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da Silva AF, Machado LC, da Silva LMI, Dezordi FZ, Wallau GL. Highly divergent and diverse viral community infecting sylvatic mosquitoes from Northeast Brazil. J Virol 2024:e0008324. [PMID: 38995042 DOI: 10.1128/jvi.00083-24] [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: 01/12/2024] [Accepted: 06/11/2024] [Indexed: 07/13/2024] Open
Abstract
Mosquitoes can transmit several pathogenic viruses to humans, but their natural viral community is also composed of a myriad of other viruses such as insect-specific viruses (ISVs) and those that infect symbiotic microorganisms. Besides a growing number of studies investigating the mosquito virome, the majority are focused on few urban species, and relatively little is known about the virome of sylvatic mosquitoes, particularly in high biodiverse biomes such as the Brazilian biomes. Here, we characterized the RNA virome of 10 sylvatic mosquito species from Atlantic forest remains at a sylvatic-urban interface in Northeast Brazil employing a metatranscriptomic approach. A total of 16 viral families were detected. The phylogenetic reconstructions of 14 viral families revealed that the majority of the sequences are putative ISVs. The phylogenetic positioning and, in most cases, the association with a high RNA-dependent RNA polymerase amino acid divergence from other known viruses suggests that the viruses characterized here represent at least 34 new viral species. Therefore, the sylvatic mosquito viral community is predominantly composed of highly divergent viruses highlighting the limited knowledge we still have about the natural virome of mosquitoes in general. Moreover, we found that none of the viruses recovered were shared between the species investigated, and only one showed high identity to a virus detected in a mosquito sampled in Peru, South America. These findings add further in-depth understanding about the interactions and coevolution between mosquitoes and viruses in natural environments. IMPORTANCE Mosquitoes are medically important insects as they transmit pathogenic viruses to humans and animals during blood feeding. However, their natural microbiota is also composed of a diverse set of viruses that cause no harm to the insect and other hosts, such as insect-specific viruses. In this study, we characterized the RNA virome of sylvatic mosquitoes from Northeast Brazil using unbiased metatranscriptomic sequencing and in-depth bioinformatic approaches. Our analysis revealed that these mosquitoes species harbor a diverse set of highly divergent viruses, and the majority comprises new viral species. Our findings revealed many new virus lineages characterized for the first time broadening our understanding about the natural interaction between mosquitoes and viruses. Finally, it also provided several complete genomes that warrant further assessment for mosquito and vertebrate host pathogenicity and their potential interference with pathogenic arboviruses.
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Affiliation(s)
- Alexandre Freitas da Silva
- Departamento de Entomologia, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil
- Núcleo de Bioinformática, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil
| | - Laís Ceschini Machado
- Departamento de Entomologia, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil
| | | | - Filipe Zimmer Dezordi
- Departamento de Entomologia, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil
- Núcleo de Bioinformática, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil
| | - Gabriel Luz Wallau
- Departamento de Entomologia, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil
- Núcleo de Bioinformática, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil
- Department of Arbovirology and Entomology, 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
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Buigues J, Viñals A, Martínez-Recio R, Monrós JS, Sanjuán R, Cuevas JM. Full-genome sequencing of dozens of new DNA viruses found in Spanish bat feces. Microbiol Spectr 2024:e0067524. [PMID: 38990026 DOI: 10.1128/spectrum.00675-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 06/26/2024] [Indexed: 07/12/2024] Open
Abstract
Bats are natural hosts of multiple viruses, many of which have clear zoonotic potential. The search for emerging viruses has been aided by the implementation of metagenomic tools, which have also enabled the detection of unprecedented viral diversity. Currently, this search is mainly focused on RNA viruses, which are largely over-represented in databases. To compensate for this research bias, we analyzed fecal samples from 189 Spanish bats belonging to 22 different species using viral metagenomics. This allowed us to identify 52 complete or near-complete viral genomes belonging to the families Adenoviridae, Circoviridae, Genomoviridae, Papillomaviridae, Parvoviridae, Polyomaviridae and Smacoviridae. Of these, 30 could constitute new species, doubling the number of viruses currently described in Europe. These findings open the door to a more thorough analysis of bat DNA viruses and their zoonotic potential. IMPORTANCE Metagenomics has become a fundamental tool to characterize the global virosphere, allowing us not only to understand the existing viral diversity and its ecological implications but also to identify new and emerging viruses. RNA viruses have a higher zoonotic potential, but this risk is also present for some DNA virus families. In our study, we analyzed the DNA fraction of fecal samples from 22 Spanish bat species, identifying 52 complete or near-complete genomes of different viral families with zoonotic potential. This doubles the number of genomes currently described in Europe. Metagenomic data often produce partial genomes that can be difficult to analyze. Our work, however, has characterized a large number of complete genomes, thus facilitating their taxonomic classification and enabling different analyses to be carried out to evaluate their zoonotic potential. For example, recombination studies are relevant since this phenomenon could play a major role in cross-species transmission.
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Affiliation(s)
- Jaime Buigues
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València and Consejo Superior de Investigaciones Científicas, València, Spain
| | - Adrià Viñals
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, València, Spain
| | - Raquel Martínez-Recio
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València and Consejo Superior de Investigaciones Científicas, València, Spain
| | - Juan S Monrós
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, València, Spain
| | - Rafael Sanjuán
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València and Consejo Superior de Investigaciones Científicas, València, Spain
- Department of Genetics, Universitat de València, València, Spain
| | - José M Cuevas
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València and Consejo Superior de Investigaciones Científicas, València, Spain
- Department of Genetics, Universitat de València, València, Spain
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Lu X, Ji L, Wang H, Zhang Q, Wang X, Liu Y, Shen Q, Yang S, Ma X, Zhang W, Shan T. Highly diverse RNA viruses and phage sequences concealed within birds. Microbiol Spectr 2024; 12:e0080224. [PMID: 38860816 PMCID: PMC11218532 DOI: 10.1128/spectrum.00802-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 04/30/2024] [Indexed: 06/12/2024] Open
Abstract
The diversity of birds in most parts of the world is very high, and thus, they may carry different types of highly differentiated and unknown viruses. Thanks to advanced sequencing technologies, studies on the diversity of bird-associated viruses have increased over the past few years. In this study, a large-scale viral metagenomics survey was performed on cloacal swabs of 2,990 birds from nine provinces of the Chinese mainland. To detect undescribed RNA viruses in birds, more than 1,800 sequences sharing relatively low (<60%) amino acid sequence identity with the best match in the GenBank database were screened. Potentially novel viruses related to vertebrates have been identified, and several potential recombination signals were found. Additionally, hundreds of RNA viral sequences related to plants, fungi, and insects were detected, including previously unknown viruses. Furthermore, we investigated the novelty, functionality, and classification of the phages examined in this study. These viruses occupied topological positions on the evolutionary trees to a certain extent and might form novel putative families, genera, or species, thus providing information to fill the phylogenetic gaps of related viruses. These findings provided new insights into bird-associated viruses, but the interactions among these viruses remain unknown and require further investigation.IMPORTANCEStudying the diversity of RNA viruses in birds and mammals is crucial due to their potential impact on human health and the global ecosystem. Many RNA viruses, such as influenza and coronaviruses, have been shown to cross the species barrier and cause zoonotic diseases. In this metagenomics study involving 2,990 birds from at least 82 species, we identified over 1,800 RNA sequences with distant relationships to known viruses, some of which are rare in birds. The study highlights the scope and diversity of RNA viruses in birds, providing data to predict disease risks and monitor potential viral threats to wildlife, livestock, and human health. This information can aid in the development of strategies for disease prevention and control.
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Affiliation(s)
- Xiang Lu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Likai Ji
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Haoning Wang
- School of Geography and Tourism, Harbin University, Harbin, Heilongjiang, China
| | - Qing Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
- Qinghai Institute of Endemic Disease Prevention and Control, Xining, Qinghai, China
| | - Xiaochun Wang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yuwei Liu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Quan Shen
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Shixing Yang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xiao Ma
- Qinghai Institute of Endemic Disease Prevention and Control, Xining, Qinghai, China
| | - Wen Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
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Gupta S, Sharma R, Williams AE, Sanchez-Vargas I, Rose NH, Zhang C, Crosbie-Villaseca A, Zhu Z, Dayama G, Gloria-Soria A, Brackney DE, Manning J, Wheeler SS, Caranci A, Reyes T, Sylla M, Badolo A, Akorli J, Aribodor OB, Ayala D, Liu WL, Chen CH, Vasquez C, Acosta CG, Ponlawat A, Magalhaes T, Carter B, Wesson D, Surin D, Younger MA, Costa-da-Silva AL, DeGennaro M, Bergman A, Lambrechts L, McBride CS, Olson KE, Calvo E, Lau NC. Global genomics of Aedes aegypti unveils widespread and novel infectious viruses capable of triggering a small RNA response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.06.597482. [PMID: 38895463 PMCID: PMC11185646 DOI: 10.1101/2024.06.06.597482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
The mosquito Aedes aegypti is a prominent vector for arboviruses, but the breadth of mosquito viruses that infects this specie is not fully understood. In the broadest global survey to date of over 200 Ae. aegypti small RNA samples, we detected viral small interfering RNAs (siRNAs) and Piwi interacting RNAs (piRNAs) arising from mosquito viruses. We confirmed that most academic laboratory colonies of Ae. aegypti lack persisting viruses, yet two commercial strains were infected by a novel tombus-like virus. Ae. aegypti from North to South American locations were also teeming with multiple insect viruses, with Anphevirus and a bunyavirus displaying geographical boundaries from the viral small RNA patterns. Asian Ae. aegypti small RNA patterns indicate infections by similar mosquito viruses from the Americas and reveal the first wild example of dengue virus infection generating viral small RNAs. African Ae. aegypti also contained various viral small RNAs including novel viruses only found in these African substrains. Intriguingly, viral long RNA patterns can differ from small RNA patterns, indicative of viral transcripts evading the mosquitoes' RNA interference (RNAi) machinery. To determine whether the viruses we discovered via small RNA sequencing were replicating and transmissible, we infected C6/36 and Aag2 cells with Ae. aegypti homogenates. Through blind passaging, we generated cell lines stably infected by these mosquito viruses which then generated abundant viral siRNAs and piRNAs that resemble the native mosquito viral small RNA patterns. This mosquito small RNA genomics approach augments surveillance approaches for emerging infectious diseases.
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Perini L, Sipes K, Zervas A, Bellas C, Lutz S, Moniruzzaman M, Mourot R, Benning LG, Tranter M, Anesio AM. Giant viral signatures on the Greenland ice sheet. MICROBIOME 2024; 12:91. [PMID: 38760842 PMCID: PMC11100222 DOI: 10.1186/s40168-024-01796-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 03/18/2024] [Indexed: 05/19/2024]
Abstract
BACKGROUND Dark pigmented snow and glacier ice algae on glaciers and ice sheets contribute to accelerating melt. The biological controls on these algae, particularly the role of viruses, remain poorly understood. Giant viruses, classified under the nucleocytoplasmic large DNA viruses (NCLDV) supergroup (phylum Nucleocytoviricota), are diverse and globally distributed. NCLDVs are known to infect eukaryotic cells in marine and freshwater environments, providing a biological control on the algal population in these ecosystems. However, there is very limited information on the diversity and ecosystem function of NCLDVs in terrestrial icy habitats. RESULTS In this study, we investigate for the first time giant viruses and their host connections on ice and snow habitats, such as cryoconite, dark ice, ice core, red and green snow, and genomic assemblies of five cultivated Chlorophyta snow algae. Giant virus marker genes were present in almost all samples; the highest abundances were recovered from red snow and the snow algae genomic assemblies, followed by green snow and dark ice. The variety of active algae and protists in these GrIS habitats containing NCLDV marker genes suggests that infection can occur on a range of eukaryotic hosts. Metagenomic data from red and green snow contained evidence of giant virus metagenome-assembled genomes from the orders Imitervirales, Asfuvirales, and Algavirales. CONCLUSION Our study highlights NCLDV family signatures in snow and ice samples from the Greenland ice sheet. Giant virus metagenome-assembled genomes (GVMAGs) were found in red snow samples, and related NCLDV marker genes were identified for the first time in snow algal culture genomic assemblies; implying a relationship between the NCLDVs and snow algae. Metatranscriptomic viral genes also aligned with metagenomic sequences, suggesting that NCLDVs are an active component of the microbial community and are potential "top-down" controls of the eukaryotic algal and protistan members. This study reveals the unprecedented presence of a diverse community of NCLDVs in a variety of glacial habitats dominated by algae.
