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Shi Y, Tang H, Zhou ZJ, Liao JY, Ge XY, Xiao CT. First detection of Tetraparvovirus ungulate 1 in diseased cattle (Chinese Simmental) from Hunan province, China. Virol J 2024; 21:132. [PMID: 38844968 PMCID: PMC11155090 DOI: 10.1186/s12985-024-02402-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 05/28/2024] [Indexed: 06/10/2024] Open
Abstract
Tetraparvovirus is an emerging parvovirus infecting a variety of mammals and humans, and associated with human diseases including severe acute respiratory infection and acute encephalitis syndrome. In the present study, a Tetraparvovirus ungulate 1 (formerly known as bovine hokovirus) strain HNU-CBY-2023 was identified and characterized from diseased Chinese Simmental from Hunan province, China. The nearly complete genome of HNU-CBY-2023 is 5346 nt in size and showed genomic identities of 85-95.5% to the known Tetraparvovirus ungulate 1 strains from GenBank, indicating a rather genetic variation. Phylogenetic and genetic divergence analyses indicated that Tetraparvovirus ungulate 1 could be divided into two genotypes (I and II), and HNU-CBY-2023 was clustered into genotype II. This study, for the first time, identified Tetraparvovirus ungulate 1 from domestic cattle from mainland China, which will be helpful to understand the prevalence and genetic diversity of Tetraparvovirus ungulate 1.
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Affiliation(s)
- Yin Shi
- Institute of Pathogen Biology and Immunology, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082, China
| | - Hui Tang
- Institute of Pathogen Biology and Immunology, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082, China
| | - Zhi-Jian Zhou
- Institute of Pathogen Biology and Immunology, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082, China
| | - Jing-Ying Liao
- Institute of Pathogen Biology and Immunology, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082, China
| | - Xing-Yi Ge
- Institute of Pathogen Biology and Immunology, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082, China
| | - Chao-Ting Xiao
- Institute of Pathogen Biology and Immunology, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082, China.
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2
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Namuwulya P, Ashraf S, Niebel M, Ssekagiri A, Tushabe P, Kakooza P, Tong L, Bukenya H, Jerome H, Davis C, Birungi M, Turyahabwe I, Mugaga A, Eliku JP, Francis A, Nakabazzi L, Nsubuga F, Katushabe E, Kisakye A, Ampeire I, Nanteza A, Kaleebu P, Bakamutumaho B, Nsamba P, Kazibwe A, da Silva Filipe A, Tweyongyere R, Bwogi J, Thomson EC. Viruses associated with measles-like illnesses in Uganda. J Infect 2024; 88:106148. [PMID: 38588959 PMCID: PMC11060986 DOI: 10.1016/j.jinf.2024.106148] [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: 08/26/2023] [Revised: 03/13/2024] [Accepted: 03/25/2024] [Indexed: 04/10/2024]
Abstract
OBJECTIVES In this study, we investigated the causes of measles-like illnesses (MLI) in the Uganda national surveillance program in order to inform diagnostic assay selection and vaccination strategies. METHODS We used metagenomic next-generation sequencing (M-NGS) on the Illumina platform to identify viruses associated with MLI (defined as fever and rash in the presence of either cough, coryza or conjunctivitis) in patient samples that had tested IgM negative for measles between 2010 and 2019. RESULTS Viral genomes were identified in 87/271 (32%) of samples, of which 44/271 (16%) contained 12 known viral pathogens. Expected viruses included rubella, human parvovirus B19, Epstein Barr virus, human herpesvirus 6B, human cytomegalovirus, varicella zoster virus and measles virus (detected within the seronegative window-period of infection) and the blood-borne hepatitis B virus. We also detected Saffold virus, human parvovirus type 4, the human adenovirus C2 and vaccine-associated poliovirus type 1. CONCLUSIONS The study highlights the presence of undiagnosed viruses causing MLI in Uganda, including vaccine-preventable illnesses. NGS can be used to monitor common viral infections at a population level, especially in regions where such infections are prevalent, including low and middle income countries to guide vaccination policy and optimize diagnostic assays.
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Affiliation(s)
| | - Shirin Ashraf
- MRC - University of Glasgow Centre for Virus Research (CVR), Glasgow, UK
| | - Marc Niebel
- MRC - University of Glasgow Centre for Virus Research (CVR), Glasgow, UK
| | | | | | | | - Lily Tong
- MRC - University of Glasgow Centre for Virus Research (CVR), Glasgow, UK
| | - Henry Bukenya
- Uganda Virus Research Institute (UVRI), Entebbe, Uganda
| | - Hanna Jerome
- MRC - University of Glasgow Centre for Virus Research (CVR), Glasgow, UK
| | - Chris Davis
- MRC - University of Glasgow Centre for Virus Research (CVR), Glasgow, UK
| | - Molly Birungi
- Uganda Virus Research Institute (UVRI), Entebbe, Uganda
| | | | - Arnold Mugaga
- Uganda Virus Research Institute (UVRI), Entebbe, Uganda
| | | | - Aine Francis
- Uganda Virus Research Institute (UVRI), Entebbe, Uganda
| | | | | | | | | | | | - Ann Nanteza
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | | | | | - Peninah Nsamba
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Anne Kazibwe
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | | | - Robert Tweyongyere
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | | | - Emma C Thomson
- MRC - University of Glasgow Centre for Virus Research (CVR), Glasgow, UK; London School of Hygiene and Tropical Medicine (LSHTM), London, UK.
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3
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Viral agents (2nd section). Transfusion 2024; 64 Suppl 1:S19-S207. [PMID: 38394038 DOI: 10.1111/trf.17630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 12/02/2023] [Indexed: 02/25/2024]
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4
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Soria-Villalba A, Pesantes N, Jiménez-Hernández N, Pons J, Moya A, Pérez-Brocal V. Comparison of Experimental Methodologies Based on Bulk-Metagenome and Virus-like Particle Enrichment: Pros and Cons for Representativeness and Reproducibility in the Study of the Fecal Human Virome. Microorganisms 2024; 12:162. [PMID: 38257988 PMCID: PMC10820677 DOI: 10.3390/microorganisms12010162] [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: 12/21/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
Studies on the human virome based on the application of metagenomic approaches involve overcoming a series of challenges and limitations inherent not only to the biological features of viruses, but also to methodological pitfalls which different approaches have tried to minimize. These approaches fall into two main categories: bulk-metagenomes and virus-like particle (VLP) enrichment. In order to address issues associated with commonly used experimental procedures to assess the degree of reliability, representativeness, and reproducibility, we designed a comparative analysis applied to three experimental protocols, one based on bulk-metagenomes and two based on VLP enrichment. These protocols were applied to stool samples from 10 adult participants, including two replicas per protocol and subject. We evaluated the performances of the three methods, not only through the analysis of the resulting composition, abundance, and diversity of the virome via taxonomical classification and type of molecule (DNA versus RNA, single stranded vs. double stranded), but also according to how the a priori identical replicas differed from each other according to the extraction methods used. Our results highlight the strengths and weaknesses of each approach, offering valuable insights and tailored recommendations for drawing reliable conclusions based on specific research goals.
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Affiliation(s)
| | - Nicole Pesantes
- Area of Genomics and Health, Foundation for the Promotion of Sanitary and Biomedical Research of Valencia Region (FISABIO-Public Health), 46020 Valencia, Spain; (N.P.); (N.J.-H.); (J.P.); (A.M.)
- Biomedical Research Networking Center for Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
| | - Nuria Jiménez-Hernández
- Area of Genomics and Health, Foundation for the Promotion of Sanitary and Biomedical Research of Valencia Region (FISABIO-Public Health), 46020 Valencia, Spain; (N.P.); (N.J.-H.); (J.P.); (A.M.)
- Biomedical Research Networking Center for Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
| | - Javier Pons
- Area of Genomics and Health, Foundation for the Promotion of Sanitary and Biomedical Research of Valencia Region (FISABIO-Public Health), 46020 Valencia, Spain; (N.P.); (N.J.-H.); (J.P.); (A.M.)
| | - Andrés Moya
- Area of Genomics and Health, Foundation for the Promotion of Sanitary and Biomedical Research of Valencia Region (FISABIO-Public Health), 46020 Valencia, Spain; (N.P.); (N.J.-H.); (J.P.); (A.M.)
- Biomedical Research Networking Center for Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia and Spanish National Research Council (CSIC), 46980 Valencia, Spain
| | - Vicente Pérez-Brocal
- Area of Genomics and Health, Foundation for the Promotion of Sanitary and Biomedical Research of Valencia Region (FISABIO-Public Health), 46020 Valencia, Spain; (N.P.); (N.J.-H.); (J.P.); (A.M.)
- Biomedical Research Networking Center for Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
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5
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Timmerman AL, Schönert ALM, van der Hoek L. Anelloviruses versus human immunity: how do we control these viruses? FEMS Microbiol Rev 2024; 48:fuae005. [PMID: 38337179 PMCID: PMC10883694 DOI: 10.1093/femsre/fuae005] [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: 11/09/2023] [Revised: 12/22/2023] [Accepted: 02/08/2024] [Indexed: 02/12/2024] Open
Abstract
One continuous companion and one of the major players in the human blood virome are members of the Anelloviridae family. Anelloviruses are probably found in all humans, infection occurs early in life and the composition (anellome) is thought to remain stable and personal during adulthood. The stable anellome implies a great balance between the host immune system and the virus. However, the lack of a robust culturing system hampers direct investigation of interactions between virus and host cells. Other techniques, however, including next generation sequencing, AnelloScan-antibody tests, evolution selection pressure analysis, and virus protein structures, do provide new insights into the interactions between anelloviruses and the host immune system. This review aims at providing an overview of the current knowledge on the immune mechanisms acting on anelloviruses and the countering viral mechanisms allowing immune evasion.
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Affiliation(s)
- Anne L Timmerman
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Postbus 22660, 1100 DD, Amsterdam, the Netherlands
| | - Antonia L M Schönert
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Postbus 22660, 1100 DD, Amsterdam, the Netherlands
| | - Lia van der Hoek
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Postbus 22660, 1100 DD, Amsterdam, the Netherlands
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6
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Ramezany H, Kheirandish M, Sharifi Z, Samiee S. Study on genotyping and coinfection rate of human parvovirus 4 among the HTLV-I/II infected blood donors in Khorasan Razavi, Iran. Heliyon 2023; 9:e21406. [PMID: 37954296 PMCID: PMC10637982 DOI: 10.1016/j.heliyon.2023.e21406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 10/19/2023] [Accepted: 10/20/2023] [Indexed: 11/14/2023] Open
Abstract
Human Parvovirus 4 (PARV4) is an emerging virus infecting individuals with other blood-borne diseases. This study aimed to determine the prevalence of PARV4 in confirmed HTLVI/II positive samples from blood donors, assessing PARV4 viral load (DNA) and genotyping. METHODS A novel qReal-Time PCR, based on a plasmid construct, was developed to simultaneously detect all three PARV4 genotypes using in-house primers and probes. Positive qPCR samples were subjected to nested PCR amplification and subsequent sequencing. Phylogenetic trees were constructed using the Neighbor-joining (N.J.) method. RESULTS The coinfection rate of PARV4-DNA in HTLVI/II confirmed infected donors, who were previously deferred, was 14.4 % (13 out of 90), with no observed association with donation status (p = 1.0). Phylogenetic analysis indicated that PARV4-positive samples closely resembled genotype 2 in Iran.qPCR quantification demonstrated significant PARV4 viral loads in positive samples, ranging between 104 and 106 DNA copies/mL of serum. CONCLUSION This study presents the first evaluation of HTLVI/II and PARV4coinfection rates among blood donors. Notably, elevated PARV4-DNA titers were detected in HTLVI/II-positive donors. Given PARV's resistance to standard plasma refinery inactivation methods and the absence of its targeted inactivation, its potential impact remains a concern.
