1
|
McClure CP, Kean K, Reid K, Mayne R, Fu MX, Rajendra P, Gates S, Breuer J, Harvala H, Golubchik T, Tarr AW, Irving WL, Makris M, Simmonds P. Reconstruction of the historic time course of blood-borne virus contamination of clotting factor concentrates, 1974-1992. J Med Virol 2024; 96:e29774. [PMID: 38953434 DOI: 10.1002/jmv.29774] [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: 04/04/2024] [Revised: 05/29/2024] [Accepted: 06/21/2024] [Indexed: 07/04/2024]
Abstract
Factor VIII and IX clotting factor concentrates manufactured from pooled plasma have been identified as potent sources of virus infection in persons with hemophilia (PWHs) in the 1970s and 1980s. To investigate the range and diversity of viruses over this period, we analysed 24 clotting factor concentrates for several blood-borne viruses. Nucleic acid was extracted from 14 commercially produced clotting factors and 10 from nonremunerated donors, preserved in lyophilized form (expiry dates: 1974-1992). Clotting factors were tested by commercial and in-house quantitative PCRs for blood-borne viruses hepatitis A, B, C and E viruses (HAV, HBV, HCV, HEV), HIV- types 1/2, parvoviruses B19V and PARV4, and human pegiviruses types 1 and 2 (HPgV-1,-2). HCV and HPgV-1 were the most frequently detected viruses (both 14/24 tested) primarily in commercial clotting factors, with frequently extremely high viral loads in the late 1970s-1985 and a diverse range of HCV genotypes. Detection frequencies sharply declined following introduction of virus inactivation. HIV-1, HBV, and HAV were less frequently detected (3/24, 1/24, and 1/24 respectively); none were positive for HEV. Contrastingly, B19V and PARV4 were detected throughout the study period, even after introduction of dry heat treatment, consistent with ongoing documented transmission to PWHs into the early 1990s. While hemophilia treatment is now largely based on recombinant factor VIII/IX in the UK and elsewhere, the comprehensive screen of historical plasma-derived clotting factors reveals extensive exposure of PWHs to blood-borne viruses throughout 1970s-early 1990s, and the epidemiological and manufacturing parameters that influenced clotting factor contamination.
Collapse
Affiliation(s)
- C Patrick McClure
- Wolfson Centre for Global Virus Research, University of Nottingham, Nottingham, UK
- National Institute for Health Research Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Kai Kean
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Kaitlin Reid
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Richard Mayne
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Michael X Fu
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Piya Rajendra
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Shannah Gates
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Judy Breuer
- Division of Infection and Immunity, University College London, London, UK
| | - Heli Harvala
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Microbiology Services, National Health Service (NHS) Blood and Transplant, London, UK
| | - Tanya Golubchik
- Sydney Infectious Diseases Institute, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
- Big Data Institute, Nuffield Department of Medicine, Universtiy of Oxford, Oxford, UK
| | - Alexander W Tarr
- Wolfson Centre for Global Virus Research, University of Nottingham, Nottingham, UK
- National Institute for Health Research Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - William L Irving
- Wolfson Centre for Global Virus Research, University of Nottingham, Nottingham, UK
- National Institute for Health Research Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Michael Makris
- School of Medicine and Population Health, University of Sheffield, Sheffield, UK
| | - Peter Simmonds
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
Munson E. Biographical Feature: Charles Y. Chiu, M.D., Ph.D. J Clin Microbiol 2024; 62:e0140523. [PMID: 38619264 PMCID: PMC11077958 DOI: 10.1128/jcm.01405-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024] Open
Affiliation(s)
- Erik Munson
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| |
Collapse
|
4
|
Orf GS, Ahouidi AD, Mata M, Diedhiou C, Mboup A, Padane A, Manga NM, Dela-del Lawson AT, Averhoff F, Berg MG, Cloherty GA, Mboup S. Next-generation sequencing survey of acute febrile illness in Senegal (2020-2022). Front Microbiol 2024; 15:1362714. [PMID: 38655084 PMCID: PMC11037400 DOI: 10.3389/fmicb.2024.1362714] [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: 12/29/2023] [Accepted: 03/13/2024] [Indexed: 04/26/2024] Open
Abstract
Introduction Acute febrile illnesses (AFI) in developing tropical and sub-tropical nations are challenging to diagnose due to the numerous causes and non-specific symptoms. The proliferation of rapid diagnostic testing and successful control campaigns against malaria have revealed that non-Plasmodium pathogens still contribute significantly to AFI burden. Thus, a more complete understanding of local trends and potential causes is important for selecting the correct treatment course, which in turn will reduce morbidity and mortality. Next-generation sequencing (NGS) in a laboratory setting can be used to identify known and novel pathogens in individuals with AFI. Methods In this study, plasma was collected from 228 febrile patients tested negative for malaria at clinics across Senegal from 2020-2022. Total nucleic acids were extracted and converted to metagenomic NGS libraries. To identify viral pathogens, especially those present at low concentration, an aliquot of each library was processed with a viral enrichment panel and sequenced. Corresponding metagenomic libraries were also sequenced to identify non-viral pathogens. Results and Discussion Sequencing reads for pathogens with a possible link to febrile illness were identified in 51/228 specimens, including (but not limited to): Borrelia crocidurae (N = 7), West Nile virus (N = 3), Rickettsia felis (N = 2), Bartonella quintana (N = 1), human herpesvirus 8 (N = 1), and Saffold virus (N = 1). Reads corresponding to Plasmodium falciparum were detected in 19 specimens, though their presence in the cohort was likely due to user error of rapid diagnostic testing or incorrect specimen segregation at the clinics. Mosquito-borne pathogens were typically detected just after the conclusion of the rainy season, while tick-borne pathogens were mostly detected before the rainy season. The three West Nile virus strains were phylogenetically characterized and shown to be related to both European and North American clades. Surveys such as this will increase the understanding of the potential causes of non-malarial AFI, which may help inform diagnostic and treatment options for clinicians who provide care to patients in Senegal.
Collapse
Affiliation(s)
- Gregory S. Orf
- Core Diagnostics, Abbott Laboratories, Abbott Park, IL, United States
- Abbott Pandemic Defense Coalition, Abbott Park, IL, United States
| | - Ambroise D. Ahouidi
- Abbott Pandemic Defense Coalition, Abbott Park, IL, United States
- Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation, Dakar, Senegal
| | - Maximillian Mata
- Core Diagnostics, Abbott Laboratories, Abbott Park, IL, United States
- Abbott Pandemic Defense Coalition, Abbott Park, IL, United States
| | - Cyrille Diedhiou
- Abbott Pandemic Defense Coalition, Abbott Park, IL, United States
- Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation, Dakar, Senegal
| | - Aminata Mboup
- Abbott Pandemic Defense Coalition, Abbott Park, IL, United States
- Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation, Dakar, Senegal
| | - Abdou Padane
- Abbott Pandemic Defense Coalition, Abbott Park, IL, United States
- Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation, Dakar, Senegal
| | - Noel Magloire Manga
- Unit of Infectious and Tropical Diseases, Université Assane Seck, Hôpital de la Paix, Ziguinchor, Senegal
| | | | - Francisco Averhoff
- Core Diagnostics, Abbott Laboratories, Abbott Park, IL, United States
- Abbott Pandemic Defense Coalition, Abbott Park, IL, United States
| | - Michael G. Berg
- Core Diagnostics, Abbott Laboratories, Abbott Park, IL, United States
- Abbott Pandemic Defense Coalition, Abbott Park, IL, United States
| | - Gavin A. Cloherty
- Core Diagnostics, Abbott Laboratories, Abbott Park, IL, United States
- Abbott Pandemic Defense Coalition, Abbott Park, IL, United States
| | - Souleymane Mboup
- Abbott Pandemic Defense Coalition, Abbott Park, IL, United States
- Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation, Dakar, Senegal
| |
Collapse
|
5
|
Zanella MC, Vu DL, Hosszu-Fellous K, Neofytos D, Van Delden C, Turin L, Poncet A, Simonetta F, Masouridi-Levrat S, Chalandon Y, Cordey S, Kaiser L. Longitudinal Detection of Twenty DNA and RNA Viruses in Allogeneic Hematopoietic Stem Cell Transplant Recipients Plasma. Viruses 2023; 15:v15040928. [PMID: 37112908 PMCID: PMC10142697 DOI: 10.3390/v15040928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 03/29/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
Metagenomics revealed novel and routinely overlooked viruses, representing sources of unrecognized infections after allogeneic hematopoietic stem cell transplantation (allo-HSCT). We aim to describe DNA and RNA virus prevalence and kinetics in allo-HSCT recipients' plasma for one year post HSCT. We included 109 adult patients with first allo-HSCT from 1 March 2017 to 31 January 2019 in this observational cohort study. Seventeen DNA and three RNA viral species were screened with qualitative and/or quantitative r(RT)-PCR assays using plasma samples collected at 0, 1, 3, 6, and 12 months post HSCT. TTV infected 97% of patients, followed by HPgV-1 (prevalence: 26-36%). TTV (median 3.29 × 105 copies/mL) and HPgV-1 (median 1.18 × 106 copies/mL) viral loads peaked at month 3. At least one Polyomaviridae virus (BKPyV, JCPyV, MCPyV, HPyV6/7) was detected in >10% of patients. HPyV6 and HPyV7 prevalence reached 27% and 12% at month 3; CMV prevalence reached 27%. HSV, VZV, EBV, HHV-7, HAdV and B19V prevalence remained <5%. HPyV9, TSPyV, HBoV, EV and HPg-V2 were never detected. At month 3, 72% of patients had co-infections. TTV and HPgV-1 infections were highly prevalent. BKPyV, MCPyV and HPyV6/7 were frequently detected relative to classical culprits. Further investigation is needed into associations between these viral infections and immune reconstitution or clinical outcomes.
Collapse
Affiliation(s)
- Marie-Céline Zanella
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1211 Geneva, Switzerland
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
| | - Diem-Lan Vu
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1211 Geneva, Switzerland
| | - Krisztina Hosszu-Fellous
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Geneva Centre for Emerging Viral Diseases, 1211 Geneva, Switzerland
| | - Dionysios Neofytos
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
| | - Chistian Van Delden
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
| | - Lara Turin
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1211 Geneva, Switzerland
| | - Antoine Poncet
- Center for Clinical Research, Department of Health and Community Medicine, University of Geneva, 1206 Geneva, Switzerland
- Division of Clinical Epidemiology, Department of Health and Community Medicine, University Hospital of Geneva, 1211 Geneva, Switzerland
| | - Federico Simonetta
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
- Division of Hematology, Department of Oncology, Geneva University Hospitals, 1211 Geneva, Switzerland
| | - Stavroula Masouridi-Levrat
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
- Division of Hematology, Department of Oncology, Geneva University Hospitals, 1211 Geneva, Switzerland
| | - Yves Chalandon
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
- Division of Hematology, Department of Oncology, Geneva University Hospitals, 1211 Geneva, Switzerland
| | - Samuel Cordey
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1211 Geneva, Switzerland
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
| | - Laurent Kaiser
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1211 Geneva, Switzerland
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
- Geneva Centre for Emerging Viral Diseases, 1211 Geneva, Switzerland
| |
Collapse
|
6
|
Abstract
The virus-encoded RNA-dependent RNA polymerase (RdRp) is responsible for viral replication, and its fidelity is closely related to viral diversity, pathogenesis, virulence, and fitness. Hepatitis C virus (HCV) and the second human pegivirus (HPgV-2) belong to the family Flaviviridae and share some features, including similar viral genome structure. Unlike HCV, HPgV-2 preserves a highly conserved genome sequence and low intrahost variation. However, the underlying mechanism remains to be elucidated. In this study, we evaluated the fidelity of HPgV-2 and HCV RdRp in an in vitro RNA polymerase reaction system. The results showed higher fidelity of HPgV-2 RdRp than HCV NS5B with respect to the misincorporation rate due to their difference in recognizing nucleoside triphosphate (NTP) substrates. Furthermore, HPgV-2 RdRp showed lower sensitivity than HCV to sofosbuvir, a nucleotide inhibitor against HCV RdRp, which explained the insusceptibility of HPgV-2 to direct-acting antiviral (DAA) therapy against HCV infection. Our results indicate that HPgV-2 could be an excellent model for studying the mechanisms involved in viral polymerase fidelity as well as RNA virus diversity and evolution. IMPORTANCE RNA viruses represent the most important pathogens for humans and animals and exhibit rapid evolution and high adaptive capacity, which is due to the high mutation rates for using the error-prone RNA-dependent RNA polymerase (RdRp) during replication. The fidelity of RdRp is closely associated with viral diversity, fitness, and pathogenesis. Previous studies have shown that the second human pegivirus (HPgV-2) exhibits a highly conserved genome sequence and low intrahost variation, which might be due to the fidelity of HPgV-2 RdRp. In this work, we used a series of in vitro RNA polymerase assays to evaluate the in vitro fidelity of HPgV-2 RdRp and compared it with that of HCV RdRp. The results indicated that HPgV-2 RdRp preserves significantly higher fidelity than HCV RdRp, which might contribute to the conservation of the HPgV-2 genome. The unique feature of HPgV-2 RdRp fidelity provides a new model for investigation of viral RdRp fidelity.
