Ebola Virus Genome Download

The viral RNA dependent RNA polymerase binds the encapsidated genome at the leader region, then sequentially transcribes each genes by recognizing start and stop signals flanking viral genes. mRNAs are capped and polyadenylated by the L protein during synthesis.

The primary product of the unedited transcript of GP gene yields a smaller non-structural glycoprotein sGP which is efficiently secreted from infected cells. RNA editing allows expression of full-length GP.

Sequence analysis of the second through the sixth genes of the Ebola virus (EBO) genome indicates that it is organized similarly to rhabdoviruses and paramyxoviruses and is virtually the same as Marburg virus (MBG). In vitro translation experiments and predicted amino acid sequence comparisons showed that the order of the EBO genes is: 3'-NP-VP35-VP40-GP-VP30-VP24-L. The transcriptional start and stop (polyadenylation) signals are conserved and all contain the sequence 3'-UAAUU. Three base intergenic sequences are present between the NP and VP35 genes (3'-GAU) and VP40 and GP genes (3'-AGC), and a large intergenic sequence of 142 bases separates the VP30 and VP24 genes. Novel gene overlaps were found between the VP35 and VP40, the GP and VP30, and the VP24 and L genes. Overlaps are 20 or 18 bases in length and are limited to the conserved sequences determined for the transcriptional signals. Stem-and-loop structures were identified in the putative (+) leader RNA and at the 5' end of each mRNA. Hybridization studies showed that a small second mRNA is transcribed from the glycoprotein gene, and is produced by termination of transcription at an atypical polyadenylation signal located in the middle of the coding region. The predicted amino acid sequence of the glycoprotein contains an N-terminal signal peptide sequence, a hydrophobic anchor sequence, and 17 potential N-linked glycosylation sites. Alignment of predicted amino acid sequences showed that the structural proteins of EBO and MBG contain large regions of homology despite the absence of serologic cross-reactivity.

Download Zip 🔥 https://tinurll.com/2y4IBG 🔥

Filoviruses such as Ebola virus continue to pose a substantial health risk to humans. Advances in the sequencing and functional characterization of both pathogen and host genomes have provided a wealth of knowledge to clinicians, epidemiologists and public health responders during outbreaks of high-consequence viral disease. Here, we describe how genomics has been historically used to investigate Ebola virus disease outbreaks and how new technologies allow for rapid, large-scale data generation at the point of care. We highlight how genomics extends beyond consensus-level sequencing of the virus to include intra-host viral transcriptomics and the characterization of host responses in acute and persistently infected patients. Similar genomics techniques can also be applied to the characterization of non-human primate animal models and to known natural reservoirs of filoviruses, and metagenomic sequencing can be the key to the discovery of novel filoviruses. Finally, we outline the importance of reverse genetics systems that can swiftly characterize filoviruses as soon as their genome sequences are available.

Infections with viruses of the mononegaviral family Filoviridae (in particular, members of the genera Ebolavirus and Marburgvirus) are an increasing threat to mankind. Until recently, the infrequent spillover of these viruses into humans and the fact that spillover often occurred in remote locations, coupled with a limited knowledge of non-human reservoir hosts, the use of low-output genomic sequencing, and biosafety and biosecurity restrictions on filovirus research, contributed to the paucity of publicly available data on filovirus genome sequences1. In December 2013, complete genome sequences for only 29 ebolaviruses and 65 marburgviruses were available2 despite the fact that 35 outbreaks of natural filovirus disease had been recorded3.

Since December 2013, atypically extensive filovirus disease outbreaks, from 2013 to 2016 in Western Africa and from 2018 to present in the Democratic Republic of the Congo, have profoundly impacted public health systems. At least 13,675 fatalities from filovirus disease were reported between December 2013 and April 5, 2020 (refs4,5). By leveraging the continued development and improvement of next-generation sequencing technology, >800 complete filovirus genome sequences and over 2,000 draft genomes (that is, genomes with >80% coverage) across classified and unclassified filovirus family members have become available since 2013 (ref.2). Indeed, among high-consequence, Risk Group 4 viruses, the genomic diversity of filoviruses is arguably becoming the best characterized.