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Affiliation(s)
- Hooman Ramezany
- Department of Immunology, Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Iranian Blood Transfusion Organization, Tehran, Tehran, Iran
| | - Maryam Kheirandish
- Department of Immunology, Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Iranian Blood Transfusion Organization, Tehran, Tehran, Iran
| | - Zohreh Sharifi
- Department of Medical Virology, Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Iran
| | - Shahram Samiee
- Department of Molecular Pathology, Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Iran
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7
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Abstract
Anelloviruses are the most common viruses infecting humans. Every human carries a nonpathogenic personal anellovirus virome (anellome), yet it is unknown which mechanisms contribute to its stability. Here, we assessed the dynamics and impact of a host antiviral defense mechanism-cytidine deaminase activity leading to C to U editing in anelloviruses-on the stability of the anellome. We investigated anellome sequence data obtained from serum samples collected every 6 months from two healthy subjects followed for more than 30 years. The subjects were infected by a total of 64 anellovirus lineages. Minus-stranded C to U editing was observed in lineages belonging to the Alpha-, Beta-, and Gammatorquevirus genera. The edited genomes were present within virus particles, therefore editing must have occurred at the late stages of the virus life cycle. Editing was favored by 5'-TC contexts in the virus genome, indicating that apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like, catalytic subunit 3 or A3 (APOBEC3) proteins are involved. Within a lineage, mutational dynamics varied over time and few fixations of mutations were detected, indicating that C to U editing is a dead end for a virus genome. We detected an editing coldspot in the GC-rich regions, suggesting that the GC-rich region is crucial for genome packaging, since only packaged virus particles were included in the analysis. Finally, we noticed a lineage-specific reduced concentration after an editing event, yet no clearance. In conclusion, cytidine deaminase activity does not clear anelloviruses, nor does it play a major role in virus evolution, but it does contribute to the stability of the anellome. IMPORTANCE Despite significant attention on anellovirus research, the interaction between the anellovirus virome and the human host remains unknown. We show the dynamics of APOBEC3-mediated cytidine deaminase activity on anelloviruses during a 30-year period of chronic infection and postulate that this antiviral mechanism controls anelloviruses. These results expand our knowledge of anellovirus-host interactions, which may be important for the design of gene therapies.
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8
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Chrzastek K, Sellers HS, Kapczynski DR. A Universal, Single-Primer Amplification Protocol to Perform Whole-Genome Sequencing of Segmented dsRNA Avian Orthoreoviruses. Avian Dis 2022; 66:479-485. [PMID: 36715482 DOI: 10.1637/aviandiseases-d-22-99999] [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: 05/31/2022] [Accepted: 05/31/2022] [Indexed: 01/15/2023]
Abstract
The Reoviridae family represents the largest family of double-stranded RNA viruses, and members have been isolated from a wide range of mammals, birds, reptiles, fishes, insects, and plants. Orthoreoviruses, one of the 15 recognized genera in the Reoviridae family, can infect humans and nearly all mammals and birds. Genomic characterization of reoviruses has not been adopted on a large scale because of the complexity of obtaining sequences for all 10 segments. In this study, we develop a time-efficient and practical method to enrich reovirus sequencing reads from isolates that allows for full-genome recovery using a single-primer amplification method coupled with next-generation sequencing. We refer to this protocol as reovirus-single-primer amplification (R-SPA). Our results demonstrate that most of the genes are covered with at least 500 reads per base space. Furthermore, R-SPA covers both the 5' and 3' ends of each reovirus genes. In summary, this study presents a universal and fast amplification protocol that yields sufficient double-stranded cDNA and facilitates and expedites the whole-genome sequencing of reoviruses.
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Affiliation(s)
- Klaudia Chrzastek
- Exotic and Emerging Avian Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, USDA, Athens, Georgia 30605,
| | - Holly S Sellers
- University of Georgia, Poultry Diagnostic & Research Center, Athens, GA 30602
| | - Darrell R Kapczynski
- Exotic and Emerging Avian Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, USDA, Athens, Georgia 30605,
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9
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Lakshmanan R, Mietzsch M, Jimenez Ybargollin A, Chipman P, Fu X, Qiu J, Söderlund-Venermo M, McKenna R. Capsid Structure of Aleutian Mink Disease Virus and Human Parvovirus 4: New Faces in the Parvovirus Family Portrait. Viruses 2022; 14:2219. [PMID: 36298773 PMCID: PMC9612331 DOI: 10.3390/v14102219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/06/2022] [Accepted: 10/07/2022] [Indexed: 11/07/2022] Open
Abstract
Parvoviruses are small, single-stranded DNA viruses with non-enveloped capsids. Determining the capsid structures provides a framework for annotating regions important to the viral life cycle. Aleutian mink disease virus (AMDV), a pathogen in minks, and human parvovirus 4 (PARV4), infecting humans, are parvoviruses belonging to the genera Amdoparvovirus and Tetraparvovirus, respectively. While Aleutian mink disease caused by AMDV is a major threat to mink farming, no clear clinical manifestations have been established following infection with PARV4 in humans. Here, the capsid structures of AMDV and PARV4 were determined via cryo-electron microscopy at 2.37 and 3.12 Å resolutions, respectively. Despite low amino acid sequence identities (10-30%) both viruses share the icosahedral nature of parvovirus capsids, with 60 viral proteins (VPs) assembling the capsid via two-, three-, and five-fold symmetry VP-related interactions, but display major structural variabilities in the surface loops when the capsid structures are superposed onto other parvoviruses. The capsid structures of AMDV and PARV4 will add to current knowledge of the structural platform for parvoviruses and permit future functional annotation of these viruses, which will help in understanding their infection mechanisms at a molecular level for the development of diagnostics and therapeutics.
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Affiliation(s)
- Renuk Lakshmanan
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32603, USA
| | - Mario Mietzsch
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32603, USA
| | - Alberto Jimenez Ybargollin
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32603, USA
| | - Paul Chipman
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32603, USA
| | - Xiaofeng Fu
- Biological Science Imaging Resource, Department of Biological Sciences, Florida State University, Tallahassee, FL 32306, USA
| | - Jianming Qiu
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | | | - Robert McKenna
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32603, USA
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Surphlis AC, Dill-Okubo JA, Harrach B, Waltzek T, Subramaniam K. Genomic characterization of psittacine adenovirus 2, a siadenovirus identified in a moribund African grey parrot (Psittacus erithacus). Arch Virol 2022; 167:911-916. [PMID: 35103853 DOI: 10.1007/s00705-021-05341-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 11/08/2021] [Indexed: 11/29/2022]
Abstract
Here, we report the complete genome sequence of psittacine adenovirus 2 from a moribund African grey parrot (Psittacus erithacus) with neurological signs and systemic inflammation. The complete siadenovirus genome is 25,386 bp in size. The results of genetic and phylogenetic analyses support its classification as a member of a novel species within the genus Siadenovirus. This study represents the first report of the genome sequence of an adenovirus from an African grey parrot.
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Affiliation(s)
- Austin C Surphlis
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA.,Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Jennifer A Dill-Okubo
- Florida Department of Agriculture and Consumer Services, Bronson Animal Disease Diagnostic Laboratory, Kissimmee, FL, USA
| | - Balázs Harrach
- Veterinary Medical Research Institute, Budapest, Hungary
| | - Thomas Waltzek
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA.,Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Kuttichantran Subramaniam
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA. .,Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.
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van Zyl GU. New Technological Developments in Identification and Monitoring of New and Emerging Infections. ENCYCLOPEDIA OF INFECTION AND IMMUNITY 2022. [PMCID: PMC8291697 DOI: 10.1016/b978-0-12-818731-9.00094-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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12
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Jager MC, Tomlinson JE, Lopez-Astacio RA, Parrish CR, Van de Walle GR. Small but mighty: old and new parvoviruses of veterinary significance. Virol J 2021; 18:210. [PMID: 34689822 PMCID: PMC8542416 DOI: 10.1186/s12985-021-01677-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 10/08/2021] [Indexed: 12/14/2022] Open
Abstract
In line with the Latin expression "sed parva forti" meaning "small but mighty," the family Parvoviridae contains many of the smallest known viruses, some of which result in fatal or debilitating infections. In recent years, advances in metagenomic viral discovery techniques have dramatically increased the identification of novel parvoviruses in both diseased and healthy individuals. While some of these discoveries have solved etiologic mysteries of well-described diseases in animals, many of the newly discovered parvoviruses appear to cause mild or no disease, or disease associations remain to be established. With the increased use of animal parvoviruses as vectors for gene therapy and oncolytic treatments in humans, it becomes all the more important to understand the diversity, pathogenic potential, and evolution of this diverse family of viruses. In this review, we discuss parvoviruses infecting vertebrate animals, with a special focus on pathogens of veterinary significance and viruses discovered within the last four years.
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Affiliation(s)
- Mason C Jager
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Joy E Tomlinson
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Robert A Lopez-Astacio
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Colin R Parrish
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Gerlinde R Van de Walle
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA.
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Asiyabi S, Marashi SM, Vahabpour R, Nejati A, Azizi-Saraji A, Mustafa AS, Baghernejad A, Shoja Z, Mansouritorghabeh H. Parvovirus 4 in Individuals with Severe Hemophilia A and Matched Control Group. Int J Hematol Oncol Stem Cell Res 2021; 15:192-198. [PMID: 35083000 PMCID: PMC8748245 DOI: 10.18502/ijhoscr.v15i3.6849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 11/29/2020] [Indexed: 11/24/2022] Open
Abstract
Background: Hemophilia is a well-known bleeding disorder with worldwide distribution. Replacement therapy, using plasma-derived or recombinant coagulation factors, comprises a gold standard regimen for the treatment. Regardless of the advancements made in viral inactivation methods in the production of plasma-derived coagulation factors, the possibility of transmission of new viral infections remained as a noticeable concern yet. The aim of the current study was to investigate the status of parvovirus 4 (PARV4) in severe hemophilia A, von Willebrand disease (vWD), and healthy control. Materials and Methods: In the current case-control study, 76 patients with hemophilia and vWD and 60 individuals from their family members entered the study. Nested PCR used to determine the presence of PARV4 in study subjects (76 cases). To characterize the PARV4 genotype, positive samples subjected to sequencing and phylogenetic analysis. Results: PARV4 genome detected in 11 (14.47%) patients with bleeding disorders. Among whom, nine patients (14.75%) were with severe hemophilia A and two (13.33%) patients with vWD. Only five healthy controls (8.33%) were positive for PARV4. All PARV4 sequences were found to be genotype 1. Conclusion: PARV4 infection in patients with hemophilia and vWD was higher than the control group. While detection of PARV4 DNA in patients with bleeding disorders may not necessarily reflect a clinical urgency, future investigations are needed to define the clinical significance of PARV4. It seems the detection of the virus immune signature of PARV4 infection, particularly in the context of acute and persistent infections, needs to focus on cellular and tissue targets.
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Affiliation(s)
- Sanaz Asiyabi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed Mahdi Marashi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Rouhollah Vahabpour
- Department of Medical Lab Technology, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ahmad Nejati
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Aliyeh Sadat Mustafa
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Asgar Baghernejad
- School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Zabiholla Shoja
- Department of Virology, Pasteur Institute of Iran, Tehran, Iran
| | - Hassan Mansouritorghabeh
- Central Diagnostic Laboratories, Ghaem Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
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14
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Kyrychenko AN, Shcherbatenko IS, Kovalenko AG. Viruses of Wild Plants and Current Metagenomic Methods for Their Investigation. CYTOL GENET+ 2021. [DOI: 10.3103/s0095452721030038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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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.
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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
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16
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Prakash S, Shukla S, Bhagat AK, Mishra H, Vangala R, Jain A. Human parvovirus 4: An emerging etiological agent in cases presenting with influenza like illness. J Med Virol 2021; 93:5158-5162. [PMID: 33017052 DOI: 10.1002/jmv.26579] [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: 02/27/2020] [Revised: 08/22/2020] [Accepted: 09/14/2020] [Indexed: 11/12/2022]
Abstract
This study was planned to study the association of parvovirus 4 (PARV4) with Influenza-like illness (ILI). A total of 1111 patients with a clinical diagnosis of ILI and 220 healthy controls were tested for Influenza A/HINI/and H3N2, Influenza B, and PARV4. Further sequencing was done to analyze the genotype distribution of parvovirus 4. Influenza A/HINI, A/H3N2, and B were detected in 334 (30.06%), 9 (0.81%), and 10 (0.9%) cases respectively. PARV4 was detected in 135 (12.15%) cases and one healthy control. Parvovirus 4 was significantly higher in cases as compared to controls (relative risk, 30.77%; p < .0006). Sequencing of 20 isolates suggests the dominance of genotype 2 in our region.
