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Saab L, DiCapua D, Zubair AS. HTLV-1 associated myelopathy/tropical spastic paraparesis (HAM/TSP): Case based discussion of risk factors, clinical, and therapeutic considerations. J Neurol Sci 2024; 459:122973. [PMID: 38520941 DOI: 10.1016/j.jns.2024.122973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 03/06/2024] [Accepted: 03/17/2024] [Indexed: 03/25/2024]
Abstract
HTLV-1 is a retrovirus virus that infects CD4+ T cells. Most people with HTLV-1 infection remain asymptomatic but some may develop conditions such as HTLV-1 associated myelopathy/tropical spastic paraparesis (HAM/TSP) or adult T-cell leukemia/lymphoma. HAM/TSP is characterized by progressive spasticity and weakness of the lower extremities, as well as loss of bladder control and sensory disturbances. The risk of developing HAM/TSP is associated with the duration of infection and the proviral load. There is currently no cure for the disease but medications can help manage symptoms and slow the progression of the disease. This is the case of a 66-year-old female who presented with nonspecific symptoms of weakness and spasticity in a hospital in Connecticut and was subsequently diagnosed with HAM/TSP. The patient's diagnosis highlights the importance of considering diseases previously confined to specific endemic regions in a globalized world where increased emigration and population mixing can occur. Early identification and management of such cases is essential for optimizing patient outcomes and quality of life.
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Affiliation(s)
- Lea Saab
- Department of Neurology, Yale University School of Medicine, 20 York Street, New Haven, CT, 06510, USA
| | - Daniel DiCapua
- Department of Neurology, Yale University School of Medicine, 20 York Street, New Haven, CT, 06510, USA
| | - Adeel S Zubair
- Department of Neurology, Yale University School of Medicine, 20 York Street, New Haven, CT, 06510, USA.
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2
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da Silva AL, Guedes BLM, Santos SN, Correa GF, Nardy A, Nali LHDS, Bachi ALL, Romano CM. Beyond pathogens: the intriguing genetic legacy of endogenous retroviruses in host physiology. Front Cell Infect Microbiol 2024; 14:1379962. [PMID: 38655281 PMCID: PMC11035796 DOI: 10.3389/fcimb.2024.1379962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 03/22/2024] [Indexed: 04/26/2024] Open
Abstract
The notion that viruses played a crucial role in the evolution of life is not a new concept. However, more recent insights suggest that this perception might be even more expansive, highlighting the ongoing impact of viruses on host evolution. Endogenous retroviruses (ERVs) are considered genomic remnants of ancient viral infections acquired throughout vertebrate evolution. Their exogenous counterparts once infected the host's germline cells, eventually leading to the permanent endogenization of their respective proviruses. The success of ERV colonization is evident so that it constitutes 8% of the human genome. Emerging genomic studies indicate that endogenous retroviruses are not merely remnants of past infections but rather play a corollary role, despite not fully understood, in host genetic regulation. This review presents some evidence supporting the crucial role of endogenous retroviruses in regulating host genetics. We explore the involvement of human ERVs (HERVs) in key physiological processes, from their precise and orchestrated activities during cellular differentiation and pluripotency to their contributions to aging and cellular senescence. Additionally, we discuss the costs associated with hosting a substantial amount of preserved viral genetic material.
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Affiliation(s)
- Amanda Lopes da Silva
- Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Bruno Luiz Miranda Guedes
- Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Samuel Nascimento Santos
- UNISA Research Center, Universidade Santo Amaro, Post-Graduation in Health Sciences, São Paulo, Brazil
| | - Giovanna Francisco Correa
- Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Ariane Nardy
- UNISA Research Center, Universidade Santo Amaro, Post-Graduation in Health Sciences, São Paulo, Brazil
| | | | - Andre Luis Lacerda Bachi
- UNISA Research Center, Universidade Santo Amaro, Post-Graduation in Health Sciences, São Paulo, Brazil
| | - Camila Malta Romano
- Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
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3
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Duran-Yelken S, Alkan F. Molecular analysis of the env, LTR, and pX regions of bovine leukemia virus in dairy cattle of Türkiye. Virus Genes 2024:10.1007/s11262-024-02058-7. [PMID: 38355991 DOI: 10.1007/s11262-024-02058-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 01/28/2024] [Indexed: 02/16/2024]
Abstract
Bovine leukemia virus is a retrovirus that causes enzootic bovine leukosis and is associated with global economic losses in the livestock industry. The aim of this study was to investigate the genotype determination of BLVs from cattle housed in 6 different farms in Türkiye and the characterization of their LTR and pX (tax, rex, R3, and G4 gene) regions. For this purpose, blood samples from 48 cattle infected with BLV were used. The phylogenetic analysis based on the env gene sequences revealed that all BLVs were clustered in genotype 1 (G1), and the sequences of the LTR (n = 48) and the pX region (n = 33) of BLVs were obtained. Also, analysis of these nucleic acid and amino acid sequences allowed assessments similar to those reported in earlier studies to be relevant to transactivation and pathogenesis. This study reports the molecular analysis of the LTR and pX region of BLVs in Türkiye for the first time.
