Plasma virome of 781 Brazilians with unexplained symptoms of arbovirus infection include a novel parvovirus and densovirus

Abstract

Plasma from patients with dengue-like symptoms was collected in 2013 to 2016 from the Brazilian states of Tocantins and Amapa. 781 samples testing negative for IgM against Dengue, Zika, and Chikungunya viruses and for flaviviruses, alphaviruses and enteroviruses RNA using RT-PCRs were analyzed using viral metagenomics. Viral particles-associated nucleic acids were enriched, randomly amplified, and deep sequenced in 102 mini-pools generating over 2 billion reads. Sequence data was analyzed for the presence of known and novel eukaryotic viral reads. Anelloviruses were detected in 80%, human pegivirus 1 in 19%, and parvovirus B19 in 17% of plasma pools. HIV and enteroviruses were detected in two pools each. Previously uncharacterized viral genomes were also identified, and their presence in single plasma samples confirmed by PCR. Chapparvovirus and ambidensovirus genomes, both in the Parvoviridae family, were partially characterized showing 33% and 34% identity in their NS1 sequences to their closest relative. Molecular surveillance using pre-existing plasma from febrile patients provides a readily scalable approach for the detection of novel, potentially emerging, viruses.

Investigating the Diversity and Host Range of Novel Parvoviruses from North American Ducks Using Epidemiology, Phylogenetics, Genome Structure, and Codon Usage Analysis

“…However, while the phylogenetic placement of the DAC sequences within a clade that is dominated by avian viruses within a genus that includes many vertebrate viruses, some of which even proven to be pathogenic [ 47 , 48 ], clearly points towards ducks as DAC hosts, such a clear conclusion cannot be made for DAAD. Densoviruses are frequently identified during metagenomic investigations of samples collected from vertebrates [ 43 , 44 , 49 ], including human plasma and cerebrospinal fluid [ 50 , 51 ], and some of the densoviruses genetically close to DAAD were also vertebrate-associated as they were detected in fecal specimens of birds, monkeys, and bats [ 43 , 44 ]. However, dipteran and lepidopteran viruses were also included in the same clade as DAAD and no proof exists that densoviruses can replicate in vertebrate hosts.…”

Meta-Transcriptomic Discovery of a Divergent Circovirus and a Chaphamaparvovirus in Captive Reptiles with Proliferative Respiratory Syndrome

“…Parvoviruses are associated with disease in a variety of host species, ranging from canines [ 47 ] to livestock [ 48 , 49 , 50 , 51 ], rodents [ 36 ], and humans [ 52 ]. Reptile parvoviruses were identified in several snake species (snake adeno-associated virus) [ 11 , 53 , 54 , 55 , 56 , 57 ] and some lizard species including bearded dragons [ 11 , 12 ].…”

Is the ZIKV Congenital Syndrome and Microcephaly Due to Syndemism with Latent Virus Coinfection?

“…In Brazil, B19V is the most frequent cause of rash/fever infections in cases where serum testing is negative for arboviruses and rubella, and several studies have shown an increase in PB19 rash/fever cases in a spatiotemporal manner compared to arboviruses and rubella [ 243 , 244 ]. Parvovirus B19 has been detected in 17% of cases when assaying the plasma of Brazilian patients with dengue fever-like symptoms, while samples were negative for arbovirus and were originally misdiagnosed (falsely positive for DENV) [ 245 , 246 , 247 , 248 , 249 ], A similar trend has also been reported for ZIKV [ 52 , 250 , 251 ].…”