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Chen MN, Ye ZX, Feng KH, Yuan JN, Chen JP, Zhang CX, Li JM, Mao QZ. Genetic Characterization of Two Novel Insect-Infecting Negative-Sense RNA Viruses Identified in a Leaf Beetle, Aulacophora indica. INSECTS 2024; 15:615. [PMID: 39194819 DOI: 10.3390/insects15080615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Revised: 08/13/2024] [Accepted: 08/14/2024] [Indexed: 08/29/2024]
Abstract
Herbivorous insects harbor a variety of insect-specific viruses (ISVs) some of which are considered to be valuable biological agents for potential applications in biological defense and control strategies. Leaf beetles with chewing mouthparts are particularly known for their capacity to disrupt plant tissue while feeding, often creating openings that can act as entry points for plant pathogens. In this study, we have identified two new negative-sense RNA viruses infecting the leaf beetle Aulacophora indica, an important member of the Chrysomelidae family. These recently discovered viruses belong to the viral families Nyamiviridae and Chuviridae and have been preliminarily named Aulacophora indica nyami-like virus 1 (AINlV1) and Aulacophora indica chu-like virus 1 (AIClV1), respectively. The complete genomic sequences of these viruses were obtained using rapid amplification of cDNA ends (RACE) techniques. Detailed analysis of their genomic structures has confirmed their similarity to other members within their respective families. Furthermore, analysis of virus-derived small interfering RNA (vsiRNA) demonstrated a high abundance and typical vsiRNA pattern of AINlV1 and AIClV1, offering substantial evidence to support their classification as ISVs. This research enhances our understanding of viral diversity within insects.
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Affiliation(s)
- Meng-Nan Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Zhuang-Xin Ye
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Ke-Hui Feng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Jing-Na Yuan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Jian-Ping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Chuan-Xi Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Jun-Min Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Qian-Zhuo Mao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
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Sun Y, Xing J, Xu S, Li Y, Zhong J, Gao H, Cheng S, Dong J, Zhang T, Lu G, Baele G, Zhang G. Demographic and zoological drivers of infectome diversity in companion cats with ascites. mSystems 2024:e0063624. [PMID: 39120143 DOI: 10.1128/msystems.00636-24] [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: 05/06/2024] [Accepted: 06/21/2024] [Indexed: 08/10/2024] Open
Abstract
Cats (Felidae) have become an integral part of many households. However, our understanding of the full spectrum of pathogens affecting cats (referred to as the infectome) is limited, mainly due to the inadequacy of commonly used diagnostic tools in capturing the complete diversity of potential pathogens and the prevalence of pathogen co-infections. In this study, we employed a meta-transcriptomic approach to simultaneously characterize the infectome contributing to different disease syndromes and to investigate spatial, demographic, and ecological factors influencing pathogen diversity and community composition in a cohort of 27 hospitalized cats and seven stray cats. We identified 15 species of pathogens, with Candidatus Rickettsia tarasevichiae and Tritrichomonas foetus representing potential spillover risks. Importantly, although most cases of ascites hyperplasia were explained by coinfection with multiple pathogens, we identified the potential novel clinical outcomes of M. aubagnense infection among cats. We demonstrated that the increase in infectome diversity can be explained by a variety of predictors including age growth, temperature increase, and a higher proportion of females, with age growth presenting the strongest effect. Fine-scale analysis indicated that a higher diversity of infectomes were harbored in young cats rather than adult ones. Our results demonstrated that most feline diseases are better explained by the presence of virus-bacteria or virus-virus coinfection. This study serves as a timely endorsement for clinical diagnosis by vets to consider the cause of a disease based on a panel of cryptical co-infecting pathogens rather than on individual infectious agents. IMPORTANCE Frequent studies reported the risks of cats as an intermediate host of zoonotic pathogens (e.g., SARS-CoV-2). Cats have a physically close interaction with their owners through activities like petting, kissing, and being licked on the cheek and hands. However, there are still limited studies that systematically investigate the infectome structure of cats. In this study, we employed a meta-transcriptomics approach to characterize 15 species of pathogens in cats, with Candidatus Rickettsia tarasevichiae first characterizing infection in diseased cats. Most feline diseases were better explained by the presence of virus-bacteria or virus-virus coinfection. The increase in infectome diversity could be influenced by a variety of predictors including age growth, temperature increase, and a higher proportion of females. A higher diversity of pathogens was harbored in young cats rather than adults. Importantly, we showed the value of linking the modern influx of meta-transcriptomics with comparative ecology and demography and of utilizing it to affirm that ecological and demographic variations impact the total infectome.
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Affiliation(s)
- Yankuo Sun
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Jiabao Xing
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Sijia Xu
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yue Li
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jianhao Zhong
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Han Gao
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Song Cheng
- CAU Dong Jun laboratory, Guangzhou, China, Guangzhou, China
| | - Jun Dong
- CAU Dong Jun laboratory, Guangzhou, China, Guangzhou, China
| | - Tianyou Zhang
- CAU Dong Jun laboratory, Guangzhou, China, Guangzhou, China
- Guangzhou Chimelong Safari Park, Guangzhou, China
| | - Gang Lu
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Guihong Zhang
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
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Maia LJ, Silva AB, de Oliveira CH, Campos FS, da Silva LA, de Abreu FVS, Ribeiro BM. Sylvatic Mosquito Viromes in the Cerrado Biome of Minas Gerais, Brazil: Discovery of New Viruses and Implications for Arbovirus Transmission. Viruses 2024; 16:1276. [PMID: 39205250 PMCID: PMC11359572 DOI: 10.3390/v16081276] [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: 06/27/2024] [Revised: 08/01/2024] [Accepted: 08/05/2024] [Indexed: 09/04/2024] Open
Abstract
Studies on animal virome have mainly concentrated on chordates and medically significant invertebrates, often overlooking sylvatic mosquitoes, constituting a major part of mosquito species diversity. Despite their potential role in arbovirus transmission, the viromes of sylvatic mosquitoes remain largely unexplored. These mosquitoes may also harbor insect-specific viruses (ISVs), affecting arboviral transmission dynamics. The Cerrado biome, known for rapid deforestation and its status as a biodiversity hotspot, offers an ideal setting for investigating mosquito viromes due to potential zoonotic spillover risks from land use changes. This study aimed to characterize the viromes of sylvatic mosquitoes collected from various locations within Minas Gerais state, Brazil. The total RNA was extracted from mosquito pools of Psorophora albipes, Sabethes albiprivus, Sa. chloropterus, Psorophora ferox, and Coquillettidia venezuelensis species, followed by high-throughput sequencing (HTS). Bioinformatic analysis included quality control, contig assembly, and viral detection. Sequencing data analysis revealed 11 near-complete viral genomes (new viruses are indicated with asterisks) across seven viral families and one unassigned genus. These included: Xinmoviridae (Ferox mosquito mononega-like virus* and Albipes mosquito Gordis-like virus*), Phasmaviridae (Sabethes albiprivus phasmavirus*), Lispiviridae (Pedras lispivirus variant MG), Iflaviridae (Sabethes albiprivus iflavivirus*), Virgaviridae (Buriti virga-like virus variant MG and Sabethes albiprivus virgavirus 1*), Flaviviridae (Psorophora ferox flavivirus*), Mesoniviridae (Alphamesonivirus cavallyense variant MG), and the genus Negevirus (Biggie virus variant MG virus and Coquillettidia venezuelensis negevirus*). Moreover, the presence of ISVs and potential novel arboviruses underscores the need for ongoing surveillance and control strategies to mitigate the risk of emerging infectious diseases.
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Affiliation(s)
- Luis Janssen Maia
- Laboratório de Baculovírus, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília (UnB), Brasília 70910-900, Brazil; (L.J.M.); (L.A.d.S.)
- Laboratório de Bioinformática e Biotecnologia, Universidade Federal do Tocantins (UFT), Gurupi 77402-970, Brazil;
| | - Arthur Batista Silva
- Laboratório de Bioinformática e Biotecnologia, Universidade Federal do Tocantins (UFT), Gurupi 77402-970, Brazil;
| | - Cirilo Henrique de Oliveira
- Laboratório de Comportamento de Insetos, Instituto Federal do Norte de Minas Gerais (IFNMG), Salinas 39560-000, Brazil;
- Programa de Pós-Graduação em Biodiversidade e Uso dos Recursos Naturais, Unimontes, Montes Claros 39401-089, Brazil
- Centro Colaborador de Entomologia/Lacoi/IFNMG/Secretaria Municipal de Saúde de Salinas, Salinas 39560-000, Brazil
| | - Fabricio Souza Campos
- Laboratório de Bioinformática e Biotecnologia, Universidade Federal do Tocantins (UFT), Gurupi 77402-970, Brazil;
- Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 90035-003, Brazil
| | - Leonardo Assis da Silva
- Laboratório de Baculovírus, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília (UnB), Brasília 70910-900, Brazil; (L.J.M.); (L.A.d.S.)
| | - Filipe Vieira Santos de Abreu
- Laboratório de Comportamento de Insetos, Instituto Federal do Norte de Minas Gerais (IFNMG), Salinas 39560-000, Brazil;
- Centro Colaborador de Entomologia/Lacoi/IFNMG/Secretaria Municipal de Saúde de Salinas, Salinas 39560-000, Brazil
| | - Bergmann Morais Ribeiro
- Laboratório de Baculovírus, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília (UnB), Brasília 70910-900, Brazil; (L.J.M.); (L.A.d.S.)
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Medina JE, Castañeda S, Camargo M, Garcia-Corredor DJ, Muñoz M, Ramírez JD. Exploring viral diversity and metagenomics in livestock: insights into disease emergence and spillover risks in cattle. Vet Res Commun 2024; 48:2029-2049. [PMID: 38865041 DOI: 10.1007/s11259-024-10403-2] [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: 10/10/2023] [Accepted: 05/01/2024] [Indexed: 06/13/2024]
Abstract
Cattle have a significant impact on human societies in terms of both economics and health. Viral infections pose a relevant problem as they directly or indirectly disrupt the balance within cattle populations. This has negative consequences at the economic level for producers and territories, and also jeopardizes human health through the transmission of zoonotic diseases that can escalate into outbreaks or pandemics. To establish prevention strategies and control measures at various levels (animal, farm, region, or global), it is crucial to identify the viral agents present in animals. Various techniques, including virus isolation, serological tests, and molecular techniques like PCR, are typically employed for this purpose. However, these techniques have two major drawbacks: they are ineffective for non-culturable viruses, and they only detect a small fraction of the viruses present. In contrast, metagenomics offers a promising approach by providing a comprehensive and unbiased analysis for detecting all viruses in a given sample. It has the potential to identify rare or novel infectious agents promptly and establish a baseline of healthy animals. Nevertheless, the routine application of viral metagenomics for epidemiological surveillance and diagnostics faces challenges related to socioeconomic variables, such as resource availability and space dedicated to metagenomics, as well as the lack of standardized protocols and resulting heterogeneity in presenting results. This review aims to provide an overview of the current knowledge and prospects for using viral metagenomics to detect and identify viruses in cattle raised for livestock, while discussing the epidemiological and clinical implications.
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Affiliation(s)
- Julián Esteban Medina
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Sergio Castañeda
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Milena Camargo
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
- Centro de Tecnología en Salud (CETESA), Innovaseq SAS, Mosquera, Cundinamarca, Colombia
| | - Diego J Garcia-Corredor
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
- Grupo de Investigación en Medicina Veterinaria y Zootecnia, Facultad de Ciencias Agropecuarias, Universidad Pedagógica y Tecnológica de Colombia, Tunja, Colombia
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia.
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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Zeng C, Wan SR, Guo M, Tan XZ, Zeng Y, Wu Q, Xie JJ, Yan P, Long Y, Zheng L, Jiang ZZ, Teng FY, Xu Y. Fecal virome transplantation: A promising strategy for the treatment of metabolic diseases. Biomed Pharmacother 2024; 177:117065. [PMID: 38971010 DOI: 10.1016/j.biopha.2024.117065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Revised: 06/27/2024] [Accepted: 06/27/2024] [Indexed: 07/08/2024] Open
Abstract
Metabolic diseases are a group of disorders caused by metabolic abnormalities, including obesity, diabetes, non-alcoholic fatty liver disease, and more. Increasing research indicates that, beyond inherent metabolic irregularities, the onset and progression of metabolic diseases are closely linked to alterations in the gut microbiota, particularly gut bacteria. Additionally, fecal microbiota transplantation (FMT) has demonstrated effectiveness in clinically treating metabolic diseases, notably diabetes. Recent attention has also focused on the role of gut viruses in disease onset. This review first introduces the characteristics and influencing factors of gut viruses, then summarizes their potential mechanisms in disease development, highlighting their impact on gut bacteria and regulation of host immunity. We also compare FMT, fecal filtrate transplantation (FFT), washed microbiota transplantation (WMT), and fecal virome transplantation (FVT). Finally, we review the current understanding of gut viruses in metabolic diseases and the application of FVT in treating these conditions. In conclusion, FVT may provide a novel and promising treatment approach for metabolic diseases, warranting further validation through basic and clinical research.
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Affiliation(s)
- Chen Zeng
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Sheng-Rong Wan
- Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Man Guo
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Xiao-Zhen Tan
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Yan Zeng
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Macao 999078, China
| | - Qi Wu
- Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Macao 999078, China; Department of Pathology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Jia-Jie Xie
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Pijun Yan
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Department of Pathology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Institute of Cardiovascular Research, Peking University, Beijing 100871, China
| | - Yang Long
- Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Lemin Zheng
- Institute of Cardiovascular Research, Peking University, Beijing 100871, China
| | - Zong-Zhe Jiang
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Fang-Yuan Teng
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China.
| | - Yong Xu
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China.
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Sun X, Lian Y, Tian T, Cui Z. Advancements in Functional Nanomaterials Inspired by Viral Particles. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2402980. [PMID: 39058214 DOI: 10.1002/smll.202402980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 06/27/2024] [Indexed: 07/28/2024]
Abstract
Virus-like particles (VLPs) are nanostructures composed of one or more structural proteins, exhibiting stable and symmetrical structures. Their precise compositions and dimensions provide versatile opportunities for modifications, enhancing their functionality. Consequently, VLP-based nanomaterials have gained widespread adoption across diverse domains. This review focuses on three key aspects: the mechanisms of viral capsid protein self-assembly into VLPs, design methods for constructing multifunctional VLPs, and strategies for synthesizing multidimensional nanomaterials using VLPs. It provides a comprehensive overview of the advancements in virus-inspired functional nanomaterials, encompassing VLP assembly, functionalization, and the synthesis of multidimensional nanomaterials. Additionally, this review explores future directions, opportunities, and challenges in the field of VLP-based nanomaterials, aiming to shed light on potential advancements and prospects in this exciting area of research.
