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Makoa-Meng M, Semmar R, Antezack A, Penant G, La Scola B, Monnet-Corti V, Colson P. Correlation of Redondovirus and Entamoeba gingivalis Detections in the Human Oral Cavity Suggests That This Amoeba Is Possibly the Redondovirus Host. Int J Mol Sci 2023; 24:ijms24076303. [PMID: 37047275 PMCID: PMC10094137 DOI: 10.3390/ijms24076303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/21/2023] [Accepted: 03/23/2023] [Indexed: 03/30/2023] Open
Abstract
The virome of the human oral cavity and the relationships between viruses and diseases such as periodontitis are scarcely deciphered. Redondoviruses were reported in the human oral cavity in 2019, including in periodontitis patients. Here, we aimed at detecting redondoviruses and at searching for a potential viral host in human saliva. Non-stimulated saliva was collected between December 2020 and June 2021. These samples were tested using real-time PCR regarding the presence of redondovirus and Entamoeba gingivalis DNA. Similarity searches were performed using BLAST against eukaryotic and prokaryotic sequences from GenBank. The redondovirus DNA was detected in 46% of the 28 human saliva samples. In addition, short fragments of redondovirus genomes were detected in silico within Entamoeba sequences. Finally, Entamoeba gingivalis DNA was detected in 46% of the 28 saliva samples, with a strong correlation between redondovirus DNA and E. gingivalis DNA detections, in 93% of the cases. Regarded together, these findings and previous ones strongly support the presence of redondoviruses in the human oral cavity and their association to E. gingivalis as their likely host.
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2
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Keeler EL, Merenstein C, Reddy S, Taylor LJ, Cobián-Güemes AG, Zankharia U, Collman RG, Bushman FD. Widespread, human-associated redondoviruses infect the commensal protozoan Entamoeba gingivalis. Cell Host Microbe 2023; 31:58-68.e5. [PMID: 36459997 PMCID: PMC9969835 DOI: 10.1016/j.chom.2022.11.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/05/2022] [Accepted: 11/04/2022] [Indexed: 12/03/2022]
Abstract
Redondoviruses are circular Rep-encoding single-stranded DNA (CRESS) viruses of high prevalence in healthy humans. Redondovirus abundance is increased in oro-respiratory samples from individuals with periodontitis, acute illness, and severe COVID-19. We investigated potential host cells supporting redondovirus replication in oro-respiratory samples and uncovered the oral amoeba Entamoeba gingivalis as a likely host. Redondoviruses are closely related to viruses of Entamoeba and contain reduced GC nucleotide content, consistent with Entamoeba hosts. Redondovirus and E. gingivalis co-occur in metagenomic data from oral disease and healthy human cohorts. When grown in xenic cultures with feeder bacteria, E. gingivalis was robustly positive for redondovirus RNA and DNA. A DNA proximity-ligation assay (Hi-C) on xenic culture cells showed enriched cross-linking of redondovirus and Entamoeba DNA, supporting E. gingivalis as the redondovirus host. While bacteria are established hosts for bacteriophages within the human virome, this work shows that eukaryotic commensals also contribute an abundant human-associated virus.
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Affiliation(s)
- Emma L Keeler
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Carter Merenstein
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Shantan Reddy
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Louis J Taylor
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Ana G Cobián-Güemes
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Urvi Zankharia
- Department of Medicine, Pulmonary, Allergy and Critical Care Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ronald G Collman
- Department of Medicine, Pulmonary, Allergy and Critical Care Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Frederic D Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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3
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Taylo LJ, Keeler EL, Bushman FD, Collman RG. The enigmatic roles of Anelloviridae and Redondoviridae in humans. Curr Opin Virol 2022; 55:101248. [PMID: 35870315 DOI: 10.1016/j.coviro.2022.101248] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/06/2022] [Accepted: 06/09/2022] [Indexed: 12/26/2022]
Abstract
Anelloviridae and Redondoviridae are virus families with small, circular, single-stranded DNA genomes that are common components of the human virome. Despite their small genome size of less than 5000 bases, they are remarkably successful - anelloviruses colonize over 90% of adult humans, while the recently discovered redondoviruses have been found at up to 80% prevalence in some populations. Anelloviruses are present in blood and many organs, while redondoviruses are found mainly in the ororespiratory tract. Despite their high prevalence, little is known about their biology or pathogenic potential. In this review, we discuss anelloviruses and redondoviruses and explore their enigmatic roles in human health and disease.
