Javaney Thomas

ENGL 21003

Michael Grove

March 23, 2018

Literature Review Draft

The Ebola Virus: How Evolution and Epidemiological Factors point to a Potential for Vaccination

Abstract

Diseases of the Filovirus family, a group of RNA based viruses, are deadly due to their progressive genetic variation and diverse nature. The Ebola virus exhibits such traits as it has caused outbreaks in African countries such as Zaire, Liberia and Sudan, with each region having high fatality rates for those infected. In this discussion, the progression of genetic diversity, epidemiological factors such as transmission and cultural practices in relation to the Ebola 2014-2016 epidemic will be examined as well as the current and future prospects to treat the disease.

Introduction

The Ebola Virus referred to as Ebola virus disease (EVD) “causes an acute hemorrhagic fever in humans with a fatality rate of up to 90%”, it is a member of the Filoviridae family[1], a family of highly fatal diseases. (EVD) was first discovered in 1976 in South Sudan and Zaire (Congo). It later reappeared with much higher mortality rates in the 2014-2016 outbreak, and spread to countries such as Liberia, Sierra Leone and Guinea, attaining epidemic status. These higher mortality rates indicate genetic change in the disease and change in its transmission. Naturally, a virus is a microscopic infective agent that replicates within the living cells of a host. During this replication, “It may reproduce errors (mutations); this ability to mutate is responsible for the ability of some viruses to change slightly in each infected person, making treatment difficult.”[2] As with (EVD), there are many ways a virus can change, such as through recombination, reassortment, or mutation.[3] This is the basis in the rapid development of the Ebola virus, as according to a) and Zaire (ZEBOV), and the commonly named Ebola from the Ebola river (EBOV).

However, with the persistent changes in the genetic sequence of the disease, there has not been a change in the way the virus affects the human body. As researchers explain in the article “Ebolavirus is evolving not changing: No evidence for functional change in EBOV from the 1976 to the 2014 outbreak” (2015) by Aboyami S. Olabode et al., stating that “none of the amino acid replacements lead to identifiable functional changes”. Additionally, all amino acid replacements are “not found in regions of the proteins associated with known functions…specifically intrinsically disordered regions,”[4] and “higher levels of variation in the (EBOV)” …were unique the 2014 outbreak (Gire et al., 2014). The higher mortality rates in the more recent outbreak compared to the 1976 incidence, and the data that portrays no functional change in proteins, indicates that the disease has genetically evolved in the adaptation and transmission in human hosts but currently has not become more fatal as there are no new symptoms.

According to Abayomi et al, “the amino acid replacements are due to incomplete purifying selection”, therefore these replacements would naturally have no function for the disease. The main EBOV proteins such as GP and VP40, were found in “disordered regions…. which only made up 27% of the protein sequence.” This lack of interaction by the viral proteins with functional sites led to “a range of amino acids contributing to the same functional role” (Nishikawa et al., 2010). Thus, creating inefficiency within the virus.

Though viral proteins are not allocated properly in the evolution process, the virus has still increased its viral fitness, as it has better adapted to the human immune system, which increases the possibility of intrahost and interhost transmission. According to Daniel J Park et al., the 2014 EBOV outbreak had three different lineages, each derived from the one prior, referred to as SL1, SL2 and SL3, with SL3 “dominating the viral population”, becoming the “most prevalent lineage” as it was best adapted to the human host. Additionally, to support the conclusion of evolution in its adaptation, the data set revealed that “97% of the genomes carry the SL3 mutation and the remainder belong to SL2” (Park et al., 2015). This is observed in the data set from the article “Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone” by Daniel J Park et al., which depicts the phylogenetic tree of the virus with the “new EBOV genomes (232 genomes, dark blue), sampled from June 16 through December 26, 2014” …which… “fills in the missing ancestry between EBOV Makona genome data sets. Tips are labeled for EBOV from five non-African health-care workers (HCWs) infected in Sierra Leone and treated in Europe (sequenced by other groups, light green).”[5] Depicted in diagram B is a “coding-complete EBOV genome alignment including 340 EBOV Makona sequences. Each colored vertex represents a sampled viral haplotype, with colors indicating countries of origin” (Daniel J Park 2015).

