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Kandathil AJ, Thomas DL. The Blood Virome: A new frontier in biomedical science. Biomed Pharmacother 2024; 175:116608. [PMID: 38703502 PMCID: PMC11184943 DOI: 10.1016/j.biopha.2024.116608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 04/12/2024] [Accepted: 04/17/2024] [Indexed: 05/06/2024] Open
Abstract
Recent advances in metagenomic testing opened a new window into the mammalian blood virome. Comprised of well-known viruses like human immunodeficiency virus, hepatitis C virus, and hepatitis B virus, the virome also includes many other eukaryotic viruses and phages whose medical significance, lifecycle, epidemiology, and impact on human health are less well known and thus regarded as commensals. This review synthesizes available information for the so-called commensal virome members that circulate in the blood of humans considering their restriction to and interaction with the human host, their natural history, and their impact on human health and physiology.
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Affiliation(s)
- Abraham J Kandathil
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David L Thomas
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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Anantharam R, Duchen D, Cox AL, Timp W, Thomas DL, Clipman SJ, Kandathil AJ. Long-Read Nanopore-Based Sequencing of Anelloviruses. Viruses 2024; 16:723. [PMID: 38793605 PMCID: PMC11125752 DOI: 10.3390/v16050723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 04/27/2024] [Accepted: 04/30/2024] [Indexed: 05/26/2024] Open
Abstract
Routinely used metagenomic next-generation sequencing (mNGS) techniques often fail to detect low-level viremia (<104 copies/mL) and appear biased towards viruses with linear genomes. These limitations hinder the capacity to comprehensively characterize viral infections, such as those attributed to the Anelloviridae family. These near ubiquitous non-pathogenic components of the human virome have circular single-stranded DNA genomes that vary in size from 2.0 to 3.9 kb and exhibit high genetic diversity. Hence, species identification using short reads can be challenging. Here, we introduce a rolling circle amplification (RCA)-based metagenomic sequencing protocol tailored for circular single-stranded DNA genomes, utilizing the long-read Oxford Nanopore platform. The approach was assessed by sequencing anelloviruses in plasma drawn from people who inject drugs (PWID) in two geographically distinct cohorts. We detail the methodological adjustments implemented to overcome difficulties inherent in sequencing circular genomes and describe a computational pipeline focused on anellovirus detection. We assessed our protocol across various sample dilutions and successfully differentiated anellovirus sequences in conditions simulating mixed infections. This method provides a robust framework for the comprehensive characterization of circular viruses within the human virome using the Oxford Nanopore.
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Affiliation(s)
- Raghavendran Anantharam
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (R.A.)
| | - Dylan Duchen
- Center for Biomedical Data Science, Yale University School of Medicine, New Haven, CT 06511, USA;
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Andrea L. Cox
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (R.A.)
| | - Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - David L. Thomas
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (R.A.)
| | - Steven J. Clipman
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (R.A.)
| | - Abraham J. Kandathil
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (R.A.)
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Thijssen M, Khamisipour G, Maleki M, Devos T, Li G, Van Ranst M, Matthijnssens J, Pourkarim MR. Characterization of the Human Blood Virome in Iranian Multiple Transfused Patients. Viruses 2023; 15:1425. [PMID: 37515113 PMCID: PMC10386462 DOI: 10.3390/v15071425] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/21/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
Blood transfusion safety is an essential element of public health. Current blood screening strategies rely on targeted techniques that could miss unknown or unexpected pathogens. Recent studies have demonstrated the presence of a viral community (virobiota/virome) in the blood of healthy individuals. Here, we characterized the blood virome in patients frequently exposed to blood transfusion by using Illumina metagenomic sequencing. The virome of these patients was compared to viruses present in healthy blood donors. A total number of 155 beta-thalassemia, 149 hemodialysis, and 100 healthy blood donors were pooled with five samples per pool. Members of the Anelloviridae and Flaviviridae family were most frequently observed. Interestingly, samples of healthy blood donors harbored traces of potentially pathogenic viruses, including adeno-, rota-, and Merkel cell polyomavirus. Viruses of the Anelloviridae family were most abundant in the blood of hemodialysis patients and displayed a higher anellovirus richness. Pegiviruses (Flaviviridae) were only observed in patient populations. An overall trend of higher eukaryotic read abundance in both patient groups was observed. This might be associated with increased exposure through blood transfusion. Overall, the findings in this study demonstrated the presence of various viruses in the blood of Iranian multiple-transfused patients and healthy blood donors.
