The unique envelope gene of the subgroup J avian leukosis virus derives from ev/J proviruses, a novel family of avian endogenous viruses

Transcriptome-wide N6-methyladenosine modification and microRNA jointly regulate the infection of avian leukosis virus subgroup J in vitro

N6-methyladenosine (m6A) methylation in transcripts has been suggested to influence tumorigenesis in liver tumors caused by the avian leukosis virus subgroup J (ALV-J). However, m6A modifications during ALV-J infection in vitro remain unclear. Herein, we performed m6A and RNA sequencing in ALV-J-infected chicken fibroblasts (DF-1). A total of 51 differentially expressed genes containing differentially methylated peaks were identified, which were markedly enriched in microRNAs (miRNAs) in cancer cells as well as apoptosis, mitophagy and autophagy, RNA degradation, and Hippo and MAPK signaling pathways. Correlation analysis indicated that YTHDC1 (m6A-reader gene) plays a key role in m6A modulation during ALV-J infection. The env gene of ALV-J harbored the strongest peak, and untranslated regions and long terminal repeats also contained peaks of different degrees. To the best of our knowledge, this is the first thorough analysis of m6A patterns in ALV-J-infected DF-1 cells. Combined with miRNA profiles, this study provides a useful basis for future research into the key pathways of ALV-J infection associated with m6A alteration.

Conservation and distribution of the DRACH motif for potential m6A sites in avian leukosis virus subgroup J

N6-methyladenosine (m6A) methylation is an internal post-transcriptional modification that has been linked to viral multiplication and pathogenicity. To elucidate the conservation patterns of potential 5'-DRACH-3' motifs in avian leukosis virus subgroup J (ALV-J), 149 ALV-J strains (139 isolates from China; ALV-J prototype HPRS-103 from the UK; and 9 strains from the USA, Russia, India, and Pakistan) available in GenBank before December 2023 were retrieved. According to the prediction results of the SRAMP web-server, these ALV-J genomes contained potential DRACH motifs, with the total number ranging from 43 to 64, which were not determined based on the isolation region and time. Conservative analysis suggested that 37 motifs exhibited a conservation of >80%, including 17 motifs with a grading above "high confidence." Although these motifs were distributed in the U5 region of LTRs and major coding regions, they were enriched in the coding regions of p27, p68, p32, and gp85. The most common m6A-motif sequence of the DRACH motif in the ALV-J genome was GGACU. The RNA secondary structure of each conserved motif predicted by SRAMP and RNAstructure web-server was mainly of two types-A-U pair (21/37) and hairpin loop (16/37)-based on the core adenosine. Considering the systematic comparative analysis performed in this study, future thorough biochemical research is warranted to determine the role of m6A modification during the replication and infection of ALV-J. These conservation and distribution analysis of the DRACH motif for potential m6A sites in ALV-J would provide a foundation for the future intervention of ALV-J infection and m6A modification.

Advances on genetic and genomic studies of ALV resistance

Avian leukosis (AL) is a general term for a variety of neoplastic diseases in avian caused by avian leukosis virus (ALV). No vaccine or drug is currently available for the disease. Therefore, the disease can result in severe economic losses in poultry flocks. Increasing the resistance of poultry to ALV may be one effective strategy. In this review, we provide an overview of the roles of genes associated with ALV infection in the poultry genome, including endogenous retroviruses, virus receptors, interferon-stimulated genes, and other immune-related genes. Furthermore, some methods and techniques that can improve ALV resistance in poultry are discussed. The objectives are willing to provide some valuable references for disease resistance breeding in poultry.

Genetic diversity of avian leukosis virus subgroup J (ALV-J): toward a unified phylogenetic classification and nomenclature system

Avian leukosis virus subgroup J (ALV-J) has infected a variety of birds, causing major economic losses in China. Understanding the comprehensive criteria of classification and nomenclature of ALV-J would be useful for the investigation of the viral evolution and also for the prevention and control of this infection. An in-depth analysis of the genetic diversity of ALV-J was performed in the present study. Four hundred and seventy-five sequences of the gp85 gene, including thirteen of avian endogenous retrovirus designated ev/J and 462 of ALV-J, were used in the phylogenetic and the evolutionary distance analysis for this classification. The study identified that the current ALV-J strains were divided into two first-order clades (Clades 1 and 2) and three second-order clades (Clades 1.1, 1.2 and 1.3). The current Chinese ALV-J strains are predominantly in Clade 1.3, and the Chinese and Egyptian chicken flocks have been facing the emerging Clade 2 viruses. This system pioneers the classification efforts for ALV-J, which uses Pilot tree for rapid classification of the new isolates and also the addition of possible new clades. The proposed unified classification system will facilitate future studies of ALV-J epidemiology and genetic evolution and of the comparison of sequences obtained across the world.

Biotic concerns in generating molecular diagnosis matrixes for 4 avian viruses with emphasis on Marek's disease virus

The great advance in the field of diagnosis of avian viruses is reflecting the highly sophisticated molecular assays of the human and general virology in providing highly sensitive and fast methods of diagnosis. The present review will discuss the biotic factors and the complexities that became evident with the evolution of the novel molecular diagnostic assays with emphasis on 4 avian viruses, chicken anemia, infectious laryngotracheitis, turkey meningoencephalitis, but mainly on Marek's disease virus. To create a biologically meaningful diagnosis, attention should be dedicated to various biotic factors and not only of the diagnostic assay. Included among the important factors are, (a) the sample examined and the sampling strategy, (b) the outcomes of the pathogen amplification ex vivo, (c) the sampling time and its reflection on the disease diagnosis, (d) the impact of simultaneous multiple virus-infections regarding the ability to demonstrate all pathogens and inter- and intra-interactions between the pathogens. A concerted consideration of the relevant factors and the use of advanced molecular diagnostic assay would yield biologically significant diagnosis in real-time that would beneficiate the poultry industry.

Molecular characteristics of avian leukosis viruses isolated from indigenous chicken breeds in China

To assess the status of avian leukosis virus (ALV) infection in indigenous chicken breeds in China, 121 plasma samples collected from various indigenous chicken breeds were tested for the presence of ALV from 2015 to 2016. A total of 14 ALV strains were isolated and identified, including two ALV-A strains, one ALV-B strain, eight ALV-J strains, and three ALV-K strains. To study the genome structure, biological characteristics, and the evolutionary relationships of the ALV-K strains with other known subgroup strains from infected chickens, we determined the complete genome sequence of the three ALV-K strains and performed comparative analysis using the whole genome sequence or selected sequence elements. The replication rates of the three ALV-K strains were markedly lower than the rates of other ALVs, and they shared a common mutation in the pol gene, which had not been previously observed. In addition, nine putative recombinant events were detected in the genomes of the three newly isolated ALV-K strains, with high statistical support. This was the first report of an ALV-K reorganization event, which has contributed to its genetic evolution. In summary, we established a robust classification system for ALV, especially for ALV-K, and revealed additional genomic diversity for the ALV strains in indigenous chicken breeds. Therefore additional works are warranted to explore ALV genomics and epidemiology.

