SARS-CoV-2 Genomics and Evolution

Since the start of the COVID-19 pandemic, the SARS-CoV-2 virus has evolved from its original RNA sequence. Using bioinformatics methods, population genetics approaches and machine learning algorithms, our laboratory at the MHI research center is analyzing the genomic sequences of the SARS-CoV-2 sequences available worldwide, from various geographic regions. Our goal is to understand SARS-CoV-2 evolution to inform genomic surveillance, as well as vaccine and treatment endeavors.


First wave genomic evolution: Spanning trees done based on subsequences derived from >50,000 consensus sequences downloaded from GISAID as of July 10th, 2020. Subsequences are formed of high frequency mutations (found at a frequency of at least 5% worldwide at a certain point in time between March 1st and July 10th).  Credit: Isabel Gamache

As part of this project, the group is involved in the following collaborations:

  • COLCORONA genetic sub-study (MHI and CRCHUL)
  • COVID-19 taskforce initiative (Collaborators: Guy Wolf, Mila; Smita Krishnaswamy, Yale University)
  • ACE2 genetics (Collaborators: Pavel Hamet and Johanne Tremblay, CRCHUM)
  • Differential Immune Responses in COVID-19 (Collaborator: Morgan Craig, Université de Montréal)


  • Pesaranghader A, Pelletier J, Grenier JC, Poujol R, Hussin JG. 2020. ImputeCoVNet: 2D ResNet Autoencoder for Imputation of SARS-CoV-2 Sequences. 15th MLCB Proceedings (pdf).
  • Hamet P, Pausova Z, Attaoua R, Hishmih C, Haloui M, Shin J, Paus T, Michal A, Gaudet D, Santucci L, Kotchen TA, Cowley AW, Hussin JG, Tremblay J. 2020. SARS-COV-2 receptor ACE2 gene is associated with hypertension and severity of COVID-19 interaction with sex, obesity and smoking. American Journal of Hypertension (here).
  • Kuchroo M. et al. 2020. Multiscale PHATE Exploration of SARS-CoV-2 Data Reveals Multimodal Signatures of Disease (biorxiv).