COMPLEXITY AND BIOSECURITY: Molecular Detection of Emerging … · COMPLEXITY AND BIOSECURITY: Molecular Detection of Emerging Threats ... MEGATRENDS - 21st CENTURY ... TESSO NILO

Presented at Workshop on Complexity and Governance,

Singapore, 18-19 July 2013

COMPLEXITY AND BIOSECURITY: Molecular Detection of Emerging Threats

Herawati Sudoyo

Eijkman Institute for Molecular Biology

• Societal Increasing wealth and urbanisation Low tolerance for risk

• Environmental Climate change

• Financial Economic crisis? Energy costs

• Biological GM technology Antibiotic resistance Emergence of zoonotics

MEGATRENDS -

21st CENTURY – THE CENTURY OF COMPLEXITY AND FEAR

Mission - To advance fundamental knowledge in the field of molecular cell biology, and to apply such knowledge to the

understanding, prevention and treatment of human diseases

SCIENCE AT THE EIJKMAN INSTITUTE SUPPORTED THE DEVELOPMENT OF DISEASE MANAGEMENT

SYSTEM

Human Genome Diversity and

Disease. Taking advantage of the

huge human genetic resource of

Indonesia, as reflected by its many

ethnic populations - as the basis for

disease genes discovery, with their

medical and biotechnological

applications.

EIJKMAN INSTITUTE and STRATEGIC RESEARCH

The peopling of the Indonesian archipelago - population markers

DNA Barcoding for speciation has been used in most animal for non-forensic context - fish and its larvae, insects, primates, marine organisms, parasites and others

Forensic DNA laboratory has established its credibility since 2004 dealing with terrorism cases

Application of forensics to wildlife crime investigation involves genetic species identification

Indonesia and Infectious Diseases – a Great Challenge to Mitigate Biorisk

Problems with emerging and reemerging

infectious diseases

Most caused mainly by environmental,

ecological or demographic factors

spread by travel and trade – Indonesia is

a maritime country with 17.504 islands,

700 languages, 33 provinces, 220 million

population

Problems with people movement

Recognize the need to develop,

strengthen and maintained the

capacity to detect, report and respond

to public health events

National Actions to Promote Capacity Building

WHAT ARE WE FACING? Indonesia – a very diverse populations – vast

genome diversity – disease management complex

Indonesia - a rapidly developing country with serious challenges in infectious (emerging and re-emerging) and zoonotic diseases

Indonesia – A Rapidly Developing Country With Serious Problems In Infectious Disease

Malaria: 15 million cases and 42,000 deaths/year (2005) - highest case number and fatality rate in the world; increasing drug resistant parasites

Tuberculosis:

ranked third in TB burden following India and China - TB is third major causes of mortality – increasing drug resistant

Estimation: 269 TB cases/100,000

Dengue: 123,174 cases,1,251 deaths (2007)

Hepatitis B: 10% of population are carriers

Moderate-to-high endemic (WHO)

Avian Influenza: highest case number and fatality rate in the world

Anthrax, Chickenpox, HIV-AIDS, Meningitis, Plaque, Hantaan and

Nipah, Ricketsiosis

NOT ONLY BIRD THAT CAN SPREAD THE FLU

THE WORLD WITHOUT BORDERS

Terms are relatively new in the region -

have not been emphasized until the introduction of anthrax powder as a bioterrorism tool

Biosecurity encompasses minimizing risk through biological harm, not least being the economic impact from spread of alien species.

The ability to implement risk management strategies through early detection system which allow prediction of species, and also monitoring is necessary.

INTRODUCTION TO BIOSAFETY AND

BIOSECURITY

BIORISK SPECTRUM (BIOLOGICAL RISK)

Biosafety

Biosecurity

Intentional Natural Accidental

Outbreak

Epidemic

Pandemic

Laboratory

acquired

infection

Containment

failure

Negligence

Sabotage

Biocriminal

Bioterorism

WHAT DO WE MEAN BY “BIOSECURITY”?

WHO sets out a limited definition of laboratory biosecurity and describes it as the "protection, control and accountability for valuable biological materials within laboratories in order to prevent their unauthorized access, loss, theft, misuse, diversion or intentional release"

BIOSECURITY

• Biosecurity - recent concept that appeared in parallel

with discussions about the growing bioterrorist threat.

• Its meaning has expanded in scope.

• Biosecurity is the objective of the whole range of

policies, mechanisms, regulations, and initiatives that

also includes export controls, biodefense, GLP, GMP,

national implementation of the BTWC including the

obligation to create national legislation relating to

biosecurity, and diplomacy etc that together minimise

the possibility that the life sciences will be misused for

hostile purposes.

Reducing risk of natural infection, accident and misuse need complex and good management

MOLECULAR DETECTION OF EMERGING THREATS: DNA BAR CODES FOR BIOSECURITY

16569 pb

COI

Molecular diagnostic tools - rapid and

accurate identification of

morphologically indistinct alien

species

DNA barcoding use information

within a single gene region common

across all taxa and to access that

information by DNA sequencing

under universal conditions.

Provide standardization and

efficiency needs – lacking in

international biosecurity community

HATARI !