Development of reliable techniques for the differential diagnosis of avian tumour viruses by immunohistochemistry and polymerase chain reaction from formalin-fixed paraffin-embedded tissue sections

A variety of techniques have been developed as diagnostic tools for the differential diagnosis of tumours produced by Marek's disease virus from those induced by avian leukosis virus and reticuloendotheliosis virus. However, most current techniques are unreliable when used in formalin-fixed paraffin-embedded (FFPE) tissues, which often is the only sample type available for definitive diagnosis. A collection of tumours was generated by the inoculation of different strains of Marek's disease virus, reticuloendotheliosis virus or avian leukosis virus singularly or in combination. FFPE tissue sections from tumour and non-tumour tissues were analysed by optimized immunohistochemistry (IHC) techniques and traditional as well as quantitative polymerase chain reaction (PCR) with newly designed primers ideal for DNA fragmented by fixation. IHC and PCR results were highly sensitive and specific in tissues from single-infected birds. Virus quantity was higher in tumours compared to non-tumour spleens from Marek's disease (MD) virus-infected birds. Thus, using FFPE sections alone may be sufficient for the diagnosis of MD by demonstration of high quantities of viral antigens or genome in tumour cells, along with the absence of other tumour viruses by traditional PCR, and if standard criteria are met based on clinical history and histology. IHC furthermore allowed detection of the specific cells that were infected with different viruses in tumours from birds that had been inoculated simultaneously with multiple viruses. Following validation with field samples, these new protocols can be applied for both diagnostic and research purposes to help accurately identify avian tumour viruses in routine FFPE tissue sections.

Residues 28 to 39 of the Extracellular Loop 1 of Chicken Na+/H+ Exchanger Type I Mediate Cell Binding and Entry of Subgroup J Avian Leukosis Virus

Chicken Na⁺/H⁺ exchanger type I (chNHE1), a multispan transmembrane protein, is a cellular receptor of the subgroup J avian leukosis virus (ALV-J). To identify the functional determinants of chNHE1 responsible for the ALV-J receptor activity, a series of chimeric receptors was created by exchanging the extracellular loops (ECL) of human NHE1 (huNHE1) and chNHE1 and by ECL replacement with a hemagglutinin (HA) tag. These chimeric receptors then were used in binding and entry assays to map the minimal ALV-J gp85-binding domain of chNHE1. We show that ECL1 of chNHE1 (chECL1) is the critical functional ECL that interacts directly with ALV-J gp85; ECL3 is also involved in ALV-J gp85 binding. Amino acid residues 28 to 39 of the N-terminal membrane-proximal region of chECL1 constitute the minimal domain required for chNHE1 binding of ALV-J gp85. These residues are sufficient to mediate viral entry into ALV-J nonpermissive cells. Point mutation analysis revealed that A30, V33, W38, and E39 of chECL1 are the key residues mediating the binding between chNHE1 and ALV-J gp85. Further, the replacement of residues 28 to 39 of huNHE1 with the corresponding chNHE1 residues converted the nonfunctional ALV-J receptor huNHE1 to a functional one. Importantly, soluble chECL1 and huECL1 harboring chNHE1 residues 28 to 39 both could effectively block ALV-J infection. Collectively, our findings indicate that residues 28 to 39 of chNHE1 constitute a domain that is critical for receptor function and mediate ALV-J entry.IMPORTANCE chNHE1 is a cellular receptor of ALV-J, a retrovirus that causes infections in chickens and serious economic losses in the poultry industry. Until now, the domains determining the chNHE1 receptor function remained unknown. We demonstrate that chECL1 is critical for receptor function, with residues 28 to 39 constituting the minimal functional domain responsible for chNHE1 binding of ALV-J gp85 and efficiently mediating ALV-J cell entry. These residues are located in the membrane-proximal region of the N terminus of chECL1, suggesting that the binding site of ALV-J gp85 on chNHE1 is probably located on the apex of the molecule; the receptor-binding mode might be different from that of retroviruses. We also found that soluble chECL1, as well as huECL1 harboring chNHE1 residues 28 to 39, effectively blocked ALV-J infection. These findings contribute to a better understanding of the ALV-J infection mechanism and also provide new insights into the control strategies for ALV-J infection.

Taishan Pinus massoniana pollen polysaccharide inhibits subgroup J avian leucosis virus infection by directly blocking virus infection and improving immunity

Subgroup J avian leucosis virus (ALV-J) generally causes neoplastic diseases, immunosuppression and subsequently increases susceptibility to secondary infection in birds. The spread of ALV-J mainly depends on congenital infection and horizontal contact. Although ALV-J infection causes enormous losses yearly in the poultry industry worldwide, effective measures to control ALV-J remain lacking. In this study, we demonstrated that Taishan Pinus massoniana pollen polysaccharide (TPPPS), a natural polysaccharide extracted from Taishan Pinus massoniana pollen, can significantly inhibit ALV-J replication in vitro by blocking viral adsorption to host cells. Electron microscopy and blocking ELISA tests revealed that TPPPS possibly blocks viral adsorption to host cells by interacting with the glycoprotein 85 protein of ALV-J. Furthermore, we artificially established a congenitally ALV-J-infected chicken model to examine the anti-viral effects of TPPPS in vivo. TPPPS significantly inhibited viral shedding and viral loads in immune organs and largely eliminated the immunosuppression caused by congenital ALV-J infection. Additionally, pre-administration of TPPPS obviously reduced the size and delayed the occurrence of tumors induced by acute oncogenic ALV-J infection. This study revealed the prominent effects and feasible mechanisms of TPPPS in inhibiting ALV-J infection, thereby providing a novel prospect to control ALV-J spread.

Genetic Diversity of NHE1, Receptor for Subgroup J Avian Leukosis Virus, in Domestic Chicken and Wild Anseriform Species

J subgroup avian leukosis virus (ALV-J) infects domestic chicken, jungle fowl, and turkey and enters the host cell through a receptor encoded by tvj locus and identified as Na+/H+ exchanger 1 (NHE1). The resistance to ALV-J in a great majority of examined galliform species was explained by deletions or substitutions of the critical tryptophan 38 in the first extracellular loop of NHE1, and genetic polymorphisms around this site predict the susceptibility or resistance of a given species or individual. In this study, we examined the NHE1 polymorphism in domestic chicken breeds and documented quantitative differences in their susceptibility to ALV-J in vitro. In a panel of chicken breeds assembled with the aim to cover the maximum variability encountered in domestic chickens, we found a completely uniform sequence of NHE1 extracellular loop 1 (ECL1) without any source of genetic variation for the selection of ALV-J-resistant poultry. In parallel, we studied the natural polymorphisms of NHE1 in wild ducks and geese because of recent reports on ALV-J positivity in feral Asian species. In anseriform species, we demonstrate a specific and highly conserved critical ECL1 sequence without any homologue of tryptophan 38 in accordance with the resistance of duck cells to prototype ALV-J. Last, we demonstrated that the new Asian strains of ALV-J have not evolved their envelope glycoprotein to the entry the duck cells. Our results contribute substantially to the current discussion of possible heterotransmission of ALV-J and its spill-over into the wild ducks and geese.