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Affiliation(s)
- Shantanu Prakash
- Department of Microbiology, King Georges Medical University, Lucknow, UP, India
| | - Suruchi Shukla
- Department of Microbiology, King Georges Medical University, Lucknow, UP, India
| | - Amit K Bhagat
- Department of Microbiology, King Georges Medical University, Lucknow, UP, India
| | - Hricha Mishra
- Department of Microbiology, King Georges Medical University, Lucknow, UP, India
| | - Ramakrishna Vangala
- Department of Microbiology, King Georges Medical University, Lucknow, UP, India
| | - Amita Jain
- Department of Microbiology, King Georges Medical University, Lucknow, UP, India
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17
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Jia J, Zhong Y, Zhang H, Yuan D, Ma L, Wang D, Zhang J, Ma Y. Identification of human parvovirus 4 genotypes 1 and 2 in Chinese source plasma pools. J Med Virol 2021; 93:4780-4785. [PMID: 33200412 PMCID: PMC8359957 DOI: 10.1002/jmv.26666] [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: 09/18/2020] [Revised: 10/23/2020] [Accepted: 11/09/2020] [Indexed: 12/16/2022]
Abstract
Human parvovirus B19 (B19V) and human parvovirus 4 (PARV4) are known to infect humans and transmit through contaminated blood and blood products. Globally, three genotypes of B19V, as well as PARV4, have been identified, respectively. The existence of different B19V genotypes in Chinese plasma donors has been investigated, however, the data regarding PARV4 were not available. The main objective of this study is to identify the genotypes of PARV4 circulating in Chinese plasma donors. By using a duplex quantitative polymerase chain reaction assay adapted for all genotypes of B19V and PARV4, 78 source plasma pools for fractionation were screened and quantified. Results showed that positive rates of B19V and PARV4 DNA in plasma pool samples were 25.64% and 14.10%, respectively. PARV4 sequences in two positive samples were next genotyped, and these two sequences belonged to PARV4 genotypes 1 and 2, respectively. In conclusion, the data present demonstrate the existence of PARV4 genotypes 1 and 2 in Chinese plasma donors for the first time and also show the relatively lower prevalence and level of PARV4 DNA in Chinese plasma donors in comparison with that of B19V DNA. At least two PARV4 genotypes, 1 and 2, were currently present in China.
The prevalence and level of PARV4 DNA in Chinese plasma donors were relatively lower in comparison with that of B19V DNA.
The rate of B19V and PARV4 coinfection in Chinese source plasma pools was low.
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Affiliation(s)
- Junting Jia
- Department of Transfusion Medicine, The First Medical Center, Chinese PLA General Hospital, Beijing, China.,NMPA Key Laboratory for Quality Control of Blood Products, Institute of Health Service and Transfusion Medicine, Academy of Military Medical Sciences, Beijing, China
| | - Yadi Zhong
- NMPA Key Laboratory for Quality Control of Blood Products, Institute of Health Service and Transfusion Medicine, Academy of Military Medical Sciences, Beijing, China.,Department of Hematology, Second Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Huan Zhang
- NMPA Key Laboratory for Quality Control of Blood Products, Institute of Health Service and Transfusion Medicine, Academy of Military Medical Sciences, Beijing, China
| | - Dian Yuan
- NMPA Key Laboratory for Quality Control of Blood Products, Institute of Health Service and Transfusion Medicine, Academy of Military Medical Sciences, Beijing, China
| | - Limin Ma
- NMPA Key Laboratory for Quality Control of Blood Products, Institute of Health Service and Transfusion Medicine, Academy of Military Medical Sciences, Beijing, China
| | - Deqing Wang
- Department of Transfusion Medicine, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Jingang Zhang
- NMPA Key Laboratory for Quality Control of Blood Products, Institute of Health Service and Transfusion Medicine, Academy of Military Medical Sciences, Beijing, China
| | - Yuyuan Ma
- NMPA Key Laboratory for Quality Control of Blood Products, Institute of Health Service and Transfusion Medicine, Academy of Military Medical Sciences, Beijing, China
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18
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Kaczorowska J, van der Hoek L. Human anelloviruses: diverse, omnipresent and commensal members of the virome. FEMS Microbiol Rev 2021; 44:305-313. [PMID: 32188999 PMCID: PMC7326371 DOI: 10.1093/femsre/fuaa007] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 03/02/2020] [Indexed: 12/12/2022] Open
Abstract
Anelloviruses are small, single stranded circular DNA viruses. They are extremely diverse and have not been associated with any disease so far. Strikingly, these small entities infect most probably the complete human population, and there are no convincing examples demonstrating viral clearance from infected individuals. The main transmission could be via fecal-oral or airway route, as infections occur at an early age. However, due to the lack of an appropriate culture system, the virus–host interactions remain enigmatic. Anelloviruses are obviously mysterious viruses, and their impact on human life is not yet known, but, with no evidence of a disease association, a potential beneficial effect on human health should also be investigated.
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Affiliation(s)
- Joanna Kaczorowska
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Location AMC, University of Amsterdam, Meibergdreef 9, Amsterdam, the Netherlands
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Location AMC, University of Amsterdam, Meibergdreef 9, Amsterdam, the Netherlands
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19
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Lazutka J, Simutis K, Matulis P, Petraitytė-Burneikienė R, Kučinskaitė-Kodzė I, Simanavičius M, Tamošiunas PL. Antigenicity study of the yeast-generated human parvovirus 4 (PARV4) virus-like particles. Virus Res 2020; 292:198236. [PMID: 33242523 DOI: 10.1016/j.virusres.2020.198236] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 11/15/2020] [Accepted: 11/16/2020] [Indexed: 11/17/2022]
Abstract
Human parvovirus 4 (PARV4) is a novel tetraparvovirus that was isolated from intravenous drug users in 2005. Recombinant PARV4 capsid protein VP2 can form stable virus-like particles (VLPs) in yeast. These VLPs could act as antigen carriers during vaccine development. Therefore, the information about PARV4 VP2 VLP antigenic sites could advance further research in this area. In this work, human parvovirus 4 VLPs obtained from yeast were used to generate monoclonal antibodies (mAbs) in mice. Epitope mapping of the obtained mAbs showed at least three distinct antigenic sites of the VP2 protein. On top of that, molecular cloning was used to replace PARV4 VP2 antigenic sites with heterologous peptides. The chimeric PARV4 VLPs bearing polyhistidine inserts obtained from yeast were observed using electron microscopy while polyhistidine-specific antibodies detected heterologous peptides of the chimeric VP2 proteins.
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Affiliation(s)
- Justas Lazutka
- Department of Eukaryote Gene Engineering, Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, Vilnius, Lithuania.
| | - Karolis Simutis
- Department of Eukaryote Gene Engineering, Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, Vilnius, Lithuania
| | - Paulius Matulis
- Department of Eukaryote Gene Engineering, Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, Vilnius, Lithuania
| | - Rasa Petraitytė-Burneikienė
- Department of Eukaryote Gene Engineering, Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, Vilnius, Lithuania
| | - Indrė Kučinskaitė-Kodzė
- Department of Immunology and Cell Biology, Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al.7, Vilnius, Lithuania
| | - Martynas Simanavičius
- Department of Immunology and Cell Biology, Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al.7, Vilnius, Lithuania
| | - Paulius Lukas Tamošiunas
- Department of Eukaryote Gene Engineering, Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, Vilnius, Lithuania
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20
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Constant companion: clinical and developmental aspects of torque teno virus infections. Arch Virol 2020; 165:2749-2757. [PMID: 33040309 DOI: 10.1007/s00705-020-04841-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 09/04/2020] [Indexed: 12/18/2022]
Abstract
Torque teno virus (TTV) is a commensal human virus observed as a circular single-negative-strand DNA molecule in various tissues and biological samples, notably in blood serum and lymphocytes. TTV has no apparent clinical significance, although it might be very useful as a prospective tool for gene delivery or as an epidemiological marker. Human populations are ubiquitously infected with TTV; the prevalence may reach 100%. The majority of babies become spontaneously infected with TTV, so that by the end of the first year of life, the prevalence reaches 'adult' values. TTV positivity in healthy early infancy and the presence of TTV in umbilical cord blood samples have been reported. The mechanism of infection and the dynamics of TTV prevalence in infants with age remain understudied. Meanwhile, the potential diagnostic and prognostic value of TTV as a marker deserves special attention and study, along with the possibility, causes and consequences of placental transmission of TTV under normal or pathological conditions.
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21
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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.
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22
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Vilmane A, Terentjeva A, Tamosiunas PL, Suna N, Suna I, Petraityte-Burneikiene R, Murovska M, Rasa-Dzelzkaleja S, Nora-Krukle Z. Human Parvoviruses May Affect the Development and Clinical Course of Meningitis and Meningoencephalitis. Brain Sci 2020; 10:brainsci10060339. [PMID: 32503112 PMCID: PMC7349785 DOI: 10.3390/brainsci10060339] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/29/2020] [Accepted: 06/01/2020] [Indexed: 12/18/2022] Open
Abstract
Meningitis and meningoencephalitis are neurological inflammatory diseases, and although routine diagnostics include testing of a wide range of pathogens, still in many cases, no causative agent is detected. Human parvovirus B19 (B19V), human bocaviruses 1–4 (HBoV1–4), and human parvovirus 4 (hPARV4) are members of the Parvoviridae family and are associated with a wide range of clinical manifestations including neurological disorders. The main aim of this study was to determine whether human parvoviruses infection markers are present among patients with meningitis/meningoencephalitis in Latvia as well as to clarify the role of these viruses on the clinical course of the mentioned diseases. Our study revealed HBoV1–4 and B19V genomic sequences in 52.38% and 16.67% of patients, respectively. Furthermore, symptoms such as the presence of a headache and its severity, fatigue, disorientation, and difficulties to concentrate were significantly frequently present in patients with active parvovirus infection in comparison with parvoviruses negative patients, therefore we suggest that HBoV1–4 and B19V infection should be included in the diagnostics to reduce the number of meningitis/meningoencephalitis with unknown/unexplained etiology.
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Affiliation(s)
- Anda Vilmane
- Institute of Microbiology and Virology, Rīga Stradiņš University, 5 Ratsupites St., LV-1067 Riga, Latvia; (A.T.); (M.M.); (S.R.-D.); (Z.N.-K.)
- Correspondence: ; Tel.: +371-67060838
| | - Anna Terentjeva
- Institute of Microbiology and Virology, Rīga Stradiņš University, 5 Ratsupites St., LV-1067 Riga, Latvia; (A.T.); (M.M.); (S.R.-D.); (Z.N.-K.)
| | - Paulius L. Tamosiunas
- Vilnius University Life Sciences Center Institute of Biotechnology, 7 Sauletekio Al., 10257 Vilnius, Lithuania; (P.L.T.); (R.P.-B.)
| | - Normunds Suna
- Department of Neurology and Neurosurgery, Riga East Clinical University Hospital “Gaiļezers”, 2 Hipokrata St., LV-1038 Riga, Latvia; (N.S.); (I.S.)
| | - Inga Suna
- Department of Neurology and Neurosurgery, Riga East Clinical University Hospital “Gaiļezers”, 2 Hipokrata St., LV-1038 Riga, Latvia; (N.S.); (I.S.)
| | - Rasa Petraityte-Burneikiene
- Vilnius University Life Sciences Center Institute of Biotechnology, 7 Sauletekio Al., 10257 Vilnius, Lithuania; (P.L.T.); (R.P.-B.)
| | - Modra Murovska
- Institute of Microbiology and Virology, Rīga Stradiņš University, 5 Ratsupites St., LV-1067 Riga, Latvia; (A.T.); (M.M.); (S.R.-D.); (Z.N.-K.)
| | - Santa Rasa-Dzelzkaleja
- Institute of Microbiology and Virology, Rīga Stradiņš University, 5 Ratsupites St., LV-1067 Riga, Latvia; (A.T.); (M.M.); (S.R.-D.); (Z.N.-K.)
| | - Zaiga Nora-Krukle
- Institute of Microbiology and Virology, Rīga Stradiņš University, 5 Ratsupites St., LV-1067 Riga, Latvia; (A.T.); (M.M.); (S.R.-D.); (Z.N.-K.)
