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David EDS, Fonseca EDC, de Carvalho JFN, Marinho RDSS, Duro RLS, Komninakis SV, Souto RNP. Metagenomics applied to the detection of diarrhea viruses in humans: Systematic Review. Acta Trop 2022; 227:106287. [PMID: 34929178 DOI: 10.1016/j.actatropica.2021.106287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 11/29/2022]
Abstract
To analyze the application of the metagenomics method in the identification of viral infectious agents that lead to diarrhea outbreaks. This study is a systematic review, which looked for publications on the following platforms: PubMed, Scientific Electronic Library Online (SciELO), LILACS and CAPES periodicals, conducted according to the PRISMA methodology, investigating in the literary composition studies related to metagenomics applied in the identification of viral infectious agents, which lead to diarrhea in humans. 1198 publications were identified. Of these, after analyzes and exclusions at different stages, 18 studies remained, which directly corresponded to the theme. Diarrhea was presented as a universal health concern. Despite the emergence of vaccines, cases of diarrhea remain persistent in poor populations. In this context, metagenomics emerges as a primary tool in detecting enteric viruses and identifying new viruses, revolutionizing health diagnoses, knowledge of viral diversity, and health surveillance, contributing to the correct etiology of infectious agents that would never be identified by conventional methods. The 18 articles studied point to advances in research in viral metagenomics of diarrheal samples, contributing to the discernment of diarrhea outbreaks, and properly associating with their etiological agents, they are presented in an innovative way for studies on the understanding of viral diversity.
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Montalban-Arques A, Katkeviciute E, Busenhart P, Bircher A, Wirbel J, Zeller G, Morsy Y, Borsig L, Glaus Garzon JF, Müller A, Arnold IC, Artola-Boran M, Krauthammer M, Sintsova A, Zamboni N, Leventhal GE, Berchtold L, de Wouters T, Rogler G, Baebler K, Schwarzfischer M, Hering L, Olivares-Rivas I, Atrott K, Gottier C, Lang S, Boyman O, Fritsch R, Manz MG, Spalinger MR, Scharl M. Commensal Clostridiales strains mediate effective anti-cancer immune response against solid tumors. Cell Host Microbe 2021; 29:1573-1588.e7. [PMID: 34453895 DOI: 10.1016/j.chom.2021.08.001] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/16/2021] [Accepted: 08/03/2021] [Indexed: 12/30/2022]
Abstract
Despite overall success, T cell checkpoint inhibitors for cancer treatment are still only efficient in a minority of patients. Recently, intestinal microbiota was found to critically modulate anti-cancer immunity and therapy response. Here, we identify Clostridiales members of the gut microbiota associated with a lower tumor burden in mouse models of colorectal cancer (CRC). Interestingly, these commensal species are also significantly reduced in CRC patients compared with healthy controls. Oral application of a mix of four Clostridiales strains (CC4) in mice prevented and even successfully treated CRC as stand-alone therapy. This effect depended on intratumoral infiltration and activation of CD8+ T cells. Single application of Roseburia intestinalis or Anaerostipes caccae was even more effective than CC4. In a direct comparison, the CC4 mix supplementation outperformed anti-PD-1 therapy in mouse models of CRC and melanoma. Our findings provide a strong preclinical foundation for exploring gut bacteria as novel stand-alone therapy against solid tumors.
