A5017731503- Viral Infections and Vectors
- Bacteriophages and microbial interactions
- Mosquito-borne diseases and control
- Plant Virus Research Studies
- Insect symbiosis and bacterial influences
- Plant and Fungal Interactions Research
- Zoonotic diseases and public health
- SARS-CoV-2 and COVID-19 Research
- Insect and Arachnid Ecology and Behavior
- RNA modifications and cancer
- Animal Disease Management and Epidemiology
- Viral gastroenteritis research and epidemiology
- Genomics and Phylogenetic Studies
- Insect and Pesticide Research
- Virology and Viral Diseases
- Yersinia bacterium, plague, ectoparasites research
- Rabies epidemiology and control
- Advanced Biosensing Techniques and Applications
- Aquaculture disease management and microbiota
- Monoclonal and Polyclonal Antibodies Research
- Poxvirus research and outbreaks
Sun Yat-sen University
2022-2025
Biocon (Switzerland)
2024
The Seventh Affiliated Hospital of Sun Yat-sen University
2022
Abstract Bats are reservoir hosts for many zoonotic viruses. Despite this, relatively little is known about the diversity and abundance of viruses within individual bats, hence frequency virus co-infection spillover among them. We characterize mammal-associated in 149 bats sampled from Yunnan province, China, using an unbiased meta-transcriptomics approach. This reveals a high (simultaneous infection bat individuals by multiple viral species) animals studied, which may turn facilitate...
Highlights•AI-based metagenomic mining greatly expands the diversity of global RNA virosphere•Developed a deep learning model that integrates sequence and structural information•161,979 putative virus species 180 supergroups were identified•RNA viruses are ubiquitous even found in most extreme environmentsSummaryCurrent tools can fail to identify highly divergent viruses. We developed algorithm, termed LucaProt, discover RNA-dependent polymerase (RdRP) sequences 10,487 metatranscriptomes...
Although metagenomic sequencing has revealed high numbers of viruses in mosquitoes sampled globally, our understanding how their diversity and abundance varies time space as well by host species gender remains unclear. To address this, we collected 23,109 over the course 12 months from a bat-dwelling cave nearby village Yunnan province, China. These samples were organized mosquito species, gender, sampling for meta-transcriptomic sequencing. A total 162 eukaryotic virus identified, which 101...
Current metagenomic tools can fail to identify highly divergent RNA viruses. We developed a deep learning algorithm, termed LucaProt, discover RNA-dependent polymerase (RdRP) sequences in 10,487 metatranscriptomes generated from diverse global ecosystems. LucaProt integrates both sequence and predicted structural information, enabling the accurate detection of RdRP sequences. Using this approach we identified 161,979 potential virus species 180 supergroups, including many previously poorly...
Abstract Bats are natural reservoirs for a wide range of microorganisms, including many notable zoonotic pathogens. However, the infectome bat kidneys remains poorly understood. To address this gap, we performed meta-transcriptomic sequencing on kidney tissues from 142 bats, spanning ten species sampled at five locations in Yunnan province, China. This analysis identified 22 viral species, 20 novel viruses, two which represented newly discovered henipaviruses closely related to highly...
Small mammals harbor a diverse array of zoonotic pathogens. To date, however, metagenomic surveys these species have primarily focused on viral diversity, with limited attention paid to bacteria and eukaryotic Additionally, the ecological determinants pathogen diversity within not been systematically examined. Herein, we employed metatranscriptomics approach survey infectome 2,408 individual samples, representing lung, liver, gut tissues from 858 animals collected throughout Guangdong...
Phlebotomus chinensis sandfly is a neglected insect vector in China that 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 the general diversity overall microbiome composition this species still very limited. Here we carried out meta-transcriptomics analysis revealed actively replicating/transcribing RNA viruses, DNA bacteria,...
Mosquito transmitted viruses are responsible for an increasing burden of human disease. Despite this, little is known about the diversity and ecology within individual mosquito hosts. Using a meta-transcriptomic approach, we analysed virome 2,438 mosquitos (79 species), spanning ~4000 km along latitudes longitudes in China. From these data identified 393 core viral species associated with mosquitos, including seven (putative) arbovirus species. We potential geographic hotspots richness...
Abstract RNA viruses are diverse components of global ecosystems. The metagenomic identification is currently limited to those with sequence similarity known viruses, such that highly divergent comprise the "dark matter" virosphere remain challenging detect. We developed a deep learning algorithm – LucaProt search for RNA-dependent polymerase (RdRP) sequences in 10,487 meta-transcriptomes. integrates both and structural information accurately efficiently detect RdRP sequences. With this...
Bats are reservoir hosts for many zoonotic viruses. Despite this, relatively little is known about the diversity and abundance of viruses within bats at level individual animals, hence frequency virus co-infection inter-species transmission. Using an unbiased meta-transcriptomics approach we characterised mammalian associated present in 149 sampled from Yunnan province, China. This revealed a high species spillover among animals studied, with 12 shared different bat species, which turn...
Abstract Bats are reservoir hosts for many zoonotic viruses. Despite this, relatively little is known about the diversity and abundance of viruses within bats at level individual animals, hence frequency virus co-infection inter-species transmission. Using an unbiased meta-transcriptomics approach we characterised mammalian associated present in 149 sampled from Yunnan province, China. This revealed a high species spillover among animals studied, with 12 shared different bat species, which...
Abstract RNA viruses exhibit vast phylogenetic diversity and can significantly impact public health agriculture. However, current bioinformatics tools for viral discovery from metagenomic data frequently generate false positive virus results, overestimate diversity, misclassify sequences. Additionally, often fail to determine virus-host associations, which hampers investigation of the potential threat posed by a newly detected virus. To address these issues we developed VirID, software tool...
Abstract Metagenomic sequencing has expanded the RNA virosphere, but many identified viral genomes remain incomplete, especially for segmented viruses. Traditional methods relying on sequence homology struggle to identify highly divergent segments and group them confidently within a single virus species. To address this, we developed new bioinformatic tool – SegFinder that identifies genome based their common co-occurrence at similar abundance successfully re-discovered all from test data...
ABSTRACT Metagenomic sequencing has transformed our understanding of viral diversity in wildlife and its threat to human health. Despite this progress, many studies have lacked systematic ecologically informed sampling, which left numerous potentially emergent viruses undiscovered, the drivers their ecology evolution poorly understood. We conducted an extensive analysis lung, spleen, gut 1,688 animals from 38 mammalian species across 428 sites Yunnan, China—a hotspot for zoonotic diseases....
Abstract RNA viruses exhibit vast phylogenetic diversity and can significantly impact public health agriculture. However, current bioinformatics tools for viral discovery from metagenomic data frequently generate false positive virus results, overestimate diversity, misclassify sequences. Additionally, often fail to determine virus–host associations, which hampers investigation of the potential threat posed by a newly detected virus. To address these issues we developed VirID, software tool...