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Other Double-Stranded DNA Viruses
Published in Paul Pumpens, Peter Pushko, Philippe Le Mercier, Virus-Like Particles, 2022
Paul Pumpens, Peter Pushko, Philippe Le Mercier
The order includes the sole Mimiviridae family with two genera, Cafeteriavirus and Mimivirus, and two species altogether (Claverie and Abergel 2012, 2018). As commented by Claverie and Abergel (2018), since 1998, when Jim van Etten’s team initiated characterization of the previously described PBCV-1 from the order Algavirales, it was the largest known DNA virus, both in terms of particle size and genome complexity. However, in 2003, the Acanthamoeba polyphaga mimivirus (APMV) from the Mimivirus genus (La Scola et al. 2003; Raoult et al. 2004, 2007) of the order Imitervirales superseded PBCV-1, opening the era of giant viruses, i.e., with virions large enough to be visible by light microscopy and with genomes encoding more proteins than many bacteria (Claverie and Abergel 2018).
The gut virome in Irritable Bowel Syndrome differs from that of controls
Published in Gut Microbes, 2021
S. Coughlan, A. Das, E. O’Herlihy, F. Shanahan, P.W. O’Toole, I.B. Jeffery
Of classified clusters, the most abundant families were those of the tailed bacteriophage viruses Siphoviridae (27.7%), Myoviridae (13%), and Podoviridae (8.9%) respectively, which are all in the Caudovirales order, in agreement with previous studies of the gut virome in healthy and disease cohorts (Table S3).17–21,24,26,27 The 4th most abundant family (6%) was the Mimiviridae family, whose members infect amoebae and protists, and whose member Mimivirus has been previously noted as a potentially dubious taxonomic classification in a study of the gut virome in ulcerative colitis.24,28 This led us to examine the confidence of the taxonomic classifications in more detail. Examination of the percentage identity and percentage coverage for each protein sequence aligned to the hit protein used for taxonomic assignment (percentage query cover) revealed a wide distribution of both scores for each family indicating that many of the classifications (Figure 1 and Figure S4) were based on low scores. While families in the Caudovirales order had high-scoring hits present, scores for most other families, including Mimiviridae were low indicating that the family-level classification was not reliable. Except for Mimiviridae, all other families with low scoring hits had very low abundances (<0.2% of total abundance at VC level and <0.6% at contig level; Tables S3 & S4, Figure 1). Ascoviridae, Iridoviridae, Marseilleviridae, Pithoviridae, and Poxviridae, all families of nucleocytoplasmic large dsDNA viruses (NCLDVs; proposed order Megavirales29) of eukaryotes had mainly low scoring hits (Figure 1) and were present in very low abundances (Figure 1; Table S1). Furthermore, Pithoviridae viruses have a diameter of 500 nm, which is larger than the 450 nm filter used to remove non-viral material in this study (Methods), and so would not be expected in our sequence data.30 Some Mimivirdae genomes are less than 450 nm and so could legitimately be present in our data. However, taxonomic assignments to families without the presence of high scoring hits or with low abundance are likely not as reliable as those for Caudovirales.