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Affiliation(s)
- Ana Montalban-Arques
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Egle Katkeviciute
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Philipp Busenhart
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Anna Bircher
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Jakob Wirbel
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Georg Zeller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Yasser Morsy
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Lubor Borsig
- Department of Physiology, University of Zurich, Zurich, Switzerland
| | | | - Anne Müller
- Institute for Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Isabelle C Arnold
- Institute for Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Mariela Artola-Boran
- Institute for Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Michael Krauthammer
- Department of Quantitative Biomedicine, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Anna Sintsova
- Department of Quantitative Biomedicine, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Nicola Zamboni
- Institute of Molecular Systems Biology, Federal Institute of Technology Zurich, Zurich, Switzerland
| | - Gabriel E Leventhal
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | | | - Gerhard Rogler
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Katharina Baebler
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Marlene Schwarzfischer
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Larissa Hering
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Ivan Olivares-Rivas
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Kirstin Atrott
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Claudia Gottier
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Silvia Lang
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Onur Boyman
- Department of Immunology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Ralph Fritsch
- Department of Medical Oncology and Hematology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Markus G Manz
- Department of Medical Oncology and Hematology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Marianne R Spalinger
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Michael Scharl
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.
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Hamza H, Hamza IA. Oncogenic papillomavirus and polyomavirus in urban sewage in Egypt. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 610-611:1413-1420. [PMID: 28854484 DOI: 10.1016/j.scitotenv.2017.08.218] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 08/19/2017] [Accepted: 08/21/2017] [Indexed: 05/23/2023]
Abstract
Recently, the occurrence of oncogenic viruses in contaminated water and their potential for waterborne transmission has been reported. We addressed an environmental surveillance of both HPyVs (JCPyV and BKPyV) and HPVs in three wastewater treatment plants in Egypt. A high level of dissemination was found for both viruses. HPyVs (JCPyV and BKPyV) were found in ~73% of examined samples, while HPVs were detected in 30.5%. Sequence analysis of HPV positive samples revealed a wide variety of circulating genotypes representing both anogenital (HPV-6, HPV-16, HPV-53, HPV-44, HPV-31, HPV-43) and cutaneous (HPV-37, HPV-21, HPV-120, HPV-111, HPV-5) types. In addition, two unclassified sequences were identified, suggesting putative types. The median concentrations of HPyVs in inflow samples were 3.03×1005, 3.9×1005, and 1.44×1005GC/l in the three WWTPs, respectively. Whereas, the viral concentration in outflow reduced by one order of magnitude in WWTP-A and WWTP-C and two orders of magnitude in WWTP-B. On the other hand, the mean concentration of the quantified HPVs positive samples was 1.68×1003GC/l for inflow and a quite similar pattern in the outflow as well. These data provide an evidence about the actual circulation pattern of both viruses in the population. Also, the high abundance of HPyVs supports its potential as a possible fecal indicator. However, further investigations are required for both viruses to elucidate the potential health risk via contaminated water.
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Affiliation(s)
- Hazem Hamza
- Environmental Virology Laboratory, Department of Water Pollution Research, National Research Centre, Cairo, Egypt; Department of Hygiene, Social- and Environmental Medicine, Ruhr-University Bochum, Germany
| | - Ibrahim Ahmed Hamza
- Environmental Virology Laboratory, Department of Water Pollution Research, National Research Centre, Cairo, Egypt.
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Escobar-Escamilla N, Ramírez-González JE, Castro-Escarpulli G, Díaz-Quiñonez JA. Utility of high-throughput DNA sequencing in the study of the human papillomaviruses. Virus Genes 2017; 54:17-24. [PMID: 29282656 DOI: 10.1007/s11262-017-1530-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 12/19/2017] [Indexed: 11/28/2022]
Abstract
The Papillomaviridae family is probably the most diverse group of viruses that affect vertebrates. The study of the relationship between infection by certain types of human papillomavirus (HPV) and the development of neoplastic epithelial lesions is of particular interest because of the high prevalence of HPV-related carcinomas in populations of developing countries. To understand the mechanisms of infection and their association with different clinical manifestations, molecular tools play an important role in the description of new types of HPV, the characterization of effector properties of the viral factors, the specific diagnosis and monitoring of HPV types, and the alteration patterns at genetic level in the host. Technological advances in the field of DNA sequencing have led to the development of different next-generation sequencing systems, allowing obtaining a large amount of data and broadening the applications to study viral diseases. In this review, we summarize the main approaches and their perspectives where the use of massively parallel sequencing has been proved as a useful tool in the research of the HPV infection.
