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Sadiq S, Holmes EC, Mahar JE. Genomic and phylogenetic features of the Picobirnaviridae suggest microbial rather than animal hosts. Virus Evol 2024; 10:veae033. [PMID: 38756987 PMCID: PMC11096803 DOI: 10.1093/ve/veae033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/27/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024] Open
Abstract
The RNA virus family Picobirnaviridae has traditionally been associated with the gastrointestinal systems of terrestrial mammals and birds, with the majority of viruses detected in animal stool samples. Metatranscriptomic studies of vertebrates, invertebrates, microbial communities, and environmental samples have resulted in an enormous expansion of the genomic and phylogenetic diversity of this family. Yet picobirnaviruses remain poorly classified, with only one genus and three species formally ratified by the International Committee of Virus Taxonomy. Additionally, an inability to culture picobirnaviruses in a laboratory setting or isolate them in animal tissue samples, combined with the presence of bacterial genetic motifs in their genomes, suggests that these viruses may represent RNA bacteriophage rather than being associated with animal infection. Utilising a data set of 2,286 picobirnaviruses sourced from mammals, birds, reptiles, fish, invertebrates, microbial communities, and environmental samples, we identified seven consistent phylogenetic clusters likely representing Picobirnavirus genera that we tentatively name 'Alpha-', 'Beta-', 'Gamma-', 'Delta-', 'Epsilon-', 'Zeta-', and 'Etapicobirnavirus'. A statistical analysis of topological congruence between virus-host phylogenies revealed more frequent cross-species transmission than any other RNA virus family. In addition, bacterial ribosomal binding site motifs were more enriched in Picobirnavirus genomes than in the two groups of established RNA bacteriophage-the Leviviricetes and Cystoviridae. Overall, our findings support the hypothesis that the Picobirnaviridae have bacterial hosts and provide a lower-level taxonomic classification for this highly diverse and ubiquitous family of RNA viruses.
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Affiliation(s)
- 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
- Laboratory of Data Discovery for Health Limited, Hong Kong, SAR, China
| | - Jackie E Mahar
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
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Vigil K, Aw TG. Comparison of de novo assembly using long-read shotgun metagenomic sequencing of viruses in fecal and serum samples from marine mammals. Front Microbiol 2023; 14:1248323. [PMID: 37808316 PMCID: PMC10556685 DOI: 10.3389/fmicb.2023.1248323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023] Open
Abstract
Introduction Viral diseases of marine mammals are difficult to study, and this has led to a limited knowledge on emerging known and unknown viruses which are ongoing threats to animal health. Viruses are the leading cause of infectious disease-induced mass mortality events among marine mammals. Methods In this study, we performed viral metagenomics in stool and serum samples from California sea lions (Zalophus californianus) and bottlenose dolphins (Tursiops truncates) using long-read nanopore sequencing. Two widely used long-read de novo assemblers, Canu and Metaflye, were evaluated to assemble viral metagenomic sequencing reads from marine mammals. Results Both Metaflye and Canu assembled similar viral contigs of vertebrates, such as Parvoviridae, and Poxviridae. Metaflye assembled viral contigs that aligned with one viral family that was not reproduced by Canu, while Canu assembled viral contigs that aligned with seven viral families that was not reproduced by Metaflye. Only Canu assembled viral contigs from dolphin and sea lion fecal samples that matched both protein and nucleotide RefSeq viral databases using BLASTx and BLASTn for Anelloviridae, Parvoviridae and Circoviridae families. Viral contigs assembled with Canu aligned with torque teno viruses and anelloviruses from vertebrate hosts. Viruses associated with invertebrate hosts including densoviruses, Ambidensovirus, and various Circoviridae isolates were also aligned. Some of the invertebrate and vertebrate viruses reported here are known to potentially cause mortality events and/or disease in different seals, sea stars, fish, and bivalve species. Discussion Canu performed better by producing the most viral contigs as compared to Metaflye with assemblies aligning to both protein and nucleotide databases. This study suggests that marine mammals can be used as important sentinels to surveil marine viruses that can potentially cause diseases in vertebrate and invertebrate hosts.
