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Sacco MA, Crosetti A. GGERV20, a recently integrated, segregating endogenous retrovirus in Gallus gallus. J Gen Virol 2020; 101:299-308. [PMID: 31916930 DOI: 10.1099/jgv.0.001379] [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] [Indexed: 11/18/2022] Open
Abstract
Endogenous retroviruses (ERVs) are widespread in vertebrate genomes. The recent availability of whole eukaryotic genomes has enabled their characterization in many organisms, including Gallus gallus (red jungle fowl), the progenitor of the domesticated chicken. Our bioinformatics analysis of a G. gallus ERV previously designated GGERV20 identified 35 proviruses with complete long terminal repeats (LTRs) and gag-pol open reading frames (ORFs) in the Genome Reference Consortium Chicken Build 6a, of which 8 showed potential for translation of functional retroviral polyproteins, including the integrase and reverse transcriptase enzymes. No elements were discovered with an env gene. Fifteen loci had LTR sequences with 100 % identity, indicative of recent integration. Chicken embryo fibroblast RNA-seq datasets showed reads representing the entire length of the GGERV20 provirus, supporting their potential for expressing viral proteins. To investigate the possibility that GGERV20 elements may not be fixed in the genome, we assessed the integration status of five loci in a meat-type chicken. PCRs targeting a GGERV20 locus on G. gallus chromosome one (GGERV201-1) reproducibly amplified both LTRs and the preintegration state, indicating that the bird from which the DNA was sampled was hemizygous at this locus. The four other loci examined only produced the preintegration state amplicons. These results reveal that GGERV20 is not fixed in the G. gallus population, and taken together with the lack of mutations seen in several provirus LTRs and their transcriptional activity, suggest that GGERV20 retroviruses have recently been and continue to be active in the chicken genome.
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Affiliation(s)
- Melanie Ann Sacco
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University, Fullerton, CA 92834-6850, USA
| | - Anna Crosetti
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University, Fullerton, CA 92834-6850, USA
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2
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Rutherford K, Meehan CJ, Langille MGI, Tyack SG, McKay JC, McLean NL, Benkel K, Beiko RG, Benkel B. Discovery of an expanded set of avian leukosis subgroup E proviruses in chickens using Vermillion, a novel sequence capture and analysis pipeline [corrected]. Poult Sci 2016; 95:2250-8. [PMID: 27354549 DOI: 10.3382/ps/pew194] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 04/08/2016] [Indexed: 01/26/2023] Open
Abstract
Transposable elements (TEs), such as endogenous retroviruses (ERVs), are common in the genomes of vertebrates. ERVs result from retroviral infections of germ-line cells, and once integrated into host DNA they become part of the host's heritable genetic material. ERVs have been ascribed positive effects on host physiology such as the generation of novel, adaptive genetic variation and resistance to infection, as well as negative effects as agents of tumorigenesis and disease. The avian leukosis virus subgroup E family (ALVE) of endogenous viruses of chickens has been used as a model system for studying the effects of ERVs on host physiology, and approximately 30 distinct ALVE proviruses have been described in the Gallus gallus genome. In this report we describe the development of a software tool, which we call Vermillion, and the use of this tool in combination with targeted next-generation sequencing (NGS) to increase the number of known proviruses belonging to the ALVE family of ERVs in the chicken genome by 4-fold, including expanding the number of known ALVE elements on chromosome 1 (Gga1) from the current 9 to a total of 40. Although we focused on the discovery of ALVE elements in chickens, with appropriate selection of target sequences Vermillion can be used to develop profiles of other families of ERVs and TEs in chickens as well as in species other than the chicken.
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Affiliation(s)
- K Rutherford
- Dalhousie University, Faculty of Computer Science, 6050 University Avenue, Halifax, NS, Canada, B3H 4R2
| | - C J Meehan
- Dalhousie University, Faculty of Computer Science, 6050 University Avenue, Halifax, NS, Canada, B3H 4R2 Institute of Tropical Medicine, Department of Biomedical Sciences, Antwerp 2000, Belgium
| | - M G I Langille
- Dalhousie University, Faculty of Computer Science, 6050 University Avenue, Halifax, NS, Canada, B3H 4R2 Dalhousie University, Faculty of Medicine, Department of Pharmacology, 5850 College St, Halifax, NS, Canada, B3H 4R2
| | - S G Tyack
- EW GROUP, 1 Hogenboegen, Visbek, Germany
| | - J C McKay
- EW GROUP, 1 Hogenboegen, Visbek, Germany
| | - N L McLean
- Dalhousie University, Faculty of Agriculture, Department of Plant and Animal Sciences, Box 550, Truro, NS, B2N 5E3
| | - K Benkel
- Dalhousie University, Faculty of Agriculture, Department of Plant and Animal Sciences, Box 550, Truro, NS, B2N 5E3
| | - R G Beiko
- Dalhousie University, Faculty of Computer Science, 6050 University Avenue, Halifax, NS, Canada, B3H 4R2
| | - B Benkel
- Dalhousie University, Faculty of Agriculture, Department of Plant and Animal Sciences, Box 550, Truro, NS, B2N 5E3
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Wragg D, Mason AS, Yu L, Kuo R, Lawal RA, Desta TT, Mwacharo JM, Cho CY, Kemp S, Burt DW, Hanotte O. Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken. BMC Genomics 2015; 16:784. [PMID: 26466991 PMCID: PMC4607243 DOI: 10.1186/s12864-015-1954-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 09/02/2015] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND EAV-HP is an ancient retrovirus pre-dating Gallus speciation, which continues to circulate in modern chicken populations, and led to the emergence of avian leukosis virus subgroup J causing significant economic losses to the poultry industry. We mapped EAV-HP integration sites in Ethiopian village chickens, a Silkie, Taiwan Country chicken, red junglefowl Gallus gallus and several inbred experimental lines using whole-genome sequence data. RESULTS An average of 75.22 ± 9.52 integration sites per bird were identified, which collectively group into 279 intervals of which 5 % are common to 90 % of the genomes analysed and are suggestive of pre-domestication integration events. More than a third of intervals are specific to individual genomes, supporting active circulation of EAV-HP in modern chickens. Interval density is correlated with chromosome length (P < 2.31(-6)), and 27 % of intervals are located within 5 kb of a transcript. Functional annotation clustering of genes reveals enrichment for immune-related functions (P < 0.05). CONCLUSIONS Our results illustrate a non-random distribution of EAV-HP in the genome, emphasising the importance it may have played in the adaptation of the species, and provide a platform from which to extend investigations on the co-evolutionary significance of endogenous retroviral genera with their hosts.