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Affiliation(s)
- Laura Perini
- Department of Environmental Science, Aarhus University, Roskilde, 4000, Denmark.
| | - Katie Sipes
- Department of Environmental Science, Aarhus University, Roskilde, 4000, Denmark
| | - Athanasios Zervas
- Department of Environmental Science, Aarhus University, Roskilde, 4000, Denmark
| | | | - Stefanie Lutz
- Department of Agroecology and Environment, Plant-Soil Interactions, Agroscope, Zurich, Switzerland
- German Research Centre for Geosciences, Helmholtz Centre Potsdam, Telegrafenberg, Potsdam, 14473, Germany
| | - Mohammad Moniruzzaman
- Department of Biological Sciences, Rosenstiel School of Marine, Atmospheric and Earth Science, University of Miami, Coral Gables, FL, USA
| | - Rey Mourot
- German Research Centre for Geosciences, Helmholtz Centre Potsdam, Telegrafenberg, Potsdam, 14473, Germany
- Department of Earth Sciences, Freie Universität Berlin, Berlin, 12249, Germany
| | - Liane G Benning
- German Research Centre for Geosciences, Helmholtz Centre Potsdam, Telegrafenberg, Potsdam, 14473, Germany
- Department of Earth Sciences, Freie Universität Berlin, Berlin, 12249, Germany
| | - Martyn Tranter
- Department of Environmental Science, Aarhus University, Roskilde, 4000, Denmark
| | - Alexandre M Anesio
- Department of Environmental Science, Aarhus University, Roskilde, 4000, Denmark
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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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Shi N, Zhu Q, Yang G, Wang P, Huang B. Prevalence and species diversity of dsRNA mycoviruses from Beauveria bassiana strains in the China's Guniujiang nature. Heliyon 2024; 10:e30186. [PMID: 38694113 PMCID: PMC11061733 DOI: 10.1016/j.heliyon.2024.e30186] [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: 09/09/2023] [Revised: 04/17/2024] [Accepted: 04/22/2024] [Indexed: 05/03/2024] Open
Abstract
We investigated the prevalence and species diversity of dsRNA mycoviruses in Beauveria bassiana isolates from the China's Guniujiang Nature Preserve. Among the 28 isolates analyzed, electropherotyping revealed viral infections in 28.6 % (8 out of 28) of the isolates. Metatranscriptomic identification and RT-PCR confirmed the presence of six putative virus species, including two novel species: Beauveria bassiana victorivirus 2 (BbV-2) and Beauveria bassiana bipartite mycovirus 2 (BbBV-2). Four previously characterized mycoviruses were also identified: Beauveria bassiana polymycovirus 4 (BbPmV4), Beauveria bassiana partitivirus 1 (BbPV-1), Beauveria bassiana bipartite mycovirus 1 (BbBV-1), and Beauveria bassiana chrysovirus 2 (BbCV-2). BbPmV4 was found to be the prevailing mycovirus among the infected isolates, and three isolates showed co-infection with both BbPmV4 and BbBV-2. This study enhances our understanding of fungal viral taxonomy and diversity, providing insights into mycovirus infections in B. bassiana populations in China's Guniujiang Nature Preserve. Furthermore, the study on the diversity of B. bassiana viruses lays the foundation for recognizing fungal viruses as potential enhancers of biocontrol agents.
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Affiliation(s)
- Najie Shi
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, 230036, China
| | - Qiuyan Zhu
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, 230036, China
| | - Guogen Yang
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, School of Plant Protection, Anhui Agricultural University, Hefei, 230036, China
| | - Ping Wang
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, 230036, China
| | - Bo Huang
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, 230036, China
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Zhou L, Zhou H, Fan Y, Wang J, Zhang R, Guo Z, Li Y, Kang R, Zhang Z, Yang D, Liu J. Metagenomics to Identify Viral Communities Associated with Porcine Respiratory Disease Complex in Tibetan Pigs in the Tibetan Plateau, China. Pathogens 2024; 13:404. [PMID: 38787256 PMCID: PMC11124006 DOI: 10.3390/pathogens13050404] [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: 03/29/2024] [Revised: 05/04/2024] [Accepted: 05/10/2024] [Indexed: 05/25/2024] Open
Abstract
Tibetan pig is a unique pig breed native to the Qinghai-Tibet Plateau. To investigate viral communities associated with porcine respiratory disease complex (PRDC), 167 respiratory samples were collected from Tibetan pigs in the Ganzi Tibetan autonomous prefecture of Sichuan province. Following library construction and Illunima Novaseq sequencing, 18 distinct viruses belonging to 15 viral taxonomic families were identified in Tibetan pigs with PRDC. Among the 18 detected viruses, 3 viruses were associated with PRDC, including porcine circovirus type 2 (PCV-2), Torque teno sus virus (TTSuV), and porcine cytomegalovirus (PCMV). The genomic sequences of two PCV-2 strains, three TTSuV strains, and one novel Porprismacovirus strain were assembled by SOAPdenovo software (v2). Sequence alignment and phylogenetic analysis showed that both PCV-2 strains belonged to PCV-2d, three TTSuVs were classified to TTSuV2a and TTSuV2b genotypes, and the Porprismacovirus strain PPMV-SCgz-2022 showed a close genetic relationship with a virus of human origin. Recombination analysis indicated that PPMV-SCgz-2022 may have originated from recombination events between Human 16,806 × 66-213 strain and Porcine 17,668 × 82-593 strain. Furthermore, the high proportion of single infection or co-infection of PCV2/TTSuV2 provides insight into PRDC infection in Tibetan pigs. This is the first report of the viral communities in PRDC-affected Tibetan pigs in this region, and the results provides reference for the prevention and control of respiratory diseases in these animals.
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Affiliation(s)
- Long Zhou
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China; (L.Z.); (H.Z.); (Y.F.); (J.W.); (R.Z.); (Z.G.); (Y.L.); (J.L.)
- Key Laboratory of Ministry of Education and Sichuan Province for Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Chengdu 610041, China
| | - Han Zhou
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China; (L.Z.); (H.Z.); (Y.F.); (J.W.); (R.Z.); (Z.G.); (Y.L.); (J.L.)
| | - Yandi Fan
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China; (L.Z.); (H.Z.); (Y.F.); (J.W.); (R.Z.); (Z.G.); (Y.L.); (J.L.)
| | - Jinghao Wang
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China; (L.Z.); (H.Z.); (Y.F.); (J.W.); (R.Z.); (Z.G.); (Y.L.); (J.L.)
| | - Rui Zhang
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China; (L.Z.); (H.Z.); (Y.F.); (J.W.); (R.Z.); (Z.G.); (Y.L.); (J.L.)
| | - Zijing Guo
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China; (L.Z.); (H.Z.); (Y.F.); (J.W.); (R.Z.); (Z.G.); (Y.L.); (J.L.)
| | - Yanmin Li
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China; (L.Z.); (H.Z.); (Y.F.); (J.W.); (R.Z.); (Z.G.); (Y.L.); (J.L.)
| | - Runmin Kang
- Sichuan Animal Science Academy, Sichuan Provincial Key Laboratory of Animal Breeding and Genetics, Chengdu 610066, China;
| | - Zhidong Zhang
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China; (L.Z.); (H.Z.); (Y.F.); (J.W.); (R.Z.); (Z.G.); (Y.L.); (J.L.)
- Key Laboratory of Ministry of Education and Sichuan Province for Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Chengdu 610041, China
| | - Danjiao Yang
- Institute of Animal Science of Ganzi Tibetan Autonomous Prefecture of Sichuan Province, Kangding 626000, China
| | - Jie Liu
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China; (L.Z.); (H.Z.); (Y.F.); (J.W.); (R.Z.); (Z.G.); (Y.L.); (J.L.)
- Key Laboratory of Ministry of Education and Sichuan Province for Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Chengdu 610041, China
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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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10
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Pan YF, Zhao H, Gou QY, Shi PB, Tian JH, Feng Y, Li K, Yang WH, Wu D, Tang G, Zhang B, Ren Z, Peng S, Luo GY, Le SJ, Xin GY, Wang J, Hou X, Peng MW, Kong JB, Chen XX, Yang CH, Mei SQ, Liao YQ, Cheng JX, Wang J, Chaolemen, Wu YH, Wang JB, An T, Huang X, Eden JS, Li J, Guo D, Liang G, Jin X, Holmes EC, Li B, Wang D, Li J, Wu WC, Shi M. Metagenomic analysis of individual mosquito viromes reveals the geographical patterns and drivers of viral diversity. Nat Ecol Evol 2024; 8:947-959. [PMID: 38519631 DOI: 10.1038/s41559-024-02365-0] [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: 08/28/2023] [Accepted: 02/11/2024] [Indexed: 03/25/2024]
Abstract
Mosquito transmitted viruses are responsible for an increasing burden of human disease. Despite this, little is known about the diversity and ecology of viruses within individual mosquito hosts. Here, using a meta-transcriptomic approach, we determined the viromes of 2,438 individual mosquitoes (81 species), spanning ~4,000 km along latitudes and longitudes in China. From these data we identified 393 viral species associated with mosquitoes, including 7 (putative) species of arthropod-borne viruses (that is, arboviruses). We identified potential mosquito species and geographic hotspots of viral diversity and arbovirus occurrence, and demonstrated that the composition of individual mosquito viromes was strongly associated with host phylogeny. Our data revealed a large number of viruses shared among mosquito species or genera, enhancing our understanding of the host specificity of insect-associated viruses. We also detected multiple virus species that were widespread throughout the country, perhaps reflecting long-distance mosquito dispersal. Together, these results greatly expand the known mosquito virome, linked viral diversity at the scale of individual insects to that at a country-wide scale, and offered unique insights into the biogeography and diversity of viruses in insect vectors.
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Affiliation(s)
- Yuan-Fei Pan
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Hailong Zhao
- BGI Research, Shenzhen, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen, China
| | - Qin-Yu Gou
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Pei-Bo Shi
- BGI Research, Shenzhen, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jun-Hua Tian
- Wuhan Center for Disease Control and Prevention, Wuhan, China
| | - Yun Feng
- Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali, China
| | - Kun Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Wei-Hong Yang
- Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali, China
| | - De Wu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Guangpeng Tang
- Guizhou Center for Disease Control and Prevention, Guiyang, China
| | - Bing Zhang
- Xinjiang Key Laboratory of Molecular Biology for Endemic Diseases, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
| | - Zirui Ren
- BGI Research, Shenzhen, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen, China
| | - Shiqin Peng
- BGI Research, Shenzhen, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen, China
| | - Geng-Yan Luo
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Shi-Jia Le
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Gen-Yang Xin
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Jing Wang
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Xin Hou
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Min-Wu Peng
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Jian-Bin Kong
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Xin-Xin Chen
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Chun-Hui Yang
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Shi-Qiang Mei
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Yu-Qi Liao
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Jing-Xia Cheng
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Juan Wang
- Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali, China
| | - Chaolemen
- Old Barag Banner Center for Disease Control and Prevention, Hulunbuir, China
| | - Yu-Hui Wu
- Old Barag Banner Center for Disease Control and Prevention, Hulunbuir, China
| | - Jian-Bo Wang
- Hulunbuir Center for Disease Control and Prevention, Hulunbuir, China
| | - Tongqing An
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Xinyi Huang
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - John-Sebastian Eden
- Centre for Virus Research, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Jun Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Deyin Guo
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, China
| | - Guodong Liang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xin Jin
- BGI Research, Shenzhen, China
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Bo Li
- Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China.
- Ministry of Education Key Laboratory for Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, China.
| | - Daxi Wang
- BGI Research, Shenzhen, China.
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen, China.
| | - Junhua Li
- BGI Research, Shenzhen, China.
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen, China.
| | - Wei-Chen Wu
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China.
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China.
| | - Mang Shi
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China.
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China.
