1
|
Olech M, Parzeniecka-Jaworska M. Detection of small ruminant Lentivirus proviral DNA in red deer from Poland. BMC Vet Res 2024; 20:195. [PMID: 38741095 DOI: 10.1186/s12917-024-04059-y] [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: 01/03/2024] [Accepted: 05/06/2024] [Indexed: 05/16/2024] Open
Abstract
Small ruminant lentiviruses (SRLVs) are widespread and infect goats and sheep. Several reports also suggest that SRLVs can infect wild ruminants. The presence of specific antibodies against SRLVs has been identified in wild ruminants from Poland, but no studies have been conducted to detect proviral DNA of SRLVs in these animals. Therefore, the purpose of this study was to examine samples from Polish wild ruminants to determine whether these animals can serve as reservoirs of SRLVs under natural conditions. A total of 314 samples were tested from red deer (n = 255), roe deer (n = 52) and fallow deer (n = 7) using nested real-time PCR. DNA from positive real-time PCR samples was subsequently used to amplify a CA fragment (625 bp) of the gag gene, a 1.2 kb fragment of the pol gene and an LTR-gag fragment. Three samples (0.95%) were positive according to nested real-time PCR using primers and probe specific for CAEV (SRLV group B). All the samples were negative for the primers and probe specific for MVV (SRLV A group). Only SRLV LTR-gag sequences were obtained from two red deer. Phylogenetic analysis revealed that these sequences were more closely related to CAEV than to MVV. Our results revealed that deer can carry SRLV proviral sequences and therefore may play a role in the epidemiology of SRLVs. To our knowledge, this is the first study describing SRLV sequences from red deer.
Collapse
Affiliation(s)
- Monika Olech
- Department of Pathology, National Veterinary Research Institute, Pulawy, 24-100, Poland.
| | - Marta Parzeniecka-Jaworska
- Department of Small Animal Diseases and Clinic, Faculty of Veterinary Medicine, Warsaw University of Life Sciences, Warsaw, 02-766, Poland
| |
Collapse
|
2
|
Schaer J, Cvetnic Z, Sukalic T, Dörig S, Grisiger M, Iscaro C, Feliziani F, Pfeifer F, Origgi F, Zanoni RG, Abril CE. Evaluation of Serological Methods and a New Real-Time Nested PCR for Small Ruminant Lentiviruses. Pathogens 2022; 11:pathogens11020129. [PMID: 35215072 PMCID: PMC8875174 DOI: 10.3390/pathogens11020129] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/05/2022] [Accepted: 01/14/2022] [Indexed: 12/04/2022] Open
Abstract
Small ruminant lentiviruses (SRLVs), i.e., CAEV and MVV, cause insidious infections with life-long persistence and a slowly progressive disease, impairing both animal welfare and productivity in affected herds. The complex diagnosis of SRLVs currently combines serological methods including whole-virus and peptide-based ELISAs and Immunoblot. To improve the current diagnostic protocol, we analyzed 290 sera of animals originating from different European countries in parallel with three commercial screening ELISAs, Immunoblot as a confirmatory assay and five SU5 peptide ELISAs for genotype differentiation. A newly developed nested real-time PCR was carried out for the detection and genotype differentiation of the virus. Using a heat-map display of the combined results, the drawbacks of the current techniques were graphically visualized and quantified. The immunoblot and the SU5-ELISAs exhibited either unsatisfactory sensitivity or insufficient reliability in the differentiation of the causative viral genotype, respectively. The new truth standard was the concordance of the results of two out of three screening ELISAs and the PCR results for serologically false negative samples along with genotype differentiation. Whole-virus antigen-based ELISA showed the highest sensitivity (92.2%) and specificity (98.9%) among the screening tests, whereas PCR exhibited a sensitivity of 75%.
