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Whitfield ZJ, Prasad AN, Ronk AJ, Kuzmin IV, Ilinykh PA, Andino R, Bukreyev A. Species-Specific Evolution of Ebola Virus during Replication in Human and Bat Cells. Cell Rep 2020; 32:108028. [PMID: 32814037 PMCID: PMC7434439 DOI: 10.1016/j.celrep.2020.108028] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 05/12/2020] [Accepted: 07/22/2020] [Indexed: 12/13/2022] Open
Abstract
Ebola virus (EBOV) causes a severe, often fatal disease in humans and nonhuman primates. Within the past decade, EBOV has caused two large and difficult-to-control outbreaks, one of which recently ended in the Democratic Republic of the Congo. Bats are the likely reservoir of EBOV, but little is known of their relationship with the virus. We perform serial passages of EBOV in human and bat cells and use circular sequencing to compare the short-term evolution of the virus. Virus populations passaged in bat cells have sequence markers indicative of host RNA editing enzyme activity, including evidence for ADAR editing of the EBOV glycoprotein. Multiple regions in the EBOV genome appear to have undergone adaptive evolution when passaged in bat and human cells. Individual mutated viruses are rescued and characterized. Our results provide insight into the host species-specific evolution of EBOV and highlight the adaptive flexibility of the virus.
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Affiliation(s)
- Zachary J Whitfield
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Abhishek N Prasad
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA; Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX, USA
| | - Adam J Ronk
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA; Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX, USA
| | - Ivan V Kuzmin
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA; Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX, USA
| | - Philipp A Ilinykh
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA; Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX, USA
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA.
| | - Alexander Bukreyev
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA; Department Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX, USA; Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX, USA.
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Abstract
Marburgviruses are closely related to ebolaviruses and cause a devastating disease in humans. In 2012, we published a comprehensive review of the first 45 years of research on marburgviruses and the disease they cause, ranging from molecular biology to ecology. Spurred in part by the deadly Ebola virus outbreak in West Africa in 2013-2016, research on all filoviruses has intensified. Not meant as an introduction to marburgviruses, this article instead provides a synopsis of recent progress in marburgvirus research with a particular focus on molecular biology, advances in animal modeling, and the use of Egyptian fruit bats in infection experiments.
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Affiliation(s)
- Judith Olejnik
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, 02118, USA.,National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, 02118, USA
| | - Elke Mühlberger
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, 02118, USA.,National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, 02118, USA
| | - Adam J Hume
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, 02118, USA.,National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, 02118, USA
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Dolan PT, Whitfield ZJ, Andino R. Mechanisms and Concepts in RNA Virus Population Dynamics and Evolution. Annu Rev Virol 2018; 5:69-92. [PMID: 30048219 DOI: 10.1146/annurev-virology-101416-041718] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
RNA viruses are unique in their evolutionary capacity, exhibiting high mutation rates and frequent recombination. They rapidly adapt to environmental changes, such as shifts in immune pressure or pharmacological challenge. The evolution of RNA viruses has been brought into new focus with the recent developments of genetic and experimental tools to explore and manipulate the evolutionary dynamics of viral populations. These studies have uncovered new mechanisms that enable viruses to overcome evolutionary challenges in the environment and have emphasized the intimate relationship of viral populations with evolution. Here, we review some of the emerging viral and host mechanisms that underlie the evolution of RNA viruses. We also discuss new studies that demonstrate that the relationship between evolutionary dynamics and virus biology spans many spatial and temporal scales, affecting transmission dynamics within and between hosts as well as pathogenesis.
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Affiliation(s)
- Patrick T Dolan
- Department of Biology, Stanford University, Stanford, California 94305, USA.,Department of Microbiology and Immunology, University of California, San Francisco, California 94143, USA;
| | - Zachary J Whitfield
- Department of Microbiology and Immunology, University of California, San Francisco, California 94143, USA;
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, California 94143, USA;
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Transcription-associated mutational pressure in the Parvovirus B19 genome: Reactivated genomes contribute to the variability of viral populations. J Theor Biol 2017; 435:199-207. [PMID: 28941869 DOI: 10.1016/j.jtbi.2017.09.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 07/12/2017] [Accepted: 09/19/2017] [Indexed: 11/22/2022]
Abstract
In this study we used non-overlapping parts of the two long open reading frames coding for nonstructural (NS) and capsid (VP) proteins of all available sequences of the Parvovirus B19 subgenotype 1a genome and found out that the rates of A to G, C to T and A to T mutations are higher in the first long reading frame (NS) of the virus than in the second one (VP). This difference in mutational pressure directions for two parts of the same viral genome can be explained by the fact of transcription of just the first long reading frame during the lifelong latency in nonerythroid cells. Adenine deamination (producing A to G and A to T mutations) and cytosine deamination (producing C to T mutations) occur more frequently in transcriptional bubbles formed by DNA "plus" strand of the first open reading frame. These mutations can be inherited only in case of reactivation of the infectious virus due to the help of Adenovirus that allows latent Parvovirus B19 to start transcription of the second reading frame and then to replicate its genome by the rolling circle mechanism using the specific origin. Results of this study provide evidence that the genomes reactivated from latency make significant contributions to the variability of Parvovirus B19.
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Khrustalev VV, Khrustaleva TA, Sharma N, Giri R. Mutational Pressure in Zika Virus: Local ADAR-Editing Areas Associated with Pauses in Translation and Replication. Front Cell Infect Microbiol 2017; 7:44. [PMID: 28275585 PMCID: PMC5319961 DOI: 10.3389/fcimb.2017.00044] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 02/07/2017] [Indexed: 12/21/2022] Open
Abstract
Zika virus (ZIKV) spread led to the recent medical health emergency of international concern. Understanding the variations in virus system is of utmost need. Using available complete sequences of ZIKV we estimated directions of mutational pressure along the length of consensus sequences of three lineages of the virus. Results showed that guanine usage is growing in ZIKV RNA plus strand due to adenine to guanine transitions, while adenine usage is growing due to cytosine to adenine transversions. Especially high levels of guanine have been found in two-fold degenerated sites of certain areas of RNA plus strand with high amount of secondary structure. The usage of cytosine in two-fold degenerated sites shows direct dependence on the amount of secondary structure in 52% (consensus sequence of East African ZIKV lineage)—32% (consensus sequence of epidemic strains) of the length of RNA minus strand. These facts are the evidences of ADAR-editing of both strands of ZIKV genome during pauses in replication. RNA plus strand can also be edited by ADAR during pauses in translation caused by the appearance of groups of rare codons. According to our results, RNA minus strand of epidemic ZIKV strain has lower number of points in which polymerase can be stalled (allowing ADAR-editing) compared to other strains. The data on preferable directions of mutational pressure in epidemic ZIKV strain is useful for future vaccine development and understanding the evolution of new strains.
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Affiliation(s)
| | - Tatyana A Khrustaleva
- Laboratory of Cellular Technologies, Institute of Physiology of the National Academy of Sciences of Belarus Minsk, Belarus
| | - Nitin Sharma
- School of Basic Sciences, Indian Institute of Technology Mandi Mandi, India
| | - Rajanish Giri
- School of Basic Sciences, Indian Institute of Technology Mandi Mandi, India
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