bioRxiv preprint doi: https://doi.org/10.1101/454314; this version posted October 29, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 An emergent Ebola virus nucleoprotein variant influences virion 2 budding, oligomerization, transcription and replication 3 Aaron E Lin1,2,3,11, William E Diehl4,11, Yingyun Cai5, Courtney Finch5, Chidiebere Akusobi6, 4 Robert N Kirchdoerfer7, Laura Bollinger5, Stephen F Schaffner2,3, Elizabeth A Brown2,3, Erica 5 Ollmann Saphire7,8, Kristian G Andersen7,9, Jens H Kuhn5,12, Jeremy Luban4,12, Pardis C 6 Sabeti1,2,3,10,12 7 8 1Harvard Program in Virology, Harvard Medical School, Boston, MA 02115, USA. 2FAS Center 9 for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, 10 Cambridge, MA 02138, USA. 3Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. 11 4Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 12 01605, USA. 5Integrated Research Facility at Fort Detrick, National Institute of Allergy and 13 Infectious Diseases, National Institutes of Health, Frederick, MD 21702. 6Department of 14 Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 15 02120, USA. 7Department of Immunology and Microbial Sciences, The Scripps Research 16 Institute, La Jolla, CA 92037, USA. 8The Skaggs Institute for Chemical Biology, The Scripps 17 Research Institute, La Jolla, CA 92037, USA. 9Scripps Translational Science Institute, La Jolla, 18 CA 92037, USA. 10Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA. 11Co-first 19 author. 12Co-last author. 1 bioRxiv preprint doi: https://doi.org/10.1101/454314; this version posted October 29, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Abstract 2 3 To investigate how Ebola virus phenotypes changed during the 2013‒2016 Western African 4 Ebola virus disease epidemic, we examined a key viral mutation that rose to high frequency: an 5 R111C substitution in the viral nucleoprotein (NP). Though NP plays many essential roles 6 during infection, there are a limited number of assays for studying these functions. We 7 developed new reporter assays to measure virion-like particle (VLP) production and NP 8 oligomerization in live cells under biosafety level 2 conditions. We found that NP-R111C 9 significantly enhanced VLP production and slightly increased NP oligomerization without 10 impairing viral transcription and replication. By contrast, a synthetic charge-reversal mutant, NP- 11 R111E, greatly increased oligomerization but dramatically reduced transcription and replication. 12 We detected an interaction of NP with the cellular clathrin adaptor protein-1 (AP-1) complex, 13 which may explain how NP facilitates VLP production. Our study provides enhanced methods to 14 study NP and indicates a complex interplay between NP's roles in virion budding, protein 15 structure, and transcription and replication. 2 bioRxiv preprint doi: https://doi.org/10.1101/454314; this version posted October 29, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Introduction 2 Given the past and current public health threats caused by Ebola virus disease (EVD) 3 outbreaks, rapidly evaluating whether Ebola virus (EBOV) genomic mutations change viral 4 phenotypes is critically important. As an RNA virus, EBOV generates many mutations over the 5 course of an outbreak. The vast majority of these mutations likely will not be adaptive and will 6 instead have negligible or negative effects on EBOV viability and replication (Holmes 2009). 7 Yet, changes in the EBOV genome over time can have important implications for clinical patient 8 care, epidemiological modeling, and vaccine development, and thus influence prospective 9 outbreak prediction and outbreak response. 10 The need to better understand EBOV evolution became clear during the 2013‒2016 11 EVD epidemic in Western Africa caused by the EBOV Makona variant. This epidemic is the 12 largest EVD epidemic on record with over 28,000 infections and more than 11,000 deaths 13 (WHO 2016). EBOV replication generated thousands of mutations over numerous rounds of 14 human-to-human transmission (Baize et al. 2014; Gire et al. 2014; Carroll et al. 2015; Ladner et 15 al. 2015; Tong et al. 2015; Park et al. 2015; Simon-Loriere et al. 2015; Kugelman et al. 2015; T. 16 Hoenen et al. 2015; Thomas Hoenen et al. 2016; Smits et al. 2015; Quick et al. 2016), but only 17 a handful