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| CADDE Project | |
|---|---|
| Name | CADDE Project |
| Established | 2010s |
| Location | São Paulo, London, Oxford |
CADDE Project
The CADDE Project was an international research initiative focused on genomic surveillance, epidemiology, and bioinformatics of viral pathogens. It combined laboratory sequencing, field epidemiology, and computational analysis to monitor viral evolution and inform public health responses for outbreaks in South America and beyond.
The CADDE Project aimed to integrate viral genomics, phylogenetics, and molecular epidemiology to track pathogen transmission, characterize novel variants, and support intervention strategies across regions including Brazil, United Kingdom, South Africa, and United States. Objectives included establishing sequencing capacity at institutions such as University of São Paulo, London School of Hygiene & Tropical Medicine, and University of Oxford; developing analytic pipelines compatible with platforms like Illumina and Oxford Nanopore Technologies; and producing data to inform agencies including World Health Organization and Pan American Health Organization. The project sought to foster collaborations with public health laboratories like Fundação Oswaldo Cruz and research centers such as Wellcome Trust Sanger Institute.
Initiated in the mid-2010s, the project expanded during events involving emerging viruses such as Zika virus and later the SARS-CoV-2 pandemic. Early phases linked researchers from University of Cambridge, Imperial College London, and University of Edinburgh with Brazilian partners at Universidade de São Paulo and Oswaldo Cruz Foundation. Funding and coordination involved stakeholders including the Wellcome Trust, Bill & Melinda Gates Foundation, and national agencies like Brazilian Ministry of Health. Technical development drew on methods from groups at Broad Institute, EMBL-EBI, and National Institutes of Health, adapting protocols first validated during outbreaks like the 2014–2016 West African Ebola epidemic.
The consortium comprised academic institutions, public health bodies, and sequencing centers: University of São Paulo, Oswaldo Cruz Foundation, FIOCRUZ, London School of Hygiene & Tropical Medicine, University of Oxford, Wellcome Sanger Institute, and national public health laboratories in Argentina and Chile. Collaborators included researchers affiliated with Imperial College London, University of Toronto, McMaster University, and regional centers such as Fiocruz Amazonas. Partnerships extended to organizations like GISAID, PLOS, and funders such as the European Commission and UK Research and Innovation.
Activities combined sample collection from hospitals and surveillance networks, high-throughput sequencing using Illumina MiSeq and Oxford Nanopore Technologies MinION, and computational analyses leveraging tools from Nextstrain, MAFFT, IQ-TREE, and BEAST. Methods included genome assembly, variant calling, phylodynamic inference, and travel-associated transmission mapping that interfaced with datasets from Ministry of Health (Brazil), hospital networks like Hospital das Clínicas, and epidemiological records from PAHO. Laboratory protocols built on standards from Centers for Disease Control and Prevention and sequencing consortia such as ARTIC Network.
The consortium produced papers documenting lineage emergence, geographic dispersal, and mutation profiles in journals and preprint servers such as Nature, Science, The Lancet, PNAS, and bioRxiv. Key outputs included descriptions of regional introductions of SARS-CoV-2 lineages into Brazil, characterizations of spike protein mutations relevant to immune escape studied alongside work from University of Oxford and LSTM (Liverpool School of Tropical Medicine), and comparative analyses with variants identified by groups at Mount Sinai Health System and Icahn School of Medicine at Mount Sinai. Findings informed technical briefs issued to WHO and were cited in modeling studies by teams at Imperial College London and London School of Hygiene & Tropical Medicine.
The project enhanced regional sequencing capacity at institutions like Fiocruz and Universidade de São Paulo, influenced surveillance policies adopted by the Brazilian Ministry of Health and regional bodies such as PAHO, and supported vaccine strategy assessments conducted by manufacturers and regulators including AstraZeneca and Brazilian Health Regulatory Agency (Anvisa). Data and pipelines were integrated into public repositories coordinated by GISAID and analytical dashboards used by institutions such as Wellcome Sanger Institute and CDC (United States), enabling real-time tracking employed during subsequent outbreaks.
Funding sources included philanthropic organizations like the Wellcome Trust and Bill & Melinda Gates Foundation, governmental grants from agencies such as UK Research and Innovation and the Brazilian National Council for Scientific and Technological Development, and institutional support from universities and research institutes including FIOCRUZ and University of Oxford. Governance relied on steering committees composed of representatives from partner institutions, ethical oversight by institutional review boards at Universidade de São Paulo and London School of Hygiene & Tropical Medicine, and data-sharing agreements aligned with standards advocated by GISAID.
Category:Virology projects