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Affiliation(s)
- Selda Duran-Yelken
- Department of Virology, Faculty of Veterinary Medicine, Kastamonu University, Kastamonu, Turkey.
| | - Feray Alkan
- Department of Virology, Faculty of Veterinary Medicine, Ankara University, Ankara, Turkey
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Levintov L, Vashisth H. Structural and computational studies of HIV-1 RNA. RNA Biol 2024; 21:1-32. [PMID: 38100535 PMCID: PMC10730233 DOI: 10.1080/15476286.2023.2289709] [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] [Accepted: 11/21/2023] [Indexed: 12/17/2023] Open
Abstract
Viruses remain a global threat to animals, plants, and humans. The type 1 human immunodeficiency virus (HIV-1) is a member of the retrovirus family and carries an RNA genome, which is reverse transcribed into viral DNA and further integrated into the host-cell DNA for viral replication and proliferation. The RNA structures from the HIV-1 genome provide valuable insights into the mechanisms underlying the viral replication cycle. Moreover, these structures serve as models for designing novel therapeutic approaches. Here, we review structural data on RNA from the HIV-1 genome as well as computational studies based on these structural data. The review is organized according to the type of structured RNA element which contributes to different steps in the viral replication cycle. This is followed by an overview of the HIV-1 transactivation response element (TAR) RNA as a model system for understanding dynamics and interactions in the viral RNA systems. The review concludes with a description of computational studies, highlighting the impact of biomolecular simulations in elucidating the mechanistic details of various steps in the HIV-1's replication cycle.
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Affiliation(s)
- Lev Levintov
- Department of Chemical Engineering & Bioengineering, University of New Hampshire, Durham, USA
| | - Harish Vashisth
- Department of Chemical Engineering & Bioengineering, University of New Hampshire, Durham, USA
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Fandiño S, Gomez-Lucia E, Benítez L, Doménech A. Comparison of Endogenous Alpharetroviruses (ALV-like) across Galliform Species: New Distant Proviruses. Microorganisms 2023; 12:86. [PMID: 38257913 PMCID: PMC10820513 DOI: 10.3390/microorganisms12010086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 12/22/2023] [Accepted: 12/25/2023] [Indexed: 01/24/2024] Open
Abstract
The Genus Alpharetrovirus contains viruses pathogenic mainly for chickens, forming the Avian Sarcoma and Leukosis Virus group (ASLV). Cells of most Galliform species, besides chickens, contain genetic elements (endogenous retroviruses, ERVs) that could recombine with other alpharetroviruses or express proteins, complementing defective ASLV, which may successfully replicate and cause disease. However, they are quite unknown, and only ALV-F, from ring-necked pheasants, has been partially published. Upon scrutiny of 53 genomes of different avian species, we found Alpharetrovirus-like sequences only in 12 different Galliformes, including six full-length (7.4-7.6 Kbp) and 27 partial sequences. Phylogenetic studies of the regions studied (LTR, gag, pol, and env) consistently resulted in five almost identical clades containing the same ERVs: Clade I (presently known ASLVs); Clade II (Callipepla spp. ERVs); Clade IIIa (Phasianus colchicus ERVs); Clade IIIb (Alectoris spp. ERVs); and Clade IV (Centrocercus spp. ERVs). The low pol identity scores suggested that each of these Clades may be considered a different species. ORF analysis revealed that putatively encoded proteins would be very similar in length and domains to those of other alpharetroviruses and thus potentially functional. This will undoubtedly contribute to better understanding the biology of defective viruses, especially in wild Galliformes, their evolution, and the danger they may represent for other wild species and the poultry industry.
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Affiliation(s)
- Sergio Fandiño
- Department of Animal Health, Veterinary Faculty, Complutense University of Madrid, Av. Puerta de Hierro s/n, 28040 Madrid, Spain; (S.F.); (A.D.)
- Department of Genetics, Physiology and Microbiology, Faculty of Biological Sciences, Complutense University of Madrid (UCM), C. de José Antonio Novais 12, 28040 Madrid, Spain;
- Research Group, “Animal Viruses” of Complutense University of Madrid, 28040 Madrid, Spain
| | - Esperanza Gomez-Lucia
- Department of Animal Health, Veterinary Faculty, Complutense University of Madrid, Av. Puerta de Hierro s/n, 28040 Madrid, Spain; (S.F.); (A.D.)
- Research Group, “Animal Viruses” of Complutense University of Madrid, 28040 Madrid, Spain
| | - Laura Benítez
- Department of Genetics, Physiology and Microbiology, Faculty of Biological Sciences, Complutense University of Madrid (UCM), C. de José Antonio Novais 12, 28040 Madrid, Spain;
- Research Group, “Animal Viruses” of Complutense University of Madrid, 28040 Madrid, Spain
| | - Ana Doménech
- Department of Animal Health, Veterinary Faculty, Complutense University of Madrid, Av. Puerta de Hierro s/n, 28040 Madrid, Spain; (S.F.); (A.D.)
