Rift Valley fever, Sudan, 2007 and 2010

Abstract

To elucidate whether Rift Valley fever virus (RVFV) diversity in Sudan resulted from multiple introductions or from acquired changes over time from 1 introduction event, we generated complete genome sequences from RVFV strains detected during the 2007 and 2010 outbreaks. Phylogenetic analyses of small, medium, and large RNA segment sequences indicated several genetic RVFV variants were circulating in Sudan, which all grouped into Kenya-1 or Kenya-2 sublineages from the 2006-2008 eastern Africa epizootic. Bayesian analysis of sequence differences estimated that diversity among the 2007 and 2010 Sudan RVFV variants shared a most recent common ancestor circa 1996. The data suggest multiple introductions of RVFV into Sudan as part of sweeping epizootics from eastern Africa. The sequences indicate recent movement of RVFV and support the need for surveillance to recognize when and where RVFV circulates between epidemics, which can make data from prediction tools easier to interpret and preventive measures easier to direct toward high-risk areas.

Figure 1

Sudan and South Sudan. States with confirmed Rift Valley fever cases are in boldface. Light gray indicates Sudan; dark gray indicates South Sudan. The Nile, White Nile, and Blue Nile Rivers are depicted in white, and other bodies of water were removed for clarity.

Figure 2

Laboratory-confirmed Rift Valley fever cases, Sudan, 2007.

Figure 3

Phylogenetic analysis of complete Rift Valley fever virus S (small) segment sequences represented as an abbreviated maximum clade credibility tree. Asterisk indicates nodes with highest posterior density >0.95. Sudan sequences are shaded. Arrow indicates reassortant viruses. Scale bar represents substitutions per site per year. The complete tree is presented in Technical Appendix Figure 1. Country names appear in boldface, and strain names appear in italics.

Figure 4

Phylogenetic analysis of complete Rift Valley fever virus M (medium) segment sequences represented as an abbreviated maximum clade credibility tree. Asterisk indicates nodes with highest posterior density >0.95. Sudan sequences are shaded. Arrow indicates reassortant viruses. Scale bar represents substitutions per site per year. The complete tree is presented in Technical Appendix Figure 2. Country names appear in boldface, and strain names appear in italics.

Figure 5

Phylogenetic analysis of complete Rift Valley fever virus L (large) segment sequences represented as an abbreviated maximum clade credibility tree. Asterisk indicates nodes with highest posterior density >0.95. Sudan sequences are shaded. Arrow indicates reassortant viruses. Scale bar represents substitutions per site per year. The complete tree is presented in Technical Appendix Figure 3. Country names appear in boldface, and strain names appear in italics.