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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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Discovery and comparative genomic analysis of a novel equine anellovirus, representing the first complete Mutorquevirus genome. Sci Rep 2023; 13:3703. [PMID: 36878942 PMCID: PMC9988894 DOI: 10.1038/s41598-023-30875-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
The complete genome of a novel torque teno virus species (Torque teno equus virus 2 (TTEqV2) isolate Alberta/2018) was obtained by high-throughput sequencing (HTS) of nucleic acid extracted from the lung and liver tissue of a Quarter Horse gelding that died of nonsuppurative encephalitis in Alberta, Canada. The 2805 nucleotide circular genome is the first complete genome from the Mutorquevirus genus and has been approved as a new species by the International Committee on Taxonomy of Viruses. The genome contains several characteristic features of torque teno virus (TTV) genomes, including an ORF1 encoding a putative 631 aa capsid protein with an arginine-rich N-terminus, several rolling circle replication associated amino acid motifs, and a downstream polyadenylation signal. A smaller overlapping ORF2 encodes a protein with an amino acid motif (WX7HX3CXCX5H) which, in general, is highly conserved in TTVs and anelloviruses. The UTR contains two GC-rich tracts, two highly conserved 15 nucleotide sequences, and what appears to be an atypical TATA-box sequence also observed in two other TTV genera. Codon usage analysis of TTEqV2 and 11 other selected anelloviruses from five host species revealed a bias toward adenine ending (A3) codons in the anelloviruses, while in contrast, A3 codons were observed at a low frequency in horse and the four other associated host species examined. Phylogenetic analysis of TTV ORF1 sequences available to date shows TTEqV2 clusters with the only other currently reported member of the Mutorquevirus genus, Torque teno equus virus 1 (TTEqV1, KR902501). Genome-wide pairwise alignment of TTEqV2 and TTEqV1 shows the absence of several highly conserved TTV features within the UTR of TTEqV1, suggesting it is incomplete and TTEqV2 is the first complete genome within the genus Mutorquevirus.
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Abstract
The COVID-19 pandemic has given the study of virus evolution and ecology new relevance. Although viruses were first identified more than a century ago, we likely know less about their diversity than that of any other biological entity. Most documented animal viruses have been sampled from just two phyla - the Chordata and the Arthropoda - with a strong bias towards viruses that infect humans or animals of economic and social importance, often in association with strong disease phenotypes. Fortunately, the recent development of unbiased metagenomic next-generation sequencing is providing a richer view of the animal virome and shedding new light on virus evolution. In this Review, we explore our changing understanding of the diversity, composition and evolution of the animal virome. We outline the factors that determine the phylogenetic diversity and genomic structure of animal viruses on evolutionary timescales and show how this impacts assessment of the risk of disease emergence in the short term. We also describe the ongoing challenges in metagenomic analysis and outline key themes for future research. A central question is how major events in the evolutionary history of animals, such as the origin of the vertebrates and periodic mass extinction events, have shaped the diversity and evolution of the viruses they carry.
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Abstract
Anelloviruses are small negative-sense single-stranded DNA viruses with genomes ranging in size from 1.6 to 3.9 kb. The family Anelloviridae comprised 14 genera before the present changes. However, in the last five years, a large number of diverse anelloviruses have been identified in various organisms. Here, we undertake a global analysis of mammalian anelloviruses whose full genome sequences have been determined and have an intact open reading frame 1 (ORF1). We established new criteria for the classification of anelloviruses, and, based on our analyses, we establish new genera and species to accommodate the unclassified anelloviruses. We also note that based on the updated species demarcation criteria, some previously assigned species (n = 10) merge with other species. Given the rate at which virus sequence data are accumulating, and with the identification of diverse anelloviruses, we acknowledge that the taxonomy will have to be dynamic and continuously evolve to accommodate new members.
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Deng Z, Delwart E. ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data. BMC Bioinformatics 2021; 22:119. [PMID: 33706720 PMCID: PMC7953547 DOI: 10.1186/s12859-021-04038-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 02/21/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Metagenomics is the study of microbial genomes for pathogen detection and discovery in human clinical, animal, and environmental samples via Next-Generation Sequencing (NGS). Metagenome de novo sequence assembly is a crucial analytical step in which longer contigs, ideally whole chromosomes/genomes, are formed from shorter NGS reads. However, the contigs generated from the de novo assembly are often very fragmented and rarely longer than a few kilo base pairs (kb). Therefore, a time-consuming extension process is routinely performed on the de novo assembled contigs. RESULTS To facilitate this process, we propose a new tool for metagenome contig extension after de novo assembly. ContigExtender employs a novel recursive extending strategy that explores multiple extending paths to achieve highly accurate longer contigs. We demonstrate that ContigExtender outperforms existing tools in synthetic, animal, and human metagenomics datasets. CONCLUSIONS A novel software tool ContigExtender has been developed to assist and enhance the performance of metagenome de novo assembly. ContigExtender effectively extends contigs from a variety of sources and can be incorporated in most viral metagenomics analysis pipelines for a wide variety of applications, including pathogen detection and viral discovery.