- Research Group, “Animal Viruses” of Complutense University of Madrid, 28040 Madrid, Spain
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Simpson J, Kozak CA, Boso G. Evolutionary conservation of an ancient retroviral gagpol gene in Artiodactyla. J Virol 2023; 97:e0053523. [PMID: 37668369 PMCID: PMC10537755 DOI: 10.1128/jvi.00535-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/28/2023] [Indexed: 09/06/2023] Open
Abstract
The genomes of mammals contain fingerprints of past infections by ancient retroviruses that invaded the germline of their ancestors. Most of these endogenous retroviruses (ERVs) contain only remnants of the original retrovirus; however, on rare occasions, ERV genes can be co-opted for a beneficial host function. While most studies of co-opted ERVs have focused on envelope genes, including the syncytins that function in placentation, there are examples of co-opted gag genes including one we recently discovered in simian primates. Here, we searched for other intact gag genes in non-primate mammalian lineages. We began by examining the genomes of extant camel species, which represent a basal lineage in the order Artiodactyla. This identified a gagpol gene with a large open reading frame (ORF) (>3,500 bp) in the same orthologous location in Artiodactyla species but that is absent in other mammals. Thus, this ERV was fixed in the common ancestor of all Artiodactyla at least 64 million years ago. The amino acid sequence of this gene, termed ARTgagpol, contains recognizable matrix, capsid, nucleocapsid, and reverse transcriptase domains in ruminants, with an RNase H domain in camels and pigs. Phylogenetic analysis and structural prediction of its reverse transcriptase and RNase H domains groups ARTgagpol with gammaretroviruses. Transcriptomic analysis shows ARTgagpol expression in multiple tissues suggestive of a co-opted host function. These findings identify the oldest and largest ERV-derived gagpol gene with an intact ORF in mammals, an intriguing milestone in the co-evolution of mammals and retroviruses. IMPORTANCE Retroviruses are unique among viruses that infect animals as they integrate their reverse-transcribed double-stranded DNA into host chromosomes. When this happens in a germline cell, such as sperm, egg, or their precursors, the integrated retroviral copies can be passed on to the next generation as endogenous retroviruses (ERVs). On rare occasions, the genes of these ERVs can be domesticated by the host. In this study we used computational similarity searches to identify an ancient ERV with an intact viral gagpol gene in the genomes of camels that is also found in the same genomic location in other even-toed ungulates suggesting that it is at least 64 million years old. Broad tissue expression and predicted preservation of the reverse transcriptase fold of this protein suggest that it may be domesticated for a host function. This is the oldest known intact gagpol gene of an ancient retrovirus in mammals.
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Affiliation(s)
- J'Zaria Simpson
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Christine A. Kozak
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Guney Boso
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
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Malli IA, Hamdan D, Aljahdali A, Almutairi A, Jar R, Alzahrani R, Khan MA. Medical Interns' Knowledge, Attitude, and Practice Toward People Living with HIV: Multicenter Experience from Saudi Arabia. HIV AIDS (Auckl) 2023; 15:571-582. [PMID: 37744212 PMCID: PMC10516208 DOI: 10.2147/hiv.s418948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 09/07/2023] [Indexed: 09/26/2023] Open
Abstract
Background Discrimination by some healthcare providers toward people living with HIV/AIDS has been documented. Differences in cultural backgrounds make it harder for future doctors, who need a lot of knowledge and a positive attitude to treat patients. In conservative countries like Saudi Arabia, not enough is known about how much medical interns know about HIV and how they feel about people living with HIV/AIDS. Methods From April to September 2021, this cross-sectional study use non-probability random sampling and utilized a self-administered questionnaire to collected the data from 346 medical interns who had graduated from five different medical schools. Results Most of the subjects correctly identified the main transmission routes, such as unprotected sex (94.57%), blood and body fluid exchange (94.19%), and sharing needles or syringes (91.47%). But they did not know what the most common co-infections were for HIV patients or how to protect themselves after exposure. This paper showed that medical interns have some stigmatizing behaviors toward patients living with HIV, as 31.1% and 22.9% agreed, respectively, that they would feel more sympathetic toward people who get AIDS from blood transfusions compared to IV drug users (IDU). Conclusion Medical interns also showed some positive attitudes, as more than half of the sample (56.2%) would not isolate beds for people living with HIV/AIDS. The study's conclusion is that HIV education and training programs should be added for medical interns, which might have a significant positive impact on their attitude.
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Affiliation(s)
- Israa Abdullah Malli
- Department of Basic Medical Sciences, College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Jeddah, 21423, Saudi Arabia
- King Abdullah International Medical Research Center, Jeddah, 22384, Saudi Arabia
- Ministry of the National Guard - Health Affairs, Jeddah, 22384, Saudi Arabia
| | - Dalia Hamdan
- Department of Basic Medical Sciences, College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Jeddah, 21423, Saudi Arabia
- King Abdullah International Medical Research Center, Jeddah, 22384, Saudi Arabia
| | - Alhanoof Aljahdali
- Department of Basic Medical Sciences, College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Jeddah, 21423, Saudi Arabia
- King Abdullah International Medical Research Center, Jeddah, 22384, Saudi Arabia
| | - Amal Almutairi
- Department of Basic Medical Sciences, College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Jeddah, 21423, Saudi Arabia
- King Abdullah International Medical Research Center, Jeddah, 22384, Saudi Arabia
| | - Raghad Jar
- Department of Basic Medical Sciences, College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Jeddah, 21423, Saudi Arabia
- King Abdullah International Medical Research Center, Jeddah, 22384, Saudi Arabia
| | - Reham Alzahrani
- Department of Basic Medical Sciences, College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Jeddah, 21423, Saudi Arabia
- King Abdullah International Medical Research Center, Jeddah, 22384, Saudi Arabia
| | - Muhammad Anwar Khan
- Department of Basic Medical Sciences, College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Jeddah, 21423, Saudi Arabia
- King Abdullah International Medical Research Center, Jeddah, 22384, Saudi Arabia
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Wang J, Han GZ. Genome mining shows that retroviruses are pervasively invading vertebrate genomes. Nat Commun 2023; 14:4968. [PMID: 37591904 PMCID: PMC10435555 DOI: 10.1038/s41467-023-40732-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 08/04/2023] [Indexed: 08/19/2023] Open
Abstract
Endogenous retroviruses (ERVs) record past retroviral infections, providing molecular archives for interrogating the evolution of retroviruses and retrovirus-host interaction. However, the vast majority of ERVs are not active anymore due to various disruptive mutations, and ongoing retroviral invasion of vertebrate genomes has been rarely documented. Here we analyze genomics data from 2004 vertebrates for mining invading ERVs (ERVi). We find that at least 412 ERVi elements representing 217 viral operational taxonomic units are invading the genomes of 123 vertebrates, 18 of which have been assessed to be threatened species. Our results reveal an unexpected prevalence of ongoing retroviral invasion in vertebrates and expand the diversity of retroviruses recently circulating in the wild. We characterize the pattern and nature of ERVi in the historical and biogeographical context of their hosts, for instance, the generation of model organisms, sympatric speciation, and domestication. We suspect that these ERVi are relevant to conservation of threatened species, zoonoses in the wild, and emerging infectious diseases in humans.