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Affiliation(s)
- Noé Escobar-Escamilla
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico.,Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Mexico City, Mexico
| | - José Ernesto Ramírez-González
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Mexico City, Mexico
| | | | - José Alberto Díaz-Quiñonez
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Mexico City, Mexico.,División de Estudios de Posgrado, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
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Simmonds P. Methods for virus classification and the challenge of incorporating metagenomic sequence data. J Gen Virol 2015; 96:1193-1206. [PMID: 26068186 DOI: 10.1099/jgv.0.000016] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The division of viruses into orders, families, genera and species provides a classification framework that seeks to organize and make sense of the diversity of viruses infecting animals, plants and bacteria. Classifications are based on similarities in genome structure and organization, the presence of homologous genes and sequence motifs and at lower levels such as species, host range, nucleotide and antigenic relatedness and epidemiology. Classification below the level of family must also be consistent with phylogeny and virus evolutionary histories. Recently developed methods such as PASC, DEMaRC and NVR offer alternative strategies for genus and species assignments that are based purely on degrees of divergence between genome sequences. They offer the possibility of automating classification of the vast number of novel virus sequences being generated by next-generation metagenomic sequencing. However, distance-based methods struggle to deal with the complex evolutionary history of virus genomes that are shuffled by recombination and reassortment, and where taxonomic lineages evolve at different rates. In biological terms, classifications based on sequence distances alone are also arbitrary whereas the current system of virus taxonomy is of utility precisely because it is primarily based upon phenotypic characteristics. However, a separate system is clearly needed by which virus variants that lack biological information might be incorporated into the ICTV classification even if based solely on sequence relationships to existing taxa. For these, simplified taxonomic proposals and naming conventions represent a practical way to expand the existing virus classification and catalogue our rapidly increasing knowledge of virus diversity.
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Affiliation(s)
- Peter Simmonds
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK
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Kocjan BJ, Bzhalava D, Forslund O, Dillner J, Poljak M. Molecular methods for identification and characterization of novel papillomaviruses. Clin Microbiol Infect 2015; 21:808-16. [PMID: 26003284 DOI: 10.1016/j.cmi.2015.05.011] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 04/27/2015] [Accepted: 05/12/2015] [Indexed: 02/02/2023]
Abstract
Papillomaviruses (PV) are a remarkably heterogeneous family of small DNA viruses that infect a wide variety of vertebrate species and are aetiologically linked with the development of various neoplastic changes of the skin and mucosal epithelia. Based on nucleotide similarity, PVs are hierarchically classified into genera, species and types. Novel human PV (HPV) types are given a unique number only after the whole genome has been cloned and deposited with the International HPV Reference Center. As of 9 March 2015, 200 different HPV types, belonging to 49 species, had been recognized by the International HPV Reference Center. In addition, 131 animal PV types identified from 66 different animal species exist. Recent advances in molecular techniques have resulted in an explosive increase in the identification of novel HPV types and novel subgenomic HPV sequences in the last few years. Among PV genera, the γ-PV genus has been growing most rapidly in recent years with 80 completely sequenced HPV types, followed by α-PV and β-PV genera that have 65 and 51 recognized HPV types, respectively. We reviewed in detail the contemporary molecular methods most often used for identification and characterization of novel PV types, including PCR, rolling circle amplification and next-generation sequencing. Furthermore, we present a short overview of 12 and 10 novel HPV types recently identified in Sweden and Slovenia, respectively. Finally, an update on the International Human Papillomavirus Reference Center is provided.
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Affiliation(s)
- B J Kocjan
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Slovenia
| | - D Bzhalava
- International Human Papillomavirus Reference Center, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - O Forslund
- Department of Laboratory Medicine, Lund University, Malmö, Sweden
| | - J Dillner
- International Human Papillomavirus Reference Center, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - M Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Slovenia.
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