Small ruminant lentivirus variants and related clinical features in goats from southeastern Brazil

•CAE is a multisystem infectious disease caused by a small ruminant lentivirus.•Little information about CAEV variants is available in Brazil.•Part of the pol gene of CAEV was amplified by nested-PCR and sequenced.•Sequences were compared with 42 reference strains previously described.•Subgroup B1 was the predominant genotype and a subgroup C-like was isolated.

Caprine arthritis encephalitis (CAE) is a multisystem infectious disease caused by a small ruminant lentivirus that is widely disseminated in the goat flock of southeastern Brazil. Little information about its variants is available in Brazil. Phylogenetic analysis was performed on the sequences of 14 clinical isolates of CAEV that obtained from mammary glands, lung, brain, milk and blood of goats with any clinical form of the disease in Sao Paulo State, Brazil. Part of the pol gene of CAEV was amplified by nested-PCR and sequenced. These sequences were compared with 42 reference strains previously described and commonly used in phylogenies. The sequences derived from this study were more related to caprine strains than to ovine strains. Additionally, subtype B of the CAEV group was detected in different clinical samples with distinct clinical symptoms. Subgroup B1 was the predominant genotype. A subgroup C-like was isolated from animals that presented interstitial indurative mastitis. Animals from which the sequences belonged to this subgroup presented interstitial mastitis induration, chronic arthritis and chronic interstitial pneumonia. Subgroup C sequences have not been reported in Brazil previously, while circulating subgroup B1 variants were already known to be present in the country. This study provides new information about CAEV variants in Brazil, since we isolated and reported the subgroup C-like. A variant from B1 subgroup was the predominant genotype. More studies are necessary in order to confirm the presence of CAEV genotype C or even a new genotype. CAEV is an important disease of goat production and all knowledge is necessary to understand its epidemiology and, prevent this illness.