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.

1. Fig trees require host‐specific agaonid fig wasps for pollination, but their figs also support numerous non‐pollinating fig wasps (NPFW) that gall fig tissues or develop as parasitoids. 2. Ficus microcarpa L. is widely naturalised outside its native range and the most invasive fig tree species. Seed predators are widely used for the biological control of invasive plants, but no obligate seed predatory (as opposed to ovule or fig wall galling) NPFW have been recorded previously from any fig trees. 3. Philotrypesis NPFW are usually regarded as parasitoids or ‘inquilines’ (parasitoids that also eat plant material) of pollinator fig wasps, but the present study provides evidence that Philotrypesis taiwanensis, a NPFW associated with F. microcarpa, is an obligate seed predator: (i) adults emerge from seeds of typical appearance, with a surrounding elaiosome; (ii) it shows no preference for figs occupied by fig wasp species, other than the pollinator; (iii) it only develops in figs that contain pollinated ovules, avoiding figs occupied by an agaonid that fails to pollinate; (iv) larvae are distributed in layers where seeds are concentrated and (v) it has a negative impact on seed but not pollinator offspring numbers. 4. Philotrypesis is a large genus, and further species are likely to be seed predators.

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