REPOSITORY > RESULTS

Abstract

Metagenomics based on high throughput sequencing (HTS) has opened a new era of discovery and genomic characterization of viruses associated with a given host or environment. The search for novel viral sequences provides an excellent opportunity to improve early detection of pathogens, and to predict viral hosts and environmental reservoirs before the occurrence of significant outbreaks. HTS-based studies of viruses are still challenging, especially in complex matrices, due to the high diversity of viruses, large fraction of unknown and yet to be discovered viruses and different properties of various sample matrices containing viruses. We used non-targeted metagenomics for virus discovery and diversity studies in complex sample matrices, addressing ecological, aetiological and biopharmaceutical perspectives of virome research.
We evaluated the composition of wastewater virome by applying an optimized virus concentration method followed by HTS and infectivity assays. We focused on plant viruses and detected representatives of 47 plant virus species, including emerging crop threats. We also demonstrated infectivity for pathogenic and economically relevant plant viruses from the genus Tobamovirus (family Virgaviridae), with pepper mild mottle virus (PMMoV) and tobacco mild green mosaic virus (TMGMV) remaining infective even after conventional wastewater treatment. These results are exposing the risks associated with the spread of viruses from the waste into the wider ecosystem and with the uncontrolled use of reclaimed water for irrigation. At the same time, the results are showing that wastewater can be used for early detection and monitoring of plant viruses.
We characterized the virome of signal crayfish (Pacifastacus leniusculus), an important freshwater invasive invertebrate species, and potential differences in viral composition and abundance along its invasion range. Study resulted in discovery of novel and divergent RNA viruses, including signal crayfish-associated reo-like, hepe-like, toti-like, and picorna-like viruses, their phylogenetic relationships and potential association with observed pathologies. Additionally the results enabled a better understanding of the potential risk of virus transmissions because of this invader’s dispersal.
In biopharmaceutical industry, viral contamination is one of the major concerns for biological products. We employed the developed metagenomics approaches to search for adventitious viruses in animal cell lines used in biopharmaceutical industry. Study of production and parental Chinese hamster ovary (CHO) cell lines of diverse origin did not indicate the presence of adventitious viral agents, however we detected an expected background of virus-like nucleic acids in the samples, which originate from remains of expression vectors, endogenized viral elements and residuals of bacteriophages. This study serves as a baseline for further investigations of CHO cell lines for adventitious viruses using HTS.