Collapse
Affiliation(s)
- Jessica Schaer
- Institute of Virology and Immunology IVI, in Cooperation with the Vetsuisse-Faculty of the University of Bern, 3012 Bern, Switzerland; (J.S.); (R.G.Z.)
| | - Zeljko Cvetnic
- Regional Veterinary Department Križevci, Croatian Veterinary Institute, Zakmandijeva 10, 48260 Križevci, Croatia; (Z.C.); (T.S.)
| | - Tomislav Sukalic
- Regional Veterinary Department Križevci, Croatian Veterinary Institute, Zakmandijeva 10, 48260 Križevci, Croatia; (Z.C.); (T.S.)
| | - Sven Dörig
- Beratungs-und Gesundheitsdienst für Kleinwiederkäuer (BGK/SSPR), 3362 Niederoenz, Switzerland;
| | | | - Carmen Iscaro
- National Reference Laboratory for Ruminant Retroviruses, Istituto Zooprofilattico, Sperimentale dell’Umbria e delle Marche Togo Rosati, 06126 Perugia, Italy; (C.I.); (F.F.)
| | - Francesco Feliziani
- National Reference Laboratory for Ruminant Retroviruses, Istituto Zooprofilattico, Sperimentale dell’Umbria e delle Marche Togo Rosati, 06126 Perugia, Italy; (C.I.); (F.F.)
| | - Folke Pfeifer
- Tierseuchenkasse/Tiergesundheitsdienst Sachsen-Anhalt, 39116 Magdeburg, Germany;
| | - Francesco Origgi
- Institute of Veterinary Pathology, Vetsuisse-Faculty of the University of Bern, 3012 Bern, Switzerland;
| | - Reto Giacomo Zanoni
- Institute of Virology and Immunology IVI, in Cooperation with the Vetsuisse-Faculty of the University of Bern, 3012 Bern, Switzerland; (J.S.); (R.G.Z.)
| | - Carlos Eduardo Abril
- Institute of Virology and Immunology IVI, in Cooperation with the Vetsuisse-Faculty of the University of Bern, 3012 Bern, Switzerland; (J.S.); (R.G.Z.)
- Correspondence: ; Tel.: +41-31-631-2423
| |
Collapse
|
3
|
Kharytonchyk S, Pedersen FS. A unique, thermostable dimer linkage structure of RD114 retroviral RNA. RNA (NEW YORK, N.Y.) 2010; 16:572-584. [PMID: 20075164 PMCID: PMC2822922 DOI: 10.1261/rna.1495110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2008] [Accepted: 11/13/2009] [Indexed: 05/28/2023]
Abstract
Retroviruses package their genome as RNA dimers linked together primarily by base-pairing between palindromic stem-loop (psl) sequences at the 5' end of genomic RNA. Retroviral RNA dimers usually melt in the range of 55 degrees C-70 degrees C. However, RNA dimers from virions of the feline endogenous gammaretrovirus RD114 were reported to melt only at 87 degrees C. We here report that the high thermal stability of RD114 RNA dimers generated from in vitro synthesized RNA is an effect of multiple dimerization sites located in the 5' region from the R region to sequences downstream from the splice donor (SD) site. By antisense oligonucleotide probing we were able to map at least five dimerization sites. Computational prediction revealed a possibility to form stems with autocomplementary loops for all of the mapped dimerization sites. Three of them were located upstream of the SD site. Mutant analysis supported a role of all five loop sequences in the formation and thermal stability of RNA dimers. Four of the five psls were also predicted in the RNA of two baboon endogenous retroviruses proposed to be ancestors of RD114. RNA fragments of the 5' R region or prolonged further downstream could be efficiently dimerized in vitro. However, this was not the case for the 3' R region linked to upstream U3 sequences, suggesting a specific mechanism of negative regulation of dimerization at the 3' end of the genome, possibly explained by a long double-stranded RNA region at the U3-R border. Altogether, these data point to determinants of the high thermostability of the dimer linkage structure of the RD114 genome and reveal differences from other retroviruses.
Collapse
|
4
|
Gherghe C, Weeks KM. The SL1-SL2 (stem-loop) domain is the primary determinant for stability of the gamma retroviral genomic RNA dimer. J Biol Chem 2006; 281:37952-61. [PMID: 16984912 DOI: 10.1074/jbc.m607380200] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Retroviral genomes are assembled from two sense-strand RNAs by noncovalent interactions at their 5' ends, forming a dimer. The RNA dimerization domain is a potential target for antiretroviral therapy and represents a compelling RNA folding problem. The fundamental dimerization unit for the Moloney murine sarcoma gamma retrovirus spans a 170-nucleotide minimal dimerization active sequence. In the dimer, two self-complementary sequences, PAL1 and PAL2, form intermolecular duplexes, and an SL1-SL2 (stem-loop) domain forms loop-loop base pairs, mediated by GACG tetraloops, and extensive tertiary interactions. To develop a framework for assembly of the retroviral RNA dimer, we quantified the stability of and established nucleotide resolution secondary structure models for sequence variants in which each motif was compromised. Base pairing and tertiary interactions between SL1-SL2 domains contribute a large free energy increment of -10 kcal/mol. In contrast, even though the PAL1 and PAL2 intermolecular duplexes span 10 and 16 bp in the dimer, respectively, they contribute only -2.5 kcal/mol to stability, roughly equal to a single new base pair. First, these results emphasize that the energetic costs for disrupting interactions in the monomer state nearly balance the PAL1 and PAL2 base pairing interactions that form in the dimer. Second, intermolecular duplex formation plays a biological role distinct from simply stabilizing the structure of the retroviral genomic RNA dimer.
