Classification of small ruminant lentivirus subtype A2, subgroups 1 and 2 based on whole genome comparisons and complex recombination patterns [version 2; revised]

Authors: Dickey, Aaron; Smith, Timothy - Tim; Clawson, Michael - Mike; Heaton, Michael - Mike; Workman, Aspen

Submitted to: F1000Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/19/2021
Publication Date: N/A
Citation: N/A

Interpretive Summary: Small ruminant lentiviruses (SRLVs) cause disease in sheep around the world. Sheep that have a specific genetic marker in their transmembrane protein 154 (TMEM154) gene are more susceptible to infection with this virus than those that do not. A genetic group of SRLVs known as subtype A2 is common in North America and A2 can be further subdivided by genetic similarity into subgroups. Two of the subgroups have been associated with variation in TMEM154; subgroup 1 viruses associate with sheep lacking the marker, and subgroup 2 viruses associate with sheep possessing it. SRLV subgroups 1 and 2 were previously classified by genetic sequence variation in a portion of their genome. The goals of this study were 1) to obtain complete virus genome sequences from both subgroups 1 and 2, and 2) to analyze and classify the complete genomes according to genetic variability and genetic recombination whereby genetic material is exchanged and mixed from two viral genomes to create a third genome with distinct traits. Twenty-three complete or near-complete genomes were assembled representing both virus subgroups 1 and 2. Analysis of these genomes with mathematical models of recombination confirmed both subgroups, revealed additional genetic groups within subgroup 2, and predicted complex patterns of recombination in several genomes. The genomes featuring the most recombination generally occurred in virus genomes from sheep with only 1 copy of the genetic marker. These virus genomes also tended to have a more diverse set of genetic changes within a single infected sheep due, in part, to multiple infection events with recombinants of the two viral subgroups. These results improve the process of classifying SRLV genomes along a continuum of recombination frequencies and suggest that sheep whose genomes contain only one copy of the TMEM154 genetic marker may facilitate recombination between subgroups 1 and 2 of the virus.

Technical Abstract: Background: Small ruminant lentiviruses (SRLVs) cause a multisystemic chronic wasting disease in sheep across much of the world. SRLV subtype A2 is prevalent in North America and further classified into multiple subgroups based on variation in the group antigens gene (gag) and envelope (env) genes. In sheep, the ovine transmembrane protein 154 (TMEM154) gene is associated with SRLV susceptibility. Ewes with at least one copy of TMEM154 encoding a full-length protein with glutamate at position 35 (E35; haplotypes 2 and 3), are highly susceptible to SRLV infection while ewes with any combination of TMEM154 haplotypes which encodes lysine (K35; haplotype 1), or truncated proteins (haplotypes 4 and 6) are several times less so. A2 subgroups 1 and 2 are associated with host TMEM154 genotypes; subgroup 1 with the K35/K35 genotype and subgroup 2 with the E35/E35 genotype. Methods: Sequence variation within and among full-length assemblies of SRLV subtype A2 subgroups 1 and 2 was analyzed to identify genome-scale recombination patterns and subgroup-specific variants. Results: Consensus viral genomes were assembled from 23 infected sheep, including animals of assorted TMEM154 genotypes comprised of haplotypes 1, 2, or 3. Viral genome analysis identified viral subgroups 1 and 2 among the samples, and revealed additional sub-structure within subgroup 2 based on models predicting complex patterns of recombination between the two subgroups in several genomes. Animals with evidence of dual subgroup infection also possessed the most diverse quasi-species and the most highly recombined consensus genomes. After accounting for recombination, 413 subgroup diagnostic single nucleotide polymorphisms (SNPs) were identified. Conclusions: The viral subgroup framework developed to classify SRLV consensus genomes along a continuum of recombination suggests that animals with the TMEM154 E35/K35 genotype may represent a reservoir for producing viral genomes representing recombination between A2 subgroups 1 and 2.