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Paietta EN, Kraberger S, Lund MC, Vargas KL, Custer JM, Ehmke E, Yoder AD, Varsani A. Diverse Circular DNA Viral Communities in Blood, Oral, and Fecal Samples of Captive Lemurs. Viruses 2024; 16:1099. [PMID: 39066262 PMCID: PMC11281440 DOI: 10.3390/v16071099] [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: 06/11/2024] [Revised: 07/01/2024] [Accepted: 07/03/2024] [Indexed: 07/28/2024] Open
Abstract
Few studies have addressed viral diversity in lemurs despite their unique evolutionary history on the island of Madagascar and high risk of extinction. Further, while a large number of studies on animal viromes focus on fecal samples, understanding viral diversity across multiple sample types and seasons can reveal complex viral community structures within and across species. Groups of captive lemurs at the Duke Lemur Center (Durham, NC, USA), a conservation and research center, provide an opportunity to build foundational knowledge on lemur-associated viromes. We sampled individuals from seven lemur species, i.e., collared lemur (Eulemur collaris), crowned lemur (Eulemur coronatus), blue-eyed black lemur (Eulemur flavifrons), ring-tailed lemur (Lemur catta), Coquerel's sifaka (Propithecus coquereli), black-and-white ruffed lemur (Varecia variegata variegata), and red ruffed lemur (Varecia rubra), across two lemur families (Lemuridae, Indriidae). Fecal, blood, and saliva samples were collected from Coquerel's sifaka and black-and-white ruffed lemur individuals across two sampling seasons to diversify virome biogeography and temporal sampling. Using viral metagenomic workflows, the complete genomes of anelloviruses (n = 4), cressdnaviruses (n = 47), caudoviruses (n = 15), inoviruses (n = 34), and microviruses (n = 537) were determined from lemur blood, feces, and saliva. Many virus genomes, especially bacteriophages, identified in this study were present across multiple lemur species. Overall, the work presented here uses a viral metagenomics approach to investigate viral communities inhabiting the blood, oral cavity, and feces of healthy captive lemurs.
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Affiliation(s)
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Michael C. Lund
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Karla L. Vargas
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Joy M. Custer
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Erin Ehmke
- Duke Lemur Center, Duke University, Durham, NC 27708, USA
| | - Anne D. Yoder
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town 7925, South Africa
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Kamga Njile D, Mugyia EA, Endegue-Zanga MC, Kfutwah JA, Djoumetio MD, Onana B, Diop OM, Njouom R, Sadeuh-Mba SA. Detection and genetic diversity of parechoviruses in children with acute flaccid paralysis in Cameroon. PLoS One 2024; 19:e0301771. [PMID: 38809876 PMCID: PMC11135751 DOI: 10.1371/journal.pone.0301771] [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: 12/24/2023] [Accepted: 03/21/2024] [Indexed: 05/31/2024] Open
Abstract
Human Parechoviruses (HPeVs) have rarely been considered in the virological investigation of Acute Flacid Paralysis (AFP) cases in Africa, where enteric infections are very common. This study investigated the prevalence and genetic diversity of HPeV in 200 children aged ≤ 15 years with AFP in Cameroon from 2018 to 2019. HPeVs were detected in their faecal RNA using 5'-untranslated real-time RT-PCR. Detected HPeVs were typed by phylogenetic comparison with homologous sequences from homotypic reference strains. Overall, HPeV RNA was detected in 11.0% (22/200) of the 200 stool samples tested. Twelve HPeVs were successfully sequenced and reliably assigned to HPeV-A1, A4, A5, A10, A14, A15, A17 and A18 genotypes. Phylogenetic analyses revealed a high genetic variability among the studied HPeVs, as well as between the studied HPeVs and their previously reported counterparts from Cameroon in 2014. These findings suggest that different HPeV genotypes co-circulate in Cameroon without documented epidemics.
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Affiliation(s)
- Daniel Kamga Njile
- Department of Virology, Centre Pasteur of Cameroon, Yaoundé, Cameroon
- Faculty of Sciences, Department of Microbiology, University of Yaoundé 1, Yaounde, Cameroon
| | - Emmanuel Akongnwi Mugyia
- Faculty of Science, Department of Microbiology and Parasitology, University of Buea, Buea, Cameroon
| | | | | | | | - Boyomo Onana
- Faculty of Sciences, Department of Microbiology, University of Yaoundé 1, Yaounde, Cameroon
| | - Ousmane Madiagne Diop
- Global Polio Eradication Initiative (GPEI), World Health Organization, Geneva, Switzerland
| | - Richard Njouom
- Department of Virology, Centre Pasteur of Cameroon, Yaoundé, Cameroon
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Mogotsi MT, Ogunbayo AE, O’Neill HG, Nyaga MM. High Detection Frequency of Vaccine-Associated Polioviruses and Non-Polio Enteroviruses in the Stools of Asymptomatic Infants from the Free State Province, South Africa. Microorganisms 2024; 12:920. [PMID: 38792747 PMCID: PMC11124149 DOI: 10.3390/microorganisms12050920] [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: 02/01/2024] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
Enterovirus (EV) infections are widespread and associated with a range of clinical conditions, from encephalitis to meningitis, gastroenteritis, and acute flaccid paralysis. Knowledge about the circulation of EVs in neonatal age and early infancy is scarce, especially in Africa. This study aimed to unveil the frequency and diversity of EVs circulating in apparently healthy newborns from the Free State Province, South Africa (SA). For this purpose, longitudinally collected faecal specimens (May 2021-February 2022) from a cohort of 17 asymptomatic infants were analysed using metagenomic next-generation sequencing. Overall, seven different non-polio EV (NPEV) subtypes belonging to EV-B and EV-C species were identified, while viruses classified under EV-A and EV-D species could not be characterised at the sub-species level. Additionally, under EV-C species, two vaccine-related poliovirus subtypes (PV1 and PV3) were identified. The most prevalent NPEV species was EV-B (16/17, 94.1%), followed by EV-A (3/17, 17.6%), and EV-D (4/17, 23.5%). Within EV-B, the commonly identified NPEV types included echoviruses 6, 13, 15, and 19 (E6, E13, E15, and E19), and coxsackievirus B2 (CVB2), whereas enterovirus C99 (EV-C99) and coxsackievirus A19 (CVA19) were the only two NPEVs identified under EV-C species. Sabin PV1 and PV3 strains were predominantly detected during the first week of birth and 6-8 week time points, respectively, corresponding with the OPV vaccination schedule in South Africa. A total of 11 complete/near-complete genomes were identified from seven NPEV subtypes, and phylogenetic analysis of the three EV-C99 identified revealed that our strains were closely related to other strains from Cameroon and Brazil, suggesting global distribution of these strains. This study provides an insight into the frequency and diversity of EVs circulating in asymptomatic infants from the Free State Province, with the predominance of subtypes from EV-B and EV-C species. This data will be helpful to researchers looking into strategies for the control and treatment of EV infection.
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Affiliation(s)
- Milton T. Mogotsi
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa; (M.T.M.); (A.E.O.)
| | - Ayodeji E. Ogunbayo
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa; (M.T.M.); (A.E.O.)
| | - Hester G. O’Neill
- Department of Microbiology and Biochemistry, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein 9300, South Africa;
| | - Martin M. Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa; (M.T.M.); (A.E.O.)
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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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Orf GS, Ahouidi AD, Mata M, Diedhiou C, Mboup A, Padane A, Manga NM, Dela-del Lawson AT, Averhoff F, Berg MG, Cloherty GA, Mboup S. Next-generation sequencing survey of acute febrile illness in Senegal (2020-2022). Front Microbiol 2024; 15:1362714. [PMID: 38655084 PMCID: PMC11037400 DOI: 10.3389/fmicb.2024.1362714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 03/13/2024] [Indexed: 04/26/2024] Open
Abstract
Introduction Acute febrile illnesses (AFI) in developing tropical and sub-tropical nations are challenging to diagnose due to the numerous causes and non-specific symptoms. The proliferation of rapid diagnostic testing and successful control campaigns against malaria have revealed that non-Plasmodium pathogens still contribute significantly to AFI burden. Thus, a more complete understanding of local trends and potential causes is important for selecting the correct treatment course, which in turn will reduce morbidity and mortality. Next-generation sequencing (NGS) in a laboratory setting can be used to identify known and novel pathogens in individuals with AFI. Methods In this study, plasma was collected from 228 febrile patients tested negative for malaria at clinics across Senegal from 2020-2022. Total nucleic acids were extracted and converted to metagenomic NGS libraries. To identify viral pathogens, especially those present at low concentration, an aliquot of each library was processed with a viral enrichment panel and sequenced. Corresponding metagenomic libraries were also sequenced to identify non-viral pathogens. Results and Discussion Sequencing reads for pathogens with a possible link to febrile illness were identified in 51/228 specimens, including (but not limited to): Borrelia crocidurae (N = 7), West Nile virus (N = 3), Rickettsia felis (N = 2), Bartonella quintana (N = 1), human herpesvirus 8 (N = 1), and Saffold virus (N = 1). Reads corresponding to Plasmodium falciparum were detected in 19 specimens, though their presence in the cohort was likely due to user error of rapid diagnostic testing or incorrect specimen segregation at the clinics. Mosquito-borne pathogens were typically detected just after the conclusion of the rainy season, while tick-borne pathogens were mostly detected before the rainy season. The three West Nile virus strains were phylogenetically characterized and shown to be related to both European and North American clades. Surveys such as this will increase the understanding of the potential causes of non-malarial AFI, which may help inform diagnostic and treatment options for clinicians who provide care to patients in Senegal.
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Affiliation(s)
- Gregory S. Orf
- Core Diagnostics, Abbott Laboratories, Abbott Park, IL, United States
- Abbott Pandemic Defense Coalition, Abbott Park, IL, United States
| | - Ambroise D. Ahouidi
- Abbott Pandemic Defense Coalition, Abbott Park, IL, United States
- Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation, Dakar, Senegal
| | - Maximillian Mata
- Core Diagnostics, Abbott Laboratories, Abbott Park, IL, United States
- Abbott Pandemic Defense Coalition, Abbott Park, IL, United States
| | - Cyrille Diedhiou
- Abbott Pandemic Defense Coalition, Abbott Park, IL, United States
- Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation, Dakar, Senegal
| | - Aminata Mboup
- Abbott Pandemic Defense Coalition, Abbott Park, IL, United States
- Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation, Dakar, Senegal
| | - Abdou Padane
- Abbott Pandemic Defense Coalition, Abbott Park, IL, United States
- Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation, Dakar, Senegal
| | - Noel Magloire Manga
- Unit of Infectious and Tropical Diseases, Université Assane Seck, Hôpital de la Paix, Ziguinchor, Senegal
| | | | - Francisco Averhoff
- Core Diagnostics, Abbott Laboratories, Abbott Park, IL, United States
- Abbott Pandemic Defense Coalition, Abbott Park, IL, United States
| | - Michael G. Berg
- Core Diagnostics, Abbott Laboratories, Abbott Park, IL, United States
- Abbott Pandemic Defense Coalition, Abbott Park, IL, United States
| | - Gavin A. Cloherty
- Core Diagnostics, Abbott Laboratories, Abbott Park, IL, United States
- Abbott Pandemic Defense Coalition, Abbott Park, IL, United States
| | - Souleymane Mboup
- Abbott Pandemic Defense Coalition, Abbott Park, IL, United States
- Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation, Dakar, Senegal
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6
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Ijeomah IM, Temitope FOC, Lander DC, Sheriff AT, Uwem GE, Bernard OA, Oluseyi OA, Elijah OI, Toluwani AG, Arthur OO, Toluwanimi AE, Bolutife PO, Damilola OG, Titilola OO, Oluwadamilola GA, Muhammad AI, Omotosho KI, Johnson AA, Jelle M, Olubusuyi AM. Classic human astrovirus 4, 8, MLB-3, and likely new genotype 5 sublineage in stool samples of children in Nigeria. J Med Virol 2024; 96:e29489. [PMID: 38402605 DOI: 10.1002/jmv.29489] [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: 08/29/2023] [Revised: 02/07/2024] [Accepted: 02/13/2024] [Indexed: 02/27/2024]
Abstract
Human astrovirus (HAstV) is a nonenveloped RNA virus and has been implicated in acute gastroenteritis among children and elderly. However, there exists a substantial dearth of information on HAstV strains circulating in Nigeria. Viral-like particles were purified from archived 254 stool samples of children with acute flaccid paralysis between January and December 2020 from five states in Nigeria, using the NetoVIR protocol. Extracted viral RNA and DNA were subjected to a reverse transcription step and subsequent random polymerase chain reaction amplification. Library preparation and Illumina sequencing were performed. Using the virome paired-end reads pipeline, raw reads were processed into genomic contigs. Phylogenetic and pairwise identity analysis of the recovered HAstV genomes was performed. Six near-complete genome sequences of HAstV were identified and classified as HAstV4 (n = 1), HAstV5 (n = 1), HAstV8 (n = 1), and MLB-3 (n = 3). The HAstV5 belonged to a yet unclassified sublineage, which we tentatively named HAstV-5d. Phylogenetic analysis of open reading frames 1a, 1b, and 2 suggested recombination events inside the MAstV1 species. Furthermore, phylogenetic analysis implied a geographic linkage between the HAstV5 strain from this study with two strains from Cameroon across all the genomic regions. We report for the first time the circulation of HAstV genotypes 4, 8, and MLB-3 in Nigeria and present data suggestive for the existence of a new sublineage of HAstV5. To further understand the burden, diversity, and evolution of HAstV, increased research interest as well as robust HAstV surveillance in Nigeria is essential.
