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. 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. 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.

中文翻译：

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土著鸡中内源性禽白血病病毒E亚组（ALVE）的多样性。

禽白血病E亚组（ALVE）插入是仅限于家禽及其野生祖细胞的内源性逆转录病毒（ERV）。在市售鸡中，已知ALVE对生产率有不利影响，并提供与外源逆转录病毒重组的来源。非商业性鸡中ALVE的广泛多样性以及这些元素在ERV衍生的免疫（EDI）中的作用尚待研究。使用最新开发的obsERVer生物信息学识别流程，从埃塞俄比亚，伊拉克和尼日利亚村庄人口的407只鸡中总共识别出974种不同的ALVE。在所有鉴定出的ALVE中，有88％是新颖的，在所有分析的鸡中，已知的ALVE整合数量已超过1300。ALVE含量是高度特定于谱系的，群体在低频下通常表现出很大的ALVE多样性，这是参与EDI的ERV的典型特征。虽然在编码区域内或附近发现了ALVE的相对耗竭，但在编码区域内或附近发现的ALVE数量明显多于偶然，这可能反映了针对有害整合的选择。这些影响不如以前对商品线鸡的分析明显。超过850种新型ALVE的鉴定使这些逆转录病毒元件的已知多样性增加了三倍。这项工作为今后的研究奠定了基础，以充分量化ALVE在抵抗外源ALV的免疫力中的作用，并为发展中经济体开发提高鸡的生产力和福利的计划提供依据。