Invasion, expansion and maintenance of Dengue & Chikungunya viruses in the

Americas.

Christine V. F. Carrington12 June 2014

DengueThe most rapidly spreading mosquito-borne viral disease

One of the most important emerging diseases of the 21st century3.5 billion people at risk

Annually: - 390 million infections (96 million clinically apparent) - 24,000 deaths- US$ 2.1 billion (Americas); US$321 million (Caribbean)

Distribution of Global Dengue Risk

Bhatt et al 2013 Nature, 496(7446), 504-507. Shepard et al (2011). Am J Trop Med Hyg. 84(2):200-7

Global Strategy for Dengue Prevention and Control, 2012-2020 Fig. 2, Page 2 http://apps.who.int/iris/bitstream/10665/75303/1/9789241504034_eng.pdf

Dengue virus (DENV)‣Family Flaviviridae, genus flavivirus‣ ~11kb single stranded positive sense RNA genome‣Five serotypes (DENV1 – 5) ‣Phylogenetically distinct genotypes within each serotypes

(Source: ViralZone:www.expasy.org/viralzone, Swiss Institute of Bioinformatics)

Outcomes of DENV infectionUp to an estimated 80% of infections are asymptomatic

DENGUE +/- WARNING SIGNS SEVERE DENGUE

with warning

signswithout

1. Severe plasma leakage2. Severe haemorrhage3. Severe organ impairment

Probable dengueLive in / travel to dengue endemic area.Fever and 2 of the following:• Nausea, vomiting• Rash• Aches and pains• Tourniquet test positive• Leukopenia• Any warning sign

Laboratory confirmed dengue

Warning signs*Abdominal pain or tendernessPersistent vomitingClinical fluid accumulationMucosal bleedingLethargy / restlessnessLiver enlargment >2cmLaboratory: increase in HCT concurrent with rapid decrease in platelet count

* Requiring strict observation and medical intervention

Life long immunity against the infecting serotypeLimited, short lived immunity against other serotypes

Increased risk of severe manifestations with 2o infection

DENGUE: GUIDELINES FOR DIAGNOSIS, TREATMENT, PREVENTION AND CONTROL: WHO, 2009

ChikungunyaRe-emerging mosquito-borne viral disease in the Old world

Recently emerging in the New World

http://www.cdc.gov/chikungunya/pdfs/ChikungunyaMap.pdf

Chikungunya virus (CHIKV)

‣Family Togaviridae, genus alphavirus‣ ~12kb single stranded positive sense RNA genome

‣Three genotypes: Western African (WAf), Eastern/Central/South African (ECSA) and Asian

(Source: ViralZone:www.expasy.org/viralzone, Swiss Institute of Bioinformatics)

Chikungunya FeverTypical symptoms• High fever (40°C/ 104°F)• Joint pain (lower back, ankle, knees, wrists or

phalanges)• Joint swelling• Rash• Headache• Muscle pain• Nausea• Fatigue

Rarely fatal. Acute symptoms typically

resolve within 7 – 10 days but some patients report persistent joint pains for months to years.

Transmission cyclesDengue virus and Chikungunya virus

Ae. aegyptiAe. albopictus

“ ”

DENV and CHIKV also exist in sylvatic cycles

• B

Ae. aegyptiAe. albopictus

Forest dwellingAedes spp.

spillover

DENV sylvatic cycle exists in SE Asia and West Africa.

Currently circulating epidemic DENV1-4 arose as a result of successful spillover events 100s of

years ago.

In Africa, during inter-epidemic periods, CHIKV is maintained in enzootic, sylvatic

cycles.

“ ”

DENV made successful cross species jumps into

human populations at least four times to give

rise to the four serotypes that are

associated with epidemic disease

globally.

DENV-5 reported by Vasilakis et al. at 3rd

International Conference on Dengue

and Dengue Haemorrhagic Fever,

Bangkok 2013

.Wang, E. et al. J. Virol. 74, 3227–3234 (2000).

Average annual no. of Dengue cases reported / countries reporting dengue,

1955–2007

WHO 2009. Dengue: Guidelines for diagnosis, treatment, prevention & control

Global emergence of Dengue

Guzman, M. G. et al. Dengue: A continuing global threat. Nature Reviews Microbiology 8, S7–S16 (2010).

