Discovery of an expanded set of avian leukosis subgroup E proviruses in chickens using Vermillion, a novel sequence capture and analysis pipeline [corrected]

Avian Leukosis: Will We Be Able to Get Rid of It?

Avian leukosis viruses (ALVs) have been virtually eradicated from commercial poultry. However, some niches remain as pockets from which this group of viruses may reemerge and induce economic losses. Such is the case of fancy, hobby, backyard chickens and indigenous or native breeds, which are not as strictly inspected as commercial poultry and which have been found to harbor ALVs. In addition, the genome of both poultry and of several gamebird species contain endogenous retroviral sequences. Circumstances that support keeping up surveillance include the detection of several ALV natural recombinants between exogenous and endogenous ALV-related sequences which, combined with the well-known ability of retroviruses to mutate, facilitate the emergence of escape mutants. The subgroup most prevalent nowadays, ALV-J, has emerged as a multi-recombinant which uses a different receptor from the previously known subgroups, greatly increasing its cell tropism and pathogenicity and making it more transmissible. In this review we describe the ALVs, their different subgroups and which receptor they use to infect the cell, their routes of transmission and their presence in different bird collectivities, and the immune response against them. We analyze the different systems to control them, from vaccination to the progress made editing the bird genome to generate mutated ALV receptors or selecting certain haplotypes.

Short communication: diversity of endogenous avian leukosis virus subgroup E elements in 11 chicken breeds

Avian leukosis virus subgroup E (ALVE) as a kind of endogenous retroviruses extensively exists in chicken genome. The insertion of ALVE has some effects on chicken production traits and appearance. Most of the work on ALVEs has been done with commercial breeds. We present here an investigation of ALVE elements in seven Chinese domestic breeds and four standard breeds. Firstly, we established an ALVE insertion site dataset by using the obsERVer pipeline to identify ALVEs from whole-genome sequence data of eleven chicken breeds, seven Chinese domestic breeds, including Beijing You (BY), Dongxiang (DX), Luxi Game (LX), Shouguang (SG), Silkie (SK), Tibetan (TB) and Wenchang (WC), four standard breeds, including White Leghorn (WL), White Plymouth Rock (WR), Cornish (CS), and Rhode Island Red (RIR). A total of 37 ALVE insertion sites were identified and 23 of them were novel. Most of these insertion sites were distributed in intergenic regions and introns. We then used locus-specific PCR to validate the insertion sites in an expanded population with 18~60 individuals in each breed. The results showed that all predicted integration sites in 11 breeds were verified by PCR. Some ALVE insertion sites were breeds specific, and 16 out of 23 novel ALVEs were found in only one Chinese domestic chicken breed. We randomly selected three ALVE insertions including ALVE_CAU005, ALVE_ros127, and ALVE_ros276, and obtained their insertion sequences by long-range PCR and Sanger sequencing. The insertion sequences were all 7525 bp, which were full-length ALVE insertion and all of them were highly homologous to ALVE1 with similarity of 99%. Our study identified the distribution of ALVE in 11 chicken breeds, which expands the current research on ALVE in Chinese domestic breeds.

The impact of endogenous Avian Leukosis Viruses (ALVE) on production traits in elite layer lines

Avian Leukosis Virus subgroup E (ALVE) integrations are endogenous retroviral elements found in the chicken genome. The presence of ALVE has been reported to have negative impacts on multiple traits, including egg production and body weight. The recent development of rapid, inexpensive and specific ALVE detection methods has facilitated their characterization in elite commercial egg production lines across multiple generations. The presence of 20 ALVE was examined in 8 elite lines, from 3 different breeds. Seventeen of these ALVE (85%) were informative and found to be segregating in at least one of the lines. To test for an association between specific ALVE inserts and traits, a large genotype by phenotype study was undertaken. Genotypes were obtained for 500 to 1500 males per line, and the phenotypes used were sire-daughter averages. Phenotype data were analyzed by line with a linear model that included the effects of generation, ALVE genotype and their interaction. If genotype effect was significant, the number of ALVE copies was fitted as a regression to estimate additive ALVE gene substitution effect. Significant associations between the presence of specific ALVE inserts and 18 commercially relevant performance and egg quality traits, including egg production, egg weight and albumen height, were observed. When an ALVE was segregating in more than one line, these associations did not always have the same impact (negative, positive or none) in each line. It is hypothesized that the presence of ALVE in the chicken genome may influence production traits by 3 mechanisms: viral protein production may modulate the immune system and impact overall production performance (virus effect); insertional mutagenesis caused by viral integration may cause direct gene alterations or affect gene regulation (gene effect); or the integration site may be within or adjacent to a quantitative trait region which impacts a performance trait (linkage disequilibrium, marker effect).