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Affiliation(s)
- David Wragg
- Ecology and Evolution, School of Life Sciences, University of Nottingham, University Park, Nottingham, UK.
- Institut National de la Recherche Agronomique (INRA), UMR 1338 GenPhySE, 31326, Castanet-Tolosan, France.
| | - Andrew S Mason
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, Edinburgh, UK.
| | - Le Yu
- GAIC Co. Ltd. Jing Chen Buiding, Science Park, South Street, Chao Yang District, Beijing, People's Republic Popular of China.
| | - Richard Kuo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, Edinburgh, UK.
| | - Raman A Lawal
- Ecology and Evolution, School of Life Sciences, University of Nottingham, University Park, Nottingham, UK.
| | - Takele Taye Desta
- Ecology and Evolution, School of Life Sciences, University of Nottingham, University Park, Nottingham, UK.
| | - Joram M Mwacharo
- Ecology and Evolution, School of Life Sciences, University of Nottingham, University Park, Nottingham, UK.
- International Centre for Agricultural Research in Dry Areas, c/o International Livestock Research Institute, Addis Ababa, Ethiopia.
| | - Chang-Yeon Cho
- Animal Genetic Resources Station, National Institute of Animal Science, Namwon, Republic of Korea.
| | - Steve Kemp
- International Livestock Research Institute, Naivasha Road, P.O. Box 30709, Nairobi, Kenya.
| | - David W Burt
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, Edinburgh, UK.
| | - Olivier Hanotte
- Ecology and Evolution, School of Life Sciences, University of Nottingham, University Park, Nottingham, UK.
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4
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Sacco MA, Nair VK. Prototype endogenous avian retroviruses of the genus Gallus. J Gen Virol 2014; 95:2060-2070. [PMID: 24903328 DOI: 10.1099/vir.0.066852-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ancient endogenous retroviruses (ERVs), designated endogenous avian retrovirus (EAVs), are present in all Gallus spp. including the chicken, and resemble the modern avian sarcoma and leukosis viruses (ASLVs). The EAVs comprise several distinct retroviruses, including EAV-0, EAV-E51 and EAV-HP, as well as a putative member previously named the avian retrotransposon of chickens (ART-CH). Thus far, only the EAV-HP elements have been well characterized. Here, we determined sequences of representative EAV-0 and EAV-E51 proviruses by cloning and data mining of the 2011 assembly of the Gallus gallus genome. Although the EAV-0 elements are primarily deleted in the env region, we identified two complete EAV-0 env genes within the G. gallus genome and prototype elements sharing identity with an EAV-E51-related clone previously designated EAV-E33. Prototype EAV-0, EAV-E51 and EAV-E33 gag, pol and env gene sequences used for phylogenetic analysis of deduced proteins showed that the EAVs formed three distinct clades, with EAV-0 sharing the last common ancestor with the ASLVs. The EAV-E51 clade showed the greatest level of divergence compared with other EAVs or ASLVs, suggesting that these ERVs represented exogenous retroviruses that evolved and integrated into the germline over a long period of time. Moreover, the degree of divergence between the chicken and red jungle fowl EAV-E51 sequences suggested that they were more ancient than the other EAVs and may have diverged through mutations that accumulated post-integration. Finally, we showed that the ART-CH elements were chimeric defective ERVs comprising portions of EAV-E51 and EAV-HP rather than authentic retrotransposons.
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Affiliation(s)
- Melanie Ann Sacco
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, CA 92834-6850, USA
| | - Venugopal K Nair
- Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN, UK
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5
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Kim YJ, Park SI, Park SJ, Kim HH, Jung YW, Kwon JT, Jang BG, Kim HK, Cho KO. Molecular analysis of endogenous avian leukosis/sarcoma virus genomes in Korean chicken embryos. J Vet Med Sci 2008; 70:17-23. [PMID: 18250567 DOI: 10.1292/jvms.70.17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Since the status of endogenous avian leucosis/sarcoma virus (ALSV) infections in Korean broiler chickens is unclear, this study examined embryonated eggs obtained from broiler farms and Korean native chicken breeds in Korea using PCR with the primer sets specific for endogenous ALSVs. The PCR assays detected the genomes of EAV, ev, ev/J and ART-CH belonging to the endogenous ALSV from all embryos tested. Phylogenetically, the Korean EAV genomes were more closely related to the prototype EAV-0 than to the other prototype, E51. The Korean ART-CH elements clustered together but were distinct from the prototype ART-CH clones, 5 and 14. Although there was comparatively little divergence in the nucleotide and amino acid sequences of the Korean ev and ev/J genomes compared with the other known ev and ev/J genomes, the Korean genomes had phylogenetically distinct branches. From these results, endogenous genomes are quite prevalent in Korean broiler chickens. In addition, the endogenous genomes circulating in Korean broiler chickens are genetically different from the other known endogenous genomes. These results are expected to provide useful information for the control and establishment of a surveillance system for endogenous ALSVs in Korea.
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Affiliation(s)
- You-Jung Kim
- Bio-Therapy Human Resources Center, College of Veterinary Medicine, Chonnam National University, Gwangju, Japan
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6
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Tarlinton RE, Meers J, Young PR. Retroviral invasion of the koala genome. Nature 2006; 442:79-81. [PMID: 16823453 DOI: 10.1038/nature04841] [Citation(s) in RCA: 254] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2006] [Accepted: 04/26/2006] [Indexed: 11/08/2022]
Abstract
Endogenous retroviruses are a common ancestral feature of mammalian genomes with most having been inactivated over time through mutation and deletion. A group of more intact endogenous retroviruses are considered to have entered the genomes of some species more recently, through infection by exogenous viruses, but this event has never been directly proved. We have previously reported koala retrovirus (KoRV) to be a functional virus that is associated with neoplasia. Here we show that KoRV also shows features of a recently inserted endogenous retrovirus that is vertically transmitted. The finding that some isolated koala populations have not yet incorporated KoRV into their genomes, combined with its high level of activity and variability in individual koalas, suggests that KoRV is a virus in transition between an exogenous and endogenous element. This ongoing dynamic interaction with a wild species provides an exciting opportunity to study the process and consequences of retroviral endogenization in action, and is an attractive model for studying the evolutionary event in which a retrovirus invades a mammalian genome.