Endogenous Retroviruses in the Genomics Era

Endogenous retroviruses comprise millions of discrete genetic loci distributed within the genomes of extant vertebrates. These sequences, which are clearly related to exogenous retroviruses, represent retroviral infections of the deep past, and their abundance suggests that retroviruses were a near-constant presence throughout the evolutionary history of modern vertebrates. Endogenous retroviruses contribute in myriad ways to the evolution of host genomes, as mutagens and as sources of genetic novelty (both coding and regulatory) to be acted upon by the twin engines of random genetic drift and natural selection. Importantly, the richness and complexity of endogenous retrovirus data can be used to understand how viruses spread and adapt on evolutionary timescales by combining population genetics and evolutionary theory with a detailed understanding of retrovirus biology (gleaned from the study of extant retroviruses). In addition to revealing the impact of viruses on organismal evolution, such studies can help us better understand, by looking back in time, how life-history traits, as well as ecological and geological events, influence the movement of viruses within and between populations.

Evaluation of a multi-epitope subunit vaccine against avian leukosis virus subgroup J in chickens

The intricate sequence and antigenic variability of avian leukosis virus subgroup J (ALV-J) have led to unprecedented difficulties in the development of vaccines. Much experimental evidence demonstrates that ALV-J mutants have caused immune evasion and pose a challenge for traditional efforts to develop effective vaccines. To investigate the potential of a multi-epitope vaccination strategy to prevent chickens against ALV-J infections, a recombinant chimeric multi-epitope protein X (rCMEPX) containing both immunodominant B and T epitope concentrated domains selected from the major structural protein of ALV-J using bioinformatics approach was expressed in Escherichia coli Rosetta (DE3). Its immunogenicity and protective efficacy was studied in chickens. The results showed that rCMEPX could elicit neutralizing antibodies and cellular responses, and antibodies induced by rCMEPX could specifically recognize host cell naturally expressed ALV-J proteins, which indicated that the rCMEPX is a good immunogen. Challenge experiments showed 80% chickens that received rCMEPX were well protected against ALV-J challenge. This is the first report of a chimeric multi-epitope protein as a potential immunogen against ALV-J.

Nonconserved tryptophan 38 of the cell surface receptor for subgroup J avian leukosis virus discriminates sensitive from resistant avian species

Subgroup J avian leukosis virus (ALV-J) is unique among the avian sarcoma and leukosis viruses in using the multimembrane-spanning cell surface protein Na(+)/H(+) exchanger type 1 (NHE1) as a receptor. The precise localization of amino acids critical for NHE1 receptor activity is key in understanding the virus-receptor interaction and potential interference with virus entry. Because no resistant chicken lines have been described until now, we compared the NHE1 amino acid sequences from permissive and resistant galliform species. In all resistant species, the deletion or substitution of W38 within the first extracellular loop was observed either alone or in the presence of other incidental amino acid changes. Using the ectopic expression of wild-type or mutated chicken NHE1 in resistant cells and infection with a reporter recombinant retrovirus of subgroup J specificity, we studied the effect of individual mutations on the NHE1 receptor capacity. We suggest that the absence of W38 abrogates binding of the subgroup J envelope glycoprotein to ALV-J-resistant cells. Altogether, we describe the functional importance of W38 for virus entry and conclude that natural polymorphisms in NHE1 can be a source of host resistance to ALV-J.

Identification of two novel multiple recombinant avian leukosis viruses in two different lines of layer chicken

Avian leukosis virus (ALV) is the most common oncogenetic retrovirus that emerges spontaneously as a result of recombination between exogenous viruses, exogenous viruses and endogenous viruses, and exogenous viruses and non-homologous cellular genes. In the present study, two natural recombinant avian leukosis viruses (rALVs) (LC110515-5 and LC110803-5) carrying a subgroup C gp85 gene, a subgroup E gp37 gene, and a subgroup J 3'UTR and 3'LTR were isolated from two different lines of layer flocks, Black-bone silky fowl (BSF) and commercial layer chicken, that suffered from myeloid leukosis. Although tumours were not observed in rALV-infected individual chickens, other non-neoplastic inflammatory lesions were evident. The two rALVs were cultured on DF-1 cells and identified by PCR, immunofluorescence assay and gene sequencing. The gp85 nucleotide sequence in the two isolates displayed a high identity (>95 %) with that of the gp85 gene in ALV-C, but the identity was less than 90 % with ALV-A/B/D/E and only 51 % with ALV-J. Phylogenetic analysis of the nucleotide and amino acid sequences confirmed that the two isolates were recombinant between ALV-C, ALV-E and ALV-J. Subgroup C ALV is rarely found in field cases. This report is the first to provide evidence that ALV-C has recombined with ALV-E and ALV-J in two different chicken lines. The source and characteristics of the two rALVs and ALV-C need to be further investigated.

Sequence analysis for the complete proviral genome of avian leukosis virus subgroup J associated with haemangiomas, leiomyosarcomas and myelomas in layer flocks

Avian leukosis virus subgroup J (ALV-J) can cause a variety of neoplasms, including mainly myeloid leukosis (myelocytomatosis) and nephromas. Other tumours, such as histiocytic sarcoma (HS), haemangiosarcoma and mesothelioma, may also develop. In a previous article we described a case in which myeloid leukosis, haemangiomas and leiomyosarcomas appeared simultaneously in a commercial layer flock with infection by ALV-J. The present research was completed to understand the molecular characteristics of the ALV-J strain that induced clinical myeloid leukosis, haemangiomas and leiomyosarcomas. Two strains of ALV-J (SDAU1001 and SDAU1002) were isolated and identified, and their full-length sequences were analysed. The complete genome nucleotide sequences of these two isolates were different in length, 7652 nt and 7636 nt, respectively. They shared 98.9% identity with each other, and 93.4% to 97.8% nucleotide identity to the reference ALV-J isolates. A 19-nucleotide repeat sequence was identified in the primer binding site (PBS) leader region of isolate SDAU1001. A base substitution mutation (base 15 C-T) in this insertion was identified. However, the identical insertion at the same site was not found in SDAU1002. The gag and pol genes of the two viruses were more conserved than the env gene. One key deletion in the E element was a common feature of SDAU1001 and SDAU1002. SDAU1001 and SDAU1002, possibly recombinants of ALV-J and another avian retrovirus, may share the same ancestor. Co-infection by SDAU1001 and SDAU1002 isolates is a possible explanation why myeloid leukosis, haemangiomas, and leiomyosarcomas appeared simultaneously in the same commercial layer flock.

Detection and molecular characterization of recombinant avian leukosis viruses in commercial egg-type chickens in China

Two natural recombinant avian leukosis viruses (ALVs) were isolated from Chinese commercial egg-type chickens in 2009, which suffered from haemangiomas and myelocytomas. Sequence analysis of the complete proviral genomes revealed several unique genetic characteristics of the present two isolates, demonstrating that the two viruses were derived from recombination between earlier Chinese ALV-J and endogenous virus sequences. The two recombinant viruses presented typical genetic organization of replication-competent genus Alpharetrovirus, and the gag and pol genes were well conserved with those of ALVs. The env genes of the two viruses were composed of the internal identical sequences (about 240 bp) of endogenous viruses, and the rest of the sequence belonged to subgroup J ALVs. The long terminal repeats of the two viruses were more closely related to HPRS-103 and earlier Chinese ALV-J than other subgroup ALVs, and multiple transcription regulatory elements of ALV-J were highly conserved. In addition, the two viruses shared an almost identical 3'-untranslated region (UTR) sequence with earlier Chinese ALV-J strains and the US strain 4817, containing a ~127 bp deletion in the E element region. However, further comparison with endogenous ALV indicated that the 3'-UTR sequences with ~127 bp deletion of ALV-J were most probably derived from endogenous viruses by recombination. These results suggested that the two isolates can be characterized as recombinant ALV-J with the internal env gene and 3'-UTR sequence of endogenous ALV.

