Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package
This publication describes the development of an open, harmonised SARS-CoV-2 contextual data specification created by PHA4GE to support interoperable metadata collection and submission to public repositories. Implemented through standardised templates, protocols, and tools, the specification improves data consistency, reuse, and integration, and is now supported by NCBI’s BioSample database to enhance global COVID-19 genomic surveillance.
Quality Control Solutions for SARS-CoV-2 Genomic Analysis
PHA4GE provides QC guidance for SARS-CoV-2 genomic sequencing, addressing common sources of variability and data quality issues in NGS workflows. The document highlights practical bioinformatics approaches to support reliable genomic surveillance.
Datasets for benchmarking antimicrobial resistance genes in bacterial metagenomic and whole genome sequencing
Whole genome sequencing (WGS) is a key tool in identifying and characterising disease-associated bacteria across clinical, agricultural, and environmental contexts.
Metagenomics-enabled microbial surveillance
Metagenomics-enabled surveillance methods offer the opportunity to improve detection of both known and yet-to-emerge pathogens.
A framework for the promotion of ethical benefit sharing in health research
This publication presents a practical framework to support the identification and implementation of benefit sharing in research programmes. Using a socioecological model and case studies from genomics research during the SARS-CoV-2 pandemic, the framework helps researchers intentionally incorporate equitable benefit sharing from project inception.
SARS-CoV-2 Contextual Data Specification
PHA4GE developed an open-source SARS-CoV-2 contextual data specification to support consistent, interoperable genomic surveillance. The standard enables harmonised data submission, improved reuse, and integrated analysis across public health systems.
PHA4GE Ethics and Data Sharing Platform
The PHA4GE Ethics and Data Sharing Platform brings together researchers, ethicists, and practitioners to engage in informed discussion and collaboration on ethics and data governance. Designed as a respectful and transparent space, the platform supports shared learning, funding opportunities, and the development of ethical research practice.
Tracking the emergence of new SARS-CoV-2 variants in South Africa
A large genomic surveillance effort in South Africa produced 1,365 high-quality whole genomes of SARS-CoV-2; this has identified 16 new lineages of the virus that had not been identified in other countries.
SARS-CoV-2 contextual data specification for open genomic epidemiology – Micro Binfie Podcast
Amid COVID-19 pandemic, experts lay out 10-point plan for a genomic revolution in public health
Pioneers of genomic epidemiology have laid out a 10-point plan for creating a well-supported scientific ecosystem — not only to fight COVID-19, but to head off future pandemics as well.