International Pathogen

Surveillance Network
Overview presentation

February 2023
The rapid expansion of pathogen genomics since 2019 presents
an opportunity to build truly global coverage

SARS-CoV-2 sequencing capability 14%

increase in one
year (54% to 68%)
• Genomic sequencing
technology has rapidly
developed in recent years,
allowing lower cost, higher
volume pathogen analysis
• COVID-19 provided an
important test case, leading
to a rapid build-out of
capacity worldwide,
• There is now an
opportunity to create an
interlinked network of high-
quality national pathogen
genomics systems, reducing
the burden of future
pandemics, and endemic
diseases
 The Challenge: pathogen genomics are not optimally
deployed to avert pandemics and reduce endemic burdens

Challenge Current efforts and gaps Implication

• Still too few countries can do sequencing at scale

Country capacity remains uneven; • Bioinformatics and links to public health decision
support efforts increasing but making often lag sequencing output
uncoordinated One health decision
• Donor support efforts have limited coverage
making still
• Risk to sustainability of domestic and donor financing
hampered by
poor/incomplete
• Limited sharing b/w human & animal health systems, data
disease areas, academia vs public health
Lots of innovation and good
• Attempts to work across siloes within more limited New pathogens &
practices but limited sharing
geographies (e.g., US CDC AMD, ACDC IPG) variants in many
• No global connector to support harmonization geographies &
disease areas still
• Insufficient incentives to share data internationally likely to be found &
Data sharing beset by problems at shared late
• PIP* was positive step for flu but in many countries &
all levels (technical, political, disease areas there remains no agreed framework
bureaucratic) • Need for WHO as global normative body to ensure trust
& global scope of sharing

* PIP : Pandemic Influenza Preparedness Framework

 In April 2022, WHO released a genomic surveillance strategy,
with five objectives to strengthen national and global systems
Strategic objectives
• Advocate for the value of genomic surveillance with policy makers
Improve access to tools for • Map and monitor capability and capacity landscape
better geographic • Deliver contextualized and sustainable technology solutions
representation • Stimulate innovation and research to address local to global needs
• Shape a sustainable and quality market to maximize access

• Roll-out training packages in genomics and bioinformatics

Strengthen the workforce to
• Promote communities of practice and knowledge exchange
deliver at speed, scale and
• Implement external quality assessment programmes
quality • Strengthen programmes for workforce development and retention

• Develop consensus on data and meta data standards

Enhance data sharing and
• Establish data sharing and access principles
utility for streamlined local
• Ensure data sharing agreements
to global public health • Harmonize norms, standards, benchmarks and reference materials
decision-making and action • Make the use of genomics routine in surveillance practice

Maximize connectivity for • Facilitate data, specimen and information sharing

timely value-add in the • Increase network linkages at local, regional and global levels
broader surveillance • Implement targeted collaboration with One Health partners
architecture • Strengthen networks in routine, epidemic and pandemic contexts

• Test the surge and stretch of genomic surveillance systems

Maintain a readiness • Establish or sustain joint projects to maintain capacities
posture for emergencies • Implement inter- or after-action reviews to strengthen practices
 IPSN was conceived by the G7 and adopted by WHO as the
major initiative of the Hub to strengthen pathogen genomics

2021: conceptualization 2022: operationalization

Concept note developed IPSN set to begin

WHO Hub for
by high-level implementation of
Pandemic and
Implementation key initiatives by
Epidemic Intelligence
Consultation Group end 2022
established

Concept of a “Global IPSN adopted by Hiring opened for

Pandemic Radar”, WHO; Pandemic leadership role within
(later termed IPSN) Hub asked to WHO Pandemic Hub and
endorsed by G7 implement SEEK Development
under UK Presidency brought on to support
implementation
 The IPSN is a new global network bringing together pathogen
genomic actors to improve public health decision making
Create a mutually supportive network of genomic
New pathogen threats detected and fully
surveillance actors with global coverage, that supports
characterized before becoming pandemics;
Vision: Mission: the development of faster and better national policy
health and economic costs of endemic,
responses, medical countermeasures and evidence-
epidemic, and pandemic diseases reduced.
based prevention, intervention and treatment.

What is IPSN? What does IPSN do? What will IPSN deliver?