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Affiliation(s)
- Zachary Deng
- Vitalant Research Institute, San Francisco, CA, 94118, USA.
- Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA, 94107, USA.
| | - Eric Delwart
- Vitalant Research Institute, San Francisco, CA, 94118, USA.
- Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA, 94107, USA.
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Wang XC, Wang H, Tan SD, Yang SX, Shi XF, Zhang W. Viral metagenomics reveals diverse anelloviruses in bone marrow specimens from hematologic patients. J Clin Virol 2020; 132:104643. [PMID: 32961430 DOI: 10.1016/j.jcv.2020.104643] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 09/11/2020] [Accepted: 09/13/2020] [Indexed: 01/01/2023]
Abstract
BACKGROUND An infectious etiology has been proposed for many human cancers, but rarely have specific agents been identified. Viral metagenomic technique is useful for identification of viral pathogens potentially existing in bone marrow specimens from hematologic patients. METHODS A total of 24 patients were included in this study, including 14 female (58.3 %) and 10 male patients (41.7 %) with a mean age of 55.20 ± 18.02 years (16-89 years).Twenty-four bone marrow specimens were collected from 24 hematologic patients (diagnosed with hypoferric anemia, diffuse large B cell lymphoma, myelodysplastic syndrome, acute myelo-monocytic leukemia, acute myelocytic leukemia with maturation, multiple myeloma, lymphoma angioimmunoblastic T cell, acute myeloid leukemia-M1, polycythemia vera/hypoferric anemia, leukocythemia, or megaloblastic anemia). Viral nucleic acid from marrow samples of hematologic patients were subjected to viral metagenomic analysis. PCR method was used to investigate the prevalence of these new viruses in this cohort of hematologic patients. Phylogenetic tree was established to elucidate the relationship of anelloviruses found here and the previously define ones. RESULTS Anelloviridae family are the main group of viruses detected in all the 4 libraries. Forty-six different species of Anelloviruses belonging to genera Alphatorquevirus, Betatorquevirus and Gammatorquevirus and unclassified anellovirus were recovered. Fifteen novel strains with complete ORF1 coding sequence were acquired and phylogenetically analyzed, indicating 8 of the 15 strains are proposed novel species belonging to genus Gammatorquevirus. Nested-PCR were then performed for these15 novel anellovirus strains in the 24 individual bone marrow samples, which showed 13 of them were present in more than one bone marrow samples. CONCLUSIONS Diverse types of anellovirus were present in bone marrow samples of hematologic patients. Whether these novel anelloviruses have association with certain hematonosis needs further investigation.
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Affiliation(s)
- Xiao-Chun Wang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, 212013, China
| | - Hao Wang
- Department of Clinical Laboratory, Huai'an Hospital, Xuzhou Medical University, Huai'an 223002, China.
| | - Shi-Dong Tan
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, 212013, China
| | - Shi-Xing Yang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, 212013, China
| | - Xiao-Feng Shi
- Department of Hematology, The Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, 212001, China
| | - Wen Zhang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, 212013, China.
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Uhl EW, Kelderhouse C, Buikstra J, Blick JP, Bolon B, Hogan RJ. New world origin of canine distemper: Interdisciplinary insights. INTERNATIONAL JOURNAL OF PALEOPATHOLOGY 2019; 24:266-278. [PMID: 30743216 DOI: 10.1016/j.ijpp.2018.12.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 11/29/2018] [Accepted: 12/31/2018] [Indexed: 06/09/2023]
Abstract
OBJECTIVE Canine distemper virus (CDV), human measles virus (HMV), and rinderpest virus (RPV) of cattle are morbilliviruses that have caused devastating outbreaks for centuries. This paper seeks to reconstruct the evolutionary history of CDV. MATERIALS AND METHODS An interdisciplinary approach is adopted, synthesizing paleopathological analysis of 96 Pre-Columbian dogs (750-1470 CE) from the Weyanoke Old Town, Virginia site, with historical reports, molecular analysis and morbilliviral epidemiology. RESULTS Both measles (c.900CE) and rinderpest (c. 376 BCE) were first reported in Eurasia, while canine distemper was initially described in South America much later (1735 CE); there are no paleopathological indications of CDV in Weyanoke Old Town dogs. Molecularly, CDV is closely related to HMV, while viral codon usage indicates CDV may have previously infected humans; South American measles epidemics occurred prior to the emergence of canine distemper and would have facilitated HMV transmission and adaptation to dogs. CONCLUSIONS The measles epidemics that decimated indigenous South American populations in the 1500-1700 s likely facilitated the establishment of CDV as a canine pathogen, which eventually spread to Europe and beyond. SIGNIFICANCE Understanding the historical and environmental conditions that have driven morbilliviral evolution provides important insights into potential future threats of animal/human cross-species infections. LIMITATIONS Interpreting historical disease descriptions is difficult and the archaeological specimens are limited. Molecular sequence data and codon usage analyses rely on modern viruses. SUGGESTIONS FOR FURTHER RESEARCH Interdisciplinary approaches are increasingly needed to understand diseases of the past and present, as critical information and knowledge is scattered in different disciplines.
