Epidemiological and Genomic Characterisation of Middelburg and Sindbis Alphaviruses Identified in Horses with Febrile and Neurological Infections, South Africa (2014-2018)

Isabel Fourie; Jumari Snyman; June Williams; Arshad Ismail; Petrus Jansen van Vuren; Marietjie Venter

doi:10.3390/v14092013

Epidemiological and Genomic Characterisation of Middelburg and Sindbis Alphaviruses Identified in Horses with Febrile and Neurological Infections, South Africa (2014-2018)

Viruses. 2022 Sep 11;14(9):2013. doi: 10.3390/v14092013.

Authors

Isabel Fourie¹, Jumari Snyman¹, June Williams², Arshad Ismail^{3

4}, Petrus Jansen van Vuren⁵, Marietjie Venter¹

Affiliations

¹ Department of Medical Virology, University of Pretoria, Pretoria 0031, South Africa.
² Department of Paraclinical Sciences, University of Pretoria, Pretoria 0110, South Africa.
³ Sequencing Core Facility, National Institute of Communicable Diseases (NICD), Johannesburg 2192, South Africa.
⁴ Department of Biochemistry and Microbiology, University of Venda, Thohoyandou 0950, South Africa.
⁵ Australian Centre for Disease Preparedness, CSIRO-Health and Biosecurity, Geelong 3220, Australia.

Abstract

Although Old World alphaviruses, Middelburg- (MIDV) and Sindbis virus (SINV), have previously been detected in horses and wildlife with neurologic disease in South Africa, the pathogenesis and clinical presentation of MIDV and SINV infections in animals are not well documented. Clinical samples from horses across South Africa with acute or fatal neurologic and febrile infections submitted between 2014-2018 were investigated. In total, 69/1084 (6.36%) and 11/1084 (1.01%) horses tested positive for MIDV and SINV, respectively, by real-time reverse transcription (RT) PCR. Main signs/outcomes for MIDV (n = 69): 73.91% neurological, 75.36% fever, 28.99% icterus and anorexia, respectively, 8.70% fatalities; SINV (n = 11): 54.54% neurological, 72.73% fever, 36.36% anorexia and 18.18% fatalities. MIDV cases peaked in the late summer/autumn across most South African provinces while SINV cases did not show a clear seasonality and were detected in fewer South African provinces. MIDV could still be detected in blood samples via RT-PCR for up to 71,417 and 21 days after onset of signs in 4 horses respectively, suggesting prolonged replication relative to SINV which could only be detected in the initial sample. Phylogenetic analyses based on partial sequences of the nsP4 (MIDV n = 59 and SINV n = 7) and E1 (MIDV n = 45) genes, as well as full genome sequences (MIDV n = 6), clustered the MIDV and SINV strains from the present study with previously detected strains. MIDV infection appears to be more prevalent in horses than SINV infection based on RT-PCR results, however, prevalence estimates might be different when also considering serological surveillance data.

Keywords: Alphavirus; Middelburg virus; Sindbis virus; arbovirus; genome; horse; zoonotic.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Alphavirus Infections* / diagnosis
Alphavirus Infections* / epidemiology
Alphavirus Infections* / veterinary
Animals
Anorexia
Genomics
Horses
Phylogeny
Sindbis Virus / genetics
South Africa / epidemiology

Grants and funding

The study was funded through Prof M. Venter’s University of Pretoria Development Fund and a grant from the EU/NRF LEAP AGRI LEARN project (Grant No: 115574; A Long term EU- Africa research and innovation Partnership on food and nutrition security and sustainable Agriculture, LEARN project: LEARN: Long-term Europe-Africa Research Network on neglected arboviral zoonotic diseases). The findings and conclusions in this manuscript are those of the author(s) and do not necessarily represent the official position of the funding agencies. The APC was funded by G7 Global Health Fund program: FKZ1368-1438TO08.