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Affiliation(s)
- Ifeorah M Ijeomah
- Department of Medical Laboratory Sciences and Center for Translation and Implementation Research, University of Nigeria Enugu Campus, Enugu, Nigeria
| | - Faleye O C Temitope
- Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - De Coninck Lander
- Laboratory of Viral Metagenomics, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Agbaje T Sheriff
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - George E Uwem
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University Ede, Ede, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Ede, Nigeria
| | - Onoja A Bernard
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Olayinka A Oluseyi
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Oni I Elijah
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Ajileye G Toluwani
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Oragwa O Arthur
- Department of Veterinary Microbiology, Faculty of Veterinary Medicine, University of Jos, Jos, Nigeria
| | - Akinleye E Toluwanimi
- Phytomedicine Unit, Department of Pharmacognosy, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria
| | - Popoola O Bolutife
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Osasona G Damilola
- Department of Medical Laboratory Sciences, Faculty of Basic Medical Sciences, Osun State and Hospitals Management Board, Redeemer's University Ede, Ado-Ekiti, Nigeria
| | - Olayinka O Titilola
- National Polio Laboratory, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | | | - Ahmed I Muhammad
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Komolafe I Omotosho
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Ede, Nigeria
| | - Adeniji A Johnson
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Infectious Disease Institute, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Matthijnssens Jelle
- Laboratory of Viral Metagenomics, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Adewumi M Olubusuyi
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Infectious Disease Institute, College of Medicine, University of Ibadan, Ibadan, Nigeria
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Alipour F, Holmes C, Lu YY, Hill KA, Kari L. Leveraging machine learning for taxonomic classification of emerging astroviruses. Front Mol Biosci 2024; 10:1305506. [PMID: 38274100 PMCID: PMC10808839 DOI: 10.3389/fmolb.2023.1305506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 12/12/2023] [Indexed: 01/27/2024] Open
Abstract
Astroviruses are a family of genetically diverse viruses associated with disease in humans and birds with significant health effects and economic burdens. Astrovirus taxonomic classification includes two genera, Avastrovirus and Mamastrovirus. However, with next-generation sequencing, broader interspecies transmission has been observed necessitating a reexamination of the current host-based taxonomic classification approach. In this study, a novel taxonomic classification method is presented for emergent and as yet unclassified astroviruses, based on whole genome sequence k-mer composition in addition to host information. An optional component responsible for identifying recombinant sequences was added to the method's pipeline, to counteract the impact of genetic recombination on viral classification. The proposed three-pronged classification method consists of a supervised machine learning method, an unsupervised machine learning method, and the consideration of host species. Using this three-pronged approach, we propose genus labels for 191 as yet unclassified astrovirus genomes. Genus labels are also suggested for an additional eight as yet unclassified astrovirus genomes for which incompatibility was observed with the host species, suggesting cross-species infection. Lastly, our machine learning-based approach augmented by a principal component analysis (PCA) analysis provides evidence supporting the hypothesis of the existence of human astrovirus (HAstV) subgenus of the genus Mamastrovirus, and a goose astrovirus (GoAstV) subgenus of the genus Avastrovirus. Overall, this multipronged machine learning approach provides a fast, reliable, and scalable prediction method of taxonomic labels, able to keep pace with emerging viruses and the exponential increase in the output of modern genome sequencing technologies.
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Affiliation(s)
- Fatemeh Alipour
- School of Computer Science, University of Waterloo, Waterloo, ON, Canada
| | - Connor Holmes
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Yang Young Lu
- School of Computer Science, University of Waterloo, Waterloo, ON, Canada
| | - Kathleen A. Hill
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Lila Kari
- School of Computer Science, University of Waterloo, Waterloo, ON, Canada
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Zhang Y, Sharma S, Tom L, Liao YT, Wu VCH. Gut Phageome-An Insight into the Role and Impact of Gut Microbiome and Their Correlation with Mammal Health and Diseases. Microorganisms 2023; 11:2454. [PMID: 37894111 PMCID: PMC10609124 DOI: 10.3390/microorganisms11102454] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
The gut microbiota, including bacteria, archaea, fungi, and viruses, compose a diverse mammalian gut environment and are highly associated with host health. Bacteriophages, the viruses that infect bacteria, are the primary members of the gastrointestinal virome, known as the phageome. However, our knowledge regarding the gut phageome remains poorly understood. In this review, the critical role of the gut phageome and its correlation with mammalian health were summarized. First, an overall profile of phages across the gastrointestinal tract and their dynamic roles in shaping the surrounding microorganisms was elucidated. Further, the impacts of the gut phageome on gastrointestinal fitness and the bacterial community were highlighted, together with the influence of diets on the gut phageome composition. Additionally, new reports on the role of the gut phageome in the association of mammalian health and diseases were reviewed. Finally, a comprehensive update regarding the advanced phage benchwork and contributions of phage-based therapy to prevent/treat mammalian diseases was provided. This study provides insights into the role and impact of the gut phagenome in gut environments closely related to mammal health and diseases. The findings provoke the potential applications of phage-based diagnosis and therapy in clinical and agricultural fields. Future research is needed to uncover the underlying mechanism of phage-bacterial interactions in gut environments and explore the maintenance of mammalian health via phage-regulated gut microbiota.
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Affiliation(s)
| | | | | | | | - Vivian C. H. Wu
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, CA 94710, USA
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9
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Kashnikov AY, Epifanova NV, Novikova NA. On the nature of picobirnaviruses. Vavilovskii Zhurnal Genet Selektsii 2023; 27:264-275. [PMID: 37293447 PMCID: PMC10244588 DOI: 10.18699/vjgb-23-32] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 06/10/2023] Open
Abstract
The picobirnaviruses (Picobirnaviridae, Picobirnavirus, PBVs) are currently thought to be animal viruses, as they are usually found in animal stool samples. However, no animal model or cell culture for their propagation has yet been found. In 2018, a hypothetical assumption about PBVs belonging to prokaryotic viruses was put forward and experimentally substantiated. This hypothesis is based on the presence of Shine-Dalgarno sequences in the genome of all PBVs before three reading frames (ORF) at the ribosomal binding site, with which the prokaryotic genome is saturated, while in the eukaryotic genome such regions occur with low frequency. The genome saturation with the Shine-Dalgarno sequences, as well as the preservation of this saturation in the progeny, according to scientists, allows us to attribute PBVs to prokaryotic viruses. On the other hand, there is a possibility that PBVs belong to viruses of eukaryotic hosts - fungi or invertebrates, since PBV-like sequences similar to the genome of fungal viruses from the families of mitoviruses and partitiviruses have been identified. In this regard, the idea arose that, in terms of reproduction mode, PBVs resemble fungal viruses. The divergence of views on the true PBV host(s) has sparked discussions among scientists and required further research to elucidate their nature. The review highlights the results of the search for a PBV host. The reasons for the occurrence of atypical sequences among the PBV genome sequences that use an alternative mitochondrial code of lower eukaryotes (fungi and invertebrates) for the translation of viral RNA-dependent RNA polymerase (RdRp) instead of the standard genetic code are analyzed. The purpose of the review was to collect arguments in support of the hypothesis about the phage nature of PBVs and to find the most realistic explanation of the reasons for identifying non-standard genomic sequences for PBVs. Based on the hypothesis about the genealogical relationship of PBVs with RNA viruses from other families with similar segmented genomes, such as Reoviridae, Cystoviridae, Totiviridae and Partitiviridae, virologists support the assumption of a decisive role in the origin of atypical PBV-like reassortment strains between PBVs and viruses of the listed families. The collected arguments given in this review indicate a high probability of a phage nature of PBVs. The data presented in the review show that the belonging of PBV-like progeny to prokaryotic or eukaryotic viruses is determined not only by its genome saturation level with a prokaryotic motif, standard or mitochondrial genetic code. The primary structure of the gene encoding the viral capsid protein responsible for the presence or absence of specific proteolytic properties of the virus that determine its ability for independent horizontal transmission into new cells may also be a decisive factor.
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Affiliation(s)
- A Yu Kashnikov
- I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russia
| | - N V Epifanova
- I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russia
| | - N A Novikova
- I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russia
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10
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Kouidhi S, Zidi O, Belkhiria Z, Rais H, Ayadi A, Ben Ayed F, Mosbah A, Cherif A, El Gaaied ABA. Gut microbiota, an emergent target to shape the efficiency of cancer therapy. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2023; 4:240-265. [PMID: 37205307 PMCID: PMC10185446 DOI: 10.37349/etat.2023.00132] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 01/04/2023] [Indexed: 05/21/2023] Open
Abstract
It is now well-acknowledged that microbiota has a profound influence on both human health and illness. The gut microbiota has recently come to light as a crucial element that influences cancer through a variety of mechanisms. The connections between the microbiome and cancer therapy are further highlighted by a number of preclinical and clinical evidence, suggesting that these complicated interactions may vary by cancer type, treatment, or even by tumor stage. The paradoxical relationship between gut microbiota and cancer therapies is that in some cancers, the gut microbiota may be necessary to maintain therapeutic efficacy, whereas, in other cancers, gut microbiota depletion significantly increases efficacy. Actually, mounting research has shown that the gut microbiota plays a crucial role in regulating the host immune response and boosting the efficacy of anticancer medications like chemotherapy and immunotherapy. Therefore, gut microbiota modulation, which aims to restore gut microbial balance, is a viable technique for cancer prevention and therapy given the expanding understanding of how the gut microbiome regulates treatment response and contributes to carcinogenesis. This review will provide an outline of the gut microbiota's role in health and disease, along with a summary of the most recent research on how it may influence the effectiveness of various anticancer medicines and affect the growth of cancer. This study will next cover the newly developed microbiota-targeting strategies including prebiotics, probiotics, and fecal microbiota transplantation (FMT) to enhance anticancer therapy effectiveness, given its significance.
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Affiliation(s)
- Soumaya Kouidhi
- Laboratory BVBGR-LR11ES31, Biotechnopole Sidi Thabet, University Manouba, ISBST, Ariana 2020, Tunisia
- Association Tunisienne de Lutte contre le Cancer (ATCC), Tunis, Tunisia
| | - Oumaima Zidi
- Laboratory BVBGR-LR11ES31, Biotechnopole Sidi Thabet, University Manouba, ISBST, Ariana 2020, Tunisia
- Department of Biologu, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis 1068, Tunisia
| | | | - Henda Rais
- Association Tunisienne de Lutte contre le Cancer (ATCC), Tunis, Tunisia
- Service d’Oncologie Médicale, Hôpital Salah-Azaïz, Tunis 1006, Tunisia
| | - Aida Ayadi
- Department of Pathology, Abderrahman Mami Hospital, University of Tunis El Manar, Ariana 2080, Tunisia
| | - Farhat Ben Ayed
- Association Tunisienne de Lutte contre le Cancer (ATCC), Tunis, Tunisia
| | - Amor Mosbah
- Laboratory BVBGR-LR11ES31, Biotechnopole Sidi Thabet, University Manouba, ISBST, Ariana 2020, Tunisia
| | - Ameur Cherif
- Laboratory BVBGR-LR11ES31, Biotechnopole Sidi Thabet, University Manouba, ISBST, Ariana 2020, Tunisia
| | - Amel Ben Ammar El Gaaied
- Laboratory of Genetics, Immunology and Human Pathology, Department of Biology, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis 1068, Tunisia
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11
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Rivera-Gutiérrez X, Morán P, Taboada B, Serrano-Vázquez A, Isa P, Rojas-Velázquez L, Pérez-Juárez H, López S, Torres J, Ximénez C, Arias CF. The fecal and oropharyngeal eukaryotic viromes of healthy infants during the first year of life are personal. Sci Rep 2023; 13:938. [PMID: 36650178 PMCID: PMC9845211 DOI: 10.1038/s41598-022-26707-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 12/19/2022] [Indexed: 01/19/2023] Open
Abstract
Using a metagenomic sequencing approach, we described and compared the diversity and dynamics of the oropharyngeal and fecal eukaryotic virome of nine asymptomatic children in a semi-rural community setting located in the State of Morelos, Mexico. Ninety oropharyngeal swabs and 97 fecal samples were collected starting 2 weeks after birth and monthly thereafter until 12 months of age. In both niches, more than 95% of the total sequence reads were represented by viruses that replicate either in humans or in plants. Regarding human viruses, three families were most abundant and frequent in the oropharynx: Herpesviridae, Picornaviridae, and Reoviridae; in fecal samples, four virus families predominated: Caliciviridae, Picornaviridae, Reoviridae, and Anelloviridae. Both niches showed a high abundance of plant viruses of the family Virgaviridae. Differences in the frequency and abundance of sequence reads and diversity of virus species were observed in both niches and throughout the year of study, with some viruses already present in the first months of life. Our results suggest that the children's virome is dynamic and likely shaped by the environment, feeding, and age. Moreover, composition analysis suggests that the virome composition is mostly individual. Whether this constant exposition to different viruses has a long-term impact on children's health or development remains to be studied.
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Affiliation(s)
- Xaira Rivera-Gutiérrez
- Instituto de Biotecnologıía, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Patricia Morán
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Blanca Taboada
- Instituto de Biotecnologıía, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico.
| | - Angélica Serrano-Vázquez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Pavel Isa
- Instituto de Biotecnologıía, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Liliana Rojas-Velázquez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Horacio Pérez-Juárez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Susana López
- Instituto de Biotecnologıía, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Javier Torres
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Cecilia Ximénez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico.
| | - Carlos F Arias
- Instituto de Biotecnologıía, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico.
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12
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Clinton NA, Hameed SA, Agyei EK, Jacob JC, Oyebanji VO, Jabea CE. 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] [MESH Headings] [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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Affiliation(s)
- Njinju Asaba Clinton
- Health and Empowerment Foundation, Cameroon
- Mbonge District Hospital, Cameroon
- University of Buea, Cameroon
| | | | - Eugene Kusi Agyei
- Faculty of Pharmacy and Pharmaceutical Sciences, Kwame Nkrumah University of Science and Technology, Ghana
| | | | | | - Cyril Ekabe Jabea
- Health and Empowerment Foundation, Cameroon
- Mbonge District Hospital, Cameroon
- University of Buea, Cameroon
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13
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Detection of human feces pecovirus in newly diagnosed HIV patients in Brazil. PLoS One 2022; 17:e0272067. [PMID: 36067165 PMCID: PMC9447917 DOI: 10.1371/journal.pone.0272067] [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: 07/09/2021] [Accepted: 07/12/2022] [Indexed: 12/04/2022] Open
Abstract
Circular single stranded DNA viruses (CRESS DNA) encoding a homologous replication-associated protein (REP) have been identified in most of eukaryotic groups. It is not clear yet the role in human diseases or details of the life cycle of these viruses. Recently, much interest has been raised in the evolutionary history of CRESS DNA owing to the increasing number of new sequences obtained by Next-Generation Sequencing (NGS) in distinct host species. In this study we describe two full-length CRESS DNA genomes obtained of two newly diagnosed HIV patients from São Paulo State, Brazil. The initial BLASTx search indicated that both sequences (named SP-FFB/2020 and SP-MJMS/2020) are highly similar (98%) to a previous CRESS DNA sequence detected in human fecal sample from Peru in 2016 and designated as pecovirus (Peruvian stool-associated circo-like virus). This study reported for the first time the Human feces pecovirus in the feces of two newly diagnosed HIV patients in Brazil. Our comparative analysis showed that although pecoviruses in South America share an identical genome structure they diverge and form distinct clades. Thus, we suggest the circulation of different species of pecoviruses in Latin America. Nevertheless, further studies must be done to examine the pathogenicity of this virus.
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14
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Kennedy EA, Holtz LR. Gut virome in early life: origins and implications. Curr Opin Virol 2022; 55:101233. [PMID: 35690009 PMCID: PMC9575407 DOI: 10.1016/j.coviro.2022.101233] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/03/2022] [Accepted: 05/05/2022] [Indexed: 12/15/2022]
Abstract
The human body is colonized by a multitude of bacteria, fungi, and viruses, which play important roles in health and disease. Microbial colonization during early life is thought to be a particularly important period with lasting consequences for health. Viral populations in the gut are particularly dynamic in early life before they stabilize in adulthood. The composition of the early-life virome is increasingly recognized as a determinant of disease later in life. Here, we review the development of the virome in healthy infants, as well as the role of the early-life virome in the development of disease states including diarrhea, malnutrition, and autoimmune diseases.
