Epidemiology and Genomic Analysis of Equine Encephalosis Virus Detected in Horses with Clinical Signs in South Africa, 2010–2017

Abstract

Equine encephalosis virus (EEV) is a neglected virus endemic to South Africa and is considered to generally result in mild disease in equines. Specimens were analyzed from live horses that presented with undefined neurological, febrile, or respiratory signs, or sudden and unexpected death. Between 2010 and 2017, 111 of 1523 (7.3%) horse samples tested positive for EEV using a nested real-time reverse transcriptase polymerase chain reaction (rRT-PCR). Clinical signs were reported in 106 (7.2%) EEV positive and 1360 negative horses and included pyrexia (77/106, 72.6%), icterus (20/106, 18.9%) and dyspnea (12/106, 11.3%). Neurological signs were inversely associated with EEV infection (OR < 1, p < 0.05) relative to EEV negative cases despite a high percentage of animals presenting with neurological abnormalities (51/106, 48.1%). Seventeen of the EEV positive horses also had coinfections with either West Nile (5/106, 4.7%), Middelburg (4/106, 3.8%) or African Horse sickness virus (8/106, 7.6%). To investigate a possible genetic link between EEV strains causing the observed clinical signs in horses, the full genomes of six isolates were compared to the reference strains. Based on the outer capsid protein (VP2), serotype 1 and 4 were identified as the predominant serotypes with widespread reassortment between the seven different serotypes.

An Investigation of Culicoides (Diptera: Ceratopogonidae) as Potential Vectors of Medically and Veterinary Important Arboviruses in South Africa

“…The high prevalence of EEV is not surprising, as Culicoides midges, specifically C. imicola and Culicoides bolitinos , are the primary vectors for EEV. Cases of febrile, neurological, and respiratory disease in horses infected with EEV were also frequently detected across South Africa during the same period [ 14 ]. Equine encephalosis virus detected in midges formed two distinct clusters with the majority grouping with the Kyalami and Northrand serotypes (clade B) and not the Bryanston and Potchefstroom serotypes, as previously reported [ 40 ].…”

“…The six vector surveillance sites were selected based on previous outbreaks of neurological disease in animals due to arbovirus infections as well as the strong humans–animal interface at these sites [ 10 , 11 , 12 , 13 , 14 , 15 ]. The highest overall MIR was reported in Lapalala Wilderness.…”

“…Spillovers of disease from wildlife to domestic animals have been reported in these areas [ 48 ]. In Boschkop and Kyalami, numerous outbreaks of WNV [ 10 ], SHUV [ 27 ], MIDV [ 18 ], and EEV [ 14 ] in horses have been reported, which consist of agricultural small holdings rather than wildlife areas. Morphological identification of Culicoides species from subsamples collected at the various surveillance sites demonstrates the high abundance of C. imicola at all sites, supporting previous findings [ 49 , 50 ].…”

“…Vector surveillance sites ( Table 1 ) were selected based on previous outbreaks of zoonotic arboviruses in animal populations in South Africa [ 10 , 11 , 12 , 13 , 14 , 15 ]. Mpumalanga and Limpopo province are primarily wildlife regions and include various national parks including Kruger National Park (KNP), Marakele Nature Reserve, and Lapalala Wilderness.…”

“…Various published reverse transcription polymerase chain reactions (RT-PCRs) were used to screen pools for arboviruses in the genera Alphavirus [ 18 ], Flavivirus , [ 19 ] Orthovirus [ 20 ], and Phlebovirus [ 20 ], as well as equine encephalosis virus (EEV) [ 14 ] and Rhabdoviridae [ 21 ]. All orthobunyavirus PCR positives were followed up with a One-Step Bunyaviridae RT-PCR.…”