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Affiliation(s)
- Elizabeth W Uhl
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602-7388, USA.
| | - Charles Kelderhouse
- Augusta University/University of Georgia Medical Partnership, Athens, GA, 30602-7388, USA.
| | - Jane Buikstra
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85287-2402, USA.
| | - Jeffrey P Blick
- Department of Government and Sociology, Georgia College and State University, Milledgeville, GA 31061-0490, USA
| | - Brad Bolon
- Department of Government and Sociology, Georgia College and State University, Milledgeville, GA 31061-0490, USA.
| | - Robert J Hogan
- Department of Veterinary Biosciences and Imaging, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602-7388, USA.
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Siqueira JD, Dominguez-Bello MG, Contreras M, Lander O, Caballero-Arias H, Xutao D, Noya-Alarcon O, Delwart E. Complex virome in feces from Amerindian children in isolated Amazonian villages. Nat Commun 2018; 9:4270. [PMID: 30323210 PMCID: PMC6189175 DOI: 10.1038/s41467-018-06502-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 09/06/2018] [Indexed: 01/22/2023] Open
Abstract
The number of viruses circulating in small isolated human populations may be reduced by viral extinctions and rare introductions. Here we used viral metagenomics to characterize the eukaryotic virome in feces from healthy children from a large urban center and from three Amerindian villages with minimal outside contact. Numerous human enteric viruses, mainly from the Picornaviridae and Caliciviridae families, were sequenced from each of the sites. Multiple children from the same villages shed closely related viruses reflecting frequent transmission clusters. Feces of isolated villagers also contained multiple viral genomes of unknown cellular origin from the Picornavirales order and CRESS-DNA group and higher levels of nematode and protozoan DNA. Despite cultural and geographic isolation, the diversity of enteric human viruses was therefore not reduced in these Amazonian villages. Frequent viral introductions and/or increased susceptibility to enteric infections may account for the complex fecal virome of Amerindian children in isolated villages.
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Affiliation(s)
- Juliana D Siqueira
- Blood Systems Research Institute, San Francisco, CA, 94118, USA.,Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, 20.231-050, Brazil
| | - Maria Gloria Dominguez-Bello
- Department of Biochemistry and Microbiology and of Anthropology, Rutgers University, New Brunswick, NJ, 08901-8554, USA
| | - Monica Contreras
- Center for Biophysics and Biochemistry, Venezuelan Institute of Scientific Research (IVIC), Caracas, 01204, Venezuela
| | - Orlana Lander
- Instituto de Medicina Tropical, Universidad Central de Venezuela, Caracas, 1051, Venezuela
| | - Hortensia Caballero-Arias
- Department of Anthropology, Venezuelan Institute of Scientific Research (IVIC), Caracas, 01204, Venezuela
| | - Deng Xutao
- Blood Systems Research Institute, San Francisco, CA, 94118, USA.,Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA, 94118, USA
| | - Oscar Noya-Alarcon
- Instituto de Medicina Tropical, Universidad Central de Venezuela, Caracas, 1051, Venezuela.,Amazonic Center for Research and Control of Tropical Diseases (CAICET), Puerto Ayacucho, 7101, Venezuela
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, CA, 94118, USA. .,Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA, 94118, USA.
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Svardal H, Jasinska AJ, Apetrei C, Coppola G, Huang Y, Schmitt CA, Jacquelin B, Ramensky V, Müller-Trutwin M, Antonio M, Weinstock G, Grobler JP, Dewar K, Wilson RK, Turner TR, Warren WC, Freimer NB, Nordborg M. Ancient hybridization and strong adaptation to viruses across African vervet monkey populations. Nat Genet 2017; 49:1705-1713. [PMID: 29083404 PMCID: PMC5709169 DOI: 10.1038/ng.3980] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 09/27/2017] [Indexed: 12/16/2022]
Abstract
Vervet monkeys are among the most widely distributed nonhuman primates, show considerable phenotypic diversity, and have long been an important biomedical model for a variety of human diseases and in vaccine research. Using whole-genome sequencing data from 163 vervets sampled from across Africa and the Caribbean, we find high diversity within and between taxa and clear evidence that taxonomic divergence was reticulate rather than following a simple branching pattern. A scan for diversifying selection across taxa identifies strong and highly polygenic selection signals affecting viral processes. Furthermore, selection scores are elevated in genes whose human orthologs interact with HIV and in genes that show a response to experimental simian immunodeficiency virus (SIV) infection in vervet monkeys but not in rhesus macaques, suggesting that part of the signal reflects taxon-specific adaptation to SIV.
