Github X-twitter Youtube Facebook Linkedin Instagram

Looking for training resources? Click here

About

Research

We publish content to enlighten our audience on the impact of genomics research and to seek feedback on PHA4GE’s work.

Subscribe to Newsletter

Publications

The publications on this page showcase the core scientific and implementation work of the Public Health Alliance for Genomic Epidemiology (PHA4GE). Together, they highlight how PHA4GE develops and shares open standards, tools, data models, and guidance to support genomic epidemiology and public health practice around the world.

Wastewater metagenomics in Africa: Opportunities and challenges

Wastewater metagenomics is transforming how we monitor microbial communities, offering a powerful and cost-effective approach for pathogen surveillance, antimicrobial resistance (AMR) tracking, and environmental health insights. In Africa, high-throughput sequencing (HTS) of wastewater can serve as an early warning system for infectious disease outbreaks—especially in densely populated areas with limited sanitation—while also supporting discovery of emerging pathogens and novel microbial functions. This overview highlights both the major opportunities and the key challenges, including infrastructure limitations, bioinformatics capacity gaps, variable wastewater composition, and data governance considerations, and outlines the collaborations and investments needed to unlock equitable public health and economic benefits.

The Mpox contextual data specification package: a data curation toolkit to support collaborative pathogen genomic surveillance

During the 2022 and 2024 global Mpox outbreaks, a standardized contextual data specification was developed to support public health genomic surveillance of MPXV. The specification defines ontology-based fields and controlled vocabularies for harmonized capture of sample metadata, epidemiological, clinical, laboratory, and methodological information, with emphasis on geo-temporal context, data provenance, and sampling strategy. Implemented within the open-source DataHarmonizer platform, the MPXV specification enables structured curation, validation, and transformation of surveillance data and is currently in use in Canada, with international applicability and extensibility to other pathogens.

Fixing the plumbing: Building interoperability between wastewater genomic surveillance datasets and systems using the PHA4GE contextual data specification

This publication presents the PHA4GE wastewater contextual data specification, an ISO-compatible, ontology-based standard developed with global partners to support interoperable wastewater genomic surveillance. Implemented through open-source tools and shared frameworks, the specification enables harmonised data integration and serves as a model for broader environmental and metagenomic surveillance standards.

See all Publications

Citations

The publications on this page demonstrate the growing scientific and policy impact of the Public Health Alliance for Genomic Epidemiology (PHA4GE). Each item represents independent work that has cited PHA4GE tools, standards, data models, or guidance, reflecting their adoption by researchers, public health laboratories, and partners around the world.

