Intra-host population dynamics of chikungunya virus in humans and naturally infected Aedes mosquitoes reveal transmission-driven diversity
Description
RNA viruses often exhibit a high mutation rate, mainly because their RNA polymerases lack proofreading, which contributes to their genetic diversity. Arboviruses, which alternate between vertebrate and invertebrate hosts, are subjected to host-specific selective pressures and population bottlenecks, mainly within mosquito vectors. Although experimental studies have brought insights about their evolutionary dynamics, data from naturally infected vectors remain limited. Here, we investigated the intra-host genetic diversity of chikungunya virus (CHIKV-ECSA lineage) through whole-genome sequencing of 19 human- and 19 mosquito-derived genomes from the 2024 outbreak in São José do Rio Preto, Brazil. Our principal component analysis revealed a greater mutation number in mosquito-derived genomes, predominantly driven by low-frequency and unique variants. Overall, intra-host genetic diversity was significantly higher in mosquito-derived than in human-derived CHIKV genomes, and protein-coding regions showed host-specific patterns. We identified 303 mutations across all CHIKV genomes. Interestingly, shared mutations were predominantly classified as synonymous, whereas unique mutations were mainly non-synonymous. Gene-wide selection analyses indicated that purifying selection predominates across CHIKV genomes from both humans and mosquitoes, suggesting that most mutations, particularly non-synonymous ones, are deleterious and subject to purifying selection. However, in mosquito-derived CHIKV genomes, evidence of relaxed purifying selection and neutral evolution, in specific proteins, such as E3 and NSP3, respectively, was observed, in contrast to the stronger purifying selection observed in human-derived CHIKV sequences. Site-specific selection analyses corroborated these results, detecting negatively selected sites in human-derived genomes but not in mosquito-derived genomes for these specific proteins. Together, our results show that these host-specific differences enable mosquitoes to act as reservoirs of genetic diversity by maintaining non-synonymous variants, likely driven by genetic drift. At the same time, human hosts may impose stronger selective pressures, contributing to preserving the genome stability. This dynamic balance between diversification in vector populations and selective constraints in vertebrate hosts likely drives CHIKV evolution and adaptation.
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Steps to reproduce
Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP, grant numbers 2022/03645-1 to MLN and 2023/14670-0 to CAB). INCT Viral Genomic Surveillance and One Health grant 405786/2022-0. Centers for Research in Emerging Infectious Diseases (CREID), via the “Coordinating Research on Emerging Arboviral Threats Encompassing the Neotropics (CREATE-NEO)” grant U01AI151807 awarded to NV by the National Institutes of Health (NIH/USA).
Institutions
- Faculdade de Medicina de Sao Jose do Rio Preto