Phylogenetic Analysis of Belgian Small Ruminant Lentiviruses Supports Cross Species Virus Transmission and Identifies New Subtype B5 Strains

Abstract

Small ruminant lentiviruses (SRLV) are a group of highly divergent viruses responsible for global and fatal infections in sheep and goats. Since the current phylogenetic classification of these viruses was proposed in 2004, it nowadays consists out of 5 genotypes and 28 subtypes. In support of our national SRLV control program, we performed the genetic characterization of SRLV strains circulating in the Belgian sheep and goat population. Fourteen sheep and 9 goat strains were sequenced in the gag-pol and pol regions using the method described by Shah. Most SRLV strains from sheep and goats belonged to prototype A1 and B1 subtypes, respectively. We, however, also found indications for cross-species transmission of SRLV strains between sheep and goats and vice versa, and identified a new subtype designated as B5. An in-depth analysis of the current SRLV phylogeny revealed that many subtypes have been defined over the years based on limited sequence information. To keep phylogeny as a useful tool, we advocate to apply more rigorous sequencing standards to ensure the correct classification of current and new emerging strains. The genetic characterization of Belgian SRLV strains will help in the development of appropriate diagnostic tools to assist the national control program.

Accurate Diagnosis of Small Ruminant Lentivirus Infection Is Needed for Selection of Resistant Sheep through TMEM154 E35K Genotyping

“…On one hand, selection of diagnosis escape mutants could explain previously described diagnostic concerns [ 9 , 11 , 27 ]. On the other hand, the antigenic spectrum of SRLV, constantly enlarged by descriptions of new genotypes and subtypes [ 28 ], is not fully covered by commercial ELISA [ 9 , 29 , 30 , 31 ], at least when applied individually [ 7 ]. Both factors account for the variable proportion of infected animals not recognized by available ELISAs, as revealed by molecular methods.…”

Vertical transmissibility of small ruminant lentivirus

“…In the present study, there was homology in the genetic sequences obtained between neonates and their mothers, and a strong relationship with the standard strain CAEV Co as well as with the Brazilian sequences BR CNPC (GenBank accession number EU300976, EU300977, EU300978, EU300979), thus proving that the isolated strains were from SRLV. This relationship is explained by the fact that the studied gene is one of the most conserved regions of the viral genome [7] and has traditionally been used in molecular analyzes [3,6,[8][9][10][11][12]. It should be…”

“…Small ruminant lentiviruses (SRLV) are viral agents that affect sheep and goats, and that share homologous sequences in the organization of the genome [1]. These viral agents belong to the Retroviridae family, which are able to transcribe ribonucleic acid (RNA) to deoxyribonucleic acid (DNA), through the action of the reverse transcriptase enzyme, and often cross the interspecific barrier between sheep and goats, with great genetic variability [2,3].…”

“…Structural (gag, pol and env) and accessories genes (vpr, rev and vif) make up the genome of SRLV [6]. Among these, the gag gene is one of the most conserved regions of the viral genome [7], and worldwide it is the target of molecular analysis [3,6,[8][9][10][11][12], allowing to properly characterize the circulating strains in the infected animal's organism due to its ideal minimum genetic variability, compared to other conserved regions of the genome [13,14].…”

Ocorrência de doenças infecciosas e parasitárias em caprinos e ovinos da região metropolitana de São Luís, Estado do Maranhão, Brasil

“…Na Bélgica, um recente estudo nacional de soroprevalência confirmou a presença de SRLV em 13% e 17% das fazendas de ovinos e caprinos, respectivamente (Michiels et al, 2020).…”