 

On an epidemiological standpoint, the cultural practices, in the early stages of the 2014 Ebola outbreak aided in the transmission of the disease to many people, driving the evolution of the virus as it adapted within hosts. According to Nell Grey et al., in the article ‘When Ebola enters a home, a family, a community’: A qualitative study of population perspectives on Ebola control measures in rural and urban areas of Sierra Leone”(2018), the cultural practices of the local people served “as barriers to an effective response, linked with accounts of people fleeing affected areas, hiding sick and dead community members, resisting healthcare services, and conducting violent attacks on screening and burial teams.”[6] This aided in human-to-human transmission as explained by Daniel J Park’s article, “we conclude that a combination of human-to-human transmission and recurrent mutations is likely responsible for the intrahost variant’s (iSNVs) pattern where … samples containing this variant often cluster on the phylogenetic tree, which means that variations in the virus are shared among two or more patients”. According to Park et al., “shared iSNVs could be explained by patient infection from multiple sources, sample contamination, recurring mutations (with or without balancing selection to reinforce mutations), or co-transmission of slightly diverged viruses that arose by mutation earlier in the transmission chain.”  The ease of transmission of the disease is a major factor in the challenge to vaccinate it. It continuously mutates today as the SL3 and SL4 strains have slight variations within groups of people as they have different genetic compositions. It is true that the disease is very aggressive, however vaccination does seem feasible.

 

 

 

Based on experimental research on gold standard models such as rodents, non-human primates (NHPs) and pigs, scientists have found several promising methods to treat the ZEBOV, SEBOV, BEBOV and MARV lineages. According to Andrea Marzi and Heinz Feldmann’s article “Ebola virus vaccines: an overview of current approaches” (2014), the classical method of using an inactivated virus has been abandoned due to its failure in protecting NHPs from lethal exposure to ZEBOV, as it only had success in guinea pigs. Now, the approach is to use virus-like particles (VLPs) that consist of “ZEBOV matrix protein VP40, glycoprotein (GP) and in some cases nucleoprotein (NP).”[7] A “100% protection from lethal ZEBOV infection” has been achieved in rodents and triple vaccination of NHPs with VLPs that contain “GP, NP, VP40 and the RIBI adjuvant” has yielded the same results. An adjuvant is “a pharmacological or immunological agent that modifies the effects of other agents.”[8] “RIBI induces cytokine production by immune cells, leading to antigen uptake and presentation.”[9] Additionally, the use of chimeric VLPs (ZEBOV-GP/MARVVP40) has been developed for cross-protection against ZEBOV and MARV with results in guinea pigs revealing protection is dependent on GP.

Secondly, researchers have turned to DNA vaccines. According to Emmie de Wit et al., in “Tackling Ebola: new Insights into prophylactic and therapeutic intervention strategies”, “DNA vaccines are purified plasmid preparations containing one or more DNA sequences of the pathogen of interest in the recipient on delivery.”[10]The advantages of this method is that “pre-existing immunity is not relevant” so the approach is reusable, “DNA vaccines have the advantage to be rapidly adapted…and pathogens and plasmids are noninfectious and easy to produce in large quantities”[11], as supported by Mazi and Feldmann in “Ebola virus vaccines: an overview of current approaches.” Both articles when cross-referenced and examined support the current data on DNA vaccines as of 2014(Ebola virus vaccines…) from 2011(Tackling Ebola…).

