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

Abstract

Phlebotomus chinensis sandfly is a neglected insect vector in China that is well-known for carrying Leishmania . Recent studies have expanded its pathogen repertoire with two novel arthropod-borne phleboviruses capable of infecting humans and animals. Despite these discoveries, our knowledge of the general pathogen diversity and overall microbiome composition of this vector species is still very limited. Here we carried out a meta-transcriptomics analysis that revealed the actively replicating/transcribing RNA viruses, DNA viruses, bacteria, and eukaryotic microbes, namely, the “total microbiome”, of several sandfly populations in China. Strikingly, “microbiome” made up 1.8% of total non-ribosomal RNA and comprised more than 87 species, among which 70 were novel, including divergent members of the genera Flavivirus and of the family Trypanosomatidae. Importantly, among these microbes we were able to reveal four distinguished types of human and/or mammalian pathogens, including two phleboviruses (hedi and wuxiang viruses), one novel Spotted fever group rickettsia, as well as a member of Leishmania donovani complex, among which hedi virus and Leishmania each had > 50% pool prevalence rate and relatively high abundance levels. Our study also showed the ubiquitous presence of an endosymbiont, namely Wolbachia , although no anti-viral or anti-pathogen effects were detected based on our data. In summary, our results uncovered the much un-explored diversity of microbes harboured by sandflies in China and demonstrated that high pathogen diversity and abundance are currently present in multiple populations, implying disease potential for exposed local human population or domestic animals.

Metatranscriptomic Sequencing Reveals Host Species as an Important Factor Shaping the Mosquito Virome

“…Wolbachia has been documented to provide resistance to the infection with some viruses, such as dengue virus and Zika virus in mosquitoes ( 21 , 22 ), and hence has been suggested as a potential tool for vector-borne disease control. However, not all Wolbachia strains have clear effects in inhibiting virus replication, and Wolbachia infection does not protect against all viruses ( 23 , 24 ). Despite this, little is known about how the ecology of hosts impacts Wolbachia diversity.…”

ViraLM: Empowering Virus Discovery through the Genome Foundation Model

“…Finally, we run all the methods on two public real metagenomic datasets and one RNA-Seq dataset released in previous studies [28, 29, 30]. These datasets, derived from distinct ecosystems such as aquatic environments, terrestrial soils, and insect populations, represent a wide range of microbial communities.…”

“…First, we downloaded complete assemblies of prokaryotes (bacteria and archaea) and eukaryotes (fungi and protozoa) from the NCBI RefSeq database. These carefully selected genomes represent typical non-viral entities commonly appearing in metagenomic data [30, 31]. Additionally, we also include the plasmid data from the RefSeq database, which are prone to be misidentified by the existing virus identification tools.…”

“…Real sequencing dataset We retrieved two public real metagenomic data and one RNA-Seq data sampled from different environments, including water [28], soil [29], and insect-associated ecosystems [30], respectively. The water metagenome is sequenced from a total of 30 surficial water samples collected from Jinghu Lake (China), a lake that is replenished by reclaimed water.…”

Metatranscriptomic Sequencing of Medically Important Mosquitoes Reveals Extensive Diversity of RNA Viruses and Other Microbial Communities in Western Australia

“…These techniques may reveal limited information regarding microbial diversity and are often laborious and time-consuming. In recent years, with advances in next-generation sequencing techniques, metatranscriptomics has evolved as a cost-effective and reliable approach to reveal microbial diversity within mosquito populations [ 7 , 8 ], enhancing disease surveillance by rapidly detecting known pathogens [ 9 ]. Metatranscriptomics has enhanced the discovery of novel microbial agents and assessment of their evolutionary history, origin, and potential to cause disease [ 7 , 10 , 11 ].…”