Through Advanced Genomic Research

Our research leverages bioinformatics to deepen our understanding of emerging pathogen evolution and to develop predictive models for preparedness against infectious diseases. Harnessing the predictive power embedded within multi-species genomic data, including the dynamic interactions between hosts and pathogens, this research axis is dedicated to enhancing the computational toolbox available for pandemic preparedness, thereby addressing the gaps in our capacity to anticipate and effectively respond to global disease outbreaks. We collaborate with the Laboratoire de Santé Publique du Québec, and we are part of the Computational Analysis, Modelling and Evolutionary Outcomes (CAMEO) group within the Coronavirus Variants Rapid Response Network (CoVaRR-Net).

First wave of SARS-CoV-2 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

Our Research Focus:

• Genomic Surveillance & Pathogen Evolution Prediction: Our group excels in the continuous surveillance of pathogen variants. Through deep viral profiling and our collaboration with the Laboratoire de Santé Publique du Québec (LSPQ), we strive to understand the genetic diversity of viruses both within and across populations globally. Our tools for data visualization and imputation enhance our capabilities in monitoring dynamic transmissions and identifying evolutionary pressures on viruses.
• Immunological Response to Emerging Pathogens: We study the interactions between pathogens and the human immune response. By exploring human leukocyte antigen (HLA) diversity and its influence on immune responses, our work is pivotal in developing strategies for T cell evasion and vaccine improvement. Integrating evolutionary biology with immunological insights, our predictive models are designed to anticipate how mutations affect pathogen evolution and immune evasion, providing critical insights for public health interventions.

Our holistic approach aids in formulating comprehensive pandemic preparedness strategies that consider both genetic diversity and health equity.

Current Group Contributors (alphabetical order):
Grenier JC, Hamelin D, Mostefai F, Poujol R, Rochefort-Boulanger C., Scicluna M.

Related Publications

• Benlarbi M, Ding S, Bélanger É, Tauzin A, Medjahed H, Poujol R, El-Ferri O, Bo Y, Bourassa C, Hussin JG, Fafard J, Pazgier M, Levade I, Abrams C, Côté M, Finzi A. 2024. Temperature-dependent Spike-ACE2 interaction of Omicron subvariants is associated with viral transmission. mBio (accepted).
• Fournelle D, Mostefai F, Brunet-Ratnasingham E, Poujol R, Grenier JC, Gálvez JH, Pagliuzza A, Levade I, Moreira S, Benlarbi M, Beaudoin-Bussières G, Gendron-Lepage G, Bourassa C, Tauzin A, Grandjean Lapierre S, Chomont N, Finzi A, Kaufmann DE, Craig M, Hussin JG. 2024. Intra-Host Evolution Analyses in an Immunosuppressed Patient Supports SARS-CoV-2 Viral Reservoir Hypothesis. Viruses 16(3), 342.
• Mostefai F, Gamache I, Huang J, N’Guessan A, Pelletier J, Pesaranghader A, Hamelin D, Murall CL, Poujol R, Grenier JC, Smith M, Craig M, Wolf G, Krishnaswamy S, Shapiro J and Hussin JG. 2022. Population Genomics Approaches for Genetic Characterization of SARS-CoV-2 Lineages. Frontiers in Medicine.
  
