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- D. Obbard (United Kingdom)
Metagenomic Strategies To Identify Sequences in the ‘Dark’ Virome
- D. Obbard (United Kingdom)
Abstract
Abstract Body
Metagenomic sequencing has dramatically expanded our knowledge of the global virome. However, the majority of metagenomic studies depend on sequence similarity to detect and classify sequences that are viral in origin. Unfortunately, the rapid divergence and ancient relationships of viruses mean that a large proportion of viral sequences may not be easily detectable in this way. This has led to the idea of the ‘dark virome’: those virus genomes, segments, and fragments that cannot be found by similarity searches. Here I present metagenomic approaches that can be used to identify and classify ‘dark’ virus sequences. I discuss their application in our studies of the Drosophila virome, and particularly the discovery of new Partitiviruses, the discovery of the ‘quenyaviruses’, and a potential new enigmatic lineage of segmented ssDNA viruses.
THE RAPIDLY EXPANDING RNA VIROSPHERE—REPLICATORS HERE, REPLICATORS THERE, REPLICATORS EVERYWHERE?
- J. H. Kuhn (United States of America)
Abstract
Background and Aims
In 2019, on the basis of a global RNA-directed RNA polymerase (RdRp) phylogeny, the International Committee on Taxonomy of Viruses (ICTV) established realm Riboviria with six distinct phyla (orthornaviran Duplornaviricota, Kitrinoviricota, Lenarviricota, Negarnaviricota, and Pisuviricota, and pararnaviran Arterviricota) to encompasses the vast majority of all then-known RNA viruses. An additional realm, Ribozyviria, was established in 2021 for an increasing number of hepatitis D-like RNA viruses (deltaviruses).
Methods
Novel large-scale RdRp phylogenies were established during large-scale metagenomic and metatranscriptomic studies.
Results
Here I will outline how the results of these studies will require major expansion and reorganization of both realms, possibly including the establishment of high-ranked riboviriad megataxa and novel ribozyviriad megataxa for “epsilonviruses” and “zetaviruses”.
Conclusions
These developments significantly expand the RNA virosphere and therefore the future scope of the ICV meeting series.
STUDYING THE VIROME OF CAMELS IN CENTRAL ASIA
- K. Karamendin (Kazakhstan)
Abstract
Background and Aims
The emergence of new pandemic strains of the MERS-CoV coronavirus in camels necessitates regular monitoring of viral populations in this animal. The goal was to identify viruses circulating among camels in Kazakhstan that pose a potential threat to human and animal health.
Methods
Molecular-genetic and serological methods were used: the isolation of nucleic acids from the camel samples, the construction of libraries for mass parallel sequencing, bioinformatic data analysis, and serological tests.
Results
As a result of virome sequencing, contigs of viruses representing the following families were found: Flaviviridae, Circoviridae, Picobirnaviridae, Astroviridae, Parvoviridae and Hepeviridae. Of these families, all but Astroviruses and Pestiviruses have previously been found in camels. Of particular interest is the detection of short sequences, hepatitis-like viral contigs, which is potentially dangerous for humans. Serological test of camels confirmed the presence of antibodies to the hepatitis E virus, which indicates its possible circulation in camels in Kazakhstan.
Conclusions
The study of viral metagenomes of camels in the close to the Middle East region is an important epidemiological task. This will make it possible to identify not only strains of coronaviruses, but also other unknown viral pathogens that are important both for domestic animals and for human health.
VIROME DIVERSITY AND MICROBIOME PROFILING OF BAT-ASSOCIATED CARIOS VESPERTILIONIS TICKS
- A. S. Ortiz-Baez (Australia)
Abstract
Background and Aims
Ticks harbour a broad spectrum of microorganisms, including viruses, bacteria and protozoans. Ticks of Carios (Argas) vespertilionis (Argasidae) are common ectoparasites of bats species in the Palearctic region and play a key vectorial role in the maintenance and transmission of zoonotic pathogens relevant to public health. The soprano pipistrelle bat (Pipistrellus pygmaeus - Vespertilionidae) is widely distributed in Europe, where it and can be found close to anthropogenic environments.
Methods
In the present study, we use meta-transcriptomics to investigate the RNA virome diversity and common microbiome pathogens present in recently blood fed C. vespertilionis ticks, collected from a soprano pipistrelle bat roosting site in Sweden.
Results
Our analysis revealed 20 newly discovered viruses classified within 12 virus families. We also identified known bat-associated and tick-borne viruses in the Nairoviridae and Picornaviridae families. Similarly, we found highly abundant bacteria and protozoans carried by C. vespertilionis, such as Delftia sp., Coxiella sp., Rickettsia sp., and Babesia sp.
Conclusions
These findings demonstrate the remarkable diversity of RNA viruses and microbiota components present in C. vespertilionis and highlight the importance of bat-associated ectoparasite surveillance.
SURVEILLANCE OF INSECT-SPECIFIC VIROME IN FIELD-CAUGHT MOSQUITOES FROM NORTHEASTERN THAILAND
- A. Burassakarn (Thailand)
Abstract
Background and Aims
Mosquitoes are the major vector of arboviruses particularly, dengue virus (DENV), zika virus (ZIKV), and chikungunya virus (CHIKV). Regardless of the failures of current arboviral vector control and prevention strategies for their transmission, alternative approaches are necessitated to further develop and improve. Recent studies have been indicated the important roles of insect-specific viruses (ISVs) in the alteration of the vector competency, serving as alternative schemes for innovative arboviral transmission control. Northeastern (NE) Thailand has a tropical climate that provides opportune settings for mosquitoes’ emergence and dissemination, supporting existing arboviruses epidemics. However, evidence concerning the representative ISVs in potential mosquito vectors of this region is lacking.
Methods
Therefore, this study aimed to survey the burden of ISVs harbored by natural mosquitoes using a Next-generation sequencing (NGS)-based metagenomic approach.
Results
Our analyses reveal that matched viral reads were highly diverse and varied in abundance among mosquito species, which were 11 taxonomic families and an unclassified group. The ISVs reads have prevailed in all mosquito species. Among these, the Guadeloupe mosquito virus (GMV) was stably found in female adults of Aedes aegypti and Culex spp. Notably, the presence of GMV contigs has firstly been suggested as a new spatial distribution of such ISV in NE Thailand as exploration with the public databases of viral metagenomic of Aedes and Culex mosquitoes.
Conclusions
Overall, this study imparts a comprehensive literacy of diverse ISV burdens circulated in the mosquito vectors from NE Thailand, which might be a potential source for innovative strategies of arboviral transmission control.