Invasion, expansion and maintenance of Dengue & Chikungunya viruses in the Americas. Christine V. F. Carrington 12 June 2014 Dengue The most rapidly spreading mosquito-borne viral disease One of the most important emerging diseases of the 21st century 3.5 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 infection Up to an estimated 80% of infections are asymptomatic DENGUE +/- WARNING SIGNS SEVERE DENGUE 1. Severe plasma leakage 2. Severe haemorrhage 3. Severe organ impairment with warning signs without Life long immunity against the infecting serotype Limited, short lived immunity against other serotypes Increased risk of severe manifestations with 2o infection Probable dengue Warning signs* Live 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 Abdominal pain or tenderness Persistent vomiting Clinical fluid accumulation Mucosal bleeding Lethargy / restlessness Liver enlargment >2cm Laboratory: increase in HCT concurrent with rapid decrease in platelet count Laboratory confirmed dengue * Requiring strict observation and medical intervention DENGUE: GUIDELINES FOR DIAGNOSIS, TREATMENT, PREVENTION AND CONTROL: WHO, 2009 Chikungunya Re-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 Fever Typical symptoms • High fever (40°C/ 104°F) • Joint pain (lower back, ankle, knees, wrists or phalanges) • Joint swelling • Rash Rarely fatal. • Headache Acute symptoms typically resolve within 7 – 10 days but some patients • Muscle pain report persistent joint pains for • Nausea months to years. • Fatigue Transmission cycles Dengue virus and Chikungunya virus Ae. aegypti Ae. albopictus “ ” DENV and CHIKV also exist in sylvatic cycles 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. Ae. aegypti Ae. albopictus spillover • B “ Forest dwelling Aedes spp. 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). . Global emergence of Dengue Average annual no. of Dengue cases reported / countries reporting dengue, 1955–2007 1970 2004 WHO 2009. Dengue: Guidelines for diagnosis, treatment, prevention & control Guzman, M. G. et al. Dengue: A continuing global threat. Nature R eviews Microbiology 8, S7–S16 (2010). Dengue emergence and changing disease pattern in the Americas A history of repeated introductions of viruses from Asia. Several DF outbreaks and epidemics; sporadic severe cases Reports of Dengue-like illness since late 1700s. Geographically restricted, self limiting outbreaks of DF Larger, more frequent epidemics with increasing numbers of severe cases 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. The strain responsible for the Indian Ocean outbreak arose from ECSA strain Maximum clade credibility (MCC) tree of 80 CHIKV strains. Volk S M et al. J. Virol. 2010;84:6497-6504 June 2014 Confirmed/Suspected Cases of Chikungunya 6000 5083 5252 5000 4218 4000 3000 2635 2000 1068 1000 487 0 January February March April May June 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. HIVassociated 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 deforestation habitat destruction high-density human populations unplanned urbanisation modern agricultural practices Factors underlying the global emergence of DENV rapid global transport WWII related troop movements and population displacement global population growth High density human populations Inadequate infrastructure unplanned urbanisation mosquito breeding sites Inadequate water supply Improper waste disposal water storage water collection Inadequate vector control + weak implementation of public health policies 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) After invasion… 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. Factors that may influence changes in mosquitoborne 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 / institutions Map 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 clinical data (n=82). Only 82 of 710 samples (11.5%) were accompanied by clinical data. 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. A Phylogenetic Approach Sample viruses from population Sequence genes / genomes from sampled individuals Field trapped vectors. host reservoirs or patient serum PCR amplification and sequencing of specific genes Create data sets of aligned sequences Newly derived + Genbank (Screening by PCR, cell culture) • Estimate rates of evolution Infer evolutionary relationships among sequences Numerous computational approaches (Maximum likelihood, Neighbour joining, Bayesian MCMC) • Estimate dates of origin for individual viruses or lineages • Reconstruct past population dynamics • Reconstruct spatial dynamics • Create and compare models describing different patterns of geographic spread and determine which, if any, best describe the inferred pattern BEAST software package (Bayesian coalescent approach) ‣ DENV 1, 2 and 4 - Strong spatial structure - Clear pattern of lineage extinction and replacement ‣ DENV2 Phylogenies inferred for DENV circulating in the Americas - Greater gene flow among countries - Less evidence of lineage turnover - Exponential growth DENV3 DENV 3 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 Allicock et al (unpublished data) 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) DENV spread in the Americas is best described by a Gravity Model Dengue 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. C Urban centres attract virus. A DEN V B Allicock et al (unpublished data) Air traffic is a good predictor of spatial diffusion patterns for DENV 1 - 3 DENV More intense gene flow C Limitations A ‣ 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) B DENV Less intense gene flow Allicock et al (unpublished data) Acknowledgements / Contributors Spatiotemporal dynamics of Dengue viruses Orchid 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