• Kuchroo M, Huang J, Wong P, Grenier JC, Shung D, Tong A, Lucas C, Klein J, Burkhardt D, Gigante S, Godavarthi A, Israelow B, Mao T, Eun Oh J, Silva J, Takahashi T, Odio CD, Casanovas-Massana A, Fournier J, Yale IMPACT Team, Farhadian S, Dela Cruz C, Ko AI, Wilson FP, Hussin JG*, Wolf G*, Iwasaki A*, Krishnaswamy S*. 2022. Multiscale PHATE identifies multimodal signatures of COVID-19. Nature Biotechnology. (*co-senior)
• Hamelin D, Fournelle D, Grenier JC, Schockaert J, Kovalchik K, Kubiniok P, Mostefai F, Duquette JD, Saab F, Sirois I, Smith MA, Pattijn S, Soudeyns H, Decaluwe H, Hussin JG*, Caron E*. 2022. The mutational landscape of SARS-CoV-2 variants diversifies T cell targets in an HLA supertype-dependent manner. Cell Systems. (*co-senior)
• Gazeau S, Deng X, Ooi JHK, Mostefai F, Hussin JG, Heffernan J, Jenner AL, Craig M. 2023. The race to understand immunopathology in COVID-19: perspectives on the impact of quantitative approaches understanding within-host interactions. Immunoinformatics.
• Arnaud N’Guessan A, Kailasam S, Mostefai F, Poujol R, Grenier JC, Contini P, De Palma R, Haber C, Stadler V, Bourque G, Hussin JG, Shapiro BJ, Fritz JH, Piccirillo CA. 2023. Selection for immune evasion in SARS-CoV-2 revealed by high-resolution epitope mapping combined with genome sequence analysis. iScience. 26(8)
• Castro E, Schweinfurth L, Mostefai F, Scicluna M, Ni S, Wolf G, Hussin JG, Krishnaswamy S. 2021. Evolution of SARS-CoV-2 ACE2-Binding Through the Lens of ReLSO. 16^th Machine Learning in Computational Biology (MLCB) proceedings 2022
• Murall C, Poujol R, Petkau A, Sobkowiak B, Zetner A, Kraemer SA, N’Guessan A, Naderi S, Gill EE, Fritz J, Brinkman F, Hussin JG, Prystajecky N, Tarah Lynch T, Croxen MA, McDonald R, MacKenzie K, Colijn C, Van Domselaar G, Otto SP, Shapiro BJ, and The Canadian COVID-19 Genomics Network (CanCOGeN) Virus Sequencing Consortium. 2021. Monitoring the evolution and spread of Delta sublineages AY.25 and AY.27 in Canada. Virological.
• Murall CL, Mostefai F, Grenier JC, Poujol R, Hussin JG, Moreira S, Shapiro BJ, on behalf of the CoVSeQ consortium. 2021. Recent evolution and international transmission of SARS-CoV-2 clade 19B (Pango A lineages). Virological. 
• Pesaranghader A, Pelletier J, Grenier JC, Poujol R, Hussin JG*. ImputeCoVNet: 2D ResNet Autoencoder for Imputation of SARS-CoV-2 Sequences. 15^th Machine Learning in Computational Biology (MLCB) proceedings. (*corresponding)
• Paré B, Rozendaal M, Morin S, Poujol R, Mostefai F, Grenier JC, Kaufmann L, Xing H, Sanchez M, Yechouron A, Racette R, Hussin JG, Wolf G, Pavlov I, Smith MA. 2021. Genomic epidemiology and associated clinical outcomes of a SARS-CoV-2 outbreak in a general adult hospital in Quebec. PLoS ONE
• Dubé MP, Lemaçon A, Barhdadi A, Lemieux Perreault LP, [25 authors], Hussin JG, Boivin G, Busseuil D, Tardif JC. 2021. Genetics of symptom remission in outpatients with COVID-19. Scientific Reports, 11,10847
• Hamet P, Pausova Z, Attaoua R, Hishmih C, Haloui M, Shin J, Paus T, Michal A, Gaudet D, Santucci L, Kotchen A., Cowley A.W, 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.
• Preprints
  1. Kovalchik K*, Hamelin D*, Kubiniok P, Bourdin B, Mostefai F, Poujol R, Paré B, Simpson S, Sidney J, Bonneil É, Courcelles M, Saini S, Kapoor S, Weitzen M, Grenier JC, Gharsallaoui B, Maréchal L, Wu Z, Savoie C, Sette A, Thibault P, Sirois I, Smith M, Decaluwe H, Hussin JG*, Lavallée-Adam M*, Caron E*. 2024. Integrating Machine Learning-Enhanced Immunopeptidomics and SARS-CoV-2 Population-Scale Analyses Unveils Novel Antigenic Features for Next-Generation COVID-19 Vaccines. 
  2. Gill E, Jia B, Murall C, Poujol R, Anwar M, John N, Richardsson J, Hobb A, Olabode A, Lepsa A, [40 authors], CPHLN consortium, CanCOGeN consortium, VirusSeq Data Portal Academic and Health network, Fiume M, Snutch T, Hussin JG, Kassen R, Joy J, Colijn C, Gordon P, Hsiao W, Poon A, Knox N, Courtot M, Stein L, Otto S, Bourque G, Shapiro BJ, Brinkman F. 2024. The Canadian VirusSeq Data Portal & Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology.
  3. Mostefai F, Grenier JC, Poujol R, Hussin JG*. 2024. Refining SARS-CoV-2 Intra-host Variation by Leveraging Large-scale Sequencing Data.