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Affiliation(s)
- Louis J Taylo
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Emma L Keeler
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Frederic D Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ronald G Collman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Medicine, Pulmonary, Allergy and Critical Care Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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4
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Abstract
Redondoviridae is a newly established family of circular Rep-encoding single-stranded (CRESS) DNA viruses found in the human ororespiratory tract. Redondoviruses were previously found in ∼15% of respiratory specimens from U.S. urban subjects; levels were elevated in individuals with periodontitis or critical illness. Here, we report higher redondovirus prevalence in saliva samples: four rural African populations showed 61 to 82% prevalence, and an urban U.S. population showed 32% prevalence. Longitudinal, limiting-dilution single-genome sequencing revealed diverse strains of both redondovirus species (Brisavirus and Vientovirus) in single individuals, persistence over time, and evidence of intergenomic recombination. Computational analysis of viral genomes identified a recombination hot spot associated with a conserved potential DNA stem-loop structure. To assess the possible role of this site in recombination, we carried out in vitro studies which showed that this potential stem-loop was cleaved by the virus-encoded Rep protein. In addition, in reconstructed reactions, a Rep-DNA covalent intermediate was shown to mediate DNA strand transfer at this site. Thus, redondoviruses are highly prevalent in humans, found in individuals on multiple continents, heterogeneous even within individuals and encode a Rep protein implicated in facilitating recombination. IMPORTANCE Redondoviridae is a recently established family of DNA viruses predominantly found in the human respiratory tract and associated with multiple clinical conditions. In this study, we found high redondovirus prevalence in saliva from urban North American individuals and nonindustrialized African populations in Botswana, Cameroon, Ethiopia, and Tanzania. Individuals on both continents harbored both known redondovirus species. Global prevalence of both species suggests that redondoviruses have long been associated with humans but have remained undetected until recently due to their divergent genomes. By sequencing single redondovirus genomes in longitudinally sampled humans, we found that redondoviruses persisted over time within subjects and likely evolve by recombination. The Rep protein encoded by redondoviruses catalyzes multiple reactions in vitro, consistent with a role in mediating DNA replication and recombination. In summary, we identify high redondovirus prevalence in humans across multiple continents, longitudinal heterogeneity and persistence, and potential mechanisms of redondovirus evolution by recombination.
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5
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Hao X, Li Y, Hu X, Fu X, Dong J, Zhang H, Zhou P, Li S. Feline Stool-Associated Circular DNA Virus (FeSCV) in Diarrheic Cats in China. Front Vet Sci 2021; 8:694089. [PMID: 34222407 PMCID: PMC8242157 DOI: 10.3389/fvets.2021.694089] [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: 04/12/2021] [Accepted: 05/17/2021] [Indexed: 11/13/2022] Open
Abstract
Feline stool-associated circular DNA virus (FeSCV) is an unclassified circular replication-associated protein-encoding single-stranded (CRESS) DNA virus that was discovered in cats in Japan in 2018. Few studies on the genomic characteristics and prevalence of FeSCV have been conducted. To investigate whether FeSCV has been circulating in domestic cats in Guangdong, China, fecal samples were collected from cats with diarrhea in an animal hospital in 2018 to promote research on FeSCV. The FeSCV genome was obtained by PCR amplification and sequencing, and the detected virus was named PY4 (GenBank No. MT732515). The genome of PY4 was 2,034 nt in size, which was 12 nt smaller than the reported genome of Japanese FeSCV strains (KU7, KU8, KU9, KU14) (2,046 nt). The PY4 strain shared 95.1 ~ 95.5% homology with Japanese FeSCV strains. Notably, the Cap protein of PY4 was mutated at 15 amino acid sites, and the PY4 genome contained a unique open reading frame 3. In addition, there were two additional base insertions in the stem-loop structure of PY4, and the nucleotide homology of the spacer region was not high. A phylogenetic tree based on Rep proteins showed that PY4, Japanese FeSCVs and rodent stool-associated circular viruses (RodSCVs) clustered together, suggesting that they might share a similar origin in their phylogenetic evolution. In this study, samples collected in Guangzhou, China, in 2018 were subjected to an etiological investigation, and 20% (2/10) of the samples were positive for FeSCV. The ORFs, stem-loop structures, Cap proteins and intergenic region sequences of PY4 were significantly different from those reported in Japan. This is the first report of FeSCV in domestic cats with diarrhea in China, and further epidemiological studies are urgently needed to assess the impact of the virus on cats.
