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. 2019 Aug 22;178(5):1057-1071.e11.
doi: 10.1016/j.cell.2019.07.018.

Travel Surveillance and Genomics Uncover a Hidden Zika Outbreak during the Waning Epidemic

Affiliations
  • PMID: 31442400
  • PMCID: PMC6716374
  • DOI: 10.1016/j.cell.2019.07.018
Free PMC article

Travel Surveillance and Genomics Uncover a Hidden Zika Outbreak during the Waning Epidemic

Nathan D Grubaugh et al. Cell. .
Free PMC article

Abstract

The Zika epidemic in the Americas has challenged surveillance and control. As the epidemic appears to be waning, it is unclear whether transmission is still ongoing, which is exacerbated by discrepancies in reporting. To uncover locations with lingering outbreaks, we investigated travel-associated Zika cases to identify transmission not captured by reporting. We uncovered an unreported outbreak in Cuba during 2017, a year after peak transmission in neighboring islands. By sequencing Zika virus, we show that the establishment of the virus was delayed by a year and that the ensuing outbreak was sparked by long-lived lineages of Zika virus from other Caribbean islands. Our data suggest that, although mosquito control in Cuba may initially have been effective at mitigating Zika virus transmission, such measures need to be maintained to be effective. Our study highlights how Zika virus may still be "silently" spreading and provides a framework for understanding outbreak dynamics. VIDEO ABSTRACT.

Keywords: Zika epidemic; Zika virus; clinical sequencing; genomic epidemiology; infectious disease genomics; phylogenetics; travel surveillance; virus sequencing.

Conflict of interest statement

The authors declare no competing interests.