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Affiliation(s)
- Hannes Svardal
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Anna J Jasinska
- Center for Neurobehavioral Genetics, University of California Los Angeles, Los Angeles, USA
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Cristian Apetrei
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Giovanni Coppola
- Center for Neurobehavioral Genetics, University of California Los Angeles, Los Angeles, USA
- Department of Neurology, University of California Los Angeles, USA
| | - Yu Huang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China
| | | | | | - Vasily Ramensky
- Center for Neurobehavioral Genetics, University of California Los Angeles, Los Angeles, USA
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | | | - Martin Antonio
- Medical Research Council (MRC), The Gambia Unit, The Gambia
| | - George Weinstock
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - J Paul Grobler
- Department of Genetics, University of the Free State, Bloemfontein, South Africa
| | - Ken Dewar
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Richard K Wilson
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, USA
- Department of Anthropology, University of Wisconsin-Milwaukee, Milwaukee, USA
| | - Trudy R Turner
- Department of Genetics, University of the Free State, Bloemfontein, South Africa
| | - Wesley C Warren
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, USA
| | - Nelson B Freimer
- Center for Neurobehavioral Genetics, University of California Los Angeles, Los Angeles, USA
| | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
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Evidence for a primate origin of zoonotic Helicobacter suis colonizing domesticated pigs. ISME JOURNAL 2017; 12:77-86. [PMID: 28885626 DOI: 10.1038/ismej.2017.145] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 05/11/2017] [Accepted: 08/04/2017] [Indexed: 12/21/2022]
Abstract
Helicobacter suis is the second most prevalent Helicobacter species in the stomach of humans suffering from gastric disease. This bacterium mainly inhabits the stomach of domesticated pigs, in which it causes gastric disease, but it appears to be absent in wild boars. Interestingly, it also colonizes the stomach of asymptomatic rhesus and cynomolgus monkeys. The origin of modern human-, pig- or non-human primate-associated H. suis strains in these respective host populations was hitherto unknown. Here we show that H. suis in pigs possibly originates from non-human primates. Our data suggest that a host jump from macaques to pigs happened between 100 000 and 15 000 years ago and that pig domestication has had a significant impact on the spread of H. suis in the pig population, from where this pathogen occasionally infects humans. Thus, in contrast to our expectations, H. suis appears to have evolved in its main host in a completely different way than its close relative Helicobacter pylori in humans.
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Zhang W, Yang S, Shan T, Hou R, Liu Z, Li W, Guo L, Wang Y, Chen P, Wang X, Feng F, Wang H, Chen C, Shen Q, Zhou C, Hua X, Cui L, Deng X, Zhang Z, Qi D, Delwart E. Virome comparisons in wild-diseased and healthy captive giant pandas. MICROBIOME 2017; 5:90. [PMID: 28780905 PMCID: PMC5545856 DOI: 10.1186/s40168-017-0308-0] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 07/13/2017] [Indexed: 05/12/2023]
Abstract
BACKGROUND The giant panda (Ailuropoda melanoleuca) is a vulnerable mammal herbivore living wild in central China. Viral infections have become a potential threat to the health of these endangered animals, but limited information related to these infections is available. METHODS Using a viral metagenomic approach, we surveyed viruses in the feces, nasopharyngeal secretions, blood, and different tissues from a wild giant panda that died from an unknown disease, a healthy wild giant panda, and 46 healthy captive animals. RESULTS The previously uncharacterized complete or near complete genomes of four viruses from three genera in Papillomaviridae family, six viruses in a proposed new Picornaviridae genus (Aimelvirus), two unclassified viruses related to posaviruses in Picornavirales order, 19 anelloviruses in four different clades of Anelloviridae family, four putative circoviruses, and 15 viruses belonging to the recently described Genomoviridae family were sequenced. Reflecting the diet of giant pandas, numerous insect virus sequences related to the families Iflaviridae, Dicistroviridae, Iridoviridae, Baculoviridae, Polydnaviridae, and subfamily Densovirinae and plant viruses sequences related to the families Tombusviridae, Partitiviridae, Secoviridae, Geminiviridae, Luteoviridae, Virgaviridae, and Rhabdoviridae; genus Umbravirus, Alphaflexiviridae, and Phycodnaviridae were also detected in fecal samples. A small number of insect virus sequences were also detected in the nasopharyngeal secretions of healthy giant pandas and lung tissues from the dead wild giant panda. Although the viral families present in the sick giant panda were also detected in the healthy ones, a higher proportion of papillomaviruses, picornaviruses, and anelloviruses reads were detected in the diseased panda. CONCLUSION This viral survey increases our understanding of eukaryotic viruses in giant pandas and provides a baseline for comparison to viruses detected in future infectious disease outbreaks. The similar viral families detected in sick and healthy giant pandas indicate that these viruses result in commensal infections in most immuno-competent animals.
