After an incubation period of 5-9 days, small (1-3 mm) raised papules, which are often not noticed, appear on the skin of the penis of stallions and the vulva of mares. Over 24-48 hours these progress to fluid-filled vesicles, which mature and rupture leaving purulent 'pox-like' craterous lesions. These may remain as individuals or may coalesce into a raw or encrusted skin erosion or ulcer, before healing usually by 10-14 days. Secondary infection with bacteria will delay healing and may require local antiseptic or antibiotic treatment. Lesions specifically on the urethral process of the stallion sometimes result in inability/unwillingness to ejaculate.
Signs of systemic illness and genital discomfort are unusual but some stallions become uncomfortable enough to be unwilling to mate until lesions have healed. Some infected stallions take longer to recover and may develop secondary complications. Mares seldom show signs of systemic illness and lesions usually heal within 10-14 days, often leaving white (depigmented) skin scars.
Latent carrier infection occurs in both mares and stallions. These individuals may or may not have shown previously recognisable signs of disease at primary or reinfection and usually do not do so at recrudescence. The anatomical site of virus latency is unproven.
A non-venereal form of EHV-3 infection occurs uncommonly in maiden colts and fillies, causing pyrexia (raised temperature) and very painful coalescing skin lesions around the anus and vulva (in fillies), over the perineum and between the hindlegs and on the scrotum (in colts).
In breeding horses the infection causes no immediate or longer term direct effect on the fertility of stallions or mares, but temporarily disrupts mating schedules while the stallion recovers and becomes no longer infectious. Where infection occurs towards the end of the breeding season, missed mating opportunities may result in reduced pregnancy rates. The virus has not been reported to cause abortion in mares.