Forensic investigation of a 1986 outbreak of osteopetrosis in commercial brown layers reveals a novel avian leukosis virus-related genome

Avian leukosis virus (ALV) is known to cause several neoplastic conditions in chickens, such as B-cell lymphomas, myelocytomas, erythroblastosis, and other types of neoplasia including osteopetrosis. We describe herein the identification of unique ALV-related proviral DNA sequences in an archived chicken bone affected with osteopetrosis. The osteopetrotic bone was obtained from an affected 46-week-old brown layer during an outbreak of osteopetrosis in Costa Rica in 1986. Analysis of proviral DNA in the 23-year-old osteopetrotic bone revealed unique exogenous ALV-related sequences that were named CR-1986 (Costa Rica, 1986). The 5' and 3' long terminal repeats (LTR) in the proviral DNA were identical to each other. The U3 regions in the LTRs were most similar to equivalent sequences in ALV-J, while U5 was identical to known endogenous ALV-E sequences. The predicted CR-1986 envelope protein was most similar to the envelope of myeloblastosis associated virus type 1 (MAV-1), although the percentage of amino acid sequence similarity to MAV-1 was low (90.4%). The variable and hypervariable regions of gp85 displayed several mutations compared to representative strains of ALV. The gp37 (transmembrane or TM) envelope protein showed three leucine to serine mutations that may represent important changes in the conformation of this protein, a finding that is currently being investigated. Several recombination events may have contributed to the emergence of CR-1986 because each analyzed segment was similar to a different ALV. CR-1986 may represent a unique ALV based on distinctive characteristics of its predicted envelope protein in comparison to previously reported ALVs.

Effects of retroviruses on host genome function

For millions of years, retroviral infections have challenged vertebrates, occasionally leading to germline integration and inheritance as ERVs, genetic parasites whose remnants today constitute some 7% to 8% of the human genome. Although they have had significant evolutionary side effects, it is useful to view ERVs as fossil representatives of retroviruses extant at the time of their insertion into the germline and not as direct players in the evolutionary process itself. Expression of particular ERVs is associated with several positive physiological functions as well as certain diseases, although their roles in human disease as etiological agents, possible contributing factors, or disease markers-well demonstrated in animal models-remain to be established. Here we discuss ERV contributions to host genome structure and function, including their ability to mediate recombination, and physiological effects on the host transcriptome resulting from their integration, expression, and other events.

Survey of endogenous virus and TVB* receptor status of commercial chicken stocks supplying specific-pathogen-free eggs

Endogenous avian leukosis virus (ALVE) and the ALVE receptor (TVB*S1) status of six commercial chicken lines supplying specific-pathogen-free eggs were analyzed. All commercial chicken lines are certified free of the avian leukosis virus (ALV) by screening for expression of the p27 protein using the standard enzyme-linked immunosorbent assay. The commercial chicken lines A, E, and F contained replication competent ALVE inserts. Line A was fixed for ALVE21, and lines E and F were segregating for ALVE10. In addition, ALVE1 was detected in all the chicken lines. Chicken lines B, D, and F were essentially fixed for the TVB*S1 allele that confers susceptibility to ALVE, whereas lines A, C, B, and E were resistant, containing either the TVB*S3 or TVB*R alleles. The results show that lines selected to be ALV p27 negative give rise to two different genotypes. One genotype lacks the TVB*S1 receptor for ALVE. Chicken lines with the TVB*S1 negative genotype can retain replication competent endogenous virus inserts such as ALVE2, 10, or 21 and still display the p27 negative phenotype. These replication competent ALVE viruses are phenotypically p27 negative in the absence of the TVB*S1 receptor because their chromosomal integration sites restrict transcription and subsequent production of the p27 protein and virus particles to levels below the detection limit. If the TVB*S1 receptor is present, the limited production of ALVE virus particles reinfects and integrates into more productive chromosomal locations in the cell. Increased production of infective virus particles and detectable levels of p27 follow this reinfection and integration into more active regions of the cells genome. The other genotype observed in the commercial lines retains the ALVE receptor (TVB*S1) but either lacks replication competent inserts or expresses the envelope encoded protein from defective inserts such as ALVE3 or ALVE6. In this phenotype, the env-coded glycoprotein encoded by the defective inserts binds to the TVB*S1 receptor and blocks the reinfection of the replication competent ALVE virus. This receptor interference stops reinfection and subsequent production of detectable virus particles and the p27 protein. Mixtures of different p27 negative phenotypes can result in the p27 positive phenotype and ALVE virus production. For example, mixtures of ALVE receptor positive (TVB*S1) but ALVE negative (p27 negative and envelope negative) chick embryo fibroblasts (CEFs) with fibroblasts that are receptor negative but ALVE positive could generate cells expressing high levels of p27 and ALVE virus. In this situation, the undetectable levels of ALVE virus from the receptor negative CEFs would infect and integrate into the receptor positive CEFs and produce detectable levels of ALVE virus. The implications of these findings for vaccine manufacturers and regulatory agencies are discussed.

Molecular and Biological Characterization of a Naturally Occurring Recombinant Subgroup B Avian Leukosis Virus with a Subgroup J–Like Long Terminal Repeat

Infection of broiler chickens with subgroup J avian leukosis virus (ALV) results in the induction of myeloid tumors. However, although egg-type chickens are susceptible to infection with ALV-J, the tumor incidence is very low, and on rare occasions the tumors observed are of the myeloid lineage. We recently described the isolation of an ALV (AF115-4) from commercial egg-type chickens suffering from myeloid leukosis. AF115-4 was initially identified as an ALV-J isolate based on PCR analysis of the long terminal repeat (LTR). However, further characterization of the viral envelope indicated that the virus is recombinant with subgroups B envelope and J LTR. Here we further characterize this recombinant virus at both the molecular and biological levels. We show that the AF115-4 isolate expresses a recombinant envelope glycoprotein encoded by a subgroup B gp85 region and a subgroup E gp37 region. The host range ofAF115-4 was analyzed using cells resistant to infection by subgroups A/B, J, or E; this shows that no ALV-J was present in the isolates obtained from the affected chickens. Additional antigenic characterization of AF115-4 using chicken sera specific for subgroups B or J indicated that no ALV-J was present in the samples examined. Inoculation of AF 115-4 into ALV-susceptible 1515 X 71 chickens resulted in the induction of lymphoid leukosis but not the expected myeloid leukosis affecting the commercial chickens. These results suggest that differences in the genetic makeup of the chickens from which AF115-4 was isolated and the line 1515 X 71 used in the present experiments may be responsible for the observed differences in pathogenicity. In addition, the results suggest that ALV-J continues to evolve by recombination, generating new viruses with different pathological properties.