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Affiliation(s)
- Elizabeth A Kennedy
- Washington University School of Medicine, Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, St. Louis, MO 63110, USA
| | - Lori R Holtz
- Washington University School of Medicine, Department of Pediatrics, St. Louis, MO 63110, USA.
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15
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Villanova F, Milagres FADP, Brustulin R, Araújo ELL, Pandey RP, Raj VS, Deng X, Delwart E, Luchs A, da Costa AC, Leal É. A New Circular Single-Stranded DNA Virus Related with Howler Monkey Associated Porprismacovirus 1 Detected in Children with Acute Gastroenteritis. Viruses 2022; 14:1472. [PMID: 35891454 PMCID: PMC9319269 DOI: 10.3390/v14071472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/17/2022] [Accepted: 06/30/2022] [Indexed: 12/04/2022] Open
Abstract
Putative replication-associated protein (REP) and capsid-like (CAP) proteins are encoded by circular single-stranded DNA viruses (CRESS DNA), which have been found in samples from most eukaryotic groups. However, the details of these viruses' life cycles and their significance in diseases have yet to be established. We presented and analyzed two full-length CRESS DNA genomes acquired from two children diagnosed with acute gastroenteritis (GI) in the northeast state of Tocantins, Brazil, using next-generation sequencing and a virus-like filtration approach. Both sequences (named SmaCV3BR08 and SmaCV3BR291) are closely similar to a prior CRESS DNA sequence discovered in the feces of a new world monkey (Alouatta caraya) from the United States in 2009 and termed Howler monkey-associated porprismacovirus 1 (Genbank ID: NC 026317). According to our comparative study, these porprismacovirus genomes deviate by 10% at the nucleotide level. For comparative reasons, the divergence between our sequences (SmaCV3BR08 and SmaCV3BR291) and a porprismacovirus recently identified in a human fecal sample from Peru is 37%. These data suggest that there is a great diversity of porprismacoviruses in South America, perhaps more than two species. In addition, the finding of closely related sequences of porprismacoviruses in humans and native monkeys highlights the zoonotic potential of these viruses.
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Affiliation(s)
- Fabiola Villanova
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, Pará, Brazil;
| | - Flávio Augusto de Padua Milagres
- Secretary of Health of Tocantins, Palmas 77453-000, Tocantins, Brazil; (F.A.d.P.M.); (R.B.)
- Public Health Laboratory of Tocantins State (LACEN/TO), Palmas 77016-330, Tocantins, Brazil
| | - Rafael Brustulin
- Secretary of Health of Tocantins, Palmas 77453-000, Tocantins, Brazil; (F.A.d.P.M.); (R.B.)
| | - Emerson Luiz Lima Araújo
- General Coordination of Public Health Laboratories of the Strategic Articulation Department of the Health Surveillance Secretariat of the Ministry of Health (CGLAB/DAEVS/SVS-MS), Brasília 70719-040, Distrito Federal, Brazil;
| | - Ramendra Pati Pandey
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat 131029, Haryana, India; (R.P.P.); (V.S.R.)
| | - V. Samuel Raj
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat 131029, Haryana, India; (R.P.P.); (V.S.R.)
| | - Xutao Deng
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA 94118, USA; (X.D.); (E.D.)
- Department Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Eric Delwart
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA 94118, USA; (X.D.); (E.D.)
- Department Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Adriana Luchs
- Enteric Disease Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo 01246-000, São Paulo, Brazil;
| | - Antonio Charlys da Costa
- Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, São Paulo, Brazil;
| | - Élcio Leal
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, Pará, Brazil;
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16
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Chu Y, Guo S, Cui D, Fu X, Ma Y. DeephageTP: a convolutional neural network framework for identifying phage-specific proteins from metagenomic sequencing data. PeerJ 2022; 10:e13404. [PMID: 35698617 PMCID: PMC9188312 DOI: 10.7717/peerj.13404] [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: 12/06/2021] [Accepted: 04/18/2022] [Indexed: 01/14/2023] Open
Abstract
Bacteriophages (phages) are the most abundant and diverse biological entity on Earth. Due to the lack of universal gene markers and database representatives, there about 50-90% of genes of phages are unable to assign functions. This makes it a challenge to identify phage genomes and annotate functions of phage genes efficiently by homology search on a large scale, especially for newly phages. Portal (portal protein), TerL (large terminase subunit protein), and TerS (small terminase subunit protein) are three specific proteins of Caudovirales phage. Here, we developed a CNN (convolutional neural network)-based framework, DeephageTP, to identify the three specific proteins from metagenomic data. The framework takes one-hot encoding data of original protein sequences as the input and automatically extracts predictive features in the process of modeling. To overcome the false positive problem, a cutoff-loss-value strategy is introduced based on the distributions of the loss values of protein sequences within the same category. The proposed model with a set of cutoff-loss-values demonstrates high performance in terms of Precision in identifying TerL and Portal sequences (94% and 90%, respectively) from the mimic metagenomic dataset. Finally, we tested the efficacy of the framework using three real metagenomic datasets, and the results shown that compared to the conventional alignment-based methods, our proposed framework had a particular advantage in identifying the novel phage-specific protein sequences of portal and TerL with remote homology to their counterparts in the training datasets. In summary, our study for the first time develops a CNN-based framework for identifying the phage-specific protein sequences with high complexity and low conservation, and this framework will help us find novel phages in metagenomic sequencing data. The DeephageTP is available at https://github.com/chuym726/DeephageTP.
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Affiliation(s)
- Yunmeng Chu
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese, Shenzhen, Guangdong, P.R. China,Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen, Fujian, P.R. China
| | - Shun Guo
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese, Shenzhen, Guangdong, P.R. China
| | - Dachao Cui
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese, Shenzhen, Guangdong, P.R. China
| | - Xiongfei Fu
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese, Shenzhen, Guangdong, P.R. China
| | - Yingfei Ma
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese, Shenzhen, Guangdong, P.R. China
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17
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Liang G, Gao H, Bushman FD. The pediatric virome in health and disease. Cell Host Microbe 2022; 30:639-649. [PMID: 35550667 DOI: 10.1016/j.chom.2022.04.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/22/2022] [Accepted: 04/11/2022] [Indexed: 11/03/2022]
Abstract
Associations between the global microbiome and diseases of children have been studied extensively; however, research on the viral component of the microbiome, the "virome," is less advanced. The analysis of disease associations with the virome is often technically challenging, requiring a close examination of the "virome dark matter." The gut is a particularly rich source of viral particles, and now multiple studies have reported intriguing associations of the virome with childhood diseases. For example, virome studies have elucidated new lineages of gut viruses that appear to be tightly associated with childhood diarrhea, and consistent patterns are starting to emerge from virome studies in pediatric IBD. In this review, we summarize the methods for studying the virome and recent research on the nature of the virome during childhood, focusing on specific studies of the intestinal virome in pediatric diseases.
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Affiliation(s)
- Guanxiang Liang
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.
| | - Hongyan Gao
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Frederic D Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6076, USA.
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18
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Portal TM, Vanmechelen B, Van Espen L, Jansen D, Teixeira DM, de Sousa ESA, da Silva VP, de Lima JS, Reymão TKA, Sequeira CG, da Silva Ventura AMR, da Silva LD, Resque HR, Matthijnssens J, Gabbay YB. Molecular characterization of the gastrointestinal eukaryotic virome in elderly people in Belem, Para, Brazil. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 99:105241. [PMID: 35150892 DOI: 10.1016/j.meegid.2022.105241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 01/24/2022] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
Acute gastroenteritis is one of the main causes of mortality and morbidity worldwide, affecting mainly children, the immunocompromised and elderly people. Enteric viruses, especially rotavirus A, are considered important etiological agents, while long-term care facilities are considered favorable environments for the occurrence of sporadic cases and outbreaks of acute gastroenteritis. Therefore, it is important to monitor the viral agents present in nursing homes, especially because studies involving the elderly population in Brazil are scarce, resulting in a lack of available virological data. As a result, the causative agent remains unidentified in a large number of reported acute gastroenteritis cases. However, the advent of next-generation sequencing provides new opportunities for viral detection and discovery. The aim of this study was to identify the viruses that circulate among elderly people with and without acute gastroenteritis, living in residential care homes in Belém, Pará, Brazil, between 2017 and 2019. Ninety-three samples were collected and screened by immunochromatography and qPCR. After, the samples were analyzed individually or in pools by next generation sequencing to identify the viruses circulating in this population. In 26 sequenced samples, members of 13 eukaryotic virus families were identified. The most abundantly present virus families were Parvoviridae, Genomoviridae and Smacoviridae. Contigs displaying similarity to pegiviruses were also detected. Furthermore, a near-complete rotavirus A genome was obtained and could be classified as G3P[8] genotype with the equine DS-1-like genetic background. Complete sequences of the VP4 and VP7 genes of a rotavirus C were also detected, belonging to G4P[2]. This study demonstrates the first characterization of the gastrointestinal virome in elderly in Northern Brazil. A diversity of viruses was found to be present in patients with and without diarrhea, reinforcing the need to monitor elderly people residing in long-term care facilities, especially in cases of acute gastroenteritis.
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Affiliation(s)
- Thayara Morais Portal
- Postgraduate Program in Virology, Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, Pará, Brazil.
| | - Bert Vanmechelen
- KU Leuven-University of Leuven, Rega Institute Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Leuven, Belgium
| | - Lore Van Espen
- KU Leuven-University of Leuven, Rega Institute Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Leuven, Belgium
| | - Daan Jansen
- KU Leuven-University of Leuven, Rega Institute Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Leuven, Belgium
| | - Dielle Monteiro Teixeira
- Postgraduate Program in Virology, Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, Pará, Brazil
| | - Emanuella Sarmento Alho de Sousa
- Scientific Initiation with CNPq and FAPESPA scholarships from Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, Pará, Brazil
| | - Victor Pereira da Silva
- Scientific Initiation with CNPq and FAPESPA scholarships from Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, Pará, Brazil
| | - Juliana Silva de Lima
- Scientific Initiation with CNPq and FAPESPA scholarships from Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, Pará, Brazil
| | - Tammy Katlhyn Amaral Reymão
- Federal University of Pará, Institute of Biological Sciences, Biology of Infectious and Parasitic Agents Graduate Program, Belém, Pará, Brazil
| | | | | | - Luciana Damascena da Silva
- Virology Section, Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, Pará, Brazil
| | - Hugo Reis Resque
- Virology Section, Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, Pará, Brazil
| | - Jelle Matthijnssens
- KU Leuven-University of Leuven, Rega Institute Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Leuven, Belgium
| | - Yvone Benchimol Gabbay
- Virology Section, Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, Pará, Brazil
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19
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Tamburini FB, Maghini D, Oduaran OH, Brewster R, Hulley MR, Sahibdeen V, Norris SA, Tollman S, Kahn K, Wagner RG, Wade AN, Wafawanaka F, Gómez-Olivé FX, Twine R, Lombard Z, Hazelhurst S, Bhatt AS. Short- and long-read metagenomics of urban and rural South African gut microbiomes reveal a transitional composition and undescribed taxa. Nat Commun 2022; 13:926. [PMID: 35194028 PMCID: PMC8863827 DOI: 10.1038/s41467-021-27917-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/25/2021] [Indexed: 12/15/2022] Open
Abstract
Human gut microbiome research focuses on populations living in high-income countries and to a lesser extent, non-urban agriculturalist and hunter-gatherer societies. The scarcity of research between these extremes limits our understanding of how the gut microbiota relates to health and disease in the majority of the world's population. Here, we evaluate gut microbiome composition in transitioning South African populations using short- and long-read sequencing. We analyze stool from adult females living in rural Bushbuckridge (n = 118) or urban Soweto (n = 51) and find that these microbiomes are taxonomically intermediate between those of individuals living in high-income countries and traditional communities. We demonstrate that reference collections are incomplete for characterizing microbiomes of individuals living outside high-income countries, yielding artificially low beta diversity measurements, and generate complete genomes of undescribed taxa, including Treponema, Lentisphaerae, and Succinatimonas. Our results suggest that the gut microbiome of South Africans does not conform to a simple "western-nonwestern" axis and contains undescribed microbial diversity.
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Affiliation(s)
| | - Dylan Maghini
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Ovokeraye H Oduaran
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Ryan Brewster
- School of Medicine, Stanford University, Stanford, CA, USA
| | - Michaella R Hulley
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa.,Division of Human Genetics, School of Pathology, Faculty of Health Sciences, National Health Laboratory Service & University of the Witwatersrand, Johannesburg, South Africa
| | - Venesa Sahibdeen
- Division of Human Genetics, School of Pathology, Faculty of Health Sciences, National Health Laboratory Service & University of the Witwatersrand, Johannesburg, South Africa
| | - Shane A Norris
- SAMRC Developmental Pathways for Health Research Unit, Department of Paediatrics, University of the Witwatersrand, Johannesburg, South Africa.,School of Human Development and Health, University of Southampton, Southampton, UK
| | - Stephen Tollman
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,INDEPTH Network, East Legon, Accra, Ghana
| | - Kathleen Kahn
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,INDEPTH Network, East Legon, Accra, Ghana
| | - Ryan G Wagner
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,INDEPTH Network, East Legon, Accra, Ghana
| | - Alisha N Wade
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Floidy Wafawanaka
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - F Xavier Gómez-Olivé
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,INDEPTH Network, East Legon, Accra, Ghana
| | - Rhian Twine
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Zané Lombard
- Division of Human Genetics, School of Pathology, Faculty of Health Sciences, National Health Laboratory Service & University of the Witwatersrand, Johannesburg, South Africa
| | | | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa. .,School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa.
| | - Ami S Bhatt
- Department of Genetics, Stanford University, Stanford, CA, USA. .,School of Medicine, Stanford University, Stanford, CA, USA. .,Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA.
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20
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Identification of missed viruses by metagenomic sequencing of clinical respiratory samples from Kenya. Sci Rep 2022; 12:202. [PMID: 34997042 PMCID: PMC8742071 DOI: 10.1038/s41598-021-03987-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 12/02/2021] [Indexed: 01/30/2023] Open
Abstract
Pneumonia remains a major cause of mortality and morbidity. Most molecular diagnoses of viruses rely on polymerase chain reaction (PCR) assays that however can fail due to primer mismatch. We investigated the performance of routine virus diagnostics in Kilifi, Kenya, using random-primed viral next generation sequencing (viral NGS) on respiratory samples which tested negative for the common viral respiratory pathogens by a local standard diagnostic panel. Among 95 hospitalised pneumonia patients and 95 household-cohort individuals, analysis of viral NGS identified at least one respiratory-associated virus in 35 (37%) and 23 (24%) samples, respectively. The majority (66%; 42/64) belonged to the Picornaviridae family. The NGS data analysis identified a number of viruses that were missed by the diagnostic panel (rhinovirus, human metapneumovirus, respiratory syncytial virus and parainfluenza virus), and these failures could be attributed to PCR primer/probe binding site mismatches. Unexpected viruses identified included parvovirus B19, enterovirus D68, coxsackievirus A16 and A24 and rubella virus. The regular application of such viral NGS could help evaluate assay performance, identify molecular causes of missed diagnoses and reveal gaps in the respiratory virus set used for local screening assays. The results can provide actionable information to improve the local pneumonia diagnostics and reveal locally important viral pathogens.