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23
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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.
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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:
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24
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Du J, Wang W, Chan JFW, Wang G, Huang Y, Yi Y, Zhu Z, Peng R, Hu X, Wu Y, Zeng J, Zheng J, Cui X, Niu L, Zhao W, Lu G, Yuen KY, Yin F. Identification of a Novel Ichthyic Parvovirus in Marine Species in Hainan Island, China. Front Microbiol 2019; 10:2815. [PMID: 31866980 PMCID: PMC6907010 DOI: 10.3389/fmicb.2019.02815] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 11/20/2019] [Indexed: 01/27/2023] Open
Abstract
Parvoviruses are a diverse group of viruses that are capable of infecting a wide range of animals. In this study, we report the discovery of a novel parvovirus, tilapia parvovirus HMU-HKU, in the fecal samples of crocodiles and intestines of tilapia in Hainan Province, China. The novel parvovirus was firstly identified from crocodiles fed with tilapia using next-generation sequencing (NGS). Screening studies revealed that the prevalence of the novel parvovirus in crocodile feces samples fed on tilapia (75–86%) was apparently higher than that in crocodiles fed with chicken (4%). Further studies revealed that the prevalence of the novel parvovirus in tilapia feces samples collected at four areas in Hainan Province was between 40 and 90%. Four stains of the novel parvovirus were identified in this study based on sequence analyses of NS1 and all the four strains were found in tilapia in contrast only two of them were detected in crocodile feces. The nearly full-length genome sequence of the tilapia parvovirus HMU-HKU-1 was determined and showed less than 45.50 and 40.38% amino acid identity with other members of Parvoviridae in NS1 and VP1 genes, respectively. Phylogenetic analysis based on the complete helicase domain amino acid sequences showed that the tilapia parvovirus HMU-HKU-1 formed a relatively independent branch in the newly proposed genus Chaphamaparvovirus in the subfamily Hamaparvovirinae according to the ICTV’s most recent taxonomic criteria for Parvoviridae classification. Tilapia parvovirus HMU-HKU-1 likely represented a new species within the new genus Chaphamaparvovirus. The identification of tilapia parvovirus HMU-HKU provides further insight into the viral and genetic diversity of parvoviruses and its infections in tilapia populations need to be evaluated in terms of pathogenicity and production losses in tilapia farming.
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Affiliation(s)
- Jiang Du
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China.,Department of Pathogen Biology, Hainan Medical University, Haikou, China
| | - Wenqi Wang
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
| | - Jasper Fuk-Woo Chan
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong.,Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong.,Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam, Hong Kong
| | - Gaoyu Wang
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
| | - Yi Huang
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
| | - Yufang Yi
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
| | - Zheng Zhu
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong.,Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong.,Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam, Hong Kong
| | - Ruoyan Peng
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
| | - Xiaoyuan Hu
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
| | - Yue Wu
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
| | - Jifeng Zeng
- Key Laboratory of Tropical Animal Breeding and Epidemic Disease Research of Hainan Province, Hainan University, Haikou, China.,Key Laboratory of Tropical Biological Resources of Ministry of Education, Haikou, China
| | - Jiping Zheng
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| | - Xiuji Cui
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China.,Department of Pathogen Biology, Hainan Medical University, Haikou, China
| | - Lina Niu
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China.,Department of Pathogen Biology, Hainan Medical University, Haikou, China
| | - Wei Zhao
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China.,Department of Pathogen Biology, Hainan Medical University, Haikou, China
| | - Gang Lu
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China.,Department of Pathogen Biology, Hainan Medical University, Haikou, China
| | - Kwok-Yung Yuen
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong.,Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong.,Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam, Hong Kong
| | - Feifei Yin
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China.,Department of Pathogen Biology, Hainan Medical University, Haikou, China
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25
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No JS, Kim WK, Cho S, Lee SH, Kim JA, Lee D, Song DH, Gu SH, Jeong ST, Wiley MR, Palacios G, Song JW. Comparison of targeted next-generation sequencing for whole-genome sequencing of Hantaan orthohantavirus in Apodemus agrarius lung tissues. Sci Rep 2019; 9:16631. [PMID: 31719616 PMCID: PMC6851128 DOI: 10.1038/s41598-019-53043-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 10/26/2019] [Indexed: 01/06/2023] Open
Abstract
Orthohantaviruses, negative-sense single-strand tripartite RNA viruses, are a global public health threat. In humans, orthohantavirus infection causes hemorrhagic fever with renal syndrome or hantavirus cardiopulmonary syndrome. Whole-genome sequencing of the virus helps in identification and characterization of emerging or re-emerging viruses. Next-generation sequencing (NGS) is a potent method to sequence the viral genome, using molecular enrichment methods, from clinical specimens containing low virus titers. Hence, a comparative study on the target enrichment NGS methods is required for whole-genome sequencing of orthohantavirus in clinical samples. In this study, we used the sequence-independent, single-primer amplification, target capture, and amplicon NGS for whole-genome sequencing of Hantaan orthohantavirus (HTNV) from rodent specimens. We analyzed the coverage of the HTNV genome based on the viral RNA copy number, which is quantified by real-time quantitative PCR. Target capture and amplicon NGS demonstrated a high coverage rate of HTNV in Apodemus agrarius lung tissues containing up to 103–104 copies/μL of HTNV RNA. Furthermore, the amplicon NGS showed a 10-fold (102 copies/μL) higher sensitivity than the target capture NGS. This report provides useful insights into target enrichment NGS for whole-genome sequencing of orthohantaviruses without cultivating the viruses.
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Affiliation(s)
- Jin Sun No
- Department of Microbiology, College of Medicine, Korea University, Seoul, 02841, Republic of Korea
| | - Won-Keun Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, 24252, Republic of Korea.,Center for Medical Science Research, College of Medicine, Hallym University, Chuncheon, 24252, Republic of Korea
| | - Seungchan Cho
- Department of Microbiology, College of Medicine, Korea University, Seoul, 02841, Republic of Korea
| | - Seung-Ho Lee
- Department of Microbiology, College of Medicine, Korea University, Seoul, 02841, Republic of Korea
| | - Jeong-Ah Kim
- Department of Microbiology, College of Medicine, Korea University, Seoul, 02841, Republic of Korea
| | - Daesang Lee
- 4th R&D Institute, Agency for Defense Development, Daejeon, 34186, Republic of Korea
| | - Dong Hyun Song
- 4th R&D Institute, Agency for Defense Development, Daejeon, 34186, Republic of Korea
| | - Se Hun Gu
- 4th R&D Institute, Agency for Defense Development, Daejeon, 34186, Republic of Korea
| | - Seong Tae Jeong
- 4th R&D Institute, Agency for Defense Development, Daejeon, 34186, Republic of Korea
| | - Michael R Wiley
- The Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases at Fort Detrick, Frederick, MD, 21702, USA
| | - Gustavo Palacios
- The Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases at Fort Detrick, Frederick, MD, 21702, USA
| | - Jin-Won Song
- Department of Microbiology, College of Medicine, Korea University, Seoul, 02841, Republic of Korea.
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26
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Prakash S, Shukla S, Ramakrishna V, Mishra H, Bhagat AK, Jain A. Human Parvovirus 4: A harmless bystander or a pathogen of severe acute respiratory illness. Int J Infect Dis 2019; 90:21-25. [PMID: 31605808 PMCID: PMC7172059 DOI: 10.1016/j.ijid.2019.10.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 09/30/2019] [Accepted: 10/01/2019] [Indexed: 01/13/2023] Open
Abstract
Severe Acute Respiratory Infection (SARI) is an important cause of morbidity and mortality worldwide. We investigated the association of PARV4 virus with SARI. PARV4 was detected in 26.55% of cases and only in one healthy control (0.68%). Detection of PARV4 is seen in a significantly large number of SARI cases. PARV4 genotype 2 was the only genotype detected from cases as well as controls.
Introduction Severe Acute Respiratory Infection (SARI) is an important cause of morbidity and mortality worldwide, caused by a large number of viral and bacterial agents. PARV4 is a recently identified virus detected in human blood and variety of tissues, but its disease association with SARI could not be established. Objective In the present case control study, we aim to investigate the association of PARV4 with SARI. Methods The Nasal and Throat swab (NS/TS) samples of 241 cases and 146 healthy controls were tested for most common respiratory viruses and PARV4 by real-time PCR. Results PARV4 was detected in 64(26.55%) SARI cases and only one healthy control (0.68%). PARV4 was the most common viral agent detected in SARI cases. A strong association of PARV4 is seen with severe respiratory illness. Conclusion Detection of PARV4 in a significantly higher number of SARI cases, in comparison with controls, suggests association of PARV4 with SARI. PARV4 genotype 2 is the only circulating strain detected in our study.
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Affiliation(s)
- Shantanu Prakash
- Department of Microbiology, King Georges Medical University, Lucknow, UP, 226003, India.
| | - Suruchi Shukla
- Department of Microbiology, King Georges Medical University, Lucknow, UP, 226003, India.
| | - Vangala Ramakrishna
- Department of Microbiology, King Georges Medical University, Lucknow, UP, 226003, India.
| | - Hricha Mishra
- Department of Microbiology, King Georges Medical University, Lucknow, UP, 226003, India.
| | - Amit K Bhagat
- Department of Microbiology, King Georges Medical University, Lucknow, UP, 226003, India.
| | - Amita Jain
- Department of Microbiology, King Georges Medical University, Lucknow, UP, 226003, India.
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27
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Souza LDC, Blawid R, Silva JMF, Nagata T. Human virome in nasopharynx and tracheal secretion samples. Mem Inst Oswaldo Cruz 2019; 114:e190198. [PMID: 31596309 PMCID: PMC6779266 DOI: 10.1590/0074-02760190198] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 09/20/2019] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND In Brazil the implementation of the Sentinel Surveillance System of
Influenza began in 2000. Central public health laboratories use reverse
transcription-quantitative polymerase chain reaction (RT-qPCR) for diagnosis
of respiratory viruses, but this protocol identifies only specific targets,
resulted in inconclusive diagnosis for many samples. Thus, high-throughput
sequencing (HTS) would be complementary method in the identification of
pathogens in inconclusive samples for RT-qPCR or other specific detection
protocols. OBJECTIVES This study aimed to detect unidentified viruses using HTS approach in
negative samples of nasopharynx/tracheal secretions by the standard RT-qPCR
collected in the Federal District, Brazil. METHODS Nucleic acids were extracted from samples collected in winter period of 2016
and subjected to HTS. The results were confirmed by the multiplex PR21
RT-qPCR, which identifies 21 respiratory pathogens. FINDINGS The main viruses identified by HTS were of families
Herpesviridae, Coronaviridae,
Parvoviridae and Picornaviridae, with
the emphasis on rhinoviruses. The presence of respiratory viruses in the
samples was confirmed by the PR21 multiplex RT-qPCR. Coronavirus,
enterovirus, bocavirus and rhinovirus were found by multiplex RT-qPCR as
well as by HTS analyses. MAIN CONCLUSIONS Wide virus diversity was found by different methodologies and high frequency
of rhinovirus occurrence was confirmed in population in winter, showing its
relevance for public health.