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Affiliation(s)
- Xiangqi Hao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, China.,Guangdong Provincial Pet Engineering Technology Research Center, Guangzhou, China
| | - Yanchao Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, China.,Guangdong Provincial Pet Engineering Technology Research Center, Guangzhou, China
| | - Xinkai Hu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, China.,Guangdong Provincial Pet Engineering Technology Research Center, Guangzhou, China
| | - Xueying Fu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, China.,Guangdong Provincial Pet Engineering Technology Research Center, Guangzhou, China
| | - Jie Dong
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, China.,Guangdong Provincial Pet Engineering Technology Research Center, Guangzhou, China
| | - Haoyang Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, China.,Guangdong Provincial Pet Engineering Technology Research Center, Guangzhou, China
| | - Pei Zhou
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, China.,Guangdong Provincial Pet Engineering Technology Research Center, Guangzhou, China
| | - Shoujun Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, China.,Guangdong Provincial Pet Engineering Technology Research Center, Guangzhou, China
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6
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Redondoviridae: High Prevalence and Possibly Chronic Shedding in Human Respiratory Tract, But No Zoonotic Transmission. Viruses 2021; 13:v13040533. [PMID: 33804837 PMCID: PMC8063800 DOI: 10.3390/v13040533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 03/19/2021] [Accepted: 03/19/2021] [Indexed: 01/06/2023] Open
Abstract
Redondoviridae is a recently discovered DNA virus family consisting of two species, vientovirus and brisavirus. Here we used PCR amplification and sequencing to characterize redondoviruses in nasal/throat swabs collected longitudinally from a cohort of 58 individuals working with animals in Vietnam. We additionally analyzed samples from animals to which redondovirus DNA-positive participants were exposed. Redondoviruses were detected in approximately 60% of study participants, including 33% (30/91) of samples collected during episodes of acute respiratory disease and in 50% (29/58) of baseline samples (with no respiratory symptoms). Vientovirus (73%; 24/33) was detected more frequently in samples than brisaviruses (27%; 9/33). In the 23 participants with at least 2 redondovirus-positive samples among their longitudinal samples, 10 (43.5%) had identical redondovirus replication-gene sequences detected (sampling duration: 35–132 days). We found no identical redondovirus replication genes in samples from different participants, and no redondoviruses were detected in 53 pooled nasal/throat swabs collected from domestic animals. Phylogenetic analysis described no large-scale geographical clustering between viruses from Vietnam, the US, Spain, and China, indicating that redondoviruses are highly genetically diverse and have a wide geographical distribution. Collectively, our study provides novel insights into the Redondoviridae family in humans, describing a high prevalence, potentially associated with chronic shedding in the respiratory tract with lack of evidence of zoonotic transmission from close animal contacts. The tropism and potential pathogenicity of this viral family remain to be determined.