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21
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Viral metagenomics reveals diverse viruses in the fecal samples of children with diarrhea. Virol Sin 2022; 37:82-93. [PMID: 35234620 PMCID: PMC8922427 DOI: 10.1016/j.virs.2022.01.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 12/06/2021] [Indexed: 01/12/2023] Open
Abstract
Diarrhea is the third leading cause of death in developing countries in children under the age of five. About half a million children die of diarrhea every year, most of which in developing countries. Viruses are the main pathogen of diarrhea. In China, the fecal virome of children with diarrhea has been rarely studied. Using an unbiased viral metagenomics approach, we analyzed the fecal virome in children with diarrhea. Many DNA or RNA viruses associated with diarrhea identified in those fecal samples were mainly from six families of Adenoviridae, Astroviridae, Caliciviridae, Parvoviridae, Picornaviridae, and Reoviridae. Among them, the family of Caliciviridae accounts for the largest proportion of 78.42%, following with Adenoviridae (8.94%) and Picornaviridae (8.36%). In addition to those diarrhea-related viruses that have already been confirmed to cause human diarrhea, the viruses not associated with diarrhea were also identified including anellovirus and picobirnavirus. This study increased our understanding of diarrheic children fecal virome and provided valuable information for the prevention and treatment of viral diarrhea in this area. Many DNA or RNA viruses associated with diarrhea were identified in this study. Viruses belonging to the family of Caliciviridae were the most main pathogen that induced children diarrhea. In addition to those diarrhea-related viruses, the viruses not associated with diarrhea were also identified.
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22
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Bonny P, Schaeffer J, Besnard A, Desdouits M, Ngang JJE, Le Guyader FS. Human and Animal RNA Virus Diversity Detected by Metagenomics in Cameroonian Clams. Front Microbiol 2021; 12:770385. [PMID: 34917052 PMCID: PMC8669915 DOI: 10.3389/fmicb.2021.770385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/18/2021] [Indexed: 11/13/2022] Open
Abstract
Many recent pandemics have been recognized as zoonotic viral diseases. While their origins remain frequently unknown, environmental contamination may play an important role in emergence. Thus, being able to describe the viral diversity in environmental samples contributes to understand the key issues in zoonotic transmission. This work describes the use of a metagenomic approach to assess the diversity of eukaryotic RNA viruses in river clams and identify sequences from human or potentially zoonotic viruses. Clam samples collected over 2years were first screened for the presence of norovirus to verify human contamination. Selected samples were analyzed using metagenomics, including a capture of sequences from viral families infecting vertebrates (VirCapSeq-VERT) before Illumina NovaSeq sequencing. The bioinformatics analysis included pooling of data from triplicates, quality filtering, elimination of bacterial and host sequences, and a deduplication step before de novo assembly. After taxonomic assignment, the viral fraction represented 0.8–15% of reads with most sequences (68–87%) remaining un-assigned. Yet, several mammalian RNA viruses were identified. Contigs identified as belonging to the Astroviridae were the most abundant, with some nearly complete genomes of bastrovirus identified. Picobirnaviridae sequences were related to strains infecting bats, and few others to strains infecting humans or other hosts. Hepeviridae sequences were mostly related to strains detected in sponge samples but also strains from swine samples. For Caliciviridae and Picornaviridae, most of identified sequences were related to strains infecting bats, with few sequences close to human norovirus, picornavirus, and genogroup V hepatitis A virus. Despite a need to improve the sensitivity of our method, this study describes a large diversity of RNA virus sequences from clam samples. To describe all viral contaminants in this type of food, and being able to identify the host infected by viral sequences detected, may help to understand some zoonotic transmission events and alert health authorities of possible emergence.
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Affiliation(s)
- Patrice Bonny
- Laboratoire de Microbiologie, LSEM/SG2M, Ifremer, Nantes, France.,Département de Microbiologie, Université de Yaoundé I, Yaoundé, Cameroon.,Centre de Recherche en Alimentation et Nutrition, IMPM, Yaoundé, Cameroon
| | - Julien Schaeffer
- Laboratoire de Microbiologie, LSEM/SG2M, Ifremer, Nantes, France
| | - Alban Besnard
- Laboratoire de Microbiologie, LSEM/SG2M, Ifremer, Nantes, France
| | - Marion Desdouits
- Laboratoire de Microbiologie, LSEM/SG2M, Ifremer, Nantes, France
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23
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Allali I, Abotsi RE, Tow LA, Thabane L, Zar HJ, Mulder NM, Nicol MP. Human microbiota research in Africa: a systematic review reveals gaps and priorities for future research. MICROBIOME 2021; 9:241. [PMID: 34911583 PMCID: PMC8672519 DOI: 10.1186/s40168-021-01195-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 11/14/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND The role of the human microbiome in health and disease is an emerging and important area of research; however, there is a concern that African populations are under-represented in human microbiome studies. We, therefore, conducted a systematic survey of African human microbiome studies to provide an overview and identify research gaps. Our secondary objectives were: (i) to determine the number of peer-reviewed publications; (ii) to identify the extent to which the researches focused on diseases identified by the World Health Organization [WHO] State of Health in the African Region Report as being the leading causes of morbidity and mortality in 2018; (iii) to describe the extent and pattern of collaborations between researchers in Africa and the rest of the world; and (iv) to identify leadership and funders of the studies. METHODOLOGY We systematically searched Medline via PubMed, Scopus, CINAHL, Academic Search Premier, Africa-Wide Information through EBSCOhost, and Web of Science from inception through to 1st April 2020. We included studies that characterized samples from African populations using next-generation sequencing approaches. Two reviewers independently conducted the literature search, title and abstract, and full-text screening, as well as data extraction. RESULTS We included 168 studies out of 5515 records retrieved. Most studies were published in PLoS One (13%; 22/168), and samples were collected from 33 of the 54 African countries. The country where most studies were conducted was South Africa (27/168), followed by Kenya (23/168) and Uganda (18/168). 26.8% (45/168) focused on diseases of significant public health concern in Africa. Collaboration between scientists from the United States of America and Africa was most common (96/168). The first and/or last authors of 79.8% of studies were not affiliated with institutions in Africa. Major funders were the United States of America National Institutes of Health (45.2%; 76/168), Bill and Melinda Gates Foundation (17.8%; 30/168), and the European Union (11.9%; 20/168). CONCLUSIONS There are significant gaps in microbiome research in Africa, especially those focusing on diseases of public health importance. There is a need for local leadership, capacity building, intra-continental collaboration, and national government investment in microbiome research within Africa. Video Abstract.
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Affiliation(s)
- Imane Allali
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Centre of Human Pathologies, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Rabat, Morocco
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Regina E Abotsi
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Cape Town, South Africa
- Department of Pharmaceutical Microbiology, School of Pharmacy, University of Health and Allied Sciences, Ho, Ghana
| | - Lemese Ah Tow
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Lehana Thabane
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario, Canada
- Biostatistics Unit, Father Sean O'Sullivan Research Centre, St Joseph's Healthcare, Hamilton, Ontario, Canada
- Departments of Paediatrics and Anaesthesia, McMaster University, Hamilton, Ontario, Canada
- Centre for Evaluation of Medicine, St Joseph's Healthcare, Hamilton, Ontario, Canada
- Population Health Research Institute, Hamilton Health Sciences, Hamilton, Ontario, Canada
- Centre for Evidence-based Health Care, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa
- Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Heather J Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, Cape Town, South Africa
- MRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Nicola M Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Mark P Nicol
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
- School of Biomedical Sciences, University of Western Australia, M504, Perth, WA, 6009, Australia.
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24
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Novel Cyclovirus Species in Dogs with Hemorrhagic Gastroenteritis. Viruses 2021; 13:v13112155. [PMID: 34834961 PMCID: PMC8622408 DOI: 10.3390/v13112155] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 11/21/2022] Open
Abstract
Nested PCRs with circovirus/cyclovirus pan-rep (replicase gene) primers detected eukaryotic circular Rep-encoding single-stranded DNA (CRESS DNA) viruses in three (samples CN9E, CN16E and CN34) of 18 canine parvovirus-2-positive fecal samples from household dogs with hemorrhagic gastroenteritis on the Caribbean island of Nevis. The complete genomes of CRESS DNA virus CN9E, CN16E and CN34 were determined by inverse nested PCRs. Based on (i) genome organization, (ii) location of the putative origin of replication, (iii) pairwise genome-wide sequence identities, (iv) the presence of conserved motifs in the putative replication-associated protein (Rep) and the arginine-rich region in the amino terminus of the putative capsid protein (Cp) and (v) a phylogenetic analysis, CN9E, CN16E and CN34 were classified as cycloviruses. Canine-associated cycloviruses CN16E and CN34 were closely related to each other and shared low genome-wide nucleotide (59.642–59.704%), deduced Rep (35.018–35.379%) and Cp (26.601%) amino acid sequence identities with CN9E. All the three canine-associated cycloviruses shared < 80% genome-wide pairwise nucleotide sequence identities with cycloviruses from other animals/environmental samples, constituting two novel species (CN9E and CN16E/34) within the genus Cyclovirus. Considering the feeding habits of dogs, we could not determine whether the cycloviruses were of dietary origin or infected the host. Interestingly, the CN9E putative Rep-encoding open reading frame was found to use the invertebrate mitochondrial genetic code with an alternative initiation codon (ATA) for translation, corroborating the hypothesis that cycloviruses are actually arthropod-infecting viruses. To our knowledge, this is the first report on the detection and complete genome analysis of cycloviruses from domestic dogs.
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25
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Van Espen L, Bak EG, Beller L, Close L, Deboutte W, Juel HB, Nielsen T, Sinar D, De Coninck L, Frithioff-Bøjsøe C, Fonvig CE, Jacobsen S, Kjærgaard M, Thiele M, Fullam A, Kuhn M, Holm JC, Bork P, Krag A, Hansen T, Arumugam M, Matthijnssens J. A Previously Undescribed Highly Prevalent Phage Identified in a Danish Enteric Virome Catalog. mSystems 2021; 6:e0038221. [PMID: 34665009 PMCID: PMC8525569 DOI: 10.1128/msystems.00382-21] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 09/02/2021] [Indexed: 01/06/2023] Open
Abstract
Gut viruses are important, yet often neglected, players in the complex human gut microbial ecosystem. Recently, the number of human gut virome studies has been increasing; however, we are still only scratching the surface of the immense viral diversity. In this study, 254 virus-enriched fecal metagenomes from 204 Danish subjects were used to generate the Danish Enteric Virome Catalog (DEVoC) containing 12,986 nonredundant viral scaffolds, of which the majority was previously undescribed, encoding 190,029 viral genes. The DEVoC was used to compare 91 healthy DEVoC gut viromes from children, adolescents, and adults that were used to create the DEVoC. Gut viromes of healthy Danish subjects were dominated by phages. While most phage genomes (PGs) only occurred in a single subject, indicating large virome individuality, 39 PGs were present in more than 10 healthy subjects. Among these 39 PGs, the prevalences of three PGs were associated with age. To further study the prevalence of these 39 prevalent PGs, 1,880 gut virome data sets of 27 studies from across the world were screened, revealing several age-, geography-, and disease-related prevalence patterns. Two PGs also showed a remarkably high prevalence worldwide-a crAss-like phage (20.6% prevalence), belonging to the tentative AlphacrAssvirinae subfamily, and a previously undescribed circular temperate phage infecting Bacteroides dorei (14.4% prevalence), called LoVEphage because it encodes lots of viral elements. Due to the LoVEphage's high prevalence and novelty, public data sets in which the LoVEphage was detected were de novo assembled, resulting in an additional 18 circular LoVEphage-like genomes (67.9 to 72.4 kb). IMPORTANCE Through generation of the DEVoC, we added numerous previously uncharacterized viral genomes and genes to the ever-increasing worldwide pool of human gut viromes. The DEVoC, the largest human gut virome catalog generated from consistently processed fecal samples, facilitated the analysis of the 91 healthy Danish gut viromes. Characterizing the biggest cohort of healthy gut viromes from children, adolescents, and adults to date confirmed the previously established high interindividual variation in human gut viromes and demonstrated that the effect of age on the gut virome composition was limited to the prevalence of specific phage (groups). The identification of a previously undescribed prevalent phage illustrates the usefulness of developing virome catalogs, and we foresee that the DEVoC will benefit future analysis of the roles of gut viruses in human health and disease.
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Affiliation(s)
- Lore Van Espen
- KU Leuven, Department of Microbiology, Immunology, & Transplantation, Rega Institute, Division of Clinical & Epidemiological Virology, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Emilie Glad Bak
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Leen Beller
- KU Leuven, Department of Microbiology, Immunology, & Transplantation, Rega Institute, Division of Clinical & Epidemiological Virology, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Lila Close
- KU Leuven, Department of Microbiology, Immunology, & Transplantation, Rega Institute, Division of Clinical & Epidemiological Virology, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Ward Deboutte
- KU Leuven, Department of Microbiology, Immunology, & Transplantation, Rega Institute, Division of Clinical & Epidemiological Virology, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Helene Bæk Juel
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Trine Nielsen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Deniz Sinar
- KU Leuven, Department of Microbiology, Immunology, & Transplantation, Rega Institute, Division of Clinical & Epidemiological Virology, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Lander De Coninck
- KU Leuven, Department of Microbiology, Immunology, & Transplantation, Rega Institute, Division of Clinical & Epidemiological Virology, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Christine Frithioff-Bøjsøe
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Children’s Obesity Clinic, accredited European Centre for Obesity Management, Department of Paediatrics, Copenhagen University Hospital Holbaek, Holbaek, Denmark
| | - Cilius Esmann Fonvig
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Children’s Obesity Clinic, accredited European Centre for Obesity Management, Department of Paediatrics, Copenhagen University Hospital Holbaek, Holbaek, Denmark
| | - Suganya Jacobsen
- Department of Gastroenterology and Hepatology, Centre for Liver Research, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Maria Kjærgaard
- Department of Gastroenterology and Hepatology, Centre for Liver Research, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Maja Thiele
- Department of Gastroenterology and Hepatology, Centre for Liver Research, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Anthony Fullam
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Michael Kuhn
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jens-Christian Holm
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Children’s Obesity Clinic, accredited European Centre for Obesity Management, Department of Paediatrics, Copenhagen University Hospital Holbaek, Holbaek, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, Berlin, Germany
- Yonsei Frontier Lab (YFL), Yonsei University, Seoul, South Korea
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Aleksander Krag
- Department of Gastroenterology and Hepatology, Centre for Liver Research, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Manimozhiyan Arumugam
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jelle Matthijnssens
- KU Leuven, Department of Microbiology, Immunology, & Transplantation, Rega Institute, Division of Clinical & Epidemiological Virology, Laboratory of Viral Metagenomics, Leuven, Belgium
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26
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Glud HA, George S, Skovgaard K, Larsen LE. Zoonotic and reverse zoonotic transmission of viruses between humans and pigs. APMIS 2021; 129:675-693. [PMID: 34586648 PMCID: PMC9297979 DOI: 10.1111/apm.13178] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 08/28/2021] [Indexed: 12/30/2022]
Abstract
Humans and pigs share a close contact relationship, similar biological traits, and one of the highest estimated number of viruses compared to other mammalian species. The contribution and directionality of viral exchange between humans and pigs remain unclear for some of these viruses, but their transmission routes are important to characterize in order to prevent outbreaks of disease in both host species. This review collects and assesses the evidence to determine the likely transmission route of 27 viruses between humans and pigs.
