SummaryThe 2013–2015 Ebola virus disease (EVD) epidemic is caused by the Makona variant of Ebola virus (EBOV). Early in the epidemic, genome sequencing provided insights into virus evolution and transmission and offered important information for outbreak response. Here, we analyze sequences from 232 patients sampled over 7 months in Sierra Leone, along with 86 previously released genomes from earlier in the epidemic. We confirm sustained human-to-human transmission within Sierra Leone and find no evidence for import or export of EBOV across national borders after its initial introduction. Using high-depth replicate sequencing, we observe both host-to-host transmission and recurrent emergence of intrahost genetic variants. We trace the increasing impact of purifying selection in suppressing the accumulation of nonsynonymous mutations over time. Finally, we note changes in the mucin-like domain of EBOV glycoprotein that merit further investigation. These findings clarify the movement of EBOV within the region and describe viral evolution during prolonged human-to-human transmission.

The internal FECV→FIPV mutation theory and three of its correlates were tested in four sibs/half-sib kittens, a healthy contact cat, and in four unrelated cats that died of FIP at geographically disparate regions. Coronavirus from feces and extraintestinal FIP lesions from the same cat were always >99% related in accessory and structural gene sequences. SNPs and deletions causing a truncation of the 3c gene product were found in almost all isolates from the diseased tissues of the eight cats suffering from FIP, whereas most, but not all fecal isolates from these same cats had intact 3c genes. Other accessory and structural genes appeared normal in both fecal and lesional viruses. Deliterious mutations in the 3c gene were unique to each cat, indicating that they did not originate in one cat and were subsequently passed horizontally to the others. Compartmentalization of the parental and mutant forms was not absolute; virus of lesional type was sometimes found in feces of affected cats and virus identical to fecal type was occasionally identified in diseased tissues. Although 3c gene mutants in this study were not horizontally transmitted, the parental fecal virus was readily transmitted by contact from a cat that died of FIP to its housemate. There was a high rate of mutability in all structural and accessory genes both within and between cats, leading to minor genetic variants. More than one variant could be identified in both diseased tissues and feces of the same cat. Laboratory cats inoculated with a mixture of two closely related variants from the same FIP cat developed disease from one or the other variant, but not both. Significant genetic drift existed between isolates from geographically distinct regions of the Western US.

Rift Valley fever virus (RVFV) is a mosquito-borne human and veterinary pathogen causing large outbreaks of severe disease throughout Africa and the Arabian Peninsula. Safe and effective vaccines are critically needed, especially those that can be used in a targeted one-health approach to prevent both livestock and human disease. We report here on the safety, immunogenicity, and efficacy of the ⌬NSs-⌬NSm recombinant RVFV (rRVFV) vaccine (which lacks the NSs and NSm virulence factors) in a total of 41 sheep, including 29 timed-pregnant ewes. This vaccine was proven safe and immunogenic for adult animals at doses ranging from Rift Valley fever virus (RVFV) (family Bunyaviridae, genus Phlebovirus) is a mosquito-borne human and veterinary pathogen associated with large outbreaks of severe disease throughout Africa and the Arabian Peninsula. The virus was first identified following the sudden death of approximately 4,700 lambs and ewes on a single farm along the shores of Lake Naivasha in the Great Rift Valley of Kenya over a 4-week period in 1931 (15). Since then, RVFV has caused numerous economically devastating epizootics often characterized by sweeping "abortion storms," neonatal animal mortality approaching 100%, and significant mortality (ϳ10 to 20%) among adult ruminant livestock, especially sheep and cattle (7,13,14,28,32). Human infections are typically self-limiting febrile illnesses that, in 1 to 2% of affected individuals, can progress to more severe disease that includes fulminant hepatitis, encephalitis, retinitis, blindness, or a hemorrhagic syndrome. Fatality ratios in hospitalized patients are 10 to 20% (22,24).RVFV is uniquely suitable for a one-health approach to prevent both livestock and human disease through animal vaccination. Livestock provide two key ecological links between the transovarially infected Aedes sp. floodwater mosquito and the human population. First, infected livestock rapidly develop high viremias, allowing the spillover of RVFV into secondary vectors (Culex and Anopheles sp. mosquitoes) that are more likely to feed on humans. Second, the high virus loads found in livestock are also a significant risk factor for human infection by direct contact with contaminated blood, tissues, and aborted fetal materials (1). A vaccination strategy targeted at preventing the virus amplification step in livestock could provide a window of opportunity to interrupt nascent RVFV outbreaks by both reducing the potential for secondary vector spillover and eliminating the threat posed by infected livestock tissues.Currently, no RVFV vaccine has been approved for veterinary use outside areas of endemicity, although a variety of vaccines for either human or livestock use have been developed since RVFV was first isolated (9, 29). Problems with prior RVFV vaccines include poor immunogenicity, requiring multiple vaccination doses; difficulties with manufacturing; and