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11
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Ullah Khan N, Sadiq A, Khan J, Basharat N, Hassan ZU, Ali I, Shah TA, Bourhia M, Bin Jardan YA, Wondmie GF. Molecular characterization of plasma virome of hepatocellular carcinoma (HCC) patients. AMB Express 2024; 14:46. [PMID: 38664337 PMCID: PMC11045709 DOI: 10.1186/s13568-024-01696-2] [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: 01/23/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
Hepatocellular carcinoma (HCC) stands as the most common cancer type, arising from various causes, and responsible for a substantial number of cancer-related fatalities. Recent advancements in viral metagenomics have empowered scientists to delve into the intricate diversity of the virosphere, viral evolution, interactions between viruses and their hosts, and the identification of viral causes behind disease outbreaks, the development of specific symptoms, and their potential role in altering the host's physiology. The present study had the objective of "Molecular Characterization of HBV, HCV, anelloviruses, CMV, SENV-D, SENV-H, HEV, and HPV viruses among individuals suffering from HCC." A total of 381 HCC patients contributed 10 cc of blood each for this study. The research encompassed the assessment of tumor markers, followed by molecular characterization of HBV, HCV, Anelloviruses (TTV, TTMV, and TTMDV), SENV-H and SENV-D viruses, HEV, CMV, and HPV, as well as histopathological examinations. The outcomes of this study revealed that majority of the HCC patients 72.4% (276/381) were male as compared to females. HCV infection, at 76.4% (291 out of 381), exhibited a significant association (p < 0.05) with HCC. Most patients displayed singular lesions in the liver, with Child Pugh Score Type B being the predominant finding in 45.2% of cases. Plasma virome analysis indicated the prevalence of TTMDV (75%), followed by TTMV (70%) and TTV (42.1%) among anelloviruses in HCC patients. Similarly, SENV-H (52%) was followed by SENV-D (20%), with co-infections at 15%. The presence of CMV and HEV among the HCC patients was recorded 5% each however 3.5% of the patients showed the presence of HPV. In conclusion, this study underscores that HCC patients serve as reservoirs for various pathogenic and non-pathogenic viruses, potentially contributing to the development, progression, and severity of the disease.
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Affiliation(s)
- Niamat Ullah Khan
- Molecular Virology Laboratory, Department of Biosciences, COMSATS University, Islamabad, Pakistan
| | - Asma Sadiq
- Department of Microbiology, University of Jhang, Punjab, Pakistan
| | - Jadoon Khan
- Molecular Virology Laboratory, Department of Biosciences, COMSATS University, Islamabad, Pakistan.
- Department of Allied Health Sciences, Iqra University, Chak Shahzad Campus, Islamabad, Pakistan.
| | - Nosheen Basharat
- Department of Microbiology, University of Jhang, Punjab, Pakistan
| | - Zulfiqar Ul Hassan
- Department of Allied Health Sciences, Iqra University, Chak Shahzad Campus, Islamabad, Pakistan
| | - Ijaz Ali
- Molecular Virology Laboratory, Department of Biosciences, COMSATS University, Islamabad, Pakistan
- Center for Applied Mathematics and Bioinformatics (CAMB), Gulf University for Science and Technology, West Mishref, Kuwait
| | - Tawaf Ali Shah
- College of Agriculture Engineering and Food Science, Shandong University of Technology, Zibo, 255000, China
| | - Mohammed Bourhia
- Laboratory of Biotechnology and Natural Resources Valorization, Faculty of Sciences, Ibn Zohr University, Agadir, 80060, Morocco.
| | - Yousef A Bin Jardan
- Department of Pharmaceutics, College of Pharmacy, King Saud University, P.O. Box 11451, Riyadh, Saudi Arabia
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12
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Waller SJ, Egan E, Crow S, Charsley A, Lokman PM, Williams EK, Holmes EC, Geoghegan JL. Host and geography impact virus diversity in New Zealand's longfin and shortfin eels. Arch Virol 2024; 169:85. [PMID: 38546898 PMCID: PMC10978610 DOI: 10.1007/s00705-024-06019-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/17/2024] [Indexed: 04/01/2024]
Abstract
The fishing and aquaculture industry is vital for global food security, yet viral diseases can result in mass fish die-off events. Determining the viromes of traditionally understudied species, such as fish, enhances our understanding of the global virosphere and the factors that influence virome composition and disease emergence. Very little is known about the viruses present in New Zealand's native fish species, including the shortfin eel (Anguilla australis) and the longfin eel (Anguilla dieffenbachii), both of which are fished culturally by Māori (the indigenous population of New Zealand) and commercially. Through a total RNA metatranscriptomic analysis of longfin and shortfin eels across three different geographic locations in the South Island of New Zealand, we aimed to determine whether viruses had jumped between the two eel species and whether eel virome composition was impacted by life stage, species, and geographic location. We identified nine viral species spanning eight different families, thereby enhancing our understanding of eel virus diversity in New Zealand and the host range of these viral families. Viruses of the family Flaviviridae (genus Hepacivirus) were widespread and found in both longfin and shortfin eels, indicative of cross-species transmission or virus-host co-divergence. Notably, both host specificity and geographic location appeared to influence eel virome composition, highlighting the complex interaction between viruses, hosts, and their ecosystems. This study broadens our understanding of viromes in aquatic hosts and highlights the importance of gaining baseline knowledge of fish viral abundance and diversity, particularly in aquatic species that are facing population declines.
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Affiliation(s)
- Stephanie J Waller
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Eimear Egan
- National Institute of Water and Atmospheric Research, Auckland, 1010, New Zealand
| | - Shannan Crow
- National Institute of Water and Atmospheric Research, Auckland, 1010, New Zealand
| | - Anthony Charsley
- National Institute of Water and Atmospheric Research, Auckland, 1010, New Zealand
| | - P Mark Lokman
- Department of Zoology, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand
| | - Erica K Williams
- National Institute of Water and Atmospheric Research, Auckland, 1010, New Zealand
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Jemma L Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand.
- Institute of Environmental Science and Research, Wellington, New Zealand.
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13
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Ji J, Li C, Hu T, Tian Z, Li J, Xu L, Zhou H, Holmes EC, Shi W. Diverse RNA viruses in the venom-related microenvironment of different animal phyla. Virus Evol 2024; 10:veae024. [PMID: 38827419 PMCID: PMC11141596 DOI: 10.1093/ve/veae024] [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: 08/08/2023] [Revised: 02/17/2024] [Accepted: 02/28/2024] [Indexed: 06/04/2024] Open
Abstract
Venom is known as the source of natural antimicrobial products. Previous studies have largely focused on the expression of venom-related genes and the biochemical components of venom. With the advent of metagenomic sequencing, many more microorganisms, especially viruses, have been identified in highly diverse environments. Herein, we investigated the RNA virome in the venom-related microenvironment through analysis of a large volume of venom-related RNA-sequencing data mined from public databases. From this, we identified viral sequences belonging to thirty-six different viruses, of which twenty-two were classified as 'novel' as they exhibited less than 90 per cent amino acid identity to known viruses in the RNA-dependent RNA polymerase. Most of these novel viruses possessed genome structures similar to their closest relatives, with specific alterations in some cases. Phylogenetic analyses revealed that these viruses belonged to at least twenty-two viral families or unclassified groups, some of which were highly divergent from known taxa. Although further analysis failed to find venom-specific viruses, some viruses seemingly had much higher abundance in the venom-related microenvironment than in other tissues. In sum, our study provides insights into the RNA virome of the venom-related microenvironment from diverse animal phyla.
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Affiliation(s)
- Jingkai Ji
- School of Life Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, No. 619 Changcheng Road, Taian 271000, China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, No. 2 Yingshengdonglu, Taian 271000, China
| | - Cixiu Li
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, No. 2 Yingshengdonglu, Taian 271000, China
- School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, No. 6699 Qingdao Road, Ji’nan 250117, China
| | - Tao Hu
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, No. 2 Yingshengdonglu, Taian 271000, China
| | - Zhongshuai Tian
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, No. 2 Yingshengdonglu, Taian 271000, China
- School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, No. 6699 Qingdao Road, Ji’nan 250117, China
| | - Juan Li
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, No. 2 Yingshengdonglu, Taian 271000, China
- School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, No. 6699 Qingdao Road, Ji’nan 250117, China
| | - Lin Xu
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, No. 2 Yingshengdonglu, Taian 271000, China
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, No. 6699 Qingdao Road, Ji’nan 250117, China
| | - Hong Zhou
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, No. 2 Yingshengdonglu, Taian 271000, China
- School of Clinical and Basic Medical Sciences, 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, Australia
- School of Life & Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Weifeng Shi
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, No. 2 Yingshengdonglu, Taian 271000, China
- 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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14
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Skene KR. Systems theory, thermodynamics and life: Integrated thinking across ecology, organization and biological evolution. Biosystems 2024; 236:105123. [PMID: 38244715 DOI: 10.1016/j.biosystems.2024.105123] [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: 12/02/2023] [Revised: 01/15/2024] [Accepted: 01/15/2024] [Indexed: 01/22/2024]
Abstract
In this paper we explore the relevance and integration of system theory and thermodynamics in terms of the Earth system. It is proposed that together, these fields explain the evolution, organization, functionality and directionality of life on Earth. We begin by summarizing historical and current thinking on the definition of life itself. We then investigate the evidence for a single unit of life. Given that any definition of life and its levels of organization are intertwined, we explore how the Earth system is structured and functions from an energetic perspective, by outlining relevant thermodynamic theory relating to molecular, metabolic, cellular, individual, population, species, ecosystem and biome organization. We next investigate the fundamental relationships between systems theory and thermodynamics in terms of the Earth system, examining the key characteristics of self-assembly, self-organization (including autonomy), emergence, non-linearity, feedback and sub-optimality. Finally, we examine the relevance of systems theory and thermodynamics with reference to two specific aspects: the tempo and directionality of evolution and the directional and predictable process of ecological succession. We discuss the importance of the entropic drive in understanding altruism, multicellularity, mutualistic and antagonistic relationships and how maximum entropy production theory may explain patterns thought to evidence the intermediate disturbance hypothesis.
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Affiliation(s)
- Keith R Skene
- Biosphere Research Institute, Angus, United Kingdom.
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15
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Nweze JE, Schweichhart JS, Angel R. Viral communities in millipede guts: Insights into the diversity and potential role in modulating the microbiome. Environ Microbiol 2024; 26:e16586. [PMID: 38356108 DOI: 10.1111/1462-2920.16586] [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: 09/08/2023] [Accepted: 01/22/2024] [Indexed: 02/16/2024]
Abstract
Millipedes are important detritivores harbouring a diverse microbiome. Previous research focused on bacterial and archaeal diversity, while the virome remained neglected. We elucidated the DNA and RNA viral diversity in the hindguts of two model millipede species with distinct microbiomes: the tropical Epibolus pulchripes (methanogenic, dominated by Bacillota) and the temperate Glomeris connexa (non-methanogenic, dominated by Pseudomonadota). Based on metagenomic and metatranscriptomic assembled viral genomes, the viral communities differed markedly and preferentially infected the most abundant prokaryotic taxa. The majority of DNA viruses were Caudoviricetes (dsDNA), Cirlivirales (ssDNA) and Microviridae (ssDNA), while RNA viruses consisted of Leviviricetes (ssRNA), Potyviridae (ssRNA) and Eukaryotic viruses. A high abundance of subtypes I-C, I-B and II-C CRISPR-Cas systems was found, primarily from Pseudomonadota, Bacteroidota and Bacillota. In addition, auxiliary metabolic genes that modulate chitin degradation, vitamins and amino acid biosynthesis and sulphur metabolism were also detected. Lastly, we found low virus-to-microbe-ratios and a prevalence of lysogenic viruses, supporting a Piggyback-the-Winner dynamic in both hosts.