1970

2004

Reports of Dengue-like illness since late 1700s.

Geographically restricted, self limiting

outbreaks of DF

Several DF outbreaks and

epidemics; sporadic severe cases

Larger, more frequent epidemics with increasing numbers of severe cases

Dengue emergence and changing disease pattern in the AmericasA history of repeated introductions of viruses from

Asia.

Figure adapted from Allicock et al (2012) Mol. Biol. Evol. 29(6):1533–1543.

Global expansion of CHIKV• Pre 1950s: Africa and Asia• 1953: virus isolated (Tanzania)• 1950s & 60s: Large outbreaks on Indian subcontinent;

disappeared 1970.• 2005: Urban epidemic in Indian Ocean; spread to

subcontinent.• 2006 onwards: imported cases in Europe, USA and

Caribbean; outbreak in Italy, • Dec 2013: St. Martin outbreak; spread to other countries in

region.

Maximum clade credibility (MCC) tree of 80 CHIKV strains.

Volk S M et al. J. Virol. 2010;84:6497-6504

The strain responsible for the Indian Ocean outbreak arose from ECSA strain

June 2014

January February March April May June 0

1000

2000

3000

4000

5000

6000

4871068

2635

4218

5083 5252

Confirmed/Suspected Cases of Chikungunya

Phylogeny of Chikungunya viruses associated with outbreak in Saint-Martin

Leparc-Goffart I, Nougairede A, Cassadou S, Prat C, de Lamballerie X. Chikungunya in the Americas. Lancet 2014; 383: 514.

Factors underlying viral emergence

• Emergence is a result of:– Evolutionary changes affecting host range,

virulence, transmissibility / infectivity, drug resistance.

– Changes in host population susceptibility e.g. HIV-associated immunodeficiency, malnutrition, reduced vaccine coverage.

– Ecological changes that increase the probability of exposure of susceptible individuals/populations to infected reservoir hosts or vectors.

Majority of disease emergence is driven ecological factors associated with

human activity

rapid global transport networks

high-density human populations unplanned urbanisation

deforestationhabitat destruction

modern agricultural practices

Inadequate vector control + weak implementation of public health policies

Factors underlying the global emergence of DENV

mosquito breeding sites

global population growthHigh density human

populationsInadequate infrastructure unplanned urbanisation

Inadequate water supply

Improper waste disposal

water storagewater collection

rapid global transport

WWII related troop movements and

population displacement

Factors underlying the recent global emergence of CHIKV

Increased tourism Rapid global transport

Evolutionary changes(adaptive E gene mutation favours replication in Ae.

albopictus)

Immune landscape(Introduction in naïve populations)

What factors underlie epidemic behaviour following introduction?

What determines rates and directions of viral spread ?

What are the peculiarities of viral gene flow in an island - mainland setting?

Identification of the factors underlying the pathogen spatiotemporal dynamics and their

relative contributions would allows us to better model disease spread and thus facilitate better

surveillance and control.

After invasion…

Factors that may influence changes in mosquito-borne virus population size and

patterns of spread‣ Rate and direction of human movement

- Geographic distance- Connectivity (Extent of road network / Air traffic / Shipping

traffic)- Historical and socioeconomic links

‣ Rate and direction of mosquito movement- Geographic distance [Short (unassisted); Long (assisted)]- Mosquito population density- Opportunities for assisted movement

‣ Availability of susceptible human hosts- Immune landscape - Human population density

‣ Availability of appropriate mosquito vector‣ Presence of Ae. Aegypti or Ae. Albopictus‣ Mosquito population density

Traditional epidemiological approach

Understanding factors underlying viral spatiotemporal dynamics

‣ Requires extensive surveillance- Labour intensive- Costly - Time consuming

‣ Deficiencies in public health infrastructure frustrate collection of accurate and timely data- basic information often delayed,

unavailable or unreliable- Type and quality of data varies

between countries / institutionsMap used to link cholera deaths in London to contaminated water from the Broad Street

pump in 1854

Data accompanying samples sent to TPHL for dengue testing during the 2011 dengue season

Samples with demographic data (n =525).

