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Order Martellivirales: Virgaviridae
Published in Paul Pumpens, Peter Pushko, Philippe Le Mercier, Virus-Like Particles, 2022
Paul Pumpens, Peter Pushko, Philippe Le Mercier
The Virgaviridae members infect a wide range of herbaceous and mono- and dicotyledonous plant species, but the host range of individual members is usually limited. All members can be transmitted experimentally by mechanical inoculation, and for those in the genus Tobamovirus this is the only known means of transmission (Adams et al. 2017).
Epilogue
Published in Paul Pumpens, Single-Stranded RNA Phages, 2020
Therefore, the list of the RNA phages, as presented in Table 1.1 of Chapter 1, appears in the novel light as greatly limited, and the brilliant metagenomic methodology provokes fresh interest in the advanced search of the RNA phage representatives in ocean, soil, and animal ecosystems. Krishnamurthy and Wang (2017) presented thereupon a systematic roadmap for the investigation and accurate classification of viral dark matter, namely, the metagenomic sequences that originate from viruses but do not align to any reference virus sequences. This paper paved the first steps in the direction to the comprehensive defining of the virome with the single-stranded RNA phages as an essential part of it. The authors estimated the viral dark matter between 40% and 90% of the metagenomic sequences and identified three factors that contribute to the existence of viral dark matter: the divergence and length of virus sequences, the limitations of alignment-based classification, and limited representation of viruses in reference sequence databases. Thus, reducing the extent of viral dark matter, the knowledge of the single-stranded RNA phages will progress inevitably. Moreover, high capabilities of the novel sequencing approaches, such as single-cell RNA sequencing (Saliba et al. 2017) and nanopore sequencing (Viehweger et al. 2018; Harel et al. 2019; Wongsurawat et al. 2019) are inspiring scientists to perform total refreshing and resequencing of older data. In this connection, the general history of DNA sequencing, or sequence of sequencers, would be recommended (Heather and Chain 2016). The growing interest resulted in a special recent review on the RNA phages in the global metagenomic era (Callanan et al. 2018). Moreover, the modern metagenomics protocols are adjusted especially to the accurate isolation of the putative RNA phage genomes (Grasis 2018). Nevertheless, it is necessary to take into account real difficulties with the RNA phage detection by metagenomic analysis, which could appear with the RNA virus-search targeted protocols. Thus, Shkoporov et al. (2018) acknowledged that the attempt to artificially spike fecal samples with the phage Qβ did not result in recovery of any reads aligning to its genome. This suggested that although some larger rod-shaped plant RNA viruses of the Virgaviridae family were detected using the protocol, the latter failed to quantitatively recover the smaller RNA phage Qβ. Further, Shkoporov and Hill (2019) acknowledged that they were unable to detect the RNA phages in gut phage communities, likely because of low viral loads and unsuitable nucleic acid extraction procedures.
Metagenomic analysis of intestinal mucosa revealed a specific eukaryotic gut virome signature in early-diagnosed inflammatory bowel disease
Published in Gut Microbes, 2019
Federica Ungaro, Luca Massimino, Federica Furfaro, Valeria Rimoldi, Laurent Peyrin-Biroulet, Silvia D’Alessio, Silvio Danese
Conversely, other viral families, such as Polydnaviridae and Tymoviridae in UC, and Virgaviridae in CD, that we observed to be less enriched in IBD patients and to negatively correlate with the presence of other viruses, might be somehow considered protective in the human host.15 This is interesting, because Polydnaviridae, Tymoviridae, and Virgaviridae are viruses that typically infects plants and insects and may have reached the gut through the diet.3 The trans-kingdom interaction15 between viruses and hosts, such as plant and insect viruses that colonize human tissues, has already been reported in the past for Tobacco Mosaic Virus (TMV), against which antibodies were found in human sera.42 Unlike animal viruses, plant viruses cannot replicate in humans or other animals because of the lack of specific receptors. Nevertheless, they still can induce the host immune response, as shown for the cowpea mosaic virus in mice.43,44
Integrated gut virome and bacteriome dynamics in COVID-19 patients
Published in Gut Microbes, 2021
Jiabao Cao, Cheng Wang, Yuqing Zhang, Guanglin Lei, Kun Xu, Na Zhao, Jingjing Lu, Fanping Meng, Linxiang Yu, Jin Yan, Changqing Bai, Shaogeng Zhang, Ning Zhang, Yuhuan Gong, Yuhai Bi, Yi Shi, Zhu Chen, Lianpan Dai, Jun Wang, Penghui Yang
Alpha – and beta-diversity analyses based on the Shannon index and Bray-Curtis distance, respectively, showed no significant differences between COVID-19 patients and healthy controls regarding the composition of the baseline virome (Figure 2b, P = .168, PERMANOVA). Comparison of baseline viromes from COVID-19 patients with healthy individuals using the Wilcoxon rank-sum test showed that the abundance of some phages (including Inviridae and Microviridae) and a plant-RNA virus (Virgaviridae) identified by blastn as cucumber green mottle mosaic virus (CGMMV) as well as unclassified viruses were significantly higher in COVID-19 patients than in healthy subjects (Figure 2c). Notably, we found that the virome was relatively stable across multiple time points in patients (Fig. S1a). To study shifts in viral abundance over the course of treatment, we traced viral groups that differed significantly between COVID-19 patients and healthy controls and found that the alteration in viral abundance over time was inconsistent (Figure 2d). Nevertheless, we found a strong correlation between the composition of viral and bacterial communities in both COVID-19 patients and healthy controls, as determined by Procrustes analysis (Fig. S2a, P = .001). Additional network analysis demonstrated that bacterial species, including Bacteroides vulgatus, Faecalibacterium prausnitzii, and Ruminococcus gnavus, and three Microviridae bacteriophages, that is, Microviridae__sp._ctmin955, Microviridae__sp._ctvbz116, and Microviridae__sp.ctjA9876, compose central network nodes and potential keystone species that could play important roles in mediating the interactions between the viral and bacterial communities (Fig. S2b); none of the eukaryotic viruses, however, was determined to be central in terms of network structure.