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Affiliation(s)
- Julius Eyiuche Nweze
- Institute of Soil Biology and Biogeochemistry, Biology Centre CAS, České Budějovice, Czechia
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia in České Budějovice, České Budějovice, Czechia
| | - Johannes Sergej Schweichhart
- Institute of Soil Biology and Biogeochemistry, Biology Centre CAS, České Budějovice, Czechia
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia in České Budějovice, České Budějovice, Czechia
| | - Roey Angel
- Institute of Soil Biology and Biogeochemistry, Biology Centre CAS, České Budějovice, Czechia
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16
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Kovalev MA, Gladysh NS, Bogdanova AS, Bolsheva NL, Popchenko MI, Kudryavtseva AV. Editing Metabolism, Sex, and Microbiome: How Can We Help Poplar Resist Pathogens? Int J Mol Sci 2024; 25:1308. [PMID: 38279306 PMCID: PMC10816636 DOI: 10.3390/ijms25021308] [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: 11/18/2023] [Revised: 01/14/2024] [Accepted: 01/19/2024] [Indexed: 01/28/2024] Open
Abstract
Poplar (Populus) is a genus of woody plants of great economic value. Due to the growing economic importance of poplar, there is a need to ensure its stable growth by increasing its resistance to pathogens. Genetic engineering can create organisms with improved traits faster than traditional methods, and with the development of CRISPR/Cas-based genome editing systems, scientists have a new highly effective tool for creating valuable genotypes. In this review, we summarize the latest research data on poplar diseases, the biology of their pathogens and how these plants resist pathogens. In the final section, we propose to plant male or mixed poplar populations; consider the genes of the MLO group, transcription factors of the WRKY and MYB families and defensive proteins BbChit1, LJAMP2, MsrA2 and PtDef as the most promising targets for genetic engineering; and also pay attention to the possibility of microbiome engineering.
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Affiliation(s)
- Maxim A. Kovalev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (M.A.K.); (N.S.G.); (A.S.B.); (N.L.B.); (M.I.P.)
- Department of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Natalya S. Gladysh
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (M.A.K.); (N.S.G.); (A.S.B.); (N.L.B.); (M.I.P.)
| | - Alina S. Bogdanova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (M.A.K.); (N.S.G.); (A.S.B.); (N.L.B.); (M.I.P.)
- Institute of Agrobiotechnology, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, 127434 Moscow, Russia
| | - Nadezhda L. Bolsheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (M.A.K.); (N.S.G.); (A.S.B.); (N.L.B.); (M.I.P.)
| | - Mikhail I. Popchenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (M.A.K.); (N.S.G.); (A.S.B.); (N.L.B.); (M.I.P.)
| | - Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (M.A.K.); (N.S.G.); (A.S.B.); (N.L.B.); (M.I.P.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia
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Wang H, Chao S, Yan Q, Zhang S, Chen G, Mao C, Hu Y, Yu F, Wang S, Lv L, Yang B, He J, Zhang S, Zhang L, Simmonds P, Feng G. Genetic diversity of RNA viruses infecting invertebrate pests of rice. SCIENCE CHINA. LIFE SCIENCES 2024; 67:175-187. [PMID: 37946067 DOI: 10.1007/s11427-023-2398-y] [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: 05/19/2023] [Accepted: 06/26/2023] [Indexed: 11/12/2023]
Abstract
Invertebrate species are a natural reservoir of viral genetic diversity, and invertebrate pests are widely distributed in crop fields. However, information on viruses infecting invertebrate pests of crops is limited. In this report, we describe the deep metatranscriptomic sequencing of 88 invertebrate samples covering all major invertebrate pests in rice fields. We identified 296 new RNA viruses and 13 known RNA viruses. These viruses clustered within 31 families, with many highly divergent viruses constituting potentially new families and genera. Of the identified viruses, 13 RNA viruses clustered within the Fiersviridae family of bacteriophages, and 48 RNA viruses clustered within families and genera of mycoviruses. We detected known rice viruses in novel invertebrate hosts at high abundances. Furthermore, some novel RNA viruses have genome structures closely matching to known plant viruses and clustered within genera of several plant virus species. Forty-five potential insect pathogenic RNA viruses were detected in invertebrate species. Our analysis revealed that host taxonomy plays a major role and geographical location plays an important role in structuring viral diversity. Cross-species transmission of RNA viruses was detected between invertebrate hosts. Newly identified viral genomes showed extensive variation for invertebrate viral families or genera. Together, the large-scale metatranscriptomic analysis greatly expands our understanding of RNA viruses in rice invertebrate species, the results provide valuable information for developing efficient strategies to manage insect pests and virus-mediated crop diseases.
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Affiliation(s)
- Haoran Wang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 311400, China
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shufen Chao
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 311400, China
| | - Qing Yan
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 311400, China
| | - Shu Zhang
- Institute of Plant Protection & Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Guoqing Chen
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 311400, China
| | - Chonghui Mao
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 311400, China
| | - Yang Hu
- Institute of Plant Protection, Guizhou Academy of Agricultural Sciences, Guiyang, 550000, China
| | - Fengquan Yu
- Institute of Plant Protection, Liaoning Academy of Agricultural Sciences, Shenyang, 110161, China
| | - Shuo Wang
- Sanya Agricultural Technology Extension and Service Centre, Sanya, 572000, China
| | - Liang Lv
- Institute of Plant Protection & Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Baojun Yang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 311400, China
| | - Jiachun He
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 311400, China
| | - Songbai Zhang
- College of Agriculture, Yangtze University, Jingzhou, 434000, China
| | - Liangsheng Zhang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310012, China
| | - Peter Simmonds
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, OX1 3SY, UK
| | - Guozhong Feng
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 311400, China.
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18
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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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19
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Zhang W, Li R, Li S, Li SY, Niu J, Wang JJ. RNA virus diversity in three parasitoid wasps of tephritid flies: insights from novel and known species. Microbiol Spectr 2023; 11:e0313923. [PMID: 37930041 PMCID: PMC10714968 DOI: 10.1128/spectrum.03139-23] [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: 08/20/2023] [Accepted: 09/29/2023] [Indexed: 11/07/2023] Open
Abstract
IMPORTANCE Parasitoid wasp populations have developed persistent beneficial symbiotic relationships with several viruses through repeated evolution. However, there have been limited reports on RNA viruses in parasitoid wasps of tephritid flies, a significant pest group affecting fruits and vegetables. This study explores the diversity of RNA viruses in three parasitoid wasps of tephritid flies and highlights the potential biological significance of specific viruses in Diachasmimorpha longicaudata. These findings have important implications for the development of sustainable pest management strategies and the enhancement of artificial rearing techniques for parasitoid wasps.
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Affiliation(s)
- Wei Zhang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Rong Li
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
| | - Shuai Li
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
| | - Shao-Yang Li
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
| | - Jinzhi Niu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Jin-Jun Wang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China
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20
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Fan Y, Hou Y, Li Q, Dian Z, Wang B, Xia X. RNA virus diversity in rodents. Arch Microbiol 2023; 206:9. [PMID: 38038743 DOI: 10.1007/s00203-023-03732-4] [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: 09/07/2023] [Revised: 11/01/2023] [Accepted: 11/02/2023] [Indexed: 12/02/2023]
Abstract
Many zoonotic disease emergencies are associated with RNA viruses in rodents that substantially impact public health. With the widespread application of meta-genomics and meta-transcriptomics for virus discovery over the last decade, viral sequences deposited in public databases have expanded rapidly, and the number of novel viruses discovered in rodents has increased. As important reservoirs of zoonotic viruses, rodents have attracted increasing attention for the risk of potential spillover of rodent-borne viruses. However, knowledge of rodent viral diversity and the major factors contributing to the risk of zoonotic epidemic outbreaks remains limited. Therefore, this study analyzes the diversity and composition of rodent RNA viruses using virus records from the Database of Rodent-associated Viruses (DRodVir/ZOVER), which covers the published literatures and records in GenBank database, reviews the main rodent RNA virus-induced human infectious diseases, and discusses potential challenges in this field.
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Affiliation(s)
- Yayu Fan
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, 650500, People's Republic of China
| | - Yutong Hou
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, 650500, People's Republic of China
| | - Qian Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, 650500, People's Republic of China
| | - Ziqin Dian
- Department of Clinical Laboratory, The First People's Hospital of Yunnan Province, Kunming, Yunnan, 650032, People's Republic of China
| | - Binghui Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, 650500, People's Republic of China.
| | - Xueshan Xia
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, 650500, People's Republic of China.
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21
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Rozo-Lopez P, Brewer W, Käfer S, Martin MM, Parker BJ. Untangling an insect's virome from its endogenous viral elements. BMC Genomics 2023; 24:636. [PMID: 37875824 PMCID: PMC10594914 DOI: 10.1186/s12864-023-09737-z] [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: 07/06/2023] [Accepted: 10/12/2023] [Indexed: 10/26/2023] Open
Abstract
BACKGROUND Insects are an important reservoir of viral biodiversity, but the vast majority of viruses associated with insects have not been discovered. Recent studies have employed high-throughput RNA sequencing, which has led to rapid advances in our understanding of insect viral diversity. However, insect genomes frequently contain transcribed endogenous viral elements (EVEs) with significant homology to exogenous viruses, complicating the use of RNAseq for viral discovery. METHODS In this study, we used a multi-pronged sequencing approach to study the virome of an important agricultural pest and prolific vector of plant pathogens, the potato aphid Macrosiphum euphorbiae. We first used rRNA-depleted RNAseq to characterize the microbes found in individual insects. We then used PCR screening to measure the frequency of two heritable viruses in a local aphid population. Lastly, we generated a quality draft genome assembly for M. euphorbiae using Illumina-corrected Nanopore sequencing to identify transcriptionally active EVEs in the host genome. RESULTS We found reads from two insect-specific viruses (a Flavivirus and an Ambidensovirus) in our RNAseq data, as well as a parasitoid virus (Bracovirus), a plant pathogenic virus (Tombusvirus), and two phages (Acinetobacter and APSE). However, our genome assembly showed that part of the 'virome' of this insect can be attributed to EVEs in the host genome. CONCLUSION Our work shows that EVEs have led to the misidentification of aphid viruses from RNAseq data, and we argue that this is a widespread challenge for the study of viral diversity in insects.
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Affiliation(s)
- Paula Rozo-Lopez
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37916, USA.
| | - William Brewer
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37916, USA
| | - Simon Käfer
- Institut Für Biologie Und Umweltwissenschaften, Carl Von Ossietzky Universität Oldenburg, 26129, Oldenburg, Germany
| | - McKayla M Martin
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37916, USA
| | - Benjamin J Parker
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37916, USA.
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22
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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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23
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Le Lay C, Stott MB, Shi M, Sadiq S, Holmes EC. A metatranscriptomic analysis of geothermal hot springs reveals diverse RNA viruses including the phylum Lenarviricota. Virology 2023; 587:109873. [PMID: 37647722 DOI: 10.1016/j.virol.2023.109873] [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: 05/07/2023] [Revised: 08/08/2023] [Accepted: 08/21/2023] [Indexed: 09/01/2023]
Abstract
Little is known about the diversity of RNA viruses in geothermal systems. We generated total RNA sequencing data from two hot springs in Kuirau Park, Rotorua, New Zealand. In one data set, from a 71.8 °C pool, we observed a microbial community that was 98.5% archaea. The second data set, representing a cooler 36.8 °C geothermal hot spring, had a more diverse microbial profile: 58% bacteria, 34.5% eukaryotes and 7.5% archaea. Within this latter pool, we detected sequences likely representing 23 RNA viruses from the families Astroviridae, Tombusviridae, Polycipiviridae, Discistroviridae, Partitiviridae, and Mitoviridae, as well as from unclassified clades of the orders Tolivirales, Picornavirales, and Ghabrivirales. Most viruses had uncertain host associations. Of particular note, we identified four novel RNA viruses from the phylum Lenarviricota, commonly associated with bacteria and fungi, that occupied a divergent phylogenetic position within unclassified clades and may represent an ancient order-level taxon of unknown host association.
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Affiliation(s)
- Callum Le Lay
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Matthew B Stott
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Mang Shi
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Sabrina Sadiq
- Sydney Institute for Infectious Diseases, School of Medical 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, NSW, 2006, Australia.
