Molecular epidemiology of Rift Valley fever virus

Abstract

Phylogenetic relationships were examined for 198 Rift Valley fever virus isolates and 5 derived strains obtained from various sources in Saudi Arabia and 16 countries in Africa during a 67-year period (1944-2010). A maximum-likelihood tree prepared with sequence data for a 490-nt section of the Gn glycoprotein gene showed that 95 unique sequences sorted into 15 lineages. A 2010 isolate from a patient in South Africa potentially exposed to co-infection with live animal vaccine and wild virus was a reassortant. The potential influence of large-scale use of live animal vaccine on evolution of Rift Valley fever virus is discussed.

Figure 1

Annual sales of Smithburn neurotropic strain animal vaccine produced in South Africa in relation to cumulative viral lineages isolated and human deaths in major outbreaks of Rift Valley fever (RVF) in Africa and Saudi Arabia, 1944–2010. Broken arrows indicate RVF outbreaks without human deaths recorded, and solid arrows indicate RVF outbreaks with human deaths. RSA, Republic of South Africa; NAM, Namibia; ZIM, Zimbabwe; MOZ, Mozambique; KEN, Kenya; EGY, Egypt; SUD, Sudan; ZAM, Zambia; MAU, Mauritania; MAD, Madagascar; TAN, Tanzania; SOM, Somalia; SAU, Saudi Arabia; YEM, Yemen.

Figure 2

Recent outbreaks of Rift Valley fever in South Africa. Lineage C virus (yellow areas), which caused a small outbreak in Kruger National Park in 1999, was associated with scattered outbreaks of disease in adjacent parts of northeastern South Africa in 2008 and limited outbreaks to the south in KwaZulu-Natal Province early in 2009. Lineage H virus (blue area), which was first encountered in the Caprivi Strip of Namibia in 2004, caused focal outbreaks in the Northern Cape Province late in 2009, and was associated with coalescing outbreaks over much of interior South Africa in 2010. Lines indicate province boundaries.

Figure A1

Maximum-likelihood tree for a 490-nt section of the Gn glycoprotein gene of 111 isolates and derived strains of Rift Valley fever virus from Africa and Saudi Arabia, 1944–2010. The 95 unique sequences sorted into 15 lineages (A–O). Mean pairwise distances (p-distances) were <0.017 within lineages, and bootstrap values were >70%. Scale bar indicates substitutions per site. CAR, Central African Republic; SNS, Smithburn neurotropic strain.