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

Author(s)

Fahsbender, Elizabeth ^{[1, 2]} ; da-Costa, Antonio Charlys ^{[3, 4]} ; Gill, Danielle Elise ^{[3, 4]} ; Milagres, Flavio Augusto de Padua ^{[5, 6]} ; Brustulin, Rafael ^{[5, 6]} ; Monteiro, Fred Julio Costa ^[7] ; Rego, Marlisson Octavio da Silva ^[7] ; Ribeiro, Edcelha Soares D'Athaide ^[7] ; Sabino, Ester Cerdeira ^{[3, 4]} ; Delwart, Eric ^{[1, 2]}

Affiliation

^[1] Univ Calif San Francisco, Dept Lab Med, San Francisco, CA 94110 - USA

^[2] Vitalant Res Inst, San Francisco, CA 94118 - USA

^[3] Univ Sao Paulo, Sch Med, Infect Dis, Sao Paulo - Brazil

^[4] Univ Sao Paulo, Inst Trop Med, Infect Dis, Sao Paulo - Brazil

^[5] Fed Univ Tocantins, Palmas, Tocantins - Brazil

^[6] Hlth Tocantins, Publ Hlth Lab State LACEN TO, Palmas, TO - Brazil

^[7] Hlth Amapa, Publ Hlth Lab State LACEN AP, Macapa, AP - Brazil

• Document type: Journal article
• Source: PLoS One; v. 15, n. 3 MAR 5 2020.
• Web of Science Citations: 0

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. (AU)

• FAPESP's process: 17/00021-9 - Viral metagenomics to track, explain and predict the transmission and spatiotemporal spread of Dengue and Chikungunya viruses in Brazil
• Grantee: Antonio Charlys da Costa
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• FAPESP's process: 16/01735-2 - Viral metagenomics to track, explain and predict the transmission and spatiotemporal spread of Dengue and Chikungunya viruses in Brazil
• Grantee: Ester Cerdeira Sabino
• Support Opportunities: Regular Research Grants