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Affiliation(s)
| | - Tiong Gim Aw
- Department of Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States
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Desdouits M, Reynaud Y, Philippe C, Guyader FSL. A Comprehensive Review for the Surveillance of Human Pathogenic Microorganisms in Shellfish. Microorganisms 2023; 11:2218. [PMID: 37764063 PMCID: PMC10537662 DOI: 10.3390/microorganisms11092218] [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: 08/04/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
Bivalve molluscan shellfish have been consumed for centuries. Being filter feeders, they may bioaccumulate some microorganisms present in coastal water, either naturally or through the discharge of human or animal sewage. Despite regulations set up to avoid microbiological contamination in shellfish, human outbreaks still occur. After providing an overview showing their implication in disease, this review aims to highlight the diversity of the bacteria or enteric viruses detected in shellfish species, including emerging pathogens. After a critical discussion of the available methods and their limitations, we address the interest of technological developments using genomics to anticipate the emergence of pathogens. In the coming years, further research needs to be performed and methods need to be developed in order to design the future of surveillance and to help risk assessment studies, with the ultimate objective of protecting consumers and enhancing the microbial safety of bivalve molluscan shellfish as a healthy food.
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Affiliation(s)
| | | | | | - Françoise S. Le Guyader
- Ifremer, Unité Microbiologie Aliment Santé et Environnement, RBE/LSEM, 44311 Nantes, France; (M.D.); (Y.R.); (C.P.)
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Schaeffer J, Desdouits M, Besnard A, Le Guyader FS. Looking into sewage: how far can metagenomics help to detect human enteric viruses? Front Microbiol 2023; 14:1161674. [PMID: 37180249 PMCID: PMC10166864 DOI: 10.3389/fmicb.2023.1161674] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/03/2023] [Indexed: 05/16/2023] Open
Abstract
The impact of human sewage on environmental and food contamination constitutes an important safety issue. Indeed, human sewage reflects the microbiome of the local population, and a variety of human viruses can be detected in wastewater samples. Being able to describe the diversity of viruses present in sewage will provide information on the health of the surrounding population health and will help to prevent further transmission. Metagenomic developments, allowing the description of all the different genomes present in a sample, are very promising tools for virome analysis. However, looking for human enteric viruses with short RNA genomes which are present at low concentrations is challenging. In this study we demonstrate the benefits of performing technical replicates to improve viral identification by increasing contig length, and the set-up of quality criteria to increase confidence in results. Our approach was able to effectively identify some virus sequences and successfully describe the viral diversity. The method yielded full genomes either for norovirus, enterovirus and rotavirus, even if, for these segmented genomes, combining genes remain a difficult issue. Developing reliable viromic methods is important as wastewater sample analysis provides an important tool to prevent further virus transmission by raising alerts in case of viral outbreaks or emergence.
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Affiliation(s)
| | | | | | - Françoise S. Le Guyader
- Ifremer, Laboratoire de Microbiologie, U. Microbiologie Aliment Santé et Environnement, Nantes, France
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Orf GS, Olivo A, Harris B, Weiss SL, Achari A, Yu G, Federman S, Mbanya D, James L, Mampunza S, Chiu CY, Rodgers MA, Cloherty GA, Berg MG. Metagenomic Detection of Divergent Insect- and Bat-Associated Viruses in Plasma from Two African Individuals Enrolled in Blood-Borne Surveillance. Viruses 2023; 15:v15041022. [PMID: 37113001 PMCID: PMC10145552 DOI: 10.3390/v15041022] [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: 03/23/2023] [Revised: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 04/29/2023] Open
Abstract
Metagenomic next-generation sequencing (mNGS) has enabled the high-throughput multiplexed identification of sequences from microbes of potential medical relevance. This approach has become indispensable for viral pathogen discovery and broad-based surveillance of emerging or re-emerging pathogens. From 2015 to 2019, plasma was collected from 9586 individuals in Cameroon and the Democratic Republic of the Congo enrolled in a combined hepatitis virus and retrovirus surveillance program. A subset (n = 726) of the patient specimens was analyzed by mNGS to identify viral co-infections. While co-infections from known blood-borne viruses were detected, divergent sequences from nine poorly characterized or previously uncharacterized viruses were also identified in two individuals. These were assigned to the following groups by genomic and phylogenetic analyses: densovirus, nodavirus, jingmenvirus, bastrovirus, dicistrovirus, picornavirus, and cyclovirus. Although of unclear pathogenicity, these viruses were found circulating at high enough concentrations in plasma for genomes to be assembled and were most closely related to those previously associated with bird or bat excrement. Phylogenetic analyses and in silico host predictions suggested that these are invertebrate viruses likely transmitted through feces containing consumed insects or through contaminated shellfish. This study highlights the power of metagenomics and in silico host prediction in characterizing novel viral infections in susceptible individuals, including those who are immunocompromised from hepatitis viruses and retroviruses, or potentially exposed to zoonotic viruses from animal reservoir species.