Of 710 samples, 525 (73.9%) were accompanied by demographic data.

Sahadeo NSD, Brown A, Carrington L, Carrington CVF. Challenges to dengue reporting & surveillance in Trinidad & Tobago. Presented at the ASTMH 61st Annual Meeting. Nov 11-15, 2012. Atlanta, Georgia USA.

Samples with clinical data (n=82).

Only 82 of 710 samples (11.5%) were accompanied by clinical data.

Sample virusesfrom population

Sequence genes / genomes from sampled

individuals

Infer evolutionary relationships among

sequences

Create data sets of aligned

sequencesField trapped vectors. host reservoirs or patient

serum(Screening by PCR, cell

culture)

PCR amplification and sequencing of specific

genes

Numerous computational

approaches(Maximum likelihood,

Neighbour joining, Bayesian MCMC)

BEAST software package (Bayesian coalescent approach)

A Phylogenetic Approach

Newly derived

+ Genbank

• Estimate dates of origin for individual viruses or lineages

• Reconstruct past population dynamics

• Estimate rates of evolution

• Reconstruct spatial dynamics

• Create and compare models describing different patterns of geographic spread and determine which, if any, best describe the inferred pattern

Phylogenies inferred for DENV circulating in the

Americas‣ DENV 1, 2 and 4

- Strong spatial structure- Clear pattern of lineage

extinction and replacement

‣ DENV 3- Greater gene flow among

countries- Less evidence of lineage

turnover- Exponential growth

DENV

2DE

NV3

Allicock et al. unpublished data; Allicock et al (2012) Mol. Biol. Evol. 29(6):1533–

1543.

Inferred dates and location for most recent common ancestors (MRCA) & evolutionary

rates

‣ Each strain of the serotypes investigated arose from a single introduction

‣ Introductions occurred a mean of 2 - 4 years before 1st epidemiological reports

‣ Locations of MRCA - DENV-3, DENV-4: country of 1st report- DENV 2: neighbouring country (Jamaica and Cuba)- DENV 1: Grenada 5 yrs before 1st reported in Jamaica- Detection threshold may be quite high due to poor surveillance in many

countries. Allicock et al. unpublished data; Allicock et al (2012) Mol. Biol. Evol. 29(6):1533–

1543.

Spread of DENV 1 inferred from sequence data.Rapid dispersal followed by more localized maintenance

Allicock et al (unpublished data)

Correlations between predictors & rates of DENV geographic spread

within the Americas

More intense virus movement• between nearby regions (DENV 1 and 3) • between countries with more air traffic between them (DENV 1-3)• from smaller to larger populations (DENV 1 and 3)Less intense virus movement • out of countries with high % urban populations (DENV 1 – 3)• out of countries with higher human development indices (DENV 3)

Allicock et al (unpublished data)

A B

C

DENV

DENV

DENV spread in the Americas is best described by a Gravity

ModelDengue virus in a given location is more likely to move to a nearby and larger human

population than to a smaller or more distant population.

Urban centres attract virus.

Allicock et al (unpublished data)

A B

CDENV

DENVLess intense gene flow

Air traffic is a good predictor of spatial

diffusion patterns for DENV 1 - 3

Limitations‣ Used total air traffic over

30 years; cannot currently incorporate predictors that change over time.

‣ Indirect movement not captured (some countries have no direct airline links)

Allicock et al (unpublished data)

More intense gene flow

Acknowledgements / Contributors

Spatiotemporal dynamics of Dengue virusesOrchid M. Allicock, Philippe Lemey, Andrew J. Tatem,,Oliver G. Pybus, Shannon N. Bennett,Brandi A. Mueller, Marc A. Suchard,Jerome E. Foster Andrew Rambaut, Christine V. F. Carrington

Challenges to dengue reporting & surveillance in Trinidad & Tobago. Nikita Sahadeo, Arianne Brown A, Leslie Carrington, Christine V.F. Carrington.

Provision of DENV isolates and sera. CARPHA (CAREC), Trinidad Public Health Laboratories

Funding: UWI-RDI Fund, Commonwealth Scholarship Commission, Caribbean Health Research Council, UWI Campus Research & Publications Fund, International Society for Infectious Disease