Transcriptional Analysis of Infection With Early or Late Isolates From the 2013–2016 West Africa Ebola Virus Epidemic Does Not Suggest Attenuated Pathogenicity as a Result of Genetic Variation

The 2013–2016 West Africa Ebola virus (EBOV) epidemic caused by the EBOV-Makona isolate is the largest and longest recorded to date. It incurred over 28,000 infections and ∼11,000 deaths. Early in this epidemic, several mutations in viral glycoprotein (A82V), nucleoprotein (R111C), and polymerase L (D759G) emerged and stabilized. In vitro studies of these new EBOV-Makona isolates showed enhanced fitness and viral replication capacity. However, in vivo studies in mice and rhesus macaques did not provide any evidence of enhanced viral fitness or shedding. Infection with late isolates carrying or early isolates lacking (early) these mutations resulted in uniformly lethal disease in nonhuman primates (NHPs), albeit with slightly delayed kinetics with late isolates. The recent report of a possible reemergence of EBOV from a persistent infection in a survivor of the epidemic highlights the urgency for understanding the impact of genetic variation on EBOV pathogenesis. However, potential molecular differences in host responses remain unknown. To address this gap in knowledge, we conducted the first comparative analysis of the host responses to lethal infection with EBOV-Mayinga and EBOV-Makona isolates using bivariate, longitudinal, regression, and discrimination transcriptomic analyses. Our analysis shows a conserved core of differentially expressed genes (DEGs) involved in antiviral defense, immune cell activation, and inflammatory processes in response to EBOV-Makona and EBOV-Mayinga infections. Additionally, EBOV-Makona and EBOV-Mayinga infections could be discriminated based on the expression pattern of a small subset of genes. Transcriptional responses to EBOV-Makona isolates that emerged later during the epidemic, specifically those from Mali and Liberia, lacked signatures of profound lymphopenia and excessive inflammation seen following infection with EBOV-Mayinga and early EBOV-Makona isolate C07. Overall, these findings provide novel insight into the mechanisms underlying the lower case fatality rate (CFR) observed with EBOV-Makona compared to EBOV-Mayinga.

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The Ebola outbreak, 2013–2016: old lessons for new epidemics

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2016.0297 ◽

2017 ◽

Vol 372 (1721) ◽

pp. 20160297 ◽

Cited By ~ 114

Author(s):

Cordelia E. M. Coltart ◽

Benjamin Lindsey ◽

Isaac Ghinai ◽

Anne M. Johnson ◽

David L. Heymann

Keyword(s):

Decision Making ◽

West Africa ◽

Disease Control ◽

Ebola Virus ◽

Case Fatality ◽

West African ◽

Lessons Learned ◽

Haemorrhagic Fever ◽

Chronological Order ◽

Epidemiological Parameters

Ebola virus causes a severe haemorrhagic fever in humans with high case fatality and significant epidemic potential. The 2013–2016 outbreak in West Africa was unprecedented in scale, being larger than all previous outbreaks combined, with 28 646 reported cases and 11 323 reported deaths. It was also unique in its geographical distribution and multicountry spread. It is vital that the lessons learned from the world's largest Ebola outbreak are not lost. This article aims to provide a detailed description of the evolution of the outbreak. We contextualize this outbreak in relation to previous Ebola outbreaks and outline the theories regarding its origins and emergence. The outbreak is described by country, in chronological order, including epidemiological parameters and implementation of outbreak containment strategies. We then summarize the factors that led to rapid and extensive propagation, as well as highlight the key successes, failures and lessons learned from this outbreak and the response. This article is part of the themed issue ‘The 2013–2016 West African Ebola epidemic: data, decision-making and disease control’.

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Maternal and Infant Death and the rVSV-ZEBOV Vaccine Through Three Recent Ebola Virus Epidemics-West Africa, DRC Équateur and DRC Kivu: 4 Years of Excluding Pregnant and Lactating Women and Their Infants from Immunization

Current Tropical Medicine Reports ◽

10.1007/s40475-019-00195-w ◽

2019 ◽

Vol 6 (4) ◽

pp. 213-222 ◽

Cited By ~ 9

Author(s):

David A. Schwartz

Keyword(s):