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Affiliation(s)
- Gregory S Orf
- Infectious Disease Research, Abbott Diagnostics, Abbott Park, IL 60004, USA
- Abbott Pandemic Defense Coalition, Abbott Park, IL 60004, USA
| | - Ana Olivo
- Infectious Disease Research, Abbott Diagnostics, Abbott Park, IL 60004, USA
- Abbott Pandemic Defense Coalition, Abbott Park, IL 60004, USA
| | - Barbara Harris
- Infectious Disease Research, Abbott Diagnostics, Abbott Park, IL 60004, USA
- Abbott Pandemic Defense Coalition, Abbott Park, IL 60004, USA
| | - Sonja L Weiss
- Infectious Disease Research, Abbott Diagnostics, Abbott Park, IL 60004, USA
- Abbott Pandemic Defense Coalition, Abbott Park, IL 60004, USA
| | - Asmeeta Achari
- Abbott Pandemic Defense Coalition, Abbott Park, IL 60004, USA
- Department of Laboratory Medicine, University of California-San Francisco, San Francisco, CA 94143, USA
| | - Guixia Yu
- Abbott Pandemic Defense Coalition, Abbott Park, IL 60004, USA
- Department of Laboratory Medicine, University of California-San Francisco, San Francisco, CA 94143, USA
| | - Scot Federman
- Abbott Pandemic Defense Coalition, Abbott Park, IL 60004, USA
- Department of Laboratory Medicine, University of California-San Francisco, San Francisco, CA 94143, USA
| | - Dora Mbanya
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé P.O. Box 1364, Cameroon
| | - Linda James
- School of Medicine, Université Protestante au Congo, Kinshasa P.O. Box 4745, Democratic Republic of the Congo
| | - Samuel Mampunza
- School of Medicine, Université Protestante au Congo, Kinshasa P.O. Box 4745, Democratic Republic of the Congo
| | - Charles Y Chiu
- Abbott Pandemic Defense Coalition, Abbott Park, IL 60004, USA
- Department of Laboratory Medicine, University of California-San Francisco, San Francisco, CA 94143, USA
- Department of Medicine, University of California-San Francisco, San Francisco, CA 94143, USA
| | - Mary A Rodgers
- Infectious Disease Research, Abbott Diagnostics, Abbott Park, IL 60004, USA
- Abbott Pandemic Defense Coalition, Abbott Park, IL 60004, USA
| | - Gavin A Cloherty
- Infectious Disease Research, Abbott Diagnostics, Abbott Park, IL 60004, USA
- Abbott Pandemic Defense Coalition, Abbott Park, IL 60004, USA
| | - Michael G Berg
- Infectious Disease Research, Abbott Diagnostics, Abbott Park, IL 60004, USA
- Abbott Pandemic Defense Coalition, Abbott Park, IL 60004, USA
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First Discovery of Phenuiviruses within Diverse RNA Viromes of Asiatic Toad (Bufo gargarizans) by Metagenomics Sequencing. Viruses 2023; 15:v15030750. [PMID: 36992458 PMCID: PMC10056474 DOI: 10.3390/v15030750] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/10/2023] [Accepted: 03/11/2023] [Indexed: 03/17/2023] Open
Abstract
Most zoonotic pathogens originate from mammals and avians, but viral diversity and related biosafety risk assessment in lower vertebrates also need to be explored. Amphibians are an important group of lower vertebrates that played a momentous role in animal evolution. To elucidate the diversity of RNA viruses in one important species of amphibians, the Asiatic toad (Bufo gargarizans), we obtained 44 samples including lung, gut, liver, and kidney tissues from Asiatic toads in Sichuan and Jilin provinces, China, for viral metagenomics sequencing. More than 20 novel RNA viruses derived from the order Bunyavirales and 7 families of Astroviridae, Dicistroviridae, Leviviridae, Partitiviridae, Picornaviridae, Rhabdoviridae, and Virgaviridae were discovered, which were distinct from previously described viruses and formed new clusters, as revealed by phylogenetic analyses. Notably, a novel bastrovirus, AtBastV/GCCDC11/2022, of the family Astroviridae was identified from the gut library, the genome of which contains three open reading frames, with the RNA-dependent RNA polymerase (RdRp) coded by ORF1 closely related to that of hepeviruses, and ORF2 encoding an astrovirus-related capsid protein. Notably, phenuiviruses were discovered for the first time in amphibians. AtPhenV1/GCCDC12/2022 and AtPhenV2/GCCDC13/2022 clustered together and formed a clade with the group of phenuiviruses identified from rodents. Picornaviruses and several invertebrate RNA viruses were also detected. These findings improve our understanding of the high RNA viral diversity in the Asiatic toad and provide new insights in the evolution of RNA viruses in amphibians.
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