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"Mapping the future of infectious diseases of the tropics" by Prof. Simon I. Hay, RSTMH

The 52nd Presidential Address to the Royal Society of Tropical Medicine and Hygiene was given at St Johns College, Oxford on 19 September 2013. It looks at the history and modern day role of the RSTMH in tropical public health.

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Transcript of "Mapping the future of infectious diseases of the tropics" by Prof. Simon I. Hay, RSTMH

Mapping the Future
Mapping the Present
The Global Burden of Disease
Scaling up ABRAID
52nd Presidential Address
Royal Society of Tropical Medicine and Hygiene

Mapping the future of infectious diseases of the tropics
i) comprehensive collection of occurrence data
ii) evidence-based consensus
iii) bespoke environmental covariates data
Disease occurrence mapping
Global changes
the tropics are not isolated
Dengue Acknowledgements
Why map dengue?
Larvae and adults thrive in urban areas
Urbanization trends are good for dengue
spreads readily on boats
Dengue virus spreads rapidly in humans on aircraft
~ as malaria declines, dengue rises
Anders & Hay (2012). , (12): 977-984
Tropics are a worthy focus
Global energy consumption -
Btoe - billion tonnes oil equivalent
Energy consumption from >3 Btoe to >12 Btoe (1965-2013)
Projected >18 Btoe in 2040 with no indication of a plateau (IEO 2013)
Pair probability of occurrence with cohort studies to infer inapparent (n=54) and apparent (n=39) incidence per pixel
Then pair with population surfaces for 2010 to sum up global totals
Consistent global estimates for BMGF, GAVI and surfaces for GBD2013
Bhatt (2013). , (7446): 504-507.
The International Research Consortium on Dengue Risk Assessment, Management and Surveillance (IDAMS: http://www.idams.eu) is funded by the European Commission Seventh Framework Programme
Green open-access with European PubMed Central ID: PMC3651993

: Presidential aims

demographically and geographically
Two peer-reviewed journals
(monthly, launched 1907)
(quarterly, launched 2009)
: Today
Biennial – next is in Oxford in 2014 - more later
Annual Research in Progress meeting for young scientists (today)
Not-tropics: 0.93 B DALYs
Tropics: 1.56 B DALYs
DALYs in 2010
GBD regions
GBD defines 21 regions of epidemiological homogeneity and geographical contiguity

Grouped into “tropics” (green) and “not-tropics” (blue)

volume (December 2012)
Data and visualizations: http://www.healthmetricsandevaluation.org/
44/51 published
Encourage you to read
RSTMH made all open access today

Forgive only a cursory treatment
Hay and McHugh (2013) ,
(10): 603-607.

Global air network -
Air traffic and ~dengue (Massey 1933)
Air traffic and dengue today (IATA 2010)
Tropics are not isolated, circle >50% global population
Globally in 2011 - livestock (34) : humans (15) : wildlife (1)
Tropical livestock >40 Mt to >80 Mt in 50 years; accelerating production
Various sources; inspiration Prof. Marius Gilbert
Global host biomass -
Global population -
From >7 BN today to >9 BN in 2050; plateaux ~10 BN but uncertain
Tropical population > not-tropical in 2007
More than 50% of people urban in tropics ~ 2030
Motto – Zonae torridae tutamen
Founded in 1907
Designated a Royal Society in 1920
by Sir James Cantlie and Dr George Carmichael Low
The current Royal Patron is Her Majesty Queen Elizabeth II
HRH The Princess Royal is an Honorary Fellow
106 years, 51 presidents (two have served two terms)
51/51 white, 50/51 male, 46/51 medically qualified
15/51 FRS; military and civil honours too numerous to document
Median age at inauguration = 62
I have the honour of being the 52nd President; and not its oldest
Guardians of the torrid zone ~ protectors of the tropics
Very established and very “establishment”
Look for Cantlie and Low in movie
Bruce’s work on trypanosomiases and Brucellosis
Leishman’s descriptions of the parasites
Manson and Ross to follow

Full annotated bibliography
A “Who’s Who” of tropical medicine
Prof. Simon I. Hay
19 September 2013
St John’s College, University of Oxford