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Affiliation(s)
- Helena Aagaard Glud
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Sophie George
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kerstin Skovgaard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Lars Erik Larsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
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27
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Luchs A, Tardy K, Tahmasebi R, Morillo SG, Milagres FADP, Morais VDS, Brustulin R, Teles MDAR, de Azevedo LS, de Souza EV, Medeiros RS, de Souza YFVP, Araújo ELL, Witkin SS, Deng X, Delwart E, Sabino EC, Leal E, da Costa AC. Human astrovirus types 1, 4 and 5 circulating among children with acute gastroenteritis in a rural Brazilian state, 2010-2016. Arch Virol 2021; 166:3165-3172. [PMID: 34417874 DOI: 10.1007/s00705-021-05206-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 06/22/2021] [Indexed: 11/30/2022]
Abstract
This study combined conventional epidemiology of human astroviruses. From 2010 to 2016, 232 stool samples from children under 5 years of age were screened using NGS and conventional RT-PCR followed by genetic analysis in order to investigate the genotypic diversity of classical human astrovirus (HAstV) circulating in Tocantins State, Brazil. HAstV was detected in 16 cases (6.9%). Seven specimens (43.7%; 7/16) were positive according RT-PCR and next-generation sequencing (NGS) to investigate the molecular to both NGS and RT-PCR. NGS and RT-PCR individually revealed six (37.5%; 6/16) and three (18.8%; 3/16) additional positive samples, respectively. Sequencing of the HAstV-positive samples revealed HAstV-1a (9/16), HAstV-4c (3/16), and HAstV-5c (4/16) lineages.
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Affiliation(s)
- Adriana Luchs
- Instituto Adolfo Lutz, Centro de Virologia, Núcleo de Doenças Entéricas, Av. Dr Arnaldo, nº 355, São Paulo, SP, 01246-902, Brazil.
| | - Kaelan Tardy
- Instituto de Medicina Tropical, Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar, nº 470, São Paulo, SP, 05403-000, Brazil
| | - Roozbeh Tahmasebi
- Instituto de Medicina Tropical, Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar, nº 470, São Paulo, SP, 05403-000, Brazil
| | - Simone Guadagnucci Morillo
- Instituto Adolfo Lutz, Centro de Virologia, Núcleo de Doenças Entéricas, Av. Dr Arnaldo, nº 355, São Paulo, SP, 01246-902, Brazil
| | - Flavio Augusto de Pádua Milagres
- Universidade Federal do Tocantins, Tocantins, Brazil.,Laboratório Central de Saúde Pública do Tocantins (Lacen-TO), Tocantins, Brazil
| | - Vanessa Dos Santos Morais
- Instituto de Medicina Tropical, Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar, nº 470, São Paulo, SP, 05403-000, Brazil
| | - Rafael Brustulin
- Universidade Federal do Tocantins, Tocantins, Brazil.,Laboratório Central de Saúde Pública do Tocantins (Lacen-TO), Tocantins, Brazil
| | | | - Lais Sampaio de Azevedo
- Instituto Adolfo Lutz, Centro de Virologia, Núcleo de Doenças Entéricas, Av. Dr Arnaldo, nº 355, São Paulo, SP, 01246-902, Brazil
| | - Ellen Viana de Souza
- Instituto Adolfo Lutz, Centro de Virologia, Núcleo de Doenças Entéricas, Av. Dr Arnaldo, nº 355, São Paulo, SP, 01246-902, Brazil
| | - Roberta Salzone Medeiros
- Instituto Adolfo Lutz, Centro de Virologia, Núcleo de Doenças Entéricas, Av. Dr Arnaldo, nº 355, São Paulo, SP, 01246-902, Brazil
| | | | - Emerson Luiz Lima Araújo
- Coordenação Geral de Laboratórios de Saúde Pública, Departamento de Articulação Estratégica de Vigilância em Saúde da Secretaria de Vigilância em Saúde do Ministério da Saúde do Brasil (CGLAB/DAEVS/SVS-MS), Brasília, Brazil
| | - Steven S Witkin
- Instituto de Medicina Tropical, Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar, nº 470, São Paulo, SP, 05403-000, Brazil.,Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, USA
| | - Xutao Deng
- Vitalant Research Institute, San Francisco, USA.,Department Laboratory Medicine, University of California San Francisco, San Francisco, USA
| | - Eric Delwart
- Vitalant Research Institute, San Francisco, USA.,Department Laboratory Medicine, University of California San Francisco, San Francisco, USA
| | - Ester Cerdeira Sabino
- Instituto de Medicina Tropical, Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar, nº 470, São Paulo, SP, 05403-000, Brazil
| | - Elcio Leal
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Pará, Brazil
| | - Antonio Charlys da Costa
- Instituto de Medicina Tropical, Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar, nº 470, São Paulo, SP, 05403-000, Brazil.
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Molecular Epidemiology and Characterization of Picobirnavirus in Wild Deer and Cattle from Australia: Evidence of Genogroup I and II in the Upper Respiratory Tract. Viruses 2021; 13:v13081492. [PMID: 34452357 PMCID: PMC8402760 DOI: 10.3390/v13081492] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/23/2021] [Accepted: 07/27/2021] [Indexed: 12/23/2022] Open
Abstract
Picobirnaviruses (PBVs) have been detected in several species of animals worldwide; however, data pertaining to their presence in Australian wild and domestic animals are limited. Although PBVs are mostly found in faecal samples, their detection in blood and respiratory tract samples raises questions concerning their tropism and pathogenicity. We report here PBV detection in wild deer and cattle from southeastern Australia. Through metagenomics, the presence of PBV genogroups I (GI) and II (GII) were detected in deer serum and plasma. Molecular epidemiology studies targeting the partial RNA-dependent RNA polymerase gene were performed in a wide range of specimens (serum, faeces, spleen, lung, nasal swabs, and trachea) collected from wild deer and cattle, with PCR amplification obtained in all specimen types except lung and spleen. Our results reveal the predominance of GI and concomitant detection of both genogroups in wild deer and cattle. In concordance with other studies, the detected GI sequences displayed high genetic diversity, however in contrast, GII sequences clustered into three distinct clades. Detection of both genogroups in the upper respiratory tract (trachea and nasal swab) of deer in the present study gives more evidence about the respiratory tract tropism of PBV. Although much remains unknown about the epidemiology and tropism of PBVs, our study suggests a wide distribution of these viruses in southeastern Australia.
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29
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Tisza MJ, Buck CB. A catalog of tens of thousands of viruses from human metagenomes reveals hidden associations with chronic diseases. Proc Natl Acad Sci U S A 2021; 118:e2023202118. [PMID: 34083435 PMCID: PMC8201803 DOI: 10.1073/pnas.2023202118] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Despite remarkable strides in microbiome research, the viral component of the microbiome has generally presented a more challenging target than the bacteriome. This gap persists, even though many thousands of shotgun sequencing runs from human metagenomic samples exist in public databases, and all of them encompass large amounts of viral sequence data. The lack of a comprehensive database for human-associated viruses has historically stymied efforts to interrogate the impact of the virome on human health. This study probes thousands of datasets to uncover sequences from over 45,000 unique virus taxa, with historically high per-genome completeness. Large publicly available case-control studies are reanalyzed, and over 2,200 strong virus-disease associations are found.
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Affiliation(s)
- Michael J Tisza
- Laboratory of Cellular Oncology, National Cancer Institute, NIH, Bethesda, MD 20892
| | - Christopher B Buck
- Laboratory of Cellular Oncology, National Cancer Institute, NIH, Bethesda, MD 20892
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30
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Rahman R, Rahman S, Afrad MMH, Talha M, Islam D, Uddin KMM, Ahmed S, Afrad MH, Faruque ASG, Hossian ME, Rahman M. Epidemiology and genetic characterization of human sapovirus among hospitalized acute diarrhea patients in Bangladesh, 2012-2015. J Med Virol 2021; 93:6220-6228. [PMID: 34081341 DOI: 10.1002/jmv.27125] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 11/09/2022]
Abstract
Human sapovirus, which causes acute gastroenteritis, is not well studied and poorly understood. This study aims to investigate the contribution of sapovirus in diarrhea, their clinical association, and genotypic diversity. Fecal specimens (n = 871) were randomly selected from diarrheal patients who attended International Centre for Diarrhoeal Disease Research, Bangladesh hospital in Dhaka, Bangladesh during January 2012-December 2015 and tested for the presence of sapovirus RNA using real-time polymerase chain reaction. Sapovirus RNA was identified in 2.3% (n = 20) of the samples. Seventy-five percent of the sapovirus positive cases were coinfected with other pathogens, such as rotavirus, norovirus, enterotoxigenic Escherichia coli, adenovirus, Shigella spp., and Vibrio cholerae. A vast genetic diversity was observed among sapovirus with at least seven common genotypes (GI.1, GI.2, GI.7, GII.1, GII.4, GII.6, and GIV), and a new genotype GII.NA1. Some of the GI.1 strains detected were similar to GI.4 in the polymerase region sequence and were confirmed as recombinant strains. Our findings suggest that the overall contribution of sapovirus in hospitalized diarrheal illness is low but highlight enormous genetic diversity.
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Affiliation(s)
- Rajibur Rahman
- Virology Laboratory, Infectious Diseases Division (IDD), International Centre for Diarrhoeal Disease Research (ICDDR), Bangladesh, Dhaka, Bangladesh
| | - Sezanur Rahman
- Virology Laboratory, Infectious Diseases Division (IDD), International Centre for Diarrhoeal Disease Research (ICDDR), Bangladesh, Dhaka, Bangladesh
| | - Md M H Afrad
- Virology Laboratory, Infectious Diseases Division (IDD), International Centre for Diarrhoeal Disease Research (ICDDR), Bangladesh, Dhaka, Bangladesh
| | - Muhammad Talha
- Virology Laboratory, Infectious Diseases Division (IDD), International Centre for Diarrhoeal Disease Research (ICDDR), Bangladesh, Dhaka, Bangladesh
| | - Deen Islam
- Virology Laboratory, Infectious Diseases Division (IDD), International Centre for Diarrhoeal Disease Research (ICDDR), Bangladesh, Dhaka, Bangladesh
| | - K M Main Uddin
- Virology Laboratory, Infectious Diseases Division (IDD), International Centre for Diarrhoeal Disease Research (ICDDR), Bangladesh, Dhaka, Bangladesh
| | - Shahnawaz Ahmed
- Nutrition and Clinical Services Division (NCSD), International Centre for Diarrhoeal Disease Research (ICDDR), Bangladesh, Dhaka, Bangladesh
| | - Mokibul H Afrad
- Virology Laboratory, Infectious Diseases Division (IDD), International Centre for Diarrhoeal Disease Research (ICDDR), Bangladesh, Dhaka, Bangladesh
| | - Abu S G Faruque
- Nutrition and Clinical Services Division (NCSD), International Centre for Diarrhoeal Disease Research (ICDDR), Bangladesh, Dhaka, Bangladesh
| | - Mohammad E Hossian
- Virology Laboratory, Infectious Diseases Division (IDD), International Centre for Diarrhoeal Disease Research (ICDDR), Bangladesh, Dhaka, Bangladesh
| | - Mustafizur Rahman
- Virology Laboratory, Infectious Diseases Division (IDD), International Centre for Diarrhoeal Disease Research (ICDDR), Bangladesh, Dhaka, Bangladesh
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31
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Song K, Lin X, Liu Y, Ji F, Zhang L, Chen P, Zhao C, Song Y, Tao Z, Xu A. Detection of Human Sapoviruses in Sewage in China by Next Generation Sequencing. FOOD AND ENVIRONMENTAL VIROLOGY 2021; 13:270-280. [PMID: 33755873 PMCID: PMC7985922 DOI: 10.1007/s12560-021-09469-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 02/25/2021] [Indexed: 06/12/2023]
Abstract
Human sapovirus (SaV) is an important causative agent of nonbacterial gastroenteritis in humans. However, little is known about its circulation in China. To study the prevalence and diversity of human SaV genotypes circulating in eastern China, a 3-year environmental surveillance combined with next generation sequencing (NGS) technology was conducted. A total of 36 raw sewage samples were collected from January 2017 to December 2019 in Jinan and processed. Thirty-five (97.22%) samples were positive for human SaV genome in quantitative RT-PCR assay; 33 (91.67%) samples were positive in nested RT-PCR assay on partial capsid VP1 sequence and all amplicons were further analyzed separately by NGS. Among those, ten genotypes belonging to the genogroups of GI, GII, GIV, and GV were identified by NGS, including 4 major genotypes (GI.2, GI.1, GV.1 and GI.3) and 6 uncommon genotypes (GII.5, GII.1, GII.NA1, GII.3, GI.6 and GIV.1). A temporal switch of predominant genotype was observed from GI.2 to GI.1 around June 2019. Local and foreign sequences clustered together in some branches according to phylogenetic analysis, indicating frequent transmission of various lineages in different regions of the world. Environmental surveillance provides a comprehensive picture of human SaV in China. NGS-based environmental surveillance improves our knowledge on human SaV circulating in communities greatly and should be encouraged as a sensitive surveillance tool.
