Alliance for Pandemic Preparedness

May 20, 2020

Emerging Phylogenetic Structure of the SARS-CoV-2 Pandemic



  • Fountain-Jones et al. studied the phylogenetic structures underlying the SARS-CoV-2 pandemic and find support for three distinct lineages, each having different demographic trajectories. While the majority of sequences classified in Lineage A and B originated in China and have been subsequently found in Washington State and throughout the US, Lineage C was predominantly European with no evidence that it circulated in China. 
  • Demographic dynamics of the lineages are also concordant with known epidemiologic factors – for instance mutations affecting the increase in viral mutation rate specific to Lineage C support the hypothesis that Lineage C may have increased transmissibility compared to other lineages  

Fountain-Jones et al. (May 19, 2020). Emerging Phylogenetic Structure of the SARS-CoV-2 Pandemic. Pre-print downloaded May 20 from