Figures

None
Graphical abstract
Figure 1
Figure 1
International Travel Cases Reveal Unreported Zika Outbreak in Cuba in 2017 Local and travel-associated Zika cases were used to determine whether outbreaks were still occurring during 2017. (A) Monthly local Zika cases (left y axis) reported by the Pan American Health Organization (PAHO) and monthly travel-associated Zika cases (right y axis) reported by the Florida Department of Health (FL-DOH) and the European Centre for Disease Prevention and Control (ECDC) were sorted by origin of exposure. The vertical lines represent the months the last local and travel cases were reported per region and the month that the World Health Organization (WHO) Public Health Emergency of International Concern status was lifted for the Zika epidemic (November 2017). In each region, travel cases and local cases were correlated (Pearson r range = 0.542–0.976; each comparison can be found in Data S1). (B) The total number of Zika cases reported by the FL-DOH and the ECDC associated with travel originating in the Caribbean are shown (black line) and are shaded by the top 5 origin locations (all other placed in the “other Caribbean” category). (C) Zika cases associated with travel from Cuba, diagnosed by the GeoSentinel Surveillance Network, were sorted by month of clinic visit. Travel cases diagnosed by the GeoSentinel Surveillance Network originating from other parts of the Americas are not shown. See also Figure S1. The data used for this figure can be found in Data S1.
Figure S1
Figure S1
Increase in Travel Zika Cases from Cuba Is Not Due to an Increase in Travel, Related to Figure 1 To assess if the 2016 to 2017 increase in Zika cases reported from travelers who recently visited Cuba were due to a Zika outbreak in Cuba or an increase in air travel passengers leaving Cuba, we compared the yearly travel volumes from Cuba to Florida, Spain, and Italy to the travel Zika cases from Cuba reported by the same countries during 2016 and 2017. The greater increase from 2016 to 2017 of travel cases compared to travel volume suggests that a Zika outbreak in Cuba was the cause.
Figure 2
Figure 2
The Zika Outbreak in Cuba during 2017 Was Similar in Size to Others during 2016 Infections of international travelers were used to estimate the size of the Zika outbreak in Cuba. (A) The local Zika virus incidence rates for each country and territory were calculated by the number of locally reported cases per month per 100,000 population. The travel Zika virus incidence rates for each country/territory of presumed exposure origin and reporting country (i.e., travel destination) pair were calculated by the number of travel-associated cases per month per 100,000 air passenger travelers entering the destination country from the origin. When there were at least 20 travel-associated Zika cases (Figure S2), there was a positive correlation between travel and local incidence for all exposure origin and reporting country (i.e., travel destination) pairs (mean Pearson r = 0.769; range = 0.121–0.984; Data S1). (B) The number of Zika cases per month (mean, interquartile range, and 95% posterior predictive interval [PPI]) in Cuba during 2016 to 2017 were estimated by using fitted relationships between estimated local and travel incidence rates in countries with both sets of data to estimate what the local incidence rate in Cuba would have been if local data were available (Figures S4 and S5). This local incidence rate was then used to estimate local per capita incidence rates and subsequent number of Zika cases per month in Cuba. (C) The estimated number of Zika cases from Cuba (mean from B) and the total reported number of Zika cases during 2016 to 2017 from all countries and territories in the Americas with Zika virus transmission were plotted with the human population size from each region. Highlighted are the other large Caribbean countries/territories (D.R., Dominican Republic). See also Figures S2, S3, S4, and S5. The data used for this figure can be found in Data S1.
Figure S2
Figure S2
Relationship between the Number of Travel-Associated Zika Cases and the Correlation between Local and Travel Incidence Rates, Related to Figure 2 To determine the number of travel-associated infections needed to infer the shape of a local outbreak, we compared the total travel-associated Zika cases from each exposure-reporting country/territory combination (x axis) with Pearson correlation between the local and travel incidence rates corresponding to the combination (y axis). The travel-associated Zika cases were totaled from 2016-2017. For the Pearson correlations between local-travel incidence rates, monthly incidence values from 2016-2017 were compared. When there were > 20 travel-associated cases, the local-travel Pearson r was > 0.5, indicating a strong positive correlation and that the travel cases can help determine the shape of the local outbreak. The lone exception to that finding was from travelers from Barbados diagnosed in the United Kingdom (UK) because the travel cases miss the locally reported Zika virus peak during January-February, 2016, but they correlate with the second local peak during July-October, 2016 (Figure 2A). In our dataset, there were 25 Zika virus infections diagnosed in Italy with recent travel to Cuba, 30 diagnosed in Spain, and 98 diagnosed in Florida. These totals are all within the range of strong positive correlations between local and travel incidence, justifying their use to infer the local Zika outbreak dynamics in Cuba (Figure 2B).
Figure S3
Figure S3
Cruise Ship Travel from Cuba to Florida Is Minimal Compared to Air Travel, Related to Figure 2 Cruise ships may be a mechanism for infected individuals to travel to other countries, thus we investigated if we should incorporated cruise ship passenger volumes for calculating travel Zika incidence. The ∼7 × smaller volume of scheduled monthly cruise ship travel from 2019 compared to air travel in 2017 suggested that this would minimally impact our estimates and the data was not included in our final analyses.
Figure S4
Figure S4
Posterior Predictions of Estimated Total Travel Incidence from Origin Country into Florida, Related to Figure 2 These distributions were used to inform the joint distribution between travel incidence and local incidence that was used to estimate local incidence in Cuba. Empirical total travel cases per country indicated by red vertical line. All of the countries shown above, besides Cuba, had > 0.25 correlation between local incidence and travel incidence and had the observed value fall within the 95% posterior predictive interval of the distribution.
Figure S5
Figure S5