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Affiliation(s)
- Rachael E Tarlinton
- School of Molecular and Microbial Sciences, University of Queensland, St Lucia 4072, Queensland, Australia
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7
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Savolainen P, Fitzsimmons C, Arvestad L, Andersson L, Lundeberg J. ESTs from brain and testis of White Leghorn and red junglefowl: annotation, bioinformatic classification of unknown transcripts and analysis of expression levels. Cytogenet Genome Res 2005; 111:79-87. [PMID: 16093725 DOI: 10.1159/000085674] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2004] [Accepted: 11/30/2004] [Indexed: 11/19/2022] Open
Abstract
We report the generation, assembly and annotation of expressed sequence tags (ESTs) from four chicken cDNA libraries, constructed from brain and testis tissue dissected from red junglefowl and White Leghorn. 21,285 5'-end ESTs were generated and assembled into 2,813 contigs and 9,737 singletons, giving 12,549 tentative unique transcripts. The transcripts were annotated using BLAST by matching to known chicken genes or to putative homologues in other species using the major gene/protein databases. The results for these similarity searches are available on www.sbc.su.se/~arve/chicken. 4,129 (32.9%) of the transcripts remained without a significant match to gene/protein databases, a proportion of unmatched transcripts similar to earlier non-mammalian EST studies. To estimate how many of these transcripts may represent novel genes, they were studied for the presence of coding sequence. It was shown that most of the unique chicken transcripts do not contain coding parts of genes, but it was estimated that at least 400 of the transcripts contain coding sequence, indicating that 3.2% of avian genes belong to previously unknown gene families. Further BLAST search against dbEST left 1,649 (13.1%) of the transcripts unmatched to any library. The number of completely unmatched transcripts containing coding sequence was estimated at 180, giving a measure of the number of putative novel chicken genes identified in this study. 84.3% of the identified transcripts were found only in testis tissue, which has been poorly studied in earlier chicken EST studies. Large differences in expression levels were found between the brain and testis libraries for a large number of transcripts, and among the 525 most frequently represented transcripts, there were at least 20 transcripts with significant difference in expression levels between red junglefowl and White Leghorn.
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Affiliation(s)
- P Savolainen
- Department of Biotechnology, Royal Institute of Technology, Stockholm, Sweden.
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8
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Borisenko LG, Rynditch AV, Bernardi G. Distribution and expression of chicken endogenous retroviruses in the host genome. ACTA ACUST UNITED AC 2004. [DOI: 10.7124/bc.000690] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- L. G. Borisenko
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
| | - A. V. Rynditch
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
| | - G. Bernardi
- Laboratorio di Evoluzione Molecolare, Stazione Zoologica Anton Dohrn
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9
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Johnson JA, Hussain A, Heneine W. Expression of a recombinant gag protein from endogenous avian virus and its use in screening for antibody reactivity in recipients of chick-derived vaccines. Vaccine 2003; 21:3738-45. [PMID: 12922106 DOI: 10.1016/s0264-410x(03)00391-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Virions incorporating endogenous avian virus (EAV) RNA have been identified in chick-derived biological products, including the vaccines used to protect against measles, mumps, and yellow fever. The presence of EAV in these vaccines raises safety concerns regarding transmission to vaccine recipients. Development of a serologic assay to detect antibodies to EAV required the discovery of a diagnostic EAV antigen and reactive antiserum. For this purpose, we have identified and expressed an EAV capsid sequence that was found to have a 66.9% amino acid identity to avian myeloblastosis virus (AMV) p27 capsid. An AMV capsid antiserum that cross-reacted to the EAV protein in both Western blot (WB) and ELISA-based testing was selected as a positive control reagent. Using our assay, we evaluated sera from 200 measles-mumps-rubella (MMRII) and 43 yellow fever (YF(FIOCRUZ)) vaccine recipients and found none of the samples were reactive to EAV capsid. The results support a lack of EAV infection in the vaccine recipients.
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Affiliation(s)
- Jeffrey A Johnson
- HIV and Retrovirology Branch, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
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10
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Abstract
The retroviral capacity for integration into the host genome can give rise to endogenous retroviruses (ERVs): retroviral sequences that are transmitted vertically as part of the host germ line, within which they may continue to replicate and evolve. ERVs represent both a unique archive of ancient viral sequence information and a dynamic component of host genomes. As such they hold great potential as informative markers for studies of both virus evolution and host genome evolution. Numerous novel ERVs have been described in recent years, particularly as genome sequencing projects have advanced. This review discusses the evolution of ERV lineages, considering the processes by which ERV distribution and diversity is generated. The diversity of ERVs isolated so far is summarised in terms of both their distribution across host taxa, and their relationships to recognised retroviral genera. Finally the relevance of ERVs to studies of genome evolution, host disease and viral ecology is considered, and recent findings discussed.