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24
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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: 0] [Impact Index Per Article: 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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Andika IB, Tian M, Bian R, Cao X, Luo M, Kondo H, Sun L. Cross-Kingdom Interactions Between Plant and Fungal Viruses. Annu Rev Virol 2023; 10:119-138. [PMID: 37406341 DOI: 10.1146/annurev-virology-111821-122539] [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: 07/07/2023]
Abstract
The large genetic and structural divergences between plants and fungi may hinder the transmission of viruses between these two kingdoms to some extent. However, recent accumulating evidence from virus phylogenetic analyses and the discovery of naturally occurring virus cross-infection suggest the occurrence of past and current transmissions of viruses between plants and plant-associated fungi. Moreover, artificial virus inoculation experiments showed that diverse plant viruses can multiply in fungi and vice versa. Thus, virus cross-infection between plants and fungi may play an important role in the spread, emergence, and evolution of both plant and fungal viruses and facilitate the interaction between them. In this review, we summarize current knowledge related to cross-kingdom virus infection in plants and fungi and further discuss the relevance of this new virological topic in the context of understanding virus spread and transmission in nature as well as developing control strategies for crop plant diseases.
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Affiliation(s)
- Ida Bagus Andika
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China;
| | - Mengyuan Tian
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China;
| | - Ruiling Bian
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China;
| | - Xinran Cao
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China;
| | - Ming Luo
- College of Agronomy, Xinjiang Agricultural University, Urumqi, China
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan;
| | - Liying Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China;
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan;
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26
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Pan YF, Zhao H, Gou QY, Shi PB, Tian JH, Feng Y, Li K, Yang WH, Wu D, Tang G, Zhang B, Ren Z, Peng S, Luo GY, Le SJ, Xin GY, Wang J, Hou X, Peng MW, Kong JB, Chen XX, Yang CH, Mei SQ, Liao YQ, Cheng JX, Wang J, Chaolemen, Wu YH, Wang JB, An T, Huang X, Eden JS, Li J, Guo D, Liang G, Jin X, Holmes EC, Li B, Wang D, Li J, Wu WC, Shi M. Metagenomic analysis of individual mosquitos reveals the ecology of insect viruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.28.555221. [PMID: 37732272 PMCID: PMC10508733 DOI: 10.1101/2023.08.28.555221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Mosquito transmitted viruses are responsible for an increasing burden of human disease. Despite this, little is known about the diversity and ecology of viruses within individual mosquito hosts. Using a meta-transcriptomic approach, we analysed the virome of 2,438 individual mosquitos (79 species), spanning ~4000 km along latitudes and longitudes in China. From these data we identified 393 core viral species associated with mosquitos, including seven (putative) arbovirus species. We identified potential species and geographic hotspots of viral richness and arbovirus occurrence, and demonstrated that host phylogeny had a strong impact on the composition of individual mosquito viromes. Our data revealed a large number of viruses shared among mosquito species or genera, expanding our knowledge of host specificity of insect-associated viruses. We also detected multiple virus species that were widespread throughout the country, possibly facilitated by long-distance mosquito migrations. Together, our results greatly expand the known mosquito virome, linked the viral diversity at the scale of individual insects to that at a country-wide scale, and offered unique insights into the ecology of viruses of insect vectors.
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Affiliation(s)
- Yuan-fei Pan
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Hailong Zhao
- BGI Research, Shenzhen 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen 518083, China
| | - Qin-yu Gou
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Pei-bo Shi
- BGI Research, Shenzhen 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen 518083, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
| | - Jun-hua Tian
- Wuhan Center for Disease Control and Prevention, Wuhan 430024, China
| | - Yun Feng
- Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali 671099, China
| | - Kun Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Wei-hong Yang
- Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali 671099, China
| | - De Wu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou 511430, China
| | - Guangpeng Tang
- Guizhou Center for Disease Control and Prevention, Guiyang 550004, China
| | - Bing Zhang
- Xinjiang Key Laboratory of Molecular Biology for Endemic Diseases, School of Basic Medical Sciences Xinjiang Medical University, Urumqi 830011, China
| | - Zirui Ren
- BGI Research, Shenzhen 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen 518083, China
| | - Shiqin Peng
- BGI Research, Shenzhen 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen 518083, China
| | - Geng-yan Luo
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Shi-jia Le
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Gen-yang Xin
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Jing Wang
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Xin Hou
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Min-wu Peng
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Jian-bin Kong
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Xin-xin Chen
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Chun-hui Yang
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Shi-qiang Mei
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Yu-qi Liao
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Jing-xia Cheng
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Juan Wang
- Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali 671099, China
| | - Chaolemen
- Old Barag Banner Center for Disease Control and Prevention, Hulunbuir 021500, China
| | - Yu-hui Wu
- Old Barag Banner Center for Disease Control and Prevention, Hulunbuir 021500, China
| | - Jian-bo Wang
- Hulunbuir Center for Disease Control and Prevention, Hulunbuir 021008, China
| | - Tongqing An
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Xinyi Huang
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - John-Sebastian Eden
- Centre for Virus Research, Westmead Institute for Medical Research, Westmead, NSW 2145, Australia
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jun Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Deyin Guo
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou 510000, China
| | - Guodong Liang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Xin Jin
- BGI Research, Shenzhen 518083, China
| | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Bo Li
- Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
| | - Daxi Wang
- BGI Research, Shenzhen 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen 518083, China
| | - Junhua Li
- BGI Research, Shenzhen 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen 518083, China
| | - Wei-chen Wu
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Mang Shi
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
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Raghwani J, Faust CL, François S, Nguyen D, Marsh K, Raulo A, Hill SC, Parag KV, Simmonds P, Knowles SCL, Pybus OG. Seasonal dynamics of the wild rodent faecal virome. Mol Ecol 2023; 32:4763-4776. [PMID: 36367339 PMCID: PMC7614976 DOI: 10.1111/mec.16778] [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: 04/21/2022] [Revised: 09/23/2022] [Accepted: 11/03/2022] [Indexed: 11/13/2022]
Abstract
Viral discovery studies in wild animals often rely on cross-sectional surveys at a single time point. As a result, our understanding of the temporal stability of wild animal viromes remains poorly resolved. While studies of single host-virus systems indicate that host and environmental factors influence seasonal virus transmission dynamics, comparable insights for whole viral communities in multiple hosts are lacking. Utilizing noninvasive faecal samples from a long-term wild rodent study, we characterized viral communities of three common European rodent species (Apodemus sylvaticus, A. flavicollis and Myodes glareolus) living in temperate woodland over a single year. Our findings indicate that a substantial fraction of the rodent virome is seasonally transient and associated with vertebrate or bacteria hosts. Further analyses of one of the most common virus families, Picornaviridae, show pronounced temporal changes in viral richness and evenness, which were associated with concurrent and up to ~3-month lags in host density, ambient temperature, rainfall and humidity, suggesting complex feedbacks from the host and environmental factors on virus transmission and shedding in seasonal habitats. Overall, this study emphasizes the importance of understanding the seasonal dynamics of wild animal viromes in order to better predict and mitigate zoonotic risks.
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Affiliation(s)
- Jayna Raghwani
- Department of BiologyUniversity of OxfordOxfordUK
- Department of Pathobiology and Population SciencesThe Royal Veterinary CollegeLondonUK
| | - Christina L. Faust
- Institute of Biodiversity, Animal Health, and Comparative MedicineUniversity of GlasgowGlasgowUK
| | | | - Dung Nguyen
- Nuffield Department of MedicineUniversity of OxfordOxfordUK
| | - Kirsty Marsh
- School of BiosciencesUniversity of ExeterExeterUK
| | - Aura Raulo
- Department of BiologyUniversity of OxfordOxfordUK
- University of TurkuTurkuFinland
| | - Sarah C. Hill
- Department of Pathobiology and Population SciencesThe Royal Veterinary CollegeLondonUK
| | | | - Peter Simmonds
- Nuffield Department of MedicineUniversity of OxfordOxfordUK
| | | | - Oliver G. Pybus
- Department of BiologyUniversity of OxfordOxfordUK
- Department of Pathobiology and Population SciencesThe Royal Veterinary CollegeLondonUK
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28
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Le Lay C, Hamm JN, Williams TJ, Shi M, Cavicchioli R, Holmes EC. Viral community composition of hypersaline lakes. Virus Evol 2023; 9:vead057. [PMID: 37692898 PMCID: PMC10492444 DOI: 10.1093/ve/vead057] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/03/2023] [Accepted: 08/29/2023] [Indexed: 09/12/2023] Open
Abstract
Despite their widespread distribution and remarkable antiquity no RNA viruses definitively associated with the domain Archaea have been identified. In contrast, 17 families of DNA viruses are known to infect archaea. In an attempt to uncover more of the elusive archaeal virosphere, we investigated the metatranscriptomes of hypersaline lakes that are a rich source of archaea. We sequenced RNA extracted from water filter samples of Lake Tyrrell (Victoria, Australia) and cultures seeded from four lakes in Antarctica. To identify highly divergent viruses in these data, we employed a variety of search tools, including Hidden Markov models (HMMs) and position-specific scoring matrices (PSSMs). From this, we identified 12 highly divergent, RNA virus-like candidate sequences from the virus phyla Artverviricota, Duplornaviricota, Kitrinoviricota, Negarnaviricota, and Pisuviricota, including those with similarity to the RNA-dependent RNA polymerase (RdRp). An additional analysis with an artificial intelligence (AI)-based approach that utilises both sequence and structural information identified seven putative and highly divergent RdRp sequences of uncertain phylogenetic position. A sequence matching the Pisuviricota from Deep Lake in Antarctica had the strongest RNA virus signal. Analyses of the dinucleotide representation of the virus-like candidates in comparison to that of potential host species were in some cases compatible with an association to archaeal or bacterial hosts. Notably, however, the use of archaeal CRISPR spacers as a BLAST database failed to detect any RNA viruses. We also described DNA viruses from the families Pleolipoviridae, Sphaerolipoviridae, Halspiviridae, and the class Caudoviricetes. Although we were unable to provide definitive evidence the existence of an RNA virus of archaea in these hypersaline lakes, this study lays the foundations for further investigations of highly divergent RNA viruses in natural environments.
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Affiliation(s)
- Callum Le Lay
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | | | - Timothy J Williams
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Mang Shi
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, P.O. Box 59, Den Burg NL-1790 AB, The Netherlands
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29
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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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30
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Zhang ZF, Liu LR, Pan YP, Pan J, Li M. Long-read assembled metagenomic approaches improve our understanding on metabolic potentials of microbial community in mangrove sediments. MICROBIOME 2023; 11:188. [PMID: 37612768 PMCID: PMC10464287 DOI: 10.1186/s40168-023-01630-x] [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: 04/15/2023] [Accepted: 07/21/2023] [Indexed: 08/25/2023]
Abstract
BACKGROUND Mangrove wetlands are coastal ecosystems with important ecological features and provide habitats for diverse microorganisms with key roles in nutrient and biogeochemical cycling. However, the overall metabolic potentials and ecological roles of microbial community in mangrove sediment are remained unanswered. In current study, the microbial and metabolic profiles of prokaryotic and fungal communities in mangrove sediments were investigated using metagenomic analysis based on PacBio single-molecule real time (SMRT) and Illumina sequencing techniques. RESULTS Comparing to Illumina short reads, the incorporation of PacBio long reads significantly contributed to more contiguous assemblies, yielded more than doubled high-quality metagenome-assembled genomes (MAGs), and improved the novelty of the MAGs. Further metabolic reconstruction for recovered MAGs showed that prokaryotes potentially played an essential role in carbon cycling in mangrove sediment, displaying versatile metabolic potential for degrading organic carbons, fermentation, autotrophy, and carbon fixation. Mangrove fungi also functioned as a player in carbon cycling, potentially involved in the degradation of various carbohydrate and peptide substrates. Notably, a new candidate bacterial phylum named as Candidatus Cosmopoliota with a ubiquitous distribution is proposed. Genomic analysis revealed that this new phylum is capable of utilizing various types of organic substrates, anaerobic fermentation, and carbon fixation with the Wood-Ljungdahl (WL) pathway and the reverse tricarboxylic acid (rTCA) cycle. CONCLUSIONS The study not only highlights the advantages of HiSeq-PacBio Hybrid assembly for a more complete profiling of environmental microbiomes but also expands our understanding of the microbial diversity and potential roles of distinct microbial groups in biogeochemical cycling in mangrove sediment. Video Abstract.
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Affiliation(s)
- Zhi-Feng Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Present Address: Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Li-Rui Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Yue-Ping Pan
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Jie Pan
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China.
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China.