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Affiliation(s)
- Marijn Thijssen
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium
| | - Gholamreza Khamisipour
- Department of Hematology, Faculty of Allied Medicine, Bushehr University of Medical Sciences, Bushehr 75146-33196, Iran
| | - Mohammad Maleki
- Blood Transfusion Research Centre, High Institute for Research and Education in Transfusion Medicine, Tehran 14665-1157, Iran
| | - Timothy Devos
- Laboratory of Molecular Immunology (Rega Institute), Department of Hematology, Department of Microbiology and Immunology, University Hospitals Leuven, KU Leuven, 3000 Leuven, Belgium
| | - Guangdi Li
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410083, China
| | - Marc Van Ranst
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium
| | - Jelle Matthijnssens
- Laboratory of Viral Metagenomics, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium
| | - Mahmoud Reza Pourkarim
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium
- Blood Transfusion Research Centre, High Institute for Research and Education in Transfusion Medicine, Tehran 14665-1157, Iran
- Health Policy Research Centre, Institute of Health, Shiraz University of Medical Sciences, Shiraz 71348-14336, Iran
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Thijssen M, Tacke F, Van Espen L, Cassiman D, Naser Aldine M, Nevens F, Van Ranst M, Matthijnssens J, Pourkarim MR. Plasma virome dynamics in chronic hepatitis B virus infected patients. Front Microbiol 2023; 14:1172574. [PMID: 37228370 PMCID: PMC10203228 DOI: 10.3389/fmicb.2023.1172574] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/19/2023] [Indexed: 05/27/2023] Open
Abstract
The virome remains an understudied domain of the human microbiome. The role of commensal viruses on the outcome of infections with known pathogens is not well characterized. In this study we aimed to characterize the longitudinal plasma virome dynamics in chronic hepatitis B virus (HBV) infected patients. Eighty-five longitudinal plasma samples were collected from 12 chronic HBV infected individuals that were classified in the four stages of HBV infection. The virome was characterized with an optimized viral extraction protocol and deep-sequenced on a NextSeq 2500 platform. The plasma virome was primarily composed of members of the Anello- Flavi-, and Hepadnaviridae (HBV) families. The virome structure and dynamics did not correlate with the different stages of chronic HBV infection nor with the administration of antiviral therapy. We observed a higher intrapersonal similarity of viral contigs. Genomic analysis of viruses observed in multiple timepoint demonstrated the presence of a dynamic community. This study comprehensively assessed the blood virome structure in chronic HBV infected individuals and provided insights in the longitudinal development of this viral community.