A network of pathogen genomic actors Communities of practice to solve Increased harmonization and
(human and animal health), including: common challenges innovation in pathogen genomics

✓ National and international lab Country scale-up accelerator to align Increased scale and efficiency of
networks & disease programs efforts & enable South-South exchange country capacity building efforts
✓ Public and veterinary health systems
✓ Academic groups Grant funding to enable equity and Increased political attention and
✓ Private sector power IPSN projects financing efficiency
✓ Philanthropy & civil society
✓ International standard organizations High-level advocacy & comms to keep
✓ Platform providers PGS on the agenda Stronger national and international
surveillance systems better able to
Convened and supported by a secretariat Global partner forum for genomic detect and characterize new threats
led by the WHO Pandemic Hub surveillance and reduce endemic burdens
 IPSN’s bodies of work will produce outputs that strengthen
surveillance systems to enable better public health outcomes
Theory of Change

Stronger
Health and
IPSN Stronger pathogen pathogen Better public
IPSN bodies of work economic
outputs genomics system genomics health response
impact
outcomes

Community of practice Better tools and standards

(Data) for data More effective,
interoperable
Country scale up systems
Improved efficiency and
accelerator effectiveness of country Enhanced Faster and better:
capacity building efforts Higher volume and identification ✓ policy responses Lives saved
quality of data and tracking of Economic
sharing new and ✓ medical product
Grant funding More resources, more development losses averted
efficiently spent existing
pathogens ✓ patient care
More capacity,
High-level advocacy More political attention, more more equitably
sustainable funding distributed across
countries
Global partner forum A better-connected network
 A range of ambitious outputs have been proposed

IPSN hypothesis products 2023 2024 2025

Gap analysis for data Proposed global agreement on data

Communities of practice to standards and protocols and benefit sharing put forward for
solve common challenges member states
Landscaping of tools and
platforms used in countries Communities of practice launch collaborative
Grant funding to enable equity products on a rolling basis
Optimal use cases across
and power IPSN projects country contexts
Workforce
Partners design and implement joint initiatives, in & across
Country scale-up accelerator competencies
regions, facilitated and funded by IPSN secretariat & donors
to align efforts & enable
Maturity model for
South-South exchange
country capacity

High-level advocacy & comms Launch of global Flagship annual

to keep genomics on the investment case for report: progress on
agenda PGS IC + call to action

Global partner forum for Formal launch Annual

genomic surveillance of IPSN partners forum
IPSN governance, based on current hypotheses

IPSN
leadership
Co-chairs Pandemic
committee
(ADG) Hub

Guides
Convenes

Informs
Operational bodies

IPSN
Funders Country scale- Communities
secretariat
forum (FF) up accelerator of practice Convenes
(CSUA) (COPs)
So far, 24 leaders have agreed to join the IPSN
community of practice on genomics data
Organization CoP member Organization CoP member
Chantel Lin
Asia-Pacific Pathogen Genomics Nigeria Centre for Disease Control Ifedayo Adetifa
Raymond Lin
Network
Ben Howden Noguchi Memorial Institute for
William Ampofo
Africa CDC Institute of Pathogen Medical Research, Ghana
Sofonias Kifle Tessema
Genomics
Robert Koch Institute Johana Hanefeld
American University of Beirut Nada M. Melhem
South African National Bioinformatics
Alan Christoffels
Bill & Melinda Gates Foundation Simon Harris Institute
Tata Institute for Genetics and Society,
Patrick Ayscue Rakesh Mishra
Chan Zuckerberg Biohub India
Cristina Tato Peter Goodhand
CSIR-Institute of Genomics and The Global Alliance for Genomics and
Debasis Dash Neerjah
Integrative Biology Health
Skantharajah
Erasmus Netherlands Marion Koopmans UK Health Security Agency Steven Riley

European Centre for Disease

Erik Alm University of Edinburgh Andrew Rambaut
Prevention and Control
US Centers for Disease Control and Duncan
Global.health Moritz Kraemer Prevention MacCannell

Food and Agricultural Wellcome Sanger Institute John Sillitoe

Keith Sumption
Organization Former US Centers for Disease
Greg Armstrong
Control and Prevention
So far, 21 leaders have agreed to join the IPSN Country
Scale Up Accelerator
Organisation CSUA member Organisation CSUA member
Africa CDC Institute of Pathogen
Sofonias Kifle Tessema
Genomics, Ethiopia Robert Koch Institute, Germany Johana Hanefeld
Asia-Pacific Pathogen Genomics
Ben Howden
Network
American University of Beirut, Tata Institute for Genetics and
Nada M. Melhem Rakesh Mishra
Lebanon Society (TIGS), India

CSIR-Institute of Genomics and

Debasis Dash UK Health Security Agency - New
Integrative Biology, India Leena Inamdar
Variant Assessment Platform
Cristina Tato
Chan Zuckerberg Biohub
Patrick Ayscue
US Center for Disease Control and
Duncan MacCannell
Food and Agricultural Organization Keith Sumption Prevention

Nisia Verônica Trindade

Lima Wellcome Connecting Michelle Bishop
Fiocruz, Brazil Sciences
Marilda Agudo Mendonça
Teixeira de Siqueira John Sillitoe
Wellcome Sanger Institute Sónia Morgado
Institut Pasteur de Dakar, Senegal Amadou Sall Kevin Howe

