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Jesse Shapiro Person1 #679756 Jesse Shapiro is an Associate Professor in the Faculty of Medicine and Health Sciences at McGill University. Jesse’s research uses genomics to understand the ecology and evolution of microbes, ranging from freshwater bacterioplankton to the human gut microbiome. His work has helped elucidate the origins of bacterial species, leading to a more unified species concept across domains of life, and has developed genome-wide association study (GWAS) methods tailored for bacteria. | - He is particularly interested in pathogen evolution, and their evolution within patients, and interactions with members of the resident microbiome.
- His laboratory currently has projects on the ecology and evolution of toxic cyanobacterial blooms, cholera infections, and antimicrobial resistance, among others.

- Jesse Shapiro did his undergrad in Biology at McGill, followed by an MSc in Integrative Bioscience at Oxford. He then completed a PhD in Computational and Systems Biology at MIT with Eric Alm, where he developed methods to detect signatures of natural selection, recombination, and speciation in bacterial genomes. He went on to a postdoc with Pardis Sabeti at the Broad Institute and Harvard University, where he studied the evolutionary genomics of Mycobacterium tuberculosis and Lassa virus.
- After seven years as Canada Research Chair in Microbial Evolutionary Genomics at Université de Montréal, he returned to McGill as an associate professor in the Department of Microbiology and Immunology and the Genome Centre.
Tags: B. Jessie Shapiro |
+Citations (5) - CitationsAdd new citationList by: CiterankMapLink[2] Zooanthroponotic transmission of SARS-CoV-2 and host-specific viral mutations revealed by genome-wide phylogenetic analysis
Author: Sana Naderi, Peter E Chen, Carmen Lia Murall, Raphael Poujol, Susanne Kraemer, Bradley S Pickering, Selena M Sagan, B Jesse Shapiro Publication date: 4 April 2023 Publication info: eLife, 4 April 2023 Cited by: David Price 4:50 PM 16 November 2023 GMT Citerank: (5) 701020CANMOD – PublicationsPublications by CANMOD Members144B5ACA0, 703961Zoonosis859FDEF6, 704045Covid-19859FDEF6, 708734Genomics859FDEF6, 715351Sana NaderiSana is a PhD student in the Shapiro Lab in the McGill Genome Center and the Department of Microbiology and Immunology at McGill University.10019D3ABAB URL: DOI: https://doi.org/10.7554/eLife.83685
| Excerpt / Summary [eLife, 4 April 2023]
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a generalist virus, infecting and evolving in numerous mammals, including captive and companion animals, free-ranging wildlife, and humans. Transmission among non-human species poses a risk for the establishment of SARS-CoV-2 reservoirs, makes eradication difficult, and provides the virus with opportunities for new evolutionary trajectories, including the selection of adaptive mutations and the emergence of new variant lineages. Here, we use publicly available viral genome sequences and phylogenetic analysis to systematically investigate the transmission of SARS-CoV-2 between human and non-human species and to identify mutations associated with each species. We found the highest frequency of animal-to-human transmission from mink, compared with lower transmission from other sampled species (cat, dog, and deer). Although inferred transmission events could be limited by sampling biases, our results provide a useful baseline for further studies. Using genome-wide association studies, no single nucleotide variants (SNVs) were significantly associated with cats and dogs, potentially due to small sample sizes. However, we identified three SNVs statistically associated with mink and 26 with deer. Of these SNVs, approx ⅔ were plausibly introduced into these animal species from local human populations, while the remaining approx ⅓ were more likely derived in animal populations and are thus top candidates for experimental studies of species-specific adaptation. Together, our results highlight the importance of studying animal-associated SARS-CoV-2 mutations to assess their potential impact on human and animal health. |
Link[3] Selection for immune evasion in SARS-CoV-2 revealed by high-resolution epitope mapping and sequence analysis
