its selective advantage is more likely to result from a higher
transmission than from a longer infectious period. Our work illustrates
how the analysis of the joint epidemiological and evolutionary dynamics of
infectious diseases can help understand the phenotypic evolution driving
pathogen adaptation.

自2019年末首次出现以来，严重急性呼吸综合征冠状病毒2型（SARS-CoV-2）已在全球范围内传播，引发了持续至今的新型冠状病毒肺炎（COVID-19）大流行。2020年秋季，Alpha变异株（谱系B.1.1.7）在英国被首次检出，随后快速传播并取代了此前的主流病毒谱系。然而，目前学界对可解释该选择性优势的感染过程潜在修饰机制仍知之甚少。
本研究旨在量化Alpha变异株与其亲代毒株在两项表型特征上的差异：传播速率与感染期时长。为此，我们以非药物干预（Non-Pharmaceutical Interventions）程度的量化指标——防控严格指数（Stringency Index）为变量，分析了传染病的联合流行病学与进化动力学特征。
假设此类公共卫生防控措施可降低人群接触率与病毒传播效率，我们开发了基于SEIR模型（Susceptible-Exposed-Infected-Recovered model）的两步分析方法，并结合流行病学与进化信息开展联合分析。第一步，我们量化了防控严格指数与病毒传播降低幅度之间的关联关系；第二步，基于SEIR模型中选择梯度的全新理论推导，我们通过Alpha变异株的种群频率变化推断其表型特征。
研究结果表明，相较于更长的感染期，Alpha变异株的选择性优势更可能源于更高的传播能力。本研究展示了，对传染病的联合流行病学与进化动力学开展分析，如何助力学界解析驱动病原体适应性进化的表型演化机制。