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Affiliation(s)
- Xianxun Sun
- College of Life Science, Jiang Han University, Wuhan, 430056, China
| | - Yindong Lian
- College of Life Science, Jiang Han University, Wuhan, 430056, China
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Tao Tian
- College of Life Science, Jiang Han University, Wuhan, 430056, China
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Zongqiang Cui
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
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Tian Z, Hu T, Holmes EC, Ji J, Shi W. Analysis of the genetic diversity in RNA-directed RNA polymerase sequences: implications for an automated RNA virus classification system. Virus Evol 2024; 10:veae059. [PMID: 39119135 PMCID: PMC11306317 DOI: 10.1093/ve/veae059] [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: 02/05/2024] [Revised: 06/21/2024] [Accepted: 07/24/2024] [Indexed: 08/10/2024] Open
Abstract
RNA viruses are characterized by a broad host range and high levels of genetic diversity. Despite a recent expansion in the known virosphere following metagenomic sequencing, our knowledge of the species rank genetic diversity of RNA viruses, and how often they are misassigned and misclassified, is limited. We performed a clustering analysis of 7801 RNA-directed RNA polymerase (RdRp) sequences representing 1897 established RNA virus species. From this, we identified substantial genetic divergence within some virus species and inconsistency in RNA virus assignment between the GenBank database and The International Committee on Taxonomy of Viruses (ICTV). In particular, 27.57% virus species comprised multiple virus operational taxonomic units (vOTUs), including Alphainfluenzavirus influenzae, Mammarenavirus lassaense, Apple stem pitting virus, and Rotavirus A, with each having over 100 vOTUs. In addition, the distribution of average amino acid identity between vOTUs within single assigned species showed a relatively low threshold: <90% and sometimes <50%. However, when only exemplar sequences from virus species were analyzed, 1889 of the ICTV-designated RNA virus species (99.58%) were clustered into a single vOTU. Clustering of the RdRp sequences from different virus species also revealed that 17 vOTUs contained two distinct virus species. These potential misassignments were confirmed by phylogenetic analysis. A further analysis of average nucleotide identity (ANI) values ranging from 70% to 97.5% revealed that at an ANI of 82.5%, 1559 (82.18%) of the 1897 virus species could be correctly clustered into one single vOTU. However, at ANI values >82.5%, an increasing number of species were clustered into two or more vOTUs. In sum, we have identified some inconsistency and misassignment of the RNA virus species based on the analysis of RdRp sequences alone, which has important implications for the development of an automated RNA virus classification system.
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Affiliation(s)
- Zhongshuai Tian
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, No. 6699 Qingdao Road, Ji’nan 250117, China
- Shanghai Institute of Virology, Shanghai Jiao Tong University School of Medicine, No. 227 Chongqingnanlu, Shanghai 200025, China
| | - Tao Hu
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, No. 6699 Qingdao Road, Ji’nan 250117, China
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
- Laboratory of Data Discovery for Health Limited, 19 Science Park West Avenue, Hong Kong 999077, China
| | - Jingkai Ji
- School of Life Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, No. 619 Changcheng Road, Taian 271000, China
| | - Weifeng Shi
- Shanghai Institute of Virology, Shanghai Jiao Tong University School of Medicine, No. 227 Chongqingnanlu, Shanghai 200025, China
- Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijinerlu, Shanghai 200025, China
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8
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Petrone ME, Grove J, Mélade J, Mifsud JCO, Parry RH, Marzinelli EM, Holmes EC. A ~40-kb flavi-like virus does not encode a known error-correcting mechanism. Proc Natl Acad Sci U S A 2024; 121:e2403805121. [PMID: 39018195 PMCID: PMC11287256 DOI: 10.1073/pnas.2403805121] [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: 02/22/2024] [Accepted: 06/13/2024] [Indexed: 07/19/2024] Open
Abstract
It is commonly held that there is a fundamental relationship between genome size and error rate, manifest as a notional "error threshold" that sets an upper limit on genome sizes. The genome sizes of RNA viruses, which have intrinsically high mutation rates due to a lack of mechanisms for error correction, must therefore be small to avoid accumulating an excessive number of deleterious mutations that will ultimately lead to population extinction. The proposed exceptions to this evolutionary rule are RNA viruses from the order Nidovirales (such as coronaviruses) that encode error-correcting exonucleases, enabling them to reach genome lengths greater than 40 kb. The recent discovery of large-genome flavi-like viruses (Flaviviridae), which comprise genomes up to 27 kb in length yet seemingly do not encode exonuclease domains, has led to the proposal that a proofreading mechanism is required to facilitate the expansion of nonsegmented RNA virus genomes above 30 kb. Herein, we describe a ~40 kb flavi-like virus identified in a Haliclona sponge metatranscriptome that does not encode a known exonuclease. Structural analysis revealed that this virus may have instead captured cellular domains associated with nucleic acid metabolism that have not been previously found in RNA viruses. Phylogenetic inference placed this virus as a divergent pesti-like lineage, such that we have provisionally termed it "Maximus pesti-like virus." This virus represents an instance of a flavi-like virus achieving a genome size comparable to that of the Nidovirales and demonstrates that RNA viruses have evolved multiple solutions to overcome the error threshold.
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Affiliation(s)
- Mary E. Petrone
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW2006, Australia
- Laboratory of Data Discovery for Health Limited, Hong Kong Special Administrative Region, China
| | - Joe Grove
- MRC-University of Glasgow Centre for Virus Research, GlasgowG61 1QH, United Kingdom
| | - Julien Mélade
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW2006, Australia
| | - Jonathon C. O. Mifsud
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW2006, Australia
| | - Rhys H. Parry
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD4067, Australia
| | - Ezequiel M. Marzinelli
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW2006, Australia
- Laboratory of Data Discovery for Health Limited, Hong Kong Special Administrative Region, China
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9
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Pavon JAR, da Silva Neves NA, Pinho JB, de Souza VJ, Patroca da Silva S, Ribeiro Cruz AC, de Almeida Medeiros DB, Teixeira Nunes MR, Slhessarenko RD. Disclosing the virome of Aedes, Anopheles and Culex female mosquitoes, Alto Pantanal of Mato Grosso, Brazil, 2019. Virology 2024; 598:110182. [PMID: 39033587 DOI: 10.1016/j.virol.2024.110182] [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: 03/06/2024] [Revised: 07/02/2024] [Accepted: 07/12/2024] [Indexed: 07/23/2024]
Abstract
Using Illumina NextSeq sequencing and bioinformatics, we identified and characterized thirty-three viral sequences of unsegmented and multipartite viral families in Aedes spp., Culex sp. and Anopheles darlingi female mosquito pools from Porto São Luiz and Pirizal, Alto Pantanal. Seventeen sequences belong to unsegmented viral families, twelve represent putative novel insect-specific viruses (ISVs) within families Chuviridae (3/33; partial genomes) and coding-complete sequences of Xinmoviridae (1/33), Rhabdoviridae (2/33) and Metaviridae (6/33); and five coding-complete sequences of already-known ISVs. Notably, two putative novel rhabdoviruses, Corixo rhabdovirus 1 and 2, were phylogenetically related to Coxipo dielmovirus, but separated from other Alpharhabdovirinae genera, sharing Anopheles spp. as host. Regarding multipartite families, sixteen segments of different putative novel viruses were identified (13 coding-complete segments) within Durnavirales (4/33), Elliovirales (1/33), Hareavirales (3/33) and Reovirales (8/33) orders. Overall, this study describes twenty-eight (28/33) putative novel ISVs and five (5/33) already described viruses using metagenomics approach.
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Affiliation(s)
- Janeth Aracely Ramirez Pavon
- Programa de Pós-graduação em Ciências da Saúde, Faculdade de Medicina, Universidade Federal de Mato Grosso, CEP 78060-900, Cuiabá, Mato Grosso, Brazil
| | - Nilvanei Aparecido da Silva Neves
- Programa de Pós-graduação em Ciências da Saúde, Faculdade de Medicina, Universidade Federal de Mato Grosso, CEP 78060-900, Cuiabá, Mato Grosso, Brazil
| | - João Batista Pinho
- Instituto de Biociências, Laboratório de Ecologia de Aves e Biodiversidade, Universidade Federal de Mato Grosso, Cuiabá, CEP 78060-900, Mato Grosso, Brazil
| | - Vilma Juscineide de Souza
- Coordenadoria de Vigilância Ambiental, Secretaria Estadual de Saúde, Centro Político Administrativo de Mato Grosso, Palácio Paiaguás, CEP 78049-902, Cuiabá, Mato Grosso, Brazil
| | | | | | | | - Márcio Roberto Teixeira Nunes
- Laboratório de Tecnologia Biomolecular, Centro de Ciências Biológicas, Universidade Federal Do Pará, CEP 66075-110, Belém, Pará, Brazil
| | - Renata Dezengrini Slhessarenko
- Programa de Pós-graduação em Ciências da Saúde, Faculdade de Medicina, Universidade Federal de Mato Grosso, CEP 78060-900, Cuiabá, Mato Grosso, Brazil.
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10
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Wickenhagen A, van Tol S, Munster V. Molecular determinants of cross-species transmission in emerging viral infections. Microbiol Mol Biol Rev 2024:e0000123. [PMID: 38912755 DOI: 10.1128/mmbr.00001-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024] Open
Abstract
SUMMARYSeveral examples of high-impact cross-species transmission of newly emerging or re-emerging bat-borne viruses, such as Sudan virus, Nipah virus, and severe acute respiratory syndrome coronavirus 2, have occurred in the past decades. Recent advancements in next-generation sequencing have strengthened ongoing efforts to catalog the global virome, in particular from the multitude of different bat species. However, functional characterization of these novel viruses and virus sequences is typically limited with regard to assessment of their cross-species potential. Our understanding of the intricate interplay between virus and host underlying successful cross-species transmission has focused on the basic mechanisms of entry and replication, as well as the importance of host innate immune responses. In this review, we discuss the various roles of the respective molecular mechanisms underlying cross-species transmission using different recent bat-borne viruses as examples. To delineate the crucial cellular and molecular steps underlying cross-species transmission, we propose a framework of overall characterization to improve our capacity to characterize viruses as benign, of interest, or of concern.
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Affiliation(s)
- Arthur Wickenhagen
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Sarah van Tol
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Vincent Munster
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
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11
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Telengech P, Hyodo K, Ichikawa H, Kuwata R, Kondo H, Suzuki N. Replication of single viruses across the kingdoms, Fungi, Plantae, and Animalia. Proc Natl Acad Sci U S A 2024; 121:e2318150121. [PMID: 38865269 PMCID: PMC11194502 DOI: 10.1073/pnas.2318150121] [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: 10/24/2023] [Accepted: 05/10/2024] [Indexed: 06/14/2024] Open
Abstract
It is extremely rare that a single virus crosses host barriers across multiple kingdoms. Based on phylogenetic and paleovirological analyses, it has previously been hypothesized that single members of the family Partitiviridae could cross multiple kingdoms. Partitiviridae accommodates members characterized by their simple bisegmented double-stranded RNA genome; asymptomatic infections of host organisms; the absence of an extracellular route for entry in nature; and collectively broad host range. Herein, we show the replicability of single fungal partitiviruses in three kingdoms of host organisms: Fungi, Plantae, and Animalia. Betapartitiviruses of the phytopathogenic fungusRosellinia necatrix could replicate in protoplasts of the carrot (Daucus carota), Nicotiana benthamiana and Nicotiana tabacum, in some cases reaching a level detectable by agarose gel electrophoresis. Moreover, betapartitiviruses showed more robust replication than the tested alphapartitiviruses. One of the fungal betapartitiviruses, RnPV18, could persistently and stably infect carrot plants regenerated from virion-transfected protoplasts. Both alpha- and betapartitiviruses, although with different host preference, could replicate in two insect cell lines derived from the fall armyworm Spodoptera frugiperda and the fruit fly Drosophila melanogaster. Our results indicate the replicability of single partitiviruses in members of three kingdoms and provide insights into virus adaptation, host jumping, and evolution.
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Affiliation(s)
- Paul Telengech
- Agrivirology Laboratory, Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama710-0046, Japan
| | - Kiwamu Hyodo
- Agrivirology Laboratory, Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama710-0046, Japan
| | - Hiroaki Ichikawa
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki305-8634, Japan
| | - Ryusei Kuwata
- Faculty of Veterinary Medicine, Okayama University of Science, Imabari, Ehime794-8555, Japan
| | - Hideki Kondo
- Agrivirology Laboratory, Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama710-0046, Japan
| | - Nobuhiro Suzuki
- Agrivirology Laboratory, Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama710-0046, Japan
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12
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Kandathil AJ, Thomas DL. The Blood Virome: A new frontier in biomedical science. Biomed Pharmacother 2024; 175:116608. [PMID: 38703502 PMCID: PMC11184943 DOI: 10.1016/j.biopha.2024.116608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 04/12/2024] [Accepted: 04/17/2024] [Indexed: 05/06/2024] Open
Abstract
Recent advances in metagenomic testing opened a new window into the mammalian blood virome. Comprised of well-known viruses like human immunodeficiency virus, hepatitis C virus, and hepatitis B virus, the virome also includes many other eukaryotic viruses and phages whose medical significance, lifecycle, epidemiology, and impact on human health are less well known and thus regarded as commensals. This review synthesizes available information for the so-called commensal virome members that circulate in the blood of humans considering their restriction to and interaction with the human host, their natural history, and their impact on human health and physiology.
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Affiliation(s)
- Abraham J Kandathil
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David L Thomas
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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13
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Alfonso P, Butković A, Fernández R, Riesgo A, Elena SF. Unveiling the hidden viromes across the animal tree of life: insights from a taxonomic classification pipeline applied to invertebrates of 31 metazoan phyla. mSystems 2024; 9:e0012424. [PMID: 38651902 PMCID: PMC11097642 DOI: 10.1128/msystems.00124-24] [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: 01/26/2024] [Accepted: 03/26/2024] [Indexed: 04/25/2024] Open
Abstract
Invertebrates constitute the majority of animal species on Earth, including most disease-causing agents or vectors, with more diverse viromes when compared to vertebrates. Recent advancements in high-throughput sequencing have significantly expanded our understanding of invertebrate viruses, yet this knowledge remains biased toward a few well-studied animal lineages. In this study, we analyze invertebrate DNA and RNA viromes for 31 phyla using 417 publicly available RNA-Seq data sets from diverse environments in the marine-terrestrial and marine-freshwater gradients. This study aims to (i) estimate virome compositions at the family level for the first time across the animal tree of life, including the first exploration of the virome in several phyla, (ii) quantify the diversity of invertebrate viromes and characterize the structure of invertebrate-virus infection networks, and (iii) investigate host phylum and habitat influence on virome differences. Results showed that a set of few viral families of eukaryotes, comprising Retroviridae, Flaviviridae, and several families of giant DNA viruses, were ubiquitous and highly abundant. Nevertheless, some differences emerged between phyla, revealing for instance a less diverse virome in Ctenophora compared to the other animal phyla. Compositional analysis of the viromes showed that the host phylum explained over five times more variance in composition than its habitat. Moreover, significant similarities were observed between the viromes of some phylogenetically related phyla, which could highlight the influence of co-evolution in shaping invertebrate viromes.IMPORTANCEThis study significantly enhances our understanding of the global animal virome by characterizing the viromes of previously unexamined invertebrate lineages from a large number of animal phyla. It showcases the great diversity of viromes within each phylum and investigates the role of habitat shaping animal viral communities. Furthermore, our research identifies dominant virus families in invertebrates and distinguishes phyla with analogous viromes. This study sets the road toward a deeper understanding of the virome across the animal tree of life.
