Although the recent Zika virus (ZIKV) epidemic in the Americas and its link to birth defects have attracted a great deal of attention1,2, much remains unknown about ZIKV disease epidemiology and ZIKV evolution, in part owing to a lack of genomic data. Here we address this gap in knowledge by using multiple sequencing approaches to generate 110 ZIKV genomes from clinical and mosquito samples from 10 countries and territories, greatly expanding the observed viral genetic diversity from this outbreak. We analysed the timing and patterns of introductions into distinct geographic regions; our phylogenetic evidence suggests rapid expansion of the outbreak in Brazil and multiple introductions of outbreak strains into Puerto Rico, Honduras, Colombia, other Caribbean islands, and the continental United States. We find that ZIKV circulated undetected in multiple regions for many months before the first locally transmitted cases were confirmed, highlighting the importance of surveillance of viral infections. We identify mutations with possible functional implications for ZIKV biology and pathogenesis, as well as those that might be relevant to the effectiveness of diagnostic tests.

Zika virus (ZIKV) is causing an unprecedented epidemic linked to severe congenital syndromes1,2. In July 2016, mosquito-borne ZIKV transmission was reported in the continental United States and since then, hundreds of locally-acquired infections have been reported in Florida3,4. To gain insights into the timing, source, and likely route(s) of ZIKV introduction, we tracked the virus from its first detection in Florida by sequencing ZIKV genomes from infected patients and Aedes aegypti mosquitoes. We show that at least four introductions, but potentially as many as 40, contributed to the outbreak in Florida and that local transmission likely started in the spring of 2016 - several months before initial detection. By analyzing surveillance and genetic data, we discovered that ZIKV moved among transmission zones in Miami. Our analyses show that most introductions are linked to the Caribbean, a finding corroborated by the high incidence rates and traffic volumes from the region into the Miami area. Our study provides an understanding of how ZIKV initiates transmission in new regions.

During the first 6 months of 2016, large outbreaks of Zika virus disease caused by local mosquito-borne transmission occurred in Puerto Rico and other U.S. territories, but local mosquito-borne transmission was not identified in the continental United States (1,2). As of July 22, 2016, the Florida Department of Health had identified 321 Zika virus disease cases among Florida residents and visitors, all occurring in either travelers from other countries or territories with ongoing Zika virus transmission or sexual contacts of recent travelers.* During standard case investigation of persons with compatible illness and laboratory evidence of recent Zika virus infection (i.e., a specimen positive by real-time reverse transcription-polymerase chain reaction [rRT-PCR], or positive Zika immunoglobulin M [IgM] with supporting dengue serology [negative for dengue IgM antibodies and positive for dengue IgG antibodies], or confirmation of Zika virus neutralizing antibodies by plaque reduction neutralization testing [PRNT]) (3), four persons were identified in Broward and Miami-Dade counties whose infections were attributed to likely local mosquito-borne transmission. Two of these persons worked within 120 meters (131 yards) of each other but had no other epidemiologic connections, suggesting the possibility of a local community-based outbreak. Further epidemiologic and laboratory investigations of the worksites and surrounding neighborhood identified a total of 29 persons with laboratory evidence of recent Zika virus infection and likely exposure during late June to early August, most within an approximate 6-block area. In response to limited impact on the population of Aedes aegypti mosquito vectors from initial ground-based mosquito control efforts, aerial ultralow volume spraying with the organophosphate insecticide naled was applied over a 10 square-mile area beginning in early August and alternated with aerial larviciding with Bacillus thuringiensis subspecies israelensis (Bti), a group biologic control agent, in a central 2 square-mile area. No additional cases were identified after implementation of this mosquito control strategy. No increases in emergency department (ED) patient visits associated with aerial spraying were reported, including visits for asthma, reactive airway disease, wheezing, shortness of breath, nausea, vomiting, or diarrhea. Local and state health departments serving communities where Ae. aegypti, the primary vector of Zika virus, is found should continue to actively monitor for local transmission of the virus.(†).

Global increases in temperatures and urbanization are impacting the epidemiology of mosquito-borne diseases. Urbanization processes create suitable habitats for vector mosquitoes in which there are a reduced number of predators, and human hosts are widely available. We hypothesize that mosquito vector species, especially Aedes aegypti, are locally concentrated primarily in those specific habitats at the neighborhood levels that provide suitable conditions and environmental resources needed for mosquito survival. Determining how mosquito vector species composition and abundance depend on environmental resources across habitats addresses where different types of vector control need to be applied. Therefore, our goal was to analyze and identify the most productive aquatic habitats for mosquitoes in Miami-Dade County, Florida. Immature mosquito surveys were conducted throughout Miami-Dade County from April 2018 to June 2019, totaling 2,488 inspections. Mosquitoes were collected in 76 different types of aquatic habitats scattered throughout 141 neighborhoods located in the urbanized areas of Miami-Dade County. A total of 44,599 immature mosquitoes were collected and Ae. aegypti was the most common and abundant species, comprising 43% of all specimens collected. Aedes aegypti was primarily found in buckets, bromeliads, and flower pots, concentrated in specific neighborhoods. Our results showed that aquatic habitats created by anthropogenic land-use modifications (e.g., ornamental bromeliads, buckets, etc.) were positively correlated with the abundance of Ae. aegypti. This study serves to identify how vector mosquitoes utilize the resources available in urban environments and to determine the exact role of these specific urban features in supporting populations of vector mosquito species. Ultimately, the identification of modifiable urban features will allow the development of targeted mosquito control strategies optimized to preventatively control vector mosquitoes in urban areas.

Vector-borne diseases are a heavy burden to human-kind. Global warming and urbanization have a significant impact on vector-borne disease transmission, resulting in more severe outbreaks, and outbreaks in formerly non-endemic areas. Miami-Dade County, Florida was the most affected area in the continental United States during the 2016 Zika virus outbreak. Miami is an important gateway and has suitable conditions for mosquitoes year-round. Therefore, it was critical to establish and validate a surveillance system to guide and improve mosquito control operations. Here we assess two years of mosquito surveillance in Miami established after the 2016 Zika virus outbreak. Our results show that the most abundant mosquito species are either well adapted to urban environments or are adapting to it. The five most abundant species comprised 85% of all specimens collected, with four of them being primary vectors of arboviruses. Aedes aegypti and Culex quinquefasciatus were found year-round throughout Miami regardless of urbanization level, vegetation, or socioeconomic variations. This study serves as a foundation for future efforts to improve mosquito surveillance and control operations.