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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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da Paz TYB, Hernández LHA, Silva SPD, Silva FSD, Barros BCVD, Casseb LMN, Guimarães RJDPSE, Vasconcelos PFDC, Cruz ACR. Novel Rodent Arterivirus Detected in the Brazilian Amazon. Viruses 2023; 15:v15051150. [PMID: 37243236 DOI: 10.3390/v15051150] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/19/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023] Open
Abstract
As part of a continuous effort to investigate the viral communities associated with wild mammals at the human-animal interface in an Amazonian metropolitan region, this study describes the detection of a novel rodent-borne arterivirus. A sample containing pooled organs of Oecomys paricola was submitted to RNA sequencing, and four sequences taxonomically assigned as related to the Arteriviridae family were recovered, corresponding to an almost complete genome of nearly 13 kb summed. In the phylogenetic analysis with the standard domains used for taxa demarcation in the family, the tentatively named Oecomys arterivirus 1 (OAV-1) was placed within the clade of rodent- and porcine-associated viruses, corresponding to the Variarterivirinae subfamily. The divergence analysis, based on the same amino acid alignment, corroborated the hypothesis that the virus may represent a new genus within the subfamily. These findings contribute to the expansion of the current knowledge about the diversity, host and geographical range of the viral family. Arterivirids are non-human pathogens and are usually species-specific, but the susceptibility of cell lines derived from different organisms should be conducted to confirm these statements for this proposed new genus in an initial attempt to assess its spillover potential.
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Affiliation(s)
- Thito Y Bezerra da Paz
- Parasite Biology in the Amazon Region Graduate Program, Pará State University, Belém 66087-670, Brazil
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, Brazil
| | - Leonardo H Almeida Hernández
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, Brazil
| | - Sandro Patroca da Silva
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, Brazil
| | - Fábio Silva da Silva
- Parasite Biology in the Amazon Region Graduate Program, Pará State University, Belém 66087-670, Brazil
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, Brazil
| | - Bruno C Veloso de Barros
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, Brazil
| | - Livia M Neves Casseb
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, Brazil
| | - Ricardo J de Paula Souza E Guimarães
- Geoprocessing Laboratory, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, Brazil
| | - Pedro F da Costa Vasconcelos
- Parasite Biology in the Amazon Region Graduate Program, Pará State University, Belém 66087-670, Brazil
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, Brazil
| | - Ana C Ribeiro Cruz
- Parasite Biology in the Amazon Region Graduate Program, Pará State University, Belém 66087-670, Brazil
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, Brazil
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Wilson A, Bogie B, Chaaban H, Burge K. The Nonbacterial Microbiome: Fungal and Viral Contributions to the Preterm Infant Gut in Health and Disease. Microorganisms 2023; 11:909. [PMID: 37110332 PMCID: PMC10144239 DOI: 10.3390/microorganisms11040909] [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: 03/03/2023] [Revised: 03/27/2023] [Accepted: 03/30/2023] [Indexed: 04/29/2023] Open
Abstract
The intestinal microbiome is frequently implicated in necrotizing enterocolitis (NEC) pathogenesis. While no particular organism has been associated with NEC development, a general reduction in bacterial diversity and increase in pathobiont abundance has been noted preceding disease onset. However, nearly all evaluations of the preterm infant microbiome focus exclusively on the bacterial constituents, completely ignoring any fungi, protozoa, archaea, and viruses present. The abundance, diversity, and function of these nonbacterial microbes within the preterm intestinal ecosystem are largely unknown. Here, we review findings on the role of fungi and viruses, including bacteriophages, in preterm intestinal development and neonatal intestinal inflammation, with potential roles in NEC pathogenesis yet to be determined. In addition, we highlight the importance of host and environmental influences, interkingdom interactions, and the role of human milk in shaping fungal and viral abundance, diversity, and function within the preterm intestinal ecosystem.
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Affiliation(s)
| | | | - Hala Chaaban
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Kathryn Burge
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
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Shakir S, Zaidi SSEA, Hashemi FSG, Nyirakanani C, Vanderschuren H. Harnessing plant viruses in the metagenomics era: from the development of infectious clones to applications. TRENDS IN PLANT SCIENCE 2023; 28:297-311. [PMID: 36379846 DOI: 10.1016/j.tplants.2022.10.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 10/17/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Recent metagenomic studies which focused on virus characterization in the entire plant environment have revealed a remarkable viral diversity in plants. The exponential discovery of viruses also requires the concomitant implementation of high-throughput methods to perform their functional characterization. Despite several limitations, the development of viral infectious clones remains a method of choice to understand virus biology, their role in the phytobiome, and plant resilience. Here, we review the latest approaches for efficient characterization of plant viruses and technical advances built on high-throughput sequencing and synthetic biology to streamline assembly of viral infectious clones. We then discuss the applications of plant viral vectors in fundamental and applied plant research as well as their technical and regulatory limitations, and we propose strategies for their safer field applications.
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Affiliation(s)
- Sara Shakir
- Plant Genetics and Rhizosphere Processes Laboratory, TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium.
| | - Syed Shan-E-Ali Zaidi
- Plant Genetics and Rhizosphere Processes Laboratory, TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Farahnaz Sadat Golestan Hashemi
- Plant Genetics and Rhizosphere Processes Laboratory, TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Chantal Nyirakanani
- Plant Genetics and Rhizosphere Processes Laboratory, TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium; Department of Crop Science, School of Agriculture, University of Rwanda, Musanze, Rwanda
| | - Hervé Vanderschuren
- Plant Genetics and Rhizosphere Processes Laboratory, TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium; Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, Biosystems Department, KU Leuven, Leuven, Belgium.
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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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Yang Z, Wang H, Yang S, Wang X, Shen Q, Ji L, Zeng J, Zhang W, Gong H, Shan T. Virome diversity of ticks feeding on domestic mammals in China. Virol Sin 2023; 38:208-221. [PMID: 36781125 PMCID: PMC10176445 DOI: 10.1016/j.virs.2023.02.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 02/08/2023] [Indexed: 02/13/2023] Open
Abstract
Ticks are considered the second most common pathogen vectors transmitting a broad range of vital human and veterinary viruses. From 2017 to 2018, 640 ticks were collected in eight different provinces in central and western China. Six species were detected, including H.longicornis, De.everestianus, Rh.microplus, Rh.turanicus, Rh.sanguineous, and Hy.asiaticum. Sixty-four viral metagenomic libraries were constructed on the MiSeq Illumina platform, resulting in 13.44 G (5.88 × 107) of 250-bp-end reads, in which 2,437,941 are viral reads. We found 27 nearly complete genome sequences, including 16 genome sequences encoding entire protein-coding regions (lack of 3' or 5' end non-coding regions) and complete viral genomes, distributed in the arboviral family (Chuviridae, Rhabdoviridae, Nairoviridae, Phenuiviridae, Flaviviridae, Iflaviridae) as well as Parvoviridae and Polyomaviridae that cause disease in mammals and even humans. In addition, 13 virus sequences found in Chuviridae, Nairoviridae, Flaviviridae, Iflaviridae, Hepeviridae, Parvoviridae, and Polyomaviridae were identified as belonging to a new virus species in the identified viral genera. Besides, an epidemiological survey shows a high prevalence (9.38% and 15.63%) of two viruses (Ovine Copiparvovirus and Bovine parvovirus 2) in the tick cohort.
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Affiliation(s)
- Zijun Yang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China; Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, China; Center of Clinical Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, 215006, China
| | - Hao Wang
- Department of Clinical Laboratory, Huai'an Hospital, Xuzhou Medical University, Huai'an, 223002, China
| | - Shixing Yang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Xiaochun Wang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Quan Shen
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Likai Ji
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Jian Zeng
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Wen Zhang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, China.
| | - Haiyan Gong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China.
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China.
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Sáez C, Pagán I. When plants are Trojan horses for viruses. THE NEW PHYTOLOGIST 2023; 237:1071-1073. [PMID: 36478567 PMCID: PMC10108265 DOI: 10.1111/nph.18571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
This article is a Commentary on Verhoeven et al. (2023), pp. 1146–1153.
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Affiliation(s)
- Cristina Sáez
- Centro de Biotecnología y Genómica de Plantas UPM‐INIA and E.T.S. Ingeniería Agronómica, Alimentaria y de BiosistemasUniversidad Politécnica de MadridMadrid28223Spain
| | - Israel Pagán
- Centro de Biotecnología y Genómica de Plantas UPM‐INIA and E.T.S. Ingeniería Agronómica, Alimentaria y de BiosistemasUniversidad Politécnica de MadridMadrid28223Spain
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Wu Q, Guo C, Li XK, Yi BY, Li QL, Guo ZM, Lu JH. A meta-transcriptomic study of mosquito virome and blood feeding patterns at the human-animal-environment interface in Guangdong Province, China. One Health 2023; 16:100493. [PMID: 36817976 PMCID: PMC9932184 DOI: 10.1016/j.onehlt.2023.100493] [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: 09/24/2022] [Revised: 01/25/2023] [Accepted: 01/26/2023] [Indexed: 02/04/2023] Open
Abstract
Mosquitoes are a formidable reservoir of viruses and important vectors of zoonotic pathogens. Blood-fed mosquitoes have been utilized to determine host infection status, overcoming the difficulties associated with sampling from human and animal populations. Comprehensive surveillance of potential pathogens at the interface of humans, animals, and the environment is currently an accredited method to provide an early warning of emerging or re-emerging infectious diseases and to proactively respond to them. Herein we performed comprehensive sampling of mosquitoes from seven habitats (residential areas, hospital, airplane, harbor, zoo, domestic sheds, and forest park) across five cities in Guangdong Province, China. Our aim was to characterize the viral communities and blood feeding patterns at the human-animal-environment interface and analyze the potential risk of cross-species transmission using meta-transcriptomic sequencing. 1898 female adult mosquitoes were collected, including 1062 Aedes and 836 Culex mosquitoes, of which approximately 12% (n = 226) were satiated with blood. Consequently, 101 putative viruses were identified, which included DNA and RNA viruses, and positive-stranded RNA viruses (+ssRNA) were the most abundant. According to viral diversity analysis, the composition of the viral structure was highly dependent on host species, and Culex mosquitoes showed richer viral diversity than Aedes mosquitoes. Although the virome of mosquitoes from different sampling habitats showed an overlap of 39.6%, multiple viruses were specific to certain habitats, particularly at the human-animal interface. Blood meal analysis found four mammals and one bird bloodmeal source, including humans, dogs, cats, poultry, and rats. Further, the blood feeding patterns of mosquitoes were found to be habitat dependent, and mosquitoes at the human-animal interface and from forests had a wider choice of hosts, including humans, domesticated animals, and wildlife, which in turn considerably increases the risk of spillover of potential zoonotic pathogens. To summarize, we are the first to investigate the virome of mosquitoes from multiple interfaces based on the One Health concept. The characteristics of viral community and blood feeding patterns of mosquitoes at the human-animal-environment interface were determined. Our findings should support surveillance activities to identify known and potential pathogens that are pathogenic to vertebrates.
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Affiliation(s)
- Qin Wu
- School of Public Health, Sun Yat-Sen University, Guangzhou 510080, China,One Health Center of Excellence for Research & Training, Sun Yat-Sen University, Guangzhou 510080, China
| | - Cheng Guo
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York 10032, USA
| | - Xiao-kang Li
- School of Public Health, Sun Yat-Sen University, Guangzhou 510080, China,One Health Center of Excellence for Research & Training, Sun Yat-Sen University, Guangzhou 510080, China
| | - Bo-Yang Yi
- School of Public Health, Sun Yat-Sen University, Guangzhou 510080, China,One Health Center of Excellence for Research & Training, Sun Yat-Sen University, Guangzhou 510080, China
| | - Qian-Lin Li
- School of Public Health, Sun Yat-Sen University, Guangzhou 510080, China,One Health Center of Excellence for Research & Training, Sun Yat-Sen University, Guangzhou 510080, China
| | - Zhong-Min Guo
- Laboratory Animal Center, Sun Yat-Sen University, Guangzhou 510080, China,Corresponding author.
| | - Jia-Hai Lu
- School of Public Health, Sun Yat-Sen University, Guangzhou 510080, China,One Health Center of Excellence for Research & Training, Sun Yat-Sen University, Guangzhou 510080, China,National Medical Products Administration Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, Guangzhou 510080, China,Hainan Key Novel Thinktank “Hainan Medical University ‘One Health’ Research Center”, Haikou 571199, China,Key Laboratory of Tropical Diseases Control, Sun Yat-Sen University, Ministry of Education, Guangzhou 510080, China,Corresponding author at: School of Public Health, Sun Yat-Sen University, Guangzhou 510080, China.