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Affiliation(s)
- Jianhua Wang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Guan-Zhu Han
- College of Life Sciences, Nanjing Normal University, Nanjing, China.
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Dunay E, Rukundo J, Atencia R, Cole MF, Cantwell A, Emery Thompson M, Rosati AG, Goldberg TL. Viruses in saliva from sanctuary chimpanzees (Pan troglodytes) in Republic of Congo and Uganda. PLoS One 2023; 18:e0288007. [PMID: 37384730 PMCID: PMC10310015 DOI: 10.1371/journal.pone.0288007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/16/2023] [Indexed: 07/01/2023] Open
Abstract
Pathogen surveillance for great ape health monitoring has typically been performed on non-invasive samples, primarily feces, in wild apes and blood in sanctuary-housed apes. However, many important primate pathogens, including known zoonoses, are shed in saliva and transmitted via oral fluids. Using metagenomic methods, we identified viruses in saliva samples from 46 wild-born, sanctuary-housed chimpanzees at two African sanctuaries in Republic of Congo and Uganda. In total, we identified 20 viruses. All but one, an unclassified CRESS DNA virus, are classified in five families: Circoviridae, Herpesviridae, Papillomaviridae, Picobirnaviridae, and Retroviridae. Overall, viral prevalence ranged from 4.2% to 87.5%. Many of these viruses are ubiquitous in primates and known to replicate in the oral cavity (simian foamy viruses, Retroviridae; a cytomegalovirus and lymphocryptovirus; Herpesviridae; and alpha and gamma papillomaviruses, Papillomaviridae). None of the viruses identified have been shown to cause disease in chimpanzees or, to our knowledge, in humans. These data suggest that the risk of zoonotic viral disease from chimpanzee oral fluids in sanctuaries may be lower than commonly assumed.
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Affiliation(s)
- Emily Dunay
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Joshua Rukundo
- Ngamba Island Chimpanzee Sanctuary / Chimpanzee Trust, Entebbe, Uganda
| | - Rebeca Atencia
- Jane Goodall Institute Congo, Pointe-Noire, Republic of Congo
| | - Megan F. Cole
- Department of Anthropology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Averill Cantwell
- Department of Psychology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Melissa Emery Thompson
- Department of Anthropology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Alexandra G. Rosati
- Department of Psychology, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Anthropology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Tony L. Goldberg
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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Ruivinho C, Gama-Carvalho M. Small non-coding RNAs encoded by RNA viruses: old controversies and new lessons from the COVID-19 pandemic. Front Genet 2023; 14:1216890. [PMID: 37415603 PMCID: PMC10322155 DOI: 10.3389/fgene.2023.1216890] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 06/07/2023] [Indexed: 07/08/2023] Open
Abstract
The recurring outbreaks caused by emerging RNA viruses have fostered an increased interest in the research of the mechanisms that regulate viral life cycles and the pathological outcomes associated with infections. Although interactions at the protein level are well-studied, interactions mediated by RNA molecules are less explored. RNA viruses can encode small non-coding RNAs molecules (sncRNAs), including viral miRNAs (v-miRNAs), that play important roles in modulating host immune responses and viral replication by targeting viral or host transcripts. Starting from the analysis of public databases compiling the known repertoire of viral ncRNA molecules and the evolution of publications and research interests on this topic in the wake of the COVID-19 pandemic, we provide an updated view on the current knowledge on viral sncRNAs, with a focus on v-miRNAs encoded by RNA viruses, and their mechanisms of action. We also discuss the potential of these molecules as diagnostic and prognostic biomarkers for viral infections and the development of antiviral therapies targeting v-miRNAs. This review emphasizes the importance of continued research efforts to characterize sncRNAs encoded by RNA viruses, identifies the most relevant pitfalls in the study of these molecules, and highlights the paradigm changes that have occurred in the last few years regarding their biogenesis, prevalence and functional relevance in the context of host-pathogen interactions.
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Romerio F. Origin and functional role of antisense transcription in endogenous and exogenous retroviruses. Retrovirology 2023; 20:6. [PMID: 37194028 DOI: 10.1186/s12977-023-00622-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/30/2023] [Indexed: 05/18/2023] Open
Abstract
Most proteins expressed by endogenous and exogenous retroviruses are encoded in the sense (positive) strand of the genome and are under the control of regulatory elements within the 5' long terminal repeat (LTR). A number of retroviral genomes also encode genes in the antisense (negative) strand and their expression is under the control of negative sense promoters within the 3' LTR. In the case of the Human T-cell Lymphotropic Virus 1 (HTLV-1), the antisense protein HBZ has been shown to play a critical role in the virus lifecycle and in the pathogenic process, while the function of the Human Immunodeficiency Virus 1 (HIV-1) antisense protein ASP remains unknown. However, the expression of 3' LTR-driven antisense transcripts is not always demonstrably associated with the presence of an antisense open reading frame encoding a viral protein. Moreover, even in the case of retroviruses that do express an antisense protein, such as HTLV-1 and the pandemic strains of HIV-1, the 3' LTR-driven antisense transcript shows both protein-coding and noncoding activities. Indeed, the ability to express antisense transcripts appears to be phylogenetically more widespread among endogenous and exogenous retroviruses than the presence of a functional antisense open reading frame within these transcripts. This suggests that retroviral antisense transcripts may have originated as noncoding molecules with regulatory activity that in some cases later acquired protein-coding function. Here, we will review examples of endogenous and exogenous retroviral antisense transcripts, and the ways through which they benefit viral persistence in the host.