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Affiliation(s)
- Robert Gifford
- Department of Biological Sciences, Imperial College, Silwood Park, Buckhurst Road, Ascot Berkshire, SL5 7PY, UK
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12
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Hussain AI, Johnson JA, Da Silva Freire M, Heneine W. Identification and characterization of avian retroviruses in chicken embryo-derived yellow fever vaccines: investigation of transmission to vaccine recipients. J Virol 2003; 77:1105-11. [PMID: 12502826 PMCID: PMC140796 DOI: 10.1128/jvi.77.2.1105-1111.2003] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
All currently licensed yellow fever (YF) vaccines are propagated in chicken embryos. Recent studies of chick cell-derived measles and mumps vaccines show evidence of two types of retrovirus particles, the endogenous avian retrovirus (EAV) and the endogenous avian leukosis virus (ALV-E), which originate from the chicken embryonic fibroblast substrates. In this study, we investigated substrate-derived avian retrovirus contamination in YF vaccines currently produced by three manufacturers (YF-vax [Connaught Laboratories], Stamaril [Aventis], and YF-FIOCRUZ [FIOCRUZ-Bio-Manguinhos]). Testing for reverse transcriptase (RT) activity was not possible because of assay inhibition. However, Western blot analysis of virus pellets with anti-ALV RT antiserum detected three distinct RT proteins in all vaccines, indicating that more than one source is responsible for the RTs present in the vaccines. PCR analysis of both chicken substrate DNA and particle-associated RNA from the YF vaccines showed no evidence of the long terminal repeat sequences of exogenous ALV subgroups A to D in any of the vaccines. In contrast, both ALV-E and EAV particle-associated RNA were detected at equivalent titers in each vaccine by RT-PCR. Quantitative real-time RT-PCR revealed 61,600, 348,000, and 1,665,000 ALV-E RNA copies per dose of Stamaril, YF-FIOCRUZ, and YF-vax vaccines, respectively. ev locus-specific PCR testing of the vaccine-associated chicken substrate DNA was positive both for the nondefective ev-12 locus in two vaccines and for the defective ev-1 locus in all three vaccines. Both intact and ev-1 pol sequences were also identified in the particle-associated RNA. To investigate the risks of transmission, serum samples from 43 YF vaccine recipients were studied. None of the samples were seropositive by an ALV-E-based Western blot assay or had detectable EAV or ALV-E RNA sequences by RT-PCR. YF vaccines produced by the three manufacturers all have particles containing EAV genomes and various levels of defective or nondefective ALV-E sequences. The absence of evidence of infection with ALV-E or EAV in 43 YF vaccine recipients suggests low risks for transmission of these viruses, further supporting the safety of these vaccines.
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Affiliation(s)
- Althaf I Hussain
- HIV and Retrovirology Branch, Division of AIDS, STD, and TB Laboratory Research, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
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13
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Johnson JA, Heneine W. Characterization of endogenous avian leukosis viruses in chicken embryonic fibroblast substrates used in production of measles and mumps vaccines. J Virol 2001; 75:3605-12. [PMID: 11264350 PMCID: PMC114852 DOI: 10.1128/jvi.75.8.3605-3612.2001] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2000] [Accepted: 01/12/2001] [Indexed: 12/26/2022] Open
Abstract
Previous findings of low levels of reverse transcriptase (RT) activity in chick cell-derived measles and mumps vaccines showed this activity to be associated with virus particles containing RNA of both subgroup E endogenous avian leukosis viruses (ALV-E) and endogenous avian viruses (EAV). These particles originate from chicken embryonic fibroblast (CEF) substrates used for propagating vaccine strains. To better characterize vaccine-associated ALV-E, we examined the endogenous ALV proviruses (ev loci) present in a White Leghorn CEF substrate pool by restriction fragment length polymorphism. Five ev loci were detected, ev-1, ev-3, ev-6, ev-18, andev-19. Both ev-18 and ev-19 can express infectious ALV-E, while ev-1, ev-3, and ev-6 are defective. We analyzed the full-length sequence of ev-1 and identified an adenosine insertion within the pol RT-beta region at position 5026, which results in a truncated RT-beta and integrase. We defined the 1,692-bp deletion in the gag-pol region of ev-3, and we found that in ev-6, sequences from the 5' long terminal repeat to the 5' pol region were absent. Based on the sequences of the ev loci, RT-PCR assays were developed to examine expression of ALV-E particles (EV) in CEF supernatants. Both ev-1- and ev-3-like RNA sequences were identified, as well as two other RNA sequences with intact pol regions, presumably of ev-18 and ev-19 origin. Inoculation of susceptible quail fibroblasts with CEF culture supernatants from both 5-azacytidine-induced and noninduced CEF led to ALV infection, confirming the presence of infectious ALV-E. Our data demonstrate that both defective and nondefective ev loci can be present in CEF vaccine substrates and suggest that both ev classes may contribute to the ALV present in vaccines.
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Affiliation(s)
- J A Johnson
- HIV and Retrovirology Branch, Division of AIDS, STD, and TB Laboratory Research, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
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14
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Abstract
The EAV-HP group of chicken endogenous retrovirus elements was previously shown to be defective, with large deletions of the pol gene. In this report, we demonstrate that genomes of other Gallus species also maintain EAV-HP elements with similar deletions. The chicken EAV-HP1 locus was detected in both red (Gallus gallus gallus) and Sonnerat's (Gallus sonneratii) jungle fowl with identical integration sites, indicating that these elements had integrated before separation of the Gallus species. Furthermore, we demonstrate for the first time that the G. sonneratii genome carries EAV-HP elements with intact pol regions.
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Affiliation(s)
- M A Sacco
- Institute for Animal Health, Compton, Newbury, Berkshire RG20 7NN, United Kingdom
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15
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Shahabuddin M, Sears JF, Khan AS. No evidence of infectious retroviruses in measles virus vaccines produced in chicken embryo cell cultures. J Clin Microbiol 2001; 39:675-84. [PMID: 11158127 PMCID: PMC87796 DOI: 10.1128/jcm.39.2.675-684.2001] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2000] [Accepted: 10/30/2000] [Indexed: 12/22/2022] Open
Abstract
All vaccines that are prepared in chicken embryo fibroblasts (CEFs) contain a low level of particle-associated reverse transcriptase (RT) activity, which is produced from the avian cell substrate. The RNAs present in the particles have sequence homology to viral DNAs belonging to the ancient endogenous avian virus (EAV) family or to the avian sarcoma-leukosis virus (ALV)-related subgroup E endogenous virus loci. Although no replication-competent retrovirus has been associated with the RT activity produced from CEFs, there have been some theoretical safety concerns regarding potential consequences of integration of EAV and ALV sequences in human DNA, which may result from nonproductive infection with replication-defective particles or infection with EAV and ALV pseudotypes bearing measles virus envelopes. To address these possibilities, we have analyzed EAV and ALV particles in a measles virus vaccine equivalent (MVVE) preparation, obtained from a U.S. manufacturer, for integration and for replication in human peripheral blood mononuclear cells (PBMCs). The results show the absence of EAV and ALV integrants in DNA prepared from MVVE-inoculated human cells by direct DNA PCR and Alu PCR assays and no propagation of retrovirus in 18-day cultures of MVVE-inoculated human PBMCs by a highly sensitive PCR-based RT assay. These results provide further confidence regarding the safety of chicken RT activity in live viral vaccines and support the continued use of chick-cell-derived vaccines in humans.
