RESUMEN
Subgroup K avian leukosis virus (ALV-K) is a new subgroup of avian leukosis virus (ALV) that was first defined in 2012 and has been become prevalent in Chinese native chickens in recent years. An in-depth analysis of the genetic diversity of ALV-K was performed in the study. By Blast analysis, the env gene and the sequences of the 25 ALV-K isolates we isolated were found to be closely related to the isolates from Guangdong, Hebei, Jiangsu, and Hubei provinces, China. Further eighty-nine sequences of the gp85 gene of ALV-K strains available were used in the phylogenetic and genetic distance analyses for the classification. ALV-K was divided into two second-order clades (Clades 1.1 and 1.2) and three third-order clades (Clades 1.2.1, 1.2.2, and 1.2.3), indicating that not only 1.1 and 1.2.3, the two old clades which are prevalent in Japan, but also two new clades (1.2.1, 1.2.2), are co-prevalent in China. The representative strains of each clade were defined for the first time. Notably, Clade 1.2.2 was found to have a deletion of an amino acid residue in the gp85 gene, which was obviously different from Clades 1.1, 1.2.1, and 1.2.3. The proposed classification method will facilitate future studies of ALV-K epidemiology and the comparison of sequences obtained across the world. The first global comprehensive molecular epidemiological analysis was accomplished on the emerging ALV-K.
RESUMEN
Avian hepatitis E virus (HEV) is a major pathogen associated with hepatitis splenomegaly syndrome in chickens and has been reported in China. Phylogenetic trees, Bayesian analysis, positive selection sites screening, and recombination analysis were first used to comprehend the global avian HEVs. All the avian HEV strains, including a new isolate named GX20A1 got from Donglan Black chicken in Guangxi, China, were uniformly defined into four genotypes, and GX20A1, belongs to Genotype 3. The topology of the phylogenetic tree based on the sequences of a 339-bp fragment (coding the helicase) in open reading frame (ORF) 1 of the avian HEVs was consistent with that based on the full-genome sequence. The estimated evolution rate of avian HEVs is 2.73 × 10-3 substitution/site/year (95% confidence interval (CI): 8.01 × 10-4-4.91 × 10-3), and the estimated genetic diversity of the strains experienced a declining phase from 2010 to 2017 and stabilized after 2017. It was further found that the Genotype 3 HEVs, including isolates from Hungary and China, likely originated in the 1930s. Notably, GX20A1 was gathered in the same branch with a Genotype 3 Guangdong isolate CaHEV-GDSZ01, which appeared earlier than GX20A1. In addition, two positive selection sites were identified, one for each of ORF1 and ORF2. Overall, the study revealed that avian HEVs were uniformly defined into four genotypes, and a 339-bp fragment in ORF1 of the viral genome could be used for the classification. A Genotype 3 isolate GX20A1 was first found from Donglan Black chicken and most likely originated from Guangdong.
RESUMEN
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 ß-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.
