Phylodynamics of dengue virus 2 in Nicaragua leading up to the 2019 epidemic reveals a role for lineage turnover

BMC Ecology and Evolution

Research

Saira Saborío¹  Angel Balmaseda¹  Shannon N. Bennett²  Eva Harris³  Sandra Bos³  Panpim Thongsripong⁴  Sean V. Edgerton⁵  Guillermina Kuan⁶ 

[1] Centro Nacional de Diagnóstico y Referencia, Laboraorio Nacional de Virología, Ministry of Health, Managua, Nicaragua;Sustainable Sciences Institute, Managua, Nicaragua;Department of Microbiology, California Academy of Sciences, San Francisco, CA, USA;Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA;Florida Medical Entomology Laboratory, Institute of Food and Agricultural Sciences, University of Florida, Vero Beach, FL, USA;Interdisciplinary Studies Graduate Program, The University of British Columbia, Vancouver, BC, Canada;Sustainable Sciences Institute, Managua, Nicaragua;Centro de Salud Sócrates Flores Vivas, Ministry of Health, Managua, Nicaragua;

关键词: Dengue virus;    Virus evolution;    Lineage turnover;    Clade replacement;    Natural selection;    Phylodynamics;    Nicaragua;   

DOI  :  10.1186/s12862-023-02156-4

 received in 2022-09-07, accepted in 2023-08-21,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundDengue is a mosquito-borne viral disease posing a significant threat to public health. Dengue virus (DENV) evolution is often characterized by lineage turnover, which, along with ecological and immunological factors, has been linked to changes in dengue phenotype affecting epidemic dynamics. Utilizing epidemiologic and virologic data from long-term population-based studies (the Nicaraguan Pediatric Dengue Cohort Study and Nicaraguan Dengue Hospital-based Study), we describe a lineage turnover of DENV serotype 2 (DENV-2) prior to a large dengue epidemic in 2019. Prior to this epidemic, Nicaragua had experienced relatively low levels of DENV transmission from 2014 to 2019, a period dominated by chikungunya in 2014/15 and Zika in 2016.ResultsOur phylogenetic analyses confirmed that all Nicaraguan DENV-2 isolates from 2018 to 2019 formed their own clade within the Nicaraguan lineage of the Asian/American genotype. The emergence of the new DENV-2 lineage reflects a replacement of the formerly dominant clade presiding from 2005 to 2009, a lineage turnover marked by several shared derived amino acid substitutions throughout the genome. To elucidate evolutionary drivers of lineage turnover, we performed selection pressure analysis and reconstructed the demographic history of DENV-2. We found evidence of adaptive evolution by natural selection at the codon level as well as in branch formation.ConclusionsThe timing of its emergence, along with a statistical signal of adaptive evolution and distinctive amino acid substitutions, the latest in the NS5 gene, suggest that this lineage may have increased fitness relative to the prior dominant DENV-2 strains. This may have contributed to the intensity of the 2019 DENV-2 epidemic, in addition to previously identified immunological factors associated with pre-existing Zika virus immunity.

【 授权许可】

CC BY   
© BioMed Central Ltd., part of Springer Nature 2023

【 图 表 】

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