Nigeria Centre for Disease National Center of Genomics and

Ifedayo Adetifa Josefina Campos
Control Bioinformatics, Argentina
 The Community of Practice can focus on 3 potential areas to address
challenges facing optimal harnessing of pathogen genomic data
Challenge Current efforts and gaps Areas for the COP to focus on

• Great variation across countries and diseases Data standards and protocols
Different are further harmonized,
• PHA4GE and others have done important
protocols and leveraging the power of the
work and there is now an opportunity to
standards network to amplify the existing
accelerate
work of PHA4GE and others

• Data sharing platforms (e.g., GISAID, PulseNet, New bioinformatics tools or

Rapid growth in EBI) useful but no unified vision of the future modules that are filling identified
platforms and
• New bioinformatics tools developed (e.g., CZ gaps are prioritised and
tools; limited
Biohub, Oxford University), but risk of developed by members of the
coordination
duplication and gaps community

Reciprocal • Data sharing limited by fears of losing Proposals for data and benefits
agreements academic credit, price gouging, or shutting sharing are worked up, brought
needed on data borders to the wider IPSN network for
and benefits • Need for comprehensive political data and consultation and then raised
sharing benefits sharing agreement with countries & WHA
 The Accelerator can focus on global goods and supporting delivery
to tackle challenges in country capacity

Challenge Current efforts and gaps Impact areas for the country accelerator
• Domestic and donor budgets have grown but
Resources Global goods that can benefit countries and
still too few countries have well-developed
insufficient and development actors, including:
systems to properly coordinate funding
may not be a. Use-case models that demonstrate the
sustainable • Countries may not always see sufficient value optimal use of genomics – and the ROI – in
in maintaining investments in “peacetime” different country contexts
Country b. A country maturity model and playbook
• Hardware procurement has often moved for developing pathogen genomic
investments not faster than human capital, or sequencing
always sequenced surveillance
volumes have overtaken bioinformatics c. A unified approach to competencies
optimally
required to strengthen workforce
development and planning
Many trainings • NPHIs have many trainings to chose from,
but limited but limited focus in strengthening the
attention to workforce i.e., addressing the workforce Supporting delivery:
career paths competency gaps a. Coordinated action for target countries,
aligning existing actors and ensuring no
overlap or gaps
• A range of skilled actors, esp. in LMICs, are
Unharnessed b. A brokering function provided by the
willing and able to support other NPHIs but
“supply” of peer- secretariat, to bring in new actors and
may require support brokering connections,
to-peer support establish new support relationships,
and small amounts of funding
including peer-to-peer NPHI linkages
 The IPSN Funders’ Forum can maximize the impact of the IPSN
by providing catalytic support and increasing coordination
Challenge Current efforts and gaps Areas of work for the funders’ forum

Country capacity • Still too few countries can do sequencing at scale

remains uneven; • Bioinformatics and links to public health decision
support efforts making often lag sequencing output Catalytic funding to
increasing but • Donor support efforts have limited coverage support the activities of
uncoordinated
• Risk to sustainability of domestic and donor financing the IPSN and ensure
there is equity of
• Limited sharing b/w human & animal health systems, participation
Lots of innovation and disease areas, academia vs public health
good practices but • Attempts to work across siloes within more limited
limited sharing geographies (e.g., US CDC AMD, ACDC IPG)
• No global connector to support harmonization

• Insufficient incentives to share data internationally

Coordination to
Data sharing beset by identify and deconflict
problems at all levels • PIP* was positive step for flu but in many countries &
disease areas there remains no agreed framework around larger funding
(technical, political, opportunities
bureaucratic) • Need for WHO as global normative body to ensure
trust & global scope of sharing