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7
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Abbas A, Taylor LJ, Collman RG, Bushman FD, Ictv Report Consortium. ICTV Virus Taxonomy Profile: Redondoviridae. J Gen Virol 2020; 102. [PMID: 33258767 PMCID: PMC8116785 DOI: 10.1099/jgv.0.001526] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Viruses in the family Redondoviridae have a circular genome of 3.0 kb with three open reading frames. The packaged genome is inferred to be single-stranded DNA by analogy to related viruses. Redondoviruses were discovered through metagenomic sequencing methods in samples from human subjects and are inferred to replicate in humans. Evidence of redondovirus infection is associated with periodontitis and critical illness, but redondoviruses have not been shown to be the causative agent of any diseases. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Redondoviridae, which is available at ictv.global/report/redondoviridae.
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Affiliation(s)
- Arwa Abbas
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Louis J Taylor
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ronald G Collman
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
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8
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Spezia PG, Macera L, Mazzetti P, Curcio M, Biagini C, Sciandra I, Turriziani O, Lai M, Antonelli G, Pistello M, Maggi F. Redondovirus DNA in human respiratory samples. J Clin Virol 2020; 131:104586. [PMID: 32841923 PMCID: PMC7428698 DOI: 10.1016/j.jcv.2020.104586] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/25/2020] [Accepted: 08/09/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND Redondovirus (ReDoV) is a recently discovered circular, Rep-encoding single-stranded DNA (CRESS-DNA) virus in humans. Its pathogenesis and clinical associations are still completely unknown. METHODS The presence of ReDoV DNA was investigated in biological specimens of 543 Italian subjects by in-house developed PCR assays. RESULTS The overall ReDoV prevalence was about 4% (23 of 543 samples). The virus was detected in 22 of 209 (11 %) respiratory samples. One stool sample was also ReDoV positive. Viral DNA was not found in blood samples from immunocompetent and immunosuppressed subjects and cerebrospinal fluids from patients with neurological diseases. Genomic nucleotide differences were detected among the ReDoV isolates by sequencing a 582-nucleotide fragment of the capsid gene of the viral genome. CONCLUSIONS The results demonstrate that ReDoV is mainly present in the respiratory tract of infected people. Further investigations are needed to reveal possible clinical implications of this new CRESS-DNA virus in humans.
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Affiliation(s)
| | - Lisa Macera
- Department of Translational Research, University of Pisa, Italy; Virology Division, Pisa University Hospital, Pisa, Italy
| | - Paola Mazzetti
- Virology Division, Pisa University Hospital, Pisa, Italy
| | - Michele Curcio
- Immunohematology 2, Pisa University Hospital, Pisa, Italy
| | - Chiara Biagini
- Immunohematology 2, Pisa University Hospital, Pisa, Italy
| | - Ilaria Sciandra
- National Institute of Gastrenterology "S. De Bellis" Research Hospital Castellana, Bari, Italy
| | | | - Michele Lai
- Department of Translational Research, University of Pisa, Italy
| | | | - Mauro Pistello
- Department of Translational Research, University of Pisa, Italy; Virology Division, Pisa University Hospital, Pisa, Italy
| | - Fabrizio Maggi
- Department of Translational Research, University of Pisa, Italy; Virology Division, Pisa University Hospital, Pisa, Italy.