The impact and importance of genomics in pathogen characterization is routinely demonstrated, but the rapid prediction of, response to and mitigation of outbreaks requires more detailed genomic information than virus consensus-genome sequencing. Indeed, as predicted6, metagenomic sequencing has become a powerful tool for identifying novel viruses and, crucially, for predicting pathogen emergence7. Targeted or unbiased sequencing of individual clinical samples aids in the identification of outbreaks, the determination of outbreak aetiology and the definition of virus transmission chains by identifying chain-defining single nucleotide polymorphisms (SNPs). Furthermore, field transcriptomics improves our understanding of host responses to virus infection and will be important in deciphering the differences between asymptomatic and symptomatic disease states and in predicting whether patients with acute and chronic disease will survive8. Functional genomics is becoming the tool of choice for the rapid characterization of patient-specific viruses that have not been isolated in culture or that cannot be equitably shared among laboratories across borders9. Finally, the genomic analysis of patient-specific viruses also enables precision medicine by predicting the efficacy of available medical countermeasures (MCMs) against these individual viruses.

Here, we review how recent advances in genomic technologies have shaped past and current responses to outbreaks of Ebola virus disease (EVD), including insights into filovirus diversity and evolution. We emphasize the importance of accurate and rapid large-scale data generation and its implications for the development of MCMs and outbreak response. We also examine the phenomena of Ebola virus (EBOV) persistence in human hosts and provide an overview of recent genomic advances in threat characterization, vaccine development and immunotherapy. Although we focus primarily on EBOV, these practices can apply to all pathogenic filoviruses and other high-consequence viruses capable of sustaining human-to-human transmission.

Although the global distribution and diversity of filoviruses remains largely undefined, metagenomic sequencing is becoming a valuable tool for identifying filovirus reservoirs. Until 1989, disease outbreaks owing to infection by ebolaviruses (including EBOV, Sudan virus (SUDV) and marburgviruses (including Marburg virus (MARV) and Ravn virus (RAVV)) had only been recorded on the African continent (Fig. 1). As the natural reservoir hosts of all of these viruses remained unidentified, despite extensive ecological studies, filoviruses were thought to be African viruses1. This view changed after 1989, when Reston virus (RESTV; of the genus Ebolavirus) was discovered and repeatedly identified as a lethal pathogen of captive crab-eating macaques (Macaca fascicularis) in non-human primate (NHP) breeding facilities in the Philippines10,11,12 (Fig. 1). However, although RESTV can infect humans, it appears to be apathogenic13. RESTV was subsequently considered to be an Asian anomaly to the African filovirus dogma.

a | Outbreaks of Ebola virus disease (EVD) in Africa, including the number of confirmed cases, the case fatality rates and the number of publicly available Ebola virus (EBOV) draft genome sequences per outbreak, are depicted3. Circles represent the relative size (in terms of the number of cases) of the outbreaks. Documented accidental laboratory-acquired infections have been excluded from this figure. b | Overview of global filovirus distribution, excluding EBOV. The place of isolation, known or suspected reservoir host and year of discovery are shown. The description of the distribution of non-EBOV filovirus disease outbreaks includes the total number of confirmed cases and the case fatality rate. BDBV, Bundibugyo virus; BOMV, Bombali virus; HUJV, Hungjio virus; LLOV, Lloviu virus; MARV, Marburg virus; MLAV, Mngl virus; RAVV, Ravn virus; RESTV, Reston virus; SUDV, Sudan virus; TAFV, Ta Forest virus; XILV, Xlng virus.

Classical filovirus-targeted genome sequencing and, later, unbiased broad-scale metagenomic sequencing, shed new light on filovirus ecology. In 2009, the sequencing of samples obtained from Egyptian rousettes (Rousettus aegyptiacus) in Africa revealed that these bats, which are cavernicolous and frugivorous pteropodids, are natural reservoir hosts of both MARV and RAVV. Coding-complete or complete genomic sequences of both viruses were repeatedly obtained from Egyptian rousette populations in Uganda, Sierra Leone and South Africa14,15,16,17, and genomic fragments of these viruses were also detected in populations of these bats in the Democratic Republic of the Congo18 and in Zambia19.

Complete or coding-complete filovirus genome sequences have been obtained from cave-dwelling and house-dwelling bats and highly diverse fish on the African, Asian and European continents (see Fig. 1 for continental distribution). The pathogenic potential of most filoviruses remains unclear, as does the transmission route of pathogenic filoviruses proven to infect humans and pigs or of pathogenic filoviruses suspected to infect chimpanzees, duikers and gorillas. Animals that have been proven to be infected by filoviruses are indicated in black; grey animals are suspected but unproven reservoirs of the indicated viruses. Solid arrows indicate highly likely transmission routes; dashed arrows indicate hypothesized transmission routes. BDBV, Bundibugyo virus; BOMV, Bombali virus; EBOV, Ebola virus; HUJV, Hungjio virus; LLOV, Lloviu virus; MARV, Marburg virus; MLAV, Mngl virus; RAVV, Ravn virus; RESTV, Reston virus; SUDV, Sudan virus; TAFV, Ta Forest virus; XILV, Xlng virus. e24fc04721