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Affiliation(s)
- Fabio Romerio
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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12
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Di Nunzio F, Uversky VN, Mouland AJ. Biomolecular condensates: insights into early and late steps of the HIV-1 replication cycle. Retrovirology 2023; 20:4. [PMID: 37029379 PMCID: PMC10081342 DOI: 10.1186/s12977-023-00619-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 03/16/2023] [Indexed: 04/09/2023] Open
Abstract
A rapidly evolving understanding of phase separation in the biological and physical sciences has led to the redefining of virus-engineered replication compartments in many viruses with RNA genomes. Condensation of viral, host and genomic and subgenomic RNAs can take place to evade the innate immunity response and to help viral replication. Divergent viruses prompt liquid-liquid phase separation (LLPS) to invade the host cell. During HIV replication there are several steps involving LLPS. In this review, we characterize the ability of individual viral and host partners that assemble into biomolecular condensates (BMCs). Of note, bioinformatic analyses predict models of phase separation in line with several published observations. Importantly, viral BMCs contribute to function in key steps retroviral replication. For example, reverse transcription takes place within nuclear BMCs, called HIV-MLOs while during late replication steps, retroviral nucleocapsid acts as a driver or scaffold to recruit client viral components to aid the assembly of progeny virions. Overall, LLPS during viral infections represents a newly described biological event now appreciated in the virology field, that can also be considered as an alternative pharmacological target to current drug therapies especially when viruses become resistant to antiviral treatment.
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Affiliation(s)
- Francesca Di Nunzio
- Advanced Molecular Virology Unit, Department of Virology, Institut Pasteur, Université Paris Cité, 75015, Paris, France
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Andrew J Mouland
- Lady Davis Institute at the Jewish General Hospital, Montréal, QC, H3T 1E2, Canada.
- Department of Microbiology and Immunology, McGill University, Montréal, QC, H3A 2B4, Canada.
- Department of Medicine, McGill University, Montréal, QC, H4A 3J1, Canada.
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Simmonds P, Adriaenssens EM, Zerbini FM, Abrescia NGA, Aiewsakun P, Alfenas-Zerbini P, Bao Y, Barylski J, Drosten C, Duffy S, Duprex WP, Dutilh BE, Elena SF, García ML, Junglen S, Katzourakis A, Koonin EV, Krupovic M, Kuhn JH, Lambert AJ, Lefkowitz EJ, Łobocka M, Lood C, Mahony J, Meier-Kolthoff JP, Mushegian AR, Oksanen HM, Poranen MM, Reyes-Muñoz A, Robertson DL, Roux S, Rubino L, Sabanadzovic S, Siddell S, Skern T, Smith DB, Sullivan MB, Suzuki N, Turner D, Van Doorslaer K, Vandamme AM, Varsani A, Vasilakis N. Four principles to establish a universal virus taxonomy. PLoS Biol 2023; 21:e3001922. [PMID: 36780432 PMCID: PMC9925010 DOI: 10.1371/journal.pbio.3001922] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Abstract
A universal taxonomy of viruses is essential for a comprehensive view of the virus world and for communicating the complicated evolutionary relationships among viruses. However, there are major differences in the conceptualisation and approaches to virus classification and nomenclature among virologists, clinicians, agronomists, and other interested parties. Here, we provide recommendations to guide the construction of a coherent and comprehensive virus taxonomy, based on expert scientific consensus. Firstly, assignments of viruses should be congruent with the best attainable reconstruction of their evolutionary histories, i.e., taxa should be monophyletic. This fundamental principle for classification of viruses is currently included in the International Committee on Taxonomy of Viruses (ICTV) code only for the rank of species. Secondly, phenotypic and ecological properties of viruses may inform, but not override, evolutionary relatedness in the placement of ranks. Thirdly, alternative classifications that consider phenotypic attributes, such as being vector-borne (e.g., "arboviruses"), infecting a certain type of host (e.g., "mycoviruses," "bacteriophages") or displaying specific pathogenicity (e.g., "human immunodeficiency viruses"), may serve important clinical and regulatory purposes but often create polyphyletic categories that do not reflect evolutionary relationships. Nevertheless, such classifications ought to be maintained if they serve the needs of specific communities or play a practical clinical or regulatory role. However, they should not be considered or called taxonomies. Finally, while an evolution-based framework enables viruses discovered by metagenomics to be incorporated into the ICTV taxonomy, there are essential requirements for quality control of the sequence data used for these assignments. Combined, these four principles will enable future development and expansion of virus taxonomy as the true evolutionary diversity of viruses becomes apparent.
