Entamoeba and Giardia parasites implicated as hosts of CRESS viruses

Abstract

Metagenomic techniques have enabled genome sequencing of unknown viruses without isolation in cell culture, but information on the virus host is often lacking, preventing viral characterisation. High-throughput methods capable of identifying virus hosts based on genomic data alone would aid evaluation of their medical or biological relevance. Here, we address this by linking metagenomic discovery of three virus families in human stool samples with determination of probable hosts. Recombination between viruses provides evidence of a shared host, in which genetic exchange occurs. We utilise networks of viral recombination to delimit virus-host clusters, which are then anchored to specific hosts using (1) statistical association to a host organism in clinical samples, (2) endogenous viral elements in host genomes, and (3) evidence of host small RNA responses to these elements. This analysis suggests two CRESS virus families (Naryaviridae and Nenyaviridae) infect Entamoeba parasites, while a third (Vilyaviridae) infects Giardia duodenalis. The trio supplements five CRESS virus families already known to infect eukaryotes, extending the CRESS virus host range to protozoa. Phylogenetic analysis implies CRESS viruses infecting multicellular life have evolved independently on at least three occasions.

Comparison of gut viral communities in diarrhoea and healthy dairy calves

“…To date, some studies have shown that certain CRESS-DNA viruses (like circovirus) may be related to animal diseases [64,65], but it is not clear whether these viruses can infect mammalian cells and directly cause calf diarrhoea. Recently, a high-throughput approach to identifying viral hosts using genomic data alone will help us address this challenge in the future [63]. In this study, most of the reads related to smacovirus, circovirus and other unclassified CRESS-DNA viruses were detected in the healthy group.…”

“…CRESS-DNA viruses are ubiquitous in the virome of many ecosystems and have been suspected of infecting a wide range of organisms such as vertebrates, plants, fungi, and diatoms [60][61][62][63]. To date, some studies have shown that certain CRESS-DNA viruses (like circovirus) may be related to animal diseases [64,65], but it is not clear whether these viruses can infect mammalian cells and directly cause calf diarrhoea.…”

Feline Stool-Associated Circular DNA Virus (FeSCV) in Diarrheic Cats in China

“…It is worth noting that the bootstrap value between unclassified CRESS DNA viruses and other viruses was 100, indicating that these newly discovered viruses shared common characteristics with the previously studied viruses. Recently, it has been suggested that parasites may be potential hosts for CRESS DNA viruses; however, the parasite genomes did not actually contain CRESS endogenous viral elements ( 30 ). Coincidentally, a sequence of Giardia intestinalis was indeed found in the FeSCV genome.…”

The International Virus Bioinformatics Meeting 2020

“…To address this issue, computational methods for identifying hosts of metagenomic virus species are needed. To illustrate one approach, we describe the recent discovery of three circular Rep-encoding single-stranded (CRESS) DNA virus families (phylum Cressdnaviricota) in human clinical samples, and the determination of their hosts, being pathogenic human gut parasites [65]. In that study, host determination was achieved by (1) identifying recombination events between viral genomes to delimit groups overlapping in their host range, and (2) linking groups to a specific host or higher level taxon using endogenous viral elements in host genomes (see Figure 8), host small RNAs, and a case-control based examination of clinical samples.…”