Identification and characterisation of endogenous Avian Leukosis Virus subgroup E (ALVE) insertions in chicken whole genome sequencing data

Background

Endogenous retroviruses (ERVs) are the remnants of retroviral infections which can elicit prolonged genomic and immunological stress on their host organism. In chickens, endogenous Avian Leukosis Virus subgroup E (ALVE) expression has been associated with reductions in muscle growth rate and egg production, as well as providing the potential for novel recombinant viruses. However, ALVEs can remain in commercial stock due to their incomplete identification and association with desirable traits, such as ALVE21 and slow feathering. The availability of whole genome sequencing (WGS) data facilitates high-throughput identification and characterisation of these retroviral remnants.

Results

We have developed obsERVer, a new bioinformatic ERV identification pipeline which can identify ALVEs in WGS data without further sequencing. With this pipeline, 20 ALVEs were identified across eight elite layer lines from Hy-Line International, including four novel integrations and characterisation of a fast feathered phenotypic revertant that still contained ALVE21. These bioinformatically detected sites were subsequently validated using new high-throughput KASP assays, which showed that obsERVer was highly precise and exhibited a 0% false discovery rate. A further fifty-seven diverse chicken WGS datasets were analysed for their ALVE content, identifying a total of 322 integration sites, over 80% of which were novel. Like exogenous ALV, ALVEs show site preference for proximity to protein-coding genes, but also exhibit signs of selection against deleterious integrations within genes.

Conclusions

obsERVer is a highly precise and broadly applicable pipeline for identifying retroviral integrations in WGS data. ALVE identification in commercial layers has aided development of high-throughput diagnostic assays which will aid ALVE management, with the aim to eventually eradicate ALVEs from high performance lines. Analysis of non-commercial chicken datasets with obsERVer has revealed broad ALVE diversity and facilitates the study of the biological effects of these ERVs in wild and domesticated populations.

Diversity of endogenous avian leukosis virus subgroup E (ALVE) insertions in indigenous chickens

Background

Avian leukosis virus subgroup E (ALVE) insertions are endogenous retroviruses (ERV) that are restricted to the domestic chicken and its wild progenitor. In commercial chickens, ALVE are known to have a detrimental effect on productivity and provide a source for recombination with exogenous retroviruses. The wider diversity of ALVE in non-commercial chickens and the role of these elements in ERV-derived immunity (EDI) are yet to be investigated.

Results

In total, 974 different ALVE were identified from 407 chickens sampled from village populations in Ethiopia, Iraq, and Nigeria, using the recently developed obsERVer bioinformatics identification pipeline. Eighty-eight percent of all identified ALVE were novel, bringing the known number of ALVE integrations to more than 1300 across all analysed chickens. ALVE content was highly lineage-specific and populations generally exhibited a large diversity of ALVE at low frequencies, which is typical for ERV involved in EDI. A significantly larger number of ALVE was found within or near coding regions than expected by chance, although a relative depletion of ALVE was observed within coding regions, which likely reflects selection against deleterious integrations. These effects were less pronounced than in previous analyses of chickens from commercial lines.

Conclusions

Identification of more than 850 novel ALVE has trebled the known diversity of these retroviral elements. This work provides the basis for future studies to fully quantify the role of ALVE in immunity against exogenous ALV, and development of programmes to improve the productivity and welfare of chickens in developing economies.