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Affiliation(s)
- Pau Alfonso
- Instituto de Biología Integrativa de Sistemas (CSIC-Universitat de València), Paterna, València, Spain
| | - Anamarija Butković
- Institut Pasteur, Université Paris Cité, CNRS UMR6047 Archaeal Virology Unit, Paris, France
| | - Rosa Fernández
- Instituto de Biología Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Ana Riesgo
- Museo Nacional de Ciencias Naturales (CSIC), Madrid, Spain
- Department of Life Sciences, Natural History Museum of London, London, United Kingdom
| | - Santiago F. Elena
- Instituto de Biología Integrativa de Sistemas (CSIC-Universitat de València), Paterna, València, Spain
- The Santa Fe Institute, Santa Fe, New Mexico, USA
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14
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Blanco-Melo D, Campbell MA, Zhu H, Dennis TPW, Modha S, Lytras S, Hughes J, Gatseva A, Gifford RJ. A novel approach to exploring the dark genome and its application to mapping of the vertebrate virus fossil record. Genome Biol 2024; 25:120. [PMID: 38741126 PMCID: PMC11089739 DOI: 10.1186/s13059-024-03258-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 04/22/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Genomic regions that remain poorly understood, often referred to as the dark genome, contain a variety of functionally relevant and biologically informative features. These include endogenous viral elements (EVEs)-virus-derived sequences that can dramatically impact host biology and serve as a virus fossil record. In this study, we introduce a database-integrated genome screening (DIGS) approach to investigate the dark genome in silico, focusing on EVEs found within vertebrate genomes. RESULTS Using DIGS on 874 vertebrate genomes, we uncover approximately 1.1 million EVE sequences, with over 99% originating from endogenous retroviruses or transposable elements that contain EVE DNA. We show that the remaining 6038 sequences represent over a thousand distinct horizontal gene transfer events across 10 virus families, including some that have not previously been reported as EVEs. We explore the genomic and phylogenetic characteristics of non-retroviral EVEs and determine their rates of acquisition during vertebrate evolution. Our study uncovers novel virus diversity, broadens knowledge of virus distribution among vertebrate hosts, and provides new insights into the ecology and evolution of vertebrate viruses. CONCLUSIONS We comprehensively catalog and analyze EVEs within 874 vertebrate genomes, shedding light on the distribution, diversity, and long-term evolution of viruses and reveal their extensive impact on vertebrate genome evolution. Our results demonstrate the power of linking a relational database management system to a similarity search-based screening pipeline for in silico exploration of the dark genome.
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Affiliation(s)
- Daniel Blanco-Melo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
- Herbold Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
| | | | - Henan Zhu
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow, G61 1QH, UK
| | - Tristan P W Dennis
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow, G61 1QH, UK
| | - Sejal Modha
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow, G61 1QH, UK
| | - Spyros Lytras
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow, G61 1QH, UK
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow, G61 1QH, UK
| | - Anna Gatseva
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow, G61 1QH, UK
| | - Robert J Gifford
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow, G61 1QH, UK.
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.
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15
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Wang Y, Zhai J, Tang B, Dong Y, Sun S, He S, Zhao W, Lancuo Z, Jia Q, Wang W. Metagenomic comparison of gut communities between wild and captive Himalayan griffons. Front Vet Sci 2024; 11:1403932. [PMID: 38784654 PMCID: PMC11112026 DOI: 10.3389/fvets.2024.1403932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
Introduction Himalayan griffons (Gyps himalayensis), known as the scavenger of nature, are large scavenging raptors widely distributed on the Qinghai-Tibetan Plateau and play an important role in maintaining the balance of the plateau ecosystem. The gut microbiome is essential for host health, helping to maintain homeostasis, improving digestive efficiency, and promoting the development of the immune system. Changes in environment and diet can affect the composition and function of gut microbiota, ultimately impacting the host health and adaptation. Captive rearing is considered to be a way to protect Himalayan griffons and increase their population size. However, the effects of captivity on the structure and function of the gut microbial communities of Himalayan griffons are poorly understood. Still, availability of sequenced metagenomes and functional information for most griffons gut microbes remains limited. Methods In this study, metagenome sequencing was used to analyze the composition and functional structures of the gut microbiota of Himalayan griffons under wild and captive conditions. Results Our results showed no significant differences in the alpha diversity between the two groups, but significant differences in beta diversity. Taxonomic classification revealed that the most abundant phyla in the gut of Himalayan griffons were Fusobacteriota, Proteobacteria, Firmicutes_A, Bacteroidota, Firmicutes, Actinobacteriota, and Campylobacterota. At the functional level, a series of Kyoto Encyclopedia of Genes and Genome (KEGG) functional pathways, carbohydrate-active enzymes (CAZymes) categories, virulence factor genes (VFGs), and pathogen-host interactions (PHI) were annotated and compared between the two groups. In addition, we recovered nearly 130 metagenome-assembled genomes (MAGs). Discussion In summary, the present study provided a first inventory of the microbial genes and metagenome-assembled genomes related to the Himalayan griffons, marking a crucial first step toward a wider investigation of the scavengers microbiomes with the ultimate goal to contribute to the conservation and management strategies for this near threatened bird.
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Affiliation(s)
- You Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - Jundie Zhai
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - Boyu Tang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - Yonggang Dong
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - Shengzhen Sun
- Animal Disease Prevention and Control Center of Qinghai Province, Xining, Qinghai, China
| | - Shunfu He
- Xining Wildlife Park of Qinghai Province, Xining, Qinghai, China
| | - Wenxin Zhao
- Xining Wildlife Park of Qinghai Province, Xining, Qinghai, China
| | - Zhuoma Lancuo
- College of Finance and Economics, Qinghai University, Xining, Qinghai, China
| | - Qiangqiang Jia
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
| | - Wen Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
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16
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Kobayashi D, Inoue Y, Suzuki R, Matsuda M, Shimoda H, Faizah AN, Kaku Y, Ishijima K, Kuroda Y, Tatemoto K, Virhuez-Mendoza M, Harada M, Nishino A, Inumaru M, Yonemitsu K, Kuwata R, Takano A, Watanabe M, Higa Y, Sawabe K, Maeda K, Isawa H. Identification and epidemiological study of an uncultured flavivirus from ticks using viral metagenomics and pseudoinfectious viral particles. Proc Natl Acad Sci U S A 2024; 121:e2319400121. [PMID: 38687787 PMCID: PMC11087778 DOI: 10.1073/pnas.2319400121] [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: 11/06/2023] [Accepted: 03/20/2024] [Indexed: 05/02/2024] Open
Abstract
During their blood-feeding process, ticks are known to transmit various viruses to vertebrates, including humans. Recent viral metagenomic analyses using next-generation sequencing (NGS) have revealed that blood-feeding arthropods like ticks harbor a large diversity of viruses. However, many of these viruses have not been isolated or cultured, and their basic characteristics remain unknown. This study aimed to present the identification of a difficult-to-culture virus in ticks using NGS and to understand its epidemic dynamics using molecular biology techniques. During routine tick-borne virus surveillance in Japan, an unknown flaviviral sequence was detected via virome analysis of host-questing ticks. Similar viral sequences have been detected in the sera of sika deer and wild boars in Japan, and this virus was tentatively named the Saruyama virus (SAYAV). Because SAYAV did not propagate in any cultured cells tested, single-round infectious virus particles (SRIP) were generated based on its structural protein gene sequence utilizing a yellow fever virus-based replicon system to understand its nationwide endemic status. Seroepidemiological studies using SRIP as antigens have demonstrated the presence of neutralizing antibodies against SAYAV in sika deer and wild boar captured at several locations in Japan, suggesting that SAYAV is endemic throughout Japan. Phylogenetic analyses have revealed that SAYAV forms a sister clade with the Orthoflavivirus genus, which includes important mosquito- and tick-borne pathogenic viruses. This shows that SAYAV evolved into a lineage independent of the known orthoflaviviruses. This study demonstrates a unique approach for understanding the epidemiology of uncultured viruses by combining viral metagenomics and pseudoinfectious viral particles.
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Affiliation(s)
- Daisuke Kobayashi
- Department of Medical Entomology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
- Management Department of Biosafety, Laboratory Animal, and Pathogen Bank, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
| | - Yusuke Inoue
- Department of Veterinary Science, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
- Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi City, Yamaguchi753-8515, Japan
| | - Ryosuke Suzuki
- Department of Virology II, National Institute of Infectious Diseases, Musashimurayama City, Tokyo208-0011, Japan
| | - Mami Matsuda
- Department of Virology II, National Institute of Infectious Diseases, Musashimurayama City, Tokyo208-0011, Japan
| | - Hiroshi Shimoda
- Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi City, Yamaguchi753-8515, Japan
| | - Astri Nur Faizah
- Department of Medical Entomology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
| | - Yoshihiro Kaku
- Department of Veterinary Science, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
| | - Keita Ishijima
- Department of Veterinary Science, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
| | - Yudai Kuroda
- Department of Veterinary Science, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
- Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi City, Yamaguchi753-8515, Japan
| | - Kango Tatemoto
- Department of Veterinary Science, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
- Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi City, Yamaguchi753-8515, Japan
| | - Milagros Virhuez-Mendoza
- Department of Veterinary Science, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
- Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi City, Yamaguchi753-8515, Japan
| | - Michiko Harada
- Department of Veterinary Science, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
- Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi City, Yamaguchi753-8515, Japan
| | - Ayano Nishino
- Department of Veterinary Science, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
- Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi City, Yamaguchi753-8515, Japan
| | - Mizue Inumaru
- Department of Medical Entomology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
| | - Kenzo Yonemitsu
- Management Department of Biosafety, Laboratory Animal, and Pathogen Bank, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
- Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi City, Yamaguchi753-8515, Japan
| | - Ryusei Kuwata
- Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi City, Yamaguchi753-8515, Japan
- Faculty of Veterinary Medicine, Okayama University of Science, Imabari City, Ehime794-8555, Japan
| | - Ai Takano
- Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi City, Yamaguchi753-8515, Japan
| | - Mamoru Watanabe
- Department of Medical Entomology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
| | - Yukiko Higa
- Department of Medical Entomology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
| | - Kyoko Sawabe
- Department of Medical Entomology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
- Management Department of Biosafety, Laboratory Animal, and Pathogen Bank, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
| | - Ken Maeda
- Department of Veterinary Science, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
- Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi City, Yamaguchi753-8515, Japan
| | - Haruhiko Isawa
- Department of Medical Entomology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
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Chukwudozie KI, Wang H, Wang X, Lu C, Xue J, Zhang W, Shan T. Viral metagenomic analysis reveals diverse viruses and a novel bocaparvovirus in the enteric virome of snow leopard ( Panthera uncia). Heliyon 2024; 10:e29799. [PMID: 38681641 PMCID: PMC11053277 DOI: 10.1016/j.heliyon.2024.e29799] [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: 09/23/2023] [Revised: 04/14/2024] [Accepted: 04/15/2024] [Indexed: 05/01/2024] Open
Abstract
The enteric virome, comprising a complex community of viruses inhabiting the gastrointestinal tract, plays a significant role in health and disease dynamics. In this study, the fecal sample of a wild snow leopard was subjected to viral metagenomic analysis using a double barcode Illumina MiSeq platform. The resulting reads were de novo assembled into contigs with SOAPdenovo2 version r240. Additional bioinformatic analysis of the assembled genome and genome annotation was done using the Geneious prime software (version 2022.0.2). Following viral metagenomic analysis and bioinformatic analysis, a total of 7 viral families and a novel specie of bocaparvovirus tentatively named Panthera uncia bocaparvovirus (PuBOV) with GenBank accession number OQ627713 were identified. The complete genome of PuBOV was predicted to contain 3 open reading frames (ORFs), contains 5433 nucleotides and has a G + C content of 47.40 %. BLASTx analysis and pairwise sequence comparison indicated the novel virus genome was a new species in the genus Bocaparvovirus based on the species demarcation criteria of the International Committee on the Taxonomy of Viruses. This study provides valuable insights into the diversity and composition of the enteric virome in wild endangered snow leopards. The identification and characterization of viruses in wildlife is crucial for developing effective strategies to manage and mitigate potential zoonotic and other viral disease threats to human and animal health.
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Affiliation(s)
- Kingsley Ikechukwu Chukwudozie
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang. Zip code: 212300, PR China
- Department of Microbiology, University of Nigeria, Zip code: 410001, PR China
| | - Haoning Wang
- Heilongjiang cold Region Wetland Ecology and Environment Research key laboratory, school of geography and tourism, Harbin university, 109 zhongxing Road, Harbin, 150086, Heilongjiang province, PR China
- School of Geography and Tourism, Harbin University, Harbin 150086, Heilongjiang province, PR China
| | - Xiaolong Wang
- The Key Laboratory of Wildlife Diseases and Biosecurity Management of Heilongjiang Province. Zip code: 154100, PR China
| | - Chunying Lu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang. Zip code: 212300, PR China
| | - Jiaxin Xue
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang. Zip code: 212300, PR China
| | - Wen Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang. Zip code: 212300, PR China
| | - Tongling Shan
- Department of Swine Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, PR China
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18
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Liu X, Liu Y, Liu J, Zhang H, Shan C, Guo Y, Gong X, Cui M, Li X, Tang M. Correlation between the gut microbiome and neurodegenerative diseases: a review of metagenomics evidence. Neural Regen Res 2024; 19:833-845. [PMID: 37843219 PMCID: PMC10664138 DOI: 10.4103/1673-5374.382223] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/19/2023] [Accepted: 06/17/2023] [Indexed: 10/17/2023] Open
Abstract
A growing body of evidence suggests that the gut microbiota contributes to the development of neurodegenerative diseases via the microbiota-gut-brain axis. As a contributing factor, microbiota dysbiosis always occurs in pathological changes of neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. High-throughput sequencing technology has helped to reveal that the bidirectional communication between the central nervous system and the enteric nervous system is facilitated by the microbiota's diverse microorganisms, and for both neuroimmune and neuroendocrine systems. Here, we summarize the bioinformatics analysis and wet-biology validation for the gut metagenomics in neurodegenerative diseases, with an emphasis on multi-omics studies and the gut virome. The pathogen-associated signaling biomarkers for identifying brain disorders and potential therapeutic targets are also elucidated. Finally, we discuss the role of diet, prebiotics, probiotics, postbiotics and exercise interventions in remodeling the microbiome and reducing the symptoms of neurodegenerative diseases.
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Affiliation(s)
- Xiaoyan Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Yi Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
- Institute of Animal Husbandry, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu Province, China
| | - Junlin Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Hantao Zhang
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Chaofan Shan
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Yinglu Guo
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Xun Gong
- Department of Rheumatology & Immunology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Mengmeng Cui
- Department of Neurology, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong Province, China
| | - Xiubin Li
- Department of Neurology, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong Province, China
| | - Min Tang
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
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Costa VA, Ronco F, Mifsud JCO, Harvey E, Salzburger W, Holmes EC. Host adaptive radiation is associated with rapid virus diversification and cross-species transmission in African cichlid fishes. Curr Biol 2024; 34:1247-1257.e3. [PMID: 38428417 DOI: 10.1016/j.cub.2024.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/18/2023] [Accepted: 02/06/2024] [Indexed: 03/03/2024]
Abstract
Adaptive radiations are generated through a complex interplay of biotic and abiotic factors. Although adaptive radiations have been widely studied in the context of animal and plant evolution, little is known about how they impact the evolution of the viruses that infect these hosts, which in turn may provide insights into the drivers of cross-species transmission and hence disease emergence. We examined how the rapid adaptive radiation of the cichlid fishes of African Lake Tanganyika over the last 10 million years has shaped the diversity and evolution of the viruses they carry. Through metatranscriptomic analysis of 2,242 RNA sequencing libraries, we identified 121 vertebrate-associated viruses among various tissue types that fell into 13 RNA and 4 DNA virus groups. Host-switching was commonplace, particularly within the Astroviridae, Metahepadnavirus, Nackednavirus, Picornaviridae, and Hepacivirus groups, occurring more frequently than in other fish communities. A time-calibrated phylogeny revealed that hepacivirus diversification was not constant throughout the cichlid radiation but accelerated 2-3 million years ago, coinciding with a period of rapid cichlid diversification and niche packing in Lake Tanganyika, thereby providing more closely related hosts for viral infection. These data depict a dynamic virus ecosystem within the cichlids of Lake Tanganyika, characterized by rapid virus diversification and frequent host jumping, and likely reflecting their close phylogenetic relationships that lower the barriers to cross-species virus transmission.