Susceptibility of various parental lines of commercial white leghorn layers to infection with a naturally occurring recombinant avian leukosis virus containing subgroup B envelope and subgroup J long terminal repeat

Chickens from seven different parental lines of commercial White Leghorn layer flocks from three independent breeders were inoculated with a naturally occurring avian leukosis virus (ALV) containing an ALV-B envelope and an ALV-J long terminal repeat (LTR) termed ALV-B/J. Additional groups of chickens from the same seven parental lines were inoculated with ALV-B. Chickens were tested for ALV viremia and antibody at 0, 4, 8, 16, and 32 wk postinfection. Chickens from all parental lines studied were susceptible to infection with ALV-B with 40%-100% of inoculated chickens positive for ALV at hatch following embryo infection. Similarly, infection of egg layer flocks with the ALV-B/J recombinant virus at 8 days of embryonation induced tolerance to ALV with 86%-100% of the chickens viremic, 40%-75% of the chickens shedding virus, and only 2/125 (2%) of the chickens producing serum-neutralizing antibodies against homologous ALV-B/J recombinant virus at 32 wk postinfection. In contrast, when infected with the ALV-B/J recombinant virus at hatch, 33%-82% of the chickens were viremic, 28%-47% shed virus, and 0%-56% produced serum-neutralizing antibodies against homologous ALV-B/J recombinant virus at 32 wk postinfection. Infection with the ALV-B/J recombinant virus at embryonation and at hatch induced predominately lymphoid leukosis (LL), along with other common ALV neoplasms, including erythroblastosis, osteopetrosis, nephroblastomas, and rhabdosarcomas. No incidence of myeloid leukosis (ML) was observed in any of the commercial White Leghorn egg layer flocks infected with ALV-B/J in the present study. Data suggest that the parental line of commercial layers may influence development of ALV-B/J-induced viremia and antibody, but not tumor type. Differences in type of tumors noted in the present study and those noted in the field case where the ALV-B/J was first isolated may be attributed to differences in the genetics of the commercial layer flock in which ML was first diagnosed and the present commercial layer flocks tested in the present study.

E (XSR) element contributes to the oncogenicity of Avian leukosis virus (subgroup J)

Among the six subgroups of Avian leukosis virus (ALV) that infect chickens, subgroup J (ALV-J) was isolated from meat-type chickens where it predominantly induces myeloid leukosis (ML) and erythroblastosis (EB). The sequence of HPRS-103, the ALV-J prototype virus, shows several distinct features, one of which is the presence of a distinct hairpin stem-loop structure called the E (also called XSR) element in the 3' untranslated region. In order to determine the role of the E element in ALV-induced pathogenicity, a comparison was made of the oncogenicity of viruses derived from the provirus clones of parental and E element-deleted HPRS-103 viruses in two genetically distinct lines of birds. In line 15I birds, deletion of the E element had profound effects on virus replication in vivo, as only 55 % of birds showed evidence of infection, compared with 100 % infection by the parental virus. Furthermore, none of the line 15I birds infected with this virus developed tumours, indicating that the E element does contribute to the oncogenicity of the virus. On the other hand, deletion of the E element had only a marginal effect on the incidence of tumours in line 0 birds. These results indicate that, although the E element per se is not absolutely essential for tumour induction by this subgroup of viruses, it does contribute to oncogenicity in certain genetic lines of chicken.

Experimental Infection with Avian Leukosis Virus Isolated from Marek's Disease Vaccines

Recently, avian leukosis virus (ALV) was isolated from four lots of Marek's disease vaccine produced by two laboratories. The ALVs isolated were characterized by examination of their interactions with cells of two phenotypes (C/E and C/A,E), subgroup-specific polymerase chain reaction (PCR), virus neutralization, envelope gene sequencing, and phylogenetic analysis. All four ALVs are exogenous, belong to subgroup A, and appear to be virtually identical to each other based on PCR and envelope gene nucleotide sequences. We describe herein the characterization of the contaminant viruses in vivo by means of experimental infection in chickens. The contaminant viruses established transient viremia in specified pathogen-free (SPF) Leghorn chickens and elicited a robust and lasting antibody response detectable by enzyme-linked immunosorbent assay. None of the contaminant ALVs induced tumors up to 31 wk of age, and mortality was insignificant. Despite a strong antibody response against the contaminant ALVs, vertical (congenital) transmission to the progeny of experimentally infected SPF chickens took place, albeit at a very low rate (< or = 1.6%). Experimental infection in meat-type chicken embryos resulted in viremia at hatch, suggesting that some meat-type chickens are susceptible to infection and support virus replication.

Na+/H+ exchanger type 1 is a receptor for pathogenic subgroup J avian leukosis virus

Subgroup J avian leukosis virus (ALV-J) is a recently identified avian oncogenic retrovirus responsible for severe economic losses worldwide. In contrast with the other ALV subgroups, ALV-J predominantly induces myeloid leukosis in meat-type chickens. Despite significant homology with the other ALV subgroups across most of the genome, the envelope protein of ALV-J (EnvJ) shares low homology with the others. Pathogenicity and myeloid leukosis induction map to the env gene of ALV-J. A chimeric protein composed of the surface domain of EnvJ fused to the constant region of a rabbit IgG and mass spectrometry were used to identify the chicken Na(+)/H(+) exchanger type 1 (chNHE1) as a binding protein for ALV-J. Flow cytometry analysis and coprecipitation experiments demonstrated a specific interaction between EnvJ and chNHE1. When introduced into nonpermissive human 293T cells and quail QT6 cells, chNHE1 conferred susceptibility to EnvJ-mediated infection. Furthermore, 293T cells expressing chNHE1 fused with 293T cells expressing EnvJ in a low-pH-dependent manner. Together, these data identify chNHE1 as a cellular receptor for the highly pathogenic ALV-J.

Detection of avian leukosis virus subgroup J in chicken flocks from Malaysia and their molecular characterization

Previously we have shown that avian leukosis virus subgroup J (ALV-J) might be present in chicken flocks from Malaysia based on serological study and also on detection of tissue samples with myelocytic infiltration. In this study, the polymerase chain reaction was used to detect ALV-J sequences from archived frozen samples. Out of 21 tissue samples examined, 16 samples were positive for proviral DNA and four samples for ALV-J RNA. However, only nine samples were found positive for myelocytic infiltration. A total of 465 base pairs equivalent to positions 5305 to 5769 of HPRS-103 from each of the viral RNA positive samples were characterized. Sequence analysis indicated that the samples showed high identity (95.9 to 98.2%) and were close to HPRS-103 with identities between 97.4 and 99.3%. This study indicates that ALV-J-specific sequences can be detected by polymerase chain reaction from frozen tissue samples with and without myelocytic infiltration.

Assessing the roles of endogenous retrovirus EAV-HP in avian leukosis virus subgroup J emergence and tolerance

Avian leukosis virus (ALV) subgroup J is thought to have emerged through a recombination event between an unknown exogenous ALV and the endogenous retrovirus elements designated EAV-HP. All EAV-HP elements identified to date in the chicken genome show large deletions, including that of the entire pol gene. Here we report the identification of four segregating chicken EAV-HP proviruses with complete pol genes, one of which shows exceptionally high sequence identity and a close phylogenetic relationship with ALV-J with respect to the env gene. Embryonic expression of EAV-HP env has been suggested as a factor associated with immunological tolerance induction in a proportion of ALV-J-infected meat-type chickens. In support of this, env gene transcripts expressed from two of the four newly identified EAV-HP proviruses were demonstrated in chicken embryos. However, when ALV-J-infected outbred meat-type chickens were assessed, the presence of intact EAV-HP proviruses failed to directly correlate with ALV-J tolerance. This association was further examined using F(2) progeny of two inbred lines of layer chicken that differed in EAV-HP status and immunological responses to ALV-J. Immunological tolerance developed in a small proportion of F(2) progeny birds, reflecting the expected phenotypic ratio for inheritance of a double-recessive genotype; however, the status of tolerance did not show any direct correlation with the presence of the intact EAV-HP sequence. Nevertheless, identification of an intact chicken EAV-HP locus showing a uniquely close relationship to the ALV-J prototype clone HPRS-103 in the env region provides the strongest evidence of its contribution to the emergence of ALV-J by recombination.