The Effort to Mitigate Emerging Infectious

Pathogens of Wildlife

Danger (Swahili)

The long road to Tesso Nilo

Palm oil tree plantation along the way

Fro

m U

ryu e

t al. 2

007

Tesso Nilo, Riau – August 2012 (Doc. WWF ID) - Elephant’s habitat replaced by palm oil plantation

WHERE DO THE WILDLIFE LIVE NOW?

From: Uryu et al. 2007

ELEPHANT POPULATION ESTIMATE IN RIAU FROM

1995 – 2007

http://www.zgf.de

Sumatran Elephant Population Analysis using Genetic Approach

http://www.zgf.de

TESSO NILO NATIONAL PARK, RIAU

-249 fecal sample

-Multiplex PCR

-13 microsatellite markers

- 3 sex-associated markers

-Ongoing analysis on 108 sample

64 female, 19 male

BUKIT TIGAPULUH

NATIONAL PARK, JAMBI

-357 fecal samples

-Multiplex PCR

-14 microsatellite markers

- 3 sex-associated markers

-Latest results:

101 individuals

74 female, 29 male, 1 ND

WAY KAMBAS NATIONAL

PARK, LAMPUNG

-310 fecal samples -Multiplex PCR

-13 microsatellite markers

- 3 sex-associated markers

-Latest results:

139 individuals

117 female, 21 male

1 ND http://www.wcs.org

Aim : 1. “Best-practice” for the extraction and genetic analysis of DNA

from dung samples. 2. The use of genetic markers (mtDNA, microsatelite, sex

determination) for capture-recapture analyses and the estimation of population size – provide scientific basis for conservation purposes

3. Provide estimates of genetic diversity for each of 6 sampled populations.

June 8th 2013

HOW MANY OF THEM LEFT ?

IUCN 2007: Sumatran orang utan – critically endangered; Bornean – endangered

Exploitation of forest area without respect reduce the size of natural habitat

Geographically Origin of Borneo Orang Utan

Based on Taxonomy • Sumatra (Pongo pygmaeus abelii) • Borneo (Pongo pygmaeus pygmaeus)

Based on cranial and dental morphologies; and MtDNA control region- Borneo Orangutan further classification: • Serawak and Northwest

Kalimantan (P. pygmaeus

pygmaeus)

• Central and Southwest Kalimantan (P. pygmaeus wurmbii)

• East Kalimantan and Sabah (P. pygmaeus morio)

Conservation = Rescue + Release

Sample Collection (blood): 1. ORC Nyaru Menteng, Central Kalimantan (94) 2. ORC Samboja Lestari, East Kalimantan (6)

The orangutan subpopulations should be protected in each geographic region to ensure their genetic diversity and survival

Samboja Lestari

Nyaru Menteng

Rehabilitation and reintroduction of orangutan need a specific attention related to genetic, health, behavioral contamination and geography.

Result • 6 distinct subpopulations within Bornean orangutans • Sequence motif to differentiate between Sumatran and Borneo

orangutan subspecies • Specific motif:

• East (8) • Central A (2) • Central B (1) • Central and Southwest (89) Kalimantan

PvivaxEI Psimium Pvivax

Pknowlesi PknowlesiEI

Psimiovale Pfieldi Pcynomolgi PcynomolgiEI

Pfragile Pcoatneyi Pinui Phylobati

Pgonderi Pmalariae PmalariaeEI

Povale PovaleEI

Pchabaudi PchabaudiEI

Pyoelli PyoeliEI Pberghei PbergheiEI

Pmexicanum Pjuxtanucleare

Pfloridense Pgalinnaceum PgallinaceumEI Pfalciparum PfalciparumEI

Preichinowi PreichinowiEI

Theileria prava 100

100

100

100

100

100

100

100

100

100

80

95

56 81

33

16

90

38

100

97

100

92

98

36

28

41

11

29

16 18

0.05

CONSENSUS

0 100 200 300 400 500 600 bp

PHYLOGENETIC TREE AND BARCODE DIAGRAM

INDICATE COI GENE CAN DIFFERENTIATE SPECIES OF

MALARIA PARASITE

Human Malaria Parasites Primate Malaria Parasites Rodent Malaria Parasites

Avian Malaria Parasites Reptile Malaria Parasites Theileria prava - Outgroup

Phylogenetic tree of 19 orangutan’s malaria parasite

showing 3 different clusters of ovale, malaria and

falciparum-types PvivaxNC007243 PsimiumNC007233 PvivaxAF055587 PvivaxAY598140 PsimiumAY800110 PvivaxY17721

PknowlesiAY722797 PknowlesiAY598141 PknowlesiNC007232

PcoatneyiAB354575 PfragileAY722799

PcynomolgiAY800108 PfieldiAB354574

PsimiovaleAY800109 Valent-12 Kejutan-48

KetutSatrio-6 PhylobatiAB354573 PinuiAB354572

Mayfalica-14 Bulan-13 Eropa-1 Lomon-5 Dogie-2 Eka-8 Shiba-41 Asapa-9 Puput-49 Yuyu-11 Pink-4 Susi-42 MissTut-3 Gilang-47 Romeo-50