At Risk ◽

Clinical Trials ◽

West Africa ◽

Pregnant Women ◽

Ebola Virus ◽

Disease Outbreaks ◽

Case Fatality ◽

Viral Disease ◽

Lactating Women ◽

Health Communities

Abstract Purpose of Review Ebola virus infection has one of the highest overall case fatality rates of any viral disease. It has historically had an especially high case mortality rate among pregnant women and infants—greater than 90% for pregnant women in some outbreaks and close to 100 % in fetuses and newborns. The Merck recombinant vaccine against Ebola virus, termed rVSV-ZEBOV, underwent clinical trials during the 2013–2015 West Africa Ebola epidemic where it was found to be 100% efficacious. It was subsequently used during the 2018 DRC Équateur outbreak and in the 2018 DRC Kivu Ebola which is still ongoing, where its efficacy is 97.5 %. Pregnant and lactating women and their infants have previously been excluded from the design, clinical trials, and administration of many vaccines and drugs. This article critically examines the development of the rVSV-ZEBOV vaccine and its accessibility to pregnant and lactating women and infants as a life-saving form of prevention through three recent African Ebola epidemics—West Africa, DRC Équateur, and DRC Kivu. Recent Findings Pregnant and lactating women and their infants were excluded from participation in the clinical trials of rVSV-ZEBOV conducted during the West Africa epidemic. This policy of exclusion was continued with the occurrence of the DRC Équateur outbreak in 2018, in spite of calls from the public health and global maternal health communities to vaccinate this population. Following the onset of the DRC Kivu epidemic, the exclusion persisted. Eventually, the policy was reversed to include vaccination of pregnant and lactating women. However, it was not implemented until June 2019, 10 months after the start of the epidemic, placing hundreds of women and infants at risk for this highly fatal infection. Summary The historical policy of excluding pregnant and lactating women and infants from vaccine design, clinical trials, and implementation places them at risk, especially in situations of infectious disease outbreaks. In the future, all pregnant women, regardless of trimester, breastfeeding mothers, and infants, should have access to the Ebola vaccine.

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Transcriptional analysis of lymphoid tissues from infected nonhuman primates reveals the basis for attenuation and immunogenicity of an Ebola virus encoding a mutant VP35 protein

Journal of Virology ◽

10.1128/jvi.01995-20 ◽

2021 ◽

Author(s):

Amanda Pinski ◽

Courtney Woolsey ◽

Allen Jankeel ◽

Robert Cross ◽

Christopher F. Basler ◽

...

Keyword(s):

Immune Response ◽

Nonhuman Primates ◽

Ebola Virus ◽

Transcriptional Response ◽

Transcriptional Analysis ◽

Lymphoid Tissues ◽

High Dose ◽

Type I ◽

Wild Type ◽

Transcriptional Responses

Infection with Zaire ebolavirus (EBOV), a member of the Filoviridae family, causes a disease characterized by high levels of viremia, aberrant inflammation, coagulopathy, and lymphopenia. EBOV initially replicates in lymphoid tissues and disseminates via dendritic cells (DCs) and monocytes to liver, spleen, adrenal gland and other secondary organs. EBOV protein VP35 is a critical immune evasion factor that inhibits type I interferon signaling and DC maturation. Nonhuman primates immunized with a high dose (5x105 PFU) of recombinant EBOV containing a mutated VP35 (VP35m) are protected from challenge with wild-type (wt)EBOV. This protection is accompanied by a transcriptional response in the peripheral blood reflecting a regulated innate immune response and a robust induction of adaptive immune genes. However, the host transcriptional response to VP35m in lymphoid tissues has not been evaluated. Therefore, we conducted a transcriptional analysis of axillary and inguinal lymph nodes, and spleen tissues of NHPs infected with a low dose (2x104 PFU) of VP35m and then backchallenged with a lethal dose of wtEBOV. VP35m induced early transcriptional responses in lymphoid tissues that are distinct from those observed in wtEBOV challenge. Specifically, we detected robust antiviral innate and adaptive responses and fewer transcriptional changes in genes with roles in angiogenesis, apoptosis and inflammation. Two of three macaques survived wtEBOV backchallenge, with only the nonsurvivor displaying a transcriptional response reflecting Ebola virus disease. These data suggest that VP35 is a key modulator of early host responses in lymphoid tissues, thereby regulating disease progression and severity following EBOV challenge. IMPORTANCE Zaire Ebola virus (EBOV) infection causes a severe and often fatal disease characterized by inflammation, coagulation defects, and organ failure driven by a defective host immune response. Lymphoid tissues are key sites of EBOV pathogenesis and generation of an effective immune response to infection. A recent study demonstrated that infection with an EBOV encoding a mutant VP35, a viral protein that antagonizes host immunity, can protect nonhuman primates (NHPs) against lethal EBOV challenge. However, no studies have examined the response to this mutant EBOV in lymphoid tissues. Here, we characterize the gene expression of lymphoid tissues from NHPs challenged with the mutant EBOV and subsequently with wild-type EBOV to identify signatures of a protective host response. Our findings are critical for elucidating viral pathogenesis, mechanisms of host antagonism and the role of lymphoid organs in protective responses to EBOV to improve the development of antivirals and vaccines against EBOV.