Collapse
Affiliation(s)
- Cristina Gherghe
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA
| | | |
Collapse
|
5
|
Bjarnadottir H, Gudmundsson B, Gudnason J, Jonsson JJ. Encapsidation determinants located downstream of the major splice donor in the maedi-visna virus leader region. J Virol 2006; 80:11743-55. [PMID: 16971429 PMCID: PMC1642619 DOI: 10.1128/jvi.01284-06] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We investigated the role of the 5'-untranslated region between the primer binding site and the gag initiation codon in ovine lentivirus maedi-visna virus (MVV) genomic RNA encapsidation. We identified five computer-predicted stem-loops, three of which were highly conserved in primary sequence and structure. One stable 83-nucleotide (nt) stem-loop (SL4) was not conserved in the primary sequence, but phylogenetic analysis revealed several base pair covariations. The deletion of individual stem-loops did not markedly affect the relative encapsidation efficiency (REE). Only one mutant, carrying a disruption of a 31-nt stem-loop (SL5), had 58% REE in fetal ovine synovial (FOS) cells. A 168-nt deletion (Delta3MSD) downstream of the major splice donor (MSD) which removed three stem-loops, including SL5, resulted in 24% and 20% REE in FOS and 293T cells, respectively. A 100-nt deletion (Delta5MSD) upstream of the MSD resulted in 15-fold lower cellular genomic RNA levels than the wild-type levels in 293T cells. The Delta5MSD mutant and a double mutant (DM) (Delta5MSD and Delta3MSD) did not express detectable levels of virion proteins in 293T cells. In contrast, the region deleted in Delta5MSD was dispensable in FOS cells, and the DM had the same REE as the Delta3MSD virus. Thus, the region upstream of the MSD contains sequences critical for RNA and protein expression in a cell type-specific fashion. Our results indicate that MVV encapsidation determinants are located downstream of the MSD. These results provide comparative insight into lentiviral encapsidation and can be utilized in the design of MVV-based gene transfer vectors.
Collapse
Affiliation(s)
- Helga Bjarnadottir
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, IS-101 Reykjavik, Iceland
| | | | | | | |
Collapse
|
6
|
Badorrek CS, Weeks KM. RNA flexibility in the dimerization domain of a gamma retrovirus. Nat Chem Biol 2005; 1:104-11. [PMID: 16408007 DOI: 10.1038/nchembio712] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2005] [Accepted: 05/16/2005] [Indexed: 11/08/2022]
Abstract
Retroviruses are the causative agents of serious diseases, such as acquired immunodeficiency syndromes and several cancers, and are also useful gene therapy vectors. Retroviruses contain two sense-strand RNA genomes, which become linked at their 5' ends to form an RNA dimer. Understanding the molecular basis for dimerization may yield new approaches for controlling viral infectivity. Because this RNA domain is highly conserved within retrovirus groups, it has not been possible to define a consensus structure for the 5' dimerization domain by comparative sequence analysis. Here, we defined a 170-nucleotide minimal dimerization active sequence (MiDAS) for a representative gamma retrovirus, the Moloney murine sarcoma virus, by stringent competitive dimerization. We then analyzed the structure at every nucleotide in the MiDAS monomeric starting state with quantitative selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) chemistry. Notably, SHAPE analysis demonstrated that the RNA monomer contains an extensive flexible domain spanning 50 nucleotides. These findings support a structural model in which RNA flexibility directly facilitates retroviral genome dimerization by reducing the energetic cost of disrupting pre-existing base pairings in the monomer.
Collapse
Affiliation(s)
- Christopher S Badorrek
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA
| | | |
Collapse
|