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Affiliation(s)
- Larissa da Costa Souza
- Universidade de Brasília, Departamento de Biologia Celular, Pós-Graduação em Biologia Microbiana, Brasília, DF, Brasil.,Laboratório Central de Saúde Pública do Distrito Federal, Brasília, DF, Brasil
| | - Rosana Blawid
- Universidade Federal Rural de Pernambuco, Departamento de Agronomia, Recife, PE, Brasil
| | - João Marcos Fagundes Silva
- Universidade de Brasília, Departamento de Biologia Celular, Pós-Graduação em Biologia Molecular, Brasília, DF, Brasil
| | - Tatsuya Nagata
- Universidade de Brasília, Departamento de Biologia Celular, Pós-Graduação em Biologia Microbiana, Brasília, DF, Brasil.,Universidade de Brasília, Departamento de Biologia Celular, Pós-Graduação em Biologia Molecular, Brasília, DF, Brasil
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28
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Chaves A, Ibarra-Cerdeña CN, López-Pérez AM, Monge O, Avendaño R, Ureña-Saborio H, Chavarría M, Zaldaña K, Sánchez L, Ortíz-Malavassi E, Suzan G, Foley J, Gutiérrez-Espeleta GA. Bocaparvovirus, Erythroparvovirus and Tetraparvovirus in New World Primates from Central America. Transbound Emerg Dis 2019; 67:377-387. [PMID: 31529612 DOI: 10.1111/tbed.13357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 09/02/2019] [Accepted: 09/07/2019] [Indexed: 12/20/2022]
Abstract
Parvoviruses in the genera Bocaparvovirus (HBoV), Erythroparvovirus (B19) and Tetraparvovirus (PARV4) are the only autonomous parvoviruses known to be associated with human and non-human primates based on studies and clinical cases in humans worldwide and non-human primates in Asia and Africa. Here, the presence of these agents with pathogenic potential was assessed by PCR in blood and faeces from 55 howler monkeys, 112 white-face monkeys, 3 squirrel monkeys and 127 spider monkeys in Costa Rica and El Salvador. Overall, 3.7% (11/297) of the monkeys had HboV DNA, 0.67% (2/297) had B19 DNA, and 14.1% (42/297) had PARV4 DNA, representing the first detection of these viruses in New World Primates (NWP). Sex was significantly associated with the presence of HBoV, males having greater risk up to nine times compared with females. Captivity was associated with increased prevalence for PARV4 and when all viruses were analysed together. This study provides compelling molecular evidence of parvoviruses in NWPs and underscores the importance of future research aimed at understanding how these viruses behave in natural environments of the Neotropics and what variables may favour their presence and transmission.
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Affiliation(s)
- Andrea Chaves
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, USA.,Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica
| | - Carlos N Ibarra-Cerdeña
- Departamento de Ecología Humana, Centro de Investigación y de Estudios Avanzados del IPN (Cinvestav), Unidad Mérida, Mérida, México
| | - Andrés M López-Pérez
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, USA.,Departamento de Etología, Fauna Silvestre y Animales de Laboratorio, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad Universitaria, México D.F, México
| | - Otto Monge
- Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica
| | - Roberto Avendaño
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, Costa Rica
| | - Hilary Ureña-Saborio
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, Costa Rica
| | - Max Chavarría
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, Costa Rica.,Escuela de Química & CIPRONA, Universidad de Costa Rica, San José, Costa Rica
| | - Karla Zaldaña
- Asociación Territorios Vivos El Salvador, San Salvador, El Salvador
| | - Lucía Sánchez
- Asociación Territorios Vivos El Salvador, San Salvador, El Salvador
| | - Edgar Ortíz-Malavassi
- Escuela de Ingienería Forestal, Instituto Tecnológico de Costa Rica, Cartago, Costa Rica
| | - Gerardo Suzan
- Departamento de Etología, Fauna Silvestre y Animales de Laboratorio, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad Universitaria, México D.F, México
| | - Janet Foley
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, USA
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29
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Abstract
Parvoviruses are structurally simple viruses with linear single-stranded DNA genomes and nonenveloped icosahedral capsids. They infect a wide range of animals from insects to humans. Parvovirus B19 is a long-known human pathogen, whereas adeno-associated viruses are nonpathogenic. Since 2005, many parvoviruses have been discovered in human-derived samples: bocaviruses 1-4, parvovirus 4, bufavirus, tusavirus, and cutavirus. Some human parvoviruses have already been shown to cause disease during acute infection, some are associated with chronic diseases, and others still remain to be proven clinically relevant-or harmless commensals, a distinction not as apparent as it might seem. One initially human-labeled parvovirus might not even be a human virus, whereas another was originally overlooked due to inadequate diagnostics. The intention of this review is to follow the rocky road of emerging human parvoviruses from discovery of a DNA sequence to current and future clinical status, highlighting the perils along the way.
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30
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Arankalle VA, Srivastava N, Kushwaha KP, Sen A, Ramdasi AY, Patel PA, Kuthe S, Haldipur B, Sakpal GN, Lole KS, Ingle NB. Detection of human parvovirus 4 DNA in the patients with acute encephalitis syndrome during seasonal outbreaks of the disease in Gorakhpur, India. Emerg Microbes Infect 2019; 8:130-138. [PMID: 30866767 PMCID: PMC6455185 DOI: 10.1080/22221751.2018.1563455] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Seasonal outbreaks of acute encephalitis syndrome (AES) at Gorakhpur, India have been recognized since 2006. So far, the causative agent has not been identified. Use of next generation sequencing identified human parvovirus 4 (HPARV4) sequences in a CSF/plasma pool. These sequences showed highest identity with sequences earlier identified in similar patients from south India. Real-time PCR detected HPARV4 DNA in 20/78 (25.6%) CSF and 6/31 (19.3%) plasma of AES patients. Phylogenetic analysis classified three almost complete genomes and 24 partial NS1 sequences as genotype 2A. The observed association of HPARV4 with AES needs further evaluation. ELISAs for the detection of IgM and IgG antibodies against scrub typhus (Orientia tsutsugamushi, OT) showed ∼70% IgM/IgG positivity suggestive of etiologic association. Prospective, comprehensive studies are needed to confirm association of these agents, singly or in combination with AES in Gorakhpur region.
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Affiliation(s)
- Vidya A Arankalle
- a National Institute of Virology, Microbial Containment Complex , Pune , India.,b Interactive Research School for Health Affairs , Pune , India
| | - Navin Srivastava
- a National Institute of Virology, Microbial Containment Complex , Pune , India
| | | | - Agnibha Sen
- a National Institute of Virology, Microbial Containment Complex , Pune , India
| | - Ashwini Y Ramdasi
- a National Institute of Virology, Microbial Containment Complex , Pune , India
| | - Priyanka A Patel
- a National Institute of Virology, Microbial Containment Complex , Pune , India
| | - Sumeet Kuthe
- a National Institute of Virology, Microbial Containment Complex , Pune , India
| | - Bangari Haldipur
- a National Institute of Virology, Microbial Containment Complex , Pune , India.,b Interactive Research School for Health Affairs , Pune , India
| | - Gajanan N Sakpal
- a National Institute of Virology, Microbial Containment Complex , Pune , India
| | - Kavita S Lole
- a National Institute of Virology, Microbial Containment Complex , Pune , India
| | - Nilesh B Ingle
- a National Institute of Virology, Microbial Containment Complex , Pune , India
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31
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Li J, Li D. The Discovery Process of SFTS in China. SEVERE FEVER WITH THROMBOCYTOPENIA SYNDROME 2019. [PMCID: PMC7121134 DOI: 10.1007/978-981-13-9562-8_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Heightened surveillance of acute febrile illness in China since 2004 led to the identification of a severe fever with thrombocytopenia syndrome (SFTS) with unknown etiology. Sporadic patients hospitalized with SFTS in 2009 and 2010 were identified and serum samples were collected. Sequence from a novel species of phlebovirus was identified by sequence independent single primer amplification (SISPA) from the serum of a patient with SFTS. The virus was isolated in Vero cell culture and its complete genome sequence was determined, only distantly related to other known phleboviruses. Electron microscopic analysis revealed a virion morphologically characteristic of phleboviruses. The virus was named as SFTS virus. The viral RNA and/or specific antibodies were detected from the blood of patients with SFTS. Serological assays demonstrated a virus-specific immune response in pairs of sera collected from patients at acute and convalescent phases. The pathogenic mechanisms of thrombocytopenia in human SFTS disease was resembled in a mouse model. The results had been collected to demonstrate that SFTS virus was etiologically associated with an acute and novel infectious disease, SFTS in humans.
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32
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Safdar A. Rare and Emerging Viral Infections in the Transplant Population. PRINCIPLES AND PRACTICE OF TRANSPLANT INFECTIOUS DISEASES 2019. [PMCID: PMC7119999 DOI: 10.1007/978-1-4939-9034-4_45] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Viral infections account for a large proportion of emerging infectious diseases, and the agents included in this group consist of recently identified viruses as well as previously identified viruses with an apparent increase in disease incidence. In transplant recipients, this group can include viruses with no recognized pathogenicity in immunocompetent patients and those that result in atypical or more severe disease presentations in the immunocompromised host. In this chapter, we begin by discussing viral diagnostics and techniques used for viral discovery, specifically as they apply to emerging and rare infections in this patient population. Focus then shifts to specific emerging and re-emerging viruses in the transplant population, including human T-cell leukemia virus 1, rabies, lymphocytic choriomeningitis virus, human bocavirus, parvovirus 4, measles, mumps, orf, and dengue. We have also included a brief discussion on emerging viruses and virus families with few or no reported cases in transplant recipients: monkeypox, nipah and hendra, chikungunya and other alphaviruses, hantavirus and the Bunyaviridae, and filoviruses. Finally, concerns regarding infectious disease complications in xenotransplantation and the reporting of rare viral infections are addressed. With the marked increase in the number of solid organ and hematopoietic stem cell transplants performed worldwide, we expect a corresponding rise in the reports of emerging viral infections in transplant hosts, both from known viruses and those yet to be identified.
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Affiliation(s)
- Amar Safdar
- Clinical Associate Professor of Medicine, Texas Tech University Health Sciences Center El Paso, Paul L. Foster School of Medicine, El Paso, TX USA
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33
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Overview of Trends in the Application of Metagenomic Techniques in the Analysis of Human Enteric Viral Diversity in Africa's Environmental Regimes. Viruses 2018; 10:v10080429. [PMID: 30110939 PMCID: PMC6115975 DOI: 10.3390/v10080429] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 08/03/2018] [Accepted: 08/10/2018] [Indexed: 12/19/2022] Open
Abstract
There has been an increase in the quest for metagenomics as an approach for the identification and study of the diversity of human viruses found in aquatic systems, both for their role as waterborne pathogens and as water quality indicators. In the last few years, environmental viral metagenomics has grown significantly and has enabled the identification, diversity and entire genome sequencing of viruses in environmental and clinical samples extensively. Prior to the arrival of metagenomics, traditional molecular procedures such as the polymerase chain reaction (PCR) and sequencing, were mostly used to identify and classify enteric viral species in different environmental milieu. After the advent of metagenomics, more detailed reports have emerged about the important waterborne viruses identified in wastewater treatment plant effluents and surface water. This paper provides a review of methods that have been used for the concentration, detection and identification of viral species from different environmental matrices. The review also takes into consideration where metagenomics has been explored in different African countries, as well as the limitations and challenges facing the approach. Procedures including sample processing, experimental design, sequencing technology, and bioinformatics analysis are discussed. The review concludes by summarising the current thinking and practices in the field and lays bare key issues that those venturing into this field need to consider and address.
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34
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Fouts DE. Amplification for Whole Genome Sequencing of Bacteriophages from Single Isolated Plaques Using SISPA. Methods Mol Biol 2018; 1681:165-178. [PMID: 29134594 DOI: 10.1007/978-1-4939-7343-9_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Genomics has greatly transformed our understanding of phage biology; however, traditional methods of DNA isolation for whole genome sequencing have required phages to be grown to high titers in large-scale preparations, potentially selecting for only those phages that can grow efficiently under laboratory conditions. This may also select for mutations or deletions that enable more efficient growth in culture. The ability to sequence a bacteriophage genome from a single isolated plaque reduces these risks while decreasing the time and complexity of bacteriophage genome sequencing. A method of amplification and library preparation is described, utilizing Sequence Independent Single Primer Amplification (SISPA), that can be used for whole genome shotgun sequencing of bacteriophages from a single isolated plaque.
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Affiliation(s)
- Derick E Fouts
- J. Craig Venter Institute, 9714 Medical Center Dr, Rockville, MD, 20850, USA.
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35
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Li W, Yang S, Wang Y, Zhu W, Ni P, Zhu S, Xu J, Lu R, Zhou C. A novel torque teno mini virus in the blood of the patient with lymphoma. Future Virol 2018. [DOI: 10.2217/fvl-2017-0113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: To characterize a novel anellovirus and analyze the relationship of the novel anellovirus with other anelloviruses. Materials & methods: Twenty-one serum samples of lymphoma patients were collected and viral metagenomics method was used to identify the novel anellovirus; CLUSTALW1.8 and MEGA6.0 was used to perform phylogenetic analysis; prevalence investigation was performed by nest PCR. Results: A novel anellovirus was discovered from two patients with lymphoma. The complete genome of torque teno mini virus (TTMV)-SHA is 2880 nt in length. Phylogenetic analysis based on ORF1 indicated that TTMV-SHA clusters with EF538882 sharing 62.5% sequence similarity, and the sequences divergence is 54%. Conclusion: TTMV (SHA) belonged to a novel anellovirus species, whether this novel anellovirus is associated with lymphoma needs further studies.
