Computational Analysis, Modelling and Evolutionary Outcomes (CAMEO)Neal Evan Caminsky2022-11-17T11:57:42-05:00
Computational Analysis, Modelling and Evolutionary Outcomes (CAMEO)
CAMEO (CoVaRR-Net’s Computational Analysis, Modelling and Evolutionary Outcomes 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. In addition, our group works to address emerging bioinformatic and computational tool needs.
CAMEO is composed of academic researchers and members of the Public Health Agency of Canada (PHAC). We collaborate with PHAC, the Canadian Public Health Laboratory Network (CPHLN), and academic researchers with diverse subject expertise from across the country. Our members conduct analyses on SARS-CoV-2 genome sequences and wastewater data from various jurisdictions.
CAMEO aims to achieve a unified Canadian network for the detection, molecular characterization, and epidemiological modelling of emerging pathogens within our borders. Our vision is to make genomic epidemiology actionable in real time, for the benefit of the research community and public health practitioners. Our team strives to build relationships, computational tools, and data standards, as well as train highly qualified personnel to realize this vision.
1. Mathematical and Phylogenetic Approaches to Characterize Variants
We are continuously analyzing SARS-CoV-2 genomic sequence data to identify and characterize the epidemiology of new and existing variants. These activities allow us to predict the variants’ rate of spread and their potential impact on health care systems across the country. We communicate this information across CoVaRR-Net pillars and to PHAC to assist in public health decision-making.
Duotang is a continually updated web-based notebook that contains genomic epidemiology and mathematical modelling analyses. Its purpose is to explore SARS-CoV-2 evolution in Canada with the aim of spurring further research discussion across pillars, supporting discussions with public health authorities, and sharing with the science communication team for eventual public dissemination. The data for Duotang is compiled from the Canadian VirusSeq Data Portal and DNAStack’s Viral AI.
3. Data Sharing
CAMEO is committed to working with the Canadian VirusSeq Data Portal to ensure that Canadian SARS-CoV-2 genome sequences generated by the Canadian Public Health Laboratory Network (CPHLN) and regional health authorities are publicly available without restriction to encourage data re-use for scientific discovery and innovation. We will work with the VirusSeq Data Portal to explore more flexible and comprehensive ways of sharing contextual data in a trusted environment. This will be done by building on the Canadian COVID Genomics Network (CanCOGeN) and CHARGES (Canadian public Health Alliance for Research in Genomic Epidemiology and Surveillance – a CPHLN-led consortium to implement genomic based infectious disease surveillance) efforts to standardize and harmonize contextual information critical for genomics analysis. Our collaboration is focused on ensuring the Data Portal is as user-friendly as possible, while working to add features that are useful to researchers seeking to analyze the data in the Portal. We are also working towards supporting the analyses and visualization of wastewater data from across the country and national priority pathogens.
COVID-MVP is an interactive heatmap-based visualization tool for SARS-CoV-2.
It tracks the prevalence of SARS-CoV-2 mutations, offering annotations of the functional impact of these mutations in variants of concern (VOCs), variants of interest (VOIs), and user-defined subpopulations in near-real time.
Pokay is also maintained by our team and is regularly updated by curating new functions from the literature.
5. SARS-CoV-2 Evolution in Animal Reservoirs
We are in the process of analyzing about 2000 SARS-CoV-2 genome sequences of animal origin and inferring their phylogenetic relationships with roughly 2000 matched human sequences. The number of animal-to-human transmission events that have happened during the pandemic will then be estimated, and a genome-wide association study will be conducted to identify any animal-associated mutations. We will then develop methods to track these mutations in wastewater.
6. Environmental Monitoring and Sequencing
In collaboration with the CUBE project and the CoVaRR-Net Wastewater Surveillance Research Group (WWSRG), we are working to develop, benchmark and apply methods to track SARS-CoV-2 mutations and variants in the built environment and in wastewater. These data streams are increasingly important in contexts with limited clinical sampling, and now is the time to validate and compare them to clinical sequence data while it is still available. Working with environmental mixtures of viruses, often at low biomass, poses computational challenges which we are working to address, and modelling how these data types track with cases and hospitalizations is also an active area of research.
Sarah (Sally) Otto
Computational Analysis, Modelling and Evolutionary Outcomes (CAMEO) Pillar Co-Lead
Killam University Professor and Canada Research Chair, University of British Columbia
Sarah (Sally) Otto, PhD, investigates how biological systems evolve using mathematical models to investigate the selective forces acting on genetic systems and modes of reproduction. Complementing this approach, her group tracks yeast as they evolve to test evolutionary theories, from the genomic level to the population level. Recent work, both theoretical and experimental, has focused on evolutionary dynamics in rapidly changing environments. Sally’s research has resulted in over 200 publications and a book.
How interactions between hosts and parasites are shaped by evolution is a particular area of Sally’s research interests. During the COVID-19 pandemic, she has been a team member of the BC COVID-19 modelling group, as well as on the External Modelling Experts Group of the Public Health Agency of Canada. Her expertise in evolutionary analysis, population genetics, and phylogenetics will be instrumental to CoVaRR-Net.