Development of quantitative competitive-reverse transcriptase-polymerase chain reaction for detection and quantitation of avian leukosis virus subgroup J

Infection with avian leukosis virus subgroup J (ALV-J) causes severe economic losses in the broiler industry by increasing mortality, producing tumors, and decreasing weight gain in chickens. The quantitation of ALV-J is difficult because of its failure to produce a cytopathic effect in cell culture systems and the nonspecificity of antigen-capture enzyme-linked immunosorbent assay (ELISA) tests. This study was performed to develop a quantitative competitive-reverse transcriptase-polymerase chain reaction (QC-RT-PCR) method based on coamplification of ALV-J genomic RNA and a known amount of a synthesized RNA competitor. The 369 bp RNA competitor was constructed by restriction enzyme treatment of an ALV-J specific 545 bp PCR product, ligation, transformation into Escherichia coli, and in vitro transcription. The competitor contained the same amplification primer annealing sites and sequence as the original viral RNA, except that it had a 176 bp internal deletion. Coamplified RT-PCR products were visualized by electrophoresis and ethidium bromide staining, and fluorescences were quantified using computer-assisted image analysis. The sensitivity of this new QC-RT-PCR method was 25 fg of viral RNA, and 10-fold dilutions were differentiable. This method allowed absolute and relative quantification of ALV-J RNA copy numbers and was simpler than previously published methods for ALV-J quantification.

Response of white leghorn chickens of various genetic lines to infection with avian leukosis virus subgroup J

In Experiment 1, chickens from various white leghorn experimental lines were inoculated with strain ADOL-Hcl of subgroup J avian leukosis virus (ALV-J) either as embryos or at 1 day of age. At various ages, chickens were tested for ALV-J induced viremia, antibody, and packed cell volume (PCV). Also, at 4 and 10 wk of age, bursal tissues were examined for avian leukosis virus (ALV)-induced preneoplastic lesions with the methyl green-pyronine (MGP) stain. In Experiment 2, chickens harboring or lacking endogenous virus 21 (EV21) were inoculated with strain ADOL-Hcl of ALV-J at hatch. All embryo-inoculated chickens in Experiment 1 tested positive for ALV-J and lacked antibody throughout the experimental period of 30 wk and were considered viremic tolerant, regardless of line of chickens. By 10 wk of age, the incidence of ALV-J viremia in chickens inoculated with virus at hatch varied from 0 (line 0 chickens) to 97% (line 1515); no influence of ALV-J infection was noted on PCV. Results from microscopic examination of MGP-stained bursal tissues indicate that ALV-J can induce typical ALV-induced transformation in bursal follicles of white leghorn chickens. Lymphoid leukosis and hemangiomas were the most common ALV-J-induced tumors noted in chickens in Experiment 1. At termination of Experiment 2 (31 wk of age), 54% of chickens harboring EV21 were viremic tolerant compared with 5% of chickens lacking EV21 after inoculation with ALV-J at hatch. The data indicate that genetic differences among lines of white leghorn chickens, including the presence or absence of EV21, can influence response of chickens to infection with ALV-J.

Comparison of Chinese field strains of avian leukosis subgroup J viruses with prototype strain HPRS-103 and United States strains

Eight Chinese field strains of subgroup J avian leukosis viruses (ALV-J) were isolated from broilers or parent stocks during January 1999 to April 2001. One strain, SD9902, was an acute transforming virus, able to induce typical myelocytomatosis in 22-38 days after inoculation of 1-day-old meat-type chicks. The envelope protein and 3'-untranslated region (UTR) of the eight field strains were compared with the U.K. prototype HPRS-103 and several U.S. field strains isolated in 1993-97. All Chinese strains shared an almost identical deletion with the U.S. strain 4817 in the E element region of 3'-UTR when compared with the prototype HPRS-103, indicating that they have a very close phylogenic relationship. Every year, China has to import grandparent stocks of meat-type chickens, mainly from the United States. Chinese isolates should represent a part in the phylogenic tree of U.S. ALV-J evolution. Envelope protein gp85 amino acid sequence analysis demonstrated that, interestingly, all recent Chinese isolates were more closely related to HPRS-103 and the earliest U.S. isolates but not to the late U.S. isolates. The result implies that envelope gp85 may not have diverged from prototype and older strains. It is also possible that some recently imported birds could have been infected by the older viruses that were introduced in the late 1990s.

Patterns of gene expression in the developing chick thymus

Gene expression in thymic T cells during late embryogenesis and early growth in chicks was examined using cDNA microarrays. Gene expression patterns were profiled into nine clusters by using self-organizing maps (SOM) clustering analysis. The expression patterns for a set of genes confirmed current information on the development of immune response. Expression of cell surface markers (MHC class I alpha chain, MHC class II associated invariant chain, CD8 beta chain, CD18, and beta2-microglobulin), and genes involved in the innate immune response (NK lysin-like) increased with age, and these patterns were consistent with an increase in the immune responsiveness of the young chick. The expression of cytokine receptor common gamma chain (gammac), death receptor-3 (DR3), and TCR alpha chain increased up to 1 day of age and then decreased. DR3 could play a role in the apoptosis during T-cell maturation, while the differential expression of TCR genes could reflect regulation of the rearrangement of TCR genes and TCR-mediated signal transduction during T cell development. Three genes coding for previously uncharacterized proteins are included in the clusters. These gene expression profiling studies provide background information on the developing chick immune system and provide preliminary functional information on unknown proteins.

Interference between avian endogenous ev/J 4.1 and exogenous ALV-J retroviral envelopes

A new family of avian retroviral endogenous sequences designated ev/J or EAV-HP has been identified recently. Here an additional avian ev/J 4.1 endogenous sequence, ev/J 4.1 Rb, is reported. ev/J 4.1 Rb has the most extensive amino acid identity ever described for an endogenous envelope protein with the ALV-J avian leukosis virus. Here, we also demonstrate that ev/J 4.1 Rb functionally pseudotypes murine leukaemia virions and leads to a complete reciprocal interference with ALV-J envelopes. This is the first demonstration of such a high level of envelope interference between endogenous and exogenous avian retroviruses. Our results provide additional clues on the co-evolution of retroviral sequences among vertebrates.

Expression of a recombinant gag protein from endogenous avian virus and its use in screening for antibody reactivity in recipients of chick-derived vaccines

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.