* PIP : Pandemic Influenza Preparedness Framework

 Consultations held- page one
Organization Name Organization Name
Africa CDC Institute of Pathogen Genomics Joseph Wangendo Institut Pasteur de Dakar, Senegal Amadou Sall
Africa CDC Institute of Pathogen Genomics Sofonias Kifle Tessema Institut Pasteur de Dakar, Senegal Karine Belondrade
Asia-Pacific Pathogen Genomics Network (APGN) Chantel Lin Institut Pasteur de Dakar, Senegal Xavier Berthet
Lin Tzer Pin Raymond Mailmann School of Public Health Salim Abdool Karim
Asia-Pacific Pathogen Genomics Network (APGN)
Valentine Nigeria Centre for Disease Control (NCDC) Ifedayo Adetifa
Bill & Melinda Gates Foundation (BMGF) David Blazes Nigeria Centre for Disease Control (NCDC) Tarik Mohammed
Bill & Melinda Gates Foundation (BMGF) Scott Dowell Oxford Big Data Institute David Aanensen
Bill & Melinda Gates Foundation (BMGF) Simon Harris Oxford Big Data Institute Heather Halls
Centre for Pathogen Genomics, University of Oxford Big Data Institute Stephen Smith
Ben Howden
Melbourne Public Health Alliance for Genomic Epidemiology
Allen Christoffels
Centre for Pathogen Genomics, University of (PHA4GE)
Le Tuyet Hoang
Melbourne Resolve to Save Lives Chris Lee
Chan Zuckerberg (CZ) Biohub Cristina Tato Robert Kosch Institute (RKI) Johanna Hanefeld
Chan Zuckerberg (CZ) Biohub Patrick Ayscue South African National Bioinformatics Institute (SANBI) Alan Christoffels
Erasmus Netherlands Marion Koopmans The Global Alliance for Genomics and Health (GA4GH) Neejah Skantharajah
European Centre for Disease Prevention and Control The Global Alliance for Genomics and Health (GA4GH) Peter Goodhand
Daniel Palm
(ECDC) The National Institute For Communicable Diseases Of
Lucille Blumberg
European Centre for Disease Prevention and Control South Africa (NICD)
Helen DeFoer
(ECDC) The Rockefeller Foundation Bruce Gellin
European Centre for Disease Prevention and Control The Rockefeller Foundation Manisha Bhinge
Jevgenijs Golovcuks
(ECDC) The Rockefeller Foundation Naveen Rao
Fiocruz Brazil David Brown The Surveillance and Epidemiology of Drug-resistant
Sharon Peacock
Fiocruz Brazil Luana Bermudez Infections Consortium (SEDRIC)
Tony Blair Institute for Global Change Adam Bradshaw
Fiocruz Brazil Marilda Agudo Tony Blair Institute for Global Change Henry Dowlen
Fiocruz Brazil Nisia Verônica Trindade Lima UK Health Security Agency (UKHSA) Bethan Sanderson
Fiocruz Brazil Pedro burger UK Health Security Agency (UKHSA) Dame Jenny Harries
Fiocruz Brazil Valber da Silva UK Health Security Agency (UKHSA) Gurnam Johal
UK Health Security Agency (UKHSA) Joe Littlewood
Global Health Envoy Germany Bernhard Schwartlander
UK Health Security Agency (UKHSA) Melanie Smith
Global Institute for Disease Elimination (GLIDE) Simon Bland UK Health Security Agency (UKHSA) Neil Squires
 Consultations held- page 2
Organization Name Organization Name
UK Health Security Agency (UKHSA) Rachel Cooper Wellcome Sanger Institute - Peru Pablo Tsukayama
UK Health Security Agency (UKHSA) Robert Dalford Wellcome Sanger Institute - Thailand Claire Chewapreecha
UK Health Security Agency (UKHSA) - NVAP (New Wellcome Sanger Institute - The Gambia Alfred Ngwa
Leena Inamdar
Variant Assessment Platform) Wellcome Sanger Institute - Uruguay Gregorio Iraola
University of Birmingham Nick Loman Wellcome Trust Alycia Draper
University of Cambridge Julian Rayner Wellcome Trust Becky Edmunds
University of Edinburgh Andrew Rambaut Wellcome Trust Bilal Mateen
US Centers for Disease Control and Prevention Wellcome Trust Edward Whiting
Anne Purfield
(USCDC) - CGH Wellcome Trust Jennifer Hart
US Centers for Disease Control and Prevention Wellcome Trust Jeremy Knox
Elizabeth Hunsperger
(USCDC) - CGH Wellcome Trust Josie Golding
US Centers for Disease Control and Prevention WHO Hub Julia Fitzner
Leonard Peruski
(USCDC) - CGH WHO Global Outbreak Alert and Response Network
Pat Drury
US Centers for Disease Control and Prevention (GOARN)
Duncan MacCannell
(USCDC) - NCEZID WHO Hub - Epidemic Intelligence from Open Sources
Phillip Abdulmalik
US Centers for Disease Control and Prevention (EIOS)
Gregory Armstrong
(USCDC) - NCEZID WHO Lyon Office Lisa Carter
Wellcome Connecting Sciences Michelle Bishop WHO Pandemic Influenza Preparedness (PIP) IPSN
Gina Samaan
Wellcome Sanger Institute Ewan Harrison Secretariat
Wellcome Sanger Institute John Sillitoe
Wellcome Sanger Institute Mara Lawniczak
Wellcome Sanger Institute Nicholas Robert Thompson
Wellcome Sanger Institute Stephen Bentley
Wellcome Sanger Institute - Argentina Josefina Campos