MEM INST OSWALDO CRUZ, RIO DE JANEIRO, 112(3) March 2017
PAGES: 175-181 DOI: 10.1590/0074-02760160312 Full paper
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

Silvana Beres Castrignano1,+, Teresa Keico Nagasse-Sugahara1, Patrícia Garrafa2, Telma Alves Monezi2, Karina Medici Barrella2, Dolores Ursula Mehnert2

1Instituto Adolfo Lutz, Centro de Virologia, Núcleo de Doenças Respiratórias, São Paulo, SP, Brasil
2Universidade de São Paulo, Departamento de Microbiologia, São Paulo, SP, Brasil

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.

Financial support: Adolfo Lutz Institute, FAPESP (nº 2004/15120-2).
+ Corresponding author: This e-mail address is being protected from spambots. You need JavaScript enabled to view it.
SBC and TKN-S contributed equally to this work.
Received 11 July 2016
Accepted 9 November 2016

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