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9
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Fur Seal Feces-Associated Circular DNA Virus Identified in Pigs in Anhui, China. Virol Sin 2020; 36:25-32. [PMID: 32488409 PMCID: PMC7973343 DOI: 10.1007/s12250-020-00232-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 03/07/2020] [Indexed: 11/08/2022] Open
Abstract
Fur seal feces-associated circular DNA virus (FSfaCV) is an unclassified circular replication-associated protein (Rep)-encoding single-stranded (CRESS) DNA virus that has been detected in mammals (fur seals and pigs). The biology and epidemiology of the virus remain largely unknown. To investigate the virus diversity among pigs in Anhui Province, China, we pooled 600 nasal samples in 2017 and detected viruses using viral metagenomic methods. From the assembled contigs, 12 showed notably high nucleotide acid sequence similarities to the genome sequences of FSfaCVs. Based on these sequences, a full-length genome sequence of the virus was then obtained using overlapping PCR and sequencing, and the virus was designated as FSfaCV-CHN (GenBank No. MK462122). This virus shared 91.3% and 90.9% genome-wide nucleotide sequence similarities with the New Zealand fur seal strain FSfaCV-as50 and the Japanese pig strain FSfaCV-JPN1, respectively. It also clustered with the two previously identified FSfaCVs in a unique branch in the phylogenetic tree based on the open reading frame 2 (ORF2), Rep-coding gene, and the genome of the reference CRESS DNA viruses. Further epidemiological investigation using samples collected in 2018 showed that the overall positive rate for the virus was 56.4% (111/197) in Anhui Province. This is the first report of FSfaCVs identified in pigs in China, and further epidemiological studies are warranted to evaluate the influence of the virus on pigs.
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10
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Lu L, Robertson G, Ashworth J, Pham Hong A, Shi T, Ivens A, Thwaites G, Baker S, Woolhouse M. Epidemiology and Phylogenetic Analysis of Viral Respiratory Infections in Vietnam. Front Microbiol 2020; 11:833. [PMID: 32499763 PMCID: PMC7242649 DOI: 10.3389/fmicb.2020.00833] [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] [Received: 12/20/2019] [Accepted: 04/07/2020] [Indexed: 12/18/2022] Open
Abstract
Acute respiratory infections (ARIs) impose a major public health burden on fragile healthcare systems of developing Southeast Asian countries such as Vietnam. The epidemiology, genetic diversity and transmission patterns of respiratory viral pathogens that circulate in this region are not well characterized. We used RT-PCR to screen for 14 common respiratory viruses in nasal/throat samples from 4326 ARI patients from 5 sites in Vietnam during 2012-2016. 64% of patients tested positive for viruses; 14% tested positive multiple co-infecting viruses. The most frequently detected viruses were Respiratory syncytial virus (RSV, 23%), Human Rhinovirus (HRV, 13%), Influenza A virus (IAV, 11%) and Human Bocavirus (HBoV, 7%). RSV infections peaked in July to October, were relatively more common in children <1 year and in the northernmost hospital. IAV infections peaked in December to February and were relatively more common in patients >5 years in the central region. Coinfection with IAV or RSV was associated with increased disease severity compared with patients only infected with HBoV or HRV. Over a hundred genomes belonging to 13 families and 24 genera were obtained via metagenomic sequencing, including novel viruses and viruses less commonly associated with ARIs. Phylogenetic and phylogeographic analyses further indicated that neighboring countries were the most likely source of many virus lineages causing ARIs in Vietnam and estimated the period that specific lineages have been circulating. Our study illustrates the value of applying the state-of-the-art virus diagnostic methods (multiplex RT-PCR and metagenomic sequencing) and phylodynamic analyses at a national level to generate an integrated picture of viral ARI epidemiology.
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Affiliation(s)
- Lu Lu
- Usher Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Gail Robertson
- Statistical Consultancy Unit, School of Mathematics, The University of Edinburgh, Edinburgh, United Kingdom
| | - Jordan Ashworth
- Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh, United Kingdom
| | - Anh Pham Hong
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Ting Shi
- Usher Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Alasdair Ivens
- Institute of Immunology and Infection Research, The University of Edinburgh, Edinburgh, United Kingdom
| | - Guy Thwaites
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Mark Woolhouse
- Usher Institute, The University of Edinburgh, Edinburgh, United Kingdom
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11
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Metagenomic Detection of Two Vientoviruses in a Human Sputum Sample. Viruses 2020; 12:v12030327. [PMID: 32197299 PMCID: PMC7150755 DOI: 10.3390/v12030327] [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] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 03/06/2020] [Accepted: 03/17/2020] [Indexed: 02/02/2023] Open
Abstract
We used metagenomics to analyze one sputum sample from a patient with symptoms of a respiratory infection that yielded negative results for all pathogens tested. We detected two viral genomes that could be assembled and showed sequence similarity to redondoviruses, a recently described group within the CRESS-DNA viruses. One hundred sputum samples were screened for the presence of these viruses using specific primers. One sample was positive for the same two viruses, and another was positive for one of them. These findings raise questions about a possible role of redondoviruses in respiratory infections in humans.