See all Citations

Most Recent Citations

18929432 Y8S2H8IN 1 modern-language-association 2 default desc 11858 https://pha4ge.org/wp-content/plugins/zotpress/
%7B%22status%22%3A%22success%22%2C%22updateneeded%22%3Afalse%2C%22instance%22%3Afalse%2C%22meta%22%3A%7B%22request_last%22%3A0%2C%22request_next%22%3A0%2C%22used_cache%22%3Atrue%7D%2C%22data%22%3A%5B%7B%22key%22%3A%229U3NX2EJ%22%2C%22library%22%3A%7B%22id%22%3A18929432%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Poulin-Laprade%20et%20al.%22%2C%22parsedDate%22%3A%222025%22%2C%22numChildren%22%3A1%7D%2C%22bib%22%3A%22%26lt%3Bdiv%20class%3D%26quot%3Bcsl-bib-body%26quot%3B%20style%3D%26quot%3Bline-height%3A%202%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%26quot%3B%26gt%3B%5Cn%20%20%26lt%3Bdiv%20class%3D%26quot%3Bcsl-entry%26quot%3B%26gt%3BPoulin-Laprade%2C%20D.%2C%20et%20al.%20%26%23x201C%3BRequirements%20and%20Considerations%20for%20Effective%20Implementation%20of%20Integrated%20One%20Health%20Antimicrobial%20Resistance%20Research.%26%23x201D%3B%20%26lt%3Bi%26gt%3BCanadian%20Journal%20of%20Microbiology%26lt%3B%5C%2Fi%26gt%3B%2C%20vol.%2071%2C%202025%2C%20Scopus%2C%20%26lt%3Ba%20class%3D%26%23039%3Bzp-DOIURL%26%23039%3B%20href%3D%26%23039%3Bhttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1139%5C%2Fcjm-2024-0194%26%23039%3B%26gt%3Bhttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1139%5C%2Fcjm-2024-0194%26lt%3B%5C%2Fa%26gt%3B.%26lt%3B%5C%2Fdiv%26gt%3B%5Cn%26lt%3B%5C%2Fdiv%26gt%3B%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Requirements%20and%20considerations%20for%20effective%20implementation%20of%20integrated%20One%20Health%20antimicrobial%20resistance%20research%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22D.%22%2C%22lastName%22%3A%22Poulin-Laprade%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22J.%22%2C%22lastName%22%3A%22Broadbent%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22D.%22%2C%22lastName%22%3A%22Biot-Pelletier%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22S.%22%2C%22lastName%22%3A%22Kraemer%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22E.J.%22%2C%22lastName%22%3A%22Griffiths%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22A.%22%2C%22lastName%22%3A%22Kumar%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22X.-Z.%22%2C%22lastName%22%3A%22Li%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22C.D.%22%2C%22lastName%22%3A%22Carrillo%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22R.%22%2C%22lastName%22%3A%22Zaheer%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22T.%22%2C%22lastName%22%3A%22McAllister%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22S.%22%2C%22lastName%22%3A%22Kullik%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22E.%22%2C%22lastName%22%3A%22Li%5Cu00e9bana%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22N.%22%2C%22lastName%22%3A%22Ricker%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22A.%22%2C%22lastName%22%3A%22Langlois%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22R.%22%2C%22lastName%22%3A%22Reid-Smith%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22S.P.%22%2C%22lastName%22%3A%22Faucher%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22G.%22%2C%22lastName%22%3A%22Flores-Vargas%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22E.%22%2C%22lastName%22%3A%22B%5Cu00e9dard%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22J.K.%22%2C%22lastName%22%3A%22Summers%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22V.%22%2C%22lastName%22%3A%22Jarocki%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22T.%22%2C%22lastName%22%3A%22Thongthum%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22C.A.