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Buigues J, Viñals A, Martínez-Recio R, Monrós JS, Sanjuán R, Cuevas JM. Full-genome sequencing of dozens of new DNA viruses found in Spanish bat feces. Microbiol Spectr 2024; 12:e0067524. [PMID: 38990026 DOI: 10.1128/spectrum.00675-24] [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: 03/13/2024] [Accepted: 06/26/2024] [Indexed: 07/12/2024] Open
Abstract
Bats are natural hosts of multiple viruses, many of which have clear zoonotic potential. The search for emerging viruses has been aided by the implementation of metagenomic tools, which have also enabled the detection of unprecedented viral diversity. Currently, this search is mainly focused on RNA viruses, which are largely over-represented in databases. To compensate for this research bias, we analyzed fecal samples from 189 Spanish bats belonging to 22 different species using viral metagenomics. This allowed us to identify 52 complete or near-complete viral genomes belonging to the families Adenoviridae, Circoviridae, Genomoviridae, Papillomaviridae, Parvoviridae, Polyomaviridae and Smacoviridae. Of these, 30 could constitute new species, doubling the number of viruses currently described in Europe. These findings open the door to a more thorough analysis of bat DNA viruses and their zoonotic potential. IMPORTANCE Metagenomics has become a fundamental tool to characterize the global virosphere, allowing us not only to understand the existing viral diversity and its ecological implications but also to identify new and emerging viruses. RNA viruses have a higher zoonotic potential, but this risk is also present for some DNA virus families. In our study, we analyzed the DNA fraction of fecal samples from 22 Spanish bat species, identifying 52 complete or near-complete genomes of different viral families with zoonotic potential. This doubles the number of genomes currently described in Europe. Metagenomic data often produce partial genomes that can be difficult to analyze. Our work, however, has characterized a large number of complete genomes, thus facilitating their taxonomic classification and enabling different analyses to be carried out to evaluate their zoonotic potential. For example, recombination studies are relevant since this phenomenon could play a major role in cross-species transmission.
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Affiliation(s)
- Jaime Buigues
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València and Consejo Superior de Investigaciones Científicas, València, Spain
| | - Adrià Viñals
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, València, Spain
| | - Raquel Martínez-Recio
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València and Consejo Superior de Investigaciones Científicas, València, Spain
| | - Juan S Monrós
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, València, Spain
| | - Rafael Sanjuán
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València and Consejo Superior de Investigaciones Científicas, València, Spain
- Department of Genetics, Universitat de València, València, Spain
| | - José M Cuevas
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València and Consejo Superior de Investigaciones Científicas, València, Spain
- Department of Genetics, Universitat de València, València, Spain
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Alamri AM, Alkhilaiwi FA, Ullah Khan N. Era of Molecular Diagnostics Techniques before and after the COVID-19 Pandemic. Curr Issues Mol Biol 2022; 44:4769-4789. [PMID: 36286040 PMCID: PMC9601158 DOI: 10.3390/cimb44100325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 09/28/2022] [Accepted: 10/05/2022] [Indexed: 11/17/2022] Open
Abstract
Despite the growth of molecular diagnosis from the era of Hippocrates, the emergence of COVID-19 is still remarkable. The previously used molecular techniques were not rapid enough to screen a vast population at home, in offices, and in hospitals. Additionally, these techniques were only available in advanced clinical laboratories.The pandemic outbreak enhanced the urgency of researchers and research and development companies to invent more rapid, robust, and portable devices and instruments to screen a vast community in a cost-effective and short time. There has been noteworthy progress in molecular diagnosing tools before and after the pandemic. This review focuses on the advancements in molecular diagnostic techniques before and after the emergence of COVID-19 and how the pandemic accelerated the implantation of molecular diagnostic techniques in most clinical laboratories towardbecoming routine tests.
