The Emergence, Diversification, and Transmission of Subgroup J Avian Leukosis Virus Reveals that the Live Chicken Trade Plays a Critical Role in the Adaption and Endemicity of Viruses to the Yellow-Chickens

Abstract

The geographical spread and inter-host transmission of the subgroup J avian leukosis virus (ALV-J) may be the most important issues for epidemiology. An integrated analysis, including phylogenetic trees, homology modeling, evolutionary dynamics, selection analysis and viral transmission, based on the gp85 gene sequences of the 665 worldwide ALV-J isolates during 1988-2020, was performed. A new Clade 3 has been emerging and was evolved from the dominating Clade 1.3 of the Chinese Yellow-chicken, and the loss of a α-helix or β-sheet of the gp85 protein monomer was found by the homology modeling. The rapid evolution found in Clades 1.3 and 3 may be closely associated with the adaption and endemicity of viruses to the Yellow-chickens. The early U.S. strains from Clade 1.1 acted as an important source for the global spread of ALV-J and the earliest introduction into China was closely associated with the imported chicken breeders in the 1990s. The dominant outward migrations of Clades 1.1 and 1.2, respectively, from the Chinese northern White-chickens and layers to the Chinese southern Yellow-chickens, and the dominating migration of Clade 1.3 from the Chinese southern Yellow-chickens to other regions and hosts, indicated that the long-distance movement of these viruses between regions in China was associated with the live chicken trade. Furthermore, Yellow-chickens have been facing the risk of infections of the emerging Clades 2 and 3. Our findings provide new insights for the epidemiology and help to understand the critical factors involved in ALV-J dissemination. IMPORTANCE Although the general epidemiology of ALV-J is well studied, the ongoing evolutionary and transmission dynamics of the virus remain poorly investigated. The phylogenetic differences and relationship of the clades and subclades were characterized, and the epidemics and factors driving the geographical spread and inter-host transmission of different ALV-J clades were explored for the first time. The results indicated that the earliest ALV-J (Clade 1.1) from the United States, acted as the source for global spreads, and Clades 1.2, 1.3 and 3 were all subsequently evolved. Also the epidemiological investigation showed that the early imported breeders and the inter-region movements of live chickens facilitated the ALV-J dispersal throughout China and highlighted the needs to implement more effective containment measures.

Keywords: Avian leukosis virus subgroup J; clades/subclades; diversification; emergence; geographical spread; gp85 gene; inter-host transmission; live chicken trade.

FIG 1

Geographic region and host distribution of ALV-J viruses during 1988–2020. Geographic region distribution of ALV-J virus in the world (A) and in China (B). Host distribution in 7 different regions of China (C). W: White-chickens; L: layers; Y: Yellow-chickens; N: unrecorded breeds; 817: a crossbred meat-type chicken; WB: wild birds; G: gamecock; V: contaminated live vaccines.

FIG 2

Phylogenetic analysis was performed based on the nucleotide sequences of ALV-J gp85 gene. (A) Two radial trees were constructed based on the gp85 sequences (n = 572) to identify the first-order clades with IQ-TREE (right) and RAxML (left) software, respectively. (B) Two radial trees were constructed based on the gp85 sequences (n = 530) to identify the second-order clades of Clade 1 with IQ-TREE (right) and RAxML (left) software, respectively. The trees were drawn to scale, with branch lengths measured in the number of substitutions per site.

FIG 3

Display the differences on the amino acid (aa) residuals of the gp85 protein monomer in different Clades by three-dimensional structure. (A) Display of aa-mutation residuals at position 40–79 of Clades 1 and 2, and at position 117–194 of Clades 1 and 3, respectively; (B) Three-dimensional structure of strain HPRS103 gp85 protein from Clade 1; (C) Three-dimensional structure of gp85 protein of the strain AF88 from Clade 2. (D) Three-dimensional structure of strain HPRS103 from Clade 1; (E) Three-dimensional structure of strain GD17ZQ08 from Clade 3; (F) Three-dimensional structure of strain JX19DX14 from Clade 3.

FIG 4

Evolution of ALV-J viruses and structural mapping of the positively selected sites on the gp85 molecule. (A) Bayesian phylogenetic analysis of the 257 sequences of gp85 in Clade 1 during 1988–2020; (B) Bayesian phylogenetic analysis of the 24 sequences of gp85 in Clade 2 during 1997–2020; Bayesian Skygrid demographic reconstruction of Clades 1 (C) and 2 (D), respectively. The vertical axis shows the effective number of infections (Ne) multiplied by mean viral generation time (τ). The solid line and shaded region represent the median and 95% credibility interval, respectively, of the inferred N_eτ through time. Three-dimensional structures of the gp85 of strains HPRS103 (E), JS09GY2 (F), GD14J2 (G), GX10GL08 (H), and AF88 (I). Mapping of positively selected aa-sites identified onto the three-dimensional structure of the gp85, and their locations in the three-dimensional structure are indicated with blue (E-I).

FIG 5

Spatial diffusion and host transmission of the ALV-J Clades 1.1, 1.2, 1.3 and 2 viruses. Spatial diffusion pathways and histograms of total number of state transitions (A, B, E, F, I, J, M and N); Host transmission pathways and histograms of total number of state transitions (C, D, G, H, K, L, O and P). Green arrows, supported rates with 3 ≤ BF < 10; blue arrows, strongly supported rates with 10 ≤ BF < 100; purple arrows, very strongly supported rates with 100 ≤ BF < 1,000 and red arrows, decisive rates with BF ≥ 1,000. W: White-chickens; L: layers; Y: Yellow-chickens; WB: wild bird; 817: a crossbred meat-type chicken; N: unrecorded breeds.