%22%2C%22lastName%22%3A%22Carson%22%7D%5D%2C%22abstractNote%22%3A%22%22%2C%22date%22%3A%222025%22%2C%22section%22%3A%22%22%2C%22partNumber%22%3A%22%22%2C%22partTitle%22%3A%22%22%2C%22DOI%22%3A%2210.1139%5C%2Fcjm-2024-0194%22%2C%22citationKey%22%3A%22%22%2C%22url%22%3A%22https%3A%5C%2F%5C%2Fwww.scopus.com%5C%2Finward%5C%2Frecord.uri%3Feid%3D2-s2.0-105014098459%26doi%3D10.1139%252Fcjm-2024-0194%26partnerID%3D40%26md5%3D2671ed8bcbf83dc297635cbe8a6b021f%22%2C%22PMID%22%3A%22%22%2C%22PMCID%22%3A%22%22%2C%22ISSN%22%3A%22%22%2C%22language%22%3A%22%22%2C%22collections%22%3A%5B%22Y8S2H8IN%22%5D%2C%22dateModified%22%3A%222025-11-21T15%3A17%3A27Z%22%7D%7D%2C%7B%22key%22%3A%22CAVWVWCB%22%2C%22library%22%3A%7B%22id%22%3A18929432%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Cameron%20et%20al.%22%2C%22parsedDate%22%3A%222025%22%2C%22numChildren%22%3A1%7D%2C%22bib%22%3A%22%26lt%3Bdiv%20class%3D%26quot%3Bcsl-bib-body%26quot%3B%20style%3D%26quot%3Bline-height%3A%202%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%26quot%3B%26gt%3B%5Cn%20%20%26lt%3Bdiv%20class%3D%26quot%3Bcsl-entry%26quot%3B%26gt%3BCameron%2C%20R.%2C%20et%20al.%20%26%23x201C%3BSARS-CoV-2%20Genomic%20Contextual%20Data%20Harmonization%3A%20Recommendations%20from%20a%20Mixed%20Methods%20Analysis%20of%20COVID-19%20Case%20Report%20Forms%20across%20Canada.%26%23x201D%3B%20%26lt%3Bi%26gt%3BArchives%20of%20Public%20Health%26lt%3B%5C%2Fi%26gt%3B%2C%20vol.%2083%2C%20no.%201%2C%202025%2C%20Scopus%2C%20%26lt%3Ba%20class%3D%26%23039%3Bzp-DOIURL%26%23039%3B%20href%3D%26%23039%3Bhttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1186%5C%2Fs13690-025-01604-5%26%23039%3B%26gt%3Bhttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1186%5C%2Fs13690-025-01604-5%26lt%3B%5C%2Fa%26gt%3B.%26lt%3B%5C%2Fdiv%26gt%3B%5Cn%26lt%3B%5C%2Fdiv%26gt%3B%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22SARS-CoV-2%20genomic%20contextual%20data%20harmonization%3A%20recommendations%20from%20a%20mixed%20methods%20analysis%20of%20COVID-19%20case%20report%20forms%20across%20Canada%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22R.%22%2C%22lastName%22%3A%22Cameron%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22S.%22%2C%22lastName%22%3A%22Savi%5Cu0107-Kalles%5Cu00f8e%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22E.J.%22%2C%22lastName%22%3A%22Griffiths%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22D.%22%2C%22lastName%22%3A%22Dooley%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22A.%22%2C%22lastName%22%3A%22Sridhar%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22A.%22%2C%22lastName%22%3A%22Sehar%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22L.C.%22%2C%22lastName%22%3A%22Tindale%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22W.W.L.%22%2C%22lastName%22%3A%22Hsiao%22%7D%5D%2C%22abstractNote%22%3A%22%22%2C%22date%22%3A%222025%22%2C%22section%22%3A%22%22%2C%22partNumber%22%3A%22%22%2C%22partTitle%22%3A%22%22%2C%22DOI%22%3A%2210.1186%5C%2Fs13690-025-01604-5%22%2C%22citationKey%22%3A%22%22%2C%22url%22%3A%22https%3A%5C%2F%5C%2Fwww.scopus.com%5C%2Finward%5C%2Frecord.uri%3Feid%3D2-s2.0-105003875604%26doi%3D10.1186%252Fs13690-025-01604-5%26partnerID%3D40%26md5%3D41a317d6358649be3b456033e0198ee6%22%2C%22PMID%22%3A%22%22%2C%22PMCID%22%3A%22%22%2C%22ISSN%22%3A%22%22%2C%22language%22%3A%22%22%2C%22collections%22%3A%5B%22Y8S2H8IN%22%5D%2C%22dateModified%22%3A%222025-11-21T15%3A17%3A27Z%22%7D%7D%5D%7D
Poulin-Laprade, D., et al. “Requirements and Considerations for Effective Implementation of Integrated One Health Antimicrobial Resistance Research.” Canadian Journal of Microbiology, vol. 71, 2025, Scopus, https://doi.org/10.1139/cjm-2024-0194.
Cameron, R., et al. “SARS-CoV-2 Genomic Contextual Data Harmonization: Recommendations from a Mixed Methods Analysis of COVID-19 Case Report Forms across Canada.” Archives of Public Health, vol. 83, no. 1, 2025, Scopus, https://doi.org/10.1186/s13690-025-01604-5.

