A comparative genome analysis of Rift Valley Fever virus isolates from foci of the disease outbreak in South Africa in 2008-2010

Abstract

Rift Valley fever (RVF) is a re-emerging zoonotic disease responsible for major losses in livestock production, with negative impact on the livelihoods of both commercial and resource-poor farmers in sub-Sahara African countries. The disease remains a threat in countries where its mosquito vector thrives. Outbreaks of RVF usually follow weather conditions which favour increase in mosquito populations. Such outbreaks are usually cyclical, occurring every 10–15 years. Recent outbreaks of the disease in South Africa have occurred unpredictably and with increased frequency. In 2008, outbreaks were reported in Mpumalanga, Limpopo and Gauteng provinces, followed by 2009 outbreaks in KwaZulu-Natal, Mpumalanga and Northern Cape provinces and in 2010 in the Eastern Cape, Northern Cape, Western Cape, North West, Free State and Mpumalanga provinces. By August 2010, 232 confirmed infections had been reported in humans, with 26 confirmed deaths.To investigate the evolutionary dynamics of RVF viruses (RVFVs) circulating in South Africa, we undertook complete genome sequence analysis of isolates from animals at discrete foci of the 2008–2010 outbreaks. The genome sequences of these viruses were compared with those of the viruses from earlier outbreaks in South Africa and in other countries. The data indicate that one 2009 and all the 2008 isolates from South Africa and Madagascar (M49/08) cluster in Lineage C or Kenya-1. The remaining of the 2009 and 2010 isolates cluster within Lineage H, except isolate M259_RSA_09, which is a probable segment M reassortant. This information will be useful to agencies involved in the control and management of Rift Valley fever in South Africa and the neighbouring countries.

Preliminary Evaluation of a Recombinant Rift Valley Fever Virus Glycoprotein Subunit Vaccine Providing Full Protection against Heterologous Virulent Challenge in Cattle

“…Rift Valley fever is one of these arboviral diseases which was detected for the first time outside its traditional boundaries in Africa when it was found in the Arabian Peninsula in 2003 [ 2 , 29 ]. Additional outbreaks occurred in South Africa (2008–2010) [ 30 ] and reemergence in 2018 [ 31 ]. Niger and Uganda were free of reported human RVFV cases for many years, but the disease has re-occurred there in 2016 [ 32 , 33 ].…”

Insights into the Pathogenesis of Viral Haemorrhagic Fever Based on Virus Tropism and Tissue Lesions of Natural Rift Valley Fever

“…Rift Valley fever virus is an enveloped, single-stranded RNA virus with only one serotype and multiple lineages [48][49][50]. The viral genome consists of three segments, large, medium, and small (L, M, and S) [51].…”

“…The viral genome consists of three segments, large, medium, and small (L, M, and S) [51]. Similar to other arboviruses such as bluetongue and epizootic haemorrhagic disease virus, RVFV's genome has low substitution rates, with genomic diversity largely driven by reassortment [49]. The L RNA segment codes for the viral RNA-dependent RNA polymerase while the M segment codes for the two envelope glycoproteins, carboxy-terminus glycoprotein (GC) and amino terminus glycoprotein (GN), as well as two non-structural proteins, NSm1 and NSm2 [52].…”

Rift valley fever: diagnostic challenges and investment needs for vaccine development

“…Sequencing of the RVFV genome has been used to monitor virus epidemiological spread and geographic distribution of different strains. 6 The ability to perform whole-genome sequencing on clinical specimens can aid the identification of new strains as well as the mapping of virus evolution and transmission. Despite the presence of a single serotype, there are 15 RVFV lineages identified 43 and they show certain differences in virulence and pathogenicity in animal models, 30 44 highlighting the importance of comprehensive genetic characterisation of RVFV for disease management as well.…”

“…A large number of detected cases in humans is usually preceded by an outbreak in animals; detected or not. Despite the sporadic nature of outbreaks in humans and the limited antigenic diversity of the virus with the presence of a single serotype, 6 RVFV is listed as one of the priority pathogens in WHO Blueprint list due to its epidemic potential and lack of effective countermeasures. RVFV is also considered a select agent by the Centers for Disease Control and Prevention (CDC) and US Department of Agriculture.…”