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Genome-Wide Patterns of Intrahuman Dengue Virus Diversity Reveal Associations with Viral Phylogenetic Clade and Interhost Diversity

Journal of Virology ◽

10.1128/jvi.00736-12 ◽

2012 ◽

Vol 86 (16) ◽

pp. 8546-8558 ◽

Cited By ~ 58

Author(s):

Poornima Parameswaran ◽

Patrick Charlebois ◽

Yolanda Tellez ◽

Andrea Nunez ◽

Elizabeth M. Ryan ◽

...

Keyword(s):

Genetic Variation ◽

Dengue Virus ◽

Strong Association ◽

Viral Fitness ◽

Envelope Gene ◽

Specific Method ◽

Coding Region ◽

Virus Diversity ◽

Genome Wide ◽

The Impact

Analogous to observations in RNA viruses such as human immunodeficiency virus, genetic variation associated with intrahost dengue virus (DENV) populations has been postulated to influence viral fitness and disease pathogenesis. Previous attempts to investigate intrahost genetic variation in DENV characterized only a few viral genes or a limited number of full-length genomes. We developed a whole-genome amplification approach coupled with deep sequencing to capture intrahost diversity across the entire coding region of DENV-2. Using this approach, we sequenced DENV-2 genomes from the serum of 22 Nicaraguan individuals with secondary DENV infection and captured ∼75% of the DENV genome in each sample (range, 40 to 98%). We identified and quantified variants using a highly sensitive and specific method and determined that the extent of diversity was considerably lower than previous estimates. Significant differences in intrahost diversity were detected between genes and also between antigenically distinct domains of the Envelope gene. Interestingly, a strong association was discerned between the extent of intrahost diversity in a few genes and viral clade identity. Additionally, the abundance of viral variants within a host, as well as the impact of viral mutations on amino acid encoding and predicted protein function, determined whether intrahost variants were observed at the interhost level in circulating Nicaraguan DENV-2 populations, strongly suggestive of purifying selection across transmission events. Our data illustrate the value of high-coverage genome-wide analysis of intrahost diversity for high-resolution mapping of the relationship between intrahost diversity and clinical, epidemiological, and virological parameters of viral infection.

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The impact of malaria coinfection on Ebola virus disease outcomes: A systematic review and meta-analysis

PLoS ONE ◽

10.1371/journal.pone.0251101 ◽

2021 ◽

Vol 16 (5) ◽

pp. e0251101

Author(s):

Hannah M. Edwards ◽

Helen Counihan ◽

Craig Bonnington ◽

Jane Achan ◽

Prudence Hamade ◽

...

Keyword(s):

Systematic Review ◽

Ebola Virus ◽

Virus Disease ◽

Meta Analysis ◽

Case Fatality ◽

The Body ◽

Diagnostic Methods ◽

Ebola Virus Disease ◽

Significant Difference ◽

The Impact

Introduction Viral outbreaks present a particular challenge in countries in Africa where there is already a high incidence of other infectious diseases, including malaria which can alter immune responses to secondary infection. Ebola virus disease (EVD) is one such problem; understanding how Plasmodium spp. and Ebolavirus (EBOV) interact is important for future outbreaks. Methods We conducted a systematic review in PubMed and Web of Science to find peer-reviewed papers with primary data literature to determine 1) prevalence of EBOV/Plasmodium spp. coinfection, 2) effect of EBOV/Plasmodium spp. coinfection on EVD pathology and the immune response, 3) impact of EBOV/Plasmodium spp. coinfection on the outcome of EVD-related mortality. Random effects meta-analyses were conducted with the R package meta to produce overall proportion and effect estimates as well as measure between-study heterogeneity. Results From 322 peer-reviewed papers, 17 were included in the qualitative review and nine were included in a meta-analysis. Prevalence of coinfection was between 19% and 72%. One study reported significantly lower coagulatory response biomarkers in coinfected cases but no difference in inflammatory markers. Case fatality rates were similar between EBOV(+)/Pl(+) and EBOV(+)/Pl(-) cases (62.8%, 95% CI 49.3–74.6 and 56.7%, 95% CI 53.2–60.1, respectively), and there was no significant difference in risk of mortality (RR 1.09, 95% CI 0.90–1.31) although heterogeneity between studies was high. One in vivo mouse model laboratory study found no difference in mortality by infection status, but another found prior acute Plasmodium yoeli infection was protective against morbidity and mortality via the IFN-γ signalling pathway. Conclusion The literature was inconclusive; studies varied widely and there was little attempt to adjust for confounding variables. Laboratory studies may present the best option to answer how pathogens interact within the body but improvement in data collection and analysis and in diagnostic methods would aid patient studies in the future.

