Both Epistasis and Diversifying Selection Drive the Structural Evolution of the Ebola Virus Glycoprotein Mucin-Like Domain

Abstract

Throughout the last 3 decades, Ebola virus (EBOV) outbreaks have been confined to isolated areas within Central Africa; however, the 2014 variant reached unprecedented transmission and mortality rates. While the outbreak was still under way, it was reported that the variant leading up to this outbreak evolved faster than previous EBOV variants, but evidence for diversifying selection was undetermined. Here, we test this selection hypothesis and show that while previous EBOV outbreaks were preceded by bursts of diversification, evidence for site-specific diversifying selection during the emergence of the 2014 EBOV clade is weak. However, we show strong evidence supporting an interplay between selection and correlated evolution (epistasis), particularly in the mucin-like domain (MLD) of the EBOV glycoprotein. By reconstructing ancestral structures of the MLD, we further propose a structural mechanism explaining how the substitutions that accumulated between 1918 and 1969 distorted the MLD, while more recent epistatic substitutions restored part of the structure, with the most recent substitution being adaptive. We suggest that it is this complex interplay between weak selection, epistasis, and structural constraints that has shaped the evolution of the 2014 EBOV variant. IMPORTANCEThe role that selection plays in the emergence of viral epidemics remains debated, particularly in the context of the 2014 EBOV outbreak. Most critically, should such evidence exist, it is generally unclear how this relates to function and increased virulence. Here, we show that the viral lineage leading up to the 2014 outbreak underwent a complex interplay between selection and correlated evolution (epistasis) in a protein region that is critical for immune evasion. We then reconstructed the three-dimensional structure of this domain and showed that the initial mutations in this lineage deformed the structure, while subsequent mutations restored part of the structure. Along this mutational path, the first and last mutations were adaptive, while the intervening ones were epistatic. Altogether, we provide a mechanistic model that explains how selection and epistasis acted on the structural constraints that materialized during the 2014 EBOV outbreak. The five viruses that constitute the genus Ebolavirus (Zaire ebolavirus [EBOV], Sudan ebolavirus, Bundibugyo ebolavirus, Reston ebolavirus, and Tai Forest ebolavirus) have been the cause of a major public health concern in sub-Saharan Africa for over 3 decades (1). Historically, outbreaks have been confined to isolated areas within Central Africa; however, the 2014 outbreak reached an unprecedented level, making this the largest outbreak since the discovery of the virus in 1976 (2).The primary analysis of EBOV isolates conducted by Gire and colleagues found a large number of nonsynonymous mutations between the 2014 EBOV sequences and all previously published EBOV sequences (3). In particular, 50 fixed nonsynonymous changes were observed, all of which were distinct to the 2014 EBOV vari...

Widespread Historical Contingency in Influenza Viruses

“…With this good statistical behavior, further analyses of independent influenza data sets showed a consistent pattern: (i) many pairs of correlated sites are involved in epistatic interactions, (ii) these pairs of sites form extensive networks of sites, consistent with Poon et al (2007b), but that are also affected by substitutions that occur sequentially -showing evidence for historical contingency in fast-evolving organismsand (iii), more intriguingly, that these epistatic pairs of sites form long-range spatial interactions. This latter point precludes the idea of a close physical link as in the case of tRNA molecules (Kimura, 1985;Chen et al, 1999), so that these long-range interactions must bring about stability (Thomas et al, 2010) and/or conformational (Mitraki et al, 1991;Newcomb et al, 1997;Harms and Thornton, 2014) and/or functional changes, as in the case of the M2 data set or in the case of the Ebola virus (Ibeh et al, 2016). While there is evidence that epistasis can be prevalent in RNA viruses (at least 31% in (Shapiro et al, 2006)) and in bacteria (15% in (Weinreich et al, 2006)), it is not impossible that epistasis reflects an evolutionary constraint stronger in RNA viruses than in organisms with larger and more redundant genomes: because these viruses have a small genome, mutations are expected to have large fitness effects, which can be alleviated by compensatory mutations (Sanjuán and Elena, 2006).…”

Episodic diversifying selection and intragenomic interactions shape the evolution of DNA and RNA viruses

“…While previous work showed that both diversifying selection and correlated evolution can affect the same gene and even the same site in a viral genome such as Ebola’s (Ibeh et al ., 2016), a ssRNA virus, the generality of this association is still unknown. At the gene level, we found strong heterogeneity among all four viral types for gene numbers showing evidence for selection, correlated evolution or both ( X 2 = 206.54, df = 6, P < 2.2×10 −16 ).…”

“…This last point suggests that a seldom explored evolutionary process, correlated evolution, might play a key role in the evolution of these single-stranded viruses. Indeed, recent work uncovered pervasive evidence for correlated evolution in influenza viruses (Nshogozabahizi et al ., 2017), and both the Zika (Aris-Brosou et al ., 2017) and the Ebola viruses (Ibeh et al ., 2016), with evidence in the latter that sites evolving in a correlated manner can also be under episodic diversifying selection. However, this recent body of evidence is so far limited to a small number of ssRNA viruses, so that the combined role of correlated evolution and selection is difficult to generalize.…”

Existing Host Range Mutations Constrain Further Emergence of RNA Viruses

“…The constraining effects of larger and smaller beneficial mutational neighborhoods were elegantly demonstrated in 6 by Burch and Chao, who noted that the high mutation rate of 6 was not sufficient to allow constrained genotypes to traverse a rugged fitness landscape (33). The ruggedness of viral fitness landscapes has been demonstrated for many viruses, including HIV (31), influenza virus A (34,35), and Ebola virus (36), and the phenomenon of mutational neighborhoods constraining evolutionary trajectories has been demonstrated in cellular organisms as well (37)(38)(39). Many of these studies involved prolonged experimental evolution, whereas our study used a very narrow window of lethal selection: a single night's selection on a novel host.…”