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Affiliation(s)
- Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | | | - F. Murilo Zerbini
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Nicola G. A. Abrescia
- Structure and Cell Biology of Viruses Lab, Center for Cooperative Research in Biosciences—BRTA, Derio, Spain
- Basque Foundation for Science, IKERBASQUE, Bilbao, Spain
| | - Pakorn Aiewsakun
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | | | - Yiming Bao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jakub Barylski
- Department of Molecular Virology, Adam Mickiewicz University, Poznan, Poland
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt University, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers The State University of New Jersey, New Brunswick, New Jersey, United States of America
| | - W. Paul Duprex
- The Center for Vaccine Research, University of Pittsburgh School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Bas E. Dutilh
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich-Schiller-University, Jena, Germany
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Utrecht, the Netherlands
| | - Santiago F. Elena
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, Valencia, Spain
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
| | - Maria Laura García
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET, UNLP, La Plata, Argentina
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt University, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Aris Katzourakis
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France
| | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick (IRF-Frederick), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, United States of America
| | - Amy J. Lambert
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
| | - Elliot J. Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Małgorzata Łobocka
- Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, Warsaw, Poland
| | - Cédric Lood
- Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Jennifer Mahony
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Jan P. Meier-Kolthoff
- Department of Bioinformatics and Databases, Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Arcady R. Mushegian
- Division of Molecular and Cellular Biosciences, National Science Foundation, Alexandria, Virginia, United States of America
| | - Hanna M. Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Minna M. Poranen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Alejandro Reyes-Muñoz
- Max Planck Tandem Group in Computational Biology, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
| | - David L. Robertson
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Simon Roux
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Luisa Rubino
- Istituto per la Protezione Sostenibile delle Piante, CNR, UOS Bari, Bari, Italy
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Stuart Siddell
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Tim Skern
- Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria
| | - Donald B. Smith
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Matthew B. Sullivan
- Departments of Microbiology and Civil, Environmental, and Geodetic Engineering, Ohio State University, Columbus, Ohio, United States of America
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
| | - Dann Turner
- School of Applied Sciences, College of Health, Science and Society, University of the West of England, Bristol, United Kingdom
| | - Koenraad Van Doorslaer
- School of Animal and Comparative Biomedical Sciences, Department of Immunobiology, BIO5 Institute, and University of Arizona Cancer Center, Tucson, Arizona, United States of America
| | - Anne-Mieke Vandamme
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Leuven, Belgium
- Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, United States of America
| | - Nikos Vasilakis
- Department of Pathology, Center of Vector-Borne and Zoonotic Diseases, Institute for Human Infection and Immunity and World Reference Center for Emerging Viruses and Arboviruses, The University of Texas Medical Branch, Galveston, Texas, United States of America
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Hogan V, Johnson WE. Unique Structure and Distinctive Properties of the Ancient and Ubiquitous Gamma-Type Envelope Glycoprotein. Viruses 2023; 15:v15020274. [PMID: 36851488 PMCID: PMC9967133 DOI: 10.3390/v15020274] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/13/2023] [Accepted: 01/15/2023] [Indexed: 01/20/2023] Open
Abstract
After the onset of the AIDS pandemic, HIV-1 (genus Lentivirus) became the predominant model for studying retrovirus Env glycoproteins and their role in entry. However, HIV Env is an inadequate model for understanding entry of viruses in the Alpharetrovirus, Gammaretrovirus and Deltaretrovirus genera. For example, oncogenic model system viruses such as Rous sarcoma virus (RSV, Alpharetrovirus), murine leukemia virus (MLV, Gammaretrovirus) and human T-cell leukemia viruses (HTLV-I and HTLV-II, Deltaretrovirus) encode Envs that are structurally and functionally distinct from HIV Env. We refer to these as Gamma-type Envs. Gamma-type Envs are probably the most widespread retroviral Envs in nature. They are found in exogenous and endogenous retroviruses representing a broad spectrum of vertebrate hosts including amphibians, birds, reptiles, mammals and fish. In endogenous form, gamma-type Envs have been evolutionarily coopted numerous times, most notably as placental syncytins (e.g., human SYNC1 and SYNC2). Remarkably, gamma-type Envs are also found outside of the Retroviridae. Gp2 proteins of filoviruses (e.g., Ebolavirus) and snake arenaviruses in the genus Reptarenavirus are gamma-type Env homologs, products of ancient recombination events involving viruses of different Baltimore classes. Distinctive hallmarks of gamma-type Envs include a labile disulfide bond linking the surface and transmembrane subunits, a multi-stage attachment and fusion mechanism, a highly conserved (but poorly understood) "immunosuppressive domain", and activation by the viral protease during virion maturation. Here, we synthesize work from diverse retrovirus model systems to illustrate these distinctive properties and to highlight avenues for further exploration of gamma-type Env structure and function.
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15
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Role of TLRs in HIV-1 Infection and Potential of TLR Agonists in HIV-1 Vaccine Development and Treatment Strategies. Pathogens 2023; 12:pathogens12010092. [PMID: 36678440 PMCID: PMC9866513 DOI: 10.3390/pathogens12010092] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/28/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023] Open
Abstract
Toll-like receptors (TLRs), as a family of pattern recognition receptors, play an important role in the recognition of HIV-1 molecular structures by various cells of the innate immune system, but also provide a functional association with subsequent mechanisms of adaptive immunity. TLR7 and TLR8 play a particularly important role in the innate immune response to RNA viruses due to their ability to recognise GU-rich single-stranded RNA molecules and subsequently activate intracellular signalling pathways resulting in expression of genes coding for various biological response modifiers (interferons, proinflammatory cytokines, chemokines). The aim of this review is to summarise the most recent knowledge on the role of TLRs in the innate immune response to HIV-1 and the role of TLR gene polymorphisms in the biology and in the clinical aspects of HIV infections. In addition, the role of TLR agonists as latency reversing agents in research to treat HIV infections and as immunomodulators in HIV vaccine research will be discussed.