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Ebola virus is evolving but not changing: no evidence for functional change in EBOV from 1976 to the 2014 outbreak

10.1101/014480 ◽

2015 ◽

Cited By ~ 1

Author(s):

Abayomi S Olabode ◽

Xiaowei Jiang ◽

David L Robertson ◽

Simon C Lovell

Keyword(s):

Genetic Variation ◽

Protein Structure ◽

Amino Acid ◽

West Africa ◽

Ebola Virus ◽

Functional Change ◽

Minimal Effect ◽

Functional Changes ◽

Epidemiological Factors ◽

The Difference

The Ebola epidemic is having a devastating impact in West Africa. Sequencing of Ebola viruses from infected individuals has revealed extensive genetic variation, leading to speculation that the virus may be adapting to the human host and accounting for the scale of the 2014 outbreak. We show that so far there is no evidence for adaptation of EBOV to humans. We analyze the putatively functional changes associated with the current and previous Ebola outbreaks, and find no significant molecular changes. Observed amino acid replacements have minimal effect on protein structure, being neither stabilizing nor destabilizing. Replacements are not found in regions of the proteins associated with known functions and tend to occur in disordered regions. This observation indicates that the difference between the current and previous outbreaks is not due to the observed evolutionary change of the virus. Instead, epidemiological factors must be responsible for the unprecedented spread of EBOV.

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VSV-EBOV Induces Temporal and Dose-Dependent Transcriptional Responses in Non-human Primates

Frontiers in Virology ◽

10.3389/fviro.2021.747198 ◽

2021 ◽

Vol 1 ◽

Author(s):

Amanda N. Pinski ◽

Kevin J. Maroney ◽

Andrea Marzi ◽

Ilhem Messaoudi

Keyword(s):

Cell Activation ◽

Ebola Virus ◽

Virus Disease ◽

Lethal Dose ◽

Transcriptional Analysis ◽

B Cell Activation ◽

Transcriptional Responses ◽

Transcriptional Signature ◽

Before And After ◽

Ebov Infection

Zaire Ebola virus (EBOV), the causative agent of Ebola virus disease (EVD), is a member of the Filoviridae family. EVD is characterized by innate and adaptive immune dysregulation that leads to excessive inflammation, coagulopathy, lymphopenia, and multi-organ failure. Recurrent outbreaks of EBOV emphasize the critical need for effective and deployable anti-EBOV vaccines. The FDA-approved VSV-EBOV vaccine protects non-human primates (NHPs) and humans from EBOV when given at a 10–20 million PFU dose. We recently demonstrated that a dose as small as 10 PFU protected NHPs from lethal EBOV infection. Furthermore, 1 PFU of VSV-EBOV protected 75% of vaccinated NHPs. In this study, we performed a comparative transcriptional analysis of the whole blood transcriptome in NHPs vaccinated with doses of VSV-EBOV associated with complete protection (10M PFU), protection with mild EVD (10 PFU), and break-through protection (1 PFU) before and after challenge with a lethal dose of EBOV Makona. Transcriptional findings demonstrated that, regardless of dose, vaccination significantly attenuated the upregulation of genes associated with fatal EVD. Genes involved in T- and B-cell activation were more highly expressed in groups receiving 10 or 10M PFU than in 1 PFU–vaccinated animals. Furthermore, the singular vaccinated (1 PFU) non-survivor exhibited a transcriptional signature distinct from both surviving vaccinated animals and controls that received an irrelevant vaccine. These findings provide additional insight into mechanisms of vaccine-mediated protection and informing public policy on vaccine distribution during outbreaks.

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Early Transcriptional Changes within Liver, Adrenal Gland, and Lymphoid Tissues Significantly Contribute to Ebola Virus Pathogenesis in Cynomolgus Macaques

Journal of Virology ◽

10.1128/jvi.00250-20 ◽

2020 ◽

Vol 94 (11) ◽

Author(s):

Allen Jankeel ◽

Andrea R. Menicucci ◽

Courtney Woolsey ◽

Karla A. Fenton ◽

Norma Mendoza ◽

...

