Understanding patterns of variant emergence and spread in an ongoing epidemic

Area of Science:

• Epidemiology
• Virology
• Evolutionary Biology

Background:

• The COVID-19 pandemic has been characterized by the emergence and spread of novel SARS-CoV-2 variants.
• While variant genotypes and phenotypes are known, the evolutionary drivers of their emergence patterns remain unclear.

Purpose of the Study:

• To investigate how variant invasion dynamics are influenced by phenotype (transmissibility, immune evasion), introduction source, timing, population susceptibility, and contact network structure.
• To model the evolutionary factors governing SARS-CoV-2 variant emergence patterns.

Main Methods:

• Utilized a stochastic multi-strain epidemic model.
• Systematically analyzed the impact of variant phenotype, introduction source, timing, population susceptibility, and contact network characteristics on invasion dynamics.

Main Results:

• Strains with increased transmissibility emerge early and dominate rapidly.
• Immune-evasive variants emerge later, persist undetected, and outcompete existing strains as population immunity increases.
• Network heterogeneity and clustering result in more punctuated evolutionary dynamics.

Conclusions:

• Variant phenotype significantly impacts emergence timing and dominance patterns.
• Contact network structure plays a crucial role in shaping viral evolution.
• Findings offer insights into past SARS-CoV-2 dynamics and inform future epidemic modeling.