Genome characterization of the Caprine arthritis-encephalitis virus in China: A retrospective genomic analysis of the earliest Chinese isolates

Caprine arthritis-encephalitis virus (CAEV) is an under-studied virus infecting caprines and ovines worldwide. Over the last four decades, CAEV has spread in China, obtaining genomic data on CAEV strains circulating in China is of importance for developing diagnostic methods and eradicating associated diseases. However, there is limited information on the genome, including characterizations, and the probable origin. This work aimed to characterize Chinese CAEV genomes and population structures. Five CAEV strains isolated from infected dairy goats between 1989 and 1994 in Gansu, Guizhou, Shaanxi, Shandong and Sichuan provinces were cloned and sequenced. The Chinese CAEV had a 58–93％ genome similarities to strains outside of China, and they belonged to subgenotype B1. The highest similarity levels (98.3–99.3％) were with two other Chinese strains, and they shared a 91.8–92.3％ similarity with the strain Clements (GenBank accession no. NC_001463.1) from outside of China. The Chinese CAEV strains isolated from different provinces over five years were still highly homologous and contained unique ancestral population components, indicating that these Chinese strains had a common origin that differed from other known strains. Our results provide genomic data on circulating Chinese CAEV strains and will be useful for future epidemiological investigations and CAEV eradication programs.