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Whole-genome sequence analysis of a novel orthobunyavirus isolated in Japan in the 1980s. Arch Virol 2023; 168:67. [PMID: 36653513 DOI: 10.1007/s00705-022-05639-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/28/2022] [Indexed: 01/20/2023]
Abstract
Two viruses isolated from Culicoides biting midges in Japan and preserved in a frozen state for over three decades were genetically characterized by next-generation sequencing. The viruses have a tripartite RNA genome with the typical coding strategy of orthobunyaviruses. They also share a high level of genetic similarity and are thus regarded as isolates of the same virus. Pairwise sequence comparisons and phylogenetic analysis including viruses of the Simbu serogroup demonstrated that the new viruses are members of clade A of this serogroup. In addition, a discrepancy in the phylogenetic trees indicated that a genetic reassortment had occurred in the evolution of the studied viruses. The L protein of the virus reported here showed no more than 94.6% amino acid sequence identity to that of any other Simbu serogroup virus, indicating that it should be regarded as a novel virus according to a criterion for species definition in the genus Orthobunyavirus. Therefore, this novel virus is tentatively named 'Taniyama virus' based on the location where the infected midges were collected.
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Evolution and emergence of mosquito-borne viruses of medical importance: towards a routine metagenomic surveillance approach. JOURNAL OF TROPICAL ECOLOGY 2023. [DOI: 10.1017/s0266467423000019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Abstract
During the last two decades, the world has witnessed the emergence and re-emergence of arthropod-borne viruses, better known as arboviruses. The close contact between sylvatic, rural and peri-urban vector species and humans has been mainly determined by the environment-modifying human activity. The resulting interactions have led to multiple dead-end host infections and have allowed sylvatic arboviruses to eventually adapt to new vectors and hosts, contributing to the establishment of urban transmission cycles of some viruses with enormous epidemiologic impact. The metagenomic next-generation sequencing (NGS) approach has allowed obtaining unbiased sequence information of millions of DNA and RNA molecules from clinical and environmental samples. Robust bioinformatics tools have enabled the assembly of individual sequence reads into contigs and scaffolds partially or completely representing the genomes of the microorganisms and viruses being present in biological samples of clinical relevance. In this review, we describe the different ecological scenarios for the emergence of viral diseases, the virus adaptation process required for the establishment of a new transmission cycle and the usefulness of NGS and computational methods for the discovery and routine genomic surveillance of mosquito-borne viruses in their ecosystems.
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Liao M, Xie Y, Shi M, Cui J. Over two decades of research on the marine RNA virosphere. IMETA 2022; 1:e59. [PMID: 38867898 PMCID: PMC10989941 DOI: 10.1002/imt2.59] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/30/2022] [Accepted: 09/14/2022] [Indexed: 06/14/2024]
Abstract
RNA viruses (realm: Riboviria), including RNA phages and eukaryote-infecting RNA viruses, are essential components of marine ecosystems. A large number of marine RNA viruses have been discovered in the last two decades because of the rapid development of next-generation sequencing (NGS) technology. Indeed, the combination of NGS and state-of-the-art meta-omics methods (viromics, the study of all viruses in a specific environment) has led to a fundamental understanding of the taxonomy and genetic diversity of RNA viruses in the sea, suggesting the complex ecological roles played by RNA viruses in this complex ecosystem. Furthermore, comparisons of viromes in the context of highly variable marine niches reveal the biogeographic patterns and ecological impact of marine RNA viruses, whose role in global ecology is becoming increasingly clearer. In this review, we summarize the characteristics of the global marine RNA virosphere and outline the taxonomic hierarchy of RNA viruses with a specific focus on their ancient evolutionary history. We also review the development of methodology and the major progress resulting from its applications in RNA viromics. The aim of this review is not only to provide an in-depth understanding of multifaceted aspects of marine RNA viruses, but to offer future perspectives on developing a better methodology for discovery, and exploring the evolutionary origin and major ecological significance of marine RNA virosphere.
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Affiliation(s)
- Meng‐en Liao
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Center for Biosafety Mega‐ScienceChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yunyi Xie
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Center for Biosafety Mega‐ScienceChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Mang Shi
- School of MedicineSun Yat‐sen UniversityShenzhen Campus of Sun Yat‐sen UniversityShenzhenChina
| | - Jie Cui
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Center for Biosafety Mega‐ScienceChinese Academy of SciencesShanghaiChina
- Laboatory for Marine Biology and BiotechnologyPilot National Laboratory for Marine Science and Technology (Qingdao)QingdaoChina
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Yang S, Mao Q, Wang Y, He J, Yang J, Chen X, Xiao Y, He Y, Zhao M, Lu J, Yang Z, Dai Z, Liu Q, Yao Y, Lu X, Li H, Zhou R, Zeng J, Li W, Zhou C, Wang X, Shen Q, Xu H, Deng X, Delwart E, Shan T, Zhang W. Expanding known viral diversity in plants: virome of 161 species alongside an ancient canal. ENVIRONMENTAL MICROBIOME 2022; 17:58. [PMID: 36437477 PMCID: PMC9703751 DOI: 10.1186/s40793-022-00453-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 11/17/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Since viral metagenomic approach was applied to discover plant viruses for the first time in 2006, many plant viruses had been identified from cultivated and non-cultivated plants. These previous researches exposed that the viral communities (virome) of plants have still largely uncharacterized. Here, we investigated the virome in 161 species belonging to 38 plant orders found in a riverside ecosystem. RESULTS We identified 245 distinct plant-associated virus genomes (88 DNA and 157 RNA viruses) belonging to 27 known viral families, orders, or unclassified virus groups. Some viral genomes were sufficiently divergent to comprise new species, genera, families, or even orders. Some groups of viruses were detected that currently are only known to infect organisms other than plants. It indicates a wider host range for members of these clades than previously recognized theoretically. We cannot rule out that some viruses could be from plant contaminating organisms, although some methods were taken to get rid of them as much as possible. The same viral species could be found in different plants and co-infections were common. CONCLUSIONS Our data describe a complex viral community within a single plant ecosystem and expand our understanding of plant-associated viral diversity and their possible host ranges.
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Affiliation(s)
- Shixing Yang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
- International Genome Center, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Qingqing Mao
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yan Wang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Jingxian He
- Suzhou Medical College of Soochow University, Suzhou, 215123, China
| | - Jie Yang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Xu Chen
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yuqing Xiao
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yumin He
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Min Zhao
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Juan Lu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Zijun Yang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Ziyuan Dai
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Qi Liu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yuxin Yao
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Xiang Lu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Hong Li
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Rui Zhou
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Jian Zeng
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Wang Li
- Department of Laboratory Medicine, Jiangsu Taizhou People's Hospital, Taizhou, 225300, Jiangsu, China
| | - Chenglin Zhou
- Department of Laboratory Medicine, Jiangsu Taizhou People's Hospital, Taizhou, 225300, Jiangsu, China
| | - Xiaochun Wang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Quan Shen
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Hui Xu
- The Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, Jiangsu, China
| | - Xutao Deng
- Vitalant Research Institute, San Francisco, CA, 94118, USA
| | - Eric Delwart
- Vitalant Research Institute, San Francisco, CA, 94118, USA
- Department of Laboratory Medicine, University of California, San Francisco, CA, 94118, USA
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China.
| | - Wen Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
- International Genome Center, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
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43
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Xie FL, Zhou XY, Xiao R, Zhang CJ, Zhong J, Zhou Q, Liu F, Zhu HJ. Discovery and exploration of widespread infection of mycoviruses in Phomopsis vexans, the causal agent of phomopsis blight of eggplant in China. FRONTIERS IN PLANT SCIENCE 2022; 13:996862. [PMID: 36438156 PMCID: PMC9685175 DOI: 10.3389/fpls.2022.996862] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/11/2022] [Indexed: 06/01/2023]
Abstract
Phomopsis vexans, which causes Phomopsis blight of eggplant, has been reported worldwide. To study the biocontrol of this disease, 162 leaf and fruit samples of eggplant Phomopsis blight were collected from Hunan, Hubei, Jiangxi, Sichuan, Zhejiang, Fujian, Guangdong and Anhui Provinces from 2017 to 2019. Eighty-seven pathogenic fungus isolates were identified as P. vexans. The following studies were conducted: screening of sporulation medium, spore morphology analysis, mycovirus detection and identification of novel mycoviruses in these isolates. The results showed that eggplant tissue medium was the most suitable medium for rapid sporulation, and all isolates had mycoviruses consisting of mainly mixed infections. The genome of these mycoviruses varied from 1-15 kb. Five novel mycoviruses infecting P. vexans were obtained, including "Phomopsis vexans fusarivirus 1" (PvFV1), "Phomopsis vexans ourmia-like virus 1" (PvOLV1), "Phomopsis vexans endornavirus 2" (PvEV2), "Phomopsis vexans partitivirus 1" (PvPV1) and "Phomopsis vexans victorivirus L1" (PvVVL1). Thus, PvVVL1 displays a unique genome structure, and this is the first report of a victorivirus consisting of two segments and of a deltapartitivirus infecting the fungus host.