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Affiliation(s)
- Wang Li
- Clinical Laboratory Center, Taizhou People's Hospital, Hailing District, Taizhou, Jiangsu 225300, China
| | - Shixing Yang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Yanchun Wang
- Department of Clinical Laboratory, Shanghai Cancer Center, Fudan University, Shanghai 200032, China
| | - Wenjun Zhu
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Ping Ni
- Clinical Laboratory Center, Taizhou People's Hospital, Hailing District, Taizhou, Jiangsu 225300, China
| | - Shuai Zhu
- Clinical Laboratory Center, Taizhou People's Hospital, Hailing District, Taizhou, Jiangsu 225300, China
| | - Juan Xu
- Clinical Laboratory Center, Taizhou People's Hospital, Hailing District, Taizhou, Jiangsu 225300, China
| | - Renquan Lu
- Department of Clinical Laboratory, Shanghai Cancer Center, Fudan University, Shanghai 200032, China
| | - Chenglin Zhou
- Clinical Laboratory Center, Taizhou People's Hospital, Hailing District, Taizhou, Jiangsu 225300, China
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36
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Ilyas M, Mietzsch M, Kailasan S, Väisänen E, Luo M, Chipman P, Smith JK, Kurian J, Sousa D, McKenna R, Söderlund-Venermo M, Agbandje-McKenna M. Atomic Resolution Structures of Human Bufaviruses Determined by Cryo-Electron Microscopy. Viruses 2018; 10:E22. [PMID: 29300333 PMCID: PMC5795435 DOI: 10.3390/v10010022] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 12/18/2017] [Accepted: 12/28/2017] [Indexed: 11/29/2022] Open
Abstract
Bufavirus strain 1 (BuV1), a member of the Protoparvovirus genus of the Parvoviridae, was first isolated from fecal samples of children with acute diarrhea in Burkina Faso. Since this initial discovery, BuVs have been isolated in several countries, including Finland, the Netherlands, and Bhutan, in pediatric patients exhibiting similar symptoms. Towards their characterization, the structures of virus-like particles of BuV1, BuV2, and BuV3, the current known genotypes, have been determined by cryo-electron microscopy and image reconstruction to 2.84, 3.79, and 3.25 Å, respectively. The BuVs, 65-73% identical in amino acid sequence, conserve the major viral protein, VP2, structure and general capsid surface features of parvoviruses. These include a core β-barrel (βB-βI), α-helix A, and large surface loops inserted between these elements in VP2. The capsid contains depressions at the icosahedral 2-fold and around the 5-fold axes, and has three separated protrusions surrounding the 3-fold axes. Structure comparison among the BuVs and to available parvovirus structures revealed capsid surface variations and capsid 3-fold protrusions that depart from the single pinwheel arrangement of the animal protoparvoviruses. These structures provide a platform to begin the molecular characterization of these potentially pathogenic viruses.
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Affiliation(s)
- Maria Ilyas
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32611, USA.
- Center for Structural Biology, The McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA.
| | - Mario Mietzsch
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32611, USA.
- Center for Structural Biology, The McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA.
| | - Shweta Kailasan
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32611, USA.
- Center for Structural Biology, The McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA.
| | - Elina Väisänen
- Department of Virology, University of Helsinki, P.O. Box 21 (Haartmaninkatu 3), University of Helsinki, FIN-00014 Helsinki, Finland.
| | - Mengxiao Luo
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32611, USA.
- Center for Structural Biology, The McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA.
| | - Paul Chipman
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32611, USA.
- Center for Structural Biology, The McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA.
| | - J Kennon Smith
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32611, USA.
- Center for Structural Biology, The McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA.
| | - Justin Kurian
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32611, USA.
- Center for Structural Biology, The McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA.
| | - Duncan Sousa
- Biological Science Imaging Resource, Department of Biological Sciences, The Florida State University, 89 Chieftan Way, Rm 119, Tallahassee, FL 32306, USA.
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32611, USA.
- Center for Structural Biology, The McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA.
| | - Maria Söderlund-Venermo
- Department of Virology, University of Helsinki, P.O. Box 21 (Haartmaninkatu 3), University of Helsinki, FIN-00014 Helsinki, Finland.
| | - Mavis Agbandje-McKenna
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32611, USA.
- Center for Structural Biology, The McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA.
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Brown JR, Bharucha T, Breuer J. Encephalitis diagnosis using metagenomics: application of next generation sequencing for undiagnosed cases. J Infect 2018; 76:225-240. [PMID: 29305150 PMCID: PMC7112567 DOI: 10.1016/j.jinf.2017.12.014] [Citation(s) in RCA: 150] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 12/22/2017] [Indexed: 12/27/2022]
Abstract
BACKGROUND Current estimates suggest that even in the most resourced settings, the aetiology of encephalitis is identified in less than half of clinical cases. It is acknowledged that filling this gap needs a combination of rigorous sampling and improved diagnostic technologies. Next generation sequencing (NGS) methods are powerful tools with the potential for comprehensive and unbiased detection of pathogens in clinical samples. We reviewed the use of this new technology for the diagnosis of suspected infectious encephalitis, and discuss the feasibility for introduction of NGS methods as a frontline diagnostic test. METHODS A systematic literature review was performed, using MESH and text word searches for variants of "sequencing" and "encephalitis" in Medline and EMbase, and searching bibliographies and citations using the Web of Science database. Two authors independently reviewed, extracted and summarised data. FINDINGS The review identified 25 articles reporting 44 case reports of patients with suspected encephalitis for whom NGS was used as a diagnostic tool. We present the data and highlight themes arising from these cases. There are no randomly controlled trials to assess the utility of NGS as a diagnostic tool. INTERPRETATION There is increasing evidence of a role for NGS in the work-up of undiagnosed encephalitis. Lower costs and increasing accessibility of these technologies will facilitate larger studies of these patients. We recommend NGS should be considered as a front-line diagnostic test in chronic and recurring presentations and, given current sample-to-result turn-around times, as second-line in acute cases of encephalitis.
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Affiliation(s)
- Julianne R Brown
- Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital for Children NHS Foundation Trust, UK.
| | - Tehmina Bharucha
- Infectious Diseases and Microbiology, Royal Free London NHS Foundation Trust, UK; Division of Infection and Immunity, University College London, UK
| | - Judith Breuer
- Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital for Children NHS Foundation Trust, UK; Division of Infection and Immunity, University College London, UK
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Rastegarpouyani H, Mohebbi SR, Hosseini SM, Azimzadeh P, beyraghie S, Sharifian A, Asadzadeh-Aghdaei H, Arshi S, Zali MR. Detection ofParvovirus4 in Iranian patients with HBV, HCV, HIV mono-infection, HIV and HCV co-infection. GASTROENTEROLOGY AND HEPATOLOGY FROM BED TO BENCH 2018; 11:138-144. [PMID: 29910855 PMCID: PMC5990921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
AIM In this study, we investigated the prevalence of PARV4 virus among the healthy population and four other groups of HBV infected, HCV infected, HIV infected and HIV/HCV co-infected individuals in Iran. BACKGROUND Parvovirus 4 (PARV4) was first discovered in 2005, in a hepatitis B virus-infected injecting drug user (IDU). To date, the best evidence about PARV4 transmission is parenteral roots which comes from IDU individuals. It seems that the prevalence of the virus in the normal population is very low. METHODS A total of 613 patients, including chronic HCV (n=103), HBV (n=193), HIV (n=180) infected individuals, HIV/HCV (n=34) co-infected patients and 103 healthy controls, were studied by using nested-PCR and also real-time PCR techniques. RESULTS Of those 180 samples were positive for HIV RNA, co-infection of PARV4 was detected in 3 cases (1.66%). All these three patients were male with the age of 28, 32 and 36 years (mean: 32). No statistical differences were found between HIV positive group and the healthy individuals. (P>0.05) The result of PARV4 PCR was negative in all other samples and healthy controls as well. CONCLUSION This study is the first to investigate the occurrence of PARV4 among these groups in Iran. The results show that the virus is not significant in Iranian population, even in patients with blood born infections such as HCV, HBV or even HIV patients. Further studies in other areas and various groups are required.
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Affiliation(s)
- Hosna Rastegarpouyani
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases Shahid Beheshti University of Medical Sciences, 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
| | - Seyed Masoud Hosseini
- Department of Microbiology and microbial biotechnology, Faculty of life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Pedram Azimzadeh
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sedigheh beyraghie
- Shahid Jafari HIV Reference Laboratory, Deputy of Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Afsaneh Sharifian
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Asadzadeh-Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shahnam Arshi
- Shahid Jafari HIV Reference Laboratory, Deputy of Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Javanmard D, Ziaee M, Ghaffari H, Namaei MH, Tavakoli A, Mollaei H, Moghoofei M, Mortazavi HS, Monavari SH. Human parvovirus B19 and parvovirus 4 among Iranian patients with hemophilia. Blood Res 2017; 52:311-315. [PMID: 29333409 PMCID: PMC5762743 DOI: 10.5045/br.2017.52.4.311] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 05/15/2017] [Accepted: 06/14/2017] [Indexed: 01/26/2023] Open
Abstract
Background Human parvovirus B19 (B19V) is one of the smallest DNA viruses and shows great resistance to most disinfectants. Therefore, it is one of the common contaminant pathogens present in blood and plasma products. Parvovirus 4 (PARV4) is a newly identified parvovirus, which is also prevalent in parenteral transmission. In this study, we aimed to evaluate the prevalence of B19V and PARV4 DNA among patients with hemophilia in Birjand County in eastern Iran. Methods This was a cross-sectional epidemiological study comprising nearly all people with hemophilia in this region. Whole blood samples were taken after patient registration and sent for plasma isolation. After nucleic acid extraction, B19V was detected with real-time polymerase chain reaction, PARV4 DNA was then detected using sensitive semi-nested PCR. Results In total, there were 86 patients with hemophilia, with mean age 28.5±1.5 years. Of these, 90.7% were men and 9.3% women; 84.9% had hemophilia A and 7.0% had hemophilia B. We found 11 patients (12.8%) were positive for B19V DNA and 8 were positive (9.3%) for PARV4 DNA. The prevalence of B19V was higher in middle-aged groups rather than younger people, whereas PARV4 infection was more common in younger patients (P <0.05). Conclusion There was a high prevalence of B19V and PARV4 infection in this high-risk group of patients with hemophilia. Due to the clinical significance of the B19 virus, imposing more precautionary measures for serum and blood products is recommended.
