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KI and WU Polyomaviruses: Seroprevalence Study and DNA Prevalence in SARS-CoV-2 RNA Positive and Negative Respiratory Samples. Microorganisms 2022; 10:microorganisms10040752. [PMID: 35456801 PMCID: PMC9031565 DOI: 10.3390/microorganisms10040752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/25/2022] [Accepted: 03/29/2022] [Indexed: 11/17/2022] Open
Abstract
The aim of this work was to study the possible co-infection of KI and WU polyomavirus (KIPyV and WUPyV, respectively) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in respiratory samples and to detect the seroprevalence of KIPyV and WUPyV. A total of 1030 nasopharyngeal samples were analyzed from SARS-CoV-2 RNA positive (n = 680) and negative (n = 350) adults and children (age: 1 day to 94.2 years) collected from August 2020 to October 2021. KIPyV DNA was detected in two SARS-CoV-2-positive samples (2/680, 0.29%) and in three SARS-CoV-2-negative samples (3/350, 0.86%). WUPyV DNA was observed in one-one samples from both groups (1/680, 0.15% vs. 1/350, 0.29%). We did not find an association between SARS-CoV-2 and KIPyV or WUPyV infection, and we found low DNA prevalence of polyomaviruses studied after a long-term lockdown in Hungary. To exclude a geographically different distribution of these polyomaviruses, we studied the seroprevalence of KIPyV and WUPyV by enzyme-linked immunosorbent assay among children and adults (n = 692 for KIPyV and n = 705 for WUPyV). Our data confirmed that primary infections by KIPyV and WUPyV occur mainly during childhood; the overall seropositivity of adults was 93.7% and 89.2% for KIPyV and WUPyV, respectively. Based on our data, we suggest that the spread of KIPyV and WUPyV might have been restricted in Hungary by the lockdown.
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Prezioso C, Moens U, Oliveto G, Brazzini G, Piacentini F, Frasca F, Viscido A, Scordio M, Guerrizio G, Rodio DM, Pierangeli A, d’Ettorre G, Turriziani O, Antonelli G, Scagnolari C, Pietropaolo V. KI and WU Polyomavirus in Respiratory Samples of SARS-CoV-2 Infected Patients. Microorganisms 2021; 9:microorganisms9061259. [PMID: 34207902 PMCID: PMC8229673 DOI: 10.3390/microorganisms9061259] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/01/2021] [Accepted: 06/08/2021] [Indexed: 11/19/2022] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has been declared a global pandemic. Our goal was to determine whether co-infections with respiratory polyomaviruses, such as Karolinska Institutet polyomavirus (KIPyV) and Washington University polyomavirus (WUPyV) occur in SARS-CoV-2 infected patients. Oropharyngeal swabs from 150 individuals, 112 symptomatic COVID-19 patients and 38 healthcare workers not infected by SARS-CoV-2, were collected from March 2020 through May 2020 and tested for KIPyV and WUPyV DNA presence. Of the 112 SARS-CoV-2 positive patients, 27 (24.1%) were co-infected with KIPyV, 5 (4.5%) were positive for WUPyV, and 3 (2.7%) were infected simultaneously by KIPyV and WUPyV. Neither KIPyV nor WUPyV DNA was detected in samples of healthcare workers. Significant correlations were found in patients co-infected with SARS-CoV-2 and KIPyV (p < 0.05) and between SARS-CoV-2 cycle threshold values and KIPyV, WUPyV and KIPyV and WUPyV concurrently detected (p < 0.05). These results suggest that KIPyV and WUPyV may behave as opportunistic respiratory pathogens. Additional investigations are needed to understand the epidemiology and the prevalence of respiratory polyomavirus in COVID-19 patients and whether KIPyV and WUPyV could potentially drive viral interference or influence disease outcomes by upregulating SARS-CoV-2 replicative potential.
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Affiliation(s)
- Carla Prezioso
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00185 Rome, Italy; (C.P.); (G.B.); (F.P.); (G.d.)
- IRCSS San Raffaele Pisana, Microbiology of Chronic Neuro-Degenerative Pathologies, 00163 Rome, Italy
| | - Ugo Moens
- Department of Medical Biology, Faculty of Health Sciences, University of Tromsø—The Arctic University of Norway, 9037 Tromsø, Norway;
| | - Giuseppe Oliveto
- Laboratory of Microbiology and Virology, Department of Molecular Medicine, “Sapienza” University of Rome, 00161 Rome, Italy; (G.O.); (F.F.); (A.V.); (M.S.); (G.G.); (D.M.R.); (A.P.); (O.T.); (G.A.); (C.S.)
