Evolution and emergence of mosquito-borne viruses of medical importance: towards a routine metagenomic surveillance approach

Abstract

During the last two decades, the world has witnessed the emergence and re-emergence of arthropod-borne viruses, better known as arboviruses. The close contact between sylvatic, rural and peri-urban vector species and humans has been mainly determined by the environment-modifying human activity. The resulting interactions have led to multiple dead-end host infections and have allowed sylvatic arboviruses to eventually adapt to new vectors and hosts, contributing to the establishment of urban transmission cycles of some viruses with enormous epidemiologic impact. The metagenomic next-generation sequencing (NGS) approach has allowed obtaining unbiased sequence information of millions of DNA and RNA molecules from clinical and environmental samples. Robust bioinformatics tools have enabled the assembly of individual sequence reads into contigs and scaffolds partially or completely representing the genomes of the microorganisms and viruses being present in biological samples of clinical relevance. In this review, we describe the different ecological scenarios for the emergence of viral diseases, the virus adaptation process required for the establishment of a new transmission cycle and the usefulness of NGS and computational methods for the discovery and routine genomic surveillance of mosquito-borne viruses in their ecosystems.

Long-term co-circulation of multiple arboviruses in southeast Australia revealed by xeno-monitoring and metatranscriptomics

“…The key transmission pathways and distributions of specific genetic lineages remains unknown (Gyawali et al, 2019). Nonetheless, there is increasing awareness of the crucial nature of molecular xeno-monitoring in response to the emergence and re-emergence of neglected arboviruses (Hill et al, 2023; Laiton-Donato et al, 2023). This is of particular significance on the Australian continent where a large number of ecosystems, at huge geographic scales, are under constant environmental disturbance potentially favoring arbovirus emergence and dispersal through dynamic changes in mosquito vector populations, reservoir distribution, and human proximity to those reservoirs and vectors.…”

“…The simultaneous circulation of multiple arboviruses and a limited understanding of temporal transmission dynamics indicate that improved, well-designed surveillance programs of arboviruses that include genomic surveillance, are needed. Curation of longitudinal, consistent data sets that are shared with the scientific community are invaluable (Cameron and Ramesh, 2021; Laiton-Donato et al, 2023). To gain a comprehensive understanding of Australian arboviruses phylogeography and movement patterns across the country, routine sampling and sequencing of viruses from the different states and territories, over time is necessary.…”