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
The Second Human Pegivirus, a Non-Pathogenic RNA Virus with Low Prevalence and Minimal Genetic Diversity. Viruses 2022; 14:v14091844. [PMID: 36146649 PMCID: PMC9503178 DOI: 10.3390/v14091844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/14/2022] [Accepted: 08/18/2022] [Indexed: 02/02/2023] Open
Abstract
The second human pegivirus (HPgV-2) is a virus discovered in the plasma of a hepatitis C virus (HCV)-infected patient in 2015 belonging to the pegiviruses of the family Flaviviridae. HPgV-2 has been proved to be epidemiologically associated with and structurally similar to HCV but unrelated to HCV disease and non-pathogenic, but its natural history and tissue tropism remain unclear. HPgV-2 is a unique RNA virus sharing the features of HCV and the first human pegivirus (HPgV-1 or GBV-C). Moreover, distinct from most RNA viruses such as HCV, HPgV-1 and human immunodeficiency virus (HIV), HPgV-2 exhibits much lower genomic diversity, with a high global sequence identity ranging from 93.5 to 97.5% and significantly lower intra-host variation than HCV. The mechanisms underlying the conservation of the HPgV-2 genome are not clear but may include efficient innate immune responses, low immune selection pressure and, possibly, the unique features of the viral RNA-dependent RNA polymerase (RdRP). In this review, we summarize the prevalence, pathogenicity and genetic diversity of HPgV-2 and discuss the possible reasons for the uniformity of its genome sequence, which should elucidate the implications of RNA virus fidelity for attenuated viral vaccines.
Collapse
|
9
|
Stapleton JT. Human Pegivirus Type 1: A Common Human Virus That Is Beneficial in Immune-Mediated Disease? Front Immunol 2022; 13:887760. [PMID: 35707535 PMCID: PMC9190258 DOI: 10.3389/fimmu.2022.887760] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/03/2022] [Indexed: 12/25/2022] Open
Abstract
Two groups identified a novel human flavivirus in the mid-1990s. One group named the virus hepatitis G virus (HGV) and the other named it GB Virus type C (GBV-C). Sequence analyses found these two isolates to be the same virus, and subsequent studies found that the virus does not cause hepatitis despite sharing genome organization with hepatitis C virus. Although HGV/GBV-C infection is common and may cause persistent infection in humans, the virus does not appear to directly cause any other known disease state. Thus, the virus was renamed “human pegivirus 1” (HPgV-1) for “persistent G” virus. HPgV-1 is found primarily in lymphocytes and not hepatocytes, and several studies found HPgV-1 infection associated with prolonged survival in people living with HIV. Co-infection of human lymphocytes with HPgV-1 and HIV inhibits HIV replication. Although three viral proteins directly inhibit HIV replication in vitro, the major effects of HPgV-1 leading to reduced HIV-related mortality appear to result from a global reduction in immune activation. HPgV-1 specifically interferes with T cell receptor signaling (TCR) by reducing proximal activation of the lymphocyte specific Src kinase LCK. Although TCR signaling is reduced, T cell activation is not abolished and with sufficient stimulus, T cell functions are enabled. Consequently, HPgV-1 is not associated with immune suppression. The HPgV-1 immunomodulatory effects are associated with beneficial outcomes in other diseases including Ebola virus infection and possibly graft-versus-host-disease following stem cell transplantation. Better understanding of HPgV-1 immune escape and mechanisms of inflammation may identify novel therapies for immune-based diseases.
Collapse
Affiliation(s)
- Jack T. Stapleton
- Medicine Service, Iowa City Veterans Administration Healthcare, Iowa City, IA, United States
- Departments of Internal Medicine, Microbiology & Immunology, University of Iowa, Iowa City, IA, United States
- *Correspondence: Jack T. Stapleton,
| |
Collapse
|
10
|
Samadi M, Salimi V, Haghshenas MR, Miri SM, Mohebbi SR, Ghaemi A. Clinical and molecular aspects of human pegiviruses in the interaction host and infectious agent. Virol J 2022; 19:41. [PMID: 35264187 PMCID: PMC8905790 DOI: 10.1186/s12985-022-01769-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 01/16/2022] [Indexed: 12/11/2022] Open
Abstract
Background Human pegivirus 1 (HPgV-1) is a Positive-sense single-stranded RNA (+ ssRNA) virus, discovered in 1995 as a Flaviviridae member, and the closest human virus linked to HCV. In comparison to HCV, HPgV-1 seems to be lymphotropic and connected to the viral group that infects T and B lymphocytes. HPgV-1 infection is not persuasively correlated to any known human disease; nevertheless, multiple studies have reported a connection between chronic HPgV-1 infection and improved survival in HPgV-1/HIV co-infected patients with a delayed and favorable impact on HIV infection development. While the process has not been thoroughly clarified, different mechanisms for these observations have been proposed. HPgV-1 is categorized into seven genotypes and various subtypes. Infection with HPgV-1 is relatively common globally. It can be transferred parenterally, sexually, and through vertical ways, and thereby its co-infection with HIV and HCV is common. In most cases, the clearance of HPgV-1 from the body can be achieved by developing E2 antibodies after infection. Main body In this review, we thoroughly discuss the current knowledge and recent advances in understanding distinct epidemiological, molecular, and clinical aspects of HPgV-1. Conclusion Due to the unique characteristics of the HPgV-1, so advanced research on HPgV-1, particularly in light of HIV co-infection and other diseases, should be conducted to explore the essential mechanisms of HIV clearance and other viruses and thereby suggest novel strategies for viral therapy in the future.
Collapse
Affiliation(s)
- Mehdi Samadi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.,Department of Microbiology, Molecular and Cell-Biology Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Vahid Salimi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Haghshenas
- Department of Microbiology, Molecular and Cell-Biology Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Seyed Mohammad Miri
- Department of Virology, Pasteur Institute of Iran, P.O. Box: 1316943551, Tehran, Iran
| | - Seyed Reza Mohebbi
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amir Ghaemi
- Department of Virology, Pasteur Institute of Iran, P.O. Box: 1316943551, Tehran, Iran.
| |
Collapse
|
11
|
Yu Y, Wan Z, Wang JH, Yang X, Zhang C. Review of human pegivirus: Prevalence, transmission, pathogenesis, and clinical implication. Virulence 2022; 13:324-341. [PMID: 35132924 PMCID: PMC8837232 DOI: 10.1080/21505594.2022.2029328] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Human pegivirus (HPgV-1), previously known as GB virus C (GBV-C) or hepatitis G virus (HGV), is a single-stranded positive RNA virus belonging to the genus Pegivirus of the Flaviviridae family. It is transmitted by percutaneous injuries (PIs), contaminated blood and/or blood products, sexual contact, and vertical mother-to-child transmission. It is widely prevalent in general population, especially in high-risk groups. HPgV-1 viremia is typically cleared within the first 1–2 years of infection in most healthy individuals, but may persist for longer periods of time in immunocompromised individuals and/or those co-infected by other viruses. A large body of evidences indicate that HPgV-1 persistent infection has a beneficial clinical effect on many infectious diseases, such as acquired immunodeficiency syndrome (AIDS) and hepatitis C. The beneficial effects seem to be related to a significant reduction of immune activation, and/or the inhabitation of co-infected viruses (e.g. HIV-1). HPgV-1 has a broad cellular tropism for lymphoid and myeloid cells, and preferentially replicates in bone marrow and spleen without cytopathic effect, implying a therapeutic potential. The paper aims to summarize the natural history, prevalence and distribution characteristics, and pathogenesis of HPgV-1, and discuss its association with other human viral diseases, and potential use in therapy as a biovaccine or viral vector.
Collapse
Affiliation(s)
- Yaqi Yu
- College of Life Sciences, Henan Normal University, Xinxiang, China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Zhenzhou Wan
- Medical Laboratory of Taizhou Fourth People's Hospital, Taizhou, China
| | - Jian-Hua Wang
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Xianguang Yang
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Chiyu Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| |
Collapse
|
12
|
Averhoff F, Berg M, Rodgers M, Osmanov S, Luo X, Anderson M, Meyer T, Landay A, Gamkrelidze A, Kallas EG, Ciuoderis K, Hernandez JP, Henry JH, Osorio J, Lindo J, Deshommes J, Anzinger J, Manasa J, Alkashvili M, Souleyman M, Kaleebu P, Correa-Oliveira R, Solomon S, de Olivera T, Suputtamongkol Y, Cloherty G. The Abbott Pandemic Defense Coalition: a unique multisector approach adds to global pandemic preparedness efforts. Int J Infect Dis 2022; 117:356-360. [PMID: 35134559 PMCID: PMC8817457 DOI: 10.1016/j.ijid.2022.02.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/31/2022] [Accepted: 02/01/2022] [Indexed: 12/15/2022] Open
Abstract
Detection and epidemiologic characterization of infectious disease outbreaks are key for early identification and response to potential pandemic threats. The rapid global spread of severe SARS-CoV-2 in 2020 highlighted the critical role of diagnostics in understanding the epidemiology of the virus early in the pandemic. As a natural extension of Abbott's work in diagnostics, virus discovery, and virus surveillance, the Abbott Pandemic Defense Coalition (APDC) was launched in early 2021. The APDC is a global multisector scientific and public health partnership whose primary objective is the early detection and mitigation of infectious disease threats of pandemic potential. As of January 2022, the APDC network has partners on 5 continents including academic institutions, governmental, and nongovernmental organizations. A novel element of the APDC is the capacity for early development and rapid deployment of scalable, quality diagnostics targeting newly identified pathogens of pandemic potential.
Collapse
Affiliation(s)
| | | | | | | | - Xinxin Luo
- Abbott Diagnostics, Abbott Park, IL, USA
| | | | - Todd Meyer
- Abbott Diagnostics, Abbott Park, IL, USA
| | - Alan Landay
- Rush University Medical Center, Chicago, IL, USA
| | | | | | - Karl Ciuoderis
- Colombia Wisconsin One Health, University of Wisconsin & National University of Colombia, Medellin, Colombia
| | - Juan Pablo Hernandez
- Colombia Wisconsin One Health, University of Wisconsin & National University of Colombia, Medellin, Colombia
| | | | - Jorge Osorio
- Colombia Wisconsin One Health, University of Wisconsin & National University of Colombia, Medellin, Colombia
| | - John Lindo
- University of the West Indies, Kingston, Jamaica
| | | | | | | | | | - Mboup Souleyman
- Institute for Health Research, Epidemiologic Surveillance and Training (IRESSEF), Dakar, Senegal
| | | | | | - Sunil Solomon
- Johns Hopkins University School of Medicine, USA & YRG CARE, Chennai, India
| | - Tulio de Olivera
- Centre for Epidemic Response and Innovation, Stellenbosch University, Stellenbosch, South Africa
| | | | | |
Collapse
|
13
|
Mrzljak A, Simunov B, Balen I, Jurekovic Z, Vilibic-Cavlek T. Human pegivirus infection after transplant: Is there an impact? World J Transplant 2022; 12:1-7. [PMID: 35096551 PMCID: PMC8771596 DOI: 10.5500/wjt.v12.i1.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 10/25/2021] [Accepted: 01/06/2022] [Indexed: 02/06/2023] Open
Abstract
The microbiome's role in transplantation has received growing interest, but the role of virome remains understudied. Pegiviruses are single-stranded positive-sense RNA viruses, historically associated with liver disease, but their path-ogenicity is controversial. In the transplantation setting, pegivirus infection does not seem to have a negative impact on the outcomes of solid-organ and hematopoietic stem cell transplant recipients. However, the role of pegiviruses as proxies in immunosuppression monitoring brings novelty to the field of virome research in immunocompromised individuals. The possible immunomodulatory effect of pegivirus infections remains to be elucidated in further trials.
Collapse
Affiliation(s)
- Anna Mrzljak
- Department of Gastroenterology and Hepatology, University Hospital Center Zagreb, School of Medicine, University of Zagreb, Zagreb 10000, Croatia
| | - Bojana Simunov
- Department of Medicine, Merkur University Hospital, Zagreb 10000, Croatia
| | - Ivan Balen
- Department of Gastroenterology and Endocrinology, General Hospital “Dr. Josip Bencevic”, Slavonski Brod 35000, Croatia
| | - Zeljka Jurekovic
- Department of Medicine, Merkur University Hospital, Zagreb 10000, Croatia
| | - Tatjana Vilibic-Cavlek
- Department of Virology, Croatian Institute of Public Health, School of Medicine, University of Zagreb, Zagreb 10000, Croatia
| |
Collapse
|
14
|
Plasma virome and the risk of blood-borne infection in persons with substance use disorder. Nat Commun 2021; 12:6909. [PMID: 34824209 PMCID: PMC8617242 DOI: 10.1038/s41467-021-26980-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 10/25/2021] [Indexed: 11/29/2022] Open
Abstract
There is an urgent need for innovative methods to reduce transmission of bloodborne pathogens like HIV and HCV among people who inject drugs (PWID). We investigate if PWID who acquire non-pathogenic bloodborne viruses like anelloviruses and pegiviruses might be at greater risk of acquiring a bloodborne pathogen. PWID who later acquire HCV accumulate more non-pathogenic viruses in plasma than matched controls who do not acquire HCV infection. Additionally, phylogenetic analysis of those non-pathogenic virus sequences reveals drug use networks. Here we find first in Baltimore and confirm in San Francisco that the accumulation of non-pathogenic viruses in PWID is a harbinger for subsequent acquisition of pathogenic viruses, knowledge that may guide the prioritization of the public health resources to combat HIV and HCV. Spread of bloodborne infections, such as HCV and HIV, is a problem, particularly amongst people who inject drugs (PWID). Here, the authors describe and then confirm in observational PWID cohorts that those with more non-pathogenic viruses in plasma were more likely later to acquire HCV than PWID who had fewer of these non-pathogenic viruses.