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Acevedo-Jiménez GE, Sarmiento-Silva RE, Alonso-Morales RA, Córdova-Ponce R, Ramírez-Álvarez H. Detection and genetic characterization of feline retroviruses in domestic cats with different clinical signs and hematological alterations. Arch Virol 2023. [DOI: https:/doi.org/10.1007/s00705-022-05627-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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17
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Kimla LJ, Clark TG, Banerjee S, Campino S. JC Polyomavirus T-antigen protein expression and the risk of colorectal cancer: Systematic review and meta-analysis of case-control studies. PLoS One 2023; 18:e0283642. [PMID: 37000859 PMCID: PMC10065230 DOI: 10.1371/journal.pone.0283642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 03/14/2023] [Indexed: 04/03/2023] Open
Abstract
JC Polyomavirus (JCV) is a human polyomavirus encoding T-antigen protein, which is implicated in carcinogenesis. JCV is prevalent in the upper and lower gastrointestinal track. Several studies have reported JCV associations with the risk of developing colorectal cancer (CRC), however, these findings remain controversial. Since JCV DNA may be present in healthy tissues as well as transformed tissues, JCV T-antigen expression could be a more useful measure of JCV's association with cancer development. The aim of this study is to conduct a meta-analysis of case-control studies to investigate if there is a significant association between JCV T-antigen protein expression and risk of CRC. A systematic review was performed to identify studies reporting JCV DNA prevalence in CRC and JCV T-antigen expression. The strength of the association was estimated by odds ratios (ORs). Five (of 66) studies satisfied analysis inclusion criteria, and spanned years 1999 to 2022. Random effects meta-analysis of CRC cases versus controls showed an 11-fold increased risk of CRC development in JCV DNA positive samples with JCV T-antigen expression versus normal tissues (OR 10.95; 95% CI: 2.48-48.24; P = 0.0016). The results of this meta-analysis of JCV infection followed by JCV T-antigen protein expression for the risk of CRC support the argument that JCV infection significantly increases the risk of colorectal cancer in tissues where the JCV T-antigen protein is expressed. Further research with JCV T-antigen expression in relation to CRC development is needed.
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Affiliation(s)
- Lenka J. Kimla
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Walden University, Minneapolis, Minnesota, United States of America
- * E-mail: ,
| | - Taane G. Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Sri Banerjee
- Walden University, Minneapolis, Minnesota, United States of America
- Ross University School of Medicine, Miramar, Florida, United States of America
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
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18
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Dezordi FZ, Coutinho GB, Dias YJM, Wallau GL. Ancient origin of Jingchuvirales derived glycoproteins integrated in arthropod genomes. Genet Mol Biol 2023; 46:e20220218. [PMID: 37036390 PMCID: PMC10084718 DOI: 10.1590/1678-4685-gmb-2022-0218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 02/11/2023] [Indexed: 04/11/2023] Open
Abstract
Endogenous virus elements (EVEs) are viral-derived sequences integrated into their host genomes. EVEs of the Jingchuvirales order were detected in a wide range of insect genomes covering several distantly related families. Moreover, Jingchuvirales-derived glycoproteins were recently associated by our group with the origin of a putative new retrovirus based on a glycoprotein captured by a mosquito retrotransposon. But, except for mosquitoes, there is a lack of a more detailed understanding of the endogenization mechanism, timing, and frequency per Jingchuvirales viral lineages. Here we screened Jingchuvirales glycoprotein-derived EVEs (Jg-EVEs) in eukaryotic genomes. We found six distinct endogenization events of Jg-EVEs, that belong to two out of five known Jingchuvirales families (Chuviridae and Natareviridae). For seven arthropod families bearing Jg-EVEs there is no register of bona fide circulating chuvirus infection. Hence, our results show that Jingchuvirales viruses infected or still infect these host families. Although we found abundant evidence of LTR-Gypsy retrotransposons fragments associated with the glycoprotein in Hymenoptera and other insect orders, our results show that the widespread distribution of Jingchuvirales glycoproteins in extant Arhtropods is a result of multiple ancient endogenization events and that these virus fossils are being vertically inherited in Arthropods genomes for millions of years.
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Affiliation(s)
- Filipe Zimmer Dezordi
- Fundação Oswaldo Cruz (FIOCRUZ), Instituto Aggeu Magalhães (IAM), Departamento de Entomologia, Recife, PE, Brazil
- Fundação Oswaldo Cruz (FIOCRUZ), Instituto Aggeu Magalhães (IAM), Núcleo de Bioinformática, Recife, PE, Brazil
| | - Gutembergmann Batista Coutinho
- Fundação Oswaldo Cruz (FIOCRUZ), Instituto Aggeu Magalhães (IAM), Departamento de Entomologia, Recife, PE, Brazil
- Universidade Federal de Pernambuco, Centro de Biociências, Recife, PE, Brazil
| | - Yago José Mariz Dias
- Fundação Oswaldo Cruz (FIOCRUZ), Instituto Aggeu Magalhães (IAM), Departamento de Entomologia, Recife, PE, Brazil
- Fundação Oswaldo Cruz (FIOCRUZ), Instituto Aggeu Magalhães (IAM), Núcleo de Bioinformática, Recife, PE, Brazil
- Universidade Federal de Pernambuco, Centro de Biociências, Recife, PE, Brazil
| | - Gabriel Luz Wallau
- Fundação Oswaldo Cruz (FIOCRUZ), Instituto Aggeu Magalhães (IAM), Departamento de Entomologia, Recife, PE, Brazil
- Fundação Oswaldo Cruz (FIOCRUZ), Instituto Aggeu Magalhães (IAM), Núcleo de Bioinformática, Recife, PE, Brazil
- WHO Collaborating Center for Arbovirus and Hemorrhagic Fever Reference and Research, Bernhard Nocht Institute for Tropical Medicine, Department of Arbovirology, Hamburg, Germany
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19
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Detection and genetic characterization of feline retroviruses in domestic cats with different clinical signs and hematological alterations. Arch Virol 2023; 168:2. [DOI: 10.1007/s00705-022-05627-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 10/17/2022] [Indexed: 12/23/2022]
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20