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12
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Redondoviridae, a Family of Small, Circular DNA Viruses of the Human Oro-Respiratory Tract Associated with Periodontitis and Critical Illness. Cell Host Microbe 2019; 25:719-729.e4. [PMID: 31071295 DOI: 10.1016/j.chom.2019.04.001] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/24/2019] [Accepted: 04/01/2019] [Indexed: 12/21/2022]
Abstract
The global virome is largely uncharacterized but is now being unveiled by metagenomic DNA sequencing. Exploring the human respiratory virome, in particular, can provide insights into oro-respiratory diseases. Here, we use metagenomics to identify a family of small circular DNA viruses-named Redondoviridae-associated with human diseases. We first identified two redondovirus genomes from bronchoalveolar lavage samples from human lung donors. We then queried thousands of metagenomic samples and recovered 17 additional complete redondovirus genomes. Detections were exclusively in human samples and mostly from respiratory tract and oro-pharyngeal sites, where Redondoviridae was the second most prevalent eukaryotic DNA virus family. Redondovirus sequences were associated with periodontal disease, and abundances decreased with treatment. Some critically ill patients in a medical intensive care unit were found to harbor high levels of redondoviruses in respiratory samples. These results suggest that redondoviruses colonize human oro-respiratory sites and can bloom in several human disorders.
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13
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Pérez-Sautu U, Wiley MR, Iglesias-Caballero M, Pozo F, Prieto K, Chitty JA, García-García ML, Calvo C, Casas I, Palacios G. Target-independent high-throughput sequencing methods provide evidence that already known human viral pathogens play a main role in respiratory infections with unexplained etiology. Emerg Microbes Infect 2019; 8:1054-1065. [PMID: 31335277 PMCID: PMC6691886 DOI: 10.1080/22221751.2019.1640587] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Despite the advanced PCR-based assays available, a fraction of the pediatric respiratory infections remain unexplained every epidemic season, and there is a perception that novel viruses might be present in these specimens. We systematically collected samples from a prospective cohort of pediatric patients with respiratory infections, that returned negative results by validated molecular RT–PCR assays, and studied them with a target-independent, high-throughput sequencing-based approach. We also included a matched cohort of children with no symptoms of respiratory infection, as a contrast study population. More than fifty percent of the specimens from the group of patients with unexplained respiratory infections were resolved. However, the higher rate of detection was not due to the presence of novel viruses, but to the identification of well-known viral respiratory pathogens. Our results show that already known viral pathogens are responsible for the majority of cases that remain unexplained after the epidemic season. High-throughput sequencing approaches that use pathogen-specific probes are easier to standardize because they ensure reproducible library enrichment and sequencing. In consequence, these techniques might be desirable from a regulatory standpoint for diagnostic laboratories seeking to benefit from the many advantages of these sequencing technologies.