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Affiliation(s)
- Ke Song
- Department of Microbiology, School of Public Health, Cheeloo College of Medicine, Shandong University, No. 44 Wenhuaxi Road, Jinan, 250012, People's Republic of China
| | - Xiaojuan Lin
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, No. 16992 Jingshi Road, Jinan, 250014, People's Republic of China
| | - Yao Liu
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, No. 16992 Jingshi Road, Jinan, 250014, People's Republic of China
| | - Feng Ji
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, No. 16992 Jingshi Road, Jinan, 250014, People's Republic of China
| | - Li Zhang
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, No. 16992 Jingshi Road, Jinan, 250014, People's Republic of China
| | - Peng Chen
- School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University, 44-1 Wenhuaxi Road, Jinan, 250012, People's Republic of China
| | - Chenxu Zhao
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, No. 44 Wenhuaxi Road, Jinan, 250012, People's Republic of China
| | - Yanyan Song
- Department of Microbiology, School of Public Health, Cheeloo College of Medicine, Shandong University, No. 44 Wenhuaxi Road, Jinan, 250012, People's Republic of China.
| | - Zexin Tao
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, No. 16992 Jingshi Road, Jinan, 250014, People's Republic of China.
| | - Aiqiang Xu
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, No. 16992 Jingshi Road, Jinan, 250014, People's Republic of China
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, No. 44 Wenhuaxi Road, Jinan, 250012, People's Republic of China
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32
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Cinek O, Kramna L, Odeh R, Alassaf A, Ibekwe MAU, Ahmadov G, Elmahi BME, Mekki H, Lebl J, Abdullah MA. Eukaryotic viruses in the fecal virome at the onset of type 1 diabetes: A study from four geographically distant African and Asian countries. Pediatr Diabetes 2021; 22:558-566. [PMID: 33786936 DOI: 10.1111/pedi.13207] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/21/2020] [Accepted: 02/26/2021] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES Studies of the fecal virome in type 1 diabetes (T1D) have been limited to populations of Europe and the United States. We therefore sought to characterize the stool virome in children after onset of T1D and in matched control subjects from four geographically distant African and Asian countries. METHODS Samples of stool were collected from 73 children and adolescents shortly after T1D onset (Azerbaijan 19, Jordan 20, Nigeria 14, Sudan 20) and 105 matched control subjects of similar age and locale. Metagenomic sequencing of the DNA and RNA virome was performed, and virus positivity was defined as more than 0.001% of reads of the sample. Selected viruses were also quantified using real-time PCR. Conditional logistic regression was used to model associations with eukaryotic virus positivity. RESULTS Signals of 387 different viral species were detected; at least one eukaryotic virus was detected in 71% case and 65% control samples. Neither of observed eukaryotic virus species or genera differed in frequency between children with T1D and controls. There was a suggestive association of the total count of different viral genera per sample between cases (1.45 genera) and controls (1.10 genera, OR 1.24, 95%CI 0.98-1.57), and an unplanned subanalysis suggested marginally more frequent endogenous retrovirus signal in cases (in 28.8% vs. in 8.6% controls, OR = 4.55, 95%CI 1.72-12). CONCLUSIONS No clear and consistent association with T1D was observed in the fecal viromes from four distant non-European populations. The finding of borderline associations of human endogenous retroviruses merits further exploration.
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Affiliation(s)
- Ondrej Cinek
- Department of Pediatrics, Second Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
| | - Lenka Kramna
- Department of Pediatrics, Second Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
| | - Rasha Odeh
- Department of Pediatrics, School of Medicine, University of Jordan, Amman, Jordan
| | - Abeer Alassaf
- Department of Pediatrics, School of Medicine, University of Jordan, Amman, Jordan
| | - Mary Ann Ugochi Ibekwe
- Department of Pediatrics, Federal Teaching Hospital Abakaliki, Ebonyi State University, Abakaliki, Nigeria
| | | | - Bashir Mukhtar Elwasila Elmahi
- Department of Paediatrics and Child Health, Faculty of Medicine, University of Khartoum, Khartoum, Sudan.,Sudan Childhood Diabetes Center, Khartoum, Sudan
| | - Hanan Mekki
- Department of Paediatrics and Child Health, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Jan Lebl
- Department of Pediatrics, Second Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
| | - Mohammed Ahmed Abdullah
- Department of Paediatrics and Child Health, Faculty of Medicine, University of Khartoum, Khartoum, Sudan.,Sudan Childhood Diabetes Center, Khartoum, Sudan
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33
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Hedžet S, Rupnik M, Accetto T. Novel Siphoviridae Bacteriophages Infecting Bacteroides uniformis Contain Diversity Generating Retroelement. Microorganisms 2021; 9:microorganisms9050892. [PMID: 33919474 PMCID: PMC8143477 DOI: 10.3390/microorganisms9050892] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/19/2021] [Accepted: 04/19/2021] [Indexed: 11/25/2022] Open
Abstract
Intestinal phages are abundant and important components of gut microbiota, yet the isolated and characterized representatives that infect abundant gut bacteria are sparse. Here we describe the isolation of human intestinal phages infecting Bacteroidesuniformis. Bacteroides is one of the most common bacterial groups in the global human gut microbiota; however, to date not many Bacteroides specific phages are known. Phages isolated in this study belong to a novel viral genus, Bacuni, within the Siphoviridae family. Their genomes encode diversity-generating retroelements (DGR), which were shown in other bacteriophages to promote phage adaptation to rapidly changing environmental conditions and to broaden their host range. Three isolated phages showed 99.83% genome identity but one of them infected a distinct B. uniformis strain. The tropism of Bacuni phages appeared to be dependent on the interplay of DGR mediated sequence variations of gene encoding putative phage fimbrial tip proteins and mutations in host genes coding for outer-membrane proteins. We found prophages with up to 85% amino acid similarity over two-thirds of the Bacuni phage genome in the B. acidifaciens and Prevotella sp. genomes. Despite the abundance of Bacteroides within the human microbiome, we found Bacuni phages only in a limited subset of published gut metagenomes.
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Affiliation(s)
- Stina Hedžet
- Centre for Medical Microbiology, Department for Microbiological Research, National Laboratory for Health, Environment and Food (NLZOH), 2000 Maribor, Slovenia; (S.H.); (M.R.)
| | - Maja Rupnik
- Centre for Medical Microbiology, Department for Microbiological Research, National Laboratory for Health, Environment and Food (NLZOH), 2000 Maribor, Slovenia; (S.H.); (M.R.)
- Faculty of Medicine, University of Maribor, 2000 Maribor, Slovenia
| | - Tomaž Accetto
- Animal Science Department, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
- Correspondence:
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34
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Fulci V, Stronati L, Cucchiara S, Laudadio I, Carissimi C. Emerging Roles of Gut Virome in Pediatric Diseases. Int J Mol Sci 2021; 22:4127. [PMID: 33923593 PMCID: PMC8073368 DOI: 10.3390/ijms22084127] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/14/2021] [Accepted: 04/15/2021] [Indexed: 12/15/2022] Open
Abstract
In the last decade, the widespread application of shotgun metagenomics provided extensive characterization of the bacterial "dark matter" of the gut microbiome, propelling the development of dedicated, standardized bioinformatic pipelines and the systematic collection of metagenomic data into comprehensive databases. The advent of next-generation sequencing also unravels a previously underestimated viral population (virome) present in the human gut. Despite extensive efforts to characterize the human gut virome, to date, little is known about the childhood gut virome. However, alterations of the gut virome in children have been linked to pathological conditions such as inflammatory bowel disease, type 1 diabetes, malnutrition, diarrhea and celiac disease.
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Affiliation(s)
- Valerio Fulci
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.F.); (L.S.)
| | - Laura Stronati
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.F.); (L.S.)
| | - Salvatore Cucchiara
- Department of Women’s and Children’s Health, Sapienza University of Rome, 00161 Rome, Italy;
| | - Ilaria Laudadio
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.F.); (L.S.)
| | - Claudia Carissimi
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.F.); (L.S.)
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35
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Lambisia AW, Phan MVT, de Laurent ZR, Cotten M, Nokes DJ, Agoti CN. Near-Complete Genome Sequences of Eight Human Astroviruses Recovered from Diarrheal Stool Samples of Hospitalized Children in Coastal Kenya in 2019. Microbiol Resour Announc 2021; 10:e00162-21. [PMID: 33858926 PMCID: PMC8050968 DOI: 10.1128/mra.00162-21] [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: 02/11/2021] [Accepted: 03/16/2021] [Indexed: 11/20/2022] Open
Abstract
Here, using a sequence-independent sequencing approach (M. V. Phan, P. Hong Anh, N. Van Cuong, B. Oude Munnink, et al., Virus Evol 2:vew027, 2016, https://doi.org/10.1093/ve/vew027), we determined human astrovirus (HAstV) genome sequences from eight diarrheal stool samples collected in coastal Kenya in 2019. Phylogenetic analysis identified the following 4 genotypes: HAstV-1 (n = 4), HAstV-2 (n = 1), HAstV-3 (n = 1), and HAstV-5 (n = 2).
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Affiliation(s)
- Arnold W Lambisia
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - My V T Phan
- UK Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - Zaydah R de Laurent
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Matthew Cotten
- UK Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - D James Nokes
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
- School of Life Sciences and Zeeman Institute (SBIDER), University of Warwick, Coventry, United Kingdom
| | - Charles N Agoti
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
- School of Health and Human Sciences, Pwani University, Kilifi, Kenya
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36
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Taboada B, Morán P, Serrano-Vázquez A, Iša P, Rojas-Velázquez L, Pérez-Juárez H, López S, Torres J, Ximenez C, Arias CF. The gut virome of healthy children during the first year of life is diverse and dynamic. PLoS One 2021; 16:e0240958. [PMID: 33852569 PMCID: PMC8046192 DOI: 10.1371/journal.pone.0240958] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 03/30/2021] [Indexed: 01/21/2023] Open
Abstract
In this work, we determined the diversity and dynamics of the gut virome of infants during the first year of life. Fecal samples were collected monthly, from birth to one year of age, from three healthy children living in a semi-rural village in Mexico. Most of the viral reads were classified into six families of bacteriophages including five dsDNA virus families of the order Caudovirales, with Siphoviridae and Podoviridae being the most abundant. Eukaryotic viruses were detected as early as two weeks after birth and remained present all along the first year of life. Thirty-four different eukaryotic virus families were found, where eight of these families accounted for 98% of all eukaryotic viral reads: Anelloviridae, Astroviridae, Caliciviridae, Genomoviridae, Parvoviridae, Picornaviridae, Reoviridae and the plant-infecting viruses of the Virgaviridae family. Some viruses in these families are known human pathogens, and it is surprising that they were found during the first year of life in infants without gastrointestinal symptoms. The eukaryotic virus species richness found in this work was higher than that observed in previous studies; on average between 7 and 24 virus species were identified per sample. The richness and abundance of the eukaryotic virome significantly increased during the second semester of life, probably because of an increased environmental exposure of infants with age. Our findings suggest an early and permanent contact of infants with a diverse array of bacteriophages and eukaryotic viruses, whose composition changes over time. The bacteriophages and eukaryotic viruses found in these children could represent a metastable virome, whose potential influence on the development of the infant's immune system or on the health of the infants later in life, remains to be investigated.
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Affiliation(s)
- Blanca Taboada
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Patricia Morán
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Angélica Serrano-Vázquez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Pavel Iša
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Liliana Rojas-Velázquez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Horacio Pérez-Juárez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Susana López
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Javier Torres
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México
- * E-mail: (CFA); (CX); (JT)
| | - Cecilia Ximenez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
- * E-mail: (CFA); (CX); (JT)
| | - Carlos F. Arias
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
- * E-mail: (CFA); (CX); (JT)
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Abstract
Picobirnaviruses (PBVs) are bisegmented double-stranded RNA viruses that have been detected in a wide variety of animal species including invertebrates and in environmental samples. Since PBVs are ubiquitous in feces/gut contents of humans and other animals with or without diarrhea, they were considered as opportunistic enteric pathogens of mammals and avian species. However, the virus remains to be propagated in animal cell cultures, or in gnotobiotic animals. Recently, the classically defined prokaryotic motif, the ribosomal binding site sequence, has been identified upstream of putative open reading frame/s in PBV and PBV-like sequences from humans, various animals, and environmental samples, suggesting that PBVs might be prokaryotic viruses. On the other hand, based on the detection of some novel PBV-like RNA-dependent RNA polymerase sequences that use the alternative mitochondrial genetic code (that of mold or invertebrates) for translation, and principal component analysis of codon usage bias for these sequences, it has been proposed that PBVs might be fungal viruses with a lifestyle reminiscent of mitoviruses. These contradicting observations warrant further studies to ascertain the true host/s of PBVs, which still remains controversial. In this minireview, we have focused on the various findings that have raised a debate on the true host/s of PBVs.
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Affiliation(s)
- Souvik Ghosh
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
| | - Yashpal S Malik
- College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Science University, Ludhiana, India
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38
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Massimino L, Lovisa S, Antonio Lamparelli L, Danese S, Ungaro F. Gut eukaryotic virome in colorectal carcinogenesis: Is that a trigger? Comput Struct Biotechnol J 2020; 19:16-28. [PMID: 33363706 PMCID: PMC7750180 DOI: 10.1016/j.csbj.2020.11.055] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/24/2020] [Accepted: 11/28/2020] [Indexed: 02/07/2023] Open
Abstract
The human gut microbiota is composed of bacteria and viruses that might be associated with colorectal cancer (CRC) onset and progression. Indeed, although viral infections have been reported to be the primary trigger in many diseases, the role of eukaryotic viruses populating the gut mucosa during early colorectal carcinogenesis is underinvestigated. Human eukaryotic viruses in the gut were found to induce alterations of the immune homeostasis so that some viral-dependent mechanisms likely able to induce DNA alterations in the bowel wall have been proposed, although no demonstration is available yet. However, thanks to the latest advancements in computational biology and the implementation of the bioinformatic pipelines, the option of establishing a direct causative link between intestinal virome and CRC will be possible soon, hopefully paving the way to innovative therapeutic strategies blocking or reverting the CRC pathogenesis.
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Affiliation(s)
- Luca Massimino
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
| | - Sara Lovisa
- IBD Center, Laboratory of Gastrointestinal Immunopathology, Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | | | - Silvio Danese
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
- IBD Center, Laboratory of Gastrointestinal Immunopathology, Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | - Federica Ungaro
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
- IBD Center, Laboratory of Gastrointestinal Immunopathology, Humanitas Clinical and Research Center, Rozzano, Milan, Italy
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Mombo IM, Boundenga L, Suquet E, Ngoubangoye B, Maganga GD, Leroy EM, Charpentier MJ, Rougeron V. Natural infection of free-ranging mandrills (Mandrillus sphinx) by enteroviruses and astroviruses in southern Gabon. Microb Pathog 2020; 150:104659. [PMID: 33249166 DOI: 10.1016/j.micpath.2020.104659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/19/2020] [Accepted: 11/20/2020] [Indexed: 10/22/2022]
Abstract
Enteroviruses (Picornaviridae) and astroviruses (Astroviridae) cause various diseases in humans and animals, including in non-human primates (NHPs). Some enteroviruses and astroviruses detected in NHPs are genetically related to those infecting humans, indicating the occurrence of interspecies transmissions. In this study, we screened 200 fecal samples of 56 free-ranging mandrills (Mandrillus sphinx) by nested reverse transcription-PCR with primers targeting the VP1 and RdRp genes, to evaluate the diversity of enterovirus and astrovirus infection, respectively, and the associated zoonotic risk. Overall, ten samples from six mandrills were enterovirus-positive (5%), and three samples from three mandrills were astrovirus-positive (1.5%). This is the first evidence of astrovirus infection in mandrills. Phylogenetic analyses based on the VP1 sequences revealed that all ten enterovirus sequences were part of the species Enterovirus J, suggesting low zoonotic risk. Phylogenetic analysis of the three astrovirus sequences showed that they all belonged to the Mamastrovirus genus. Two astrovirus sequences were highly divergent from all human astrovirus sequences (63.4-73% nucleotide identity), while one sequence (AstV-5) suggested cross-species transmission from humans to mandrills. Additional studies are needed to better characterize the identified astroviruses and to confirm whether mandrills are host of astroviruses than can be transmitted to humans.