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Affiliation(s)
- Ahmad M. Alamri
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha 61413, Saudi Arabia
- Cancer Research Unit, King Khalid University, Abha 61413, Saudi Arabia
| | - Faris A. Alkhilaiwi
- Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Regenerative Medicine Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Najeeb Ullah Khan
- Institute of Biotechnology and Genetic Engineering (Health Division), The University of Agriculture, Peshawar 25130, Pakistan
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Gilbertson MLJ, Fountain-Jones NM, Craft ME. Incorporating genomic methods into contact networks to reveal new insights into animal behavior and infectious disease dynamics. BEHAVIOUR 2019; 155:759-791. [PMID: 31680698 DOI: 10.1163/1568539x-00003471] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Utilization of contact networks has provided opportunities for assessing the dynamic interplay between pathogen transmission and host behavior. Genomic techniques have, in their own right, provided new insight into complex questions in disease ecology, and the increasing accessibility of genomic approaches means more researchers may seek out these tools. The integration of network and genomic approaches provides opportunities to examine the interaction between behavior and pathogen transmission in new ways and with greater resolution. While a number of studies have begun to incorporate both contact network and genomic approaches, a great deal of work has yet to be done to better integrate these techniques. In this review, we give a broad overview of how network and genomic approaches have each been used to address questions regarding the interaction of social behavior and infectious disease, and then discuss current work and future horizons for the merging of these techniques.
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Affiliation(s)
- Marie L J Gilbertson
- Department of Veterinary Population Medicine, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Nicholas M Fountain-Jones
- Department of Veterinary Population Medicine, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Meggan E Craft
- Department of Veterinary Population Medicine, University of Minnesota, Minneapolis, Minnesota 55455, USA
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Franke N, Bette M, Marquardt A, Briese T, Lipkin WI, Kurz C, Ehrenreich J, Mack E, Baying B, Beneš V, Rodepeter FR, Neff A, Teymoortash A, Eivazi B, Geisthoff U, Stuck BA, Bakowsky U, Mandic R. Virome Analysis Reveals No Association of Head and Neck Vascular Anomalies with an Active Viral Infection. In Vivo 2018; 32:1323-1331. [PMID: 30348684 DOI: 10.21873/invivo.11382] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 09/20/2018] [Accepted: 09/28/2018] [Indexed: 11/10/2022]
Abstract
BACKGROUND/AIM Vascular anomalies encompass different vascular malformations [arteriovenous (AVM), lymphatic (LM), venous lymphatic (VLM), venous (VM)] and vascular tumors such as hemangiomas (HA). The pathogenesis of vascular anomalies is still poorly understood. Viral infection was speculated as a possible underlying cause. MATERIALS AND METHODS A total of 13 human vascular anomalies and three human skin control tissues were used for viral analysis. RNA derived from AVM (n=4) and normal skin control (n=3) tissues was evaluated by RNA sequencing. The Virome Capture Sequencing Platform for Vertebrate Viruses (VirCapSeq-VERT) was deployed on 10 tissues with vascular anomalies (2×AVM, 1×HA, 1×LM, 2×VLM, 4×VM). RESULTS RNA sequencing did not show any correlation of AVM with viral infection. By deploying VirCapSeq-VERT, no consistent viral association was seen in the tested tissues. CONCLUSION The analysis does not point to the presence of an active viral infection in vascular anomalies. However, transient earlier viral infections, e.g. during pregnancy, cannot be excluded with this approach.