of mutations became common enough to have had a sizeable impact on the epidemic 18 (Baize et al. 2014; Gire et al. 2014; Park et al. 2015; Carroll et al. 2015; Ladner et al. 2015; 19 Tong et al. 2015; Simon-Loriere et al. 2015). These mutations define four distinct genetic EBOV 20 Makona clades, which emerged as the outbreak was accelerating in May 2014. Each of the 21 clades, termed “SL1” through “SL4,” descended from one another sequentially (e.g., SL2 22 derived from SL1), with a subsequent increase in EVD cases. Because non-synonymous 23 mutations directly change protein sequence, we focused on the only two non-synonymous 24 clade-defining mutations—one each defining the SL1 and SL2 clades. 25 3 bioRxiv preprint doi: https://doi.org/10.1101/454314; this version posted October 29, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 The SL1 clade-defining mutation, C6283U, results in an A82V substitution in the EBOV 2 glycoprotein (GP-A82V) and has been studied extensively through well-established biosafety 3 level 2 (BSL-2) surrogate model systems and live virus BSL-4 studies. Because EBOV GP 4 mediates EBOV particle entry into cells and is a major target for host antibodies, GP-A82V is an 5 obvious priority for experimental studies. During outbreaks of other viral diseases, mutation in 6 viral surface proteins such as GP has altered cell tropism (e.g., Zika virus (Yuan et al. 2017)) or 7 host tropism (e.g., chikungunya virus (Tsetsarkin et al. 2007)). Based on multiple in vitro 8 studies, GP-A82V increases EBOV infectivity for a variety of human and non-human primate 9 cell types. These data suggest that the mutation confers a selective advantage to EBOV (Diehl 10 et al. 2016; Urbanowicz et al. 2016; Dietzel et al. 2017; Ueda et al. 2017; Hoffmann et al. 2017; 11 Wang et al. 2017), which however has not yet been demonstrated clearly in vivo (Marzi et al. 12 2018; Wong et al. 2018). 13 The SL2 clade-defining mutation, C800U, results in an R111C substitution in the EBOV 14 nucleoprotein (NP-R111C) and has not been thoroughly studied because, though NP has many 15 functions, there are a limited number of assays for studying these functions. While surface 16 glycoproteins like EBOV GP alter viral tropism primarily by affecting cell susceptibility (e.g., 17 increased viral entry), mutations in non-glycoproteins can also affect viral tropism by changing 18 cell permissiveness (e.g., increased viral genome replication) (Cauldwell et al. 2014; Kirmaier et 19 al. 2010; Krupp et al. 2013; Zimmermann et al. 2011). For this study, we focused our attention 20 on EBOV NP. 21 The N-terminus of EBOV NP, which contains the R111 residue, interacts with viral RNA 22 and connects multiple viral phenotypes such as virion structure, and transcription and 23 replication. During virion assembly and budding, the EBOV matrix protein VP40 dimerizes in the 24 cytoplasm, traffics to the cell membrane, and oligomerizes. VP40 oligomers engage with the 25 EBOV ribonucleoprotein (RNP) complex composed of NP, polymerase cofactor VP35, 26 transcription regulator VP30, and RNA-dependent polymerase L, and shape the cell's plasma 4 bioRxiv preprint doi: https://doi.org/10.1101/454314; this version posted October 29, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 membrane around them into EBOV virions, which exit the cell by budding (Luke D. Jasenosky 2 and Kawaoka 2004). Expression of VP40 in the absence of other viral proteins generates 3 similarly shaped particles, dubbed virion-like particles (VLPs) (Harty et al. 2000; L. D. Jasenosky 4 et al. 2001; Noda et al. 2002). Co-expression of VP40 with NP or other viral proteins 5 significantly increases the number of VLPs in cellular supernatant (Licata et al. 2004), 6 suggesting that NP plays a structural role in assembling and stabilizing VLPs. Mutations in NP 7 that affect its ability to enhance VLP production are not known. 8 EBOV NP also plays an essential role in viral transcription and replication. By directly 9 interacting with EBOV RNA, VP35, and VP30, NP recruits L to enact both of these essential 10 functions (Groseth et al. 2009). Based on EBOV NP structural data, homology modeling versus 11 other viral nucleoproteins, and site-directed mutagenesis experiments, key EBOV NP residues 12 that interact with EBOV RNA (Dong et al.