Collapse
|
15
|
Liang Y, Hu F, Fan H, Li L, Wan Z, Wang H, Shui J, Zhou Y, Tong Y, Cai W, Tang S. Difference of Intrahost Dynamics of the Second Human Pegivirus and Hepatitis C Virus in HPgV-2/HCV-Coinfected Patients. Front Cell Infect Microbiol 2021; 11:728415. [PMID: 34466405 PMCID: PMC8403064 DOI: 10.3389/fcimb.2021.728415] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 07/26/2021] [Indexed: 01/02/2023] Open
Abstract
Background The second human pegivirus (HPgV-2) and hepatitis C virus (HCV) belong to the Flaviviridae family and share some common genome features. However, the two viruses exhibit significantly different genetic diversity. The comparison of intrahost dynamics of HPgV-2 and HCV that mainly reflect virus-host interactions is needed to elucidate their intrahost difference of genetic diversity and the possible mechanisms. Methods Intrahost single nucleotide variations (iSNVs) were identified by means of next-generation sequencing from both cross-sectional and longitudinal samples from HPgV-2- and HCV-coinfected patients. The levels of human cytokines were quantified in the patient before and after HCV elimination by the treatment of direct-acting antivirals (DAA). Results Unlike HCV, the viral sequences of HPgV-2 are highly conserved among HPgV-2-infected patients. However, iSNV analysis confirmed the intrahost variation or quasispecies of HPgV-2. Almost all iSNVs of HPgV-2 did not accumulate or transmit within host over time, which may explain the highly conserved HPgV-2 consensus sequence. Intrahost variation of HPgV-2 mainly causes nucleotide transition in particular at the 3rd codon position and synonymous substitutions, indicating purifying or negative selection posed by host immune system. Cytokine data further indicate that HPgV-2 infection alone may not efficiently stimulate innate immune responses since proinflammatory cytokine expression dramatically decreased with elimination of HCV. Conclusion This study provided new insights into the intrahost genomic variations and evolutionary dynamics of HPgV-2 as well as the impact of host immune selection and virus polymerase on virus evolution. The different genetic diversity of HPgV-2 and HCV makes HPgV-2 a potential new model to investigate RNA virus diversity and the mechanism of viral polymerase in modulating virus replication.
Collapse
Affiliation(s)
- Yuanhao Liang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Fengyu Hu
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Hang Fan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Linghua Li
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Zhengwei Wan
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Haiying Wang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Jingwei Shui
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Yuanping Zhou
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yigang Tong
- School of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Weiping Cai
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Shixing Tang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China.,Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, China
| |
Collapse
|
16
|
Zhen W, Wu Y, Zhang W, Wang M, Jia R, Zhu D, Liu M, Zhao X, Yang Q, Wu Y, Zhang S, Liu Y, Zhang L, Yu Y, Pan L, Chen S, Cheng A. Emergence of a novel pegivirus species in southwest China showing a high rate of coinfection with parvovirus and circovirus in geese. Poult Sci 2021; 100:101251. [PMID: 34175799 PMCID: PMC8254001 DOI: 10.1016/j.psj.2021.101251] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/03/2021] [Accepted: 05/03/2021] [Indexed: 12/27/2022] Open
Abstract
Previously, we isolated a novel strain of goose pegivirus (GPgV) that infects geese and shows high levels of lymphotropism. This novel pegivirus strain is phylogenetically distinct from previously known Pegivirus species, Pegivirus A-K, and qualifies as a candidate new Pegivirus species, GPgV. GPgV is tentatively named Pegivirus M. Here, to better understand the epidemic of GPgV infection and the coinfection of this virus with other viruses in Southwest China, 25 geese in poor health from Sichuan Province and 24 geese in poor health from the municipality of Chongqing were collected. The geese were tested for 9 types of goose viruses (goose hemorrhagic polyomavirus, GPgV, astrovirus, parvovirus, circovirus, reovirus, coronavirus, paramyxovirus, and avian influenza virus) by RT-PCR or nested RT-PCR. GPgV RNA was detected in 2 out of 25 monoinfections and 8 out of 25 coinfections with other viruses on Sichuan farms and 2 out of 24 monoinfections and 10 out of 24 coinfections on Chongqing farms. Overall, 22 of the 49 (44.9%) geese were positive for GPgV, which indicated a high infection rate. To the best of our knowledge, this is the first report of GPgV coinfection with other epidemic viruses. This study enhances our understanding of the emergence and epidemiology of Pegivirus.
Collapse
Affiliation(s)
- Wu Zhen
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan Province, 611130, China
| | - Yuanyuan Wu
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan Province, 611130, China
| | - Wei Zhang
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan Province, 611130, China
| | - Mingshu Wang
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan Province, 611130, China; Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan Province, 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu City, Sichuan Province, 611130, China
| | - Renyong Jia
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan Province, 611130, China; Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan Province, 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu City, Sichuan Province, 611130, China
| | - Dekang Zhu
- Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan Province, 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu City, Sichuan Province, 611130, China
| | - Mafeng Liu
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan Province, 611130, China; Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan Province, 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu City, Sichuan Province, 611130, China
| | - Xinxin Zhao
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan Province, 611130, China; Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan Province, 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu City, Sichuan Province, 611130, China
| | - Qiao Yang
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan Province, 611130, China; Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan Province, 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu City, Sichuan Province, 611130, China
| | - Ying Wu
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan Province, 611130, China; Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan Province, 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu City, Sichuan Province, 611130, China
| | - ShaQiu Zhang
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan Province, 611130, China; Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan Province, 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu City, Sichuan Province, 611130, China
| | - YunYa Liu
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan Province, 611130, China
| | - Ling Zhang
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan Province, 611130, China
| | - YanLing Yu
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan Province, 611130, China
| | - Leichang Pan
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan Province, 611130, China
| | - Shun Chen
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan Province, 611130, China; Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan Province, 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu City, Sichuan Province, 611130, China.
| | - Anchun Cheng
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan Province, 611130, China; Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan Province, 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu City, Sichuan Province, 611130, China
| |
Collapse
|
17
|
Nishizawa T, Usui R, Narabu Y, Takahashi M, Murata K, Okamoto H. Identification of a novel pegivirus in pet cats (Felis silvestris catus) in Japan. Virus Res 2021; 301:198452. [PMID: 33971193 DOI: 10.1016/j.virusres.2021.198452] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/03/2021] [Accepted: 05/04/2021] [Indexed: 12/01/2022]
Abstract
We report a novel pegivirus in pet cats (Felis silvestris catus) in Japan. This virus was only 44.0-49.6 % identical to the reported viruses in the 11 current Pegivirus species and an unclassified pegivirus in dolphins within the entire protein-coding nucleotide sequence and was detected in 1.6 % of pet cats.
Collapse
Affiliation(s)
- Tsutomu Nishizawa
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Shimotsuke, Tochigi 329-0498, Japan
| | - Reiko Usui
- Usui Dog and Cat Hospital, Utsunomiya, Tochigi 321-0136, Japan
| | - Yoko Narabu
- Narabu Animal Hospital, Mibu-machi, Shimotsuga-gun, Tochigi 321-0227, Japan
| | - Masaharu Takahashi
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Shimotsuke, Tochigi 329-0498, Japan
| | - Kazumoto Murata
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Shimotsuke, Tochigi 329-0498, Japan
| | - Hiroaki Okamoto
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Shimotsuke, Tochigi 329-0498, Japan.
| |
Collapse
|
18
|
Fama A, Larson MC, Link BK, Habermann TM, Feldman AL, Call TG, Ansell SM, Liebow M, Xiang J, Maurer MJ, Slager SL, Nowakowski GS, Stapleton JT, Cerhan JR. Human Pegivirus Infection and Lymphoma Risk: A Systematic Review and Meta-analysis. Clin Infect Dis 2021; 71:1221-1228. [PMID: 31671178 DOI: 10.1093/cid/ciz940] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 09/20/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Human pegivirus (HPgV) is a single-strand RNA virus belonging to the Flaviviridae. Although no definitive association between HPgV infection and disease has been identified, previous studies have suggested an association of HPgV viremia with risk of lymphomas. METHODS We conducted a systematic review and meta-analysis, including 1 cohort study and 14 case-control studies, assessing the association of HPgV viremia with adult lymphomas. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated using a random-effects model, overall and by geographic region and lymphoma subtype. RESULTS The overall OR for lymphoma was 2.85 (95% CI, 1.98-4.11), with statistically significantly elevated ORs observed in 8 of 15 studies. There was a small amount of heterogeneity among studies (I2 = 28.9%; Q = 18.27, P = .16), and the funnel plot provided no evidence for publication bias. The strongest association with lymphoma risk was observed for studies from Southern Europe (OR, 5.68 [95% CI, 1.98-16.3]), whereas weaker ORs (with 95% CIs) were observed for studies from North America (2.24 [1.76-2.85]), Northern Europe (2.90 [.45-18.7), and the Middle East (2.51 [.87-7.27]), but all of similar magnitude. Participants with HPgV viremia had statistically significantly increased risks (OR [95% CI]) for developing diffuse large B-cell (3.29 [1.63-6.62]), follicular (3.01 [1.95-4.63]), marginal zone (1.90 [1.13-3.18]), and T-cell (2.11 [1.17-3.89]) lymphomas, while the risk for Hodgkin lymphoma (3.53 [.48-25.9]) and chronic lymphocytic leukemia (1.45 [.45-4.66]) were increased but did not achieve statistical significance. CONCLUSIONS This meta-analysis supports a positive association of HPgV viremia with lymphoma risk, overall and for the major lymphoma subtypes.
Collapse
Affiliation(s)
- Angelo Fama
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Ematologia, Azienda Unità Sanitaria Locale, Istituto di Ricovero e Cura a Carattere Scientifico di Reggio Emilia, Reggio Emilia, Italy
| | - Melissa C Larson
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Brian K Link
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Thomas M Habermann
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Andrew L Feldman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Timothy G Call
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Stephen M Ansell
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Mark Liebow
- Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Jinhua Xiang
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, USA.,Iowa City Veterans Affairs Medical Center, Iowa City, Iowa, USA
| | - Matthew J Maurer
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Susan L Slager
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Grzegorz S Nowakowski
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Jack T Stapleton
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, USA.,Iowa City Veterans Affairs Medical Center, Iowa City, Iowa, USA
| | - James R Cerhan
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| |
Collapse
|
19
|
Akimkin VG, Alimov AV, Zakharova YA, Bolgarova EV, Piterskiy MV, Sisin EI. [Review of current issues of diagnosis and prevention of blood-borne nosocomial viral infections.]. Vopr Virusol 2021; 64:262-267. [PMID: 32168439 DOI: 10.36233/0507-4088-2019-64-6-262-267] [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: 10/08/2019] [Accepted: 11/28/2019] [Indexed: 11/05/2022]
Abstract
Provision of infection security in transplantology and transfusiology is a challenging and significant problem that depends on the quality of medical donor selection and laboratory diagnosis of the blood collected. At present, a large number of blood-borne viruses are known; nevertheless, in Russia, the list of viral agents to be tested during the examination by the blood service boils down to three ones: HIV, hepatitis C and hepatitis B viruses. The review article demonstrates the need for implementation of additional laboratory tests for the agents of the priority healthcare-associated blood-borne infections (HAI) using a risk-based approach, i.e., on specified sites and in high risk groups. It presents a methodology for determination of a quantitative blood-induced infection residual risk (BIRR) index to be used while evaluating the efficiency of viral security provision in the blood service.
Collapse
Affiliation(s)
- V G Akimkin
- Central Institute of Epidemiology, Moscow, 111123, Russia
| | - A V Alimov
- Yekaterinburg Research Institute of Viral Infections, Yekaterinburg, 620030, Russia
| | - Y A Zakharova
- Yekaterinburg Research Institute of Viral Infections, Yekaterinburg, 620030, Russia
| | - E V Bolgarova
- Yekaterinburg Research Institute of Viral Infections, Yekaterinburg, 620030, Russia
| | - M V Piterskiy
- Yekaterinburg Research Institute of Viral Infections, Yekaterinburg, 620030, Russia
| | - E I Sisin
- Yekaterinburg Research Institute of Viral Infections, Yekaterinburg, 620030, Russia
| |
Collapse
|
20
|
Coller KE, Bruce V, Cassidy M, Gersch J, Frankel MB, Vallari A, Cloherty G, Hackett J, Evans JL, Page K, Dawson GJ. Chronic Human Pegivirus 2 without Hepatitis C Virus Co-infection. Emerg Infect Dis 2021; 26:265-272. [PMID: 31961294 PMCID: PMC6986836 DOI: 10.3201/eid2602.190434] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Most human pegivirus 2 (HPgV-2) infections are associated with past or current hepatitis C virus (HCV) infection. HPgV-2 is thought to be a bloodborne virus: higher prevalence of active infection has been found in populations with a history of parenteral exposure to viruses. We evaluated longitudinally collected blood samples obtained from injection drug users (IDUs) for active and resolved HPgV-2 infections using a combination of HPgV-2–specific molecular and serologic tests. We found evidence of HPgV-2 infection in 11.2% (22/197) of past or current HCV-infected IDUs, compared with 1.9% (4/205) of an HCV-negative IDU population. Testing of available longitudinal blood samples from HPgV-2–positive participants identified 5 with chronic infection (>6 months viremia in >3 timepoints); 2 were identified among the HCV-positive IDUs and 3 among the HCV-negative IDUs. Our findings indicate that HPgV-2 can establish chronic infection and replicate in the absence of HCV.
