Identification of circo-like virus-Brazil genomic sequences in raw sewage from the metropolitan area of São Paulo: evidence of circulation two and three years after the first detection

Abstract

BACKGROUND Two novel viruses named circo-like virus-Brazil (CLV-BR) hs1 and hs2 were previously discovered in a Brazilian human fecal sample through metagenomics. CLV-BR hs1 and hs2 possess a small circular DNA genome encoding a replication initiator protein (Rep), and the two genomes exhibit 92% nucleotide identity with each other. Phylogenetic analysis based on the Rep protein showed that CLV-BRs do not cluster with circoviruses, nanoviruses, geminiviruses or cycloviruses.OBJECTIVE The aim of this study was to search for CLV-BR genomes in sewage and reclaimed water samples from the metropolitan area of São Paulo, Brazil, to verify whether the first detection of these viruses was an isolated finding.METHODS Sewage and reclaimed water samples collected concomitantly during the years 2005-2006 were purified and concentrated using methodologies designed for the study of viruses. A total of 177 treated reclaimed water samples were grouped into five pools, as were 177 treated raw sewage samples. Nucleic acid extraction, polymerase chain reaction (PCR) amplification and Sanger sequencing were then performed.eFINDINGS CLV-BR genomes were detected in two pools of sewage samples, p6 and p9. Approximately 28% and 51% of the CLV-BR genome was amplified from p6 and p9, respectively, including 76% of the Rep gene. The detected genomes are most likely related to CLV-BR hs1. Comparative analysis showed several synonymous substitutions within Rep-encoding sequences, suggesting purifying selection for this gene, as has been observed for other eukaryotic circular Rep-encoding single-stranded DNA (CRESS-DNA) viruses.MAIN CONCLUSION The results therefore indicated that CLV-BR has continued to circulate in Brazil two and three years after first being detected.

Viral Metagenomic Profiling of Croatian Bat Population Reveals Sample and Habitat Dependent Diversity

“…: MK241555) has been described by our research group previously in the context of a genome announcement [ 35 ]. It indicated a similarity to Circo-like viruses Brazil HS1 and HS2, which were identified in human feces [ 48 , 49 ].…”

Viral metagenomics revealed diverse CRESS-DNA virus genomes in faeces of forest musk deer

“…The Rep protein sequences of these novel virus were homology alignment with the reference sequences in GenBank using the ClustalW program in MEGA7.0. Phylogenetic analyses were constructed using fulllength rep protein of novel virus and other genetically close relatives [22,46]. Save the aligned sequence as a Nexus form file, which was used to construct the phylogenetic tree using Bayes' theorem in Mrbayes3.2.7 program.…”

A comprehensive genealogy of the replication associated protein of CRESS DNA viruses reveals a single origin of intron-containing Rep

“…The training set was used to estimate an amino acid substitution matrix with a modified HyPhy batch file from Nickle et al (Nickle et al, 2007a) (https://github.com/lzhao-virevol/matrix) and FastMG (Dang et al, 2014). We used two matrices to seed our matrix estimation: VT, the best-fitting matrix to the full dataset and LG, the most recent general amino acid substitution matrix (Le and Gascuel, 2008), which is frequently used to describe CRESS DNA virus evolution (Bistolas et al, 2017;Castrignano et al, 2017;Kaszab et al, 2018;Male et al, 2016). The HyPhy estimated matrices initiated with LG and VT are named fitLG and fitVT matrices.…”

“…Our analysis included RefSeq sequences for each CRESS DNA viral species, including from the Geminiviridae, which is the most speciose viral family, while most researchers use only a small number of representative geminiviruses in a dataset, and these representatives most often come from Begomovirus, which comprises 75% of the annotated geminivirus species (https://talk.ictvonline.org/taxonomy/). Begomovirus Reps do not contain an intron, so often the sequence diversity of geminivirus Reps was inadequately represented (Castrignano et al, 2017;Simmonds et al, 2017;Varsani and Krupovic, 2018). Interestingly, when we reduced the number of Begomovirus Reps in our dataset to the same size as the largest intron-containing genus, Mastrevirus (n=37), the single origin of intron-containing geminivirus and genomovirus Reps loses support, and nanoviruses group within the alpha-satellites instead of being reciprocally monophyletic ( Figure 4).…”