Mapping Past
: Presidential addresses

CEO Gerri McHugh and immediate past-president Prof Peter Winstanley
RSTMH is governed by a board of 12 trustees (9 fellows, 3 with additional skills)
Formally welcome three new trustees today: Dr Peter Horby, Dr Nynke Van den Broek and Dr John Dusabe
Formally welcome a new VP: Dr Simon Cathcart
1264 fellows, 89 countries
554 UK, 151 USA
Charitable objects
: Today
Manson Medal: 1923, triennial, contributions to tropical medicine, highest honour : Prof. David Molyneux
Chalmers Medal: 1923, annual, contributions to tropical medicine, <46 : Prof. Joanne Webster
George MacDonald Medal: 1972, triennial, contributions to tropical hygiene
Sir Rickard Christophers Medal: 1979, triennial, practical and field applications
Donald Mackay Medal: 1990, annual, health of workers in tropics

Honours and awards
Strong foundation
Renew five-year plan
Improve communication with the existing fellowship
Advocate to and for a wider fellowship
benefit from constitutional restructuring and stable resources
draft, consult, review, implement
web presence, social media, meetings
International health and development policy development
Monitor key revenue generators
Encourage, embrace and improve the journal stock
impact factor, open access
investment review, subscriptions, journals
increase the activities of the RSTMH and its fellows
Mortality and morbidity audit for 2010
Attributes 53 million deaths to 235 diseases and injuries
DALY allows direct comparison of deaths and non-fatal health outcomes
DALY = disability-adjusted life year = YLL + YLD
YLL: years of life lost due to mortality
YLD: years lived with disability
Data from formal and informal sources of vital registration
By age, sex and geographical region for specific points in time
Causes categorised as
To compare life prospects in tropics and not-tropics
Ecological theory
What is disease occurrence mapping?
Dengue as an example
Why map dengue?
Disease occurrence mapping: how does it work?
Not just pretty maps
From probability of occurrence to new burden estimations
“Borrows” directly from rich ecological theory
assume disease observations approximate the realized niche of pathogen
correlate with covariates where known and use statistical model to predict extensively
It is clearly not perfect
i) sampling – do we capture enough of the realized distribution?
ii) biotic interactions, biogeography and human impact – especially important at the global scale
iii) environment – is our covariate suite representative?
Mitigated from the outset
Uncertain distribution and burden
Mild to fatal disease with no cure
Day-biting vectors hard to avoid
Control is extremely difficult
A disease of the future
From dengue risk to burden
Archive Volume
Update Volume
Where is the big signal?
Audited in 2012 by John Brownstein and Nigel Collier
Large amount of unused geo-positioned occurrence data
Hundreds of new records daily
web reporting systems
Vast amount of unused high provenance data
Software to automate extraction of data and geopositioning from PubMed abstracts and GenBank records
Number and distribution of geo-positioned entries (13%)
National Center for Biotechnology
~1400 species of pathogens have been described in humans
Aetiological agents for ~350 diseases
174 should be mapped, only 4% have been
Can we generate a global atlas of all infectious diseases?
We have seen data retrieval and geo-positioning are the main bottlenecks
Concept, targets, timeline, collaborators, audience
Restate the problem
What data can we harvest?
Where is the big data / big signal?
How can we automate?
What is ABRAID?
Opportunity for low-cost surveys
Intervention opportunities (i.e. vaccine sentiment “vaccination”)
: social media
New low provenance data sources
Twitter as an example
There are and will be others
High volume
>150 million tweets daily and increasing
5% are geopositioned and increasing
Tweetping movie – every minute for 7 hours
Assumption is it contains lots of occurrence data
Future problems change from obtaining data to extracting signal from noise
Note Tweeting is bidirectional
ABRAID concept
ABRAID details
Automate data retrieval
Machine learning (provenance and geo-positioning)
Automate mapping
BRT and derivatives in a feed-back loop
Extensive validation
Crowd-source checking
Geo-wiki integrated with Global Health Network (http://tghn.org) user groups
Additional expert panel of arbiters
Main audiences
Standard map users: (i) atlas; (ii) spatial audit; (iii) advocacy; (iv) travel health
GBD partner: (i) supply disease landscape covariates; (ii) improve timeliness
Biosurveillance: (i) geo-spatial triage of outbreak risk; (ii) abraid = to awaken
: Sir Patrick Manson



Discovered the role of mosquitoes in the transmission of filarial worms (1877)

Founder of LSHTM

“Father of tropical medicine”

First president
: Sir Ronald Ross



Discovered the life-cycle of avian malaria

Nobel Prize in Physiology and Medicine (1902)

First Briton to receive the prize

Among the first infectious disease modellers

Second president
Childhood mortality has more than halved in my lifetime
Not-tropics from 5-1M , thus effective “interventions” exist
Existing tools could have a profound impact
That opportunity for impact is still great