Collapse
|
21
|
Silva ADSN, Silva CP, Barata RR, da Silva PVR, Monteiro PDJ, Lamarão L, Burbano RMR, Nunes MRT, de Lima PDL. Human pegivirus (HPgV, GBV-C) RNA in volunteer blood donors from a public hemotherapy service in Northern Brazil. Virol J 2020; 17:153. [PMID: 33054824 PMCID: PMC7556973 DOI: 10.1186/s12985-020-01427-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 10/06/2020] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Human pegivirus (HPgV)-formerly known as GBV-C-is a member of the Flaviviridae family and belongs to the species Pegivirus C. It is a non-pathogenic virus and is transmitted among humans mainly through the exposure to contaminated blood and is often associated with human immunodeficiency virus (HIV) infection, among other viruses. This study aimed to determine the prevalence of HPgV viremia, its association with HIV and clinical epidemiological factors, as well as the full-length sequencing and genome characterization of HPgV recovered from blood donors of the HEMOPA Foundation in Belém-PA-Brazil. METHODS Plasma samples were obtained from 459 donors, tested for the presence of HPgV RNA by the RT-qPCR. From these, a total of 26 RT-qPCR positive samples were submitted to the NGS sequencing approach in order to obtain the full genome. Genome characterization and phylogenetic analysis were conducted. RESULTS The prevalence of HPgV was 12.42%. We observed the highest prevalences among donors aged between 18 and 30 years old (16.5%), with brown skin color (13.2%) and men (15.8%). The newly diagnosed HIV-1 prevalence was 26.67%. The HPgV genotype 2 (2a and 2b) was identified. No data on viral load value was found to corroborate the protective effect of HPgV on HIV evolution. CONCLUSIONS This study provided information regarding the HPgV infection among blood donors from HEMOPA Foundation. Furthermore, we genetically characterized the HPgV circulating strains and described by the first time nearly complete genomes of genotype 2 in Brazilian Amazon.
Collapse
Affiliation(s)
- Aniel de Sarom Negrão Silva
- Center for Life Science and Health, Pará State University, Travessa. Perebebuí, 2623, Marco, Belém, Pará, 66087-662, Brazil.
| | - Clayton Pereira Silva
- Evandro Chagas Institute, Rodovia BR-316, km 7 s/n, Levilândia, Ananindeua , Pará, 67030-000, Brazil
| | - Rafael Ribeiro Barata
- Evandro Chagas Institute, Rodovia BR-316, km 7 s/n, Levilândia, Ananindeua , Pará, 67030-000, Brazil
| | - Pedro Victor Reis da Silva
- Center for Life Science and Health, Pará State University, Travessa. Perebebuí, 2623, Marco, Belém, Pará, 66087-662, Brazil
| | - Patrícia Danin Jordão Monteiro
- Foundation Center for Hemotherapy and Hematology of Pará (HEMOPA Foundation), Travessa Padre Eutíquio, 2109, Batista Campos, Belém, Pará, 66033-000, Brazil
| | - Letícia Lamarão
- Foundation Center for Hemotherapy and Hematology of Pará (HEMOPA Foundation), Travessa Padre Eutíquio, 2109, Batista Campos, Belém, Pará, 66033-000, Brazil
| | | | | | - Patrícia Danielle Lima de Lima
- Center for Life Science and Health, Pará State University, Travessa. Perebebuí, 2623, Marco, Belém, Pará, 66087-662, Brazil
| |
Collapse
|
22
|
The First Nonmammalian Pegivirus Demonstrates Efficient In Vitro Replication and High Lymphotropism. J Virol 2020; 94:JVI.01150-20. [PMID: 32759314 DOI: 10.1128/jvi.01150-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 07/28/2020] [Indexed: 11/20/2022] Open
Abstract
Members of the Pegivirus genus, family Flaviviridae, widely infect humans and other mammals, including nonhuman primates, bats, horses, pigs, and rodents, but are not associated with disease. Here, we report a new, genetically distinct pegivirus in goose (Anser cygnoides), the first identified in a nonmammalian host species. Goose pegivirus (GPgV) can be propagated in goslings, embryonated goose eggs, and primary goose embryo fibroblasts, and is thus the first pegivirus that can be efficiently cultured in vitro Experimental infection of GPgV in goslings via intravenous injection revealed robust replication and high lymphotropism. Analysis of the tissue tropism of GPgV revealed that the spleen and thymus were the organs bearing the highest viral loads. Importantly, GPgV could promote clinical manifestations of goose parvovirus infection, including reduced weight gain and 7% mortality. This finding contrasts with the lack of pathogenicity that is characteristic of previously reported pegiviruses.IMPORTANCE Members of the Pegivirus genus, family Flaviviridae, widely infect humans and other mammals, but are described as causing persistent infection and lacking pathogenicity. The efficiency of in vitro replication systems for pegivirus is poor, thus limiting investigation into viral replication steps. Because of that, the pathogenesis, cellular tropism, route of transmission, biology, and epidemiology of pegiviruses remain largely uncovered. Here, we report a phylogenetically distinct goose pegivirus (GPgV) that should be classified as a new species. GPgV proliferated in cell culture in a species- and cell-type-specific manner. Animal experiments show GPgV lymphotropism and promote goose parvovirus clinical manifestations. This study provides the first cell culture model for pegivirus, opening new possibilities for studies of pegivirus molecular biology. More importantly, our findings stand in contrast to the lack of identified pathogenicity of previously reported pegiviruses, which sheds lights on the pathobiology of pegivirus.
Collapse
|
23
|
Beyond Cytomegalovirus and Epstein-Barr Virus: a Review of Viruses Composing the Blood Virome of Solid Organ Transplant and Hematopoietic Stem Cell Transplant Recipients. Clin Microbiol Rev 2020; 33:33/4/e00027-20. [PMID: 32847820 DOI: 10.1128/cmr.00027-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Viral primary infections and reactivations are common complications in patients after solid organ transplantation (SOT) and hematopoietic stem cell transplantation (HSCT) and are associated with high morbidity and mortality. Among these patients, viral infections are frequently associated with viremia. Beyond the usual well-known viruses that are part of the routine clinical management of transplant recipients, numerous other viral signatures or genomes can be identified in the blood of these patients. The identification of novel viral species and variants by metagenomic next-generation sequencing has opened up a new field of investigation and new paradigms. Thus, there is a need to thoroughly describe the state of knowledge in this field with a review of all viral infections that should be scrutinized in high-risk populations. Here, we review the eukaryotic DNA and RNA viruses identified in blood, plasma, or serum samples of pediatric and adult SOT/HSCT recipients and the prevalence of their detection, with a particular focus on recently identified viruses and those for which their potential association with disease remains to be investigated, such as members of the Polyomaviridae, Anelloviridae, Flaviviridae, and Astroviridae families. Current knowledge of the clinical significance of these viral infections with associated viremia among transplant recipients is also discussed. To ensure a comprehensive description in these two populations, individuals described as healthy (mostly blood donors) are considered for comparative purposes. The list of viruses that should be on the clinicians' radar is certainly incomplete and will expand, but the challenge is to identify those of possible clinical significance.
Collapse
|
24
|
Berg MG, Olivo A, Forberg K, Harris BJ, Yamaguchi J, Shirazi R, Gozlan Y, Sauleda S, Kaptue L, Rodgers MA, Mor O, Cloherty GA. Advanced molecular surveillance approaches for characterization of blood borne hepatitis viruses. PLoS One 2020; 15:e0236046. [PMID: 32678844 PMCID: PMC7367454 DOI: 10.1371/journal.pone.0236046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 06/26/2020] [Indexed: 12/27/2022] Open
Abstract
Defining genetic diversity of viral infections directly from patient specimens is the ultimate goal of surveillance. Simple tools that can provide full-length sequence information on blood borne viral hepatitis viruses: hepatitis C, hepatitis B and hepatitis D viruses (HCV, HBV and HDV) remain elusive. Here, an unbiased metagenomic next generation sequencing approach (mNGS) was used for molecular characterization of HCV infections (n = 99) from Israel which yielded full-length HCV sequences in 89% of samples, with 7 partial sequences sufficient for classification. HCV genotypes were primarily 1b (68%) and 1a (19%), with minor representation of genotypes 2c (1%) and 3a (8%). HBV/HDV coinfections were characterized by suppressed HBV viral loads, resulting in sparse mNGS coverage. A probe-based enrichment approach (xGen) aiming to increase HBV and HDV coverage was validated on a panel of diverse genotypes, geography and titers. The method extended HBV genome coverage a median 61% (range 8–84%) and provided orders of magnitude boosts in reads and sequence depth for both viruses. When HBV-xGen was applied to Israeli samples, coverage was improved by 28–73% in 4 samples and identified HBV genotype A1, A2, D1 specimens and a dual B/D infection. Abundant HDV reads in mNGS libraries yielded 18/26 (69%) full genomes and 8 partial sequences, with HDV-xGen only providing minimal extension (3–11%) of what were all genotype 1 genomes. Advanced molecular approaches coupled to virus-specific capture probes promise to enhance surveillance of viral infections and aid in monitoring the spread of local subtypes.
Collapse
Affiliation(s)
- Michael G. Berg
- Infectious Diseases Research, Abbott Diagnostics, Abbott Park, Illinois, United States of America
- * E-mail:
| | - Ana Olivo
- Infectious Diseases Research, Abbott Diagnostics, Abbott Park, Illinois, United States of America
| | - Kenn Forberg
- Infectious Diseases Research, Abbott Diagnostics, Abbott Park, Illinois, United States of America
| | - Barbara J. Harris
- Infectious Diseases Research, Abbott Diagnostics, Abbott Park, Illinois, United States of America
| | - Julie Yamaguchi
- Infectious Diseases Research, Abbott Diagnostics, Abbott Park, Illinois, United States of America
| | - Rachel Shirazi
- Central Virology Laboratory, National HIV and Viral Hepatitis Reference Center, Public Health Services, Ministry of Health, Tel-Hashomer, Ramat-Gan, Israel
| | - Yael Gozlan
- Central Virology Laboratory, National HIV and Viral Hepatitis Reference Center, Public Health Services, Ministry of Health, Tel-Hashomer, Ramat-Gan, Israel
| | - Silvia Sauleda
- Transfusion Safety Laboratory, Banc de Sang i Teixits, Servei Català de la Salut, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | | | - Mary A. Rodgers
- Infectious Diseases Research, Abbott Diagnostics, Abbott Park, Illinois, United States of America
| | - Orna Mor
- Central Virology Laboratory, National HIV and Viral Hepatitis Reference Center, Public Health Services, Ministry of Health, Tel-Hashomer, Ramat-Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Israel
| | - Gavin A. Cloherty
- Infectious Diseases Research, Abbott Diagnostics, Abbott Park, Illinois, United States of America
| |
Collapse
|
25
|
Tomlinson JE, Wolfisberg R, Fahnøe U, Sharma H, Renshaw RW, Nielsen L, Nishiuchi E, Holm C, Dubovi E, Rosenberg BR, Tennant BC, Bukh J, Kapoor A, Divers TJ, Rice CM, Van de Walle GR, Scheel TKH. Equine pegiviruses cause persistent infection of bone marrow and are not associated with hepatitis. PLoS Pathog 2020; 16:e1008677. [PMID: 32649726 PMCID: PMC7375656 DOI: 10.1371/journal.ppat.1008677] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 07/22/2020] [Accepted: 06/02/2020] [Indexed: 12/20/2022] Open
Abstract
Pegiviruses frequently cause persistent infection (as defined by >6 months), but unlike most other Flaviviridae members, no apparent clinical disease. Human pegivirus (HPgV, previously GBV-C) is detectable in 1–4% of healthy individuals and another 5–13% are seropositive. Some evidence for infection of bone marrow and spleen exists. Equine pegivirus 1 (EPgV-1) is not linked to disease, whereas another pegivirus, Theiler’s disease-associated virus (TDAV), was identified in an outbreak of acute serum hepatitis (Theiler’s disease) in horses. Although no subsequent reports link TDAV to disease, any association with hepatitis has not been formally examined. Here, we characterized EPgV-1 and TDAV tropism, sequence diversity, persistence and association with liver disease in horses. Among more than 20 tissue types, we consistently detected high viral loads only in serum, bone marrow and spleen, and viral RNA replication was consistently identified in bone marrow. PBMCs and lymph nodes, but not liver, were sporadically positive. To exclude potential effects of co-infecting agents in experimental infections, we constructed full-length consensus cDNA clones; this was enabled by determination of the complete viral genomes, including a novel TDAV 3’ terminus. Clone derived RNA transcripts were used for direct intrasplenic inoculation of healthy horses. This led to productive infection detectable from week 2–3 and persisting beyond the 28 weeks of study. We did not observe any clinical signs of illness or elevation of circulating liver enzymes. The polyprotein consensus sequences did not change, suggesting that both clones were fully functional. To our knowledge, this is the first successful extrahepatic viral RNA launch and the first robust reverse genetics system for a pegivirus. In conclusion, equine pegiviruses are bone marrow tropic, cause persistent infection in horses, and are not associated with hepatitis. Based on these findings, it may be appropriate to rename the group of TDAV and related viruses as EPgV-2. Transmissible hepatitis in horses (Theiler’s disease) has been known for 100 years without knowledge of causative infectious agents. Recently, two novel equine pegiviruses (EPgV) were discovered. Whereas EPgV-1 was not associated to disease, the other was identified in an outbreak of acute serum hepatitis and therefore named Theiler’s disease-associated virus (TDAV). This finding was surprising since human and monkey pegiviruses typically cause long-term infection without associated clinical disease. Whereas no subsequent reports link TDAV to disease, the original association to hepatitis has not been formally examined. Here, we studied EPgV-1 and TDAV and found that their natural history of infection in horses were remarkably similar. Examination of various tissues identified the bone marrow as the primary site of replication for both viruses with no evidence of replication in the liver. To exclude potential effects of other infectious agents, we developed molecular full-length clones for EPgV-1 and TDAV and were able to initiate infection in horses using derived synthetic viral genetic material. This demonstrated long-term infection, but no association with hepatitis. These findings call into question the connection between TDAV, liver infection, and hepatitis in horses.