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Affiliation(s)
- M Shahabuddin
- Laboratory of Retrovirus Research, Division of Viral Products, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Bethesda, Maryland 20892, USA
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16
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Dimcheff DE, Krishnan M, Mindell DP. Evolution and characterization of tetraonine endogenous retrovirus: a new virus related to avian sarcoma and leukosis viruses. J Virol 2001; 75:2002-9. [PMID: 11160701 PMCID: PMC115148 DOI: 10.1128/jvi.75.4.2002-2009.2001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In a previous study, we found avian sarcoma and leukosis virus (ASLV) gag genes in 19 species of birds in the order Galliformes including all grouse and ptarmigan (Tetraoninae) surveyed. Our data suggested that retroviruses had been transmitted horizontally among some host species. To further investigate these elements, we sequenced a replication-defective retrovirus, here named tetraonine endogenous retrovirus (TERV), from Bonasa umbellus (ruffed grouse). This is the first report of a complete, replication-defective ASLV provirus sequence from any bird other than the domestic chicken. We found a replication-defective proviral sequence consisting of putative Gag and Env proteins flanked by long terminal repeats. Reverse transcription-PCR analysis showed that retroviral gag sequences closely related to TERV are transcribed, supporting the hypothesis that TERV is an active endogenous retrovirus. Phylogenetic analyses suggest that TERV may have arisen via recombination between different retroviral lineages infecting birds. Southern blotting using gag probes showed that TERV occurs in tetraonines but not in chickens or ducks, suggesting that integration occurred after the earliest phasianid divergences but prior to the radiation of tetraonine birds.
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Affiliation(s)
- D E Dimcheff
- Department of Biology, University of Michigan, Ann Arbor, Michigan 48109-1079, USA.
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Hussain AI, Shanmugam V, Switzer WM, Tsang SX, Fadly A, Thea D, Helfand R, Bellini WJ, Folks TM, Heneine W. Lack of evidence of endogenous avian leukosis virus and endogenous avian retrovirus transmission to measles, mumps, and rubella vaccine recipients. Emerg Infect Dis 2001; 7:66-72. [PMID: 11266296 PMCID: PMC2631681 DOI: 10.3201/eid0701.010111] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The identification of endogenous avian leukosis virus (ALV) and endogenous avian retrovirus (EAV) in chick cell-derived measles and mumps vaccines in current use has raised concern about transmission of these retroviruses to vaccine recipients. We used serologic and molecular methods to analyze specimens from 206 recipients of measles, mumps, and rubella (MMR) vaccine for evidence of infection with ALV and EAV. A Western blot assay for detecting antibodies to endogenous ALV was developed and validated. All serum samples were negative for antibodies to endogenous ALV by Western blot analysis. Peripheral blood lymphocyte samples from 100 vaccinees were further tested by polymerase chain reaction for both ALV and EAV proviral sequences; all were negative. Matching serum samples were tested by reverse transcriptase polymerase chain reaction for ALV and EAV RNA, and all 100 samples were negative, providing no evidence of viremia. These findings do not indicate the presence of either ALV or EAV infection in MMR vaccine recipients and provide support for current immunization policies.
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Affiliation(s)
- A I Hussain
- Centers for Disease Control and Prevention, 1600 Clifton Road, Mail Stop G19, Atlanta, GA 30333, USA.
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18
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Dimcheff DE, Drovetski SV, Krishnan M, Mindell DP. Cospeciation and horizontal transmission of avian sarcoma and leukosis virus gag genes in galliform birds. J Virol 2000; 74:3984-95. [PMID: 10756010 PMCID: PMC111912 DOI: 10.1128/jvi.74.9.3984-3995.2000] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In a study of the evolution and distribution of avian retroviruses, we found avian sarcoma and leukosis virus (ASLV) gag genes in 26 species of galliform birds from North America, Central America, eastern Europe, Asia, and Africa. Nineteen of the 26 host species from whom ASLVs were sequenced were not previously known to contain ASLVs. We assessed congruence between ASLV phylogenies based on a total of 110 gag gene sequences and ASLV-host phylogenies based on mitochondrial 12S ribosomal DNA and ND2 sequences to infer coevolutionary history for ASLVs and their hosts. Widespread distribution of ASLVs among diverse, endemic galliform host species suggests an ancient association. Congruent ASLV and host phylogenies for two species of Perdix, two species of Gallus, and Lagopus lagopus and L. mutus also indicate an old association with vertical transmission and cospeciation for these ASLVs and hosts. An inference of horizontal transmission of ASLVs among some members of the Tetraoninae subfamily (grouse and ptarmigan) is supported by ASLV monophyletic groups reflecting geographic distribution and proximity of hosts rather than host species phylogeny. We provide a preliminary phylogenetic taxonomy for the new ASLVs, in which named taxa denote monophyletic groups.
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Affiliation(s)
- D E Dimcheff
- Department of Biology and Museum of Zoology, University of Michigan, Ann Arbor, Michigan 48109-1079, USA.
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19
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Sreekumar GP, Smyth JR, Ambady S, Ponce de Leon FA. Analysis of the effect of endogenous viral genes in the Smyth line chicken model for autoimmune vitiligo. THE AMERICAN JOURNAL OF PATHOLOGY 2000; 156:1099-107. [PMID: 10702426 PMCID: PMC1876847 DOI: 10.1016/s0002-9440(10)64978-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/14/1999] [Indexed: 11/21/2022]
Abstract
The Smyth line (SL) chicken, an animal model for autoimmune human vitiligo, is characterized by a spontaneous posthatch pigment loss, determined to be the result of an autoimmune phenomenon. Because endogenous virus (EV) genes have been reported to be associated with a number of autoimmune diseases of human and animal models, we designed this experiment to investigate the role of EV in the SL vitiligo by using the complete sequence of Rous-associated virus-2 as a probe for EV. An F(2) resource population was developed by the matings of SL and parental control (BL) chickens. Linkage disequilibrium between vitiligo and EV was apparent (16.2-kb SacI fragment, P = 0.05 and a 19-kb HindIII fragment, P = 0.03). Methylation analyses revealed that the EV and endogenous avian retroviral (EAV) genes were methylated in both the SL and BL sublines of chickens; therefore, methylation does not appear to be responsible for the differences in the expression of vitiligo between SL and BL sublines. Expression of the EV genes correlated with the disease in vitiliginous SL101 birds and also in 5-Azacytidine-induced vitiliginous BL101 parental control chickens. Only one EV locus was detected in the unrelated Light Brown Leghorn control chickens (1q14) by in situ hybridization, whereas 3 EV loci were identified in SL101 and BL101 chickens (1p25, 2q26, and an unidentifiable microchromosome). Our observations indicate that EV genes may play a role in the induction of autoimmune vitiligo in the SL chicken model.
