First Laboratory-Confirmed Outbreak of Human and Animal Rift Valley Fever Virus in Uganda in 48 Years

Abstract

In March 2016, an outbreak of Rift Valley fever (RVF) was identified in Kabale district, southwestern Uganda. A comprehensive outbreak investigation was initiated, including human, livestock, and mosquito vector investigations. Overall, four cases of acute, nonfatal human disease were identified, three by RVF virus (RVFV) reverse transcriptase polymerase chain reaction (RT-PCR), and one by IgM and IgG serology. Investigations of cattle, sheep, and goat samples from homes and villages of confirmed and probable RVF cases and the Kabale central abattoir found that eight of 83 (10%) animals were positive for RVFV by IgG serology; one goat from the home of a confirmed case tested positive by RT-PCR. Whole genome sequencing from three clinical specimens was performed and phylogenetic analysis inferred the relatedness of 2016 RVFV with the 2006-2007 Kenya-2 clade, suggesting previous introduction of RVFV into southwestern Uganda. An entomological survey identified three of 298 pools (1%) of Aedes and Coquillettidia species that were RVFV positive by RT-PCR. This was the first identification of RVFV in Uganda in 48 years and the 10^th independent viral hemorrhagic fever outbreak to be confirmed in Uganda since 2010.

Figure 1.

Map showing the locations of confirmed and probable Rift Valley fever cases and locations where human, livestock, and mosquito samples were collected during the outbreak investigations in Kabale district, Uganda, 2016. This figure appears in color at www.ajtmh.org.

Figure 2.

Sequential Rift Valley fever virus (RVFV) IgM and IgG serologies and reverse transcriptase polymerase chain reaction (RT-PCR) for the three confirmed cases in Kabale district for acute clinical RVF cases AC1 (A), AC2 (B), and AC3 (C). X axis represents days post RVF symptom onset when blood sample was collected; y axis (left) represents IgG serological titer; y axis (right) represents cycle threshold (Ct) values for RT-PCR performed on each sequential clinical sample. (A) RVFV sequential serology and RT-PCR for the initial confirmed acute case (AC1). (B) RVFV sequential serology and RT-PCR for the second confirmed acute case (AC2). (C) RVFV sequential serology and RT-PCR for the third confirmed acute case (AC3). This figure appears in color at www.ajtmh.org.

Figure 3.

Phylogenetic trees comparing complete S (A), M (B), and L (C) segment sequences of RVFV using all available full genome sequences. The sequence from the three RT-PCR–positive acute human cases described here, 20160187 (AC1), 201601298 (AC2), and 201601502 (AC4), are in red type. The evolutionary history was inferred based on the SPR model with the GTR + Γ (n = 4) nucleotide substitution model. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. Branch support estimates represent bootstrap values following 1,000 replicates and are displayed as integers for branch support > 70%. Clades are labeled according to Bird et al.^, and Aradaib et al. Evolutionary analyses were conducted using phyml (v 3.0). Scale bar represents 0.005 substitutions/site. GenBank accession numbers used in tree are MG953418, MG953419, MG953420, MG953421, MG953422, MG953423, MG953424, MG953425, and MG953426. RT-PCR = reverse transcriptase polymerase chain reaction; RVFV = Rift Valley fever virus. This figure appears in color at www.ajtmh.org.