Collapse
Affiliation(s)
- Joy E. Tomlinson
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Raphael Wolfisberg
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital and Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Ulrik Fahnøe
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital and Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Himanshu Sharma
- Center for Vaccines and Immunity, Research Institute at Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Randall W. Renshaw
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Louise Nielsen
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital and Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Eiko Nishiuchi
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
| | - Christina Holm
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital and Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Edward Dubovi
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Brad R. Rosenberg
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Bud C. Tennant
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital and Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Amit Kapoor
- Center for Vaccines and Immunity, Research Institute at Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Thomas J. Divers
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Charles M. Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
| | - Gerlinde R. Van de Walle
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Troels K. H. Scheel
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital and Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
- * E-mail:
| |
Collapse
|
26
|
The Prevalence, Genetic Characterization, and Evolutionary Analysis of Porcine Pegivirus in Guangdong, China. Virol Sin 2020; 36:52-60. [PMID: 32643050 DOI: 10.1007/s12250-020-00240-3] [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: 12/07/2019] [Accepted: 04/15/2020] [Indexed: 10/23/2022] Open
Abstract
Porcine pegivirus (PPgV) is a member of the Pegivirus genus in the Flaviviridae family. PPgV is an emerging virus that has been discovered in swine herds in Germany, the United States, China, Poland, Italy, and the United Kingdom, indicating a wide geographical distribution. In this retrospective study, 339 pig serum samples were collected from 20 different commercial swine farms located in nine cities in Guangdong Province, China, from 2016 to 2018, to investigate the prevalence and genetic diversity of PPgV in this geographical region. PPgV was detected in 55% (11/20) of the farms using nested reverse transcription PCR, with 6.2% (21/339) of pigs testing positive for PPgV. The yearly PPgV-positive rate increased from 2.6% to 7.5% between 2016 and 2018. Sequencing of PPgV-positive samples identified two complete polyprotein genes and seven partial NS5B genes from different farms. Comparative analysis of the polyprotein genes revealed that PPgV sequences obtained in this study showed 87.4%-97.2% similarity at the nucleotide level and 96.5%-99.4% similarity at the amino acid level with the reference sequences. Sequence alignment and phylogenetic analysis of the complete polyprotein gene and partial NS5B and NS3 genes demonstrated a high genetic similarity with the samples from the USA. The finding of the wide distribution of PPgV in swine herds in Guangdong Province will contribute to the understanding of the epidemiological characteristics and genetic evolution of PPgV in China.
Collapse
|
27
|
Arhab Y, Bulakhov AG, Pestova TV, Hellen CU. Dissemination of Internal Ribosomal Entry Sites (IRES) Between Viruses by Horizontal Gene Transfer. Viruses 2020; 12:E612. [PMID: 32512856 PMCID: PMC7354566 DOI: 10.3390/v12060612] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/01/2020] [Accepted: 06/02/2020] [Indexed: 12/19/2022] Open
Abstract
Members of Picornaviridae and of the Hepacivirus, Pegivirus and Pestivirus genera of Flaviviridae all contain an internal ribosomal entry site (IRES) in the 5'-untranslated region (5'UTR) of their genomes. Each class of IRES has a conserved structure and promotes 5'-end-independent initiation of translation by a different mechanism. Picornavirus 5'UTRs, including the IRES, evolve independently of other parts of the genome and can move between genomes, most commonly by intratypic recombination. We review accumulating evidence that IRESs are genetic entities that can also move between members of different genera and even between families. Type IV IRESs, first identified in the Hepacivirus genus, have subsequently been identified in over 25 genera of Picornaviridae, juxtaposed against diverse coding sequences. In several genera, members have either type IV IRES or an IRES of type I, II or III. Similarly, in the genus Pegivirus, members contain either a type IV IRES or an unrelated type; both classes of IRES also occur in members of the genus Hepacivirus. IRESs utilize different mechanisms, have different factor requirements and contain determinants of viral growth, pathogenesis and cell type specificity. Their dissemination between viruses by horizontal gene transfer has unexpectedly emerged as an important facet of viral evolution.
Collapse
Affiliation(s)
| | | | | | - Christopher U.T. Hellen
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, NY 11203, USA; (Y.A.); (A.G.B.); (T.V.P.)
| |
Collapse
|
28
|
Impact of Blood Transfusion on the Prevalence of HHpgV-1, HPgV-1, and B19V Among Iranian HCV-infected Patients With Hemophilia. J Pediatr Hematol Oncol 2020; 42:e213-e218. [PMID: 31972722 DOI: 10.1097/mph.0000000000001717] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Blood-derived products from patient with hemophilia treated by factor VIII concentrates are potential sources of transfusion-transmitted infections, including human immunodeficiency virus, hepatitis, human pegivirus-1 (HPgV-1), B19 virus, and also human hepegivirus-1 (HHpgV-1). In the current study, we investigated the impact of blood transfusion on the prevalence of HHpgV-1, HPgV-1, and B19 virus in plasma of Iranian patient with hemophilia after direct-acting antiviral treatment of hepatitis C virus (HCV) infections for the first time. MATERIALS AND METHODS A total of 170 patients with hemophilia who received direct-acting antivirals were enrolled in this study. Among them, 92 patients had a history of blood transfusion. The presence of HHpgV-1, HPgV-1, and B19 virus was detected by nested polymerase chain reaction analysis using the conserved primers. The plasmids harboring 5'-UTR and NS3 were used as positive controls for HPgV-1 and HHpgV-1, respectively. RESULTS Our data identified 3 individuals with HHpgV-1 viremia (1.76%), 11 individuals with HPgV-1 viremia (6.47%), and 33 individuals with B19 viremia (19.4%). All patients were negative for hepatitis B virus, human immunodeficiency virus, and HCV infections. These findings indicated lower transmissibility or higher rates of virus clearance for HHpgV-1, HPgV-1, and B19 virus as compared with other bloodborne human flaviviruses such as HCV. However, the prevalence of B19 virus was significantly higher than the other 2 viruses. CONCLUSION In general, these findings showed that the history of blood transfusion could increase the risk of viral transmission of bloodborne viruses among patient with hemophilia.
Collapse
|
29
|
Fahsbender E, Charlys da-Costa A, Elise Gill D, Augusto de Padua Milagres F, Brustulin R, Julio Costa Monteiro F, Octavio da Silva Rego M, Soares D’Athaide Ribeiro E, Cerdeira Sabino E, Delwart E. Plasma virome of 781 Brazilians with unexplained symptoms of arbovirus infection include a novel parvovirus and densovirus. PLoS One 2020; 15:e0229993. [PMID: 32134963 PMCID: PMC7058308 DOI: 10.1371/journal.pone.0229993] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 02/19/2020] [Indexed: 12/16/2022] Open
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.
Collapse
Affiliation(s)
- Elizabeth Fahsbender
- Vitalant Research Institute, San Francisco, CA, United States of America
- UCSF Dept. of Laboratory Medicine, University of California–San Francisco, San Francisco, CA, United States of America
| | - Antonio Charlys da-Costa
- School of Medicine & Institute of Tropical Medicine, University of Sao Paulo, Infectious Disease, Sao Paulo, Brazil
| | - Danielle Elise Gill
- School of Medicine & Institute of Tropical Medicine, University of Sao Paulo, Infectious Disease, Sao Paulo, Brazil
| | - Flavio Augusto de Padua Milagres
- Public Health Laboratory State (LACEN/TO), Secretary of Health of Tocantins, Palmas, TO, Brazil
- Federal University of Tocantins, Palmas, Tocantins, Brazil
| | - Rafael Brustulin
- Public Health Laboratory State (LACEN/TO), Secretary of Health of Tocantins, Palmas, TO, Brazil
- Federal University of Tocantins, Palmas, Tocantins, Brazil
| | | | | | | | - Ester Cerdeira Sabino
- School of Medicine & Institute of Tropical Medicine, University of Sao Paulo, Infectious Disease, Sao Paulo, Brazil
| | - Eric Delwart
- Vitalant Research Institute, San Francisco, CA, United States of America
- UCSF Dept. of Laboratory Medicine, University of California–San Francisco, San Francisco, CA, United States of America
- * E-mail:
| |
Collapse
|
30
|
Wan Z, Liu J, Hu F, Shui J, Li L, Wang H, Tang X, Hu C, Liang Y, Zhou Y, Cai W, Tang S. Evidence that the second human pegivirus (HPgV-2) is primarily a lymphotropic virus and can replicate independent of HCV replication. Emerg Microbes Infect 2020; 9:485-495. [PMID: 32100631 PMCID: PMC7054972 DOI: 10.1080/22221751.2020.1730247] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The second human pegivirus HPgV-2 is a novel blood-borne virus that is strongly associated with the hepatitis C virus (HCV) infection. However, the molecular evidence for their association as well as the natural history and tissue tropism of HPgV-2 remain to be elucidated. In this longitudinal study, a total of 753 patients including 512 HIV-1 and HCV co-infected patients were enrolled to characterize the natural history of HPgV-2 infection. Peripheral blood mononuclear cells (PBMCs) and liver biopsies were collected to determine the tissue tropism of HPgV-2 using immunohistochemical staining of the HPgV-2 antigen and in situ hybridization of HPgV-2 RNA. We documented both persistent HPgV-2 infection with the presence of HPgV-2 viral RNA and antibodies up to 4.6 years and resolved HPgV-2 infection, accompanied by a simultaneous decline of anti-HPgV-2 antibodies and clearance of HPgV-2 viremia. Furthermore, we observed the clearance of HCV, but not HPgV-2, by treatment with direct-acting antivirals (DAAs). Biochemical tests and pathological analyses did not reveal any indication of hepatic impairment caused by HPgV-2. HPgV-2 RNA and nonstructural antigen were detected in the lymphocytes, but not in the hepatocytes present in the liver biopsy samples. In addition, both positive- and negative-strand HPgV-2 RNAs were detected in PBMCs, especially in B cells. The present study is the first to provide evidence that HPgV-2 is a lymphotropic, but not a hepatotropic virus and that HPgV-2 replication is independent of HCV viremia. These new findings let us gain insights into the evolution and persistent infection of RNA viruses in humans.
Collapse
Affiliation(s)
- Zhengwei Wan
- Department of Epidemiology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, People's Republic of China
| | - Junwei Liu
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Fengyu Hu
- Infectious Disease Center, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Jingwei Shui
- Department of Epidemiology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, People's Republic of China
| | - Linghua Li
- Infectious Disease Center, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Haiying Wang
- Department of Epidemiology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, People's Republic of China
| | - Xiaoping Tang
- Infectious Disease Center, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Chengguang Hu
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Yuanhao Liang
- Department of Epidemiology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, People's Republic of China
| | - Yuanping Zhou
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Weiping Cai
- Infectious Disease Center, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Shixing Tang
- Department of Epidemiology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, People's Republic of China.,Dermatology Hospital, Southern Medical University, Guangzhou, People's Republic of China
| |
Collapse
|
31
|
Li T, Tang S, Su Y, Bao Z, Wang X, Liu Y, Li H, Han J, Pei Z, Wan Z, Fan H, Tong Y, Li L, Wang N, Li J. High prevalence and viremia of human pegivirus 2 in the HIV-infected population in Honghe Prefecture, Yunnan Province. Arch Virol 2020; 165:619-626. [PMID: 31965315 DOI: 10.1007/s00705-019-04512-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 11/29/2019] [Indexed: 10/25/2022]
Abstract
Human pegivirus 2 (HPgV-2) is a recently recognized pegivirus of the family Flaviviridae. To investigate the epidemic features of HPgV-2 circulating in the human immunodeficiency virus (HIV)-infected population, we tested for antibodies and viral RNA of HPgV-2 and hepatitis C virus (HCV) with retrospective plasma samples collected from 771 HIV infections with multiple risk behaviors in Honghe Prefecture of Yunnan Province. A total of 195 subjects (25.29%) were seroreactive to HPgV-2, and 41 (5.32%) were RNA positive. Although the positive rate of HPgV-2 antibodies in HIV/HCV-coinfected individuals (27.69%) was significantly higher than that of HIV monoinfections (20.82%) (p = 0.036), this is the first report of HPgV-2 viremia in HIV-infected individuals without HCV infection and the presence of two HPgV-2 lineages in China. Our data indicate that HPgV-2 can also be transmitted sexually, which might be facilitated when combined with HCV infection, injecting drug use, and risky sexual behavior, which appear to have a synergistic effect on HPgV-2 infection. Phylogenetic analysis of 26 near-full-length genome sequences showed that the HPgV-2 strains in China are divided into two clusters.
