Virus Discovery in Desert Tortoise Fecal Samples: Novel Circular Single-Stranded DNA Viruses

Abstract

The Sonoran Desert tortoise Gopherus morafkai is adapted to the desert, and plays an important ecological role in this environment. There is limited information on the viral diversity associated with tortoises (family Testudinidae), and to date no DNA virus has been identified associated with these animals. This study aimed to assess the diversity of DNA viruses associated with the Sonoran Desert tortoise by sampling their fecal matter. A viral metagenomics approach was used to identify the DNA viruses in fecal samples from wild Sonoran Desert tortoises in Arizona, USA. In total, 156 novel single-stranded DNA viruses were identified from 40 fecal samples. Those belonged to two known viral families, the Genomoviridae (n = 27) and Microviridae (n = 119). In addition, 10 genomes were recovered that belong to the unclassified group of circular-replication associated protein encoding single-stranded (CRESS) DNA virus and five circular molecules encoding viral-like proteins.

Identification and Distribution of Novel Cressdnaviruses and Circular Molecules in Four Penguin Species in South Georgia and the Antarctic Peninsula

“…Since we identified six AntCMs with Reps that are most closely related to those of plasmids, we included a suite of plasmids grouped by Kazlauskas et al [ 35 ] for clustering the Reps using a sequence similarity network (SSN) based approach. We have found in the past [ 26 , 61 , 62 ] that an SSN analysis using EST-EFI [ 36 , 37 ] with a network threshold of 60 allows for reasonable family level clusters for families in the phylum Cressdnaviricota [ 27 ]. Based on the sequence similarity network analysis of the Rep amino acid sequences ( Figure 3 ), none of the AntV Reps cluster with known viral sequences.…”

Legionella pneumophila CRISPR-Cas suggests recurrent encounters with Gokushovirinae

“…In total, 35 L. pneumophila spacers target sequences of Microviridae origin: 25 spacers target the conserved major capsid protein VP1, target the pilot protein VP2, and 5 target the DNA replication protein VP4. One spacer targets a non-coding region (Table 3) (80,81) and Pequeñovirus (80,82).…”

“…Strikingly, nearly all the spacer targets belong to the Gokushovirinae sub-family (Figure 4). First identified as phages for intracellular pathogens such as Chlamydia and Spiroplasma, Gokushovirinae is a very abundant Microviridae subfamily found in diverse environments including marine, freshwater, soil, fecal and animal tissue environments (78)(79)(80)(81)(82)(83)(84)(85)(86)(87)(88)(89)(90), and in hosts ranging from marine bacteria (65) to enterobacteria (91). Within the Microviridae, the only additional hit is to genomes clustering with the proposed Pichovirinae sub-family; a single spacer notable mainly because it targets a non-coding region which one would not expect to be well conserved (76) (Fig S2 ).…”

“…Gokushovirinae, first characterized as phages of Chlamydia (14-17), Spiroplasma (71-74) and Bdellovibrio (75). Several additional subfamilies have been proposed in recent years including: Pichovirinae (76), Alpavirinae (77), Sukshmavirinae (78), Dragonfly-associated Microvirus "Group D" (78, 79), Parabacteroidetes group based on Parabacteroidetes prophages(80,81) …”

First detection of herpesvirus and prevalence of mycoplasma infection in free-ranging Hermann’s tortoises (Testudo hermanni), and in potential pet vectors

“…Captive individuals are frequently released into the wild, intentionally or accidentally, often carrying pathogens that may threaten native populations of tortoises (Sandmeier et al, 2009; Jacobson et al 2014; Whitfield et al, 2018). The scarcity of investigations in natural populations, except in USA, means that possible role of pet tortoises as agents of contamination is not quantified in Europe, as in most parts of the world (Jacobson and Berry, 2012; Kane et al, 2017; Orton et al, 2020).…”