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Affiliation(s)
- Nora Franke
- Department of Otolaryngology/Head and Neck Surgery, University Hospital Giessen and Marburg, Marburg, Germany
| | - Michael Bette
- Institute of Anatomy and Cell Biology, Philipps University, Marburg, Germany
| | - André Marquardt
- Department of Hematology, Oncology and Immunology, University Hospital Giessen and Marburg, Marburg, Germany
| | - Thomas Briese
- Center for Infection and Immunity, Columbia University, New York City, NY, U.S.A
| | - W Ian Lipkin
- Center for Infection and Immunity, Columbia University, New York City, NY, U.S.A
| | - Christopher Kurz
- Department of Otolaryngology/Head and Neck Surgery, University Hospital Giessen and Marburg, Marburg, Germany
| | - Jovine Ehrenreich
- Department of Otolaryngology/Head and Neck Surgery, University Hospital Giessen and Marburg, Marburg, Germany
| | - Elisabeth Mack
- Department of Hematology, Oncology and Immunology, University Hospital Giessen and Marburg, Marburg, Germany
| | - Bianka Baying
- Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Vladimir Beneš
- Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Andreas Neff
- Department of Oral and Maxillofacial Surgery, University Hospital Giessen and Marburg, Marburg, Germany
| | - Afshin Teymoortash
- Department of Otolaryngology/Head and Neck Surgery, University Hospital Giessen and Marburg, Marburg, Germany
| | - Behfar Eivazi
- Department of Otolaryngology/Head and Neck Surgery, University Hospital Giessen and Marburg, Marburg, Germany
| | - Urban Geisthoff
- Department of Otolaryngology/Head and Neck Surgery, University Hospital Giessen and Marburg, Marburg, Germany
| | - Boris A Stuck
- Department of Otolaryngology/Head and Neck Surgery, University Hospital Giessen and Marburg, Marburg, Germany
| | - Udo Bakowsky
- Department of Pharmaceutical Technology and Biopharmacy, Philipps University, Marburg, Germany
| | - Robert Mandic
- Department of Otolaryngology/Head and Neck Surgery, University Hospital Giessen and Marburg, Marburg, Germany
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First detection of human hepegivirus-1 (HHpgV-1) in Iranian patients with hemophilia. Sci Rep 2018; 8:5036. [PMID: 29568043 PMCID: PMC5864744 DOI: 10.1038/s41598-018-23490-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 03/13/2018] [Indexed: 12/15/2022] Open
Abstract
A novel blood-borne virus called the human hepegivirus 1 (HHpgV-1) was recently discovered in hemophilia patients. The present study aimed to investigate the presence of HHpgV-1 in hemophilia patients. A total of 436 serum samples were investigated for the presence of hepatitis C virus (HCV), human pegivirus-1 (HPgV-1), torque teno virus (TTV), and HHpgV-1. Out of the 436 patients, 163 (37.4%), 19 (4.4%), 76 (17.4%), and four (0.9%) patients were positive for HCV, HPgV-1, TTV, and HHpgV-1, respectively. HHpgV-1 patients had a mean viral load of 4.9 ± 0.3 log RNA copies/mL and were co-infected with HCV-1a, HPgV-1, and TTV. Moreover, three HHpgV-1-positive patients exhibited stage F0 liver fibrosis. HCV viral load in HHpgV-1-positive patients was lower than those of HHpgV-1-negative patients. Results also revealed that co-infection of HHpgV-1 with HPgV-1 and HCV may play a protective role in patients with chronic HCV. In conclusion, we detected a low frequency of HHpgV-1 infection in hemophilia patients, and results suggested that HHpgV-1 infection was correlated with the presence of other blood-borne viruses and is likely to also correlate with low HCV viral load and reduced severity of liver disease. Additional studies are required to further investigate the clinical importance of HHpgV-1.
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Abstract
Compared to classical epidemiologic methods, genomics can be used to precisely monitor virus evolution and transmission in real time across large, diverse populations. Integration of pathogen genomics with data about host genetics and global transcriptional responses to infection allows for comprehensive studies of population-level responses to infection and provides novel methods for predicting clinical outcomes. As genomic technologies become more accessible, these methods will redefine how emerging viruses are studied and outbreaks are contained. Here we review the existing and emerging genomic technologies that are enabling systems epidemiology and systems virology and making it possible to respond rapidly to emerging viruses such as Zika.
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Affiliation(s)
- Angela L Rasmussen
- Department of Microbiology, University of Washington, 960 Republican Street, Seattle, WA 98109, USA
| | - Michael G Katze
- Department of Microbiology, University of Washington, 960 Republican Street, Seattle, WA 98109, USA.
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