Collapse
Affiliation(s)
- Tianyi Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China
| | - Shixing Tang
- Southern Medical University, Guangzhou, 510515, Guangdong, China.,Guangdong Provincial Key Laboratory of Tropical Disease Research, Guangzhou, China
| | - Yingying Su
- Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Zuoyi Bao
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China
| | - Xiaolin Wang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China
| | - Yongjian Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China
| | - Hanping Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China
| | - Jingwan Han
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China
| | - Zhichao Pei
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China
| | - Zhengwei Wan
- Southern Medical University, Guangzhou, 510515, Guangdong, China.,Guangdong Provincial Key Laboratory of Tropical Disease Research, Guangzhou, China
| | - Hang Fan
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China
| | - Yigang Tong
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China
| | - Lin Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China.
| | - Ning Wang
- Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China.
| |
Collapse
|
32
|
de Albuquerque PPLF, Santos LHS, Antunes D, Caffarena ER, Figueiredo AS. Structural insights into NS5B protein of novel equine hepaciviruses and pegiviruses complexed with polymerase inhibitors. Virus Res 2020; 278:197867. [PMID: 31972246 DOI: 10.1016/j.virusres.2020.197867] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 01/15/2020] [Accepted: 01/17/2020] [Indexed: 01/09/2023]
Abstract
Infections produced by hepaciviruses have been associated with liver disease in horses. Currently, at least three viruses belonging to the Flaviviridae family are capable of producing a chronic infection in equines: non-primate hepacivirus (NPHV), Theiler's disease-associated virus (TDAV), and equine pegivirus (EPgV). The RNA-dependent RNA polymerases of viruses (RdRp) (NS5 protein), from the flavivirus family, use de novo RNA synthesis to initiate synthesis. The two antiviral drugs currently used to treat hepatitis C (HCV), sofosbuvir and dasabuvir, act on the viral NS5B polymerase as nucleoside and non-nucleoside inhibitors, respectively. Both drugs have shown significant clinical inhibition of viral response. In this work, we aimed to model the NS5B polymerase of the equine hepacivirus (EHCV) subtypes 1 and 2, TDAV and EPgV, to assess whether current direct-acting antiviral drugs against HCV interact with these proteins. Crystal structures of HCV-NS5B were used as templates for modeling target sequences in both conformations (open and closed). Also, molecular docking of sofosbuvir and dasabuvir were performed to predict their possible binding modes at the modeled NS5B polymerase binding sites. We observed that the NS5B models of the EHCV and EPgV shared well-conserved 3D structures to HCV-NS5B and other RdRps, suggesting functional conservation. Interactions of EHCV subtypes 1, 2 and TDAV polymerases with sofosbuvir showed a similar molecular interaction pattern compared to HCV-NS5B, while interactions with dasabuvir were less conserved. In silico studies of molecular interactions between these modeled structures and sofosbuvir suggest that this compound could be efficient in combating equine pathogens, thus contributing to animal welfare.
Collapse
Affiliation(s)
| | - Lucianna H S Santos
- Laboratório de Modelagem Molecular e Planejamento de Fármacos, Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Deborah Antunes
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil.
| | - Ernesto Raul Caffarena
- Grupo de Biofísica Computacional e Modelagem Molecular, Programa de Computação Científica, Fiocruz, Rio de Janeiro, Brazil
| | - Andreza Soriano Figueiredo
- Laboratório de Desenvolvimento Tecnológico em Virologia, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| |
Collapse
|
33
|
Mrzljak A, Tabain I, Premac H, Bogdanic M, Barbic L, Savic V, Stevanovic V, Jelic A, Mikulic D, Vilibic-Cavlek T. The Role of Emerging and Neglected Viruses in the Etiology of Hepatitis. Curr Infect Dis Rep 2019; 21:51. [PMID: 31754812 DOI: 10.1007/s11908-019-0709-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
PURPOSE OF REVIEW In this review, we present the overview of emerging and neglected viruses associated with liver involvement. RECENT FINDINGS Hepatitis E virus (HEV) emerged in the last two decades, causing hepatitis in many parts of the world. Moreover, liver involvement was also described in some emerging arboviral infections. Many reports showed dengue-associated liver injury; however, chikungunya, West Nile, tick-borne encephalitis, and Zika virus are rarely associated with clinically manifest liver disease. In addition, some neglected highly prevalent viruses such as adenoviruses and parvovirus B19 are capable of causing hepatitis in specific population groups. Anelloviruses (torque teno virus/torque teno mini virus/torque teno midi virus, SEN virus), human bocavirus, pegiviruses, and lymphocytic choriomeningitis virus have shown a little potential for causing hepatitis, but their role in the etiology of liver disease remains to be determined. In addition to the well-known hepatotropic viruses, many emerging and neglected viruses have been associated with liver diseases. The number of emerging zoonotic viruses has been increasingly recognized. While zoonotic potential of HEV is well documented, the recent identification of new hepatitis-related animal viruses such as HEV strains from rabbits and camels, non-primate hepaciviruses in domestic dogs and horses, as well as equine and porcine pegivirus highlights the possible zoonotic transmission in the context of "One Health." However, zoonotic potential and hepatotropism of animal hepatitis viruses remain to be determined.
Collapse
Affiliation(s)
- Anna Mrzljak
- Department of Medicine, Merkur University Hospital, Salata 3b, 10000, Zagreb, Croatia.
- School of Medicine, University of Zagreb, Zagreb, Croatia.
| | - Irena Tabain
- Department of Virology, Croatian Institute of Public Health, Zagreb, Croatia
| | - Hrvoje Premac
- Department of Medicine, Varazdin General Hospital, Varazdin, Croatia
| | - Maja Bogdanic
- Department of Virology, Croatian Institute of Public Health, Zagreb, Croatia
| | - Ljubo Barbic
- Department of Microbiology and Infectious Diseases with Clinic, Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Vladimir Savic
- Poultry Center, Laboratory for Virology and Serology, Croatian Veterinary Institute, Zagreb, Croatia
| | - Vladimir Stevanovic
- Department of Microbiology and Infectious Diseases with Clinic, Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Ana Jelic
- Department of Medicine, Merkur University Hospital, Salata 3b, 10000, Zagreb, Croatia
| | - Danko Mikulic
- Department of Surgery, Merkur University Hospital, Zagreb, Croatia
| | - Tatjana Vilibic-Cavlek
- School of Medicine, University of Zagreb, Zagreb, Croatia
- Department of Virology, Croatian Institute of Public Health, Zagreb, Croatia
| |
Collapse
|
34
|
Wang H, Wan Z, Xu R, Guan Y, Zhu N, Li J, Xie Z, Lu A, Zhang F, Fu Y, Tang S. A Novel Human Pegivirus, HPgV-2 (HHpgV-1), Is Tightly Associated With Hepatitis C Virus (HCV) Infection and HCV/Human Immunodeficiency Virus Type 1 Coinfection. Clin Infect Dis 2019; 66:29-35. [PMID: 29020289 DOI: 10.1093/cid/cix748] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 08/17/2017] [Indexed: 12/28/2022] Open
Abstract
Background Human pegivirus type 2 (HPgV-2) is a novel blood-borne human pegivirus that mainly infects hepatitis C virus (HCV)-infected subjects. We have investigated the prevalence of HPgV-2 in China, its association with HCV and human immunodeficiency virus type 1 (HIV-1), and the impact on HCV viral load and liver damage. Methods A cross-sectional study was conducted with both blood donors and HCV- and HIV-1-infected patients in Guangzhou, China. All subjects were screened for anti-HPgV-2 and HPgV-2 RNA. Demographic and clinical information were obtained from electronic medical records. Results We tested 8198 serum or plasma samples. Only 0.15% (6/4017) of healthy blood donors were positive for anti-HPgV-2 and negative for HPgV-2 RNA. No HPgV-2 viremia was detected in hepatitis B virus- or HIV-1-monoinfected individuals. The relatively high frequency of HPgV-2 infection was observed in 1.23% (30/2440) and 0.29% (7/2440) of HCV-infected persons by serological assay and reverse-transcription polymerase chain reaction, respectively. Furthermore, anti-HPgV-2 and HPgV-2 RNA were detected in 8.91% (18/202) and 3.47% (7/202), respectively, of HCV/HIV-1-coinfected subjects. HPgV-2 persistent infection was documented in about 30% of anti-HPgV-2-positive individuals. In addition, HPgV-2 infection may not affect HCV-related liver injury and HCV viral load. Conclusions Our results indicate the rarity of HPgV-2 infection in the general population and tight association with HCV, in particular with HCV/HIV-1 coinfection. HPgV-2 appears not to worsen HCV-related liver damage. Our study provides new findings about the association of HPgV-2 and HCV/HIV-1 and the impact of HPgV-2 infection on HCV replication and pathogenesis.
Collapse
Affiliation(s)
- Haiying Wang
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University
| | - Zhengwei Wan
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University
| | - Ru Xu
- Guangzhou Blood Center, Guangzhou, Guangdong, China
| | - Yujuan Guan
- Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Naling Zhu
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University
| | - Jianping Li
- Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zhiwei Xie
- Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Aiqi Lu
- Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Fuchun Zhang
- Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yongshui Fu
- Guangzhou Blood Center, Guangzhou, Guangdong, China
| | - Shixing Tang
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University
| |
Collapse
|
35
|
Jia H, Gong P. A Structure-Function Diversity Survey of the RNA-Dependent RNA Polymerases From the Positive-Strand RNA Viruses. Front Microbiol 2019; 10:1945. [PMID: 31507560 PMCID: PMC6713929 DOI: 10.3389/fmicb.2019.01945] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 08/07/2019] [Indexed: 01/15/2023] Open
Abstract
The RNA-dependent RNA polymerases (RdRPs) encoded by the RNA viruses are a unique class of nucleic acid polymerases. Each viral RdRP contains a 500–600 residue catalytic module with palm, fingers, and thumb domains forming an encircled human right hand architecture. Seven polymerase catalytic motifs are located in the RdRP palm and fingers domains, comprising the most conserved parts of the RdRP and are responsible for the RNA-only specificity in catalysis. Functional regions are often found fused to the RdRP catalytic module, resulting in a high level of diversity in RdRP global structure and regulatory mechanism. In this review, we surveyed all 46 RdRP-sequence available virus families of the positive-strand RNA viruses listed in the 2018b collection of the International Committee on Virus Taxonomy (ICTV) and chose a total of 49 RdRPs as representatives. By locating hallmark residues in RdRP catalytic motifs and by referencing structural and functional information in the literature, we were able to estimate the N- and C-terminal boundaries of the catalytic module in these RdRPs, which in turn serve as reference points to predict additional functional regions beyond the catalytic module. Interestingly, a large number of virus families may have additional regions fused to the RdRP N-terminus, while only a few of them have such regions on the C-terminal side of the RdRP. The current knowledge on these additional regions, either in three-dimensional (3D) structure or in function, is quite limited. In the five RdRP-structure available virus families in the positive-strand RNA viruses, only the Flaviviridae family has the 3D structural information resolved for such regions. Hence, future efforts to solve full-length RdRP structures containing these regions and to dissect the functional contribution of them are necessary to improve the overall understanding of the RdRP proteins as an evolutionarily integrated group, and our analyses here may serve as a guideline for selecting representative RdRP systems in these studies.
Collapse
Affiliation(s)
- Hengxia Jia
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Peng Gong
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| |
Collapse
|
36
|
Li H, Li K, Bi Z, Gu J, Song D, Lei D, Luo S, Huang D, Wu Q, Ding Z, Wang L, Ye Y, Tang Y. Development of a reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay for the detection of porcine pegivirus. J Virol Methods 2019; 270:59-65. [PMID: 31022411 PMCID: PMC7113777 DOI: 10.1016/j.jviromet.2019.04.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 04/20/2019] [Accepted: 04/21/2019] [Indexed: 02/07/2023]
Abstract
A simple and accurate reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay was developed and evaluated for the detection of porcine pegivirus (PPgV). The specific RT-LAMP primers targeting the conserved regions of NS5A genes were designed and used to detect PPgV. The optimal reaction parameter for RT-LAMP assay was 63℃ for 60 min. The detection limit of the RT-LAMP assay was 10 copies of PPgV genome, which was 100 times more sensitive than that of the conventional RT-PCR and comparable to nested RT-PCR and quantitative RT-PCR (qRT-PCR). There was no cross amplification with other related RNA viruses. In the clinical evaluation, the RT-LAMP assay exhibited a similar sensitivity with nested RT-PCR and qRT-PCR. The results indicated that RT-LAMP assay developed in this study could be a highly specific, sensitive, and cost-effective alternative for a rapid detection of PPgV in field settings.
Collapse
Affiliation(s)
- Hao Li
- Department of Preventive Veterinary Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, China; Key Laboratory for Animal Health of Jiangxi Province, Nanchang, Jiangxi, 330045, China
| | - Kai Li
- Department of Preventive Veterinary Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, China; Key Laboratory for Animal Health of Jiangxi Province, Nanchang, Jiangxi, 330045, China
| | - Zhen Bi
- Department of Preventive Veterinary Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, China; Key Laboratory for Animal Health of Jiangxi Province, Nanchang, Jiangxi, 330045, China
| | - Jun Gu
- Department of Preventive Veterinary Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, China; Key Laboratory for Animal Health of Jiangxi Province, Nanchang, Jiangxi, 330045, China
| | - Deping Song
- Department of Preventive Veterinary Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, China; Key Laboratory for Animal Health of Jiangxi Province, Nanchang, Jiangxi, 330045, China
| | - Dan Lei
- Department of Preventive Veterinary Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, China; Key Laboratory for Animal Health of Jiangxi Province, Nanchang, Jiangxi, 330045, China
| | - Suoxian Luo
- Department of Preventive Veterinary Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, China; Key Laboratory for Animal Health of Jiangxi Province, Nanchang, Jiangxi, 330045, China
| | - Dongyan Huang
- Department of Preventive Veterinary Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, China; Key Laboratory for Animal Health of Jiangxi Province, Nanchang, Jiangxi, 330045, China
| | - Qiong Wu
- Department of Preventive Veterinary Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, China; Key Laboratory for Animal Health of Jiangxi Province, Nanchang, Jiangxi, 330045, China
| | - Zhen Ding
- Department of Preventive Veterinary Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, China; Key Laboratory for Animal Health of Jiangxi Province, Nanchang, Jiangxi, 330045, China
| | - Leyi Wang
- Department of Veterinary Clinical Medicine and the Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL, 61802, USA
| | - Yu Ye
- Department of Preventive Veterinary Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, China; Key Laboratory for Animal Health of Jiangxi Province, Nanchang, Jiangxi, 330045, China.
| | - Yuxin Tang
- Department of Preventive Veterinary Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, China; Key Laboratory for Animal Health of Jiangxi Province, Nanchang, Jiangxi, 330045, China.
| |
Collapse
|
37
|
Breitwieser FP, Lu J, Salzberg SL. A review of methods and databases for metagenomic classification and assembly. Brief Bioinform 2019; 20:1125-1136. [PMID: 29028872 PMCID: PMC6781581 DOI: 10.1093/bib/bbx120] [Citation(s) in RCA: 261] [Impact Index Per Article: 52.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 08/22/2017] [Indexed: 12/13/2022] Open
Abstract
Microbiome research has grown rapidly over the past decade, with a proliferation of new methods that seek to make sense of large, complex data sets. Here, we survey two of the primary types of methods for analyzing microbiome data: read classification and metagenomic assembly, and we review some of the challenges facing these methods. All of the methods rely on public genome databases, and we also discuss the content of these databases and how their quality has a direct impact on our ability to interpret a microbiome sample.