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Kuriyama K, Tabara M, Moriyama H, Takahashi H, Fukuhara T. The essential role of the quasi-long terminal repeat sequence for replication and gene expression of an endogenous pararetrovirus, petunia vein clearing virus. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2022; 39:405-414. [PMID: 37283613 PMCID: PMC10240922 DOI: 10.5511/plantbiotechnology.22.1017a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 10/17/2022] [Indexed: 06/08/2023]
Abstract
Petunia vein clearing virus (PVCV) is a type member of the genus Petuvirus within the Caulimoviridae family and is defined as one viral unit consisting of a single open reading frame (ORF) encoding a viral polyprotein and one quasi-long terminal repeat (QTR) sequence. Since some full-length PVCV sequences are found in the petunia genome and a vector for horizontal transmission of PVCV has not been identified yet, PVCV is referred to as an endogenous pararetrovirus. Molecular mechanisms of replication, gene expression and horizontal transmission of endogenous pararetroviruses in plants are elusive. In this study, agroinfiltration experiments using various PVCV infectious clones indicated that the replication (episomal DNA synthesis) and gene expression of PVCV were efficient when the QTR sequences are present on both sides of the ORF. Whereas replacement of the QTR with another promoter and/or terminator is possible for gene expression, it is essential for QTR sequences to be on both sides for viral replication. Although horizontal transmission of PVCV by grafting and biolistic inoculation was previously reported, agroinfiltration is a useful and convenient method for studying its replication and gene expression.
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Affiliation(s)
- Kazunori Kuriyama
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo 183-8509, Japan
| | - Midori Tabara
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo 183-8509, Japan
- Ritsumeikan-Global Innovation Research Organization, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga 525-8577, Japan
| | - Hiromitsu Moriyama
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo 183-8509, Japan
| | - Hideki Takahashi
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki-Aza-Aoba, Sendai, Miyagi 980-0845, Japan
| | - Toshiyuki Fukuhara
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo 183-8509, Japan
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo 183-8509, Japan
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21
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Simpson J, Kozak CA, Boso G. Cross-species transmission of an ancient endogenous retrovirus and convergent co-option of its envelope gene in two mammalian orders. PLoS Genet 2022; 18:e1010458. [PMID: 36240227 PMCID: PMC9604959 DOI: 10.1371/journal.pgen.1010458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 10/26/2022] [Accepted: 09/30/2022] [Indexed: 11/06/2022] Open
Abstract
Endogenous retroviruses (ERVs) found in vertebrate genomes are remnants of retroviral invasions of their ancestral species. ERVs thus represent molecular fossil records of ancient retroviruses and provide a unique opportunity to study viral-host interactions, including cross-species transmissions, in deep time. While most ERVs contain the mutated remains of the original retrovirus, on rare occasions evolutionary selection pressures lead to the co-option/exaptation of ERV genes for a host function. Here, we report the identification of two ancient related non-orthologous ERV env genes, ARTenvV and CARenvV, that are preserved with large open reading frames (ORFs) in the mammalian orders Artiodactyla and Carnivora, respectively, but are not found in other mammals. These Env proteins lack a transmembrane motif, but phylogenetic analyses show strong sequence preservation and positive selection of the env surface ORF in their respective orders, and transcriptomic analyses show a broad tissue expression pattern for both ARTenvV and CARenvV, suggesting that these genes may be exapted for a host function. Multiple lines of evidence indicate that ARTenvV and CARenvV were derived from an ancient ancestral exogenous gamma-like retrovirus that was independently endogenized in two mammalian orders more than 60 million years ago, which roughly coincides with the K-Pg mass extinction event and subsequent mammalian diversification. Thus, these findings identify the oldest known retroviral cross-ordinal transmission of a gamma-like retrovirus with no known extant infectious counterpart in mammals, and the first discovery of the convergent co-option of an ERV gene derived from the same ancestral retrovirus in two different mammalian orders.
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Affiliation(s)
- J’Zaria Simpson
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Christine A. Kozak
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Guney Boso
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
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22
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Gainor K, Ghosh S. A comprehensive review of viruses in terrestrial animals from the Caribbean islands of Greater and Lesser Antilles. Transbound Emerg Dis 2022; 69:e1299-e1325. [PMID: 35578793 DOI: 10.1111/tbed.14595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/09/2022] [Accepted: 05/09/2022] [Indexed: 11/26/2022]
Abstract
Viruses pose a major threat to animal health worldwide, causing significant mortalities and morbidities in livestock, companion animals and wildlife, with adverse implications on human health, livelihoods, food safety and security, regional/national economies, and biodiversity. The Greater and Lesser Antilles consist of a cluster of islands between the North and South Americas and is habitat to a wide variety of animal species. This review is the first to put together decades of information on different viruses circulating in companion animals, livestock, and wildlife from the Caribbean islands of Greater and Lesser Antilles. Although animal viral diseases have been documented in the Caribbean region since the 1940s, we found that studies on different animal viruses are limited, inconsistent, and scattered. Furthermore, a significant number of the reports were based on serological assays, yielding preliminary data. The available information was assessed to identify knowledge gaps and limitations, and accordingly, recommendations were made, with the overall goal to improve animal health and production, and combat zoonoses in the region. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Kerry Gainor
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, St. Kitts, West Indies
| | - Souvik Ghosh
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, St. Kitts, West Indies
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