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Affiliation(s)
- Vincenzo A Costa
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Fabrizia Ronco
- Natural History Museum, University of Oslo, 0562 Oslo, Norway
| | - Jonathon C O Mifsud
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Erin Harvey
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Walter Salzburger
- Zoological Institute, Department of Environmental Sciences, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.
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20
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Cui N, Yang X, Sui H, Tan L, Wang W, Su S, Qi L, Huang Q, Hrabchenko N, Xu C. Virome characterization of diarrheic red-crowned crane (G. japonensis). Anim Microbiome 2024; 6:8. [PMID: 38419121 PMCID: PMC10902971 DOI: 10.1186/s42523-024-00299-3] [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: 09/26/2023] [Accepted: 02/26/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND The red-crowned crane is one of the vulnerable bird species. Although the captive population has markedly increased over the last decade, infectious diseases can lead to the death of young red-crowned cranes while few virological studies have been conducted. METHODS Using a viral metagenomics approach, we analyzed the virome of tissues of the dead captive red-crowned crane with diarrhea symptoms in Dongying Biosphere Reserve, Shandong Province, China and feces of individual birds breeding at the corresponding captive breeding center, which were pooled separately. RESULTS There is much more DNA and RNA viruses in the feces than that of the tissues. RNA virus belonging to the families Picornaviridae, and DNA viruses belonging to the families Parvoviridae, associated with enteric diseases were detected in the tissues and feces. Genomes of the picornavirus, genomovirus, and parvovirus identified in the study were fully characterized, which further suggested that infectious viruses of these families were possibly presented in the diseased red-crowned crane. CONCLUSION RNA virus belonging to the families Picornaviridae, and DNA viruses belonging to the families Genomoviridae and Parvoviridae were possibly the causative agent for diarrhea of red-crowned crane. This study has expanded our understanding of the virome of red-crowned crane and provides a baseline for elucidating the etiology for diarrhea of the birds.
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Affiliation(s)
- Ning Cui
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Jinan, China
| | - Xiao Yang
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Jinan, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Hong Sui
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Jinan, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Liugang Tan
- Dongying Animal Husbandry and Veterinary Station, Dongying, China
| | - Weihua Wang
- National Nature Reserve Management Committee of Shandong Yellow River Triangle, Dongying, China
| | - Shuai Su
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Lihong Qi
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Jinan, China
| | - Qinghua Huang
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China.
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Jinan, China.
| | - Nataliia Hrabchenko
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China.
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Jinan, China.
| | - Chuantian Xu
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China.
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Jinan, China.
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21
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Albuquerque NK, Silva SP, Aragão CF, Cunha TCAS, Paiva FAS, Coelho TFSB, Cruz ACR. Virome analysis of Desmodus rotundus tissue samples from the Amazon region. BMC Genomics 2024; 25:34. [PMID: 38177994 PMCID: PMC10768307 DOI: 10.1186/s12864-023-09950-w] [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: 08/21/2023] [Accepted: 12/28/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND Bats are renowned for harboring a high viral diversity, their characteristics contribute to emerging infectious diseases. However, environmental and anthropic factors also play a significant role in the emergence of zoonotic viruses. Metagenomic is an important tool for investigating the virome of bats and discovering new viruses. RESULTS Twenty-four families of virus were detected in lung samples by sequencing and bioinfomatic analysis, the largest amount of reads was focused on the Retroviridae and contigs assembled to Desmodus rotundus endogenous retrovirus, which was feasible to acquire complete sequences. The reads were also abundant for phages. CONCLUSION This lung virome of D. rotundus contributes valuable information regarding the viral diversity found in bats, which is useful for understanding the drivers of viral cycles and their ecology in this species. The identification and taxonomic categorization of viruses hosted by bats carry epidemiological significance due to the potential for viral adaptation to other animals and humans, which can have severe repercussions for public health. Furthermore, the characterization of endogenized viruses helps to understanding the host genome and the evolution of the species.
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Affiliation(s)
- Nádia K Albuquerque
- Institute of Biologic Science, Federal University of Pará, Augusto Corrêa Road, Belém, 66075-750, Pará, Brazil.
| | - Sandro P Silva
- Arbovirology and Hemorragic Fever Department, Evandro Chagas Institute, BR-316 Highway, Ananindeua, 67030-000, Pará, Brazil
| | - Carine F Aragão
- Arbovirology and Hemorragic Fever Department, Evandro Chagas Institute, BR-316 Highway, Ananindeua, 67030-000, Pará, Brazil
| | - Tânia Cristina A S Cunha
- Arbovirology and Hemorragic Fever Department, Evandro Chagas Institute, BR-316 Highway, Ananindeua, 67030-000, Pará, Brazil
| | - Francisco A S Paiva
- Arbovirology and Hemorragic Fever Department, Evandro Chagas Institute, BR-316 Highway, Ananindeua, 67030-000, Pará, Brazil
| | - Taciana F S B Coelho
- Arbovirology and Hemorragic Fever Department, Evandro Chagas Institute, BR-316 Highway, Ananindeua, 67030-000, Pará, Brazil
| | - Ana Cecília R Cruz
- Institute of Biologic Science, Federal University of Pará, Augusto Corrêa Road, Belém, 66075-750, Pará, Brazil.
- Arbovirology and Hemorragic Fever Department, Evandro Chagas Institute, BR-316 Highway, Ananindeua, 67030-000, Pará, Brazil.
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22
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Jin L, Mao Z. Living virus-based nanohybrids for biomedical applications. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2024; 16:e1923. [PMID: 37619605 DOI: 10.1002/wnan.1923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/26/2023]
Abstract
Living viruses characterized by distinctive biological functions including specific targeting, gene invasion, immune modulation, and so forth have been receiving intensive attention from researchers worldwide owing to their promising potential for producing numerous theranostic modalities against diverse pathological conditions. Nevertheless, concerns during applications, such as rapid immune clearance, altering immune activation modes, insufficient gene transduction efficiency, and so forth, highlight the crucial issues of excessive therapeutic doses and the associated biosafety risks. To address these concerns, synthetic nanomaterials featuring unique physical/chemical properties are frequently exploited as efficient drug delivery vehicles or treatments in biomedical domains. By constant endeavor, researchers nowadays can create adaptable living virus-based nanohybrids (LVN) that not only overcome the limitations of virotherapy, but also combine the benefits of natural substances and nanotechnology to produce novel and promising therapeutic and diagnostic agents. In this review, we discuss the fundamental physiochemical properties of the viruses, and briefly outline the basic construction methodologies of LVN. We then emphasize their distinct diagnostic and therapeutic performances for various diseases. Furthermore, we survey the foreseeable challenges and future perspectives in this interdisciplinary area to offer insights. This article is categorized under: Biology-Inspired Nanomaterials > Protein and Virus-Based Structures Therapeutic Approaches and Drug Discovery > Emerging Technologies.
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Affiliation(s)
- Lulu Jin
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China
| | - Zhengwei Mao
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China
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23
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Dong X, Li C, Wang Y, Hu T, Zhang F, Meng F, Gao M, Han X, Wang G, Qin J, Nauwynck H, Holmes EC, Sorgeloos P, Sui L, Huang J, Shi W. Diversity and connectedness of brine shrimp viruses in global hypersaline ecosystems. SCIENCE CHINA. LIFE SCIENCES 2024; 67:188-203. [PMID: 37922067 DOI: 10.1007/s11427-022-2366-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 05/26/2023] [Indexed: 11/05/2023]
Abstract
Brine shrimp (Artemia) has existed on Earth for 400 million years and has major ecological importance in hypersaline ecosystems. As a crucial live food in aquaculture, brine shrimp cysts have become one of the most important aquatic products traded worldwide. However, our understanding of the biodiversity, prevalence and global connectedness of viruses in brine shrimp is still very limited. A total of 143 batches of brine shrimp (belonging to seven species) cysts were collected from six continents including 21 countries and more than 100 geographic locations worldwide during 1977-2019. In total, 55 novel RNA viruses were identified, which could be assigned to 18 different viral families and related clades. Eleven viruses were dsRNA viruses, 16 were +ssRNA viruses, and 28 were-ssRNA viruses. Phylogenetic analyses of the RNA-directed RNA polymerase (RdRp) showed that brine shrimp viruses were often grouped with viruses isolated from other invertebrates and fungi. Remarkably, most brine shrimp viruses were related to those from different hosts that might feed on brine shrimp or share the same ecological niche. A notable case was the novel brine shrimp noda-like virus 3, which shared 79.25% (RdRp) and 63.88% (capsid proteins) amino acid identity with covert mortality nodavirus (CMNV) that may cause losses in aquaculture. In addition, both virome composition and phylogenetic analyses revealed global connectedness in certain brine shrimp viruses, particularly among Asia and Northern America. This highlights the incredible species diversity of viruses in these ancient species and provides essential data for the prevalence of RNA viruses in the global aquaculture industry. More broadly, these findings provide novel insights into the previously unrecognized RNA virosphere in hypersaline ecosystems worldwide and demonstrate that human activity might have driven the global connectedness of brine shrimp viruses.
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Affiliation(s)
- Xuan Dong
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences; Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory; Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs; Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Qingdao, 266071, China
| | - Cixiu Li
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, China
| | - Yiting Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences; Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory; Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs; Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Qingdao, 266071, China
- Dalian Ocean University, Dalian, 116023, China
| | - Tao Hu
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, China
| | - Fan Zhang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences; Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory; Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs; Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Qingdao, 266071, China
| | - Fanzeng Meng
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences; Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory; Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs; Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Qingdao, 266071, China
| | - Meirong Gao
- Asian Regional Artemia Reference Center, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Xuekai Han
- Asian Regional Artemia Reference Center, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Guohao Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences; Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory; Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs; Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Qingdao, 266071, China
| | - Jiahao Qin
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences; Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory; Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs; Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Qingdao, 266071, China
| | | | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, 2006, Australia
| | | | - Liying Sui
- Asian Regional Artemia Reference Center, Tianjin University of Science & Technology, Tianjin, 300457, China.
| | - Jie Huang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences; Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory; Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs; Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Qingdao, 266071, China.
- Network of Aquaculture Centres in Asia-Pacific, Bangkok, 10900, Thailand.
| | - Weifeng Shi
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, China.
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117, China.
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24
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Medina JE, Castañeda S, Páez-Triana L, Camargo M, Garcia-Corredor DJ, Gómez M, Luna N, Ramírez AL, Pulido-Medellín M, Muñoz M, Ramírez JD. High prevalence of Enterovirus E, Bovine Kobuvirus, and Astrovirus revealed by viral metagenomics in fecal samples from cattle in Central Colombia. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 117:105543. [PMID: 38135265 DOI: 10.1016/j.meegid.2023.105543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/13/2023] [Accepted: 12/16/2023] [Indexed: 12/24/2023]
Abstract
Livestock plays a crucial role in ensuring food security and driving the global economy. However, viral infections can have far-reaching consequences beyond economic productivity, affecting the health of cattle, as well as posing risks to human health and other animals. Identifying viruses present in fecal samples, a primary route of pathogen transmission, is essential for developing effective prevention, control, and surveillance strategies. Viral metagenomic approaches offer a broader perspective and hold great potential for detecting previously unknown viruses or uncovering previously undescribed agents. Ubaté Province is Colombia's dairy capital and a key center for livestock production in the country. Therefore, the purpose of this study was to characterize viral communities in fecal samples from cattle in this region. A total of 42 samples were collected from three municipalities in Ubaté Province, located in central Colombia, using a convenient non-probabilistic sampling method. We utilized metagenomic sequencing with Oxford Nanopore Technologies (ONT), combined with diversity and phylogenetic analysis. The findings revealed a consistent and stable viral composition across the municipalities, primarily comprising members of the Picornaviridae family. At the species level, the most frequent viruses were Enterovirus E (EVE) and Bovine Astrovirus (BoAstV). Significantly, this study reported, for the first time in Colombia, the presence of viruses with veterinary importance occurring at notable frequencies: EVE (59%), Bovine Kobuvirus (BKV) (52%), and BoAstV (19%). Additionally, the study confirmed the existence of Circular replicase-encoding single-stranded (CRESS) Virus in animal feces. These sequences were phylogenetically grouped with samples obtained from Asia and Latin America, underscoring the importance of having adequate representation across the continent. The virome of bovine feces in Ubaté Province is characterized by the predominance of potentially pathogenic viruses such as BoAstV and EVE that have been reported with substantial frequency and quantities. Several of these viruses were identified in Colombia for the first time. This study showcases the utility of using metagenomic sequencing techniques in epidemiological surveillance. It also paves the way for further research on the influence of these agents on bovine health and their frecuency across the country.
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Affiliation(s)
- Julián Esteban Medina
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Sergio Castañeda
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Luisa Páez-Triana
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Milena Camargo
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia; Centro de Tecnología en Salud (CETESA), Innovaseq SAS, Funza, Cundinamarca, Colombia
| | - Diego J Garcia-Corredor
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia; Grupo de Investigación en Medicina Veterinaria y Zootecnia, Facultad de Ciencias Agropecuarias, Universidad Pedagógica y Tecnológica de Colombia, Tunja, Colombia
| | - Marcela Gómez
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia; Grupo de Investigación en Ciencias Básicas (NÚCLEO) Facultad de Ciencias e Ingeniería, Universidad de Boyacá, Tunja, Colombia
| | - Nicolas Luna
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Angie L Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Martín Pulido-Medellín
- Grupo de Investigación en Medicina Veterinaria y Zootecnia, Facultad de Ciencias Agropecuarias, Universidad Pedagógica y Tecnológica de Colombia, Tunja, Colombia
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia.
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Arragain B, Pelosse M, Thompson A, Cusack S. Structural and functional analysis of the minimal orthomyxovirus-like polymerase of Tilapia Lake Virus from the highly diverged Amnoonviridae family. Nat Commun 2023; 14:8145. [PMID: 38066000 PMCID: PMC10709604 DOI: 10.1038/s41467-023-44044-x] [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: 08/10/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
Tilapia Lake Virus (TiLV), a recently discovered pathogen of tilapia fish, belongs to the Amnoonviridae family from the Articulavirales order. Its ten genome segments have characteristic conserved ends and encode proteins with no known homologues, apart from the segment 1, which encodes an orthomyxo-like RNA-dependent-RNA polymerase core subunit. Here we show that segments 1-3 encode respectively the PB1, PB2 and PA-like subunits of an active heterotrimeric polymerase that maintains all domains found in the distantly related influenza polymerase, despite an unprecedented overall size reduction of 40%. Multiple high-resolution cryo-EM structures of TiLV polymerase in pre-initiation, initiation and active elongation states, show how it binds the vRNA and cRNA promoters and performs RNA synthesis, with both transcriptase and replicase configurations being characterised. However, the highly truncated endonuclease-like domain appears inactive and the putative cap-binding domain is autoinhibited, emphasising that many functional aspects of TiLV polymerase remain to be elucidated.