Collapse
Affiliation(s)
| | | | - Steven L Salzberg
- Corresponding author: Steven L. Salzberg, Center for Computational Biology, Johns Hopkins University, 1900 E. Monument St., Baltimore, MD, 21205, USA. E-mail:
| |
Collapse
|
38
|
Abstract
Microbiome research has grown rapidly over the past decade, with a proliferation of new methods that seek to make sense of large, complex data sets. Here, we survey two of the primary types of methods for analyzing microbiome data: read classification and metagenomic assembly, and we review some of the challenges facing these methods. All of the methods rely on public genome databases, and we also discuss the content of these databases and how their quality has a direct impact on our ability to interpret a microbiome sample.
Collapse
|
39
|
Sridhar S, Yip CCY, Chew NFS, Wu S, Leung KH, Chan JFW, Cheng VCC, Yuen KY. Epidemiological and Clinical Characteristics of Human Hepegivirus 1 Infection in Patients With Hepatitis C. Open Forum Infect Dis 2019; 6:ofz329. [PMID: 31660385 PMCID: PMC6735942 DOI: 10.1093/ofid/ofz329] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 07/11/2019] [Indexed: 12/13/2022] Open
Abstract
Background Transmission of human hepegivirus 1 (HHpgV-1), a novel human pegivirus, is closely associated with hepatitis C virus (HCV). The impact of HHpgV-1 viremia on HCV infection is unknown. This study aimed to (a) evaluate the impact of HHpgV-1 viremia on HCV viral load and liver injury and (b) elucidate the clinical and molecular epidemiology of HHpgV-1 infection. Methods Individuals with HHpgV-1 viremia (cases) were identified by screening plasma from 655 HCV-infected adults. HHpgV-1 isolates were sequenced for phylogenetic analysis, and viral load was quantified. Cases were age- and sex-matched to HCV-infected individuals without HHpgV-1 viremia (controls) in a 1:3 ratio. A retrospective case–control analysis was performed to identify differences in HCV viral load and parameters of liver injury. Results Among HCV-infected adults, 16/655 (2.4%) had HHpgV-1 viremia. Risk groups for HHpgV-1 infection included intravenous drug users, blood product recipients, tattoo recipients, and men who have sex with men. Viral sequences clustered into 2 distinct HHpgV-1 genogroups. Cases had a higher mean HCV viral load than controls, with difference between means of 0.58 log10 IU/mL (P = .009). Cases were more likely to have an HCV viral load >5 log10 IU/mL (P = .028). Multiple regression demonstrated the impact of HHpgV-1 viral load and infection status on HCV viral load. HHpgV-1 infection was not associated with higher liver function tests, fibrosis scores, or imaging abnormalities. Conclusions HHpgV-1 viremia is associated with a higher HCV viral load in co-infected patients. HHpgV-1 infection does not affect progression of HCV-related liver disease.
Collapse
Affiliation(s)
- Siddharth Sridhar
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong - Shenzhen Hospital, The University of Hong Kong, Hong Kong.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong.,Department of Microbiology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong
| | - Cyril C Y Yip
- Department of Microbiology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Nicholas F S Chew
- Department of Microbiology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Shusheng Wu
- Department of Microbiology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Kit-Hang Leung
- Department of Microbiology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Jasper F W Chan
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong - Shenzhen Hospital, The University of Hong Kong, Hong Kong.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong.,Department of Microbiology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong
| | - Vincent C C Cheng
- Department of Microbiology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Kwok-Yung Yuen
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong - Shenzhen Hospital, The University of Hong Kong, Hong Kong.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong.,Department of Microbiology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong.,The Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong
| |
Collapse
|
40
|
Anh NT, Hong NTT, Nhu LNT, Thanh TT, Anscombe C, Chau LN, Thanh TTT, Lau CY, Limmathurotsakul D, Chau NVV, Rogier van Doorn H, Deng X, Rahman M, Delwart E, Le T, Thwaites G, Van Tan L. Detection and Characterization of Human Pegivirus 2, Vietnam. Emerg Infect Dis 2019; 24:2063-2067. [PMID: 30334714 PMCID: PMC6199981 DOI: 10.3201/eid2411.180668] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
We report human pegivirus 2 (HPgV-2) infection in Vietnam. We detected HPgV-2 in some patients with hepatitis C virus/HIV co-infection but not in patients with HIV or hepatitis A, B, or C virus infection, nor in healthy controls. HPgV-2 strains in Vietnam are phylogenetically related to global strains.
Collapse
|
41
|
Shui J, Liu W, Liang Y, Zhang J, Wan Z, Wang H, Qu X, Tang S. Infection of human pegivirus 2 (HPgV-2) is associated with hepatitis C virus but not hepatitis B virus infection in people who inject drugs. J Gen Virol 2019; 100:968-974. [PMID: 31090532 DOI: 10.1099/jgv.0.001266] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
We evaluated the association between human pegivirus-2 (HPgV-2) infection and hepatitis C virus (HCV)/hepatitis B virus (HBV) co-infection in 745 plasma samples collected from HCV-positive but human immunodeficiency virus type one (HIV-1)-negative people who inject drugs in Hunan, China. The prevalence of anti-HPgV-2 was 4.43 % (33/745) and, within this, the HCV 6a genotype showed significantly higher prevalence as compared with the HCV non-6a genotypes, 6.29 % (18/286) vs. 1.69 % (4/236), respectively (P=0.009). HPgV-2 RNA was detected in 2.15 % (16/745), and was not significantly different between the HCV 6a and non-6a genotypes, 2.45 % (7/286) vs. 2.54 % (6/236), respectively (P =0.945). HBV single infection did not increase the risk of HPgV-2 infection. Compared with HCV single infection, HCV/HBV co-infection increased the risk of HPgV-2 infection by about three-fold: odds ratio (OR)=3.24 [95 % confidence interval (CI) 1.34-7.82, P=0.014] according to anti-HPgV-2 positivity or OR=3.51 (95 % CI 1.15-10.74, P=0.051) according to HPgV-2 viraemia. HPgV-2 infection did not increase the levels of liver-specific enzymes. Our study provides new findings regarding the association between HPgV-2 and HCV genotypes as well as HCV/HBV co-infection.
Collapse
Affiliation(s)
- Jingwei Shui
- 1 Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, PR China
| | - Wenpei Liu
- 2 Translational Medicine Institute, The First People's Hospital of Chenzhou, University of South China, Chenzhou, Hunan, PR China
| | - Yuanhao Liang
- 1 Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, PR China
| | - Jian Zhang
- 2 Translational Medicine Institute, The First People's Hospital of Chenzhou, University of South China, Chenzhou, Hunan, PR China
| | - Zhengwei Wan
- 1 Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, PR China
| | - Haiying Wang
- 1 Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, PR China
| | - Xiaowang Qu
- 2 Translational Medicine Institute, The First People's Hospital of Chenzhou, University of South China, Chenzhou, Hunan, PR China
| | - Shixing Tang
- 1 Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, PR China
- 3 Dermatology Hospital, Southern Medical University, Guangzhou, PR China
| |
Collapse
|
42
|
Chen F, Knutson TP, Braun E, Jiang Y, Rossow S, Marthaler DG. Semi-quantitative duplex RT-PCR reveals the low occurrence of Porcine Pegivirus and Atypical Porcine Pestivirus in diagnostic samples from the United States. Transbound Emerg Dis 2019; 66:1420-1425. [PMID: 30806022 PMCID: PMC6849716 DOI: 10.1111/tbed.13154] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 01/24/2019] [Accepted: 02/16/2019] [Indexed: 02/06/2023]
Abstract
Porcine Pegivirus (PPgV) and Atypical Porcine Pestivirus (APPV) are two recently identified porcine viruses. In this study, the identification of two viruses by metagenomic sequencing, and a duplex semi‐quantitative RT‐PCR was developed to detect these pathogens simultaneously. The PPgV strain Minnesota‐1/2016 had a 95.5%–96.3% nucleotide identity and clustered with the recently identified US PPgV strains, which is a distant clade from the German PPgV strains. The APPV strain Minnesota‐1/2016 shared an 87.3%–92.0% nucleotide identity with the other global APPV strains identity but only shared an 82.8%–83.0% nucleotide identity with clade II consisting of strain identified in China. Detection of both PPgV and APPV was 9.0% of the diagnostic cases. Co‐infection of PPgV and APPV was identified in 7.5% of the diagnostic cases. The occurrence and genetic characterization of PPgV and APPV further enhance our knowledge regarding these new pathogens in the United States.
Collapse
Affiliation(s)
- Fangzhou Chen
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota.,State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Todd P Knutson
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota
| | - Eli Braun
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota
| | - Yin Jiang
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota
| | - Stephanie Rossow
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota
| | - Douglas G Marthaler
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota.,Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas
| |
Collapse
|
43
|
Wang H, Wan Z, Sun Q, Zhu N, Li T, Ren X, An X, Deng S, Wu Y, Li X, Li L, Li J, Tong Y, Tang S. Second Human Pegivirus in Hepatitis C Virus-Infected and Hepatitis C Virus/HIV-1-Co-infected Persons Who Inject Drugs, China. Emerg Infect Dis 2019; 24:908-911. [PMID: 29664364 PMCID: PMC5938795 DOI: 10.3201/eid2405.161162] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
We report the presence of the second human pegivirus (HPgV-2) in Guangdong and Sichuan Provinces in China. The prevalence of HPgV-2 in hepatitis C virus/HIV-1–co-infected persons who inject drugs was 12.9% in Guangdong and 15.9% in Sichuan. This population is at high risk for HPgV-2 infection.
Collapse
|
44
|
Rodrigues TCS, Subramaniam K, McCulloch SD, Goldstein JD, Schaefer AM, Fair PA, Reif JS, Bossart GD, Waltzek TB. Genomic characterization of a novel pegivirus species from free-ranging bottlenose dolphins (Tursiops truncatus) in the Indian River Lagoon, Florida. Virus Res 2019; 263:98-101. [PMID: 30633958 DOI: 10.1016/j.virusres.2019.01.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 01/07/2019] [Accepted: 01/08/2019] [Indexed: 11/15/2022]
Abstract
We report the discovery of the first cetacean pegivirus (family Flaviviridae) using a next-generation sequencing approach. One of two infected bottlenose dolphins had elevated activities of liver enzymes, which may suggest hepatocellular injury. Further research is needed to determine the epidemiology and pathogenicity of dolphin pegivirus.
Collapse
Affiliation(s)
| | | | - Stephen D McCulloch
- Protect Wild Dolphins Alliance, 2046 Treasure Coast Plaza, 32960, Vero Beach, FL, USA
| | - Juli D Goldstein
- Protect Wild Dolphins Alliance, 2046 Treasure Coast Plaza, 32960, Vero Beach, FL, USA
| | - Adam M Schaefer
- Florida Atlantic University, 5600 US 1, North, 34946, Fort Pierce, FL, USA
| | - Patricia A Fair
- Medical University of South Carolina, 179 Ashley Ave, 29425, Charleston, SC, USA
| | - John S Reif
- Colorado State University, 102 Administration Bldg, 80523, Fort Collins, CO, USA
| | - Gregory D Bossart
- Georgia Aquarium, 225 Baker Street, 30313, Atlanta, GA, USA; University of Miami, PO Box 016960 (R-46), 33101, Miami, FL, USA
| | - Thomas B Waltzek
- University of Florida, 2187 Mowry Road, 32611, Gainesville, FL, USA.
| |
Collapse
|
45
|
Rodgers MA, Holzmayer V, Vallari A, Olivo A, Forberg K, Fuhrman J, Coller KE, Awazi B, Kenmegne Sidje JB, Frankel MB, Berg MG, Mbanya D, Ndembi N, Cloherty GA. Hepatitis C virus surveillance and identification of human pegivirus 2 in a large Cameroonian cohort. J Viral Hepat 2019; 26:30-37. [PMID: 30187640 PMCID: PMC7379692 DOI: 10.1111/jvh.12996] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 07/20/2018] [Accepted: 08/14/2018] [Indexed: 12/11/2022]
Abstract
The prevalence of chronic hepatitis C virus (HCV) and the presence of human pegivirus 2 (HPgV-2) have not been examined in Cameroon, although HCV has been associated with HPgV-2 infections previously. Herein we aimed to characterize the burden and genetic diversity of HCV and the presence of HPgV-2 in Cameroon. Retrospective plasma specimens collected from N = 12 369 consenting subjects in South Cameroon from 2013 to 2016 were included in the study. The majority (97.1%) of participants were patients seeking health care. All specimens were screened for HCV using the Abbott RealTime HCV viral load assay and positive specimens with remaining volume were also screened for HPgV-2 antibodies on the Abbott ARCHITECT instrument, followed by molecular characterization. Overall, HCV RNA was detected in 305 (2.47%; 95% CI: 2.21%-2.75%) specimens. Notably, the prevalence of HCV RNA was 9.09% amongst participants over age 40 and 3.81% amongst males. Phylogenetic classification of N = 103 HCV sequences identified genotypes 1 (19.4%), 2 (15.5%) and 4 (65.1%) within the study cohort. Amongst HCV RNA-positive specimens, N = 28 (10.6%; 95% CI: 7.44%-14.90%) specimens also had detectable HPgV-2 antibodies. Of these, N = 2 viremic HPgV-2 infections were confirmed by sequencing and shared 93-94 median % identity with strains found on other continents. This is the first study to determine the prevalence of chronic HCV in Cameroon, and the discovery of HPgV-2 in this study cohort expands the geography of HPgV-2 to the African continent, indicating a widespread distribution exists.