Endogenous avian leukosis virus subgroup E elements of the chicken reference genome

The chicken reference genome contains 2 endogenous avian leukosis virus subgroup E (ALVE) insertions, but gaps and unresolved repetitive sequences in previous assemblies have hindered their precise characterization. Detailed analysis of the most recent reference genome (GRCg6a) now shows both ALVEs within contiguous chromosome assemblies for the first time. ALVE6 (ALVE-JFevA) and ALVE-JFevB are both located on chromosome 1, with ALVE6 close to the p-arm telomere. ALVE-JFevB is a structurally intact element containing the ALVE gag, pol, and env genes and is capable of forming replication competent viruses. In contrast, ALVE6 contains a 3,352 bp 5′ truncation and lacks the entire 5′ long terminal repeat and gag gene. Despite this, ALVE6 remains able to produce intact envelope protein, likely due to a mutation in the recognition site for a known inhibitory miRNA (miR-155). Whole genome resequencing data sets from layers, broilers, and 3 independent sources of wild-caught red junglefowl were surveyed for the presence of each of these reference genome ALVEs. ALVE-JFevB was found in no other chicken or red junglefowl genomes, whereas ALVE6 was identified in some layers, broilers, and native breeds but not within any other red junglefowl genome. Improved assembly contiguity has facilitated better characterization of the 2 ALVEs of the chicken reference genome. However, both the limited ALVE content and unique presence of ALVE-JFevB suggests that the reference individual is unrepresentative of ancestral Gallus gallus ALVE diversity.

Domestic chickens activate a piRNA defense against avian leukosis virus

PIWI-interacting RNAs (piRNAs) protect the germ line by targeting transposable elements (TEs) through the base-pair complementarity. We do not know how piRNAs co-evolve with TEs in chickens. Here we reported that all active TEs in the chicken germ line are targeted by piRNAs, and as TEs lose their activity, the corresponding piRNAs erode away. We observed de novo piRNA birth as host responds to a recent retroviral invasion. Avian leukosis virus (ALV) has endogenized prior to chicken domestication, remains infectious, and threatens poultry industry. Domestic fowl produce piRNAs targeting ALV from one ALV provirus that was known to render its host ALV resistant. This proviral locus does not produce piRNAs in undomesticated wild chickens. Our findings uncover rapid piRNA evolution reflecting contemporary TE activity, identify a new piRNA acquisition modality by activating a pre-existing genomic locus, and extend piRNA defense roles to include the period when endogenous retroviruses are still infectious.

DOI:http://dx.doi.org/10.7554/eLife.24695.001

Viruses called retroviruses can infect animal cells and merge their genetic information with those of the animal causing damage to the animal’s genetic blueprints. Once retroviruses are integrated into a cell they can sometimes get passed down through the generations over the centuries. Almost half of the human genetic code, for example, is made from ancient retroviruses and other foreign sequences. Over time many of these ancient viruses lost the ability to infect other cells and became trapped within cells but they can still jump out and damage the animal’s genetic code under certain circumstances. These trapped foreign sequences are called transposable elements.

Animal cells produce molecules called piRNAs to shut down transposable elements. Most piRNAs are produced from genetic information that originally came from integrated retroviruses and that has been hijacked to defend the cell, a similar strategy as Crisper system in bacteria. Domestic chickens produce piRNAs against a virus called avian leukosis virus (or ALV for short) – which commonly infects domestic fowl. The virus also infected the wild ancestors of chickens, known as red jungle fowl, but these birds do not produce piRNAs. This provides an ideal setting to study the evolution of piRNAs in an animal that is not too distantly related to humans (chickens and humans both have backbones, and are therefore both warm-blooded vertebrates).

Sun et al. examined cells from the testicles of domestic chickens and red jungle fowl as an example of the role of piRNAs in protecting genetic information in vertebrates. The investigation revealed that piRNAs against all previously trapped viruses in the chicken’s genetic code are produced in chickens to stop them from causing more damage. Sun et al. also observed the creation of piRNAs in chickens in response to ALV that had not yet become trapped in the chicken’s genetic code. Importantly, the piRNAs could control these retroviruses while they were still infectious.

The experiments also revealed that piRNAs against ALV are produced from a single copy of ALV that is found in both domestic and wild chickens. The results showed that cells can produce new piRNAs using these pre-existing viral copies within their own genetics. This illustrates that production of piRNA from existing genetic material can be activated in response to certain cues.

Further work will seek to discover how existing genetic information becomes a source of piRNAs. In the United States, 8 billion domestic chickens are consumed each year, and a better understanding of how these birds defend themselves against viral infections could increase the productivity of the poultry industry around the world. Moreover, because other viruses trapped in the chicken’s genetic code are related to similar viruses in humans, future discoveries made in this area could help to guide research that will benefit human health as well.

DOI:http://dx.doi.org/10.7554/eLife.24695.002