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Affiliation(s)
- Benoit Arragain
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042, Grenoble, Cedex 9, France
| | - Martin Pelosse
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042, Grenoble, Cedex 9, France
| | - Albert Thompson
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042, Grenoble, Cedex 9, France
- The Francis Crick Institute, London, UK
| | - Stephen Cusack
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042, Grenoble, Cedex 9, France.
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Parry RH, Slonchak A, Campbell LJ, Newton ND, Debat HJ, Gifford RJ, Khromykh AA. A novel tamanavirus ( Flaviviridae) of the European common frog ( Rana temporaria) from the UK. J Gen Virol 2023; 104:001927. [PMID: 38059479 PMCID: PMC10770923 DOI: 10.1099/jgv.0.001927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/19/2023] [Indexed: 12/08/2023] Open
Abstract
Flavivirids are small, enveloped, positive-sense RNA viruses from the family Flaviviridae with genomes of ~9-13 kb. Metatranscriptomic analyses of metazoan organisms have revealed a diversity of flavivirus-like or flavivirid viral sequences in fish and marine invertebrate groups. However, no flavivirus-like virus has been identified in amphibians. To remedy this, we investigated the virome of the European common frog (Rana temporaria) in the UK, utilizing high-throughput sequencing at six catch locations. De novo assembly revealed a coding-complete virus contig of a novel flavivirid ~11.2 kb in length. The virus encodes a single ORF of 3456 aa and 5' and 3' untranslated regions (UTRs) of 227 and 666 nt, respectively. We named this virus Rana tamanavirus (RaTV), as BLASTp analysis of the polyprotein showed the closest relationships to Tamana bat virus (TABV) and Cyclopterus lumpus virus from Pteronotus parnellii and Cyclopterus lumpus, respectively. Phylogenetic analysis of the RaTV polyprotein compared to Flavivirus and Flavivirus-like members indicated that RaTV was sufficiently divergent and basal to the vertebrate Tamanavirus clade. In addition to the Mitcham strain, partial but divergent RaTV, sharing 95.64-97.39 % pairwise nucleotide identity, were also obtained from the Poole and Deal samples, indicating that RaTV is widespread in UK frog samples. Bioinformatic analyses of predicted secondary structures in the 3'UTR of RaTV showed the presence of an exoribonuclease-resistant RNA (xrRNA) structure standard in flaviviruses and TABV. To examine this biochemically, we conducted an in vitro Xrn1 digestion assay showing that RaTV probably forms a functional Xrn1-resistant xrRNA.
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Affiliation(s)
- Rhys H. Parry
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Andrii Slonchak
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre (AIDRC), Brisbane, QLD, Australia
| | - Lewis J. Campbell
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Institute of Zoology, Zoological Society of London, London, UK
- Environment and Sustainability Institute, University of Exeter, Penryn, UK
| | - Natalee D. Newton
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre (AIDRC), Brisbane, QLD, Australia
| | - Humberto J. Debat
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Córdoba X5020ICA, Argentina
- Unidad de Fitopatología y Modelización Agrícola (UFYMA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba X5020ICA, Argentina
| | | | - Alexander A. Khromykh
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre (AIDRC), Brisbane, QLD, Australia
- AIDRC Global Virus Network Centre of Excellence, Brisbane, QLD, Australia
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Okoh GR, Ariel E, Whitmore D, Horwood PF. Metagenomic and Molecular Detection of Novel Fecal Viruses in Free-Ranging Agile Wallabies. ECOHEALTH 2023; 20:427-440. [PMID: 38091182 DOI: 10.1007/s10393-023-01659-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 10/26/2023] [Indexed: 02/21/2024]
Abstract
The agile wallaby (Notamacropus agilis) is one of the most abundant marsupial species in northern Queensland and a competent host for the zoonotic Ross River virus. Despite their increased proximity and interactions with humans, little is known about the viruses carried by these animals, and whether any are of conservation or zoonotic importance. Metagenomics and molecular techniques were used in a complementary manner to identify and characterize novel viruses in the fecal samples of free-ranging agile wallabies. We detected a variety of novel marsupial-related viral species including agile wallaby atadenovirus 1, agile wallaby chaphamaparvovirus 1-2, agile wallaby polyomavirus 1-2, agile wallaby associated picobirnavirus 1-9, and a known macropod gammaherpesvirus 3. Phylogenetic analyses indicate that most of these novel viruses would have co-evolved with their hosts (agile wallabies). Additionally, non-marsupial viruses that infect bacteria (phages), plants, insects, and other eukaryotes were identified. This study highlighted the utility of non-invasive sampling as well as the integration of broad-based molecular assays (consensus PCR and next generation sequencing) for monitoring the emergence of potential pathogenic viruses in wildlife species. Furthermore, the novel marsupial viruses identified in this study will enrich the diversity of knowledge about marsupial viruses, and may be useful for developing diagnostics and vaccines.
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Affiliation(s)
- God'spower Richard Okoh
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, 4811, Australia.
| | - Ellen Ariel
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, 4811, Australia
| | - David Whitmore
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, 4811, Australia
| | - Paul F Horwood
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, 4811, Australia.
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Petrone ME, Parry R, Mifsud JCO, Van Brussel K, Vorhees I, Richards ZT, Holmes EC. Evidence for an ancient aquatic origin of the RNA viral order Articulavirales. Proc Natl Acad Sci U S A 2023; 120:e2310529120. [PMID: 37906647 PMCID: PMC10636315 DOI: 10.1073/pnas.2310529120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 10/03/2023] [Indexed: 11/02/2023] Open
Abstract
The emergence of previously unknown disease-causing viruses in mammals is in part the result of a long-term evolutionary process. Reconstructing the deep phylogenetic histories of viruses helps identify major evolutionary transitions and contextualizes the emergence of viruses in new hosts. We used a combination of total RNA sequencing and transcriptome data mining to extend the diversity and evolutionary history of the RNA virus order Articulavirales, which includes the influenza viruses. We identified instances of Articulavirales in the invertebrate phylum Cnidaria (including corals), constituting a novel and divergent family that we provisionally named the "Cnidenomoviridae." We further extended the evolutionary history of the influenza virus lineage by identifying four divergent, fish-associated influenza-like viruses, thereby supporting the hypothesis that fish were among the first hosts of influenza viruses. In addition, we substantially expanded the phylogenetic diversity of quaranjaviruses and proposed that this genus be reclassified as a family-the "Quaranjaviridae." Within this putative family, we identified a novel arachnid-infecting genus, provisionally named "Cheliceravirus." Notably, we observed a close phylogenetic relationship between the Crustacea- and Chelicerata-infecting "Quaranjaviridae" that is inconsistent with virus-host codivergence. Together, these data suggest that the Articulavirales has evolved over at least 600 million years, first emerging in aquatic animals. Importantly, the evolution of the Articulavirales was likely shaped by multiple aquatic-terrestrial transitions and substantial host jumps, some of which are still observable today.
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Affiliation(s)
- Mary E. Petrone
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW2006, Australia
- Laboratory of Data Discovery for Health Limited, Hong Kong Special Administrative Region, China
| | - Rhys Parry
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD4067, Australia
| | - Jonathon C. O. Mifsud
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW2006, Australia
| | - Kate Van Brussel
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW2006, Australia
| | - Ian Vorhees
- James A. Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY14850
| | - Zoe T. Richards
- Coral Conservation and Research Group, Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA6102, Australia
- Collections and Research, Western Australian Museum, Welshpool, WA6106, Australia
| | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW2006, Australia
- Laboratory of Data Discovery for Health Limited, Hong Kong Special Administrative Region, China
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29
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Liao F, Xia Y, Gu W, Fu X, Yuan B. Comparative analysis of shotgun metagenomics and 16S rDNA sequencing of gut microbiota in migratory seagulls. PeerJ 2023; 11:e16394. [PMID: 37941936 PMCID: PMC10629391 DOI: 10.7717/peerj.16394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 10/11/2023] [Indexed: 11/10/2023] Open
Abstract
Background Shotgun metagenomic and 16S rDNA sequencing are commonly used methods to identify the taxonomic composition of microbial communities. Previously, we analysed the gut microbiota and intestinal pathogenic bacteria configuration of migratory seagulls by using 16S rDNA sequencing and culture methods. Methods To continue in-depth research on the gut microbiome and reveal the applicability of the two methods, we compared the metagenome and 16S rDNA amplicon results to further demonstrate the features of this animal. Results The number of bacterial species detected by metagenomics gradually increased from the phylum to species level, consistent with 16S rDNA sequencing. Several taxa were commonly shared by both sequencing methods. However, Escherichia, Shigella, Erwinia, Klebsiella, Salmonella, Escherichia albertii, Shigella sonnei, Salmonella enterica, and Shigella flexneri were unique taxa for the metagenome compared with Escherichia-Shigella, Hafnia-Obesumbacterium, Catellicoccus marimammalium, Lactococcus garvieae, and Streptococcus gallolyticus for 16S rDNA sequencing. The largest differences in relative abundance between the two methods were identified at the species level, which identified many pathogenic bacteria to humans using metagenomic sequencing. Pearson correlation analysis indicated that the correlation coefficient for the two methods gradually decreased with the refinement of the taxonomic levels. The high consistency of the correlation coefficient was identified at the genus level for the beta diversity of the two methods. Conclusions In general, relatively consistent patterns and reliability could be identified by both sequencing methods, but the results varied following the refinement of taxonomic levels. Metagenomic sequencing was more suitable for the discovery and detection of pathogenic bacteria of gut microbiota in seagulls. Although there were large differences in the numbers and abundance of bacterial species of the two methods in terms of taxonomic levels, the patterns and reliability results of the samples were consistent.
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Affiliation(s)
- Feng Liao
- Department of Respiratory Medicine, The First People’s Hospital of Yunnan Province, Kunming, Yunnan, China
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Yilan Xia
- Department of Infectious Diseases and Hepatology, The First People’s Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Wenpeng Gu
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Centre for Disease Control and Prevention, Kunming, Yunnan, China
| | - Xiaoqing Fu
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Centre for Disease Control and Prevention, Kunming, Yunnan, China
| | - Bing Yuan
- Department of Respiratory Medicine, The First People’s Hospital of Yunnan Province, Kunming, Yunnan, China
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
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French RK, Anderson SH, Cain KE, Greene TC, Minor M, Miskelly CM, Montoya JM, Wille M, Muller CG, Taylor MW, Digby A, Holmes EC. Host phylogeny shapes viral transmission networks in an island ecosystem. Nat Ecol Evol 2023; 7:1834-1843. [PMID: 37679456 PMCID: PMC10627826 DOI: 10.1038/s41559-023-02192-9] [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: 12/12/2022] [Accepted: 08/04/2023] [Indexed: 09/09/2023]
Abstract
Virus transmission between host species underpins disease emergence. Both host phylogenetic relatedness and aspects of their ecology, such as species interactions and predator-prey relationships, may govern rates and patterns of cross-species virus transmission and hence zoonotic risk. To address the impact of host phylogeny and ecology on virus diversity and evolution, we characterized the virome structure of a relatively isolated island ecological community in Fiordland, New Zealand, that are linked through a food web. We show that phylogenetic barriers that inhibited cross-species virus transmission occurred at the level of host phyla (between the Chordata, Arthropoda and Streptophyta) as well as at lower taxonomic levels. By contrast, host ecology, manifest as predator-prey interactions and diet, had a smaller influence on virome composition, especially at higher taxonomic levels. The virus-host community comprised a 'small world' network, in which hosts with a high diversity of viruses were more likely to acquire new viruses, and generalist viruses that infect multiple hosts were more likely to infect additional species compared to host specialist viruses. Such a highly connected ecological community increases the likelihood of cross-species virus transmission, particularly among closely related species, and suggests that host generalist viruses present the greatest risk of disease emergence.
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Affiliation(s)
- Rebecca K French
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia.
| | - Sandra H Anderson
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Kristal E Cain
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Terry C Greene
- Biodiversity Group, Department of Conservation, Christchurch, New Zealand
| | - Maria Minor
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Colin M Miskelly
- Te Papa Tongarewa Museum of New Zealand, Wellington, New Zealand
| | - Jose M Montoya
- Theoretical and Experimental Ecology Station, National Centre for Scientific Research (CNRS), Moulis, France
| | - Michelle Wille
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Chris G Muller
- Wildbase, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Michael W Taylor
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Andrew Digby
- Kākāpō Recovery Team, Department of Conservation, Invercargill, New Zealand
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia.
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31
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Fonseca BDP, Morel CM. Relevance of national, regional and global virome projects on pandemics prediction, prevention, and control: a social network analysis of GVP-citing articles. Mem Inst Oswaldo Cruz 2023; 118:e230116. [PMID: 37878831 PMCID: PMC10599233 DOI: 10.1590/0074-02760230116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 09/05/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND The Global Virome Project (GVP) was proposed in 2018 as an evolution of the USAID PREDICT project and was presented as a "collaborative scientific initiative to discover zoonotic viral threats and stop future pandemics". The immediate response was mixed, with public health and scientific communities representatives showing skepticism, if not direct opposition. OBJECTIVES The economic, social, and health consequences of the coronavirus disease 2019 (COVID-19) pandemic demonstrated how unprepared the world was in the face of new pandemics. This paper analyses the impact of the GVP on the scientific and public health communities. METHODS Published scientific articles that cited the two 2018 seminal publications proposing the project were analysed using social network analysis methods. FINDINGS Encompassing the periods before and after the onset of the Covid-19 pandemic, the results indicate that (i) the concepts of the GVP have received more support than opposition in the scientific literature; (ii) its foundations should be updated to address the specific criticisms. MAIN CONCLUSIONS Shifting focus to national virome projects can provide tangible, regional benefits that can positively contribute towards a consensus on achieving a high level of preparedness for the ever-present possibility of the following global viral pandemic.
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Affiliation(s)
- Bruna de Paula Fonseca
- Fundação Oswaldo Cruz-Fiocruz, Centro de Desenvolvimento Tecnológico em Saúde, Rio de Janeiro, RJ, Brasil
- Fundação Oswaldo Cruz-Fiocruz, Centro de Desenvolvimento Tecnológico em Saúde, Instituto Nacional de Ciência e Tecnologia de Inovação em Doenças de Populações Negligenciadas, Rio de Janeiro, RJ, Brasil
| | - Carlos Medicis Morel
- Fundação Oswaldo Cruz-Fiocruz, Centro de Desenvolvimento Tecnológico em Saúde, Rio de Janeiro, RJ, Brasil
- Fundação Oswaldo Cruz-Fiocruz, Centro de Desenvolvimento Tecnológico em Saúde, Instituto Nacional de Ciência e Tecnologia de Inovação em Doenças de Populações Negligenciadas, Rio de Janeiro, RJ, Brasil
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Chen YM, Hu SJ, Lin XD, Tian JH, Lv JX, Wang MR, Luo XQ, Pei YY, Hu RX, Song ZG, Holmes EC, Zhang YZ. Host traits shape virome composition and virus transmission in wild small mammals. Cell 2023; 186:4662-4675.e12. [PMID: 37734372 DOI: 10.1016/j.cell.2023.08.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 07/13/2023] [Accepted: 08/22/2023] [Indexed: 09/23/2023]
Abstract
Bats, rodents, and shrews are the most important animal sources of human infectious diseases. However, the evolution and transmission of viruses among them remain largely unexplored. Through the meta-transcriptomic sequencing of internal organ and fecal samples from 2,443 wild bats, rodents, and shrews sampled from four Chinese habitats, we identified 669 viruses, including 534 novel viruses, thereby greatly expanding the mammalian virome. Our analysis revealed high levels of phylogenetic diversity, identified cross-species virus transmission events, elucidated virus origins, and identified cases of invertebrate viruses in mammalian hosts. Host order and sample size were the most important factors impacting virome composition and patterns of virus spillover. Shrews harbored a high richness of viruses, including many invertebrate-associated viruses with multi-organ distributions, whereas rodents carried viruses with a greater capacity for host jumping. These data highlight the remarkable diversity of mammalian viruses in local habitats and their ability to emerge in new hosts.