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Affiliation(s)
- Wen Zhang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013 China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081 China
| | - Shixing Yang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013 China
| | - Tongling Shan
- Department of Swine Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241 China
| | - Rong Hou
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081 China
| | - Zhijian Liu
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013 China
| | - Wang Li
- Department of Laboratory Medicine, Jiangsu Taizhou People’s Hospital, Taizhou, Jiangsu 225300 China
| | - Lianghua Guo
- School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, 200240 China
| | - Yan Wang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013 China
| | - Peng Chen
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081 China
| | - Xiaochun Wang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013 China
| | - Feifei Feng
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081 China
| | - Hua Wang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013 China
| | - Chao Chen
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081 China
| | - Quan Shen
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013 China
| | - Chenglin Zhou
- Department of Laboratory Medicine, Jiangsu Taizhou People’s Hospital, Taizhou, Jiangsu 225300 China
| | - Xiuguo Hua
- School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, 200240 China
| | - Li Cui
- School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, 200240 China
| | - Xutao Deng
- Blood Systems Research Institute, Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94118 USA
| | - Zhihe Zhang
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081 China
| | - Dunwu Qi
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081 China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610000 China
| | - Eric Delwart
- Blood Systems Research Institute, Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94118 USA
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12
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Buechler CR, Bailey AL, Lauck M, Heffron A, Johnson JC, Campos Lawson C, Rogers J, Kuhn JH, O'Connor DH. Genome Sequence of a Novel Kunsagivirus ( Picornaviridae: Kunsagivirus) from a Wild Baboon ( Papio cynocephalus). GENOME ANNOUNCEMENTS 2017; 5:e00261-17. [PMID: 28473378 PMCID: PMC5477186 DOI: 10.1128/genomea.00261-17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 03/15/2017] [Indexed: 12/18/2022]
Abstract
The picornaviral genus Kunsagivirus has a single member, kunsagivirus A, which was discovered in migratory bird feces. We report here the discovery of a novel kunsagivirus in wild yellow baboon (Papio cynocephalus) blood. The genomic sequence of this virus indicates the probable need for the establishment of a second kunsagivirus species.
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Affiliation(s)
- Connor R Buechler
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, Madison, Wisconsin, USA
| | - Adam L Bailey
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, Madison, Wisconsin, USA
| | - Michael Lauck
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, Madison, Wisconsin, USA
| | - Anna Heffron
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, Madison, Wisconsin, USA
| | - Joshua C Johnson
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, USA
| | - Cristine Campos Lawson
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, USA
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, Madison, Wisconsin, USA
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13
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Pimenoff VN, de Oliveira CM, Bravo IG. Transmission between Archaic and Modern Human Ancestors during the Evolution of the Oncogenic Human Papillomavirus 16. Mol Biol Evol 2017; 34:4-19. [PMID: 28025273 PMCID: PMC5854117 DOI: 10.1093/molbev/msw214] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Every human suffers through life a number of papillomaviruses (PVs) infections, most of them asymptomatic. A notable exception are persistent infections by Human papillomavirus 16 (HPV16), the most oncogenic infectious agent for humans and responsible for most infection-driven anogenital cancers. Oncogenic potential is not homogeneous among HPV16 lineages, and genetic variation within HPV16 exhibits some geographic structure. However, an in-depth analysis of the HPV16 evolutionary history was still wanting. We have analyzed extant HPV16 diversity and compared the evolutionary and phylogeographical patterns of humans and of HPV16. We show that codivergence with modern humans explains at most 30% of the present viral geographical distribution. The most explanatory scenario suggests that ancestral HPV16 already infected ancestral human populations and that viral lineages co-diverged with the hosts in parallel with the split between archaic Neanderthal-Denisovans and ancestral modern human populations, generating the ancestral HPV16A and HPV16BCD viral lineages, respectively. We propose that after out-of-Africa migration of modern human ancestors, sexual transmission between human populations introduced HPV16A into modern human ancestor populations. We hypothesize that differential coevolution of HPV16 lineages with different but closely related ancestral human populations and subsequent host-switch events in parallel with introgression of archaic alleles into the genomes of modern human ancestors may be largely responsible for the present-day differential prevalence and association with cancers for HPV16 variants.