Endogenous retroviruses related to jaagsiekte sheep retrovirus

Ovine betaretroviruses consist of exogenous viruses [jaagsiekte sheep retrovirus (JSRV) and enzootic nasal tumor virus, (ENTV)] associated with neoplastic diseases of the respiratory tract and 15-20 endogenous viruses (enJSRV) stably integrated in the ovine and caprine genome. Phylogenetic analysis of this group of retroviruses suggests that the enJSRV can be considered as 'modern' endogenous retroviruses with active, exogenous counterparts. Sequence analysis of JSRV, ENTV and enJSRV suggests that enJSRV do not directly contribute to the pathogenesis of ovine pulmonary adenocarcinoma (OPA) or enzootic nasal tumor through large-scale recombination events, but small-scale recombination or complementation of gene function cannot be excluded; experiments involving enJSRV-free sheep, which have not been found, would be needed to investigate this possibility. Evidence of expression of enJSRV structural proteins in tissues of the reproductive tract and lung implies that they do not have a primary role in disease. However, experimental exploitation of exogenous/endogenous retrovirus sequence differences by producing chimeras has been useful in establishing the determinants of JSRV Env-induced transformation. Even if enJSRV do not have a direct role in OPA, their expression during ontogeny or in neonatal life may impact the likelihood of exogenous JSRV infection and disease outcome via the induction of immunological tolerance. Aside from any role in disease, enJSRV loci may serve as useful genetic markers in the sheep and their frequent expression in the reproductive tract of the ewe may portend an important physiologic role in sheep.

Pathogenicity of two recombinant avian leukosis viruses

We have recently described the isolation and molecular characteristics of two recombinant avian leukosis subgroup J viruses (ALV J) with an avian leukosis virus subgroup A envelope (r5701A and r6803A). In the present study, we examined the role of the subgroup A envelope in the pathogenesis of these recombinant viruses. Chickens of line 151(5) x 7(1) were inoculated at 1 day of age with r5701A, r6803A, Rous-associated virus type 1 (RAV-1), or strain ADOL-Hcl of ALV-J. At 2, 4, 10, 18, and 32 wk postinoculation (PI), chickens were tested for avian leukosis virus (ALV)-induced viremia, shedding, and neutralizing antibodies. All except one chicken inoculated with the recombinant viruses (98%) developed neutralizing antibodies by 10 wk PI compared with only 16% and 46% of the ADOL-Hcl and RAV-1-inoculated birds, respectively. ALV-induced tumors and mortality in the two groups inoculated with recombinant viruses were different. The incidence of tumors in groups inoculated with r5701A or RAV-1 was 100% compared with only 9% in the groups inoculated with r6803A or ADOL-Hcl. The data suggest that differences in pathogenicity between the two recombinant viruses might be due to differences in the sequence of the 3' untranslated region (presence or absence of the E element), and, therefore, not only the envelope but also other elements of the viral genome play an important role in the pathogenesis of ALV.

Occurrence of subgroup J avian leukosis virus in Taiwan

There are three grandparent farms for three different chicken breeds in Taiwan. One of these farms, populated by breast meat yield chickens (yield type), suffered from a severe subgroup J avian leukosis virus (ALV-J) infection in mid-1997. The affected flocks at that farm had a weekly mortality of more than 1% and a 15% drop in egg production. The broilers from that breed had a 10% condemnation rate during the first week of age, and 5% of the remaining broilers were stunted afterwards. Some chickens had myeloid leukosis lesions at 6 weeks old. Their survivability was about 85%. However, chickens at the other two grandparent farms, populated with non-yield chickens (regular type), were also infected by ALV-J and showed myeloid leukosis. However, chickens at these farms produced progeny whose survivability reached more than 95%. ALV-J caused greater economic loss in yield type chickens than in regular type chickens in Taiwan.

The viral envelope is a major determinant for the induction of lymphoid and myeloid tumours by avian leukosis virus subgroups A and J, respectively

Among the six envelope subgroups of avian leukosis virus (ALV) that infect chickens, subgroups A (ALV-A) and J (ALV-J) are the most pathogenic and widespread among commercial chicken populations. While ALV-A is predominantly associated with lymphoid leukosis (LL) and less frequently with erythroblastosis (EB), ALV-J mainly induces tumours of the myeloid lineage. In order to examine the basis for the lineage specificity of tumour induction by these two ALV subgroups, we constructed two chimeric viruses by substituting the env genes into the reciprocal proviral clones. The chimeric HPRS-103(A) virus carrying the subgroup A env gene is identical to ALV-J prototype virus HPRS-103 except for the env gene, and the chimeric RCAS(J) virus carrying the subgroup J env gene is identical to the parent replication-competent ALV-A vector RCAS except for the env gene. In experimentally inoculated chickens, HPRS-103(A) virus induced LL and EB similar to ALV-A isolates such as RAV-1, while RCAS(J) virus induced myeloid leukosis (ML) and EB, similar to ALV-J, suggesting that the env gene is the major determinant for the lineage-specific oncogenicity. There were genetic differences in susceptibility to tumour induction between line 0 and line 15(I) chickens, indicating that in addition to the env gene, other viral or host factors could also serve as determinants for oncogenicity. Induction of both LL and ML by the two chimeric viruses occurred through the activation of c-myc, while the EB tumours were induced by activation of the c-erbB oncogene.

Segregation of EAV-HP ancient endogenous retroviruses within the chicken population

Avian leukosis virus subgroup J (ALV-J), an exogenous avian retrovirus, is thought to have evolved by recombination with the highly identical env gene of the endogenous avian retrovirus EAV-HP. Embryonic expression of EAV-HP env has been suggested to be associated with the induction of immunological tolerance, a feature observed in a significant proportion of meat-type chickens infected with ALV-J. In support of this hypothesis, we demonstrate that EAV-HP loci, some of which could be associated with tolerance, are still segregating within the chicken population.

Identification and characterization of recombinant subgroup J avian leukosis viruses (ALV) expressing subgroup A ALV envelope

Three recombinant avian leukosis subgroup J viruses, ADOL 5701A, ADOL 5701ADelta, and ADOL 6803A, carrying a subgroup A envelope have been isolated and characterized. These viruses were identified by their ability to replicate in DF-1/J, a recombinant chicken embryo fibroblast (CEF) cell line expressing the subgroup J envelope that is resistant to subgroup J replication. Flow cytometric analysis of DF-1/J cells infected with ADOL 5701 and ADOL 6803, two subgroup J isolates, indicated cross-reactivity with subgroup A chicken polyclonal serum. Based on published sequences of subgroups A and J isolates, we designed a series of primers to PCR amplify the envelope and LTR of these viruses. PCR products were obtained when the forward primer was specific for subgroup A gp85 envelope protein gene and the reverse primer was specific for subgroup J LTR. Sequence analysis of the PCR products indicated that these viruses had a subgroup A gp85, a subgroup E gp37, and a subgroup J LTR. Interestingly, these viruses had previously been propagated in CEF from the alv6 chicken line, a line that carries a replication defective recombinant endogenous virus expressing a subgroup A envelope (RAV 0-A(1)). Sequence analysis of RAV 0-A(1) gp85 and gp37 envelope proteins indicated that they were almost identical to those of the recombinants ADOL 5701A and ADOL 6803A. These results indicate that these three recombinant viruses arose by recombination between exogenous subgroup J isolates and a recombinant defective endogenous virus with subgroup A envelope.