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Affiliation(s)
- G P Sreekumar
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, Massachusetts 01003, USA
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20
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Sacco MA, Flannery DM, Howes K, Venugopal K. Avian endogenous retrovirus EAV-HP shares regions of identity with avian leukosis virus subgroup J and the avian retrotransposon ART-CH. J Virol 2000; 74:1296-306. [PMID: 10627540 PMCID: PMC111464 DOI: 10.1128/jvi.74.3.1296-1306.2000] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The existence of novel endogenous retrovirus elements in the chicken genome, designated EAV-HP, with close sequence identity to the env gene of avian leukosis virus (ALV) subgroup J has been reported (L. M. Smith, A. A. Toye, K. Howes, N. Bumstead, L. N. Payne, and K. Venugopal, J. Gen. Virol. 80:261-268, 1999). To resolve the genome structure of these retroviral elements, we have determined the complete sequence of two proviral clones of EAV-HP from a line N chicken genomic DNA yeast artificial chromosome library and from a meat-type chicken line 21 lambda library. The EAV-HP sequences from the two lines were 98% identical and had a typical provirus structure. The two EAV-HP clones showed identical large deletions spanning part of the gag, the entire pol, and part of the env genes. The env region of the EAV-HP clones was 97% identical to the env sequence of HPRS-103, the prototype subgroup J ALV. The 5' region of EAV-HP comprising the R and U5 regions of the long terminal repeat (LTR), the untranslated leader, and the 5' end of the putative gag region were 97% identical to the avian retrotransposon sequence, ART-CH. The remaining gag sequence shared less than 60% identity with other ALV sequences. The U3 region of the LTR was distinct from those of other retroviruses but contained some of the conserved motifs required for functioning as a promoter. To examine the ability of this endogenous retroviral LTR to function as a transcriptional promoter, the EAV-HP and HPRS-103 LTR U3 regions were compared in a luciferase reporter gene assay. The low luciferase activity detected with the EAV-HP LTR U3 constructs, at levels close to those observed for a control vector lacking the promoter or enhancer elements, suggested that these elements function as a weak promoter, possibly accounting for their low expression levels in chicken embryos.
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Affiliation(s)
- M A Sacco
- Institute for Animal Health, Compton, Newbury, Berkshire RG20 7NN, United Kingdom
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21
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Khan AS, Maudru T, Thompson A, Muller J, Sears JF, Peden KW. The reverse transcriptase activity in cell-free medium of chicken embryo fibroblast cultures is not associated with a replication-competent retrovirus. J Clin Virol 1998; 11:7-18. [PMID: 9784139 DOI: 10.1016/s0928-0197(98)00042-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND Reverse transcriptase (RT) activity has previously been reported in concentrated medium of primary chicken embryo cell cultures using the traditional RT assay. Recently, using the newly-developed and highly-sensitive product-enhanced reverse transcriptase (PERT) assay, RT activity has been detected in live, attenuated vaccines grown in chicken cell substrates. Furthermore, this activity has been associated with particles that contain RNA related to an ancient, endogenous avian retrovirus family designated as EAV-0. OBJECTIVE To investigate whether the RT activity present in vaccines produced in specific pathogen-free chicken cell substrates is associated with an infectious retrovirus that can replicate in human cells. STUDY DESIGN The kinetics of RT activity produced by 10-day-old chicken embryo fibroblast (CEF) cultures was determined by analyzing cell-free medium in a PCR-based RT (PBRT) assay. Material containing the peak PBRT activity was used as the inoculum to infect various human cell lines and peripheral blood mononuclear cells. Filtered supernatants from control and test cultures were analyzed for the presence of replication-competent retroviruses by the PBRT assay. The cells were monitored for other adventitious agents by routine observation for cytopathic effect (CPE) and by transmission electron microscopy (TEM) at culture termination. RESULTS The PBRT activity did not increase above the background level in the human target cells through at least five cell passages, thus indicating the absence of a replicating retrovirus. No other adventitious agents were detected based upon TEM analysis and the absence of CPE. CONCLUSION The RT activity produced by chicken primary cell cultures is not associated with a retrovirus that can replicate in human cells.
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Affiliation(s)
- A S Khan
- Laboratory of Retrovirus Research, US Food and Drug Administration, Bethesda, MD 20892, USA.
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22
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Abstract
1. A study of primary wing feather development rate in guinea fowl revealed genetic control through a single pair of sex-linked alleles. The allele for slow feathering (K) was dominant over that for rapid feathering (k+). 2. Wing feather sexing showed 94% accuracy in 10-d-old keets. 3. Incidence of rapid feathering allele (k+) was higher in the population selected for high body weight compared to the unselected population.
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Affiliation(s)
- S K Pal
- Central Avian Research Institute, Izatnagar, India
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23
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Weissmahr RN, Schüpbach J, Böni J. Reverse transcriptase activity in chicken embryo fibroblast culture supernatants is associated with particles containing endogenous avian retrovirus EAV-0 RNA. J Virol 1997; 71:3005-12. [PMID: 9060660 PMCID: PMC191429 DOI: 10.1128/jvi.71.4.3005-3012.1997] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
We have recently shown that live attenuated virus vaccines produced on chicken-derived cells contain low levels of particle-associated reverse transcriptase (RT). In both virus and corresponding control harvests produced on chicken embryo fibroblasts, these activities were present at significantly higher concentrations than in the vaccines. In order to identify the putative retrovirus sequence responsible for this activity, a novel method for the selective PCR amplification of particle-associated retrovirus RNA that uses DNA primers complementary to the primer binding sites of the known exogenous retroviruses in combination with an anchor primer was applied. A product of the endogenous avian retrovirus family EAV-0, termed EAV-0(B1), was reproducibly generated with a tRNA(Trp)-derived primer from the RT peak fraction of a sucrose density gradient run with a harvest of a live attenuated measles vaccine. In contrast, no products were detected with primers derived from tRNA(Pro), tRNA(Lys)1,2 or tRNA(Lys)3. In the same fraction, genomic RNA of EAV-0(B1) was demonstrated by long PCR. Analysis of several sucrose density gradients from different harvests of various manufacturers demonstrated accumulation of, and colocalization with, RT activity for the EAV-0(B1) RNA but not for a chicken cellular mRNA. Synthesis of cDNA from EAV-0(B1) RNA was shown by endogenous RT reaction. Furthermore, complexes of naturally primed EAV-0(B1) RNA with RT were demonstrated. Taken together, these data strongly suggest that EAV-0 is able to produce virus-like particles with an active RT.