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Affiliation(s)
- Yan-Mei Chen
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai 200438, China
| | - Shu-Jian Hu
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai 200438, China
| | - Xian-Dan Lin
- Wenzhou Center for Disease Control and Prevention, Wenzhou, Zhejiang 325002, China
| | - Jun-Hua Tian
- Wuhan Center for Disease Control and Prevention, Wuhan, Hubei 430022, China
| | - Jia-Xin Lv
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai 200438, China
| | - Miao-Ruo Wang
- Longquan Center for Disease Control and Prevention, Longquan, Zhejiang 323799, China
| | - Xiu-Qi Luo
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai 200438, China
| | - Yuan-Yuan Pei
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai 200438, China
| | - Rui-Xue Hu
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai 200438, China
| | - Zhi-Gang Song
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai 200438, China
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia; Laboratory of Data Discovery for Health Limited, Hong Kong SAR, China
| | - Yong-Zhen Zhang
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai 200438, China.
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Grimwood RM, Fortune-Kelly G, Holmes EC, Ingram T, Geoghegan JL. Host specificity shapes fish viromes across lakes on an isolated remote island. Virology 2023; 587:109884. [PMID: 37757732 DOI: 10.1016/j.virol.2023.109884] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/03/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023]
Abstract
Fish viromes often provide insights into the origin and evolution of viruses affecting tetrapods, including those associated with imporant human diseases. However, despite fish being the most diverse vertebrate group, their viruses are still understudied. We investigated the viromes of fish on Chatham Island (Rēkohu), a geographically isolated island housing 9% of New Zealand's threatened endemic fish species. Using metatranscriptomics, we analyzed samples from seven host species across 16 waterbodies. We identified 19 fish viruses, including 16 potentially novel species, expanding families such as the Coronaviridae, Hantaviridae, Poxviridae, and the recently proposed Tosoviridae. Surprisingly, virome composition was not influenced by the ecological factors measured and smelt (Retropinna retropinna) viromes were consistent across lakes despite differences in host life history, seawater influence, and community richness. Overall, fish viromes across Rēkohu were highly diverse and revealed a long history of co-divergence between host and virus despite their unique and geographically isolated ecosystem.
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Affiliation(s)
- Rebecca M Grimwood
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | | | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Travis Ingram
- Department of Zoology, University of Otago, Dunedin, 9016, New Zealand
| | - Jemma L Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand; Institute of Environmental Science and Research, Wellington, 5018, New Zealand.
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Rajput M, Thakur N. Editorial: Advances in host-pathogen interactions for diseases in animals and birds. Front Vet Sci 2023; 10:1282110. [PMID: 37766859 PMCID: PMC10520279 DOI: 10.3389/fvets.2023.1282110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Affiliation(s)
- Mrigendra Rajput
- Department of Biology, University of Dayton, Dayton, OH, United States
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Pereira PDC, Diniz DG, da Costa ER, Magalhães NGDM, da Silva ADJF, Leite JGS, Almeida NIP, Cunha KDN, de Melo MAD, Vasconcelos PFDC, Diniz JAP, Brites D, Anthony DC, Diniz CWP, Guerreiro-Diniz C. Genes, inflammatory response, tolerance, and resistance to virus infections in migratory birds, bats, and rodents. Front Immunol 2023; 14:1239572. [PMID: 37711609 PMCID: PMC10497949 DOI: 10.3389/fimmu.2023.1239572] [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: 06/13/2023] [Accepted: 08/14/2023] [Indexed: 09/16/2023] Open
Abstract
Normally, the host immunological response to viral infection is coordinated to restore homeostasis and protect the individual from possible tissue damage. The two major approaches are adopted by the host to deal with the pathogen: resistance or tolerance. The nature of the responses often differs between species and between individuals of the same species. Resistance includes innate and adaptive immune responses to control virus replication. Disease tolerance relies on the immune response allowing the coexistence of infections in the host with minimal or no clinical signs, while maintaining sufficient viral replication for transmission. Here, we compared the virome of bats, rodents and migratory birds and the molecular mechanisms underlying symptomatic and asymptomatic disease progression. We also explore the influence of the host physiology and environmental influences on RNA virus expression and how it impacts on the whole brain transcriptome of seemingly healthy semipalmated sandpiper (Calidris pusilla) and spotted sandpiper (Actitis macularius). Three time points throughout the year were selected to understand the importance of longitudinal surveys in the characterization of the virome. We finally revisited evidence that upstream and downstream regulation of the inflammatory response is, respectively, associated with resistance and tolerance to viral infections.
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Affiliation(s)
- Patrick Douglas Corrêa Pereira
- Ciência e Tecnologia do Pará, Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Bragança, Pará, Brazil
| | - Daniel Guerreiro Diniz
- Seção de Hepatologia, Laboratório de Microscopia Eletrônica, Instituto Evandro Chagas, Belém, Pará, Brazil
- Instituto de Ciências Biológicas, Hospital Universitário João de Barros Barreto, Laboratório de Investigações em Neurodegeneração e Infecção, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Emanuel Ramos da Costa
- Ciência e Tecnologia do Pará, Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Bragança, Pará, Brazil
- Instituto de Ciências Biológicas, Hospital Universitário João de Barros Barreto, Laboratório de Investigações em Neurodegeneração e Infecção, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Nara Gyzely de Morais Magalhães
- Ciência e Tecnologia do Pará, Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Bragança, Pará, Brazil
| | - Anderson de Jesus Falcão da Silva
- Ciência e Tecnologia do Pará, Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Bragança, Pará, Brazil
| | - Jéssica Gizele Sousa Leite
- Ciência e Tecnologia do Pará, Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Bragança, Pará, Brazil
| | - Natan Ibraim Pires Almeida
- Ciência e Tecnologia do Pará, Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Bragança, Pará, Brazil
| | - Kelle de Nazaré Cunha
- Ciência e Tecnologia do Pará, Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Bragança, Pará, Brazil
| | - Mauro André Damasceno de Melo
- Ciência e Tecnologia do Pará, Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Bragança, Pará, Brazil
| | - Pedro Fernando da Costa Vasconcelos
- Centro de Ciências Biológicas e da Saúde, Universidade do Estado do Pará, Belém, Pará, Brazil
- Seção de Arbovirologia e Febres Hemorrágicas, Instituto Evandro Chagas, Ananindeua, Pará, Brazil
| | - José Antonio Picanço Diniz
- Seção de Hepatologia, Laboratório de Microscopia Eletrônica, Instituto Evandro Chagas, Belém, Pará, Brazil
| | - Dora Brites
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
- Department of Pharmaceutical Sciences and Medicines, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Daniel Clive Anthony
- Department of Pharmacology, Laboratory of Experimental Neuropathology, University of Oxford, Oxford, United Kingdom
| | - Cristovam Wanderley Picanço Diniz
- Instituto de Ciências Biológicas, Hospital Universitário João de Barros Barreto, Laboratório de Investigações em Neurodegeneração e Infecção, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Cristovam Guerreiro-Diniz
- Ciência e Tecnologia do Pará, Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Bragança, Pará, Brazil
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Gil P, Exbrayat A, Loire E, Rakotoarivony I, Charriat F, Morel C, Baldet T, Boisseau M, Marie A, Frances B, L’Ambert G, Bessat M, Otify Y, Goffredo M, Mancini G, Busquets N, Birnberg L, Talavera S, Aranda C, Ayari E, Mejri S, Sghaier S, Bennouna A, El Rhaffouli H, Balenghien T, Chlyeh G, Fassi Fihri O, Reveillaud J, Simonin Y, Eloit M, Gutierrez S. Spatial scale influences the distribution of viral diversity in the eukaryotic virome of the mosquito Culex pipiens. Virus Evol 2023; 9:vead054. [PMID: 37719779 PMCID: PMC10504824 DOI: 10.1093/ve/vead054] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 06/22/2023] [Accepted: 08/23/2023] [Indexed: 09/19/2023] Open
Abstract
Our knowledge of the diversity of eukaryotic viruses has recently undergone a massive expansion. This diversity could influence host physiology through yet unknown phenomena of potential interest to the fields of health and food production. However, the assembly processes of this diversity remain elusive in the eukaryotic viromes of terrestrial animals. This situation hinders hypothesis-driven tests of virome influence on host physiology. Here, we compare taxonomic diversity between different spatial scales in the eukaryotic virome of the mosquito Culex pipiens. This mosquito is a vector of human pathogens worldwide. The experimental design involved sampling in five countries in Africa and Europe around the Mediterranean Sea and large mosquito numbers to ensure a thorough exploration of virus diversity. A group of viruses was found in all countries. This core group represented a relatively large and diverse fraction of the virome. However, certain core viruses were not shared by all host individuals in a given country, and their infection rates fluctuated between countries and years. Moreover, the distribution of coinfections in individual mosquitoes suggested random co-occurrence of those core viruses. Our results also suggested differences in viromes depending on geography, with viromes tending to cluster depending on the continent. Thus, our results unveil that the overlap in taxonomic diversity can decrease with spatial scale in the eukaryotic virome of C. pipiens. Furthermore, our results show that integrating contrasted spatial scales allows us to identify assembly patterns in the mosquito virome. Such patterns can guide future studies of virome influence on mosquito physiology.
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Affiliation(s)
- Patricia Gil
- ASTRE, CIRAD, INRAE, University of Montpellier, Montpellier, Languedoc-Roussillon 34398, France
| | - Antoni Exbrayat
- ASTRE, CIRAD, INRAE, University of Montpellier, Montpellier, Languedoc-Roussillon 34398, France
| | - Etienne Loire
- ASTRE, CIRAD, INRAE, University of Montpellier, Montpellier, Languedoc-Roussillon 34398, France
| | - Ignace Rakotoarivony
- ASTRE, CIRAD, INRAE, University of Montpellier, Montpellier, Languedoc-Roussillon 34398, France
| | - Florian Charriat
- ASTRE, CIRAD, INRAE, University of Montpellier, Montpellier, Languedoc-Roussillon 34398, France
| | - Côme Morel
- ASTRE, CIRAD, INRAE, University of Montpellier, Montpellier, Languedoc-Roussillon 34398, France
| | - Thierry Baldet
- ASTRE, CIRAD, INRAE, University of Montpellier, Montpellier, Languedoc-Roussillon 34398, France
| | - Michel Boisseau
- ASTRE, CIRAD, INRAE, University of Montpellier, Montpellier, Languedoc-Roussillon 34398, France
| | | | | | | | - Mohamed Bessat
- Department of Parasitology, Faculty of Veterinary Medicine, Alexandria University, Alexandria 5410012, Egypt
| | - Yehia Otify
- Department of Parasitology, Faculty of Veterinary Medicine, Alexandria University, Alexandria 5410012, Egypt
| | - Maria Goffredo
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise ‘G. Caporale’, Teramo 64100, Italy
| | - Giuseppe Mancini
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise ‘G. Caporale’, Teramo 64100, Italy
| | - Núria Busquets
- IRTA. Programa de Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra 08193, Spain
| | - Lotty Birnberg
- IRTA. Programa de Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra 08193, Spain
| | - Sandra Talavera
- IRTA. Programa de Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra 08193, Spain
| | - Carles Aranda
- IRTA. Programa de Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra 08193, Spain
- Servei de Control de Mosquits del Consell Comarcal del Baix Llobregat, Barcelona 08980, Spain
| | - Emna Ayari
- Institut de la Recherche Vétérinaire de Tunisie - Université Tunis El Manar, Tunis 1068, Tunisia
| | - Selma Mejri
- Institut de la Recherche Vétérinaire de Tunisie - Université Tunis El Manar, Tunis 1068, Tunisia
| | - Soufien Sghaier
- Institut de la Recherche Vétérinaire de Tunisie - Université Tunis El Manar, Tunis 1068, Tunisia
| | - Amal Bennouna
- Department of Animal Pathology and Public Health, Hassan II Agronomy & Veterinary Institute, Rabat BP 6202, Morocco
| | | | - Thomas Balenghien
- ASTRE, CIRAD, INRAE, University of Montpellier, Montpellier, Languedoc-Roussillon 34398, France
- Department of Animal Pathology and Public Health, Hassan II Agronomy & Veterinary Institute, Rabat BP 6202, Morocco
| | - Ghita Chlyeh
- Département de Production, Protection et Biotechnologies Végétales, Unité de Zoologie, Institute of Agronomy and Veterinary Medicine Hassan II, Rabat BP 6202, Morocco
| | - Ouafaa Fassi Fihri
- Department of Animal Pathology and Public Health, Hassan II Agronomy & Veterinary Institute, Rabat BP 6202, Morocco
| | - Julie Reveillaud
- ASTRE, CIRAD, INRAE, University of Montpellier, Montpellier, Languedoc-Roussillon 34398, France
| | - Yannick Simonin
- ASTRE, CIRAD, INRAE, University of Montpellier, Montpellier, Languedoc-Roussillon 34398, France
- Pathogenesis and Control of Chronic Infections, University of Montpellier, INSERM, EFS, Montpellier 34394, France
| | - Marc Eloit
- Institut Pasteur, Université Paris Cité, Pathogen Discovery Laboratory, Paris 75015, France
- Institut Pasteur, The OIE Collaborating Centre for Detection and Identification in Humans of Emerging Animal Pathogens, Paris 75724, France
- École nationale vétérinaire d’Alfort, Maisons-Alfort 94700, France
| | - Serafin Gutierrez
- ASTRE, CIRAD, INRAE, University of Montpellier, Montpellier, Languedoc-Roussillon 34398, France
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Richard JC, Blevins E, Dunn CD, Leis EM, Goldberg TL. Viruses of Freshwater Mussels during Mass Mortality Events in Oregon and Washington, USA. Viruses 2023; 15:1719. [PMID: 37632061 PMCID: PMC10458741 DOI: 10.3390/v15081719] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/04/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
Freshwater mussels (Unionida) are globally imperiled, in part due to largely unexplained mass mortality events (MMEs). While recent studies have begun to investigate the possibility that mussel MMEs in the Eastern USA may be caused by infectious diseases, mussels in the Western USA have received relatively little attention in this regard. We conducted a two-year epidemiologic investigation of the role of viruses in ongoing MMEs of the Western pearlshell (Margaritifera falcata) and the Western ridged mussel (Gonidea angulata) in the Chehalis River and Columbia River watersheds in the Western USA. We characterized viromes of mussel hemolymph from 5 locations in 2018 and 2020 using metagenomic methods and identified 557 viruses based on assembled contiguous sequences, most of which are novel. We also characterized the distribution and diversity of a previously identified mussel Gammarhabdovirus related to pathogenic finfish viruses. Overall, we found few consistent associations between viruses and mussel health status. Variation in mussel viromes was most strongly driven by location, with little influence from date, species, or health status, though these variables together only explained ~1/3 of variation in virome composition. Our results demonstrate that Western freshwater mussels host remarkably diverse viromes, but no single virus or combination of viruses appears to be associated with morbidity or mortality during MMEs. Our findings have implications for the conservation of imperiled freshwater mussels, including efforts to enhance natural populations through captive propagation.