Collapse
Affiliation(s)
| | | | | | - Ana Olivo
- Abbott LaboratoriesAbbott ParkIllinoisUSA
| | | | | | | | - Bih Awazi
- Université de Yaoundé IYaoundéCameroon
| | | | | | | | - Dora Mbanya
- Université de Yaoundé IYaoundéCameroon,University of BamendaBamendaCameroon
| | | | | |
Collapse
|
46
|
Greninger AL, Naccache SN. Metagenomics to Assist in the Diagnosis of Bloodstream Infection. J Appl Lab Med 2018; 3:643-653. [PMID: 31639732 DOI: 10.1373/jalm.2018.026120] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 11/08/2018] [Indexed: 12/13/2022]
Abstract
BACKGROUND Metagenomic next-generation sequencing (mNGS) has emerged as a promising technology that enables pan-pathogen detection from any source. However, clinical utility and practical integration into the clinical microbiology work flow and a bloodstream infection detection algorithm are currently uncharted. In the context of bloodstream infections, the challenges associated with blood culture, including sensitivity, postantibiotic treatment, attaining sufficient volumes sufficient volumes, and turnaround time, are well-known. Molecular assays have helped expedite turnaround time, especially when performed directly from positive culture media bottles. mNGS offers an unbiased but more complex version of molecular testing directly from sample, but it is unclear how and if it should be implemented in the clinical microbiology laboratory today. CONTENT Here we map out the potential utility and application of mNGS tests to infectious disease diagnostics from blood sources, including intrinsic limitations of the methodology in diagnosing bloodstream infections and sepsis vs DNAemia, current barriers to integration into routine workup, and milestones that may need to be met before implementation. SUMMARY Polymerases and pores move faster than bugs divide, so the thermodynamics of mNGS adoption for bloodstream infection is favorable. Nonetheless, considerable activation barriers exist that will slow this likely diagnostic transition. We eagerly await the manufacturer who designs an integrated sample-to-answer box to do for mNGS what has been done for other aspects of molecular detection.
Collapse
Affiliation(s)
| | - Samia N Naccache
- Department of Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA
| |
Collapse
|
47
|
Virus discovery reveals frequent infection by diverse novel members of the Flaviviridae in wild lemurs. Arch Virol 2018; 164:509-522. [PMID: 30460488 DOI: 10.1007/s00705-018-4099-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 10/31/2018] [Indexed: 12/13/2022]
Abstract
Lemurs are highly endangered mammals inhabiting the forests of Madagascar. In this study, we performed virus discovery on serum samples collected from 84 wild lemurs and identified viral sequence fragments from 4 novel viruses within the family Flaviviridae, including members of the genera Hepacivirus and Pegivirus. The sifaka hepacivirus (SifHV, two genotypes) and pegivirus (SifPgV, two genotypes) were discovered in the diademed sifaka (Propithecus diadema), while other pegiviral fragments were detected in samples from the indri (Indri indri, IndPgV) and the weasel sportive lemur (Lepilemur mustelinus, LepPgV). Although data are preliminary, each viral species appeared host species-specific and frequent infection was detected (18 of 84 individuals were positive for at least one virus). The complete coding sequence and partial 5' and 3' untranslated regions (UTRs) were obtained for SifHV and its genomic organization was consistent with that of other hepaciviruses, with one unique polyprotein and highly structured UTRs. Phylogenetic analyses showed the SifHV belonged to a clade that includes several viral species identified in rodents from Asia and North America, while SifPgV and IndPgV were more closely related to pegiviral species A and C, that include viruses found in humans as well as New- and Old-World monkeys. Our results support the current proposed model of virus-host co-divergence with frequent occurrence of cross-species transmission for these genera and highlight how the discovery of more members of the Flaviviridae can help clarify the ecology and evolutionary history of these viruses. Furthermore, this knowledge is important for conservation and captive management of lemurs.
Collapse
|
48
|
Optimizing a Metatranscriptomic Next-Generation Sequencing Protocol for Bronchoalveolar Lavage Diagnostics. J Mol Diagn 2018; 21:251-261. [PMID: 30389465 DOI: 10.1016/j.jmoldx.2018.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 09/05/2018] [Accepted: 09/27/2018] [Indexed: 12/16/2022] Open
Abstract
Compared with conventional serologic, culture-based, and molecular-based diagnostic tests, next-generation sequencing (NGS) provides sequence-evidenced detection of various microbes, without prior knowledge, and thus is becoming a novel diagnostic approach. Herein we describe an RNA-based metatranscriptomic NGS (mtNGS) protocol for culture-independent detection of potential infectious pathogens, using clinical bronchoalveolar lavage specimens as an example. We present both an optimized workflow for experimental sequence data collection and a simplified pipeline for bioinformatics sequence data processing. As shown, the whole protocol takes approximately 24 to 36 hours to detect a wide range of Gram-positive and -negative bacteria and possibly other viral and/or fungal pathogens. In particular, we introduce a spike-in RNA mix as an internal control, which plays a critical role in mitigating false-positive and false-negative results of clinical diagnostic tests. Moreover, our mtNGS method can detect antibiotic resistance genes and virulence factors; although it may not be comprehensive, such information is imperative and helpful for the clinician to make better treatment decisions. Results from our preliminary testing suggest that the mtNGS approach is a useful alterative in diagnostic detection of emerging infectious pathogens in clinical laboratories. However, further improvements are needed to achieve better sensitivity and accuracy.
Collapse
|
49
|
Jordier F, Deligny ML, Barré R, Robert C, Galicher V, Uch R, Fournier PE, Raoult D, Biagini P. Human pegivirus isolates characterized by deep sequencing from hepatitis C virus-RNA and human immunodeficiency virus-RNA-positive blood donations, France. J Med Virol 2018; 91:38-44. [PMID: 30133782 DOI: 10.1002/jmv.25290] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 08/14/2018] [Indexed: 01/18/2023]
Abstract
Human pegivirus (HPgV, formerly GBV-C) is a member of the genus Pegivirus, family Flaviviridae. Despite its identification more than 20 years ago, both natural history and distribution of this viral group in human hosts remain under exploration. Analysis of HPgV genomes characterized up to now points out the scarcity of French pegivirus sequences in databases. To bring new data regarding HPgV genomic diversity, we investigated 16 French isolates obtained from hepatitis C virus-RNA and human immunodeficiency virus-RNA-positive blood donations following deep sequencing and coupled molecular protocols. Initial phylogenetic analysis of 5'-untranslated region (5'-UTR)/E2 partial sequences permitted to assign HPgV isolates to genotypes 2 (n = 15) and 1 (n = 1), with up to 16% genetic diversity observed for both regions considered. Seven nearly full-length representative genomes were characterized subsequently, with complete polyprotein coding sequences exhibiting up to 13% genetic diversity; closest nucleotide (nt) divergence with available HPgV sequences was in the range 7% to 11%. A 36 nts deletion located on the NS4B coding region (N-terminal part, 12 amino acids) of the genotype 1 HPgV genome characterized was identified, along with single nucleotide deletions in two genotype 2, 5'-UTR sequences.
Collapse
Affiliation(s)
- François Jordier
- Biologie des Groupes Sanguins, Etablissement Français du Sang Provence Alpes Côte d'Azur Corse, Aix Marseille University, CNRS, EFS, ADES, Marseille, France
| | - Marie-Laurence Deligny
- Biologie des Groupes Sanguins, Etablissement Français du Sang Provence Alpes Côte d'Azur Corse, Aix Marseille University, CNRS, EFS, ADES, Marseille, France
| | - Romain Barré
- Biologie des Groupes Sanguins, Etablissement Français du Sang Provence Alpes Côte d'Azur Corse, Aix Marseille University, CNRS, EFS, ADES, Marseille, France
| | - Catherine Robert
- UMR MEPHI, IRD, Aix Marseille University, AP-HM, IHU Méditerranée-Infection, Marseille, France
| | - Vital Galicher
- Biologie des Groupes Sanguins, Etablissement Français du Sang Provence Alpes Côte d'Azur Corse, Aix Marseille University, CNRS, EFS, ADES, Marseille, France
| | - Rathviro Uch
- Biologie des Groupes Sanguins, Etablissement Français du Sang Provence Alpes Côte d'Azur Corse, Aix Marseille University, CNRS, EFS, ADES, Marseille, France
| | - Pierre-Edouard Fournier
- UMR VITROME, IRD, Aix Marseille University, SSA, AP-HM, IHU Méditerranée-Infection, Marseille, France
| | - Didier Raoult
- UMR MEPHI, IRD, Aix Marseille University, AP-HM, IHU Méditerranée-Infection, Marseille, France
| | - Philippe Biagini
- Biologie des Groupes Sanguins, Etablissement Français du Sang Provence Alpes Côte d'Azur Corse, Aix Marseille University, CNRS, EFS, ADES, Marseille, France
| |
Collapse
|
50
|
Yamaguchi J, Olivo A, Laeyendecker O, Forberg K, Ndembi N, Mbanya D, Kaptue L, Quinn TC, Cloherty GA, Rodgers MA, Berg MG. Universal Target Capture of HIV Sequences From NGS Libraries. Front Microbiol 2018; 9:2150. [PMID: 30271393 PMCID: PMC6146096 DOI: 10.3389/fmicb.2018.02150] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 08/22/2018] [Indexed: 11/13/2022] Open
Abstract
Background: Global surveillance of viral sequence diversity is needed to keep pace with the constant evolution of HIV. Recent next generation sequencing (NGS) methods have realized the goal of sequencing circulating virus directly from patient specimens. Yet, a simple, universal approach that maximizes sensitivity and sequencing capacity remains elusive. Here we present a novel HIV enrichment strategy to yield near complete genomes from low viral load specimens. Methodology: A non-redundant biotin-labeled probe set (HIV-xGen; n = 652) was synthesized to tile all HIV-1 (groups M, N, O, and P) and HIV-2 (A and B) strains. Illumina Nextera barcoded libraries of either gene-specific or randomly primed cDNA derived from infected plasma were hybridized to probes in a single pool and unbound sequences were washed away. Captured viral cDNA was amplified by Illumina adaptor primers, sequenced on a MiSeq, and NGS reads were demultiplexed for alignment with CLC Bio software. Results: HIV-xGen probes selectively captured and amplified reads spanning the entirety of the HIV phylogenetic tree. HIV sequences clearly present in unenriched libraries of specimens but previously not observed due to high host background levels, insufficient sequencing depth or the extent of multiplexing, were now enriched by >1,000-fold. Thus, xGen selection not only substantially increased the depth of existing sequence, but also extended overall genome coverage by an average of 40%. We characterized 50 new, diverse HIV strains from clinical specimens and demonstrated a viral load cutoff of approximately log 3.5 copies/ml for full length coverage. Genome coverage was <20% for 5/10 samples with viral loads <log 3.5 copies/ml and >90% for 35/40 samples with higher viral loads. Conclusions: Characterization of >20 complete genomes at a time is now possible from a single probe hybridization and MiSeq run. With the versatility to capture all HIV strains and the sensitivity to detect low titer specimens, HIV-xGen will serve as an important tool for monitoring HIV sequence diversity.
Collapse
Affiliation(s)
- Julie Yamaguchi
- Infectious Diseases Research, Abbott Diagnostics, Chicago, IL, United States
| | - Ana Olivo
- Infectious Diseases Research, Abbott Diagnostics, Chicago, IL, United States
| | - Oliver Laeyendecker
- National Institute of Allergy and Infectious Diseases, NIH, Baltimore, MD, United States
| | - Kenn Forberg
- Infectious Diseases Research, Abbott Diagnostics, Chicago, IL, United States
| | | | - Dora Mbanya
- Université de Yaoundé 1, Yaoundé, Cameroon.,University of Bamenda, Bamenda, Cameroon
| | | | - Thomas C Quinn
- National Institute of Allergy and Infectious Diseases, NIH, Baltimore, MD, United States
| | - Gavin A Cloherty
- Infectious Diseases Research, Abbott Diagnostics, Chicago, IL, United States
| | - Mary A Rodgers
- Infectious Diseases Research, Abbott Diagnostics, Chicago, IL, United States
| | - Michael G Berg
- Infectious Diseases Research, Abbott Diagnostics, Chicago, IL, United States
| |
Collapse
|