- Microbiology and Virology Unit, “Sapienza” University Hospital “Policlinico Umberto I”, 00161 Rome, Italy
- Istituto Pasteur Italia, 00161 Rome, Italy
| | - Gabriele Brazzini
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00185 Rome, Italy; (C.P.); (G.B.); (F.P.); (G.d.)
| | - Francesca Piacentini
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00185 Rome, Italy; (C.P.); (G.B.); (F.P.); (G.d.)
| | - Federica Frasca
- Laboratory of Microbiology and Virology, Department of Molecular Medicine, “Sapienza” University of Rome, 00161 Rome, Italy; (G.O.); (F.F.); (A.V.); (M.S.); (G.G.); (D.M.R.); (A.P.); (O.T.); (G.A.); (C.S.)
- Istituto Pasteur Italia, 00161 Rome, Italy
| | - Agnese Viscido
- Laboratory of Microbiology and Virology, Department of Molecular Medicine, “Sapienza” University of Rome, 00161 Rome, Italy; (G.O.); (F.F.); (A.V.); (M.S.); (G.G.); (D.M.R.); (A.P.); (O.T.); (G.A.); (C.S.)
- Microbiology and Virology Unit, “Sapienza” University Hospital “Policlinico Umberto I”, 00161 Rome, Italy
| | - Mirko Scordio
- Laboratory of Microbiology and Virology, Department of Molecular Medicine, “Sapienza” University of Rome, 00161 Rome, Italy; (G.O.); (F.F.); (A.V.); (M.S.); (G.G.); (D.M.R.); (A.P.); (O.T.); (G.A.); (C.S.)
- Istituto Pasteur Italia, 00161 Rome, Italy
| | - Giuliana Guerrizio
- Laboratory of Microbiology and Virology, Department of Molecular Medicine, “Sapienza” University of Rome, 00161 Rome, Italy; (G.O.); (F.F.); (A.V.); (M.S.); (G.G.); (D.M.R.); (A.P.); (O.T.); (G.A.); (C.S.)
- Microbiology and Virology Unit, “Sapienza” University Hospital “Policlinico Umberto I”, 00161 Rome, Italy
| | - Donatella Maria Rodio
- Laboratory of Microbiology and Virology, Department of Molecular Medicine, “Sapienza” University of Rome, 00161 Rome, Italy; (G.O.); (F.F.); (A.V.); (M.S.); (G.G.); (D.M.R.); (A.P.); (O.T.); (G.A.); (C.S.)
- Microbiology and Virology Unit, “Sapienza” University Hospital “Policlinico Umberto I”, 00161 Rome, Italy
| | - Alessandra Pierangeli
- Laboratory of Microbiology and Virology, Department of Molecular Medicine, “Sapienza” University of Rome, 00161 Rome, Italy; (G.O.); (F.F.); (A.V.); (M.S.); (G.G.); (D.M.R.); (A.P.); (O.T.); (G.A.); (C.S.)
- Istituto Pasteur Italia, 00161 Rome, Italy
| | - Gabriella d’Ettorre
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00185 Rome, Italy; (C.P.); (G.B.); (F.P.); (G.d.)
| | - Ombretta Turriziani
- Laboratory of Microbiology and Virology, Department of Molecular Medicine, “Sapienza” University of Rome, 00161 Rome, Italy; (G.O.); (F.F.); (A.V.); (M.S.); (G.G.); (D.M.R.); (A.P.); (O.T.); (G.A.); (C.S.)
- Microbiology and Virology Unit, “Sapienza” University Hospital “Policlinico Umberto I”, 00161 Rome, Italy
| | - Guido Antonelli
- Laboratory of Microbiology and Virology, Department of Molecular Medicine, “Sapienza” University of Rome, 00161 Rome, Italy; (G.O.); (F.F.); (A.V.); (M.S.); (G.G.); (D.M.R.); (A.P.); (O.T.); (G.A.); (C.S.)
- Microbiology and Virology Unit, “Sapienza” University Hospital “Policlinico Umberto I”, 00161 Rome, Italy
- Istituto Pasteur Italia, 00161 Rome, Italy
| | - Carolina Scagnolari
- Laboratory of Microbiology and Virology, Department of Molecular Medicine, “Sapienza” University of Rome, 00161 Rome, Italy; (G.O.); (F.F.); (A.V.); (M.S.); (G.G.); (D.M.R.); (A.P.); (O.T.); (G.A.); (C.S.)
- Istituto Pasteur Italia, 00161 Rome, Italy
| | - Valeria Pietropaolo
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00185 Rome, Italy; (C.P.); (G.B.); (F.P.); (G.d.)