Author: Arnaud N’Guessan, Senthilkumar Kailasam, Fatima Mostefai, Raphaël Poujol, Jean-Christophe Grenier, Nailya Ismailova, Paola Contini, Raffaele De Palma, Carsten Haber, Volker Stadler, Guillaume Bourque, Julie G. Hussin, B. Jesse Shapiro, Jörg H. Fritz, Ciriaco A. Piccirillo Publication date: 13 July 2023 Publication info: iScience, VOLUME 26, ISSUE 8, 107394, AUGUST 18, 2023 Cited by: David Price 4:51 PM 16 November 2023 GMT Citerank: (3) 701020CANMOD – PublicationsPublications by CANMOD Members144B5ACA0, 704036Immunology859FDEF6, 704045Covid-19859FDEF6 URL: DOI: https://doi.org/10.1016/j.isci.2023.107394
| Excerpt / Summary [iScience, 13 July 2023]
Here, we exploit a deep serological profiling strategy coupled with an integrated, computational framework for the analysis of SARS-CoV-2 humoral immune responses. Applying a high-density peptide array (HDPA) spanning the entire proteomes of SARS-CoV-2 and endemic human coronaviruses allowed identification of B cell epitopes and relate them to their evolutionary and structural properties. We identify hotspots of pre-existing immunity and identify cross-reactive epitopes that contribute to increasing the overall humoral immune response to SARS-CoV-2. Using a public dataset of over 38,000 viral genomes from the early phase of the pandemic, capturing both inter- and within-host genetic viral diversity, we determined the evolutionary profile of epitopes and the differences across proteins, waves, and SARS-CoV-2 variants. Lastly, we show that mutations in spike and nucleocapsid epitopes are under stronger selection between than within patients, suggesting that most of the selective pressure for immune evasion occurs upon transmission between hosts. |
Link[4] Longitudinal genomic surveillance of multidrug-resistant Escherichia coli carriage in critical care patients
Author: Mira El Chaar, Yaralynn Khoury, Gavin M. Douglas, Samir El Kazzi, Tamima Jisr, Shatha Soussi, Georgi Merhi, Rima A. Moghnieh, B. Jesse Shapiro Publication date: 3 January 2024 Publication info: Clinical Microbiology, 3 January 2024 Cited by: David Price 9:40 PM 4 March 2024 GMT Citerank: (3) 701020CANMOD – PublicationsPublications by CANMOD Members144B5ACA0, 708734Genomics859FDEF6, 715325Pathogens859FDEF6 URL: DOI: https://doi.org/10.1128/spectrum.03128-23
| Excerpt / Summary [Clinical Microbiology, 3 January 2024]
Colonization with multidrug-resistant Escherichia coli strains causes a substantial health burden in hospitalized patients. We performed a longitudinal genomics study to investigate the colonization of resistant E. coli strains in critically ill patients and to identify evolutionary changes and strain replacement events within patients. Patients were admitted to the intensive care unit and hematology wards at a major hospital in Lebanon. Perianal swabs were collected from participants on admission and during hospitalization, which were screened for extended-spectrum beta-lactamases and carbapenem-resistant Enterobacterales. We performed whole-genome sequencing and analysis on E. coli strains isolated from patients at multiple time points. The E. coli isolates were genetically diverse, with 11 sequence types (STs) identified among 22 isolates sequenced. Five patients were colonized by E. coli sequence type 131 (ST131)-encoding CTX-M-27, an emerging clone not previously observed in clinical samples from Lebanon. Among the eight patients whose resident E. coli strains were tracked over time, five harbored the same E. coli strain with relatively few mutations over the 5 to 10 days of hospitalization. The other three patients were colonized by different E. coli strains over time. Our study provides evidence of strain diversity within patients during their hospitalization. While strains varied in their antimicrobial resistance profiles, the number of resistance genes did not increase over time. We also show that ST131-encoding CTX-M-27, which appears to be emerging as a globally important multidrug-resistant E. coli strain, is also prevalent among critical care patients and deserves further monitoring. |
Link[5] The Canadian VirusSeq Data Portal & Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology