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Affiliation(s)
- Unai Pérez-Sautu
- a Influenza and Respiratory Viruses Unit, National Center for Microbiology, Instituto de Salud Carlos III (ISCIII) , Madrid , Spain.,b Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID) , Frederick , MD , USA
| | - Michael Ross Wiley
- b Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID) , Frederick , MD , USA.,c College of Public Health, University of Nebraska Medical Center , Omaha , NE , USA
| | - María Iglesias-Caballero
- a Influenza and Respiratory Viruses Unit, National Center for Microbiology, Instituto de Salud Carlos III (ISCIII) , Madrid , Spain
| | - Francisco Pozo
- a Influenza and Respiratory Viruses Unit, National Center for Microbiology, Instituto de Salud Carlos III (ISCIII) , Madrid , Spain
| | - Karla Prieto
- b Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID) , Frederick , MD , USA.,c College of Public Health, University of Nebraska Medical Center , Omaha , NE , USA
| | - Joseph Alex Chitty
- b Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID) , Frederick , MD , USA
| | | | | | - Inmaculada Casas
- a Influenza and Respiratory Viruses Unit, National Center for Microbiology, Instituto de Salud Carlos III (ISCIII) , Madrid , Spain
| | - Gustavo Palacios
- b Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID) , Frederick , MD , USA
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14
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Zhao L, Rosario K, Breitbart M, Duffy S. Eukaryotic Circular Rep-Encoding Single-Stranded DNA (CRESS DNA) Viruses: Ubiquitous Viruses With Small Genomes and a Diverse Host Range. Adv Virus Res 2018; 103:71-133. [PMID: 30635078 DOI: 10.1016/bs.aivir.2018.10.001] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
While single-stranded DNA (ssDNA) was once thought to be a relatively rare genomic architecture for viruses, modern metagenomics sequencing has revealed circular ssDNA viruses in most environments and in association with diverse hosts. In particular, circular ssDNA viruses encoding a homologous replication-associated protein (Rep) have been identified in the majority of eukaryotic supergroups, generating interest in the ecological effects and evolutionary history of circular Rep-encoding ssDNA viruses (CRESS DNA) viruses. This review surveys the explosion of sequence diversity and expansion of eukaryotic CRESS DNA taxonomic groups over the last decade, highlights similarities between the well-studied geminiviruses and circoviruses with newly identified groups known only through their genome sequences, discusses the ecology and evolution of eukaryotic CRESS DNA viruses, and speculates on future research horizons.
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Affiliation(s)
- Lele Zhao
- Department of Ecology, Evolution and Natural Resources, Rutgers, the State University of New Jersey, New Brunswick, NJ, United States
| | - Karyna Rosario
- College of Marine Science, University of South Florida, Saint Petersburg, FL, United States
| | - Mya Breitbart
- College of Marine Science, University of South Florida, Saint Petersburg, FL, United States
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, Rutgers, the State University of New Jersey, New Brunswick, NJ, United States.
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Takano T, Yanai Y, Hiramatsu K, Doki T, Hohdatsu T. Novel single-stranded, circular DNA virus identified in cats in Japan. Arch Virol 2018; 163:3389-3393. [PMID: 30218220 PMCID: PMC7087140 DOI: 10.1007/s00705-018-4020-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 09/05/2018] [Indexed: 12/03/2022]
Abstract
We detected a novel feline stool-associated circular DNA virus (FeSCV) in fecal samples from cats with diarrhea using consensus primers matching those of circovirus and cyclovirus. FeSCV is a circular DNA virus containing a genome with a total length of 2,046 nt encoding 2 open reading frames. Phylogenetic analyses indicated that FeSCV is classified into a clade different from that of circovirus and cyclovirus. Since the FeSCVs detected in several cats in the same household had genetically similar genomes, these viruses are most likely derived from the same origin.
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Affiliation(s)
- Tomomi Takano
- Laboratory of Veterinary Infectious Disease, School of Veterinary Medicine, Kitasato University, Towada, Japan
| | - Yoshitomo Yanai
- Laboratory of Veterinary Infectious Disease, School of Veterinary Medicine, Kitasato University, Towada, Japan
| | - Kanae Hiramatsu
- Laboratory of Veterinary Infectious Disease, School of Veterinary Medicine, Kitasato University, Towada, Japan
| | - Tomoyoshi Doki
- Laboratory of Veterinary Infectious Disease, School of Veterinary Medicine, Kitasato University, Towada, Japan
| | - Tsutomu Hohdatsu
- Laboratory of Veterinary Infectious Disease, School of Veterinary Medicine, Kitasato University, Towada, Japan.
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