U5 mortality trends
GBD timeline
What is possible?
What has been done?
What can be done?
Mapping past

Why map?
From advocacy to evidence-based spatial audit of current risk
Baseline from which to measure change
Why do we need new maps?
Achilles heels of existing maps
no evidence-base
no GIS
no uncertainty
What kind of maps can we make?
Systematic review of all infectious diseases to
score maps available vs. maps possible
Infectious Diseases
How many infectious diseases are there?
~1400 (ever recorded) and 355 on
Should we map them all?
Pre-requisites for mapping
Spatial: geographically variable infectious disease occurrence
Aetiology: understand pathogen life history
Measurement: is information available to map
Utility: is it of public health interest
What infectious diseases can we map?
What infectious diseases have we mapped?
174 / 355 to map
Only 7 (4%) comprehensively mapped
What can we infer about the future?
What will be particularly important in the tropics?
Climate change
Biodiversity loss
more people, more urbanites – particularly in the tropics
more host biomass for pathogens – particularly in the tropics
Consumption and production
massive continued growth – less in the tropics
GBD timeline
GBD timeline
Glorious history and a glorious future
We have done much but still much to improve (esp. tropics)
Poor in kind and extent
Rich in kind, poor in extent
Considerable change to anticipate (esp. tropics), not isolated
Rich in kind and extent
The Department of Zoology, University of Oxford (20 years on 01/10/13)
David Rogers, Sarah Randolph, Willy Wint and Sunetra Gupta
The Wellcome Trust (15 years on 01/10/13)
St John’s College
Lab members – past, present and future …
For data, graphics and maps: Sam Bhatt, Chris Connick, Kirsten Duda, Nick Golding, Ros Howes, Tom Koch, Gerri McHugh, Janey Messina, David Pigott, Andy Tatem … apologies if I have missed you!

General acknowledgements
Oxford Town Hall

25-27 September 2014

Measuring progress
Scientists, charities, NGO, funding bodies

Alan Magill (ASTMH president)

Measuring Progress
Watch your inbox
(a) evidence consensus;
(b) occurrence;
(c) pseudo-absence;
(d) environmental / epidemiological covariates which together predict
(e) the probability of occurrence of an infectious disease
Communicable, maternal, neonatal, and nutritional disorders
Non-communicable disorders
DALYs are NOT equal between the regions (tropics > not-tropics)
Heart disease and stroke remain 1 and 2 in not-tropics
Communicable diseases 12 of top 20 in tropics
Almost 50% DALYs in tropics from communicable disease
“Tropical medicine” remains a justifiable concept

Prof. David Molyneux
Prof. Joanne Webster
Occurrence mapping
ITHG disagree on endemic status of 34 territories

Massive systematic search and treatment of evidence of transmission

Brady (2012). , (8): e1760

Gold open-access with European PubMed Central ID: PMC3413714
(a) evidence-based consensus
(b) occurrence data
Formal literature searches were conducted
-PubMed, ISI WoS and PROMED

All papers identified manually

All abstracts read manually

All occurrence data geo-positioned manually

This yielded 8309 points for mapping from 106 countries (1963-2012)

An additional 1622 points were provided by HealthMap (2007-2012)

N = 8309 from literature searches and N = 1622 from HealthMap
90% occurrence points from the tropics
Africa relatively data poor – a focus of future research

(b) occurrence data
All niche modelling techniques
These data are generated in proportion to definitive extent certainty
We explore the full effect through ensemble approaches

(c) pseudo-absence data
(d) environmental datasets
Lots of useful maps available, from climatologies to GDP
Synoptic precipitation http://www.worldclim.org
From 0 mm (yellow) to 800 mm (blue) per month
(d) environmental datasets
Synoptic mean monthly temperature http://www.worldclim.org
Converted to daily dengue transmissibility suitability for
Covariate is the annual number of days suitable for dengue transmission
(d) environmental datasets
Lots of opportunity to use “epidemiological” covariates
Geographically-based economic data
Pixel-based equivalent of gross domestic product (GDP)
BRT mapping with (i) evidence base; (ii) modern cartography and (iii) uncertainty
Statistically accurate and geographically plausible (definitive extent; ++occurrence data)
Biologically plausible: covariates selected have epidemiological relevance: precipitation (37%), temp. suitability (20%), G-econ (9%)
(e) probability of occurrence
Full transcript