Abstract
Outbreaks of Rift Valley fever (RVF) occurred in Namibia in 2010 and 2011. Complete genome characterization was obtained from virus isolates collected during disease outbreaks in southern Namibia in 2010 and from wildlife in Etosha National Park in 2011, close to the area where RVF outbreaks occurred in domestic livestock. The virus strains were sequenced using Sanger sequencing (Namibia_2010) or next generation sequencing (Namibia_2011). A sequence-independent, single-primer amplification (SISPA) protocol was used in combination with the Illumina Next 500 sequencer. Phylogenetic analysis of the sequences of the small (S), medium (M), and large (L) genome segments of RVF virus (RVFV) provided evidence that two distinct RVFV strains circulated in the country. The strain collected in Namibia in 2010 is genetically similar to RVFV strains circulating in South Africa in 2009 and 2010, confirming that the outbreaks reported in the southern part of Namibia in 2010 were caused by possible dissemination of the infection from South Africa. Isolates collected in 2011 were close to RVFV isolates from 2010 collected in humans in Sudan and which belong to the large lineage containing RVFV strains that caused an outbreak in 2006–2008 in eastern Africa. This investigation showed that the RVFV strains circulating in Namibia in 2010 and 2011 were from two different introductions and that RVFV has the ability to move across regions. This supports the need for risk-based surveillance and monitoring.
Highlights
Rift Valley fever is a severe disease of livestock, causing abortions and neonatal mortality in domestic ruminants
This study describes whole-genome sequencing and phylogenetic analysis of the RVF virus (RVFV) strains isolated in Namibia during 2010 and 2011
Genomic sequences of strains isolated in Namibia during the 2010 and 2011 outbreaks showed a high number of mismatches
Summary
Rift Valley fever is a severe disease of livestock, causing abortions and neonatal mortality in domestic ruminants. The disease is caused by RVFV, an enveloped RNA virus of the Phlebovirus genus (Family Phenuiviridae). The infection with RVFV can cause mild to severe illness in humans [1]. The disease transmission occurs primarily by mosquitoes, which are vectors and reservoirs of the virus [2,3,4]. The virus was first identified in the Great Rift Valley in Kenya in the 1930s [6,7]. RVFV isolation and serological evidence was reported in greater parts of the African continent, the disease is considered endemic to eastern and southern Africa (Sudan, Somalia, Kenya, Zimbabwe, Zambia, Mozambique, Namibia, Madagascar, Tanzania, and South Africa) and in the western countries of Mauritania, Senegal, and Niger. Substantial outbreaks have been reported in Egypt, Saudi Arabia, and Yemen [8,9], amongst others, in the past, demonstrating the potential for further spread of the pathogen into disease-free regions [10,11]
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