Maedi Visna (MV), is a lentiviral disease of sheep characterised by a chronic wasting condition which is ultimately fatal within infected animals. Caused by small ruminant lentivirus (SRLV), infection has no treatment or cure. Control of infection typically focuses on identification of infected animals followed by isolation or culling to prevent further spread. Within the UK, MV prevalence is on the rise (approximately 10%) with control strategies showing minimal efficacy. Despite this increased relevance within the current UK sheep industry, little is known regarding circulating viral strains with the most recent published genome sequence (EV1) from 1991. To address this, RNA extracted from lung and lymph tissue from 3 naturally infected rams of the same flock were sequenced by next generation sequencing technology and analysed to identify current circulating viral strains and allow comparison to historic UK and worldwide strains. Approximately 92% of SRLV sequence was obtained from obtained data. Sequence classified as genotype A and shared closest identity with EV1 (81%). Despite this, prior extensive PCR based assays targeting EV1 failed to detect this new strain. In this study we have identified a new strain of SRLV circulating recently within the UK sheep population, despite similarities with previously known strains, it has been shown to be significantly different diagnostically. This highlights the importance for strain monitoring within the UK to ensure that circulating strains are known and detectable to ensure efficacy of control strategies to counteract the steep rise in prevalence over recent years.