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Affiliation(s)
- Davod Javanmard
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Masood Ziaee
- Infectious Diseases Research Center, Birjand University of Medical Sciences, Birjand, Iran
| | - Hadi Ghaffari
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Hasan Namaei
- Infectious Diseases Research Center, Birjand University of Medical Sciences, Birjand, Iran
| | - Ahmad Tavakoli
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Hamidreza Mollaei
- Department of Microbiology and Virology, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohsen Moghoofei
- Department of Microbiology, Faculty of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran.,Student Research Committee, Iran University of Medical Sciences, Tehran, Iran
| | - Helya Sadat Mortazavi
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
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40
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Lau SKP, Ahmed SS, Tsoi HW, Yeung HC, Li KSM, Fan RYY, Zhao PSH, Lau CCC, Lam CSF, Choi KKF, Chan BCH, Cai JP, Wong SSY, Chen H, Zhang HL, Zhang L, Wang M, Woo PCY, Yuen KY. Bats host diverse parvoviruses as possible origin of mammalian dependoparvoviruses and source for bat-swine interspecies transmission. J Gen Virol 2017; 98:3046-3059. [PMID: 29106348 DOI: 10.1099/jgv.0.000969] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Compared to the enormous species diversity of bats, relatively few parvoviruses have been reported. We detected diverse and potentially novel parvoviruses from bats in Hong Kong and mainland China. Parvoviruses belonging to Amdoparvovirus, Bocaparvovirus and Dependoparvovirus were detected in alimentary, liver and spleen samples from 16 different chiropteran species of five families by PCR. Phylogenetic analysis of partial helicase sequences showed that they potentially belonged to 25 bocaparvovirus, three dependoparvovirus and one amdoparvovirus species. Nearly complete genome sequencing confirmed the existence of at least four novel bat bocaparvovirus species (Rp-BtBoV1 and Rp-BtBoV2 from Rhinolophus pusillus, Rs-BtBoV2 from Rhinolophus sinicus and Rol-BtBoV1 from Rousettus leschenaultii) and two novel bat dependoparvovirus species (Rp-BtAAV1 from Rhinolophus pusillus and Rs-BtAAV1 from Rhinolophus sinicus). Rs-BtBoV2 was closely related to Ungulate bocaparvovirus 5 with 93, 72.1 and 78.7 % amino acid identities in the NS1, NP1 and VP1/VP2 genes, respectively. The detection of bat bocaparvoviruses, including Rs-BtBoV2, closely related to porcine bocaparvoviruses, suggests recent interspecies transmission of bocaparvoviruses between bats and swine. Moreover, Rp-BtAAV1 and Rs-BtAAV1 were most closely related to human AAV1 with 48.7 and 57.5 % amino acid identities in the rep gene. The phylogenetic relationship between BtAAVs and other mammalian AAVs suggests bats as the ancestral origin of mammalian AAVs. Furthermore, parvoviruses of the same species were detected from multiple bat species or families, supporting the ability of bat parvoviruses to cross species barriers. The results extend our knowledge on the diversity of bat parvoviruses and the role of bats in parvovirus evolution and emergence in humans and animals.
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Affiliation(s)
- Susanna K P Lau
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR.,Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Syed Shakeel Ahmed
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Hoi-Wah Tsoi
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Hazel C Yeung
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Kenneth S M Li
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Rachel Y Y Fan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Pyrear S H Zhao
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Candy C C Lau
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Carol S F Lam
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Kelvin K F Choi
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Ben C H Chan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Jian-Piao Cai
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Samson S Y Wong
- Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR.,State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Honglin Chen
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR.,Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Hai-Lin Zhang
- Yunnan Institute of Endemic Disease Control and Prevention, Dali, Yunnan, PR China.,Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali, Yunnan, PR China
| | - Libiao Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangzhou, Guangdong Province, PR China.,Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangzhou, Guangdong Province, PR China.,Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong Province, PR China
| | - Ming Wang
- Guangzhou Centre for Disease Control, Guangzhou, Guangdong Province, PR China
| | - Patrick C Y Woo
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR.,Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR.,State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Kwok-Yung Yuen
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR.,State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR.,Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
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41
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Väisänen E, Fu Y, Hedman K, Söderlund-Venermo M. Human Protoparvoviruses. Viruses 2017; 9:v9110354. [PMID: 29165368 PMCID: PMC5707561 DOI: 10.3390/v9110354] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 11/17/2017] [Accepted: 11/19/2017] [Indexed: 12/22/2022] Open
Abstract
Next-generation sequencing and metagenomics have revolutionized the discovery of novel viruses. In recent years, three novel protoparvoviruses have been discovered in fecal samples of humans: bufavirus (BuV) in 2012, tusavirus (TuV) in 2014, and cutavirus (CuV) in 2016. BuV has since been studied the most, disclosing three genotypes that also represent serotypes. Besides one nasal sample, BuV DNA has been found exclusively in diarrheal feces, but not in non-diarrheal feces, suggesting a causal relationship. According to both geno- and seroprevalences, BuV appears to be the most common of the three novel protoparvoviruses, whereas TuV DNA has been found in only a single fecal sample, with antibody detection being equally rare. Moreover, the TuV sequence is closer to those of non-human protoparvoviruses, and so the evidence of TuV being a human virus is thus far insufficient. Interestingly, besides in feces, CuV has also been detected in skin biopsies of patients with cutaneous T-cell lymphoma and a patient with melanoma, while all other skin samples have tested PCR negative. Even if preliminary disease associations exist, the full etiological roles of these viruses in human disease are yet to be resolved.
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Affiliation(s)
- Elina Väisänen
- Department of Virology, University of Helsinki, Helsinki 00290, Finland.
| | - Yu Fu
- Department of Virology, University of Helsinki, Helsinki 00290, Finland.
| | - Klaus Hedman
- Department of Virology, University of Helsinki, Helsinki 00290, Finland.
- Helsinki University Hospital, Helsinki 00290, Finland.
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42
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Jia J, Zhong Y, Guo Y, Huangfu C, Zhao X, Fang C, Fan R, Ma Y, Zhang J. Simultaneous detection and differentiation of human parvovirus B19 and human parvovirus 4 by an internally controlled multiplex quantitative real-time PCR. Mol Cell Probes 2017; 36:50-57. [PMID: 28863892 DOI: 10.1016/j.mcp.2017.08.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 08/28/2017] [Accepted: 08/28/2017] [Indexed: 02/03/2023]
Abstract
Human parvovirus B19 (B19V) and human parvovirus 4 (PARV4) are two parvoviruses known to infect humans and transmit through blood and plasma derived medicinal products (PDMPs). Inactivation of the two parvoviruses has proven to be difficult and nucleic acid testing (NAT) would be an efficient means to exclude viruses. In this study, an internally controlled multiplex quantitative real-time PCR (qPCR) assay for B19V and PARV4 simultaneous detection and quantification was established and evaluated. The optimized multiplex qPCR assay allowed for simultaneous detection of all of the genotypes (1-3) of B19V and PARV4, with equal limit of quantification (LOQ) of 5 copies/μL, rather than other blood-borne viruses. It had a wide dynamic range of reliable amplification linearity of at least 8 orders of magnitude. Low standard deviations (SD) of quantification cycle (Cq) values and low coefficients of variation (CV) of copy numbers for both B19V and PARV4 suggested a high level of repeatability and reproducibility for the multiplex qPCR assay. This multiplex qPCR assay can be served as a readily applicable approach to screen plasma units intended for further manufacturing into PDMPs to reduce the risk of parvoviruses infection by such products and may also be useful for the detection of B19V/PARV4 co-infection or co-existence.
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Affiliation(s)
- Junting Jia
- Beijing Key Laboratory of Blood Safety and Supply Technologies & Blood Products and Substitute Laboratory, Beijing Institute of Transfusion Medicine, Beijing 100850, China.
| | - Yadi Zhong
- Beijing Key Laboratory of Blood Safety and Supply Technologies & Blood Products and Substitute Laboratory, Beijing Institute of Transfusion Medicine, Beijing 100850, China.
| | - Yi Guo
- Beijing Key Laboratory of Blood Safety and Supply Technologies & Blood Products and Substitute Laboratory, Beijing Institute of Transfusion Medicine, Beijing 100850, China; Shaanxi Blood Center, Xi'an 710000, China.
| | - Chaoji Huangfu
- Beijing Key Laboratory of Blood Safety and Supply Technologies & Blood Products and Substitute Laboratory, Beijing Institute of Transfusion Medicine, Beijing 100850, China.
| | - Xiong Zhao
- Beijing Key Laboratory of Blood Safety and Supply Technologies & Blood Products and Substitute Laboratory, Beijing Institute of Transfusion Medicine, Beijing 100850, China.
| | - Chi Fang
- Beijing Key Laboratory of Blood Safety and Supply Technologies & Blood Products and Substitute Laboratory, Beijing Institute of Transfusion Medicine, Beijing 100850, China.
| | - Rui Fan
- Beijing Key Laboratory of Blood Safety and Supply Technologies & Blood Products and Substitute Laboratory, Beijing Institute of Transfusion Medicine, Beijing 100850, China.
| | - Yuyuan Ma
- Beijing Key Laboratory of Blood Safety and Supply Technologies & Blood Products and Substitute Laboratory, Beijing Institute of Transfusion Medicine, Beijing 100850, China.
| | - Jingang Zhang
- Beijing Key Laboratory of Blood Safety and Supply Technologies & Blood Products and Substitute Laboratory, Beijing Institute of Transfusion Medicine, Beijing 100850, China.
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Santana Suárez A, García Rodríguez R, García Delgado R, Armas Roca M, Medina Castellano M, Romero Requejo A, Hernández Febles M, Falcón M, García Hernández J. Diagnóstico ecográfico y manejo de la infección fetal por parvovirus B19. CLINICA E INVESTIGACION EN GINECOLOGIA Y OBSTETRICIA 2017. [DOI: 10.1016/j.gine.2015.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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44
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Chrzastek K, Lee DH, Smith D, Sharma P, Suarez DL, Pantin-Jackwood M, Kapczynski DR. Use of Sequence-Independent, Single-Primer-Amplification (SISPA) for rapid detection, identification, and characterization of avian RNA viruses. Virology 2017. [PMID: 28646651 PMCID: PMC7111618 DOI: 10.1016/j.virol.2017.06.019] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Current technologies with next generation sequencing have revolutionized metagenomics analysis of clinical samples. To achieve the non-selective amplification and recovery of low abundance genetic sequences, a simplified Sequence-Independent, Single-Primer Amplification (SISPA) technique in combination with MiSeq platform was applied to target negative- and positive-sense single-stranded RNA viral sequences. This method allowed successful sequence assembly of full or near full length avian influenza virus (AIV), infectious bronchitis virus (IBV), and Newcastle disease virus (NDV) viral genome. Moreover, SISPA analysis applied to unknown clinical cases of mixed viral infections produced genome assemblies comprising 98% NDV and 99% of IBV genomes. Complete or near complete virus genome sequence was obtained with titers at or above 104.5 EID50/ml (50% embryo infectious dose), and virus identification could be detected with titers at or above 103 EID50/ml. Taken together, these studies demonstrate a simple template enrichment protocol for rapid detection and accurate characterization of avian RNA viruses. A simple, random priming technique was optimized to target viral RNA genomes. This technique allows characterization of multiple viruses in single reaction. Complete or near complete genome sequence with titers at or above 104.5 EID50/ml. The detection limit with viral titers at or above 103 EID50/ml.
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Affiliation(s)
- Klaudia Chrzastek
- US National Poultry Research Center, Agricultural Research Service, US Department of Agriculture, 934 College Station Road, Athens, GA 30605, USA
| | - Dong-Hun Lee
- US National Poultry Research Center, Agricultural Research Service, US Department of Agriculture, 934 College Station Road, Athens, GA 30605, USA
| | - Diane Smith
- US National Poultry Research Center, Agricultural Research Service, US Department of Agriculture, 934 College Station Road, Athens, GA 30605, USA
| | - Poonam Sharma
- US National Poultry Research Center, Agricultural Research Service, US Department of Agriculture, 934 College Station Road, Athens, GA 30605, USA
| | - David L Suarez
- US National Poultry Research Center, Agricultural Research Service, US Department of Agriculture, 934 College Station Road, Athens, GA 30605, USA
| | - Mary Pantin-Jackwood
- US National Poultry Research Center, Agricultural Research Service, US Department of Agriculture, 934 College Station Road, Athens, GA 30605, USA
| | - Darrell R Kapczynski
- US National Poultry Research Center, Agricultural Research Service, US Department of Agriculture, 934 College Station Road, Athens, GA 30605, USA.
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45
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Amirahmadi F, Sarvari J, Hosseini SY, Pirbonyeh N, Gorzin AA. Frequency of human parvovirus 4 (PARV4) viremia among HBV-infected patients and healthy donors in Shiraz, Iran. Turk J Med Sci 2017; 47:868-873. [PMID: 28618736 DOI: 10.3906/sag-1603-83] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Accepted: 12/06/2016] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND/AIM PARV4, a small DNA virus belonging to the family Parvoviridae, was first isolated in an HBV injecting drug user. Several studies have investigated PARV4 co-infection with HBV and HCV and its effect on the progression of liver disease. The aim of this study was to determine the frequency of PARV4 among HBV-infected patients and healthy individuals. MATERIALS AND METHODS A group of 90 HBV patients and a group of 90 healthy subjects were included in this study. Samples were selected after screening tests such as HBsAg ELISA, anti-HCV ELISA, and anti-HIV ELISA. Nested-PCRs were conducted to detect the PARV4 genome. Positive samples were then subjected to DNA sequencing. RESULTS PARV4 DNA was detected in 4.4% of HBV patients in comparison with 1.1% of healthy individuals (P-value: 0.36). DNA sequencing results revealed that PARV4 in all five positive samples was genotype I.Conclusions: Although this pilot study showed no significant difference between the frequency of PARV4 among HBV patients and healthy donors, further studies with a larger sample size are suggested to determine the association of PARV4 with HBV co-infection and the impact of this virus on the progression of liver disease in patients with hepatitis B.