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Affiliation(s)
- Marijn Thijssen
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Frank Tacke
- Department of Hepatology and Gastroenterology, Campus Virchow-Klinikum and Campus Charité Mitte, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Lore Van Espen
- Laboratory of Viral Metagenomics, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - David Cassiman
- Department of Gastroenterology and Hepatology, University Hospital Leuven, Leuven, Belgium
| | - Mahmoud Naser Aldine
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Frederik Nevens
- Department of Gastroenterology and Hepatology, University Hospital Leuven, Leuven, Belgium
| | - Marc Van Ranst
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Jelle Matthijnssens
- Laboratory of Viral Metagenomics, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Mahmoud Reza Pourkarim
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
- Health Policy Research Centre, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
- Blood Transfusion Research Centre, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
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Feng B, Liu B, Cheng M, Dong J, Hu Y, Jin Q, Yang F. An atlas of the blood virome in healthy individuals. Virus Res 2023; 323:199004. [PMID: 36402209 PMCID: PMC10194198 DOI: 10.1016/j.virusres.2022.199004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/14/2022] [Accepted: 11/15/2022] [Indexed: 11/18/2022]
Abstract
Emerging evidence indicates that gut virome plays a role in human health and disease, however, much less is known about the viral communities in blood. Here we conducted a direct metatranscriptomic sequencing of virus-like-particles in blood from 1200 healthy individuals, without prior amplification to avoid potential amplification bias and with a strictly bioinformatic and manual check for candidate viral reads to reduce false-positive matches. We identified 55 different viruses from 36 viral families, including 24 human DNA, RNA and retroviruses in 70% of the studied pools. The study showed that anelloviruses are widely distributed and dominate the blood virome in healthy individuals. Human herpesviruses and pegivirus-1 are commonly prevalent in asymptomatic humans. We identified the prevalence of RNA viruses often causing acute infection, like HEV, HPIV, RSV and HCoV-HKU1, revealing of a transmissible risk of asymptomatic infection. Several viruses possible related to transfusion safety were identified, including human Merkel cell polyomavirus, papillomavirus, parvovirus B19 and herpesvirus 8 in addition to HBV. In addition, phages in Caudovirales and Microviridae, were commonly found in pools of samples with a very low abundance; a few sequences for invertebrate, plant and giant viruses were found in some of individuals; however, the remaining 31 viruses mostly reflect extensive contamination from commercial reagents and the work environments. In conclusion, this study is the first comprehensive investigation of blood virome in healthy individuals by metatranscriptomic sequencing of VLP in China. Further investigation of potential false positives representing a major challenge for the identification of novel viruses in mNGS, will offer a systemic idea and means to reveal true viral infections of human.
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Affiliation(s)
- Bo Feng
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, CAMS&PUMC, Beijing 100730, PR China
| | - Bo Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, CAMS&PUMC, Beijing 100730, PR China
| | - Min Cheng
- China Institute of Veterinary Drug Control, Beijing 100081, PR China
| | - Jie Dong
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, CAMS&PUMC, Beijing 100730, PR China
| | - Yongfeng Hu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, CAMS&PUMC, Beijing 100730, PR China.
| | - Qi Jin
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, CAMS&PUMC, Beijing 100730, PR China.
| | - Fan Yang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, CAMS&PUMC, Beijing 100730, PR China.
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Kandathil AJ, Benner SE, Bloch EM, Shrestha R, Ajayi O, Zhu X, Caturegli PP, Shoham S, Sullivan D, Gebo K, Quinn TC, Casadevall A, Hanley D, Pekosz A, Redd AD, Balagopal A, Tobian AAR. Absence of pathogenic viruses in COVID-19 convalescent plasma. Transfusion 2023; 63:23-29. [PMID: 36268708 PMCID: PMC9840666 DOI: 10.1111/trf.17168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/03/2022] [Accepted: 10/10/2022] [Indexed: 01/27/2023]
Abstract
BACKGROUND It is important to maintain the safety of blood products by avoiding the transfusion of units with known and novel viral pathogens. It is unknown whether COVID-19 convalescent plasma (CCP) may contain pathogenic viruses (either newly acquired or reactivated) that are not routinely screened for by blood centers. METHODS The DNA virome was characterized in potential CCP donors (n = 30) using viral genome specific PCR primers to identify DNA plasma virome members of the Herpesviridae [Epstein Barr Virus (EBV), cytomegalovirus (CMV), human herpesvirus 6A/B, human herpesvirus 7] and Anelloviridae [Torque teno viruses (TTV), Torque teno mini viruses (TTMV), and Torque teno midi viruses (TTMDV)] families. In addition, the RNA plasma virome was characterized using unbiased metagenomic sequencing. Sequencing was done on a HiSeq2500 using high output mode with a read length of 2X100 bp. The sequencing reads were taxonomically classified using Kraken2. CMV and EBV seroprevalence were evaluated using a chemiluminescent immunoassay. RESULTS TTV and TTMDV were detected in 12 (40%) and 4 (13%) of the 30 study participants, respectively; TTMDV was always associated with infection with TTV. We did not observe TTMV DNAemia. Despite CMV and EBV seroprevalences of 33.3% and 93.3%, respectively, we did not detect Herpesviridae DNA among the study participants. Metagenomic sequencing did not reveal any human RNA viruses in CCP, including no evidence of circulating SARS-CoV-2. DISCUSSION There was no evidence of pathogenic viruses, whether newly acquired or reactivated, in CCP despite the presence of non-pathogenic Anelloviridae. These results confirm the growing safety data supporting CCP.