Guidance Documents & Standards

PHA4GE develops guidance documents, standards, and best-practice resources to support the effective use of genomics in public health. These outputs are created through collaborative working groups and reflect consensus-driven, evidence-based approaches informed by global public health practice.

PHA4GE Wastewater Surveillance Guidance and Resources

Ten Best Practices for Public Health Bioinformatics Pipelines

Proposed Standards for Public Health Bioinformatics Software

Bioinformatics Solutions for Mpox Genomic Analysis

See all Guidance Documents

In the Media

PHA4GE’s work in public health genomics and global disease surveillance has been featured in international media, specialist publications, and sector-focused outlets. These independent mentions reflect growing recognition of the importance of coordinated, data-driven approaches to strengthening global public health systems.

Pathoplexus: towards fair and transparent sequence sharing

This piece highlights Pathoplexus, a community-driven viral genomics database developed with input from PHA4GE to advance open data sharing, ethical use, and transparent governance in public health genomics.

Wastewater surveillance reveals disease trends in South Africa

From COVID-19 to measles, scientists are showing how wastewater surveillance can expose underreported infections and strengthen national health monitoring.

Collaboration for greater impact – PHA4GE Conference and IPSN Global Partners Forum 2025

More than 270 scientists, policy-makers, funders and public health experts from around the world attended the third International Pathogen Surveillance Network (IPSN) Global Partners Forum in Cape Town, South Africa from 27 to 29 October 2025. The forum was held jointly with the second Public Health Alliance for Genomic Epidemiology (PHA4GE) biennial conference and was co-hosted by the WHO Hub for Pandemic and Epidemic Intelligence and WHO’s Regional Office for Africa

See all Media Coverage

Videos

Watch PHA4GE videos on public health genomics, genomic epidemiology and pathogen surveillance. Our video library includes recorded conference sessions, expert talks, webinars, podcasts and training materials from the global public health genomics community.

PHA4GE’s YouTube channel provides open access to practical resources covering genomic surveillance, data standards, bioinformatics tools and capacity building for public health. These videos support learning, collaboration and real-world implementation across diverse settings.

See our YouTube Channel

Articles

The articles on this page bring together news, stories, and updates from the Public Health Alliance for Genomic Epidemiology (PHA4GE). They highlight our projects, collaborations, events, and milestones as we work with partners around the world to strengthen genomic epidemiology and public health practice.

Practical panhuman host sequence depletion for responsible data sharing Webinar

PHA4GE Conference & IPSN Global Partners Forum 2025 Summary Report

Collaboration for greater impact – PHA4GE Conference and IPSN Global Partners Forum 2025

See all Articles

Conferences

PHA4GE hosts a biennial international conference that brings together the global public health genomics community to share knowledge, align on standards, and advance the use of genomic epidemiology for public health action.

PHA4GE Conference & IPSN Global Partners Forum 2025

More than 270 scientists, policy-makers, funders, and public health experts from around the world gathered in Cape Town for the third International Pathogen Surveillance Network Global Partners Forum, held jointly with PHA4GE’s second biennial conference. Under the theme Data for Action, the meeting focused on translating genomics into public health impact through stronger surveillance systems, digital infrastructure, and equitable global data sharing.

PHA4GE Conference 2023

PHA4GE’s first-ever conference took place from 30 October to 1 November 2023 at Cavalli Estate in Cape Town, South Africa, bringing together the global public health genomics community. The meeting explored key topics including pathogen surveillance tools, data harmonisation, laboratory quality assurance, ethical data sharing, and enabling genomics in resource-limited settings.

See all PHA4GE Conferences

Newsletters

Receive Regular updates and notifications on PHA4GE’s activities.

See all Newsletters

PHA4GE Newsletter – June 2025

From regional workshops and new initiatives to behind-the-scenes tool development and dialogue, this issue highlights the collective power driving data equity and community-led public health genomics across Africa and beyond.