Molecular cloning and functional analysis of three type D endogenous retroviruses of sheep reveal a different cell tropism from that of the highly related exogenous jaagsiekte sheep retrovirus

Integrated into the sheep genome are 15 to 20 copies of type D endogenous loci that are highly related to two exogenous oncogenic viruses, jaagsiekte sheep retrovirus (JSRV) and enzootic nasal tumor virus (ENTV). The exogenous viruses cause infectious neoplasms of the respiratory tract in small ruminants. In this study, we molecularly cloned three intact type D endogenous retroviruses of sheep (enJS56A1, enJS5F16, and enJS59A1; collectively called enJRSVs) and analyzed their genomic structures, their phylogenies with respect to their exogenous counterparts, their capacity to form viral particles, and the expression specificities of their long terminal repeats (LTRs). In addition, the pattern of expression of enJSRVs in vivo was studied by in situ hybridization. All of the three enJSRV proviruses had open reading frames for at least one of the structural genes. In particular, enJS56A1 had open reading frames for all structural genes, but it could not assemble viral particles when highly expressed in human 293T cells. We localized the defect for viral assembly in the first two-thirds of the gag gene by making a series of chimeras between enJS56A1 and the exogenous infectious molecular clone JSRV(21). Phylogenetic analysis distinguished five ovine type D retroviruses: enJSRV groups A and B, ENTV, and two exogenous JSRV groups (African versus United Kingdom/North America isolates). Transient transfection assays indicated that the LTRs of the three enJSRVs were not preferentially active in differentiated lung epithelial cells. This suggests that the pulmonary tropic JSRV developed from a type D retrovirus that did not have lung specificity. Consistent with this, in situ hybridization of a panel of normal ovine tissues revealed high expression of enJSRV mRNA in the luminal epithelium and glandular epithelium of the uterus; lower expression was localized in the lamina propria of the gut and in the bronchiolar epithelium of the lungs.

Hypervariability in the envelope genes of subgroup J avian leukosis viruses obtained from different farms in the United States

Avian leukosis virus, subgroup J (ALV-J), has a wide host range, preferentially infecting meat-type birds, and produces a high incidence of myelocytomatosis and nephromas. Using the published sequences from HPRS-103 (ALV-J isolated in 1989 in Great Britain), we designed a set of PCR primers that amplified proviral DNA from nine U.S. field samples. The primers were specific for ALV-J, not amplifying DNA from uninfected cells or cells infected with ALV subgroups A-E. These primers expanded a 2.4-kb fragment that encompasses gp85, gp37, the E element, and most of the 3' LTR. We also developed a set of PCR primers that amplified a 2.1-kb fragment from ALV-J-infected cells and a 1.6-kb fragment from uninfected ev- chicken embryo fibroblasts (Line 0). Upon cloning and DNA sequencing, we determined that the 2.1- and 1.6-kb fragments contained ALV-J gp85- and gp37-like sequences. Comparison of the amino acid sequences demonstrated that the Line 0 sequences were 97.5% identical with the gp85 and gp37 of HPRS-103 and somewhat less identical with the other nine U.S. isolates. This suggests that the envelope genes of ALV-J may have arisen as a result of a recombination event between exogenous ALV and Line 0-like sequences in the chicken. Phylogenetic analysis also showed that the U.S. field isolates were closely related to one another and more distantly related to the European HPRS-103. The pattern of mutations in the U.S. field isolates suggests that the U.S. strains are slowly drifting away from their progenitor Line 0-like sequences. The development of effective vaccines and diagnostic tests is likely to become more problematic as the viruses continue to mutate.

Avian endogenous retrovirus EAV-HP shares regions of identity with avian leukosis virus subgroup J and the avian retrotransposon ART-CH

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.

A genetically engineered cell line resistant to subgroup J avian leukosis virus infection (C/J)

A cell line (DF-1¿J) expressing the envelope protein isolated from the ADOL-Hc1 strain of the avian leukosis virus subgroup J (ALV-J) was used to analyze receptor interference to six different isolates of ALV-J as well as ALV subgroups A-D. The traditional gag-specific enzyme-linked immunosorbent assay (ELISA) as well as flow cytometry was used to evaluate viral infection. The parental cell line (DF-1) was susceptible to all ALV subgroups tested while the DF-1¿J cell line was selectively resistant to the subgroup J isolates. The DF-1¿J cell line was resistant to infection by all six ALV-J isolates as determined using the gag-specific ELISA. There was no interference with the other ALV subgroups (A-D) induced by the expression of the ADOL-Hcl envelope. The ALV-J isolates used in this analysis are serologically distinct when analyzed by flow cytometry. Convalescent sera to ADOL-Hcl cross-reacts with all of the ALV-J isolates tested; however, sera to HPRS-103 did not bind to four of the six isolates. Based on the intensity and differential binding of these antisera using flow cytometry, the six ALV-J isolates used can be grouped into four categories. Thus the DF-1¿J cell line is resistant to infection by a serologically and genetically diverse group of ALV-J isolates and should be useful as a diagnostic tool.

Avian leukosis virus subgroup J: a rapidly evolving group of oncogenic retroviruses

A strain of avian leukosis virus (ALV) belonging to a new envelope subgroup J was isolated in the UK in 1988 from meat-type chickens. The disease caused by the members of this subgroup has since spread very rapidly worldwide and has become one of the major problems facing the broiler meat industry. Molecular characterisation of HPRS -103, the prototype of subgroup J, has shown that it has a structure of a typical ALV with gag, pol and env genes. However the env gene was distinct from that of other ALV s and was closely related to that of novel endogenous retroviral elements designated EAV - HP. As other regions of the genome were closely related to ALV s, it is believed that ALV-J has evolved by recombination with the env sequences of EAV - HP. ALV-J has a tropism for myeloid cells, a feature that may be associated with its ability to induce myeloid leukosis. Recent data show that ALV -J isolates evolve rapidly resulting in sequence changes within the variable regions of the env gene leading to antigenic variation. Eradication programmes established for other subgroups are proving to be effective in eradicating ALV-J from infected flocks.

Genome structure and expression of the ev/J family of avian endogenous viruses

We recently reported the identification of sequences in the chicken genome that show over 95% identity to the novel envelope gene of the subgroup J avian leukosis virus (S. J. Benson, B. L. Ruis, A. M. Fadly, and K. F. Conklin, J. Virol. 72:10157-10164, 1998). Based on the fact that the endogenous subgroup J-related env genes were associated with long terminal repeats (LTRs), we concluded that these LTR-env sequences defined a new family of avian endogenous viruses that we designated the ev/J family. In this report, we have further characterized the content and expression of the ev/J proviruses. The data obtained indicate that there are between 6 and 11 copies of ev/J proviruses in all chicken cells examined and that these proviruses fall into six classes. Of the 18 proviruses examined, all share a high degree of sequence identity and all contain an internal deletion that removes all of the pol gene and various amounts of gag and env gene sequences. Sequencing of the gag genes, LTRs, and untranslated regions of several ev/J proviruses revealed a high level of identity between isolates, indicating that they have not undergone significant sequence variation since their introduction into the avian germ line. Although the ev/J gag gene showed a relatively weak relationship (46% identity and 61% similarity at the amino acid level) to that of the avian leukosis-sarcoma virus family, it retains several sequences of demonstrated importance for virus assembly, budding, and/or infectivity. Finally, evidence was obtained that at least some members of the ev/J family are expressed and, if translated, could encode Gag- and Env-related polypeptides.