Some respiratory tract infections remain unexplained despite extensive testing for common pathogens. Nasopharyngeal aspirates (NPAs) from 120 Chilean infants from Santiago with acute lower respiratory tract infections were analysed by viral metagenomics, revealing the presence of nucleic acids from anelloviruses, adenovirus-associated virus and 12 known respiratory viral pathogens. A single sequence read showed translated protein similarity to cycloviruses. We used inverse PCR to amplify the complete circular ssDNA genome of a novel cyclovirus we named CyCV-ChileNPA1. Closely related variants were detected using PCR in the NPAs of three other affected children that also contained anelloviruses. This report increases the current knowledge of the genetic diversity of cycloviruses whose detection in multiple NPAs may reflect a tropism for human respiratory tissues.Cycloviruses, members of a proposed genus within the family Circoviridae, have a circular ssDNA genome of approximately 2 kb (Li et al., 2010). Genetically highly diverse cycloviruses were initially found in the faeces of Pakistani children with and without acute flaccid paralysis (Victoria et al., 2009), in wild chimpanzees (Li et al., 2010) and in tissues of farm animals including cows, goats, bats and chickens (Ge et al., 2011;Li et al., 2010Li et al., , 2011. Unexpectedly, other cyclovirus species have also been detected in insects, namely dragonflies and cockroaches (Dayaram et al., 2013;Padilla-Rodriguez et al., 2013;Rosario et al., 2011). In 2013, a cyclovirus species (CyCV-CN) was found initially using viral metagenomics and then by PCR in 4 % of cerebrospinal fluid (CSF) specimens from Vietnamese children with unexplained central nervous system disorder, but not in CSF from patients with non-neurological problems, as well as in 4.2 % of faeces from healthy Vietnamese children (Tan et al., 2013). CyCV-CN DNA was also detected in a throat swab (Tan et al., 2013). In this study, 58 % of faecal specimens from pigs and poultry in Vietnam were also positive for the same cyclovirus, suggesting possible sources of human infection (Tan et al., 2013). A related cyclovirus was also detected in 10 % of CSF samples and 15 % of serum samples from adult patients with paraplegia (leg paralysis) from Malawi (Smits et al., 2013). Nasopharyngeal aspirates (NPAs) from Chilean children less than 2 years old with acute lower respiratory infections were tested for respiratory syncytial virus (RSV), adenovirus, parainfluenza virus 1-3 and influenza A and B viruses by indirect immunofluorescence assays and virus isolation (Avendaño et al., 2003). From 1998 to 2000, a mean of 29 % of acute lower respiratory infections samples were positive for RSV (Avendaño et al., 2003). To initiate the characterization of the viruses in non-reactive NPA samples, viral particles were enriched by filtration, and unprotected DNA and RNA were digested using a combination of nuclease enzymes (Victoria et al., 2009). The remaining nucleic acids were then extracted using a MagMAX Viral RNA Iso...