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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
Castrignano, Silvana Beres; Nagasse-Sugahara, Teresa Keico; Garrafa, Patrícia; Monezi, Telma Alves; Barrella, Karina Medici & Mehnert, Dolores Ursula
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.
FINDINGS 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.
Keywords
circo-like virus-Brazil; circular DNA virus; single-stranded DNA virus; Rep gene; CRESS-DNA virus; sewage
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