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Chrisman BS, He C, Jung JY, Stockham N, Paskov K, Wall DP. Transmission dynamics of human herpesvirus 6A, 6B and 7 from whole genome sequences of families. Virol J 2022; 19:225. [PMID: 36566197 PMCID: PMC9789512 DOI: 10.1186/s12985-022-01941-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 11/30/2022] [Indexed: 12/25/2022] Open
Abstract
While hundreds of thousands of human whole genome sequences (WGS) have been collected in the effort to better understand genetic determinants of disease, these whole genome sequences have less frequently been used to study another major determinant of human health: the human virome. Using the unmapped reads from WGS of over 1000 families, we present insights into the human blood DNA virome, focusing particularly on human herpesvirus (HHV) 6A, 6B, and 7. In addition to extensively cataloguing the viruses detected in WGS of human whole blood and lymphoblastoid cell lines, we use the family structure of our dataset to show that household drives transmission of several viruses, and identify the Mendelian inheritance patterns characteristic of inherited chromsomally integrated human herpesvirus 6 (iciHHV-6). Consistent with prior studies, we find that 0.6% of our dataset's population has iciHHV, and we locate candidate integration sequences for these cases. We document genetic diversity within exogenous and integrated HHV species and within integration sites of HHV-6. Finally, in the first observation of its kind, we present evidence that suggests widespread de novo HHV-6B integration and HHV-7 integration and reactivation in lymphoblastoid cell lines. These findings show that the unmapped read space of WGS is a promising source of data for virology research.
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Affiliation(s)
- Brianna S. Chrisman
- grid.168010.e0000000419368956Department of Bioengineering, Stanford University, Serra Mall, Stanford, USA ,grid.266818.30000 0004 1936 914XNevada Bioinformatics Center, University of Nevada, Reno, USA
| | - Chloe He
- grid.168010.e0000000419368956Department of Biomedical Data Science, Stanford University, Serra Mall, Stanford, USA
| | - Jae-Yoon Jung
- grid.168010.e0000000419368956Department of Pediatrics (Systems Medicine), Stanford University, Serra Mall, Stanford, USA
| | - Nate Stockham
- grid.168010.e0000000419368956Department of Neuroscience, Stanford University, Serra Mall, Stanford, USA
| | - Kelley Paskov
- grid.168010.e0000000419368956Department of Biomedical Data Science, Stanford University, Serra Mall, Stanford, USA
| | - Dennis P. Wall
- grid.168010.e0000000419368956Department of Pediatrics (Systems Medicine), Stanford University, Serra Mall, Stanford, USA
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Valença IN, Santos RBD, Peronni KC, Sauvage V, Vandenbogaert M, Caro V, Silva Junior WAD, Covas DT, Silva-Pinto AC, Laperche S, Kashima S, Slavov SN. Deep sequencing applied to the analysis of viromes in patients with beta-thalassemia. Rev Inst Med Trop Sao Paulo 2021; 63:e40. [PMID: 34037156 PMCID: PMC8149102 DOI: 10.1590/s1678-9946202163040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 04/18/2021] [Indexed: 11/22/2022] Open
Abstract
To date, blood banks apply routine diagnosis to a specific spectrum of
transfusion-transmitted viruses. Even though this measure is considered highly
efficient to control their transmission, the threat imposed by emerging viruses
is increasing globally, which can impact transfusion safety, especially in the
light of the accelerated viral discovery by novel sequencing technologies. One
of the most important groups of patients, who may indicate the presence of
emerging viruses in the field of blood transfusion, is the group of individuals
who receive multiple transfusions due to hereditary hemoglobinopathies. It is
possible that they harbor unknown or unsuspected parenterally-transmitted
viruses. In order to elucidate this, nucleic acids from 30 patients with
beta-thalassemia were analyzed by Illumina next-generation sequencing and
bioinformatics analysis. Three major viral families:
Anelloviridae, Flaviviridae and
Hepadnaviridae were identified. Among
them, anelloviruses were the most representative, being detected with high
number of reads in all tested samples. Human Pegivirus 1 (HPgV-1, or GBV-C),
Hepatitis B Virus (HBV) and Hepatitis C Virus (HCV) were also identified. HBV
and HCV detection was expected due to the high seroprevalence in patients with
beta thalassemia. Our results do not confirm the presence of emerging or
unsuspected viruses threatening the transfusion safety at present, but can be
used to actively search for viruses that threaten blood transfusion safety. We
believe that the application of viral metagenomics in multiple-transfused
patients is highly useful to monitor possible viral transfusion threats and for
the annotation of their virome composition.
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Affiliation(s)
- Ian Nunes Valença
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Programa de Mestrado em Oncologia Clínica, Células-Tronco e Terapia Celular, Ribeirão Preto, São Paulo, Brazil.,Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Hemocentro de Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
| | - Rafael Bezerra Dos Santos
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Programa de Mestrado em Oncologia Clínica, Células-Tronco e Terapia Celular, Ribeirão Preto, São Paulo, Brazil.,Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Hemocentro de Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
| | - Kamila Chagas Peronni
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Hemocentro de Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
| | - Virginie Sauvage
- Centre National de Référence Risques Infectieux Transfusionnels, Institut National de la Transfusion Département d'études des Agents Transmissibles par le Sang, Paris, France
| | - Mathias Vandenbogaert
- Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence, Paris, France
| | - Valérie Caro
- Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence, Paris, France
| | - Wilson Araújo da Silva Junior
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Genética, Ribeirão Preto, São Paulo, Brazil
| | - Dimas Tadeu Covas
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Hemocentro de Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil.,Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Clínica Médica, Ribeirão Preto, São Paulo, Brazil
| | - Ana Cristina Silva-Pinto
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Hemocentro de Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
| | - Syria Laperche
- Centre National de Référence Risques Infectieux Transfusionnels, Institut National de la Transfusion Département d'études des Agents Transmissibles par le Sang, Paris, France
| | - Simone Kashima
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Hemocentro de Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
| | - Svetoslav Nanev Slavov
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Hemocentro de Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil.,Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Clínica Médica, Ribeirão Preto, São Paulo, Brazil
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