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Affiliation(s)
- Illich M Mombo
- Centre International de Recherches Médicales de Franceville (CIRMF), BP769, Franceville, Gabon.
| | - Larson Boundenga
- Centre International de Recherches Médicales de Franceville (CIRMF), BP769, Franceville, Gabon
| | - Eloise Suquet
- Centre International de Recherches Médicales de Franceville (CIRMF), BP769, Franceville, Gabon
| | - Barthélémy Ngoubangoye
- Centre International de Recherches Médicales de Franceville (CIRMF), BP769, Franceville, Gabon
| | - Gaël D Maganga
- Centre International de Recherches Médicales de Franceville (CIRMF), BP769, Franceville, Gabon
| | - Eric M Leroy
- Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle (MIVEGEC), UMR5290, Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Université de Montpellier, 34394, Montpellier, France
| | - Marie J Charpentier
- Institut des Sciences de l'Evolution de Montpellier (ISEM), UMR5554, Université de Montpellier, CNRS, IRD, EPHE, Place Eugène Bataillon (cc065), 34095, Montpellier, France
| | - Virginie Rougeron
- Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle (MIVEGEC), UMR5290, Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Université de Montpellier, 34394, Montpellier, France; Centre de Recherche en Ecologie et Evolution de la Santé (CREES), 34000, Montpellier, France
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40
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Gregory AC, Zablocki O, Zayed AA, Howell A, Bolduc B, Sullivan MB. The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut. Cell Host Microbe 2020; 28:724-740.e8. [PMID: 32841606 PMCID: PMC7443397 DOI: 10.1016/j.chom.2020.08.003] [Citation(s) in RCA: 303] [Impact Index Per Article: 75.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/14/2020] [Accepted: 08/06/2020] [Indexed: 12/12/2022]
Abstract
The gut microbiome profoundly affects human health and disease, and their infecting viruses are likely as important, but often missed because of reference database limitations. Here, we (1) built a human Gut Virome Database (GVD) from 2,697 viral particle or microbial metagenomes from 1,986 individuals representing 16 countries, (2) assess its effectiveness, and (3) report a meta-analysis that reveals age-dependent patterns across healthy Westerners. The GVD contains 33,242 unique viral populations (approximately species-level taxa) and improves average viral detection rates over viral RefSeq and IMG/VR nearly 182-fold and 2.6-fold, respectively. GVD meta-analyses show highly personalized viromes, reveal that inter-study variability from technical artifacts is larger than any "disease" effect at the population level, and document how viral diversity changes from human infancy into senescence. Together, this compact foundational resource, these standardization guidelines, and these meta-analysis findings provide a systematic toolkit to help maximize our understanding of viral roles in health and disease.
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Affiliation(s)
- Ann C Gregory
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Olivier Zablocki
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA; Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Ahmed A Zayed
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA; Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Allison Howell
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Benjamin Bolduc
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA; Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Matthew B Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA; Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH 43210, USA; Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA.
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41
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Abe H, Ushijima Y, Bikangui R, Ondo GN, Zadeh VR, Pemba CM, Mpingabo PI, Igasaki Y, de Vries SG, Grobusch MP, Loembe MM, Agnandji ST, Lell B, Yasuda J. First evidence for continuous circulation of hepatitis A virus subgenotype IIA in Central Africa. J Viral Hepat 2020; 27:1234-1242. [PMID: 32564517 PMCID: PMC7586949 DOI: 10.1111/jvh.13348] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 05/30/2020] [Accepted: 06/08/2020] [Indexed: 12/22/2022]
Abstract
Although a high seroprevalence of antibodies against hepatitis A virus (HAV) has been estimated in Central Africa, the current status of both HAV infections and seroprevalence of anti-HAV antibodies remains unclear due to a paucity of surveillance data available. We conducted a serological survey during 2015-2017 in Gabon, Central Africa, and confirmed a high seroprevalence of anti-HAV antibodies in all age groups. To identify the currently circulating HAV strains and to reveal the epidemiological and genetic characteristics of the virus, we conducted molecular surveillance in a total of 1007 patients presenting febrile illness. Through HAV detection and sequencing, we identified subgenotype IIA (HAV-IIA) infections in the country throughout the year. A significant prevalence trend emerged in the young child population, presenting several infection peaks which appeared to be unrelated to dry or rainy seasons. Whole-genome sequencing and phylogenetic analyses revealed local HAV-IIA evolutionary events in Central Africa, indicating the circulation of HAV-IIA strains of a region-specific lineage. Recombination analysis of complete genome sequences revealed potential recombination events in Gabonese HAV strains. Interestingly, Gabonese HAV-IIA possibly acquired the 5'-untranslated region (5'-UTR) of the rare subgenotype HAV-IIB in recent years, suggesting the present existence of HAV-IIB in Central Africa. These findings indicate a currently stable HAV-IIA circulation in Gabon, with a high risk of infections in children aged under 5 years. Our findings will enhance the understanding of the current status of HAV infections in Central Africa and provide new insight into the molecular epidemiology and evolution of HAV genotype II.
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Affiliation(s)
- Haruka Abe
- Department of Emerging Infectious DiseasesInstitute of Tropical Medicine (NEKKEN)Nagasaki UniversityNagasakiJapan
| | - Yuri Ushijima
- Department of Emerging Infectious DiseasesInstitute of Tropical Medicine (NEKKEN)Nagasaki UniversityNagasakiJapan
| | - Rodrigue Bikangui
- Centre de Recherches Médicales de LambarénéLambarénéGabon,Institute for Tropical MedicineUniversity of TübingenTübingenGermany
| | | | - Vahid R. Zadeh
- Department of Emerging Infectious DiseasesInstitute of Tropical Medicine (NEKKEN)Nagasaki UniversityNagasakiJapan,Graduate School of Biomedical SciencesNagasaki UniversityNagasakiJapan
| | - Christelle M. Pemba
- Department of Emerging Infectious DiseasesInstitute of Tropical Medicine (NEKKEN)Nagasaki UniversityNagasakiJapan,Graduate School of Biomedical SciencesNagasaki UniversityNagasakiJapan
| | - Patrick I. Mpingabo
- Department of Emerging Infectious DiseasesInstitute of Tropical Medicine (NEKKEN)Nagasaki UniversityNagasakiJapan,Graduate School of Biomedical SciencesNagasaki UniversityNagasakiJapan
| | - Yui Igasaki
- Department of Emerging Infectious DiseasesInstitute of Tropical Medicine (NEKKEN)Nagasaki UniversityNagasakiJapan
| | - Sophia G. de Vries
- Centre de Recherches Médicales de LambarénéLambarénéGabon,Division of Internal MedicineDepartment of Infectious DiseasesCenter of Tropical Medicine and Travel MedicineAmsterdam University Medical CentersUniversity of AmsterdamAmsterdamNetherlands
| | - Martin P. Grobusch
- Centre de Recherches Médicales de LambarénéLambarénéGabon,Institute for Tropical MedicineUniversity of TübingenTübingenGermany,Division of Internal MedicineDepartment of Infectious DiseasesCenter of Tropical Medicine and Travel MedicineAmsterdam University Medical CentersUniversity of AmsterdamAmsterdamNetherlands
| | | | - Selidji T. Agnandji
- Centre de Recherches Médicales de LambarénéLambarénéGabon,Institute for Tropical MedicineUniversity of TübingenTübingenGermany
| | - Bertrand Lell
- Centre de Recherches Médicales de LambarénéLambarénéGabon,Division of Infectious Diseases and Tropical MedicineMedical University of ViennaViennaAustria
| | - Jiro Yasuda
- Department of Emerging Infectious DiseasesInstitute of Tropical Medicine (NEKKEN)Nagasaki UniversityNagasakiJapan,Graduate School of Biomedical SciencesNagasaki UniversityNagasakiJapan,National Research Center for the Control and Prevention of Infectious Diseases (CCPID)Nagasaki UniversityNagasakiJapan
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42
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Kashnikov AY, Epifanova NV, Novikova NA. Picobirnaviruses: prevalence, genetic diversity, detection methods. Vavilovskii Zhurnal Genet Selektsii 2020; 24:661-672. [PMID: 33659852 PMCID: PMC7716564 DOI: 10.18699/vj20.660] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
This article presents a general overview of the prevalence, genetic diversity and detection methods of picobirnaviruses (PBVs), which are small, non-enveloped icosahedral viruses with a segmented double-stranded RNA genome consisting of two segments taxonomically related to the genus Picobirnavirus of the family Picobirnaviridae. This review of scientific papers published in 1988-2019 provides data on the PBV distribution in the nature and a broad host range. PBV infection is characterized as opportunistic, the lack of understanding of the etiological role of PBVs in diarrhea is emphasized, since these viruses are detected both in symptomatic and asymptomatic cases. The concept of PBV infection as a chronic disease caused by a long-lasting persistence of the virus in the host is considered. Such factors as stress syndrome, physiological conditions, immune status and host age at the time of primary PBV infection influence the virus detection rate in humans and animals. The possible zoonotic nature of human PBV infection is noted due to the capacity for interspecies PBV transmission acquired during evolution as a result of the reassortment of the genome segments of different viruses infecting the same host. Data providing evidence that PBVs belong to eukaryotes and a challenging hypothesis stating that PBVs are bacterial viruses are presented. The need to intensify work on PBV detection because of their wide distribution, despite the complexity due to the lack of the cultivation system, is emphasized. Two strategies of RT-PCR as main PBV detection methods are considered. The genomes of individual representatives of the genus isolated from different hosts are characterized. Emphasis is placed on the feasibility of developing primers with broader specificity for expanding the range of identifiable representatives of the genus PBV due to a huge variety of their genotypes. The importance of effective monitoring of PBV prevalence for studying the zoonotic and anthroponotic potential using metagenomic analysis is highlighted, and so is the possibility of using PBV as a marker for environmental monitoring.
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Affiliation(s)
- A Yu Kashnikov
- I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russia
| | - N V Epifanova
- I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russia
| | - N A Novikova
- I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russia
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43
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Rosado NCL, Santos MR, Silva LMN, Assao VS, AraÚjo EN, Gonzaga NF, Kunz AF, Takiuchi E, Bressan GC, Fietto JLR, Silva-JÚnior A. Detection and partial molecular characterization of Picobirnavirus in swine from the state of Minas Gerais, Brazil. J Vet Med Sci 2020; 82:1798-1801. [PMID: 33071251 PMCID: PMC7804044 DOI: 10.1292/jvms.19-0565] [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] [Indexed: 12/02/2022] Open
Abstract
Picobirnavirus (PBV) is a small two-segmented double-stranded RNA (dsRNA) virus that has been identified in diarrheic feces of a large range
of animal hosts, including humans. For this reason, PBV has been recognized as an opportunistic agent of gastrointestinal disease. Even under these
circumstances, there is a lack of studies regarding this pathogen. Not outstanding, in Brazil, the single description of the PBV occurrence in pigs was provided
in the 1980s. Hence, this study aimed to verify the PBV occurrence in Brazilian swine farms and to perform molecular characterization of the identified strains.
High genetic variability was found in the analyzed sequences. Further studies comprehending the infection of swine by PBV in Brazilian herds should be performed
to provide more accurate information on its epidemiology and to discuss the role of the virus in gastrointestinal diseases.
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Affiliation(s)
- Nívia Carolina Lopes Rosado
- Laboratory of Immunobiological and Animal Virology, Department of Veterinary, Federal University of Viçosa (UFV), Viçosa, Minas Gerais 36570-900, Brazil
| | - Marcus Rebouças Santos
- Laboratory of Immunobiological and Animal Virology, Department of Veterinary, Federal University of Viçosa (UFV), Viçosa, Minas Gerais 36570-900, Brazil
| | - Laura Morais Nascimento Silva
- Laboratory of Immunobiological and Animal Virology, Department of Veterinary, Federal University of Viçosa (UFV), Viçosa, Minas Gerais 36570-900, Brazil
| | - Viviane Sisdelli Assao
- Laboratory of Immunobiological and Animal Virology, Department of Veterinary, Federal University of Viçosa (UFV), Viçosa, Minas Gerais 36570-900, Brazil
| | - Elaine Nery AraÚjo
- Laboratory of Immunobiological and Animal Virology, Department of Veterinary, Federal University of Viçosa (UFV), Viçosa, Minas Gerais 36570-900, Brazil
| | - Natália Fialho Gonzaga
- Laboratory of Immunobiological and Animal Virology, Department of Veterinary, Federal University of Viçosa (UFV), Viçosa, Minas Gerais 36570-900, Brazil
| | - Andressa Fernanda Kunz
- Department of Veterinary Sciences, Federal University of Paraná-UFPR Palotina, PR, Brazil
| | - Elisabete Takiuchi
- Department of Veterinary Sciences, Federal University of Paraná-UFPR Palotina, PR, Brazil
| | - Gustavo Costa Bressan
- Laboratory of Animal Molecular Infectology, Institute of Biotechnology Applied to Agriculture, Federal University of Viçosa (UFV), Viçosa, Minas Gerais 36570-900, Brazil
| | - Juliana Lopes Rangel Fietto
- Laboratory of Animal Molecular Infectology, Institute of Biotechnology Applied to Agriculture, Federal University of Viçosa (UFV), Viçosa, Minas Gerais 36570-900, Brazil
| | - Abelardo Silva-JÚnior
- Laboratory of Immunobiological and Animal Virology, Department of Veterinary, Federal University of Viçosa (UFV), Viçosa, Minas Gerais 36570-900, Brazil
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44
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Lay CL, Shi M, Buček A, Bourguignon T, Lo N, Holmes EC. Unmapped RNA Virus Diversity in Termites and their Symbionts. Viruses 2020; 12:v12101145. [PMID: 33050289 PMCID: PMC7650761 DOI: 10.3390/v12101145] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/01/2020] [Accepted: 10/05/2020] [Indexed: 12/15/2022] Open
Abstract
Despite their ecological importance, nothing is known about the diversity and abundance of RNA viruses in termites (Termitoidae). We used a metatranscriptomics approach to determine the RNA virome structure of 50 diverse species of termite that differ in both phylogenetic position and colony composition. From these samples, we identified 67 novel RNA viruses, characterized their genomes, quantified their abundance and inferred their evolutionary history. These viruses were found within or similar to those from the Togaviridae, Iflaviridae, Polycipiviridae, Flaviviridae, Leviviridae, Narnaviridae, Mitoviridae, Lispivirdae, Phasmaviridae, Picobirnaviridae and Partitiviridae. However, all viruses identified were novel and divergent, exhibiting only 20% to 45% amino acid identity to previously identified viruses. Our analysis suggested that 17 of the viruses identified were termite-infecting, with the remainder likely associated with the termite microbiome or diet. Unclassified sobemo-like and bunya-like viruses dominated termite viromes, while most of the phylogenetic diversity was provided by the picobirna- and mitovirus-like viruses. Of note was the identification of a novel flavi-like virus most closely related to those found in marine vertebrates and invertebrates. Notably, the sampling procedure had the strongest association with virome composition, with greater RNA virome diversity in libraries prepared from whole termite bodies than those that only sampled heads.
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Affiliation(s)
- Callum Le Lay
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney 2006, New South Wales, Australia; (C.L.L.); (M.S.)