Awards include a MacArthur Fellowship, a Steacie Fellowship and Steacie Prize, and fellowship in the Royal Society of Canada, the American Academy of Arts and Sciences, and the National Academy of Sciences.
Jesse Shapiro, PhD, is Associate Professor in the Department of Microbiology and Immunology and at the Genome Centre at McGill University. He is an expert in microbial evolutionary genomics, using genomics approaches to understand the ecology and evolution of microbes. He has developed genome-wide association study methods tailored for bacteria to track evolving microbial populations in real time and understand their evolution and predict their adaptation to changing environments. Jesse co-leads the coronavirus sequencing in Quebec (www.covseq.ca), in collaboration with the Quebec Public Health Lab, and is part of the Canadian COVID-19 Genomics Network (CanCOGeN). His expertise in population genomics and phylogenetics is crucial to CoVaRR-Net.
Jesse 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 Associate Professor in the Department of Microbiology and Immunology and at the Genome Centre.
Fiona Brinkman, PhD, FRSC, is Distinguished Professor in Bioinformatics and Genomics at Simon Fraser University (SFU), most known for R&D of widely used software that aids more integrative, systems-based analyses of microbe and human genomics/transcriptomics data. She leads the data integration of a centralized database integrating CHILD cohort data (CHILDdb), to enable more integrative analysis of diverse CHILD Cohort Study data, including microbiome data. She also co-leads the development of the IRIDA platform, which is now used as the primary platform for Canada’s Public Health Agency to track infectious disease outbreaks using combined epidemiological, lab and genomics data.
All of these projects have expanded to include COVID-19 components and she is additionally now a co-lead of Viral (VirusSeq) Data Analytics for the Canadian COVID-19 Genomics Network. Fiona co-coordinates two large consortiums, involving researchers from 15 countries, enabling better genomic data sharing in an ethical framework. She has a strong interest in developing more preventative, sustainable approaches for disease control, using microbiome data as a sentinel for human, animal or ecosystem health, as well as in bioinformatics education and mentoring young scientists.
Fiona is on several committees and boards, having chaired the Scientific Advisory Board for the European Nucleotide Archive and previously being a member of the Board of Directors for Genome Canada. A fellow of the Royal Society of Canada, her awards include a TR100 award from MIT, Thompson Reuters’ “World’s Most Influential Scientific Minds” and “High Cited Researcher”, and most recently she received a Distinguished Alumni Award from the University of Waterloo and became an SFU Distinguished Professor.
Caroline Colijn, PhD, works at the interface of mathematics, evolution, infection and public health. She joined Simon Fraser University’s Mathematics Department in 2018 as a Canada 150 Research Chair in Mathematics for Infection, Evolution and Public Health.
She did her PhD in applied mathematics at the University of Waterloo, where she studied the foundations of quantum mechanics. She changed track in her postdoctoral years, working on mathematical modelling at McGill and then in infectious disease epidemiology at the Harvard School of Public Health and the Broad Institute at MIT. She moved to the Department of Engineering Mathematics in Bristol, England in 2007 and joined Imperial College London’s Department of Mathematics in 2011.
Caroline has broad interests in applications of mathematics to questions in evolution, infectious disease and public health, and was a founding member of Imperial’s Centre for the Mathematics of Precision Healthcare. She is a leading modeller on COVID-19 and supports the British Columbia Centre for Disease Control and the Public Health Agency of Canada, as well as doing independent academic research. She is a member of the Chief Science Advisor’s expert panel on COVID-19.
Jörg H. Fritz
Jörg H. Fritz, PhD, is Associate Professor in the Department of Microbiology and Immunology at McGill University. Jörg did his undergrad in Microbiology and Genetics at the University of Vienna, Austria followed by an MSc at the biotech start-up Intercell AG in Vienna. He then completed a PhD in Immunology and Vaccinology at the University of Vienna in cooperation with Intercell AG at the University of Vienna, Austria where he developed the novel vaccine adjuvant IC31, which is in phase 3 clinical trials. He furthered his training during a postdoc with Dana J. Philpott at the Institute Pasteur in Paris and with Jennifer L. Gommerman at the University of Toronto, where he studied how Nod-like receptors shape antigen-specific immune responses, and how intestinal IgA+ plasma cells are regulated.
Jörg started his own research group and program at McGill University in July 2010 focused understanding how innate host resistance regulates inflammatory and antigen-specific adaptive immune responses. In particular, his laboratory studies the priming and function of innate lymphoid cells (ILC) and B lineage cells for their role in mucosal immunity.
Jörg’s research centers on two main pillars: (i) the regulation of group 2 innate lymphoid cells (ILC2) during allergic lung inflammation and pulmonary infection; (ii) understanding antigen-specific immunity to SARS-CoV-2 infection in the context of pre-existing immunity to previous infections.