A time-series meta-transcriptomic analysis reveals the seasonal, host, and gender structure of mosquito viromes

Abstract

Although metagenomic sequencing has revealed high numbers of viruses in mosquitoes sampled globally, our understanding of how their diversity and abundance varies in time and space, as well as by host species and gender, remains unclear. To address this we collected 23,109 mosquitoes over the course of 12 months from a bat-dwelling cave and a nearby village in Yunnan province, China. These samples were organized by mosquito species, mosquito gender and sampling time for meta-transcriptomic sequencing. A total of 162 eukaryotic virus species were identified, of which 101 were novel, including representatives of 17 RNA virus multi-family supergroups and four species of DNA virus from the families Parvoviridae, Circoviridae and Nudiviridae. In addition, two known vector-borne viruses – Japanese encephalitis virus and Banna virus – were found. Analyses of the entire virome revealed strikingly different viral compositions and abundance levels in warmer compared to colder months, a strong host structure at the level of mosquito species, and no substantial differences between those viruses harbored by male and female mosquitoes. At the scale of individual viruses, some were found to be ubiquitous throughout the year and across four mosquito species, while most of the other viruses were season and/or host specific. Collectively, this study reveals the diversity, dynamics and evolution of the mosquito virome at a single location and sheds new lights on the ecology of these important vector animals.

Total RNA sequencing of Phlebotomus chinensis sandflies in China revealed viral, bacterial, and eukaryotic microbes potentially pathogenic to humans

“…chinensis ) based on the abundance levels, pool prevalence rate, and/or their phylogenetic positions, only a very small fraction is relevant for human infections (i.e. hedi virus and wuxiang virus), which is similar to the observations made in other blood-sucking arthropods, such as mosquitoes [ 20 , 22 , 41 ], ticks [ 47 ], midges [ 51 ], and batflies [ 48 ]. Also being revealed as part of the virome are a large diversity of viruses associated with parasites, endosymbionts, or foods.…”

“…chinensis in Northern China. Furthermore, the diversity and overall abundance of the pathogen in sandflies estimated in this study is much higher than another important insect vectors, mosquitoes, which mainly harboured viral pathogens with 0-0.0059% abundance levels based on the same meta-transcriptomics sequencing [ 20 , 22 , 41 ], although those studies on mosquito microbiome were performed at different regions.…”

“…chinensis sandflies. Like what has been revealed in other arthropod species, such as mosquitoes [ 20 , 22 ], ticks [ 47 ], flies [ 48 ], bees [ 49 ] and termites [ 50 ], the virome of sandflies is characterized by an enormous diversity that expands multiple viral super-groups and with a great abundance level that makes up an average of 1.67% total non-ribosomal RNA. While the majority of the virome is likely associated with the principal host (i.e.…”

“…In addition to RNA viruses, meta-transcriptomics can also reveal and characterize a wide range of DNA organisms (i.e. DNA viruses, bacteria, and eukaryotic microbes) [ 20-22 ] such that it is now the candidate method to simultaneously cover the entire spectrum of microbial organisms, namely, the “total microbiome” [ 23 ]. More importantly, the genomic/transcriptomics information uncovered by meta-transcriptomics can be further used to characterize the pathogens, including their origin, evolutionary history, and epidemiological features, and, therefore it presents a powerful tool for modern pathogen discovery works [ 23 ].…”

Characterisation of the RNA Virome of Nine Ochlerotatus Species in Finland

“…Additional topics that would be of interest to explore further include the geographic and seasonal variations in the virome, as well as differences between males and females and at different developmental stages. Seasonal variation has been observed in Aedes ( Stegomyia ) albopictus [ 101 ] and Culex mosquitoes [ 102 ], though the core virome remains similar across different life stages in Ae. albopictus [ 103 ].…”