- School of Life and Environmental Sciences, The University of Sydney, Sydney 2006, New South Wales, Australia;
- School of Medical Sciences, The University of Sydney, Sydney 2006, New South Wales, Australia
| | - Mang Shi
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney 2006, New South Wales, Australia; (C.L.L.); (M.S.)
- School of Life and Environmental Sciences, The University of Sydney, Sydney 2006, New South Wales, Australia;
- School of Medical Sciences, The University of Sydney, Sydney 2006, New South Wales, Australia
| | - Aleš Buček
- Okinawa Institute of Science and Technology Graduate University, Tancha, Onna-son, Okinawa 904-0495, Japan; (A.B.); (T.B.)
| | - Thomas Bourguignon
- Okinawa Institute of Science and Technology Graduate University, Tancha, Onna-son, Okinawa 904-0495, Japan; (A.B.); (T.B.)
- Faculty of Tropical AgriSciences, Czech University of Life Sciences, 165 00 Prague, Czech Republic
| | - Nathan Lo
- School of Life and Environmental Sciences, The University of Sydney, Sydney 2006, New South Wales, Australia;
| | - Edward C. Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney 2006, New South Wales, Australia; (C.L.L.); (M.S.)
- School of Life and Environmental Sciences, The University of Sydney, Sydney 2006, New South Wales, Australia;
- School of Medical Sciences, The University of Sydney, Sydney 2006, New South Wales, Australia
- Correspondence:
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45
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Campbell SJ, Ashley W, Gil-Fernandez M, Newsome TM, Di Giallonardo F, Ortiz-Baez AS, Mahar JE, Towerton AL, Gillings M, Holmes EC, Carthey AJR, Geoghegan JL. Red fox viromes in urban and rural landscapes. Virus Evol 2020; 6:veaa065. [PMID: 33365150 PMCID: PMC7744383 DOI: 10.1093/ve/veaa065] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The Red fox (Vulpes vulpes) has established large populations in Australia’s urban and rural areas since its introduction following European settlement. The cryptic and highly adaptable nature of foxes allows them to invade cities and live among humans whilst remaining largely unnoticed. Urban living and access to anthropogenic food resources also influence fox ecology. Urban foxes grow larger, live at higher densities, and are more social than their rural counterparts. These ecological changes in urban red foxes are likely to impact the pathogens that they harbour, and foxes could pose a disease risk to humans and other species that share these urban spaces. To investigate this possibility, we used a meta-transcriptomic approach to characterise the virome of urban and rural foxes across the Greater Sydney region in Australia. Urban and rural foxes differed significantly in virome composition, with rural foxes harbouring a greater abundance of viruses compared to their urban counterparts. We identified ten potentially novel vertebrate-associated viruses in both urban and rural foxes, some of which are related to viruses associated with disease in domestic species and humans. These included members of the Astroviridae, Picobirnaviridae, Hepeviridae, and Picornaviridae as well as rabbit haemorrhagic disease virus-2. This study sheds light on the viruses carried by urban and rural foxes and emphasises the need for greater genomic surveillance of foxes and other invasive species at the human–wildlife interface.
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Affiliation(s)
- Sarah J Campbell
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Wilbur Ashley
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Margarita Gil-Fernandez
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Thomas M Newsome
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | | | - Ayda Susana Ortiz-Baez
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Jackie E Mahar
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Alison L Towerton
- Greater Sydney Local Land Services, Sydney, New South Wales 2750, Australia
| | - Michael Gillings
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Alexandra J R Carthey
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Jemma L Geoghegan
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia.,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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46
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Harima H, Sasaki M, Kajihara M, Gonzalez G, Simulundu E, Bwalya EC, Qiu Y, Okuya K, Isono M, Orba Y, Takada A, Hang'ombe BM, Mweene AS, Sawa H. Characterization of mammalian orthoreoviruses isolated from faeces of pigs in Zambia. J Gen Virol 2020; 101:1027-1036. [PMID: 32706330 DOI: 10.1099/jgv.0.001476] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Mammalian orthoreovirus (MRV) has been identified in humans, livestock and wild animals; this wide host range allows individual MRV to transmit into multiple species. Although several interspecies transmission and genetic reassortment events of MRVs among humans, livestock and wildlife have been reported, the genetic diversity and geographic distribution of MRVs in Africa are poorly understood. In this study, we report the first isolation and characterization of MRVs circulating in a pig population in Zambia. In our screening, MRV genomes were detected in 19.7 % (29/147) of faecal samples collected from pigs by reverse transcription PCR. Three infectious MRV strains (MRV-85, MRV-96 and MRV-117) were successfully isolated, and their complete genomes were sequenced. Recombination analyses based on the complete genome sequences of the isolated MRVs demonstrated that MRV-96 shared the S3 segment with a different MRV isolated from bats, and that the L1 and M3 segments of MRV-117 originated from bat and human MRVs, respectively. Our results suggest that the isolated MRVs emerged through genetic reassortment events with interspecies transmission. Given the lack of information regarding MRVs in Africa, further surveillance of MRVs circulating among humans, domestic animals and wildlife is required to assess potential risk for humans and animals.
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Affiliation(s)
- Hayato Harima
- Hokudai Center for Zoonosis Control in Zambia, School of Veterinary Medicine, the University of Zambia, PO Box 32379, Lusaka, 10101, Zambia
| | - Michihito Sasaki
- Division of Molecular Pathobiology, Hokkaido University, Research Center for Zoonosis Control, N20 W10, Kita-ku, Sapporo, 001-0020, Japan
| | - Masahiro Kajihara
- Division of Global Epidemiology, Hokkaido University, Research Center for Zoonosis Control, N20 W10, Kita-ku, Sapporo, 001-0020, Japan.,Hokudai Center for Zoonosis Control in Zambia, School of Veterinary Medicine, the University of Zambia, PO Box 32379, Lusaka, 10101, Zambia
| | - Gabriel Gonzalez
- Division of Bioinformatics, Hokkaido University, Research Center for Zoonosis Control, N20 W10, Kita-ku, Sapporo, 001-0020, Japan
| | - Edgar Simulundu
- Department of Disease Control, School of Veterinary Medicine, the University of Zambia, PO Box 32379, Lusaka, 10101, Zambia
| | - Eugene C Bwalya
- Department of Clinical Studies, School of Veterinary Medicine, the University of Zambia, PO Box 32379, Lusaka, 10101, Zambia
| | - Yongjin Qiu
- Hokudai Center for Zoonosis Control in Zambia, School of Veterinary Medicine, the University of Zambia, PO Box 32379, Lusaka, 10101, Zambia
| | - Kosuke Okuya
- Division of Global Epidemiology, Hokkaido University, Research Center for Zoonosis Control, N20 W10, Kita-ku, Sapporo, 001-0020, Japan
| | - Mao Isono
- Division of Global Epidemiology, Hokkaido University, Research Center for Zoonosis Control, N20 W10, Kita-ku, Sapporo, 001-0020, Japan
| | - Yasuko Orba
- Division of Molecular Pathobiology, Hokkaido University, Research Center for Zoonosis Control, N20 W10, Kita-ku, Sapporo, 001-0020, Japan
| | - Ayato Takada
- Division of Global Epidemiology, Hokkaido University, Research Center for Zoonosis Control, N20 W10, Kita-ku, Sapporo, 001-0020, Japan.,Department of Disease Control, School of Veterinary Medicine, the University of Zambia, PO Box 32379, Lusaka, 10101, Zambia.,Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University Kita-ku, Sapporo, 001-0020, Japan.,Africa Center of Excellence for Infectious Diseases of Humans and Animals, the University of Zambia, PO Box 32379, Lusaka, 10101, Zambia
| | - Bernard M Hang'ombe
- Department of Para-clinical Studies, School of Veterinary Medicine, the University of Zambia, PO Box 32379, Lusaka, 10101, Zambia.,Africa Center of Excellence for Infectious Diseases of Humans and Animals, the University of Zambia, PO Box 32379, Lusaka, 10101, Zambia
| | - Aaron S Mweene
- Africa Center of Excellence for Infectious Diseases of Humans and Animals, the University of Zambia, PO Box 32379, Lusaka, 10101, Zambia.,Department of Disease Control, School of Veterinary Medicine, the University of Zambia, PO Box 32379, Lusaka, 10101, Zambia
| | - Hirofumi Sawa
- Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University Kita-ku, Sapporo, 001-0020, Japan.,Department of Disease Control, School of Veterinary Medicine, the University of Zambia, PO Box 32379, Lusaka, 10101, Zambia.,Global Virus Network, Baltimore, Maryland, 21201, 725 West Lombard St, Room S413, Baltimore, USA.,Division of Molecular Pathobiology, Hokkaido University, Research Center for Zoonosis Control, N20 W10, Kita-ku, Sapporo, 001-0020, Japan.,Africa Center of Excellence for Infectious Diseases of Humans and Animals, the University of Zambia, PO Box 32379, Lusaka, 10101, Zambia
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Intestinal fungi are causally implicated in microbiome assembly and immune development in mice. Nat Commun 2020; 11:2577. [PMID: 32444671 PMCID: PMC7244730 DOI: 10.1038/s41467-020-16431-1] [Citation(s) in RCA: 138] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 04/30/2020] [Indexed: 02/06/2023] Open
Abstract
The gut microbiome consists of a multi-kingdom microbial community. Whilst the role of bacteria as causal contributors governing host physiological development is well established, the role of fungi remains to be determined. Here, we use germ-free mice colonized with defined species of bacteria, fungi, or both to differentiate the causal role of fungi on microbiome assembly, immune development, susceptibility to colitis, and airway inflammation. Fungal colonization promotes major shifts in bacterial microbiome ecology, and has an independent effect on innate and adaptive immune development in young mice. While exclusive fungal colonization is insufficient to elicit overt dextran sulfate sodium-induced colitis, bacterial and fungal co-colonization increase colonic inflammation. Ovalbumin-induced airway inflammation reveals that bacterial, but not fungal colonization is necessary to decrease airway inflammation, yet fungi selectively promotes macrophage infiltration in the airway. Together, our findings demonstrate a causal role for fungi in microbial ecology and host immune functionality, and therefore prompt the inclusion of fungi in therapeutic approaches aimed at modulating early life microbiomes. The immunomodulatory role of commensal gut fungi and interactions with bacteria remain unclear. Here, using germ-free mice colonized with defined species of bacteria and fungi, the authors find that fungal colonization induces changes in bacterial microbiome ecology while having an independent effect on innate and adaptive immunity in mice.
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Fernandez-Garcia MD, Simon-Loriere E, Kebe O, Sakuntabhai A, Ndiaye K. Identification and molecular characterization of the first complete genome sequence of Human Parechovirus type 15. Sci Rep 2020; 10:6759. [PMID: 32317760 PMCID: PMC7174385 DOI: 10.1038/s41598-020-63467-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 03/26/2020] [Indexed: 12/29/2022] Open
Abstract
Using a metagenomics approach, we have determined the first full-length genome sequence of a human parechovirus type 15 (HPeV15) strain, isolated from a child with acute flaccid paralysis and co-infected with EV-A71. HPeV15 is a rarely reported type. To date, no full-length genome sequence of HPeV15 is available in the GenBank database, where only limited VP1 sequences of this virus are available. Pairwise comparisons of the complete VP1 nucleotide and deduced amino acid sequences revealed that the study strain belongs to type 15 as it displayed 79.6% nucleotide and 93.4% amino acid identity with the HPeV15 prototype strain. Comparative analysis of available genomic regions and phylogenetic analysis using the P2 and P3 coding regions revealed low nucleotide identity to HPeV reference genomes. Phylogenetic and similarity plot analyses showed that genomic recombination events might have occurred in the UTRs and nonstructural region during HPeV15 evolution. The study strain has high similarity features with different variants of HPeV3 suggesting intertypic recombination. Our data contributes to the scarce data available on HPeVs in Africa and provides valuable information for future studies that aim to understand the evolutionary history, molecular epidemiology or biological and pathogenic properties of HPeV15.
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Ugboko HU, Nwinyi OC, Oranusi SU, Oyewale JO. Childhood diarrhoeal diseases in developing countries. Heliyon 2020; 6:e03690. [PMID: 32322707 PMCID: PMC7160433 DOI: 10.1016/j.heliyon.2020.e03690] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 12/03/2019] [Accepted: 03/25/2020] [Indexed: 12/27/2022] Open
Abstract
Diarrhoeal diseases collectively constitute a serious public health challenge globally, especially as the leading cause of death in children (after respiratory diseases). Childhood diarrhoea affecting children under the age of five accounts for approximately 63% of the global burden. Accurate and timely detection of the aetiology of these diseases is very crucial; but conventional methods, apart from being laborious and time-consuming, often fail to identify difficult-to-culture pathogens. The aetiological agent of an average of up to 40% of cases of diarrhoea cannot be identified. This review gives an overview of the recent trends in the epidemiology and treatment of diarrhoea and aims at highlighting the potentials of metagenomics technique as a diagnostic method for enteric infections.
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Affiliation(s)
- Harriet U Ugboko
- Microbiology Research Unit, Department of Biological Sciences, Covenant University, Canaanland, KM 10, Idiroko Road, P.M.B, 1023, Ota, Ogun State, Nigeria
| | - Obinna C Nwinyi
- Microbiology Research Unit, Department of Biological Sciences, Covenant University, Canaanland, KM 10, Idiroko Road, P.M.B, 1023, Ota, Ogun State, Nigeria
| | - Solomon U Oranusi
- Microbiology Research Unit, Department of Biological Sciences, Covenant University, Canaanland, KM 10, Idiroko Road, P.M.B, 1023, Ota, Ogun State, Nigeria
| | - John O Oyewale
- Microbiology Research Unit, Department of Biological Sciences, Covenant University, Canaanland, KM 10, Idiroko Road, P.M.B, 1023, Ota, Ogun State, Nigeria
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50
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Abstract
Colorectal cancer (CRC) is a leading cause of cancer-related deaths in both the USA and the world. Recent research has demonstrated the involvement of the gut microbiota in CRC development and progression. Microbial biomarkers of disease have focused primarily on the bacterial component of the microbiome; however, the viral portion of the microbiome, consisting of both bacteriophages and eukaryotic viruses, together known as the virome, has been lesser studied. Here we review the recent advancements in high-throughput sequencing (HTS) technologies and bioinformatics, which have enabled scientists to better understand how viruses might influence the development of colorectal cancer. We discuss the contemporary findings revealing modulations in the virome and their correlation with CRC development and progression. While a variety of challenges still face viral HTS detection in clinical specimens, we consider herein numerous next steps for future basic and clinical research. Clinicians need to move away from a single infectious agent model for disease etiology by grasping new, more encompassing etiological paradigms, in which communities of various microbial components interact with each other and the host. The reporting and indexing of patient health information, socioeconomic data, and other relevant metadata will enable identification of predictive variables and covariates of viral presence and CRC development. Altogether, the virome has a more profound role in carcinogenesis and cancer progression than once thought, and viruses, specific for either human cells or bacteria, are clinically relevant in understanding CRC pathology, patient prognosis, and treatment development.
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