PgonderiAY800111 PovaleAB354571 PmalariaeAB354570 PmalariaeAF182848

PreichinowiAJ251941 PreichinowiNC002235

Sisil-17 PfalciparumAY282930 PfalciparumAJ276844 PfalciparumNC002375 PfalciparumM76611 PfalciparumAJ276845 PfalciparumAJ276847 PfalciparumAJ298788 PfalciparumM99416

Theileria prava

100

100

100

100 59

93

100

91

66

99

100

60

39

29

28

16

29

46

96

79

83

100

0.05

15 Malariae-type parasite

3 Ovale-type

Falciparum-type

Reported Cases Of Plasmodium Knowlesi

Infection In Human – Host Jumping

Naturally acquired human Plasmodium knowlesi infection, Singapore. 2008. Tek Ng et al, Emerg Infec Dis 14:814

Human infections with Plasmodium knowlesi, the Philippines. 2008. Luchavez et al. Emerg Infect Dis 14:811

Swedish traveller with Plasmodium knowlesi malaria after visiting Malaysian Borneo. 2009. Bronner et al. BMC 8:15

Human Plasmodium knowlesi infections in young children in central Vietnam. 2009. Van den Eede et al, BMC 8:249

Plasmodium knowlesi in human, Indonesian Borneo. 2010. Figtree et al, Emerg Infect Dis 16:4

First case of detection of Plasmodium knowlesi in Spain by Real time PCR in a traveller from Southeast Asia. 2010. Tang et al, Malaria J 9:219

Human

Human

Animal

Animal

Animal

Human

Anthroponosis Zoonosis

Parasite, Bakteria and Viruses

Michalak et al, Emerg Infect Dis,1998: Mycobacterium tuberculosis infection as a zoonotic disease: Transmission between humans and elephants. Three elephants from an

exotic animal farm in Illinois died of pulmonary disease due to M. tuberculosis. A fourth living elephant was culture-

positive for M. tuberculosis. Twenty two handlers were screened for TB; One culture positive active TB. Molecular

diagnosis showed that the isolates from the four elephants and the handler were the same strain. The investigation

indicates transmission of M.tuberculosis between humans and elephants

MEDIA COVERAGE - EBOLA AND AVIAN FLU

(Not Mutation but man made)

Bioterrorism is an act of bioterrorist to deliberately

release of biological agents, in order to cause death or disease in humans, animals, or plants

The motif of the bioterrorist is mostly to create fear

and/or intimidate government or societies in the pursuit of political, religious, or ideological goals.

• 353 healthy Pongo pygmaeus from central and east Kalimantan • 65/353 (18.4%) and 6/353 (1.7%) seropositive for EBOV and

MARV • Majority of sera showed specificity to Zaire, Sudan, Ivory coast

or Bundibugyo virus found in Africa

Result suggest the existence of multiple species of filoviruses or unknown filoviruses-related in Indonesia and transmission from unidentified reservoir hosts into the orang utan populations

TOWARDS ONE HEALTH

CAPACITY BUILDING IN IDENTIFICATION

AND SURVEILLANCE through EMERGING

PANDEMIC THREATS (EPT) PROGRAM

Pathogen Detection - identification of novel wildlife

pathogens that pose a significant public health threat:

Capacity building - Wildlife surveillance at human-

animal interfaces; non-invasive sampling; Technology

development and pathogen discovery/ diagnostics -

PREDICT viral family (14)

Coordination with National Committee of Zoonoses

and related government partners: Ministry of

Agriculture, Ministry of Forestry, and Ministry of

Health

PREDICT ANIMAL STUDY

• To detect new and known zoonotic pathogens

that are spilling over from wildlife into humans.

• Better understand the presence/prevalence of

emerging pandemic threats circulating in people

• Begin providing updated information to clinicians

to improve diagnosis and treatment protocols

PREDICT - HUMAN STUDY

WILDLIFE SURVEILLANCE AT HUMAN ANIMAL INTERFACE: wet markets, wild macaque colonies, national parks on bats, rodents and primates

Biosecurity in Indonesia - a multi sector issue with unique priorities and challenges

Coordination between MFA. MOH, MOA/DGLSAHS, MST, MOTI, MOD and private sector

Best practices of biorisk management system

Accountability and oversight

Awareness and Education

BUILDING CULTURE OF RESPONSIBILITY

Building Biorisk Culture in Indonesia – Challenge that We Should Face Together

unconscious

incompetent

conscious

Incompetent

conscious

competent

unconscious

competent

• heard

• not understood

• heard

• understood

• not applied

• heard

• understood

• applied

• culture

Geneva 201004 WHERE ARE WE NOW?

WHAT TO OFFER TO COMPLEXITY

SCIENCE?

The Population Dynamics of Emerging

pathogens? Emergence due to anthropogenic change,

Emergence of pathogen in an introduced species (alien),

Emergence of a potential human pathogen from

transportation of a wildlife pathogen

The environmental and social influences

on emerging infectious diseases: past,

present and future? Travel and trade, land use

and environmental change

Thank you for your kind attention