Discovery of two novel Torque Teno viruses in Callithrix penicillata provides insights on Anelloviridae diversification dynamics

Abstract

The development of high-throughput sequencing (HTS) technologies and metagenomics protocols deeply impacted the discovery of viral diversity. Moreover, the characterization of novel viruses in the Neotropical primates (NP) is central for the comprehension of viral evolution dynamics in those hosts, due to their evolutionary proximity to Old World primates, including humans. In the present work, novel anelloviruses were detected and characterized through HTS protocols in the NP Callithrix penicillata, the common black-tufted marmoset. De novo assembly of generated sequences was carried out, and a total of 15 contigs were identified with complete Anelloviridae ORF1 gene, two of them including a flanking GC-rich region, confirming the presence of two whole novel genomes of ~3 kb. The identified viruses were monophyletic within the Epsilontorquevirus genus, a lineage harboring previously reported anelloviruses infecting hosts from the Cebidae family. The genetic divergence found in the new viruses characterized two novel species, named Epsilontorquevirus callithrichensis I and II. The phylogenetic pattern inferred for the Epsilontorquevirus genus was consistent with the topology of their host species tree, echoing a virus-host diversification model observed in other viral groups. This study expands the host span of Anelloviridae and provides insights into their diversification dynamics, highlighting the importance of sampling animal viral genomes to obtain a clearer depiction of their long-term evolutionary processes.

Metagenomic analysis reveals novel dietary-related viruses in the gut virome of marmosets hybrids (Callithrix jacchus x Callithrix penicillata), Brazil

“…High throughput sequencing is a powerful tool for microbial metagenomic analysis. It has been used to discover a large diversity of novel viruses that could not have been identified by traditional methods (Cosentino et al , 2022; D’arc et al , 2020; Harvey and Holmes, 2022; Shi et al , 2016; Zayed et al , 2022). Following previous virome studies based on non-invasive samples (A Duarte et al , 2019; Bodewes et al , 2014; Wang et al , 2019), we characterized the viral metagenomic of fecal samples of C. jacchus x C. penicillata hybrids, the first virome analysis from introduced free-living marmosets.…”

“…The supernatant was discarded and approximately 0.2 mL of the sample was incubated with DNases (Promega and Epicentre, Madison, WI, USA), RNase A (Ambion, USA) and Benzonase (Sigma, USA) for 90 minutes at 37°C to digest unprotected nucleic acid. Viral nucleic acids were then isolated using QIAamp MinElute Virus Spin Kit (QIAGEN, Hilden, Germany) according to the manufacturer's instructions with some modifications described (Cosentino et al, 2022). Complementary DNA (cDNA) synthesis was performed using the Superscript III First Strand Synthesis Supermix Kit (Thermo Fisher Scientific) and for the synthesis of the second strand of cDNA was used the Klenow fragment 3'-5' exo (New England Biolabs Inc., Ipswich, MA, USA), following the manufacturer's instructions.…”

Fecal Virome ofCoendou spinosus(Paraguaian Hairy Dwarf Porcupine)

“…The next steps were viral metagenomics library construction, sequencing and computational analysis. Briefly, samples went through a viral enrichment step, followed by an indexed paired-end library preparation with the Nextera XT kit, according to the manufacturer’s instructions with some modifications described previously (Cosentino et al, 2022). Sequencing was performed on the MiSeq instrument (Illumina) with 300 cycles per sequencing pair-ended (2 × 151 bp) from the Department of Genetics at UFRJ.…”

“…Sequencing was performed on the MiSeq instrument (Illumina) with 300 cycles per sequencing pair-ended (2 × 151 bp) from the Department of Genetics at UFRJ. An in house custom bioinformatics pipeline was used for data quality control with Fastp v.0.20.1 (Chen et al, 2018), de novo assembly using SPAdes v3.15.3 (Nurk et al, 2017), taxonomic assignments were performed by Kraken2 (Wood & Salzberg, 2014) and Diamond v.2.0.14 (Buchfink et al, 2015) and interactive visualization with Krona v.2.7.1 (Ondov et al, 2011), also described previously in Cosentino et al ., (2022). The library generated a total of 2,109,411 raw reads, of which 949,294 reads (45%) passed the criteria for quality trimming and filtering.…”

Characterization of a new anellovirus species infecting an ocelot (Leopardus pardalis) in Brazil

“…A consensus sequence was used to design specific PCR primers to obtain the complete genome using genomic DNA from blood. Novel sequences were evolutionarily contextualized with a comprehensive Anelloviridae ORF1 dataset combining a dataset containing all known Anelloviridae genera ( Cosentino et al, 2022 ) and one containing 220 novel sequences from multiple Felidae species ( Kraberger et al, 2021 ). ORF1 genes were aligned by MAFFT v7.505 ( Katoh and Standley, 2013 ) and TrimAL v.1.4 ( Capella-Gutiérrez et al, 2009 ) was used to remove non informative regions with the “gappyout” option.…”