Molecular characteristics of avian leukosis viruses isolated from indigenous chicken breeds in Yunnan Province, Southwestern China

Abstract

Indigenous chicken breeds have a large market share in China due to their superior production traits, including high meat quality and disease resistance. Yunnan Province is recognized as a major source of domestic chickens globally and boasts a diverse array of indigenous chicken resources. Avian leukosis virus (ALV) induces various tumors and immunosuppression, endangering the poultry industry. However, the prevalence of ALV infection among indigenous chickens in Yunnan Province remains unclear. In this study, we aimed to investigate the presence of ALV in these breeds. To this end, we collected 1,470 plasma samples from six indigenous chicken breeds in Yunnan province, 309 of which tested positive. The results confirmed the presence of exogenous ALV in local chicken, with a positivity rate ranging from 8.20 %-41.46 %. Furthermore, eight exogenous ALV isolates were successfully identified: four ALV subtype J (ALV-J) strains, three ALV subtype A (ALV-A) strains and one ALV subtype B (ALV-B) strain. The four ALV-J strains share relatively high sequence identity (99.55 %-99.80 %) with the GX14ZS14 strain isolated from Guangxi in 2014 and was closely related to the prototype strain HPRS103 and belongs to clade 1.1. Several substitutions were observed in gp85 proteins in the three ALV-A and ALV-B strains isolated in this study. Additionally, the four ALV-J strains exhibited 203 bp deletions in the rTM and DR1 regions, a feature commonly observed in viruses in clades 1.2 and 1.3. Overall, this study confirmed the presence of multiple ALVs in these six indigenous chicken breeds from Yunnan Province. This study provides molecular characterization of ALV in indigenous chicken breeds in Yunnan Province and provides a reference for the further eradication of ALV in China. The complex background of ALV infection highlights the urgent need for intensifying eradication efforts.

Keywords: Avian leukemia virus; Genetic diversity; Molecular characterization; Yunnan local chicken.

Fig. 1

Genetic analysis of ALVs isolated from local chickens in Yunnan province. (A) Phylogenetic analysis based on gp85 gene sequences of eight ALV isolates from local chickens in Yunnan and 35 reference sequences, using the maximum likelihood method with 1000 bootstrap replicates. The eight strains isolated in this study are indicated in red. (B) Heatmap of nucleotide sequence similarity for the eight isolates, with identity values represented on a progressive color scale from 40 %–100 %.

Fig. 2

Genetic analysis of ALV-J viruses isolated from local chickens. (A) Phylogenetic analysis based on gp85 sequences of 79 ALV-J viruses isolated from local chickens using the maximum likelihood method with 1000 bootstrap replicates. The ALV-J isolates isolated in this study are indicated in red. (B) Heatmap displaying similarity analysis for the 79 ALV-J viruses isolated from local chickens (top right: amino acid sequence similarity; bottom left: nucleotide sequence similarity), with identity values represented by a progressive color scale ranging from 80 %–100 %.

Fig. 3

Characteristics of the 3′ UTR of ALV-J isolates in this study. (A) Comparative analysis of nucleotide deletions in the 3′ UTR of ALV-J isolates from clades 1.1, 1.2, and 1.3 with ALV-J strains isolated in this study. (B) Detailed comparison of 3′ UTR nucleotide deletions specifically within clade 1.1. The deletions are indicated in gray.