- Microbiology and Virology Unit, “Sapienza” University Hospital “Policlinico Umberto I”, 00161 Rome, Italy
- Correspondence: ; Tel.: +39-06-49914439
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Paskey AC, Frey KG, Schroth G, Gross S, Hamilton T, Bishop-Lilly KA. Enrichment post-library preparation enhances the sensitivity of high-throughput sequencing-based detection and characterization of viruses from complex samples. BMC Genomics 2019; 20:155. [PMID: 30808306 PMCID: PMC6390631 DOI: 10.1186/s12864-019-5543-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 02/18/2019] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Sequencing-based detection and characterization of viruses in complex samples can suffer from lack of sensitivity due to a variety of factors including, but not limited to, low titer, small genome size, and contribution of host or environmental nucleic acids. Hybridization-based target enrichment is one potential method for increasing the sensitivity of viral detection via high-throughput sequencing. RESULTS This study expands upon two previously developed panels of virus enrichment probes (for filoviruses and for respiratory viruses) to include other viruses of biodefense and/or biosurveillance concern to the U.S. Department of Defense and various international public health agencies. The newly expanded and combined panel is tested using carefully constructed synthetic metagenomic samples that contain clinically relevant amounts of viral genetic material. Target enrichment results in a dramatic increase in sensitivity for virus detection as compared to shotgun sequencing, yielding full, deeply covered viral genomes from materials with Ct values suggesting that amplicon sequencing would be likely to fail. Increased pooling to improve cost- and time-effectiveness does not negatively affect the ability to obtain full-length viral genomes, even in the case of co-infections, although as expected, it does decrease depth of coverage. CONCLUSIONS Hybridization-based target enrichment is an effective solution to obtain full-length viral genomes for samples from which virus detection would fail via unbiased, shotgun sequencing or even via amplicon sequencing. As the development and testing of probe sets for viral target enrichment expands and continues, the application of this technique, in conjunction with deeper pooling strategies, could make high-throughput sequencing more economical for routine use in biosurveillance, biodefense and outbreak investigations.
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Affiliation(s)
- Adrian C. Paskey
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, Fort Detrick, Frederick, MD 21702 USA
- Uniformed Services University of the Health Sciences, Bethesda, MD 20814 USA
- Leidos, Reston, VA 20190 USA
| | - Kenneth G. Frey
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, Fort Detrick, Frederick, MD 21702 USA
| | | | | | - Theron Hamilton
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, Fort Detrick, Frederick, MD 21702 USA
| | - Kimberly A. Bishop-Lilly
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, Fort Detrick, Frederick, MD 21702 USA
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Kamminga S, van der Meijden E, Feltkamp MCW, Zaaijer HL. Seroprevalence of fourteen human polyomaviruses determined in blood donors. PLoS One 2018; 13:e0206273. [PMID: 30352098 PMCID: PMC6198985 DOI: 10.1371/journal.pone.0206273] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 10/10/2018] [Indexed: 11/26/2022] Open
Abstract
The polyomavirus family currently includes thirteen human polyomavirus (HPyV) species. In immunocompromised and elderly persons HPyVs are known to cause disease, such as progressive multifocal leukoencephalopathy (JCPyV), haemorrhagic cystitis and nephropathy (BKPyV), Merkel cell carcinoma (MCPyV), and trichodysplasia spinulosa (TSPyV). Some recently discovered polyomaviruses are of still unknown prevalence and pathogenic potential. Because HPyVs infections persist and might be transferred by blood components to immunocompromised patients, we studied the seroprevalence of fourteen polyomaviruses in adult Dutch blood donors. For most polyomaviruses the observed seroprevalence was high (60–100%), sometimes slightly increasing or decreasing with age. Seroreactivity increased with age for JCPyV, HPyV6 and HPyV7 and decreased for BKPyV and TSPyV. The most recently identified polyomaviruses HPyV12, NJPyV and LIPyV showed low overall seroprevalence (~5%) and low seroreactivity, questioning their human tropism. Altogether, HPyV infections are common in Dutch blood donors, with an average of nine polyomaviruses per subject.