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Affiliation(s)
- Jordan C. Richard
- Department of Pathobiological Sciences and Freshwater & Marine Sciences Program, University of Wisconsin-Madison, Madison, WI 53706, USA;
- Southwestern Virginia Field Office, U.S. Fish and Wildlife Service, Abingdon, VA 24210, USA
| | - Emilie Blevins
- Xerces Society for Invertebrate Conservation, Portland, OR 97232, USA;
| | - Christopher D. Dunn
- Department of Pathobiological Sciences and Freshwater & Marine Sciences Program, University of Wisconsin-Madison, Madison, WI 53706, USA;
| | - Eric M. Leis
- La Crosse Fish Health Center, Midwest Fisheries Center, U.S. Fish and Wildlife Service, Onalaska, WI 54650, USA;
| | - Tony L. Goldberg
- Department of Pathobiological Sciences and Freshwater & Marine Sciences Program, University of Wisconsin-Madison, Madison, WI 53706, USA;
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38
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Zhai J, Wang Y, Tang B, Zheng S, He S, Zhao W, Chen H, Lin J, Li F, Bao Y, Lancuo Z, Sharshov K, Liu C, Wang W. Comparative analysis of gut DNA viromes in wild and captive Himalayan vultures. Front Microbiol 2023; 14:1120838. [PMID: 37601346 PMCID: PMC10433386 DOI: 10.3389/fmicb.2023.1120838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 07/21/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction Himalayan vultures (Gyps hinalayensis) are widely distributed on the Qinghai-Tibetan Plateau and play a crucial role in maintaining the ecological balance by feeding on decayed corpses of wild and domestic animals. Large-scale culture and metagenomics studies have broadened our understanding of viral diversity in animals' gastrointestinal tracts. However, despite the importance of gut viral communities in regulating bacterial diversity and performing symbiotic functions, no gut viral study has been conducted on Himalayan vultures. Furthermore, the impact of captivity on the gut virome of these vultures remains unknown. Methods In this study, metagenomic sequencing methods targeting DNA of virus-like particles enriched from feces were used to characterize the gut DNA viromes of wild and captive Himalayan vultures. Results In total, 22,938 unique viral operational taxonomic units (vOTUs) were identified and assigned to 140 viral genera in 41 viral families. These families included viruses associated with bacteria, animals, plants, insects, and archaea. Phage communities, including Siphoviridae, Microviridae, Myoviridae, Inoviridae, and Herelleviridae, dominated the gut virome of Himalayan vultures. Wild vultures exhibited higher viral richness and diversity compared with those in captivity. The functional capacity of the gut virome was characterized by identifying 93 KEGG pathways, which were significantly enriched in metabolism and genetic information processing. Abundant auxiliary metabolic genes, such as carbohydrate-active enzyme, and antibiotic resistance genes, were also found in the vultures' gut virome. Discussion Our findings reveal the complex and diverse viral community present in the gut virome of Himalayan vultures, which varies between wild, and captive states. The DNA virome dataset establishes a baseline for the vultures' gut virome and will serve as a reference for future virus isolation and cultivation. Understanding the impact of captivity on the gut virome contributes to our knowledge of vultures' response to captivity and aids in optimizing their rehabilitation and implementing protective measures.
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Affiliation(s)
- Jundie Zhai
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - You Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - Boyu Tang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - Sisi Zheng
- Animal Disease Prevention and Control Center of Qinghai Province, Xining, Qinghai, China
| | - Shunfu He
- Xining Wildlife Park of Qinghai Province, Xining, Qinghai, China
| | - Wenxin Zhao
- Xining Wildlife Park of Qinghai Province, Xining, Qinghai, China
| | - Hanxi Chen
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - Jun Lin
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - Feng Li
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - Yuzi Bao
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - Zhuoma Lancuo
- College of Finance and Economics, Qinghai University, Xining, Qinghai, China
| | - Kirill Sharshov
- Federal Research Center of Fundamental and Translational Medicine, Novosibirsk, Russia
| | - Chuanfa Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Wen Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
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Hollingsworth BD, Grubaugh ND, Lazzaro BP, Murdock CC. Leveraging insect-specific viruses to elucidate mosquito population structure and dynamics. PLoS Pathog 2023; 19:e1011588. [PMID: 37651317 PMCID: PMC10470969 DOI: 10.1371/journal.ppat.1011588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023] Open
Abstract
Several aspects of mosquito ecology that are important for vectored disease transmission and control have been difficult to measure at epidemiologically important scales in the field. In particular, the ability to describe mosquito population structure and movement rates has been hindered by difficulty in quantifying fine-scale genetic variation among populations. The mosquito virome represents a possible avenue for quantifying population structure and movement rates across multiple spatial scales. Mosquito viromes contain a diversity of viruses, including several insect-specific viruses (ISVs) and "core" viruses that have high prevalence across populations. To date, virome studies have focused on viral discovery and have only recently begun examining viral ecology. While nonpathogenic ISVs may be of little public health relevance themselves, they provide a possible route for quantifying mosquito population structure and dynamics. For example, vertically transmitted viruses could behave as a rapidly evolving extension of the host's genome. It should be possible to apply established analytical methods to appropriate viral phylogenies and incidence data to generate novel approaches for estimating mosquito population structure and dispersal over epidemiologically relevant timescales. By studying the virome through the lens of spatial and genomic epidemiology, it may be possible to investigate otherwise cryptic aspects of mosquito ecology. A better understanding of mosquito population structure and dynamics are key for understanding mosquito-borne disease ecology and methods based on ISVs could provide a powerful tool for informing mosquito control programs.
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Affiliation(s)
- Brandon D Hollingsworth
- Department of Entomology, Cornell University, Ithaca, New York, United States of America
- Cornell Institute for Host Microbe Interaction and Disease, Cornell University, Ithaca, New York, United States of America
| | - Nathan D Grubaugh
- Yale School of Public Health, New Haven, Connecticut, United States of America
- Yale University, New Haven, Connecticut, United States of America
| | - Brian P Lazzaro
- Department of Entomology, Cornell University, Ithaca, New York, United States of America
- Cornell Institute for Host Microbe Interaction and Disease, Cornell University, Ithaca, New York, United States of America
| | - Courtney C Murdock
- Department of Entomology, Cornell University, Ithaca, New York, United States of America
- Cornell Institute for Host Microbe Interaction and Disease, Cornell University, Ithaca, New York, United States of America
- Northeast Regional Center for Excellence in Vector-borne Diseases, Cornell University, Ithaca, New York, United States of America
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40
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Zhang P, Zhang Y, Cao L, Li J, Wu C, Tian M, Zhang Z, Zhang C, Zhang W, Li Y. A Diverse Virome Is Identified in Parasitic Flatworms of Domestic Animals in Xinjiang, China. Microbiol Spectr 2023; 11:e0070223. [PMID: 37042768 PMCID: PMC10269781 DOI: 10.1128/spectrum.00702-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 03/17/2023] [Indexed: 04/13/2023] Open
Abstract
Parasitic flatworms infect diverse vertebrates and are major threats to animal and even human health; however, little is known about the virome of these lower life forms. Using viral metagenomic sequencing, we characterized the virome of the parasitic flatworms collected from major domestic animals, including Dicrocoelium lanceatum and Taenia hydatigena, Echinococcus granulosus sensu stricto and Echinococcus multilocularis. Seven and three different viruses were discovered from D. lanceatum and T. hydatigena, respectively, and no viral sequences were found in adult tapeworms and protoscoleces of E. granulosus sensu stricto and E. multilocularis. Two out of the five parasitic flatworm species carry viruses, showing a host specificity of these viruses. These viruses belong to the Parvoviridae, Circoviridae, unclassified circular, Rep-encoding single-stranded (CRESS) DNA virus, Rhabdoviridae, Endornaviridae, and unclassified RNA viruses. The presence of multiple highly divergent RNA viruses, especially those that cluster with viruses found in marine animals, implies a deep evolutionary history of parasite-associated viruses. In addition, we found viruses with high identity to common pathogens in dogs, including canine circovirus and canine parvovirus 2. The presence of these viruses in the parasites implies that they may infect parasitic flatworms but does not completely exclude the possibility of contamination from host intestinal contents. Furthermore, we demonstrated that certain viruses, such as CRESS DNA virus may integrate into the genome of their host. Our results expand the knowledge of viral diversity in parasites of important domestic animals, highlighting the need for further investigations of their prevalence among other parasites of key animals. IMPORTANCE Characterizing the virome of parasites is important for unveiling the viral diversity, evolution, and ecology and will help to understand the "Russian doll" pattern among viruses, parasites, and host animals. Our data indicate that diverse viruses are present in specific parasitic flatworms, including viruses that may have an ancient evolutionary history and viruses currently circulating in parasite-infected host animals. These data also raise the question of whether parasitic flatworms acquire and/or carry some viruses that may have transmission potential to animals. In addition, through the study of virus-parasite-host interactions, including the influence of viral infection on the life cycle of the parasite, as well as its fitness and pathogenicity to the host, we could find new strategies to prevent and control parasitic diseases.
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Affiliation(s)
- Peng Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Yao Zhang
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, WHO-Collaborating Centre for Prevention and Care Management of Echinococcosis, Xinjiang Medical University, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Le Cao
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Jun Li
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, WHO-Collaborating Centre for Prevention and Care Management of Echinococcosis, Xinjiang Medical University, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Chuanchuan Wu
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, WHO-Collaborating Centre for Prevention and Care Management of Echinococcosis, Xinjiang Medical University, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Mengxiao Tian
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, WHO-Collaborating Centre for Prevention and Care Management of Echinococcosis, Xinjiang Medical University, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Zhuangzhi Zhang
- Veterinary Research Institute, Xinjiang Academy of Animal Sciences, Urumqi, Xinjiang, China
| | - Chiyu Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Wenbao Zhang
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, WHO-Collaborating Centre for Prevention and Care Management of Echinococcosis, Xinjiang Medical University, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
- Veterinary Research Institute, Xinjiang Academy of Animal Sciences, Urumqi, Xinjiang, China
| | - Yanpeng Li
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
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Sousa-Pimenta M, Martins Â, Machado V. Oncolytic viruses in hematological malignancies: hijacking disease biology and fostering new promises for immune and cell-based therapies. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2023; 379:189-219. [PMID: 37541724 DOI: 10.1016/bs.ircmb.2023.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/06/2023]
Abstract
The increased tropism for malignant cells of some viruses has been highlighted in recent studies, prompting their use as a strategy to modify the transcriptional profile of those cells, while sparing the healthy ones. Likewise, they have been recognized as players modulating microenvironmental immunity, namely through an increase in antigen-presenting, natural-killer, and T CD8+ cytotoxic cells by a cross-priming mechanism elicited by tumor-associated antigens. The immunomodulatory role of the oncolytic virus seems relevant in hematological malignancies, which may relapse as a result of a proliferative burst elicited by an external stimulus in progenitor or neoplastic stem cells. By reprogramming the host cells and the surrounding environment, the potential of virotherapy ranges from the promise to eradicate the minimal measurable disease (in acute leukemia, for example), to the ex vivo purging of malignant progenitor cells in the setting of autologous bone marrow transplantation. In this review, we analyze the recent advances in virotherapy in hematological malignancies, either when administered alone or together with chemotherapeutic agents or other immunomodulators.
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Affiliation(s)
- Mário Sousa-Pimenta
- Serviço de Onco-Hematologia, Instituto Português de Oncologia do Porto, Porto, Portugal; i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal; Departamento de Biomedicina, Unidade de Farmacologia e Terapêutica, Faculdade de Medicina da Universidade do Porto, Universidade do Porto, Porto, Portugal.
| | - Ângelo Martins
- Serviço de Onco-Hematologia, Instituto Português de Oncologia do Porto, Porto, Portugal
| | - Vera Machado
- Grupo de Oncologia Molecular e Patologia Viral, Centro de investigação do IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Instituto português de Oncologia do Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC), LAB2, Rua Dr António Bernardino de Almeida, Porto, Portugal
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42
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Liao F, Qian J, Yang R, Gu W, Li R, Yang T, Fu X, Yuan B, Zhang Y. Metagenomics of gut microbiome for migratory seagulls in Kunming city revealed the potential public risk to human health. BMC Genomics 2023; 24:269. [PMID: 37208617 DOI: 10.1186/s12864-023-09379-1] [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: 03/02/2023] [Accepted: 05/15/2023] [Indexed: 05/21/2023] Open
Abstract
BACKGROUND Seagull as a migratory wild bird has become most popular species in southwest China since 1980s. Previously, we analyzed the gut microbiota and intestinal pathogenic bacteria configuration for this species by using 16S rRNA sequencing and culture methods. To continue in-depth research on the gut microbiome of migratory seagulls, the metagenomics, DNA virome and RNA virome were both investigated for their gut microbial communities of abundance and diversity in this study. RESULTS The metagenomics results showed 99.72% of total species was bacteria, followed by viruses, fungi, archaea and eukaryota. In particular, Shigella sonnei, Escherichia albertii, Klebsiella pneumonia, Salmonella enterica and Shigella flexneri were the top distributed taxa at species level. PCoA, NMDS, and statistics indicated some drug resistant genes, such as adeL, evgS, tetA, PmrF, and evgA accumulated as time went by from November to January of the next year, and most of these genes were antibiotic efflux. DNA virome composition demonstrated that Caudovirales was the most abundance virus, followed by Cirlivirales, Geplafuvirales, Petitvirales and Piccovirales. Most of these phages corresponded to Enterobacteriaceae and Campylobacteriaceae bacterial hosts respectively. Caliciviridae, Coronaviridae and Picornaviridae were the top distributed RNA virome at family level of this migratory animal. Phylogenetic analysis indicated the sequences of contigs of Gammacoronavirus and Deltacoronavirus had highly similarity with some coronavirus references. CONCLUSIONS In general, the characteristics of gut microbiome of migratory seagulls were closely related to human activities, and multiomics still revealed the potential public risk to human health.
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Affiliation(s)
- Feng Liao
- Department of Respiratory Medicine, The First People's Hospital of Yunnan Province, 650022, Kunming, P.R. China
- The Affiliated Hospital of Kunming University of Science and Technology, 650500, Kunming, P.R. China
| | - Jing Qian
- The Affiliated Hospital of Kunming University of Science and Technology, 650500, Kunming, P.R. China
| | - Ruian Yang
- Department of Respiratory Medicine, The First People's Hospital of Yunnan Province, 650022, Kunming, P.R. China
| | - Wenpeng Gu
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Centre for Disease Control and Prevention, 650022, Kunming, P.R. China
| | - Rufang Li
- Department of Respiratory Medicine, The First People's Hospital of Yunnan Province, 650022, Kunming, P.R. China
| | - Tingting Yang
- Department of Respiratory Medicine, The First People's Hospital of Yunnan Province, 650022, Kunming, P.R. China
| | - Xiaoqing Fu
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Centre for Disease Control and Prevention, 650022, Kunming, P.R. China
| | - Bing Yuan
- Department of Respiratory Medicine, The First People's Hospital of Yunnan Province, 650022, Kunming, P.R. China
| | - Yunhui Zhang
- Department of Respiratory Medicine, The First People's Hospital of Yunnan Province, 650022, Kunming, P.R. China.