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Affiliation(s)
- Fereshte Amirahmadi
- Deparment of Bacteriology & Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Jamal Sarvari
- Deparment of Bacteriology & Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyed Younes Hosseini
- Deparment of Bacteriology & Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Neda Pirbonyeh
- Deparment of Bacteriology & Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ali Akbar Gorzin
- Deparment of Bacteriology & Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
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46
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Kumar A, Murthy S, Kapoor A. Evolution of selective-sequencing approaches for virus discovery and virome analysis. Virus Res 2017; 239:172-179. [PMID: 28583442 PMCID: PMC5819613 DOI: 10.1016/j.virusres.2017.06.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 12/28/2016] [Accepted: 06/02/2017] [Indexed: 12/11/2022]
Abstract
Description of virus enrichment techniques for metagenomics based virome analysis. Usefulness of recently developed virome capture sequencing techniques. Perspective on negative and positive selection approaches for virome analysis.
Recent advances in sequencing technologies have transformed the field of virus discovery and virome analysis. Once mostly confined to the traditional Sanger sequencing based individual virus discovery, is now entirely replaced by high throughput sequencing (HTS) based virus metagenomics that can be used to characterize the nature and composition of entire viromes. To better harness the potential of HTS for the study of viromes, sample preparation methodologies use different approaches to exclude amplification of non-viral components that can overshadow low-titer viruses. These virus-sequence enrichment approaches mostly focus on the sample preparation methods, like enzymatic digestion of non-viral nucleic acids and size exclusion of non-viral constituents by column filtration, ultrafiltration or density gradient centrifugation. However, recently a new approach of virus-sequence enrichment called virome-capture sequencing, focused on the amplification or HTS library preparation stage, was developed to increase the ability of virome characterization. This new approach has the potential to further transform the field of virus discovery and virome analysis, but its technical complexity and sequence-dependence warrants further improvements. In this review we discuss the different methods, their applications and evolution, for selective sequencing based virome analysis and also propose refinements needed to harness the full potential of HTS for virome analysis.
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Affiliation(s)
- Arvind Kumar
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Satyapramod Murthy
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Amit Kapoor
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA; Department of Pediatrics, College of Medicine and Public Health, Ohio State University, Columbus, OH 43210, USA.
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47
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Lewandowska DW, Schreiber PW, Schuurmans MM, Ruehe B, Zagordi O, Bayard C, Greiner M, Geissberger FD, Capaul R, Zbinden A, Böni J, Benden C, Mueller NJ, Trkola A, Huber M. Metagenomic sequencing complements routine diagnostics in identifying viral pathogens in lung transplant recipients with unknown etiology of respiratory infection. PLoS One 2017; 12:e0177340. [PMID: 28542207 PMCID: PMC5441588 DOI: 10.1371/journal.pone.0177340] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 04/26/2017] [Indexed: 12/19/2022] Open
Abstract
Background Lung transplant patients are a vulnerable group of immunosuppressed patients that are prone to frequent respiratory infections. We studied 60 episodes of respiratory symptoms in 71 lung transplant patients. Almost half of these episodes were of unknown infectious etiology despite extensive routine diagnostic testing. Methods We re-analyzed respiratory samples of all episodes with undetermined etiology in order to detect potential viral pathogens missed/not accounted for in routine diagnostics. Respiratory samples were enriched for viruses by filtration and nuclease digestion, whole nucleic acids extracted and randomly amplified before high throughput metagenomic virus sequencing. Viruses were identified by a bioinformatic pipeline and confirmed and quantified using specific real-time PCR. Results In completion of routine diagnostics, we identified and confirmed a viral etiology of infection by our metagenomic approach in four patients (three Rhinovirus A, one Rhinovirus B infection) despite initial negative results in specific multiplex PCR. Notably, the majority of samples were also positive for Torque teno virus (TTV) and Human Herpesvirus 7 (HHV-7). While TTV viral loads increased with immunosuppression in both throat swabs and blood samples, HHV-7 remained at low levels throughout the observation period and was restricted to the respiratory tract. Conclusion This study highlights the potential of metagenomic sequencing for virus diagnostics in cases with previously unknown etiology of infection and in complex diagnostic situations such as in immunocompromised hosts.
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Affiliation(s)
| | - Peter W. Schreiber
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Macé M. Schuurmans
- Division of Pulmonary Medicine, University Hospital Zurich, Zurich, Switzerland
| | - Bettina Ruehe
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Osvaldo Zagordi
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Cornelia Bayard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Michael Greiner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | | | - Riccarda Capaul
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Andrea Zbinden
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Christian Benden
- Division of Pulmonary Medicine, University Hospital Zurich, Zurich, Switzerland
| | - Nicolas J. Mueller
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
- * E-mail:
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48
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Bédarida S, Dussol B, Signoli M, Biagini P. Analysis of Anelloviridae sequences characterized from serial human and animal biological samples. INFECTION GENETICS AND EVOLUTION 2017; 53:89-93. [PMID: 28536071 DOI: 10.1016/j.meegid.2017.05.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 04/28/2017] [Accepted: 05/19/2017] [Indexed: 11/19/2022]
Abstract
Rolling-circle amplification-sequence-independent single primer amplifications (RCA-SISPA) and/or RCA-PCR-based approaches were applied to serial human plasma and animal (domestic cat) saliva samples. Complete SENV-H-related and PRA4 Anelloviridae genomes were characterized and analysed over time (~16 and 6.5years for human and animal samples, respectively). Genomic sequences and deduced putative coding regions were compared. Comparable values, i.e. ~2×10-4subs/site/year, were obtained for estimated rates of non-synonymous substitutions. A "hot-spot" of mutations located on the SENV-H-related ORF1 was identified. These results are first data concerning Anelloviridae evolution in a human and an animal host based on the analysis of complete sequences.
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Affiliation(s)
- Sandra Bédarida
- EFS Alpes-Méditerranée, Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France
| | - Bertrand Dussol
- Nephrology and Renal Transplantation Centre, CHU Conception, Marseille, France
| | | | - Philippe Biagini
- EFS Alpes-Méditerranée, Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France.
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49
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Sharp CP, Gregory WF, Hattingh L, Malik A, Adland E, Daniels S, van Zyl A, Carlson JM, Wareing S, Ogwu A, Shapiro R, Riddell L, Chen F, Ndung'u T, Goulder PJR, Klenerman P, Simmonds P, Jooste P, Matthews PC. PARV4 prevalence, phylogeny, immunology and coinfection with HIV, HBV and HCV in a multicentre African cohort. Wellcome Open Res 2017; 2:26. [PMID: 28497124 PMCID: PMC5423528 DOI: 10.12688/wellcomeopenres.11135.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Background: The seroprevalence of human parvovirus-4 (PARV4) varies considerably by region. In sub-Saharan Africa, seroprevalence is high in the general population, but little is known about the transmission routes or the prevalence of coinfection with blood-borne viruses, HBV, HCV and HIV.
Methods: To further explore the characteristics of PARV4 in this setting, with a particular focus on the prevalence and significance of coinfection, we screened a cohort of 695 individuals recruited from Durban and Kimberley (South Africa) and Gaborone (Botswana) for PARV4 IgG and DNA, as well as documenting HIV, HBV and HCV status.
Results: Within these cohorts, 69% of subjects were HIV-positive. We identified no cases of HCV by PCR, but 7.4% were positive for HBsAg. PARV4 IgG was positive in 42%; seroprevalence was higher in adults (69%) compared to children (21%) (p<0.0001) and in HIV-positive (52%) compared to HIV-negative individuals (24%) (p<0.0001), but there was no association with HBsAg status. We developed an on-line tool to allow visualization of coinfection data (
https://purl.oclc.org/coinfection-viz). We identified five subjects who were PCR-positive for PARV4 genotype-3.
Ex vivo CD8+ T cell responses spanned the entire PARV4 proteome and we propose a novel HLA-B*57:03-restricted epitope within the NS protein.
Conclusions: This characterisation of PARV4 infection provides enhanced insights into the epidemiology of infection and co-infection in African cohorts, and provides the foundations for planning further focused studies to elucidate transmission pathways, immune responses, and the clinical significance of this organism.
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Affiliation(s)
- Colin P Sharp
- Roslin Institute, University of Edinburgh, Edinburgh, EH25 9RG, UK.,Edinburgh Genomics, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | | | - Louise Hattingh
- Kimberley Hospital, Kimberley, Northern Cape, 8301, South Africa
| | - Amna Malik
- Department of Paediatrics, University of Oxford, Oxford, OX1 3SY, UK
| | - Emily Adland
- Department of Paediatrics, University of Oxford, Oxford, OX1 3SY, UK
| | - Samantha Daniels
- Kimberley Hospital, Kimberley, Northern Cape, 8301, South Africa
| | - Anriette van Zyl
- Kimberley Hospital, Kimberley, Northern Cape, 8301, South Africa
| | | | - Susan Wareing
- Department of Microbiology and Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Anthony Ogwu
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Roger Shapiro
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Lynn Riddell
- Northampton General Hospital NHS Trust, Northampton, NN1 5BD, UK
| | - Fabian Chen
- Royal Berkshire Hospital, Reading, RG1 5AN, UK
| | - Thumbi Ndung'u
- HIV Pathogenesis Program, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, KwaZulu-Natal, 4041, South Africa
| | | | - Paul Klenerman
- Department of Microbiology and Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, OX3 9DU, UK.,Nuffield Department of Medicine, University of Oxford, Oxford, OX1 3SY, UK.,NIHR Biomedical Research Centre, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, OX1 3SY, UK
| | - Pieter Jooste
- Kimberley Hospital, Kimberley, Northern Cape, 8301, South Africa
| | - Philippa C Matthews
- Department of Microbiology and Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, OX3 9DU, UK.,Nuffield Department of Medicine, University of Oxford, Oxford, OX1 3SY, UK
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50
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Matthews PC, Sharp C, Simmonds P, Klenerman P. Human parvovirus 4 'PARV4' remains elusive despite a decade of study. F1000Res 2017; 6:82. [PMID: 28184291 PMCID: PMC5288687 DOI: 10.12688/f1000research.9828.1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/23/2017] [Indexed: 12/16/2022] Open
Abstract
Human parvovirus 4 ('PARV4') is a small DNA tetraparvovirus, first reported in 2005. In some populations, PARV4 infection is uncommon, and evidence of exposure is found only in individuals with risk factors for parenteral infection who are infected with other blood-borne viruses. In other settings, seroprevalence studies suggest an endemic, age-associated transmission pattern, independent of any specific risk factors. The clinical impact of PARV4 infection remains uncertain, but reported disease associations include an influenza-like syndrome, encephalitis, acceleration of HIV disease, and foetal hydrops. In this review, we set out to report progress updates from the recent literature, focusing on the investigation of cohorts in different geographical settings, now including insights from Asia, the Middle East, and South America, and discussing whether attributes of viral or host populations underpin the striking differences in epidemiology. We review progress in understanding viral phylogeny and biology, approaches to diagnostics, and insights that might be gained from studies of closely related animal pathogens. Crucial questions about pathogenicity remain unanswered, but we highlight new evidence supporting a possible link between PARV4 and an encephalitis syndrome. The unequivocal evidence that PARV4 is endemic in certain populations should drive ongoing research efforts to understand risk factors and routes of transmission and to gain new insights into the impact of this virus on human health.
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Affiliation(s)
- Philippa C Matthews
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building for Pathogen Research, South Parks Road, Oxford, OX1 3SY, UK; Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
| | - Colin Sharp
- Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building for Pathogen Research, South Parks Road, Oxford, OX1 3SY, UK
| | - Paul Klenerman
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building for Pathogen Research, South Parks Road, Oxford, OX1 3SY, UK; Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK; NIHR Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
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