Keyword(s):

Ebola Virus ◽

Adrenal Glands ◽

Case Fatality ◽

Hemorrhagic Fever ◽

Organ Damage ◽

Host Responses ◽

Lymphoid Tissues ◽

Cynomolgus Macaques ◽

Ebov Infection ◽

Transcriptional Changes

ABSTRACT Ebola virus (EBOV) continues to pose a significant threat to human health, as evidenced by the 2013–2016 epidemic in West Africa and the ongoing outbreak in the Democratic Republic of the Congo. EBOV causes hemorrhagic fever, organ damage, and shock culminating in death, with case fatality rates as high as 90%. This high lethality combined with the paucity of licensed medical countermeasures makes EBOV a critical human pathogen. Although EBOV infection results in significant damage to the liver and the adrenal glands, little is known about the molecular signatures of injury in these organs. Moreover, while changes in peripheral blood cells are becoming increasingly understood, the host responses within organs and lymphoid tissues remain poorly characterized. To address this knowledge gap, we tracked longitudinal transcriptional changes in tissues collected from EBOV-Makona-infected cynomolgus macaques. Following infection, both liver and adrenal glands exhibited significant and early downregulation of genes involved in metabolism, coagulation, hormone synthesis, and angiogenesis; upregulated genes were associated with inflammation. Analysis of lymphoid tissues showed early upregulation of genes that play a role in innate immunity and inflammation and downregulation of genes associated with cell cycle and adaptive immunity. Moreover, transient activation of innate immune responses and downregulation of humoral immune responses in lymphoid tissues were confirmed with flow cytometry. Together, these data suggest that the liver, adrenal gland, and lymphatic organs are important sites of EBOV infection and that dysregulating the function of these vital organs contributes to the development of Ebola virus disease. IMPORTANCE Ebola virus (EBOV) remains a high-priority pathogen since it continues to cause outbreaks with high case fatality rates. Although it is well established that EBOV results in severe organ damage, our understanding of tissue injury in the liver, adrenal glands, and lymphoid tissues remains limited. We begin to address this knowledge gap by conducting longitudinal gene expression studies in these tissues, which were collected from EBOV-infected cynomolgus macaques. We report robust and early gene expression changes within these tissues, indicating they are primary sites of EBOV infection. Furthermore, genes involved in metabolism, coagulation, and adaptive immunity were downregulated, while inflammation-related genes were upregulated. These results indicate significant tissue damage consistent with the development of hemorrhagic fever and lymphopenia. Our study provides novel insight into EBOV-host interactions and elucidates how host responses within the liver, adrenal glands, and lymphoid tissues contribute to EBOV pathogenesis.

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Comparative multi-tissue profiling reveals extensive tissue-specificity in transcriptome reprogramming upon cold exposure

10.1101/2021.03.26.437139 ◽

2021 ◽

Author(s):

Noushin Hadadi ◽

Martina Spiljar ◽

Karin Steinbach ◽

Gabriela Salinas ◽

Doron Merkler ◽

...

Keyword(s):

Gene Expression ◽

Cold Exposure ◽

Tissue Specificity ◽

Gene Expression Pattern ◽

Transcriptional Analysis ◽

Transcriptional Responses ◽

Adipose Tissues ◽

Brown Adipose ◽

Wide Range ◽

The Impact

ABSTRACTCold exposure is an extensively used intervention for enhancing thermogenic and mitochondrial activity in adipose tissues. As such, it has been suggested as a potential lifestyle intervention for body weight maintenance. The metabolic consequences of cold acclimation are not limited to the adipose tissues, however the impact on rest of the tissues in context of their gene expression profile remains unclear. Here we provide a systematic characterization of cold exposure-mediated effects in a comparative multi-tissue RNA sequencing approach using wide range of organs including spleen, bone marrow, spinal cord, brain, hypothalamus, ileum, liver, subcutaneous-, visceral- and brown adipose tissues. Our findings highlight that transcriptional responses to cold exposure exhibit high degree of tissue-specificity both at the gene level and at GO enrichment gene sets, which is not directed by the basal gene expression pattern exhibited by the various organs. Our study places the cold adaptation of individual tissues in a whole-organism framework and provides an integrative transcriptional analysis necessary for understanding the cold exposure-mediated biological reprograming.

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