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Affiliation(s)
- Ville N Pimenoff
- Infections and Cancer Laboratory, Cancer Epidemiology Research Programme, Catalan Institute of Oncology, Barcelona, Spain
- Unit of Biomarkers and Susceptibility, Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain
| | - Cristina Mendes de Oliveira
- Infections and Cancer Laboratory, Cancer Epidemiology Research Programme, Catalan Institute of Oncology, Barcelona, Spain
- Virology Laboratory, Institute of Tropical Medicine, University of São Paulo, São Paulo, Brazil
| | - Ignacio G Bravo
- Infections and Cancer Laboratory, Cancer Epidemiology Research Programme, Catalan Institute of Oncology, Barcelona, Spain
- MIVEGEC (UMR CNRS 5290, IRD 224, UM), National Center for Scientific Research (CNRS), Montpellier, France
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14
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Smith DB, Becher P, Bukh J, Gould EA, Meyers G, Monath T, Muerhoff AS, Pletnev A, Rico-Hesse R, Stapleton JT, Simmonds P. Proposed update to the taxonomy of the genera Hepacivirus and Pegivirus within the Flaviviridae family. J Gen Virol 2016; 97:2894-2907. [PMID: 27692039 PMCID: PMC5770844 DOI: 10.1099/jgv.0.000612] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Proposals are described for the assignment of recently reported viruses, infecting rodents, bats and other mammalian species, to new species within the Hepacivirus and Pegivirus genera (family Flaviviridae). Assignments into 14 Hepacivirus species (Hepacivirus A–N) and 11 Pegivirus species (Pegivirus A–K) are based on phylogenetic relationships and sequence distances between conserved regions extracted from complete coding sequences for members of each proposed taxon. We propose that the species Hepatitis C virus is renamed Hepacivirus C in order to acknowledge its unique historical position and so as to minimize confusion. Despite the newly documented genetic diversity of hepaciviruses and pegiviruses, members of these genera remain phylogenetically distinct, and differ in hepatotropism and the possession of a basic core protein; pegiviruses in general lack these features. However, other characteristics that were originally used to support their division into separate genera are no longer definitive; there is overlap between the two genera in the type of internal ribosomal entry site and the presence of miR-122 sites in the 5′ UTR, the predicted number of N-linked glycosylation sites in the envelope E1 and E2 proteins, the presence of poly U tracts in the 3′ UTR and the propensity of viruses to establish a persistent infection. While all classified hepaciviruses and pegiviruses have mammalian hosts, the recent description of a hepaci-/pegi-like virus from a shark and the likely existence of further homologues in other non-mammalian species indicate that further species or genera remain to be defined in the future.
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Affiliation(s)
- Donald B Smith
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Scotland, UK
| | - Paul Becher
- Institute of Virology, University of Veterinary Medicine, Hannover, Germany
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases and Clinical Research Centre, Copenhagen University Hospital, Hvidovre, Denmark.,Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Ernest A Gould
- EHESP French School of Public Health, French Institute of Research for Development (IRD), Aix Marseille Université, EPV UMR_D 190 Emergence des Pathologies Virales, Marseille, France
| | - Gregor Meyers
- Institut für Immunologie, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Thomas Monath
- Hookipa Biotech AG, Vienna, Austria.,PaxVax Inc., Menlo Park and Redwood City, CA, USA
| | - A Scott Muerhoff
- Abbott Diagnostics Research and Development, Abbott Park, IL, USA
| | - Alexander Pletnev
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Rebecca Rico-Hesse
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Jack T Stapleton
- Medical Service, Iowa City Veterans Affairs Medical Center, Iowa City, IA, USA.,Department of Internal Medicine, University of Iowa, Iowa City, IA, USA.,Department of Microbiology, University of Iowa, Iowa City, IA, USA
| | - Peter Simmonds
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Scotland, UK.,Nuffield Department of Medicine, University of Oxford, Oxford, UK
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15
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Lam TTY, Zhu H, Guan Y, Holmes EC. Genomic Analysis of the Emergence, Evolution, and Spread of Human Respiratory RNA Viruses. Annu Rev Genomics Hum Genet 2016; 17:193-218. [PMID: 27216777 DOI: 10.1146/annurev-genom-083115-022628] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The emergence and reemergence of rapidly evolving RNA viruses-particularly those responsible for respiratory diseases, such as influenza viruses and coronaviruses-pose a significant threat to global health, including the potential of major pandemics. Importantly, recent advances in high-throughput genome sequencing enable researchers to reveal the genomic diversity of these viral pathogens at much lower cost and with much greater precision than they could before. In particular, the genome sequence data generated allow inferences to be made on the molecular basis of viral emergence, evolution, and spread in human populations in real time. In this review, we introduce recent computational methods that analyze viral genomic data, particularly in combination with metadata such as sampling time, geographic location, and virulence. We then outline the insights these analyses have provided into the fundamental patterns and processes of evolution and emergence in human respiratory RNA viruses, as well as the major challenges in such genomic analyses.
