Phylogenetic Analysis of Transmission Dynamics of Dengue in Large and Small Population Centers, Northern Ecuador

Although dengue is typically considered an urban disease, rural communities are also at high risk. To clarify dynamics of dengue virus (DENV) transmission in settings with characteristics generally considered rural (e.g., lower population density, remoteness), we conducted a phylogenetic analysis in 6 communities in northwestern Ecuador. DENV RNA was detected by PCR in 121/488 serum samples collected from febrile case-patients during 2019–2021. Phylogenetic analysis of 27 samples from Ecuador and other countries in South America confirmed that DENV-1 circulated during May 2019–March 2020 and DENV-2 circulated during December 2020–July 2021. Combining locality and isolation dates, we found strong evidence that DENV entered Ecuador through the northern province of Esmeraldas. Phylogenetic patterns suggest that, within this province, communities with larger populations and commercial centers were more often the source of DENV but that smaller, remote communities also play a role in regional transmission dynamics.

[1]  J. Eisenberg,et al.  A Chikungunya Outbreak in a Dengue-endemic Region in Rural Northern Coastal Ecuador. , 2022, The American journal of tropical medicine and hygiene.

[2]  M. Martínez-Gutiérrez,et al.  Phylogenetic and evolutionary analysis of dengue virus serotypes circulating at the Colombian–Venezuelan border during 2015–2016 and 2018–2019 , 2021, PloS one.

[3]  R. Baric,et al.  Antigenic Variation of the Dengue Virus 2 Genotypes Impacts the Neutralization Activity of Human Antibodies in Vaccinees , 2020, Cell reports.

[4]  M. Suchard,et al.  Determinants of dengue virus dispersal in the Americas , 2020, Virus evolution.

[5]  Nuno R. Faria,et al.  Genomic detection of a virus lineage replacement event of dengue virus serotype 2 in Brazil, 2019 , 2020, Memorias do Instituto Oswaldo Cruz.

[6]  J. Navarro,et al.  COVID-19 and dengue, co-epidemics in Ecuador and other countries in Latin America: Pushing strained health care systems over the edge , 2020, Travel Medicine and Infectious Disease.

[7]  Tulio de Oliveira,et al.  Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes , 2020, Bioinform..

[8]  I. Maljkovic Berry,et al.  The origins of dengue and chikungunya viruses in Ecuador following increased migration from Venezuela and Colombia , 2020, BMC Evolutionary Biology.

[9]  S. Blower,et al.  HIV transmission and source-sink dynamics in sub-Saharan Africa. , 2020, The lancet. HIV.

[10]  P. Müller,et al.  Active dispersal of Aedes albopictus: a mark-release-recapture study using self-marking units , 2019, Parasites & Vectors.

[11]  T. Shioda,et al.  Genotype replacement of dengue virus type 3 and clade replacement of dengue virus type 2 genotype Cosmopolitan in Dhaka, Bangladesh in 2017. , 2019, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[12]  Zhicong Yang,et al.  Urban villages as transfer stations for dengue fever epidemic: A case study in the Guangzhou, China , 2019, PLoS neglected tropical diseases.

[13]  J. Eisenberg,et al.  Dengue Serotype Differences in Urban and Semi-rural Communities in Ecuador , 2018, ACI Avances en Ciencias e Ingenierías.

[14]  A. Kohl,et al.  Revisiting Key Entry Routes of Human Epidemic Arboviruses into the Mainland Americas through Large-Scale Phylogenomics , 2018, International journal of genomics.

[15]  G. Chang,et al.  Inter- and intra-host sequence diversity reveal the emergence of viral variants during an overwintering epidemic caused by dengue virus serotype 2 in southern Taiwan , 2018, PLoS neglected tropical diseases.

[16]  M. Suchard,et al.  Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7 , 2018, Systematic biology.

[17]  J. Kaewkungwal,et al.  Data quality and timeliness of outbreak reporting system among countries in Greater Mekong subregion: Challenges for international data sharing , 2018, PLoS neglected tropical diseases.

[18]  C. Codeço,et al.  The introduction of dengue follows transportation infrastructure changes in the state of Acre, Brazil: A network-based analysis , 2017, PLoS neglected tropical diseases.

[19]  E. Zeng,et al.  Global Epidemiology of Dengue Outbreaks in 1990–2015: A Systematic Review and Meta-Analysis , 2017, Front. Cell. Infect. Microbiol..

[20]  Jhony Joe Real-Cotto,et al.  Evolución del virus dengue en el Ecuador. Período 2000 a 2015 , 2017 .

[21]  Y. Hsieh,et al.  Ascertaining the impact of public rapid transit system on spread of dengue in urban settings , 2017, Science of The Total Environment.

[22]  Trevor Bedford,et al.  Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples , 2017, Nature Protocols.

[23]  R. Jamal,et al.  Rural-urban comparisons of dengue seroprevalence in Malaysia , 2016, BMC Public Health.

[24]  E. Harris,et al.  Single-Reaction Multiplex Reverse Transcription PCR for Detection of Zika, Chikungunya, and Dengue Viruses , 2016, Emerging infectious diseases.

[25]  Andrew Rambaut,et al.  Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen) , 2016, Virus evolution.

[26]  P. Newton,et al.  Causes of Fever in Rural Southern Laos , 2015, The American journal of tropical medicine and hygiene.

[27]  L. Ng,et al.  2013 Dengue Outbreaks in Singapore and Malaysia Caused by Different Viral Strains , 2015, The American journal of tropical medicine and hygiene.

[28]  M. Baldeón,et al.  Transition in the Cause of Fever from Malaria to Dengue, Northwestern Ecuador, 1990–2011 , 2013, Emerging infectious diseases.

[29]  Duane J. Gubler,et al.  Dengue, Urbanization and Globalization: The Unholy Trinity of the 21st Century , 2011, Tropical medicine and health.

[30]  Philippe Buchy,et al.  Dengue Incidence in Urban and Rural Cambodia: Results from Population-Based Active Fever Surveillance, 2006–2008 , 2010, PLoS neglected tropical diseases.

[31]  E. Holmes,et al.  Evolution of dengue virus in Mexico is characterized by frequent lineage replacement , 2010, Archives of Virology.

[32]  S. Ho,et al.  Relaxed Phylogenetics and Dating with Confidence , 2006, PLoS biology.

[33]  Edward C. Holmes,et al.  Clade Replacements in Dengue Virus Serotypes 1 and 3 Are Associated with Changing Serotype Prevalence , 2005, Journal of Virology.

[34]  O. Pybus,et al.  Bayesian coalescent inference of past population dynamics from molecular sequences. , 2005, Molecular biology and evolution.

[35]  Edward C Holmes,et al.  The origin, emergence and evolutionary genetics of dengue virus. , 2003, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[36]  Laura D. Kramer,et al.  Typing of Dengue Viruses in Clinical Specimens and Mosquitoes by Single-Tube Multiplex Reverse Transcriptase PCR , 1998, Journal of Clinical Microbiology.

[37]  H. Gómez-Dantés,et al.  Dengue in the Americas: challenges for prevention and control. , 2009, Cadernos de saude publica.