Posterior Predictions of Estimated Total Local Incidence from Origin Country into Florida, Related to Figure 2 These distributions were used to inform the joint distribution between travel incidence and local incidence that was used to estimate local incidence in Cuba. Empirical total local cases per country indicated by red vertical line. Estimated local incidence of Cuba indicated in blue with no empirical value. All of the countries shown above, besides Cuba, had > 0.25 correlation between local incidence and travel incidence and had the observed value fall within the 95% posterior predictive interval of the distribution.
Figure 3
Figure 3
The Chikungunya Outbreak in Cuba during the 2014 Epidemic Was Not Delayed (A and B) Travel-associated chikungunya cases were used to investigate whether the delayed Zika outbreak in Cuba should have been expected. Travel (A) Zika and (B) chikungunya virus incidence rates were calculated by the number of travel-associated cases reported by the FL-DOH per month per 100,000 air passenger travelers entering Florida, USA from the origin. FL-DOH surveillance for Zika cases did not start until January 2016. Shown are the six largest Caribbean Islands by population plus the US Virgin Islands. All of the data used for this figure can be found in Data S1.
Figure 4
Figure 4
The Establishment of Zika Virus from Other Caribbean Islands Was Delayed in Cuba Genomics approaches were used to determine the timing and sources of the Zika virus introductions into Cuba. (A) A time-resolved maximum clade credibility (MCC) tree was constructed using 283 near-complete Zika virus protein coding sequences, including 10 sequences from travelers returning from Cuba during 2017 to 2018. (B) The zooms show the likely times of Zika virus establishment (i.e., tMRCAs) for each of the Cuba clades as well as potential introduction sources (i.e., locations of the sequences basal on the tree). The fill color on each tip represents the probable location of infection, the clade posterior probabilities at each node are indicated by white circles filled with black relative to the level of posterior support, and the gray violin plot indicates the 95% highest posterior density (HPD) interval for each tMRCA. The mean tMRCA for clade 1-Cuba was August 2016 (95% HPD = May–November 2016), the mean tMRCA for clade 2-Cuba was July 2016 (95% HPD = March–December 2016), and the mean tMRCA for clade 3-Cuba was September 2016 (95% HPD = May 2016–February 2017). Clade “Cuba-4” does not have a tMRCA estimate because it consists of a single sequence. A maximum likelihood tree and a root-to-tip molecular clock are shown in Figure S6. (C) The three separate estimated Zika virus establishment times with tMRCA estimates into Cuba are shown with the Zika virus travel incidence rates (travel cases/100,000 travelers; as calculated for Figures 2 and 3). The estimated earliest Zika virus establishment times (based on the MCC tree in A and travel incidence rates for the Dominican Republic, Puerto Rico, and the Caribbean as a whole [minus Cuba]) are shown to compare the times from establishment of the virus to outbreak peak. See also Figure S6. GenBank access numbers of Zika virus genomes sequenced during this study can be found in Data S2, the data used to create (A) and (B) can be found in Data S3, and the data used to create (C) can be found in Data S1.
Figure S6
Figure S6
Maximum Likelihood Tree and Root-to-Tip Regression of Zika Virus Genomes from Cuba and the Epidemic in the Americas, Related to Figure 4 (A) Maximum likelihood tree of publicly available Zika virus sequences (n = 269) and sequences generated in this study (n = 14). Tips are colored by location. Bootstrap support values are colored at the nodes. Divergence shown as substitutions per site. “1-3 Cuba” represent three independent introductions of Zika virus into Cuba. (B) Linear regression of sample tip dates against divergence from root based on sequences with known collection dates estimates an evolutionary rate for the Zika virus phylogeny of 5.71 × 10−3 nucleotide substitutions per site per year.
Figure 5
Figure 5
Aggressive Aedes aegypti Control May Have Delayed Zika Outbreak in Cuba (A) The potential for Zika virus introductions was assessed by total airline passenger arrivals into each of the listed countries per month from 2014 to 2017 coming from regions in the Americas known to support local Zika virus transmission (excluding the continental United States because the outbreaks were relatively small), along the distribution of likely establishment times (i.e., tMRCAs) of the initial (known) Zika virus establishment in the Caribbean (tMRCA January–September 2015) and three separate establishments in Cuba (tMRCAs March 2016–February 2017). (B) Monthly dengue virus travel incidence rates (travel cases/100,000 travelers), as reported by the FL-DOH, for Cuba and other large Caribbean Islands were shown to compare Ae. aegypti-borne virus outbreaks. (C) Analysis of dengue and Zika virus incidence, Ae. aegypti transmission potential, and the timing of a reported vector control campaign were used to investigate the delayed Zika outbreak in Cuba. Monthly dengue and Zika virus travel incidence rates (travel cases/100,000 travelers), as reported by the FL-DOH, and relative Ae. aegypti-borne virus transmission potential (mean and 95% confidence interval), determined by a temperature-sensitive model (Mordecai et al., 2017) and monthly temperature from Havana, Cuba, were used to judge the impact of the aggressive Ae. aegypti mosquito control program that was reported to have begun in Cuba during February 2016. News reports of Zika and dengue cases and the mosquito control campaign in Cuba are summarized in Data S4. The data used for this figure can be found in Data S1.
Figure 6
Figure 6
Risk of “Silent” Zika Virus Spread from the Outbreak in Cuba during 2017 Travel volumes from Cuba and Ae. aegypti suitability were used to address the potential spread of Zika virus from Cuba during the outbreak in 2017. (A) Monthly Zika cases associated with international travel reported by the FL-DOH and the ECDC, sorted by travel origins in Cuba or all other countries/territories in the Americas, were used to demonstrate that >98% of all travel-associated Zika cases during June–December of 2017 came from Cuba. (B) During June–December 2017, all countries and US states that received >20,000 airline passengers from Cuba are shown, along with the relative Ae. aegypti suitability, to represent possible destinations for Zika virus spread from Cuba. The data used for this figure can be found in Data S1.

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