Computational Analysis, Modelling and Evolutionary Outcomes (CAMEO)
About us
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.
Our Vision
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.
Policy guidance
In this presentation to the National Advisory Committee on Immunization (NACI) in March 2023, Dr. Sarah Otto summarized recent CAMEO work highlighting how SARS-CoV-2 variants have been evolving in Canada. While BQ.* variant lineages dominated in early 2023, the XBB.1.5 variant has been rising rapidly in frequency and now comprises the majority of COVID-19 cases.
XBB.1.5 is a member of the XBB* family of lineages that arose by recombination from two separate BA.2 lineages (“X” in the start of a lineage name refers to a recombined lineage). Lab studies have shown that the family of BQ.* and XBB* lineages are more immune evasive, but the fast spread of XBB.1.5 is thought to be due to its greater ability to bind to our cells’ ACE2 receptors, leading to higher transmissibility.
At present, Canada-wide immunity is high, so these variants no longer lead to big waves, but they do lead to wavelets and, more importantly, to long term rises in the “sea-level” of COVID-19 cases. Dr. Otto explores models to show how variants are expected to influence future case numbers and how measures that we take can counteract the rising sea-level of COVID-19 (e.g., through vaccinations, improved ventilation, and masking).
Current Projects
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.
2. Duotang
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.
4. COVID-MVP
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.
COVID-MVP visualization is powered through an independent, scalable and reproducible genomics workflow using functional annotations manually curated in Pokay.
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.
Members
Members
Zohaib Anwar
Simon Fraser University
Erin Gill
Pillar Lead Coordinator
Paul Gordon
University of Calgary
William Hsiao
Simon Fraser University
Julie Hussin
Université de Montréal
Rees Kassen
University of Ottawa
Justin (Baofeng) Jia
Pillar Co-Coordinator
Jeffery Joy
University of British Colombia
Carmen Lia Murall
Public Health Agency of Canada
Abayomi Olabode
Western University
Art Poon
Western University
Steven Sutcliffe
McGill University
Funded Research Results
The race to understand immunopathology in COVID-19: Perspectives on the impact of quantitative approaches to understand within-host interactions
The COVID-19 pandemic has revealed the need for the increased integration of modelling and data analysis to public health, experimental, and clinical studies.
Within-host genetic diversity of SARS-CoV-2 across animal species
Infectious disease transmission to different host species makes eradication very challenging and expands the diversity of evolutionary trajectories taken by the pathogen.
Refining SARS-CoV-2 intra-host variation by leveraging large-scale sequencing data
Understanding how the SARS-CoV-2 virus evolves within individuals during infection is key to managing the pandemic and preventing future outbreaks. In our research, we used publicly available sequencing data, originally collected for genomic surveillance, to study how the virus mutates within individual hosts. These mutations, called intra-host single nucleotide variants (iSNVs), are genetic changes that can shed light on how the virus adapts.
SMDP: SARS-CoV-2 mutation distribution profiler for rapid estimation of mutational histories of unusual lineages
The COVID-19 pandemic-causing virus SARS-CoV-2 generally changes at a steady rate over time. However, sometimes, certain versions of the virus (called lineages) develop many more mutations than we would expect for how long they have been around.
Selection for immune evasion in SARS-CoV-2 revealed by high-resolution epitope mapping combined with genome sequence analysis
Understanding how the immune system responds to SARS-CoV-2, the virus responsible for COVID-19, is crucial for developing better diagnostics, treatments, and vaccines.
The Canadian VirusSeq Data Portal and Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology
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.
Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data
Wastewater-based surveillance (WBS) is an important epidemiological and public health tool for tracking pathogens across the scale of a building, neighbourhood, city, or region.
Endemic means change as SARS-CoV-2 evolves
COVID-19 has become endemic, with dynamics that reflect the waning of immunity and re-exposure, by contrast to the epidemic phase driven by exposure in immunologically naïve populations.
A small number of early introductions seeded widespread transmission of SARS-CoV-2 in Québec, Canada
Québec was the Canadian province most impacted by COVID-19, with 401,462 cases as of September 24th, 2021, and 11,347 deaths due mostly to a very severe first pandemic wave.
Detection of prevalent SARS-CoV-2 variant lineages in wastewater and clinical sequences from cities in Québec, Canada
The ongoing pandemic wave caused by the Omicron variant of SARS-CoV-2 has overwhelmed PCR testing capacity in many parts of the world, including Canada.
Zooanthroponotic transmission of SARS-CoV-2 and host-specific viral mutations revealed by genome-wide phylogenetic analysis
Like other coronaviruses, SARS-CoV-2 can infect a broad range of animals. Since the beginning of the pandemic, there have been several reports of humans infecting animals (including pets like dogs and cats, and wild animals like deer) and a smaller number of transmissions in the other direction, from animals back to humans.
Population Genomics Approaches for Genetic Characterization of SARS-CoV-2 Lineages
Since the start of the COVID-19 pandemic, the SARS-CoV-2 genome has been sequenced at an unprecedented scale. This enables the scientific community to detect many genetic mutations that occur during its evolution, including variants of concern that have spread quickly in the human population.
Monitoring the evolution and spread of Delta sublineages AY.25 and AY.27 in Canada
Over the summer and fall of 2021, CoVaRR-Net scientists, as part of the Canadian COVID Genomics Network (CanCOGeN), partnered with the National Microbiology Laboratory (NML) and the Canadian Public Health Laboratory Network (CPHLN) to investigate the Delta variant and its diverse sub-lineages, which collectively became dominant around the world.