DNA vaccine expressing ZEBOV-GP or ZEBOV-NP exhibited a 100% positive immune response on a cellular and humoral basis in mice. This took four doses of the plasmid DNA. The cons of the approach were that “50% of the surviving animals developed viremia” and that in “strain 13 guinea pigs there was partial protection” from the virus. As for NHPs DNA vaccination alone is not sufficient. However, use of DNA with recombinant Adenovirus 5 (rAd5)-based vectors was effective enough to lead to phase I clinical trials “showing that three doses of a DNA vaccine-encoding ZEBOV-GP, -NP and SEBOV-GP are immunogenic in humans.”

Thirdly, research into the antisense therapy has shown promising potential although the “feasibility in an outbreak setting remains to be determined”, according to Wit et al., (de Wit et al. Genome Medicine 2011, 3:5). This antisense strategy “inhibits EBOV replication” which reduces the pathogenic effects in EBOV, “allowing the immune system more time to clear the infections.” It targets viral proteins such as VP24, VP35, and ZEBOV L, as studied in rodents and NHPs, leading to a “66-100% protection from lethal EBOV exposure.

Similarly, in another study, “using chemically modified oligonucleotides called phosphorodiamidate morpholino oligomers, conferred 60% protection against lethal ZEBOV challenge in NHPs following intraperitoneal, subcutaneous and intravenous administration.”

 

Treatment	Efficacy	Prophylactic	Therapeutic	Status	References
Vaccines
DNA vaccines	Rodents and NHPs	Yes	Unknown	Phase I clinical trails	[57,60]
Adenovirus	Rodents and NHPs	Yes	Unknown	Phase I clinical trails	[62,63]
rVSV-EBOV	Rodents and NHPs	Yes	Yes	Experimental	[65-68]
HPIV3-EBOV	Rodents and NHPs	Yes	Unknown	Experimental	[70]
EBOV-VLPs	Rodents and NHPs	Yes	Unknown	Experimental	[71]
Replication-deficient ZEBOV	Rodents	Yes	Unknown	Experimental	[72]
Antivirals
rhAPC	Partial in NHPs	Unknown	Yes	Licensed	[75]
rNAPc2	Partial in NHPs	Yes	Yes	Phase II clinical trails	[76]
FGI-103, FGI-104 and FGI-106	Rodents	Yes	Yes	Experimental	[81-83]
Antisense oligonucleotides	Rodents and NHPs	Yes	Yes	Experimental	[85-88]

Promising vaccine and antiviral drug development for the prevention and treatment of Ebolavirus

*Licensed for the treatment of sepsis-induced coagulation disorders. †The antithrombotic potential of rNAPc2 in orthopedic surgery and coronary revascularization was tested. ‡Only FGI-106 was tested therapeutically. Abbreviations: HPIV3, human parainfluenza virus type 3; NHP, non-human primate; rhAPC, recombinant human activated protein C; rNAPc2, nematode anticoagulant protein c2; rVSV, recombinant vesicular stomatitis virus; VLP, virus-like particle.

 

This table is taken from the document “Tackling Ebola: new insights into prophylactic and therapeutic intervention strategies” (2011) by Emmie de Wit, Heinz Feldmann and Vincent J Munster. The reference section is derived from this original document. Analysis of this table shows the recent approaches in treatment of EBOV, the success of each and to what stage in the study this success is observed, whether it be clinical, experimental or already licensed.

In conclusion, there are many feasible opportunities to vaccinate the disease in the future. According to experts in Marzi and Feldmann’s article “Tackling Ebola: …” pg. 10 (2014), “funding for GMP/GLP vaccine production and execution of Phase I and Phase II clinical trials” need to be prioritized for EBOV vaccine platforms to be successful. Additionally, the threat of EBOV being used as a bioterrorism agent is acknowledged as a major reason to prioritize these new potential vaccines. As said in the “five-year view” on page 10 of the article, “at least one of the EBOV vaccine approaches will be moved through licensing for stockpiling.” In this way there will be preparations in the case of “future outbreaks, case importations or intentional release”.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Works Cited

 

“Adjuvant.” Wikipedia, Wikimedia Foundation, 26 June 2018, en.wikipedia.org/wiki/Adjuvant.