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Affiliation(s)
- Tommy T-Y Lam
- State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong, China; , ,
- Joint Influenza Research Center and Joint Institute of Virology, Shantou University Medical College, Shantou 515041, China
- State Key Laboratory of Emerging Infectious Diseases (HKU-Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen 518112, China
| | - Huachen Zhu
- State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong, China; , ,
- Joint Influenza Research Center and Joint Institute of Virology, Shantou University Medical College, Shantou 515041, China
- State Key Laboratory of Emerging Infectious Diseases (HKU-Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen 518112, China
| | - Yi Guan
- State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong, China; , ,
- Joint Influenza Research Center and Joint Institute of Virology, Shantou University Medical College, Shantou 515041, China
- State Key Laboratory of Emerging Infectious Diseases (HKU-Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen 518112, China
- Department of Microbiology, Guangxi Medical University, Nanning 530021, China
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales 2006, Australia;
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16
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Bailey AL, Lauck M, Ghai RR, Nelson CW, Heimbruch K, Hughes AL, Goldberg TL, Kuhn JH, Jasinska AJ, Freimer NB, Apetrei C, O'Connor DH. Arteriviruses, Pegiviruses, and Lentiviruses Are Common among Wild African Monkeys. J Virol 2016; 90:6724-6737. [PMID: 27170760 PMCID: PMC4944300 DOI: 10.1128/jvi.00573-16] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 05/06/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Nonhuman primates (NHPs) are a historically important source of zoonotic viruses and are a gold-standard model for research on many human pathogens. However, with the exception of simian immunodeficiency virus (SIV) (family Retroviridae), the blood-borne viruses harbored by these animals in the wild remain incompletely characterized. Here, we report the discovery and characterization of two novel simian pegiviruses (family Flaviviridae) and two novel simian arteriviruses (family Arteriviridae) in wild African green monkeys from Zambia (malbroucks [Chlorocebus cynosuros]) and South Africa (vervet monkeys [Chlorocebus pygerythrus]). We examine several aspects of infection, including viral load, genetic diversity, evolution, and geographic distribution, as well as host factors such as age, sex, and plasma cytokines. In combination with previous efforts to characterize blood-borne RNA viruses in wild primates across sub-Saharan Africa, these discoveries demonstrate that in addition to SIV, simian pegiviruses and simian arteriviruses are widespread and prevalent among many African cercopithecoid (i.e., Old World) monkeys. IMPORTANCE Primates are an important source of viruses that infect humans and serve as an important laboratory model of human virus infection. Here, we discover two new viruses in African green monkeys from Zambia and South Africa. In combination with previous virus discovery efforts, this finding suggests that these virus types are widespread among African monkeys. Our analysis suggests that one of these virus types, the simian arteriviruses, may have the potential to jump between different primate species and cause disease. In contrast, the other virus type, the pegiviruses, are thought to reduce the disease caused by human immunodeficiency virus (HIV) in humans. However, we did not observe a similar protective effect in SIV-infected African monkeys coinfected with pegiviruses, possibly because SIV causes little to no disease in these hosts.
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Affiliation(s)
- Adam L Bailey
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, Madison, Wisconsin, USA
| | - Michael Lauck
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, Madison, Wisconsin, USA
| | - Ria R Ghai
- Odum School of Ecology, University of Georgia, Athens, Georgia, USA
| | - Chase W Nelson
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, USA
| | - Katelyn Heimbruch
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, Madison, Wisconsin, USA
| | - Austin L Hughes
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, USA
| | - Tony L Goldberg
- Wisconsin National Primate Research Center, Madison, Wisconsin, USA
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, USA
| | - Anna J Jasinska
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, California, USA
| | - Nelson B Freimer
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, California, USA
| | - Cristian Apetrei
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, Madison, Wisconsin, USA
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17
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Hrazdilová K, Slaninková E, Brožová K, Modrý D, Vodička R, Celer V. New species of Torque Teno miniviruses infecting gorillas and chimpanzees. Virology 2015; 487:207-14. [PMID: 26547037 DOI: 10.1016/j.virol.2015.10.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 10/12/2015] [Accepted: 10/15/2015] [Indexed: 10/22/2022]
Abstract
Anelloviridae family is comprised of small, non-enveloped viruses of various genome lengths, high sequence diversity, sharing the same genome organization. Infections and co-infections by different genotypes in humans are ubiquitous. Related viruses were described in number of mammalian hosts, but very limited data are available from the closest human relatives - great apes and non-human primates. Here we report the 100% prevalence determined by semi-nested PCR from fecal samples of 16 captive primate species. Only the Mandrillus sphinx, showed the prevalence only 8%. We describe three new species of gorillas׳ and four new species of chimpanzees׳ Betatorqueviruses and their co-infections in one individual. This study is also first report and analysis of nearly full length TTMV genomes infecting gorillas. Our attempts to sequence the complete genomes of anelloviruses from host feces invariably failed. Broader usage of blood /tissue material is necessary to understand the diversity and interspecies transmission of anelloviruses.