Author: Erin E. Gill, et al. - Baofeng Jia, Carmen Lia Murall, Raphaël Poujol, Muhammad Zohaib Anwar, Nithu Sara John, Justin Richardsson, Ashley Hobb, Abayomi S. Olabode, Alexandru Lepsa, Ana T. Duggan, Andrea D. Tyler, Arnaud N'Guessan, Atul Kachru, Brandon Chan, Catherine Yoshida, Christina K. Yung, David Bujold, Dusan Andric, Edmund Su, Emma J. Griffiths, Gary Van Domselaar, Gordon W. Jolly, Heather K.E. Ward, Henrich Feher, Jared Baker, Jared T. Simpson, Jaser Uddin, Jiannis Ragoussis, Jon Eubank, Jörg H. Fritz, José Héctor Gálvez, Karen Fang, Kim Cullion, Leonardo Rivera, Linda Xiang, Matthew A. Croxen, Mitchell Shiell, Natalie Prystajecky, Pierre-Olivier Quirion, Rosita Bajari, Samantha Rich, Samira Mubareka, Sandrine Moreira, Scott Cain, Steven G. Sutcliffe, Susanne A. Kraemer, Yann Joly, Yelizar Alturmessov, CPHLN consortium, CanCOGeN consortium, VirusSeq Data Portal Academic, Health network, Marc Fiume, Terrance P. Snutch, Cindy Bell, Catalina Lopez-Correa, Julie G. Hussin, Jeffrey B. Joy, Caroline Colijn, Publication date: 8 May 2024 Publication info: arXiv:2405.04734v1 Cited by: David Price 10:21 AM 19 January 2025 GMT Citerank: (4) 679761Caroline ColijnDr. Caroline Colijn works at the interface of mathematics, evolution, infection and public health, and leads the MAGPIE research group. She joined SFU's Mathematics Department in 2018 as a Canada 150 Research Chair in Mathematics for Infection, Evolution and Public Health. She has broad interests in applications of mathematics to questions in evolution and public health, and was a founding member of Imperial College London's Centre for the Mathematics of Precision Healthcare.10019D3ABAB, 679875Sarah OttoProfessor in Zoology. Theoretical biologist, Canada Research Chair in Theoretical and Experimental Evolution, and Killam Professor at the University of British Columbia.10019D3ABAB, 729380SARS-CoV-2 DuotangDuotang is a genomic epidemiology analyses and mathematical modelling notebook, built to explore Canadian SARS-CoV-2 genomic and epidemiological data.122C78CB7, 729382CAMEOCoVaRR-Net’s Computational Analysis, Modelling and Evolutionary Outcomes (CAMEO) team's goal is to use computer modelling and simulations to evaluate the genetic evolution of SARS-CoV-2 variants and how quickly they propagate in the Canadian population. We also help to flag variants of Canadian origin, highlight current variants of interest, and investigate differences in selection acting upon various lineages among regions of the country.10015D3D3AB URL: DOI: https://doi.org/10.48550/arXiv.2405.04734
| Excerpt / Summary [arXiv, 8 May 2024]
The COVID-19 pandemic led to a large global effort to sequence SARS-CoV-2 genomes from patient samples to track viral evolution and inform public health response. Millions of SARS-CoV-2 genome sequences have been deposited in global public repositories. The Canadian COVID-19 Genomics Network (CanCOGeN - VirusSeq), a consortium tasked with coordinating expanded sequencing of SARS-CoV-2 genomes across Canada early in the pandemic, created the Canadian VirusSeq Data Portal, with associated data pipelines and procedures, to support these efforts. The goal of VirusSeq was to allow open access to Canadian SARS-CoV-2 genomic sequences and enhanced, standardized contextual data that were unavailable in other repositories and that meet FAIR standards (Findable, Accessible, Interoperable and Reusable). The Portal data submission pipeline contains data quality checking procedures and appropriate acknowledgement of data generators that encourages collaboration. Here we also highlight Duotang, a web platform that presents genomic epidemiology and modeling analyses on circulating and emerging SARS-CoV-2 variants in Canada. Duotang presents dynamic changes in variant composition of SARS-CoV-2 in Canada and by province, estimates variant growth, and displays complementary interactive visualizations, with a text overview of the current situation. The VirusSeq Data Portal and Duotang resources, alongside additional analyses and resources computed from the Portal (COVID-MVP, CoVizu), are all open-source and freely available. Together, they provide an updated picture of SARS-CoV-2 evolution to spur scientific discussions, inform public discourse, and support communication with and within public health authorities. They also serve as a framework for other jurisdictions interested in open, collaborative sequence data sharing and analyses. |
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