- The Affiliated Hospital of Kunming University of Science and Technology, 650500, Kunming, P.R. China.
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Li Y, Zhang P, Ye M, Tian RR, Li N, Cao L, Ma Y, Liu FL, Zheng YT, Zhang C. Novel Circovirus in Blood from Intravenous Drug Users, Yunnan, China. Emerg Infect Dis 2023; 29:1015-1019. [PMID: 37081583 PMCID: PMC10124637 DOI: 10.3201/eid2905.221617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023] Open
Abstract
We identified a novel circovirus (human-associated circovirus 2 [HuCV2]) from the blood of 2 intravenous drug users in China who were infected with HIV-1, hepatitis C virus, or both. HuCV2 is most closely related to porcine circovirus 3. Our findings underscore the risk for HuCV2 and other emerging viruses among this population.
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Olendraite I, Brown K, Firth AE. Identification of RNA Virus-Derived RdRp Sequences in Publicly Available Transcriptomic Data Sets. Mol Biol Evol 2023; 40:msad060. [PMID: 37014783 PMCID: PMC10101049 DOI: 10.1093/molbev/msad060] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 01/15/2023] [Accepted: 03/08/2023] [Indexed: 04/05/2023] Open
Abstract
RNA viruses are abundant and highly diverse and infect all or most eukaryotic organisms. However, only a tiny fraction of the number and diversity of RNA virus species have been catalogued. To cost-effectively expand the diversity of known RNA virus sequences, we mined publicly available transcriptomic data sets. We developed 77 family-level Hidden Markov Model profiles for the viral RNA-dependent RNA polymerase (RdRp)-the only universal "hallmark" gene of RNA viruses. By using these to search the National Center for Biotechnology Information Transcriptome Shotgun Assembly database, we identified 5,867 contigs encoding RNA virus RdRps or fragments thereof and analyzed their diversity, taxonomic classification, phylogeny, and host associations. Our study expands the known diversity of RNA viruses, and the 77 curated RdRp Profile Hidden Markov Models provide a useful resource for the virus discovery community.
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Affiliation(s)
- Ingrida Olendraite
- Division of Virology, Department of Pathology, Addenbrookes Hospital, University of Cambridge, Cambridge, United Kingdom
| | - Katherine Brown
- Division of Virology, Department of Pathology, Addenbrookes Hospital, University of Cambridge, Cambridge, United Kingdom
| | - Andrew E Firth
- Division of Virology, Department of Pathology, Addenbrookes Hospital, University of Cambridge, Cambridge, United Kingdom
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Du Q, Peng F, Xiong Q, Xu K, Yang KY, Wang M, Wu Z, Li S, Cheng X, Rao X, Wang Y, Tsui SKW, Zeng X. Genomic Analysis of Amphioxus Reveals a Wide Range of Fragments Homologous to Viral Sequences. Viruses 2023; 15:v15040909. [PMID: 37112889 PMCID: PMC10145014 DOI: 10.3390/v15040909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/11/2023] [Accepted: 03/28/2023] [Indexed: 04/05/2023] Open
Abstract
Amphioxus species are considered living fossils and are important in the evolutionary study of chordates and vertebrates. To explore viral homologous sequences, a high-quality annotated genome of the Beihai amphioxus (Branchiostoma belcheri beihai) was examined using virus sequence queries. In this study, 347 homologous fragments (HFs) of viruses were identified in the genome of B. belcheri beihai, of which most were observed on 21 genome assembly scaffolds. HFs were preferentially located within protein-coding genes, particularly in their CDS regions and promoters. A range of amphioxus genes with a high frequency of HFs is proposed, including histone-related genes that are homologous to the Histone H4 or Histone H2B domains of viruses. Together, this comprehensive analysis of viral HFs provides insights into the neglected role of viral integration in the evolution of amphioxus.
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Affiliation(s)
- Qiao Du
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Fang Peng
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Qing Xiong
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, China
| | - Kejin Xu
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Kevin Yi Yang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, China
| | - Mingqiang Wang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Zhitian Wu
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Shanying Li
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaorui Cheng
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Xinjie Rao
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuyouye Wang
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Stephen Kwok-Wing Tsui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, China
| | - Xi Zeng
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
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46
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Ni Z, Chen L, Yun T, Xie R, Ye W, Hua J, Zhu Y, Zhang C. Inactivation Performance of Pseudorabies Virus as African Swine Fever Virus Surrogate by Four Commercialized Disinfectants. Vaccines (Basel) 2023; 11:vaccines11030579. [PMID: 36992163 DOI: 10.3390/vaccines11030579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/22/2023] [Accepted: 02/24/2023] [Indexed: 03/06/2023] Open
Abstract
This study was based on similar physicochemical characteristics of pseudorabies virus (PRV) and African swine fever virus (ASFV). A cellular model for evaluation of disinfectants was established with PRV as an alternative marker strain. In the present study, we evaluated the disinfection performance of commonly used commercialized disinfectants on PRV to provide a reference for the selection of good ASFV disinfectants. In addition, the disinfection (anti-virus) performances for four disinfectants were investigated based on the minimum effective concentration, onset time, action time, and operating temperature. Our results demonstrated that glutaraldehyde decamethylammonium bromide solution, peracetic acid solution, sodium dichloroisocyanurate, and povidone-iodine solution effectively inactivated PRV at concentrations 0.1, 0.5, 0.5, and 2.5 g/L on different time points 30, 5, 10, and 10 min, respectively. Specifically, peracetic acid exhibits optimized overall performance. Glutaraldehyde decamethylammonium bromide is cost effective but requires a long action time and the disinfectant activity is severely affected by low temperatures. Furthermore, povidone-iodine rapidly inactivates the virus and is not affected by environmental temperature, but its application is limited by a poor dilution ratio such as for local disinfection of the skin. This study provides a reference for the selection of disinfectants for ASFV.
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Affiliation(s)
- Zheng Ni
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Husbandry and Veterinary Sciences, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Liu Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Husbandry and Veterinary Sciences, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Tao Yun
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Husbandry and Veterinary Sciences, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Ronghui Xie
- Zhejiang Provincial Center for Animal Disease Control, Hangzhou 310018, China
| | - Weicheng Ye
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Husbandry and Veterinary Sciences, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jionggang Hua
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Husbandry and Veterinary Sciences, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Yinchu Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Husbandry and Veterinary Sciences, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Cun Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Husbandry and Veterinary Sciences, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
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48
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Wallau GL, Barbier E, Tomazatos A, Schmidt-Chanasit J, Bernard E. The Virome of Bats Inhabiting Brazilian Biomes: Knowledge Gaps and Biases towards Zoonotic Viruses. Microbiol Spectr 2023; 11:e0407722. [PMID: 36625641 PMCID: PMC9927472 DOI: 10.1128/spectrum.04077-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 12/09/2022] [Indexed: 01/11/2023] Open
Abstract
Bats host a large variety of viruses, including some that may infect other vertebrates and humans. Research on bat-borne viruses attracted significant attention in recent years mainly due to epizootics caused by viruses having bats as hosts. The characterization of the viral communities of bats was then prioritized, but despite increasing efforts, there are large disparities in the geographical ranges covered and the methodologies employed around the world. As a result, large gaps remain in our current understanding of bat viromes and their role in disease emergence. This is particularly true for megadiverse regions in Latin America. This review aims to summarize the current understanding about bat viruses that inhabit Brazilian biomes, one of the most bat species-rich and diverse regions of the globe. Taking into account all known bat-associated viral families studied in Brazilian biomes, we found that almost half of all bat species (86/181 species) were not investigated for viruses at all. Moreover, only a small fraction of viral lineages or families have been studied more in depth, usually employing targeted methods with limited power to characterize a broad virus diversity. Additionally, these studies relied on limited spatiotemporal sampling and small sample sizes. Therefore, our current understanding of bat viral communities in the Brazilian biomes is limited and biased at different levels, limiting zoonotic risk assessments of bat-borne viruses. Considering these limitations, we propose strategies to bridge the existing gaps in the near future. IMPORTANCE Bat-borne viruses have attracted much attention due to zoonotic outbreaks with large consequences to humans. Because of that, virus characterization in bats has been prioritized in tropical regions of the globe. However, bat-virus research in Latin America and particularly in Brazil, which are among the most bat species-rich regions of the world, are highly biased toward zoonotic viruses and known bat reservoir species. These results have direct implication for virus studies in general but also for new zoonotic virus and spillover events characterization. The limited knowledge we currently have about the virome of Brazilian bats drastically limits any broad assessment of zoonotic viruses they carry and calls for coordinated and large-scale studies to fill this crucial knowledge gap.
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Affiliation(s)
- Gabriel Luz Wallau
- Departamento de Entomologia and Núcleo de Bioinformática, Instituto Aggeu Magalhães (IAM) - Fundação Oswaldo Cruz (Fiocruz), Cidade Universitária, Recife, Brazil
- Department of Arbovirology, Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Center for Arbovirus and Hemorrhagic Fever Reference and Research, National Reference Center for Tropical Infectious Diseases, Hamburg, Germany
| | - Eder Barbier
- Laboratório de Ciência Aplicada à Conservação da Biodiversidade, Departamento de Zoologia, Centro de Biociências, Universidade Federal de Pernambuco, Cidade Universitária, Recife, Brazil
| | - Alexandru Tomazatos
- Department of Arbovirology, Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Center for Arbovirus and Hemorrhagic Fever Reference and Research, National Reference Center for Tropical Infectious Diseases, Hamburg, Germany
| | - Jonas Schmidt-Chanasit
- Department of Arbovirology, Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Center for Arbovirus and Hemorrhagic Fever Reference and Research, National Reference Center for Tropical Infectious Diseases, Hamburg, Germany
- Faculty of Mathematics, Informatics and Natural Sciences, University of Hamburg, Hamburg, Germany
| | - Enrico Bernard
- Laboratório de Ciência Aplicada à Conservação da Biodiversidade, Departamento de Zoologia, Centro de Biociências, Universidade Federal de Pernambuco, Cidade Universitária, Recife, Brazil
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49
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Iwama RE, Moran Y. Origins and diversification of animal innate immune responses against viral infections. Nat Ecol Evol 2023; 7:182-193. [PMID: 36635343 DOI: 10.1038/s41559-022-01951-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 11/11/2022] [Indexed: 01/14/2023]
Abstract
Immune systems are of pivotal importance to any living organism on Earth, as they protect the organism against deleterious effects of viral infections. Though the current knowledge about these systems is still biased towards the immune response in vertebrates, some studies have focused on the identification and characterization of components of invertebrate antiviral immune systems. Two classic model organisms, the insect Drosophila melanogaster and the nematode Caenorhabditis elegans, were instrumental in the discovery of several important components of the innate immune system, such as the Toll-like receptors and the RNA interference pathway. However, these two model organisms provide only a limited view of the evolutionary history of the immune system, as they both are ecdysozoan protostomes. Recent functional studies in non-classic models such as unicellular holozoans (for example, choanoflagellates), lophotrochozoans (for example, oysters) and cnidarians (for example, sea anemones) have added crucial information for understanding the evolution of antiviral systems, as they revealed unexpected ancestral complexity. This Review aims to summarize this information and present the ancestral nature of the antiviral immune response in animals. We also discuss lineage-specific adaptations and future perspectives for the comparative study of the innate immune system that are essential for understanding its evolution.
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Affiliation(s)
- Rafael E Iwama
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Yehu Moran
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, Hebrew University of Jerusalem, Jerusalem, Israel.
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50
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Miranda TDS, Schiffler FB, D'arc M, Moreira FRR, Cosentino MAC, Coimbra A, Mouta R, Medeiros G, Girardi DL, Wanderkoke V, Soares CFA, Francisco TM, Henry MD, Afonso BC, Soffiati FL, Ferreira SS, Ruiz-Miranda CR, Soares MA, Santos AFA. Metagenomic analysis reveals novel dietary-related viruses in the gut virome of marmosets hybrids (Callithrix jacchus x Callithrix penicillata), Brazil. Virus Res 2023; 325:199017. [PMID: 36565815 DOI: 10.1016/j.virusres.2022.199017] [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: 10/13/2022] [Revised: 12/02/2022] [Accepted: 12/04/2022] [Indexed: 12/24/2022]
Abstract
Viral metagenomics has contributed enormously to the characterization of a wide range of viruses infecting animals of all phyla in the last decades. Among Neotropical primates, especially those introduced, knowledge about viral diversity remains poorly studied. Therefore, using metagenomics based on virus enrichment, we explored the viral microbiota present in the feces of introduced common marmosets (Callithrix sp.) in three locations from the Silva Jardim region in the State of Rio de Janeiro, Brazil. Fecal samples were collected from nine marmosets, pooled into three sample pools, and sequenced on Illumina MiSeq platform. Sequence reads were analyzed using a viral metagenomic analysis pipeline and two novel insect viruses belonging to the Parvoviridae and Baculoviridae families were identified. The complete genome of a densovirus (Parvoviridae family) of 5,309 nucleotides (nt) was obtained. The NS1 and VP1 proteins share lower than 32% sequence identity with the corresponding proteins of known members of the subfamily Densovirinae. Phylogenetic analysis suggests that this virus represents a new genus, provisionally named Afoambidensovirus due to its discovery in the Brazilian Atlantic Forest. The novel species received the name Afoambidensovirus incertum 1. The complete circular genome of a baculovirus of 107,191 nt was also obtained, showing 60.8% sequence identity with the most closely related member of the Baculoviridae family. Phylogenetic analysis suggests that this virus represents a new species in the Betabaculovirus genus, provisionally named Betabaculovirus incertum 1. In addition, sequences from several families of arthropods in the three pools evaluated were characterized (contigs ranging from 244 to 6,750 nt), corroborating the presence of possible insect hosts with which these new viruses may be associated. Our study expands the knowledge about two viral families known to infect insects, an important component of the marmosets' diet. This identification in hosts' feces samples demonstrates one of the many uses of this type of data and could serve as a basis for future research characterizing viruses in wildlife using noninvasive samples.
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Affiliation(s)
- Thamiris Dos Santos Miranda
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | | | - Mirela D'arc
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Filipe Romero Rebello Moreira
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil; Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | | | - Amanda Coimbra
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Ricardo Mouta
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Gabriel Medeiros
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Déa Luiza Girardi
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Victor Wanderkoke
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Caique Ferreira Amaral Soares
- Associação Mico-Leão-Dourado, Silva Jardim, Rio de Janeiro, RJ, Brazil; Laboratório de Ciências Ambientais, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
| | - Talitha Mayumi Francisco
- Associação Mico-Leão-Dourado, Silva Jardim, Rio de Janeiro, RJ, Brazil; Laboratório de Ciências Ambientais, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
| | - Malinda Dawn Henry
- Laboratório de Ciências Ambientais, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
| | - Bianca Cardozo Afonso
- Associação Mico-Leão-Dourado, Silva Jardim, Rio de Janeiro, RJ, Brazil; Laboratório de Ciências Ambientais, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
| | | | | | - Carlos Ramon Ruiz-Miranda
- Associação Mico-Leão-Dourado, Silva Jardim, Rio de Janeiro, RJ, Brazil; Laboratório de Ciências Ambientais, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
| | - Marcelo Alves Soares
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil; Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil
| | - André Felipe Andrade Santos
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil.
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