 

Gray, Nell, et al. “’When Ebola Enters a Home, a Family, a Community’: A Qualitative Study of Population Perspectives on Ebola Control Measures in Rural and Urban Areas of Sierra Leone.” PLOS Medicine, Public Library of Science, 8 June 2018, journals.plos.org/plosntds/article?id=10.1371%2Fjournal.pntd.0006461.

 

Marzi, Andrea, and Heinz Feldmann. “Ebola Virus Vaccines: An Overview of Current Approaches.” HHS Public Access, Expert Rev Vaccines, Apr. 2014, www-ncbi-nlm-nih-gov.ccny-proxy1.libr.ccny.cuny.edu/pmc/articles/PMC4785864/pdf/nihms-764158.pdf.

 

Olabode, Abayomi S, et al. “Ebolavirus Is Evolving Not Changing: No Evidence for Functional Change in EBOV from the 1976 to the 2014 Outbreak.” Www-Ncbi-Nlm-Nih-Gov.ccny-proxy1.Libr.ccny.cuny.edu, Virology, Aug. 2015, www-ncbi-nlm-nih-gov.ccny-proxy1.libr.ccny.cuny.edu/pmc/articles/PMC4503884/.

 

Park, Daniel J, and Gytis Dudas. “Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone.” Www-Ncbi-Nlm-Nih-Gov.ccny-proxy1.Libr.ccny.cuny.edu, Cell, 18 June 2015, www-ncbi-nlm-nih-gov.ccny proxy1.libr.ccny.cuny.edu/pmc/articles/PMC4503805/.

“Using Ribi Adjuvant.” Antibodies: A Laboratory Manual, antibodiesmanual.org/index.php?prt=26.

Witt, E de, et al. “Tackling Ebola: New Insights into Prophylactic and Therapeutic Intervention Strategies.” Www-Ncbi-Nlm-Nih-Gov.ccny-proxy1.Libr.ccny.cuny.edu, Genome Med., 27 Jan. 2011, www-ncbi-nlm-nih-gov.ccny-proxy1.libr.ccny.cuny.edu/pubmed/?term=tackling%2Bebola%3A%2BNew%2Binsights.

 

Witt, E de, et al. “Tackling Ebola: New Insights into Prophylactic and Therapeutic Intervention Strategies.” Http://Genomemedicine.com/Content/3/1/5, BioMed Central, 2011, www-ncbi-nlm-nih-gov.ccny-proxy1.libr.ccny.cuny.edu/pmc/articles/PMC3092090/pdf/gm219.pdf.

 

 

 

 

 

 

[1] https://www-ncbi-nlm-nih-gov.ccny-proxy1.libr.ccny.cuny.edu/pmc/articles/PMC4785864/

[2] https://www.medicinenet.com/script/main/art.asp?articlekey=5997

[3] https://link.springer.com/content/pdf/10.1023%2FA%3A1007989407305.pdf

[4] https://www-ncbi-nlm-nih-gov.ccny-proxy1.libr.ccny.cuny.edu/pmc/articles/PMC4503884/

[5] https://www-ncbi-nlm-nih-gov.ccny-proxy1.libr.ccny.cuny.edu/pmc/articles/PMC4503805/

[6] http://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0006461

[7] https://www-ncbi-nlm-nih-gov.ccny-proxy1.libr.ccny.cuny.edu/pmc/articles/PMC4785864/pdf/nihms-764158.pdf

[8] https://en.wikipedia.org/wiki/Adjuvant

[9] http://antibodiesmanual.org/index.php?prt=26

[10] https://www-ncbi-nlm-nih-gov.ccny-proxy1.libr.ccny.cuny.edu/pmc/articles/PMC3092090/pdf/gm219.pdf

[11] https://www-ncbi-nlm-nih-gov.ccny-proxy1.libr.ccny.cuny.edu/pmc/articles/PMC4785864/pdf/nihms-764158.pdf