Diversity of CRESS DNA Viruses in Squamates Recapitulates Hosts Dietary and Environmental Sources of Exposure

Abstract

CRESS DNA viruses are significant pathogens of birds and pigs and have been detected repeatedly in human samples (stools, serum, and cerebrospinal fluid), both from healthy individuals and from patients with neurological disease, eliciting in 2013 a risk assessment by the European Centre for Disease Prevention and Control (ECDC). Sequences of CRESS DNA viruses previously reported in humans (TN9, TN12, and TN25), and detected in different animal species (e.g., birds, dogs, and bats) were herein detected in fecal samples of synanthropic squamates (geckos and lizards).

Circoviridae Survey in Captive Non-Human Primates, Italy

“…Upon sequence alignment and analysis of pairwise percent identities, all the sequences shared 99.1–100% nt identity to each other, whilst the overall nt identities to other CyVs ranged from 29.9% to 99.1%. The closest match (98.0–99.1% nt) was to a CyV strain (RI196/ITA) identified in the intestinal content of a Maltese wall lizard ( Podarcis filfolensis ) in Italy [ 26 ] and to human CyVs (69.7–72.4% nt) detected in nasopharyngeal aspirates from Chilean children less than 2 years old with acute lower respiratory infections [ 23 ].…”

“…Upon interrogation (January 2024) of Genbank database, the strains NHP21F/2022/ITA, NHP21S/2022/ITA, NHP39/2023/ITA, NHP40/2023/ITA and NHP41/ITA/2023 displayed the best match (98.3–98.6% pairwise genome-wide nt identity) to the lizard CyV RI196/ITA [ 26 ], with pairwise aminoacid [aa] identities of 99.6–100% and 95.8–96.6%, respectively, in the full rep and Cp proteins. The full genomes of the five NHP strains were aligned with CyV complete genomic nucleotide sequences currently available on GenBank databases using MUSCLE [ 29 ] and the alignments were used to construct the phylogenetic tree.…”

“…The full genomes of the five NHP strains were aligned with CyV complete genomic nucleotide sequences currently available on GenBank databases using MUSCLE [ 29 ] and the alignments were used to construct the phylogenetic tree. Maximum Likelihood tree ( Figure 1 ) revealed that the NHPs CyVs grouped tightly (bootstrap value 100%) with the Italian strain RI196/ITA of lizard origin [ 26 ]. These strains displayed 98.3–100% nt identity to each other and represented the cluster genetically most close (71.2–71.7% nt identity) to members of the species Cyclovirus umana (7078A, 5841A, 7046A) detected in respiratory samples from Chilean patients [ 23 ].…”

“…Partial CyV Rep sequences were obtained from all the positive samples. According to sequence analyses, the ten partial sequences shared high identity (97.6–100% nt) and displayed the closest identity (98.6–99.1%) to a lizard strain, RI196/ITA, identified in 2022 in the Sicily region [ 26 ]. When reconstructing the complete sequence and genome organization of five NHP CyVs, the closest sequence identity (98.3–98.6%) to the lizard strain was confirmed.…”

Phylogenomic analysis expands the known repertoire of single-stranded DNA viruses in benthic zones of the South Indian Ocean

“…More recently, uncharacterized groups of ssDNA viruses associated with vertebrates from terrestrial environments have become the subject of extensive research [ 29–34 ] . Although these studies have provided substantial insights regarding the diversity and versatility of ssDNA, the results have led to an overrepresentation of virus sequences from several habitats including terrestrial ecosystems and mammal derived samples [ 35–37 ].…”