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Affiliation(s)
- R N Weissmahr
- Swiss National Center for Retroviruses, University of Zurich
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24
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Aarts HJ, Leenstra FR. Association of endogenous avian viral and endogenous viral genes with feed conversion and six-week body weight in broilers. Poult Sci 1995; 74:1022-8. [PMID: 7543996 DOI: 10.3382/ps.0741022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The consistency of the effect of selection on the frequencies of endogenous avian viral (eav) and endogenous viral (ev) specific restriction fragment length polymorphism (RFLP) bands was studied in two broiler lines selected from a single base population and in an F2 population derived from a reciprocal cross of both lines. One broiler line (FC line) was selected for low feed conversion ratio and the other line (GL line) was selected for high 6-wk body weight. In the F2 population, the band frequencies were determined in groups representing separate tails of the distribution of two production traits, namely, low feed conversion ratio between 29 and 42 d of age and body weight at 42 d of age. The F2 population consisted of 288 females belonging to 24 full-sib families. To rule out family effects, the tails for these production traits were composed by either the best or by the worst female performer for each trait in each full-sib family. In total, 29 HindIII-eav, 34 MspI-eav, and 21 BamHI-ev bands could be distinguished by RFLP analysis. This report describes the influence of selection on 11 potentially interesting bands. Two bands, the 9.5-kb HindIII-eav and the 15-kb MspI-eav band, which were found both in higher frequencies in the parental FC line, were also found in higher (P < or = .05) frequencies in the F2 tail with a favorable feed conversion ratio. A third band, the 6.5-kb HindIII-eav band, present in lower frequencies in the parental GL line, was also present in lower (P < or = .05) frequencies in the F2 tail of birds with heavy body weight.
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Affiliation(s)
- H J Aarts
- DLO-Institute for Animal Science and Health, Beekbergen, The Netherlands
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25
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Abstract
The complete sequence of ART-CH, a recently found chicken retrotransposon (A. V. Gudkov, E. A. Komarova, M. A. Nikiforov, and T. E. Zaitsevskaya, J. Virol. 66:1726-1736, 1992), was characterized. ART-CH has the structure of a 3,300-bp-long provirus, including two 388-bp long terminal repeats (LTRs) (U3, 245 bp; R region, 17 bp; and U5, 126 bp), a tRNA(Trp)-binding site, and a polypurine tract, similar to avian leukosis viruses. At least some of the approximately 50 genomic copies of ART-CH are transcribed into polyadenylated RNA, which is initiated and terminated at the expected sites within the LTRs. In contrast to the regulatory sequences involved in proviral expression and replication, the internal regions of ART-CH seem to be completely defective. Several short regions of homology with avian leukosis virus genes, most of which encode gag-related sequences, were found among different reading frames of ART-CH, which are not organized like regular retroviral genes. Both sequence analysis and restriction fragment length polymorphism analysis revealed a high degree of sequence (97% homology) and structural similarity among members of the ART-CH family, indicating their common origin and recent penetration into chicken DNA. ART-CH sequences were detected in mouse cells infected with Rous sarcoma virus produced by an ART-CH-expressing Rous sarcoma. These data are consistent with the hypothesis that ART-CH belongs to a class of defective retrotransposons whose replication strategy requires the use of helper viruses. They might originate from an avian leukosis virus-related retrovirus which completely lost its coding capacities as a result of multiple mutations and deletions. These features apparently group ART-CH with the VL30 retrotransposons of rodents.
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Affiliation(s)
- M A Nikiforov
- Institute of Carcinogenesis, Cancer Research Center, Moscow, Russian Federation
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26
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Benkel BF, Gavora JS. A novel molecular fingerprint probe based on the endogenous avian retroviral element (EAV) of chickens. Anim Genet 1993; 24:409-13. [PMID: 8273914 DOI: 10.1111/j.1365-2052.1993.tb00353.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We have developed a novel molecular probe that is useful for DNA fingerprint analysis in chickens. The probe is based on the middle-repetitive, chicken endogenous retroviral (EAV) element. It consists of 1503 bp of the 3' portion of the EAV element, extending from the down-stream end of the envelope gene to the beginning of the downstream long terminal repeat (LTR). Unlike other probes that are currently in use for fingerprint analysis with chicken DNA, the EAV-based probe works well at normal levels of stringency, and with standard hybridization buffers. Digestion of chicken genomic DNA with a variety of restriction enzymes routinely yields up to 30 resolvable bands per bird in the 500 bp to 20 kbp range. In order to test the efficacy of the EAV-based fingerprint probe, we have used it to estimate the degree of inbreeding in the inbred WG strain of White Leghorns. We find that the estimates derived with the EAV probe are very similar to those reported previously for the WG strain. These results suggest that molecular probes based on endogenous retroviruses and other middle-repetitive DNA elements should be useful for fingerprint analysis in chickens, and in vertebrates in general.
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Affiliation(s)
- B F Benkel
- Centre for Food and Animal Research, Agriculture Canada, Ottawa, Ontario
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27
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Silversides FG, Tixier-Boichard M, Durand L, Mérat P. Research note: the S(al)-c mutation in the chicken is not linked to Rous-associated virus-2 related DNA sequences. Poult Sci 1993; 72:368-72. [PMID: 8382818 DOI: 10.3382/ps.0720368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
A male chicken heterozygous for a gene for sex-linked imperfect albinism (s(al)-c) was used to produce offspring in five dam families. The DNA from 23 offspring (22 females and 1 male) was cut with the restriction enzyme Sac1 and hybridized with a Rous-Associated Virus-2 probe to test for linkage between the gene and endogenous viral (ev) genes. In a second experiment, 15 albino and 15 nonalbino females resulting from 4 males mated to 11 females were studied with the enzymes Sac1 and BamHI. In the first experiment, 10 different ev genes were seen. These, plus seven additional bands were seen in the second experiment. The gene s(al)-c segregated independently of all ev genes, suggesting that it could be used for autosexing of chickens or in layer flocks without causing inherent problems previously associated with K, the gene for slow feathering, caused by essentially complete concordance between K and ev21.