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Affiliation(s)
- Sergio Kamminga
- Department of Blood-borne Infections, Sanquin Research, Amsterdam, the Netherlands
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
- * E-mail:
| | - Els van der Meijden
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Mariet C. W. Feltkamp
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Hans L. Zaaijer
- Department of Blood-borne Infections, Sanquin Research, Amsterdam, the Netherlands
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O'Flaherty BM, Li Y, Tao Y, Paden CR, Queen K, Zhang J, Dinwiddie DL, Gross SM, Schroth GP, Tong S. Comprehensive viral enrichment enables sensitive respiratory virus genomic identification and analysis by next generation sequencing. Genome Res 2018; 28:869-877. [PMID: 29703817 PMCID: PMC5991510 DOI: 10.1101/gr.226316.117] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 04/10/2018] [Indexed: 01/01/2023]
Abstract
Next generation sequencing (NGS) technologies have revolutionized the genomics field and are becoming more commonplace for identification of human infectious diseases. However, due to the low abundance of viral nucleic acids (NAs) in relation to host, viral identification using direct NGS technologies often lacks sufficient sensitivity. Here, we describe an approach based on two complementary enrichment strategies that significantly improves the sensitivity of NGS-based virus identification. To start, we developed two sets of DNA probes to enrich virus NAs associated with respiratory diseases. The first set of probes spans the genomes, allowing for identification of known viruses and full genome sequencing, while the second set targets regions conserved among viral families or genera, providing the ability to detect both known and potentially novel members of those virus groups. Efficiency of enrichment was assessed by NGS testing reference virus and clinical samples with known infection. We show significant improvement in viral identification using enriched NGS compared to unenriched NGS. Without enrichment, we observed an average of 0.3% targeted viral reads per sample. However, after enrichment, 50%–99% of the reads per sample were the targeted viral reads for both the reference isolates and clinical specimens using both probe sets. Importantly, dramatic improvements on genome coverage were also observed following virus-specific probe enrichment. The methods described here provide improved sensitivity for virus identification by NGS, allowing for a more comprehensive analysis of disease etiology.
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Affiliation(s)
- Brigid M O'Flaherty
- Centers for Disease Control and Prevention, NCIRD, DVD, Atlanta, Georgia 30329, USA.,Oak Ridge Institute for Science Education, Oak Ridge, Tennessee 37830, USA
| | - Yan Li
- Centers for Disease Control and Prevention, NCIRD, DVD, Atlanta, Georgia 30329, USA
| | - Ying Tao
- Centers for Disease Control and Prevention, NCIRD, DVD, Atlanta, Georgia 30329, USA
| | - Clinton R Paden
- Centers for Disease Control and Prevention, NCIRD, DVD, Atlanta, Georgia 30329, USA.,Oak Ridge Institute for Science Education, Oak Ridge, Tennessee 37830, USA
| | - Krista Queen
- Centers for Disease Control and Prevention, NCIRD, DVD, Atlanta, Georgia 30329, USA.,Oak Ridge Institute for Science Education, Oak Ridge, Tennessee 37830, USA
| | - Jing Zhang
- Centers for Disease Control and Prevention, NCIRD, DVD, Atlanta, Georgia 30329, USA.,IHRC Incorporated, Atlanta, Georgia 30346, USA
| | - Darrell L Dinwiddie
- Department of Pediatrics, Clinical Translational Science Center, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | | | - Gary P Schroth
- Illumina, Incorporated, San Diego, California 92122, USA
| | - Suxiang Tong
- Centers for Disease Control and Prevention, NCIRD, DVD, Atlanta, Georgia 30329, USA
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Baez CF, Brandão Varella R, Villani S, Delbue S. Human Polyomaviruses: The Battle of Large and Small Tumor Antigens. Virology (Auckl) 2017; 8:1178122X17744785. [PMID: 29238174 PMCID: PMC5721967 DOI: 10.1177/1178122x17744785] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 10/30/2017] [Indexed: 12/17/2022] Open
Abstract
About 40 years ago, the large and small tumor antigens (LT-Ag and sT-Ag) of the polyomavirus (PyVs) simian vacuolating virus 40 have been identified and characterized. To date, it is well known that all the discovered human PyVs (HPyVs) encode these 2 multifunctional and tumorigenic proteins, expressed at viral replication early stage. The 2 T-Ags are able to transform cells both in vitro and in vivo and seem to play a distinct role in the pathogenesis of some tumors in humans. In addition, they are involved in viral DNA replication, transcription, and virion assembly. This short review focuses on the structural and functional features of the HPyVs’ LT-Ag and sT-Ag, with special attention to their transforming properties.
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Affiliation(s)
- Camila Freze Baez
- Department of Preventive Medicine, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Sonia Villani
- Department of Biomedical, Surgical and Dental Sciences, University of Milano, Milano, Italy
| | - Serena Delbue
- Department of Biomedical, Surgical and Dental Sciences, University of Milano, Milano, Italy
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Biology, evolution, and medical importance of polyomaviruses: An update. INFECTION GENETICS AND EVOLUTION 2017. [DOI: 10.1016/j.meegid.2017.06.011] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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