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Affiliation(s)
- Kristýna Hrazdilová
- Department of Infectious Diseases and Microbiology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno,612 42 Brno, Czech Republic; CEITEC - Central European Institute of Technology, University of Veterinary and Pharmaceutical Sciences Brno,612 42 Brno, Czech Republic.
| | - Eva Slaninková
- Department of Infectious Diseases and Microbiology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno,612 42 Brno, Czech Republic; Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno,612 42 Brno, Czech Republic
| | - Kristýna Brožová
- Department of Infectious Diseases and Microbiology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno,612 42 Brno, Czech Republic; Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno,612 42 Brno, Czech Republic
| | - David Modrý
- CEITEC - Central European Institute of Technology, University of Veterinary and Pharmaceutical Sciences Brno,612 42 Brno, Czech Republic; Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno,612 42 Brno, Czech Republic; Biology Centre, Institute of Parasitology, Czech Academy of Sciences, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Roman Vodička
- The Prague Zoological Garden, Prague 171 00, Czech Republic
| | - Vladimír Celer
- Department of Infectious Diseases and Microbiology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno,612 42 Brno, Czech Republic; CEITEC - Central European Institute of Technology, University of Veterinary and Pharmaceutical Sciences Brno,612 42 Brno, Czech Republic
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18
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Li L, Deng X, Da Costa AC, Bruhn R, Deeks SG, Delwart E. Virome analysis of antiretroviral-treated HIV patients shows no correlation between T-cell activation and anelloviruses levels. J Clin Virol 2015; 72:106-13. [PMID: 26479202 DOI: 10.1016/j.jcv.2015.09.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 09/01/2015] [Accepted: 09/16/2015] [Indexed: 01/29/2023]
Abstract
BACKGROUND Abnormally high levels of T-cell activation can persist in HIV-infected subjects despite effective anti-retroviral therapy (ART) and has been associated with negative health outcomes. The nature of the antigenic drivers or other causes of this residual T-cell activation remain uncertain. Anelloviruses are universally acquired soon after birth, resulting in persistent viremia, and considered part of the commensal human virome. Reduced immunocompetence results in increased anellovirus levels. OBJECTIVES To test whether increased levels of anelloviruses or other viruses in plasma are associated with higher levels of persistent T-cell activation during ART. STUDY DESIGN Two amplification methods combined with next generation sequencing were used to detect all viruses and estimate relative anellovirus levels in plasma from 19 adults on effective ART who exhibited a wide range of T-cell activation levels. RESULTS Nucleic acids from HBV and HCV were detected in one patient each while pegivirus A (GBV-C) was found in three patients. Anellovirus DNA was detected in all patients with some individuals carrying up to eight different genotypes. Specific anellovirus genotypes or higher level of co-infections were not detected in subjects with higher levels of T-cell activation. No association was detected between relative plasma anellovirus DNA levels and the percentage of activated CD4 or CD8 T cells. CONCLUSIONS Human anelloviruses were detected in all HIV suppressed subjects, exhibited a wide range of viremia levels, and were genetically highly diverse. The level of persistent T-cell activation was not correlated with the level of viremia or genotypes present indicating that anellovirus antigens are unlikely to be a dominant source of antigens driving chronic T-cell activation.
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Affiliation(s)
- Linlin Li
- Blood Systems Research Institute, San Francisco, CA, USA; Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, CA, USA; Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Antonio Charlys Da Costa
- Blood Systems Research Institute, San Francisco, CA, USA; Institute of Tropical Medicine, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Roberta Bruhn
- Blood Systems Research Institute, San Francisco, CA, USA
| | - Steven G Deeks
- Positive Health Program, San Francisco General Hospital, San Francisco, CA, USA
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, CA, USA; Department of Laboratory Medicine, University of California, San Francisco, CA, USA.
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19
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Policicchio BB, Pandrea I, Apetrei C. Population Bottlenecks and Pathogen Extinction: "Make This Everyone's Mission to Mars, Including Yours". J Virol 2015; 89:8104-6. [PMID: 26018162 PMCID: PMC4524259 DOI: 10.1128/jvi.00920-15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Kapusinszky et al. (J Virol 89:8152-8161, 2015, http://dx.doi.org/10.1128/JVI.00671-15) report that host population bottlenecks may result in pathogen extinction, which provides a compelling argument for an alternative approach to vaccination for the control of virus spread. By comparing the prevalence levels of three viral pathogens in two populations of African green monkeys (AGMs) (Chlorocebus sabaeus) from Africa and two Caribbean Islands, they convincingly show that a major host bottleneck resulted in the eradication of select pathogens from a given host.
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Affiliation(s)
- Benjamin B Policicchio
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, USA Department of Infectious Diseases and Microbiology, Graduate School of Public Health, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Ivona Pandrea
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, USA Department of Infectious Diseases and Microbiology, Graduate School of Public Health, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Cristian Apetrei
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, USA Department of Infectious Diseases and Microbiology, Graduate School of Public Health, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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