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Affiliation(s)
- F G Silversides
- Laboratoire de Génétique Factorielle, Institut National de la Recherche Agronomique, Jouy-en-Josas, France
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28
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Grunder AA, Benkel B, Sabour P, Gavora JS. Research note: avian leukosis retroviral genes are not detected in geese. Poult Sci 1993; 72:363-7. [PMID: 8382817 DOI: 10.3382/ps.0720363] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Genomic DNA from four strains of geese was analyzed for the presence of endogenous viral elements using a probe that can detect over 20 Rous-associated endogenous viral genes (ev genes) in chickens, as well as a probe and protocol that detects endogenous avian viruses (EAV). Southern blot analysis of genomic DNA did not reveal any ev genes in DNA of 15 geese from Chinese, Synthetic, or two Embden goose strains. Even under low stringency conditions, using a probe that covered most of the polymerase (pol) gene of the Rous-associated virus (RAV) and that revealed EAV elements in a chicken without ev genes, no viral loci were evident in goose DNA.
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Affiliation(s)
- A A Grunder
- Centre for Food and Animal Research, Agriculture Canada, Ottawa, Ontario
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29
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Boyce-Jacino MT, O'Donoghue K, Faras AJ. Multiple complex families of endogenous retroviruses are highly conserved in the genus Gallus. J Virol 1992; 66:4919-29. [PMID: 1321278 PMCID: PMC241335 DOI: 10.1128/jvi.66.8.4919-4929.1992] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
We have analyzed the genome of the domestic chicken for the presence of genetic sequences related to the envelope protein-encoding genes of avian sarcoma/leukosis retroviruses to determine the organization, structure, potential functionality, and distribution of such sequences. We have previously identified in the genus Gallus an extensive group of endogenous avian retroviruses termed EAV-0. Southern blot and sequence analysis presented here of EAV-0 elements revealed that the majority of the EAV-0 elements in the domestic chicken genome have large deletions in their env genes. Screening of a line 0 chicken genomic DNA library for potential full-length env gene-containing endogenous elements yielded three provirus clones of a previously unrecognized group of endogenous retroviruses. These three clones, E13, E33, and E51, are more closely related to each other (80% or more sequence identity) than to other avian retroviruses (70% or less sequence identity). The E13 element has a large deletion in env, but the E51 element has full-length and highly divergent SU- and TM-coding domains. Complete sequence analysis of the E51 env gene region revealed a defective SU-coding domain and an intact TM-coding domain. Sequence analysis of the E51, E33, and E13 3' termini revealed highly distinctive long terminal repeats of approximately 360 bp which appear to be the products, in part, of long terminal repeat domain shuffling. Hybridization analysis with E51 and E33 env gene probes indicated that they are members of an extensive group of elements present in all Gallus species, and at least one element, E51, could be shown by polymerase chain reaction amplification and direct sequencing to have integrated prior to Gallus speciation.
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Affiliation(s)
- M T Boyce-Jacino
- Institute of Human Genetics, University of Minnesota, Minneapolis 55455
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30
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Abstract
A 3' region of a previously unknown retroviruslike element named ART-CH (avian retrotransposon from chicken genome) was obtained in the course of polymerase chain reaction-mediated cloning of avian leukosis virus long terminal repeats (LTRs) from DNAs of infected chicken cells. About 50 copies of ART-CH are present in the genome of chickens of different breeds. ART-CH is not found in DNA of quails, ducks, turkeys, or several other birds tested. The ART-CH element is about 3 kb in size, including 388 bp LTRs. The major class of ART-CH-specific RNA, also 3 kb in size, is detected in various organs of chickens. An ART-CH polypurine tract, a tRNA(Trp)-binding site, regions around the TATA box and polyadenylation signal, and the beginning of the putative gag gene strongly resemble the corresponding regions of avian leukosis viruses and EAV, the two described classes of chicken retroviruses. An open reading frame capable of encoding a polypeptide with a putative transmembrane domain is located upstream of the right ART-CH LTR. This sequence, as well as the U3 and U5 regions of the ART-CH LTR, has no obvious similarities with the corresponding parts of other known vertebrate retroviruses and retrotransposons. A short sequence upstream of the right LTR of ART-CH is very similar to sequences which flank the 3' ends of the oncogenes v-src, v-myc, v-fps, and v-crk in four different recombinant avian retroviruses and which are absent from the genomes of other studied avian retroviruses. Thus, ART-CH is a new endogenous chicken provirus that may participate in the formation of recombinant oncogenic retroviruses.
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Affiliation(s)
- A V Gudkov
- Laboratory of Molecular Genetics, Cancer Research Center, Moscow, Russia
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31
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Boulliou A, Le Pennec JP, Hubert G, Donal R, Smiley M. The Endogenous Retroviral ev 21 Locus in Commercial Chicken Lines and its Relationship with the Slow-Feathering Phenotype (K). Poult Sci 1992; 71:38-46. [PMID: 1347168 DOI: 10.3382/ps.0710038] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Provirus ev21 was found in both K- and k(+)-feathering Rhode Island Red commercial layers. Probe EV21-int revealed the presence of two distinct but similar regions, US (unoccupied site) and OS (occupied site). Restriction analysis showed that these regions had at least 19 kb structural homology but were distinguishable by ev21 proviral sequences, OS, and possibly three polymorphics US. The loci OS and US were both located on Chromosome Z. The k(+)-feathering birds were found to have only one site (either OS or US) per individual Z chromosome, whereas K-feathering birds had at least one Z chromosome with both regions in cis configuration. It has been possible to show that the reversion to the k(+)-feathering phenotype is accompanied by the loss of either a US or OS region that disrupts the cis configuration in K-feathering birds.
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Affiliation(s)
- A Boulliou
- Laboratoire de Génétique Moléculaire, Centre National de la Recherche Scientifique, Unite de Recherche Associée 256, Université de Rennes I, France
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