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Affiliation(s)
- Fang Ling Xie
- College of Plant Protection, Hunan Agricultural University, Changsha, China
- College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Xin Yu Zhou
- College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Rong Xiao
- Hunan Institute of Microbiology, Changsha, China
| | - Chao Jun Zhang
- College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Jie Zhong
- College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Qian Zhou
- College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Feng Liu
- College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Hong Jian Zhu
- College of Plant Protection, Hunan Agricultural University, Changsha, China
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44
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Moubset O, François S, Maclot F, Palanga E, Julian C, Claude L, Fernandez E, Rott P, Daugrois JH, Antoine-Lorquin A, Bernardo P, Blouin AG, Temple C, Kraberger S, Fontenele RS, Harkins GW, Ma Y, Marais A, Candresse T, Chéhida SB, Lefeuvre P, Lett JM, Varsani A, Massart S, Ogliastro M, Martin DP, Filloux D, Roumagnac P. Virion-Associated Nucleic Acid-Based Metagenomics: A Decade of Advances in Molecular Characterization of Plant Viruses. PHYTOPATHOLOGY 2022; 112:2253-2272. [PMID: 35722889 DOI: 10.1094/phyto-03-22-0096-rvw] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Over the last decade, viral metagenomic studies have resulted in the discovery of thousands of previously unknown viruses. These studies are likely to play a pivotal role in obtaining an accurate and robust understanding of how viruses affect the stability and productivity of ecosystems. Among the metagenomics-based approaches that have been developed since the beginning of the 21st century, shotgun metagenomics applied specifically to virion-associated nucleic acids (VANA) has been used to disentangle the diversity of the viral world. We summarize herein the results of 24 VANA-based studies, focusing on plant and insect samples conducted over the last decade (2010 to 2020). Collectively, viruses from 85 different families were reliably detected in these studies, including capsidless RNA viruses that replicate in fungi, oomycetes, and plants. Finally, strengths and weaknesses of the VANA approach are summarized and perspectives of applications in detection, epidemiological surveillance, environmental monitoring, and ecology of plant viruses are provided. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Oumaima Moubset
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | | | - François Maclot
- Plant Pathology Laboratory, Terra, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
| | - Essowè Palanga
- Institut Togolais de Recherche Agronomique (ITRA-CRASS), B.P. 129, Kara, Togo
| | - Charlotte Julian
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Lisa Claude
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Emmanuel Fernandez
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Philippe Rott
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Jean-Heinrich Daugrois
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | | | | | - Arnaud G Blouin
- Plant Pathology Laboratory, Terra, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
- Plant Protection Department, Agroscope, 1260, Nyon, Switzerland
| | - Coline Temple
- Plant Pathology Laboratory, Terra, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, U.S.A
| | - Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, U.S.A
| | - Gordon W Harkins
- South African Medical Research Council Capacity Development Unit, South African National Bioinformatics, Institute, University of the Western Cape, South Africa
| | - Yuxin Ma
- Univ. Bordeaux, INRAE, UMR BFP, 33140 Villenave d'Ornon, France
| | - Armelle Marais
- Univ. Bordeaux, INRAE, UMR BFP, 33140 Villenave d'Ornon, France
| | | | | | | | | | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, U.S.A
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Sébastien Massart
- Plant Pathology Laboratory, Terra, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
| | | | - Darren P Martin
- Division of Computational Biology, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Denis Filloux
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Philippe Roumagnac
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
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Schuettenberg A, Piña A, Metrailer M, Peláez-Sánchez RG, Agudelo-Flórez P, Lopez JÁ, Ryle L, Monroy FP, Altin JA, Ladner JT. Highly Multiplexed Serology for Nonhuman Mammals. Microbiol Spectr 2022; 10:e0287322. [PMID: 36125316 PMCID: PMC9602771 DOI: 10.1128/spectrum.02873-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 09/06/2022] [Indexed: 01/04/2023] Open
Abstract
Emerging infectious diseases represent a serious and ongoing threat to humans. Most emerging viruses are maintained in stable relationships with other species of animals, and their emergence within the human population results from cross-species transmission. Therefore, if we want to be prepared for the next emerging virus, we need to broadly characterize the diversity and ecology of viruses currently infecting other animals (i.e., the animal virosphere). High-throughput metagenomic sequencing has accelerated the pace of virus discovery. However, molecular assays can detect only active infections and only if virus is present within the sampled fluid or tissue at the time of collection. In contrast, serological assays measure long-lived antibody responses to infections, which can be detected within the blood, regardless of the infected tissues. Therefore, serological assays can provide a complementary approach for understanding the circulation of viruses, and while serological assays have historically been limited in scope, recent advancements allow thousands to hundreds of thousands of antigens to be assessed simultaneously using <1 μL of blood (i.e., highly multiplexed serology). The application of highly multiplexed serology for the characterization of the animal virosphere is dependent on the availability of reagents that can be used to capture or label antibodies of interest. Here, we evaluate the utility of commercial immunoglobulin-binding proteins (protein A and protein G) to enable highly multiplexed serology in 25 species of nonhuman mammals, and we describe a competitive fluorescence-linked immunosorbent assay (FLISA) that can be used as an initial screen for choosing the most appropriate capture protein for a given host species. IMPORTANCE Antibodies are generated in response to infections with viruses and other pathogens, and they help protect against future exposures. Mature antibodies are long lived, are highly specific, and can bind to their protein targets with high affinity. Thus, antibodies can also provide information about an individual's history of viral exposures, which has important applications for understanding the epidemiology and etiology of disease. In recent years, there have been large advances in the available methods for broadly characterizing antibody-binding profiles, but thus far, these have been utilized primarily with human samples only. Here, we demonstrate that commercial antibody-binding reagents can facilitate modern antibody assays for a wide variety of mammalian species, and we describe an inexpensive and fast approach for choosing the best reagent for each animal species. By studying antibody-binding profiles in captive and wild animals, we can better understand the distribution and prevalence of viruses that could spill over into humans.
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Affiliation(s)
- Alexa Schuettenberg
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Alejandra Piña
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Morgan Metrailer
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | | | | | - Juan Álvaro Lopez
- Microbiology School, Primary Immunodeficiencies Group, University of Antioquia, Medellín, Colombia
| | - Luke Ryle
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Fernando P. Monroy
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - John A. Altin
- The Translational Genomics Research Institute (TGen), Flagstaff, Arizona, USA
| | - Jason T. Ladner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
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Lemieux A, Colby GA, Poulain AJ, Aris-Brosou S. Viral spillover risk increases with climate change in High Arctic lake sediments. Proc Biol Sci 2022; 289:20221073. [PMID: 36259208 PMCID: PMC9579761 DOI: 10.1098/rspb.2022.1073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The host spectrum of viruses is quite diverse, as they can sustainedly infect a few species to several phyla. When confronted with a new host, a virus may even infect it and transmit sustainably in this new host, a process called ‘viral spillover’. However, the risk of such events is difficult to quantify. As climate change is rapidly transforming environments, it is becoming critical to quantify the potential for spillovers. To address this issue, we resorted to a metagenomics approach and focused on two environments, soil and lake sediments from Lake Hazen, the largest High Arctic freshwater lake in the world. We used DNA and RNA sequencing to reconstruct the lake’s virosphere in both its sediments and soils, as well as its range of eukaryotic hosts. We then estimated the spillover risk by measuring the congruence between the viral and the eukaryotic host phylogenetic trees, and show that spillover risk increases with runoff from glacier melt, a proxy for climate change. Should climate change also shift species range of potential viral vectors and reservoirs northwards, the High Arctic could become fertile ground for emerging pandemics.
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Affiliation(s)
- Audrée Lemieux
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Graham A. Colby
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Stéphane Aris-Brosou
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada
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47
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Abstract
Viruses are the most abundant biological entities on Earth, and yet, they have not received enough consideration in astrobiology. Viruses are also extraordinarily diverse, which is evident in the types of relationships they establish with their host, their strategies to store and replicate their genetic information and the enormous diversity of genes they contain. A viral population, especially if it corresponds to a virus with an RNA genome, can contain an array of sequence variants that greatly exceeds what is present in most cell populations. The fact that viruses always need cellular resources to multiply means that they establish very close interactions with cells. Although in the short term these relationships may appear to be negative for life, it is evident that they can be beneficial in the long term. Viruses are one of the most powerful selective pressures that exist, accelerating the evolution of defense mechanisms in the cellular world. They can also exchange genetic material with the host during the infection process, providing organisms with capacities that favor the colonization of new ecological niches or confer an advantage over competitors, just to cite a few examples. In addition, viruses have a relevant participation in the biogeochemical cycles of our planet, contributing to the recycling of the matter necessary for the maintenance of life. Therefore, although viruses have traditionally been excluded from the tree of life, the structure of this tree is largely the result of the interactions that have been established throughout the intertwined history of the cellular and the viral worlds. We do not know how other possible biospheres outside our planet could be, but it is clear that viruses play an essential role in the terrestrial one. Therefore, they must be taken into account both to improve our understanding of life that we know, and to understand other possible lives that might exist in the cosmos.
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Affiliation(s)
- Ignacio de la Higuera
- Department of Biology, Center for Life in Extreme Environments, Portland State University, Portland, OR, United States
| | - Ester Lázaro
- Centro de Astrobiología (CAB), CSIC-INTA, Torrejón de Ardoz, Spain
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48
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Han Z, Xiao J, Song Y, Zhao X, Sun Q, Lu H, Zhang K, Li J, Li J, Si F, Zhang G, Zhao H, Jia S, Zhou J, Wang D, Zhu S, Yan D, Xu W, Fu X, Zhang Y. Highly diverse ribonucleic acid viruses in the viromes of eukaryotic host species in Yunnan province, China. Front Microbiol 2022; 13:1019444. [PMID: 36312977 PMCID: PMC9606678 DOI: 10.3389/fmicb.2022.1019444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 09/20/2022] [Indexed: 11/17/2022] Open
Abstract
Background The diversity in currently documented viruses and their morphological characteristics indicates the need for understanding the evolutionary characteristics of viruses. Notably, further studies are needed to obtain a comprehensive landscape of virome, the virome of host species in Yunnan province, China. Materials and methods We implemented the metagenomic next-generation sequencing strategy to investigate the viral diversity, which involved in 465 specimens collected from bats, pangolins, monkeys, and other species. The diverse RNA viruses were analyzed, especially focusing on the genome organization, genetic divergence and phylogenetic relationships. Results In this study, we investigated the viral composition of eight libraries from bats, pangolins, monkeys, and other species, and found several diverse RNA viruses, including the Alphacoronavirus from bat specimens. By characterizing the genome organization, genetic divergence, and phylogenetic relationships, we identified five Alphacoronavirus strains, which shared phylogenetic association with Bat-CoV-HKU8-related strains. The pestivirus-like virus related to recently identified Dongyang pangolin virus (DYPV) strains from dead pangolin specimens, suggesting that these viruses are evolving. Some genomes showed higher divergence from known species (e.g., calicivirus CS9-Cali-YN-CHN-2020), and many showed evidence of recombination events with unknown or known strains (e.g., mamastroviruses BF2-astro-YN-CHN-2020 and EV-A122 AKM5-YN-CHN-2020). The newly identified viruses showed extensive changes and could be assigned as new species, or even genus (e.g., calicivirus CS9-Cali-YN-CHN-2020 and iflavirus Ifla-YN-CHN-2020). Moreover, we identified several highly divergent RNA viruses and estimated their evolutionary characteristics among different hosts, providing data for further examination of their evolutionary dynamics. Conclusion Overall, our study emphasizes the close association between emerging viruses and infectious diseases, and the need for more comprehensive surveys.
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Affiliation(s)
- Zhenzhi Han
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Beijing, China
| | - Jinbo Xiao
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yang Song
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiaonan Zhao
- Yunnan Center for Disease Control and Prevention, Kunming, China
| | - Qiang Sun
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Huanhuan Lu
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Keyi Zhang
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jichen Li
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Junhan Li
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Fenfen Si
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Guoyan Zhang
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hehe Zhao
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Senquan Jia
- Yunnan Center for Disease Control and Prevention, Kunming, China
| | - Jienan Zhou
- Yunnan Center for Disease Control and Prevention, Kunming, China
| | - Dongyan Wang
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shuangli Zhu
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Dongmei Yan
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Wenbo Xu
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Xiaoqing Fu
- Yunnan Center for Disease Control and Prevention, Kunming, China
- Xiaoqing Fu,
| | - Yong Zhang
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
- *Correspondence: Yong Zhang,
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Crosstalk between the Intestinal Virome and Other Components of the Microbiota, and Its Effect on Intestinal Mucosal Response and Diseases. J Immunol Res 2022; 2022:7883945. [PMID: 36203793 PMCID: PMC9532165 DOI: 10.1155/2022/7883945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 09/12/2022] [Accepted: 09/14/2022] [Indexed: 11/17/2022] Open
Abstract
In recent years, there has been ample evidence illustrating the effect of microbiota on gut immunity, homeostasis, and disease. Most of these studies have engaged more efforts in understanding the role of the bacteriome in gut mucosal immunity and disease. However, studies on the virome and its influence on gut mucosal immunity and pathology are still at infancy owing to limited metagenomic tools. Nonetheless, the existing studies on the virome have largely been focused on the bacteriophages as these represent the main component of the virome with little information on endogenous retroviruses (ERVs) and eukaryotic viruses. In this review, we describe the gut virome, and its role in gut mucosal response and disease progression. We also explore the crosstalk between the virome and other microorganisms in the gut mucosa and elaborate on how these interactions shape the gut mucosal immunity going from bacteriophages through ERVs to eukaryotic viruses. Finally, we elucidate the potential contribution of this crosstalk in the pathogenesis of inflammatory bowel diseases and colon cancer.
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50
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From Contagium vivum fluidum to Riboviria: A Tobacco Mosaic Virus-Centric History of Virus Taxonomy. Biomolecules 2022; 12:biom12101363. [PMID: 36291572 PMCID: PMC9599303 DOI: 10.3390/biom12101363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/12/2022] [Accepted: 09/19/2022] [Indexed: 11/17/2022] Open
Abstract
Viruses were discovered as agents of disease in the late 19th century, but it was not until the 1930s that the nature of these agents was elucidated. Nevertheless, as soon as viral diseases started to be recognized and cataloged, there were attempts to classify and name viruses. Although these early attempts failed to be adopted by the nascent virology community, they are evidence of the human compulsion to try to organize the natural world into well-defined categories. Different classification schemes were proposed during the 20th century, but again none were widely embraced by virologists. In 1966, with the creation of the International Committee on Nomenclature of Viruses (eventually renamed as the International Committee on Taxonomy of Viruses), a more organized effort led to an official taxonomy in which viruses were classified into families and genera. At present, a much better understanding of the evolutionary relationships among viruses has led to the establishment of a 15-rank taxonomy based primarily on these evolutionary relationships. This review of virus taxonomy will be centered on the tobacco mosaic virus (TMV), the agent of the disease studied by Dmitry Ivanovsky and the first virus to be recognized as such, which was often historically at the center of major advancements in virology during the 20th century.
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