Emergence and pandemic spread of small ruminant lentiviruses

Abstract

Small ruminant lentiviruses (SRLVs) cause chronic, persistent infections in populations of domestic sheep (Ovis aries) and goats (Capra hircus) worldwide. The vast majority of SRLV infections involve two genotypes (A and B) that spread in association with the emergence of global livestock trade. However, SRLVs have likely been present in Eurasian ruminant populations since at least the early Neolithic period. Here, we use phylogenetic and phylogeographic approaches to reconstruct the origin of pandemic SRLV strains and infer their historical pattern of global spread. We constructed an open computational resource (‘Lentivirus-GLUE’) via which an up-to-date database of published SRLV sequences, multiple sequence alignments, and sequence-associated metadata can be maintained. We used data collated in Lentivirus-GLUE to perform a comprehensive phylogenetic investigation of global SRLV diversity. Phylogenies reconstructed from genome-length alignments reveal that the deep divisions in the SRLV phylogeny are consistent with an ancient split into Eastern (A-like) and Western (B-like) lineages as agricultural systems disseminated out of domestication centres during the Neolithic period. These findings are also consistent with historical and phylogeographic evidence linking the early 20th century emergence of SRLV-A to international export of Central Asian Karakul sheep. Investigating the global diversity of SRLVs can help reveal how anthropogenic factors have impacted the ecology and evolution of livestock diseases. The open resources generated in our study can expedite these studies and can also serve more broadly to facilitate the use of genomic data in SRLV diagnostics and research.

Genetic Characterization of Small Ruminant Lentiviruses Isolated from Dairy Sheep in Greece

“…Our results also confirmed the infection of sheep with strains of genotype B, which were initially isolated from goats [50]. This finding is in agreement with previous studies, which reported cross-species transmission of A and B genotype strains between sheep and goats [11][12][13].…”

“…On the other hand, the other group of gag-pol sequences was clearly clustered with B2 strains isolated in Italy and Spain [7,[46][47][48], presenting very low values of nucleotide distance (<10%) as derived from the nucleotide pairwise comparisons. The genetic association of SRLV strains of genotypes A and B with these specific regions is consistent with previous phylogenetic studies indicating the Middle East and Central Europe as the ancestral regions of the A and B genotypes, respectively [49,50]. Nevertheless, further investigation and bioinformatics analyses of whole-genome sequence data are imperative for the exploration of the origin of SRLV strains isolated in the present study.…”

A Combined Approach for the Characterization of Small Ruminant Lentivirus Strains Circulating in the Islands and Mainland of Greece

“…The first belonged to the B2 subtype, firstly isolated in cases of arthritis in Spanish sheep [51,52] and now endemic in Mediterranean flocks without species restrictions [25,26,37,40,[53][54][55][56]. However, the majority of sequences retrieved in the study were clustered in a new A subgroup closely related to previously reported Greek and Lebanese sequences [6,57]. These sequences showed a mean genetic distance from around 13.6 to 15.8% with the A12 Polish sequence and, based on the SRLV classification reported by Shah [3], can be tentatively assigned to a new A28 viral subtype.…”

Isolation and Identification of Caprine Arthritis Encephalitis Virus from Animals in the Republic of Mordovia

“…It should be noted that only two sequences of small ruminant lentiviruses isolated in the Russian Federation are available in Genbank (MN186380.1-Mordovia 2018; JN008914.1-Tverskoy 2008). Due to the high variability of the genomes of lentiviruses, their phylogenetic analysis is complicated [46].…”