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Affiliation(s)
- Abraham J Kandathil
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Sarah E Benner
- Department of Pathology, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Evan M Bloch
- Department of Pathology, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Ruchee Shrestha
- Department of Pathology, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Olivia Ajayi
- Department of Pathology, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Xianming Zhu
- Department of Pathology, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Patrizio P Caturegli
- Department of Pathology, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Shmuel Shoham
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - David Sullivan
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA.,Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Kelly Gebo
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Thomas C Quinn
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA.,Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Daniel Hanley
- Department of Neurology, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Andrew Pekosz
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA.,Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Andrew D Redd
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA.,Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Ashwin Balagopal
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Aaron A R Tobian
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA.,Department of Pathology, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
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Altered vaginal eukaryotic virome is associated with different cervical disease status. Virol Sin 2022; 38:184-197. [PMID: 36565811 PMCID: PMC10176265 DOI: 10.1016/j.virs.2022.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
Viruses are important components of the human body. Growing evidence suggests that they are engaged in the physiology and disease status of the host. Even though the vaginal microbiome is involved in human papillomavirus (HPV) infection and cervical cancer (CC) progression, little is known about the role of the vaginal virome. In this pilot exploratory study, using unbiased viral metagenomics, we aim to investigate the vaginal eukaryotic virome in women with different levels of cervical lesions, and examine their associations with different cervical disease status. An altered eukaryotic virome was observed in women with different levels of lesions and Lactobacillus profiles. Anelloviruses and papillomaviruses are the most commonly detected eukaryotic viruses of the vaginal virome. Higher abundance and richness of anelloviruses and papillomaviruses were associated with low-grade squamous intraepithelial lesion (LSIL) and CC. Besides, higher anellovirus abundance was also associated with lactobacillus-depleted microbiome profiles and bacterial community state (CST) type IV. Furthermore, increased correlations between Anelloviridae and Papillomaviridae occurred in the women with increased cervical disease severity level from LSIL to CC. These data suggest underlying interactions between different microbes as well as the host physiology. Higher abundance and diversity of both anelloviruses and papillomaviruses shared by LSIL and CC suggest that anellovirus may be used as a potential adjunct biomarker to predict the risk of HPV persistent infection and/or CC. Future studies need to focus on the clinical relevance of anellovirus abundance with cervical disease status, and the evaluation of their potential as a new adjunct biomarker for the prediction and prognoses of CC.
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Garand M, Huang SSY, Goessling LS, Santillan DA, Santillan MK, Brar A, Wylie TN, Wylie KM, Eghtesady P. A Case of Persistent Human Pegivirus Infection in Two Separate Pregnancies of a Woman. Microorganisms 2022; 10:1925. [PMID: 36296201 PMCID: PMC9610878 DOI: 10.3390/microorganisms10101925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/15/2022] [Accepted: 09/23/2022] [Indexed: 05/26/2024] Open
Abstract
Human pegivirus (HPgV) is best known for persistent, presumably non-pathogenic, infection and a propensity to co-infect with human immunodeficiency virus or hepatitis C virus. However, unique attributes, such as the increased risk of malignancy or immune modulation, have been recently recognized for HPgV. We have identified a unique case of a woman with high levels HPgV infection in two pregnancies, which occurred 4 years apart and without evidence of human immunodeficiency virus or hepatitis C virus infection. The second pregnancy was complicated by congenital heart disease. A high level of HPgV infection was detected in the maternal blood from different trimesters by RT-PCR and identified as HPgV type 1 genotype 2 in both pregnancies. In the second pregnancy, the decidua and intervillous tissue of the placenta were positive for HPgV by PCR but not the chorion or cord blood (from both pregnancies), suggesting no vertical transmission despite high levels of viremia. The HPgV genome sequence was remarkably conserved over the 4 years. Using VirScan, sera antibodies for HPgV were detected in the first trimester of both pregnancies. We observed the same anti-HPgV antibodies against the non-structural NS5 protein in both pregnancies, suggesting a similar non-E2 protein humoral immune response over time. To the best of our knowledge, this is the first report of persistent HPgV infection involving placental tissues with no clear indication of vertical transmission. Our results reveal a more elaborate viral-host interaction than previously reported, expand our knowledge about tropism, and opens avenues for exploring the replication sites of this virus.
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Affiliation(s)
- Mathieu Garand
- Division of Pediatric Cardiothoracic Surgery, Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Susie S. Y. Huang
- Division of Pediatric Cardiothoracic Surgery, Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Lisa S. Goessling
- Division of Pediatric Cardiothoracic Surgery, Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Donna A. Santillan
- Department of Obstetrics and Gynecology, University of Iowa, Iowa City, IA 52242, USA
| | - Mark K. Santillan
- Department of Obstetrics and Gynecology, University of Iowa, Iowa City, IA 52242, USA
| | - Anoop Brar
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Todd N. Wylie
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kristine M. Wylie
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Pirooz Eghtesady
- Division of Pediatric Cardiothoracic Surgery, Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
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Plasma Virome Reveals Blooms and Transmission of Anellovirus in Intravenous Drug Users with HIV-1, HCV, and/or HBV Infections. Microbiol Spectr 2022; 10:e0144722. [PMID: 35758682 PMCID: PMC9431549 DOI: 10.1128/spectrum.01447-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Intravenous drug users (IDUs) are a high-risk group for HIV-1, hepatitis C virus (HCV), and hepatitis B virus (HBV) infections, which are the leading causes of death in IDUs. However, the plasma virome of IDUs and how it is influenced by above viral infections remain unclear. Using viral metagenomics, we determined the plasma virome of IDUs and its association with HIV-1, HCV, and/or HBV infections. Compared with healthy individuals, IDUs especially those with major viral infections had higher viral abundance and diversity. Anelloviridae dominated plasma virome. Coinfections of multiple anelloviruses were common, and anelloviruses from the same genus tended to coexist together. In this study, 4,487 anellovirus ORF1 sequences were identified, including 1,620 (36.1%) with less than 69% identity to any known sequences, which tripled the current number. Compared with healthy controls (HC), more anellovirus sequences were observed in neg-IDUs, and HIV-1, HCV, and/or HBV infections further expanded the sequence number in IDUs, which was characterized by the emergence of novel divergent taxons and blooms of resident anelloviruses. Pegivirus was mainly identified in infected IDUs. Five main pegivirus transmission clusters (TCs) were identified by phylogenetic analysis, suggesting a transmission link. Similar anellovirus profiles were observed in IDUs within the same TC, suggesting transmission of anellome among IDUs. Our data suggested that IDUs suffered higher plasma viral burden especially anelloviruses, which was associated with HIV-1, HCV, and/or HBV infections. Blooms in abundance and unprecedented diversity of anellovirus highlighted active evolution and replication of this virus in blood circulation, and an uncharacterized role it may engage with the host. IMPORTANCE Virome is associated with immune status and determines or influences disease progression through both pathogenic and resident viruses. Increased viral burden in IDUs especially those with major viral infections indicated the suboptimal immune status and high infection risks of these population. Blooms in abundance and unprecedented diversity of anellovirus highlighted its active evolution and replication in the blood circulation, and sensitive response to other viral infections. In addition, transmission cluster analysis revealed the transmission link of pegivirus among IDUs, and the individuals with transmission links shared similar anellome profiles. In-depth monitoring of the plasma virome in high-risk populations is not only needed for surveillance for emerging viruses and transmission networks of major and neglected bloodborne viruses, but also important for a better understanding of commensal viruses and their role it may engage with immune system.
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