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Article ; Online: RNA Virus Fidelity Mutants: A Useful Tool for Evolutionary Biology or a Complex Challenge?

Kautz, Tiffany F / Forrester, Naomi L

2018 Volume 10, Issue 11

Abstract: RNA viruses replicate with low fidelity due to the error-prone nature of the RNA-dependent RNA polymerase, which generates approximately one mutation per round of genome replication. Due to the large population sizes produced by RNA viruses during ... ...

Abstract	RNA viruses replicate with low fidelity due to the error-prone nature of the RNA-dependent RNA polymerase, which generates approximately one mutation per round of genome replication. Due to the large population sizes produced by RNA viruses during replication, this results in a cloud of closely related virus variants during host infection, of which small increases or decreases in replication fidelity have been shown to result in virus attenuation in vivo, but not typically in vitro. Since the discovery of the first RNA virus fidelity mutants during the mid-aughts, the field has exploded with the identification of over 50 virus fidelity mutants distributed amongst 7 RNA virus families. This review summarizes the current RNA virus fidelity mutant literature, with a focus upon the definition of a fidelity mutant as well as methods to confirm any mutational changes associated with the fidelity mutant. Due to the complexity of such a definition, in addition to reports of unstable virus fidelity phenotypes, the future translational utility of these mutants and applications for basic science are examined.
MeSH term(s)	Animals ; Biological Evolution ; Humans ; Mutation ; Protein Biosynthesis ; RNA Replicase/chemistry ; RNA Replicase/genetics ; RNA Replicase/metabolism ; RNA Stability ; RNA Virus Infections/virology ; RNA Viruses/physiology ; Structure-Activity Relationship ; Transcription, Genetic ; Virus Replication/genetics
Chemical Substances	RNA Replicase (EC 2.7.7.48)
Keywords	covid19
Language	English
Publishing date	2018-11-01
Publishing country	Switzerland
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v10110600
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Population bottlenecks and founder effects: implications for mosquito-borne arboviral emergence.

Weaver, Scott C / Forrester, Naomi L / Liu, Jianying / Vasilakis, Nikos

Nature reviews. Microbiology

2021 Volume 19, Issue 3, Page(s) 184–195

Abstract: Transmission of arthropod-borne viruses (arboviruses) involves infection and replication in both arthropod vectors and vertebrate hosts. Nearly all arboviruses are RNA viruses with high mutation frequencies, which leaves them vulnerable to genetic drift ... ...

Abstract	Transmission of arthropod-borne viruses (arboviruses) involves infection and replication in both arthropod vectors and vertebrate hosts. Nearly all arboviruses are RNA viruses with high mutation frequencies, which leaves them vulnerable to genetic drift and fitness losses owing to population bottlenecks during vector infection, dissemination from the midgut to the salivary glands and transmission to the vertebrate host. However, despite these bottlenecks, they seem to avoid fitness declines that can result from Muller's ratchet. In addition, founder effects that occur during the geographic introductions of human-amplified arboviruses, including chikungunya virus and Zika virus, can affect epidemic and endemic circulation, as well as virulence. In this Review, we discuss the role of genetic drift following population bottlenecks and founder effects in arboviral evolution and spread, and the emergence of human disease.
MeSH term(s)	Animals ; Arbovirus Infections/transmission ; Arbovirus Infections/virology ; Arboviruses/genetics ; Culicidae/virology ; Genetic Drift ; Genomics ; Humans ; Vector Borne Diseases/virology
Language	English
Publishing date	2021-01-11
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	2139054-X
ISSN	1740-1534 ; 1740-1526
ISSN (online)	1740-1534
ISSN	1740-1526
DOI	10.1038/s41579-020-00482-8
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Article ; Online: Multiple Lineages of Hantaviruses Harbored by the Iberian Mole (

Gu, Se Hun / Miñarro, Marcos / Feliu, Carlos / Hugot, Jean-Pierre / Forrester, Naomi L / Weaver, Scott C / Yanagihara, Richard

Viruses

2023 Volume 15, Issue 6

Abstract: The recent detection of both Nova virus (NVAV) and Bruges virus (BRGV) in European moles ( ...

Abstract	The recent detection of both Nova virus (NVAV) and Bruges virus (BRGV) in European moles (
MeSH term(s)	Animals ; Moles ; Phylogeny ; Spain ; Orthohantavirus/genetics ; Bayes Theorem ; Hantavirus Infections/veterinary
Language	English
Publishing date	2023-06-02
Publishing country	Switzerland
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v15061313
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Article ; Online: A Low Fidelity Virus Shows Increased Recombination during the Removal of an Alphavirus Reporter Gene.

Kautz, Tiffany F / Jaworski, Elizabeth / Routh, Andrew / Forrester, Naomi L

Viruses

2020 Volume 12, Issue 6

Abstract: Reporter genes for RNA viruses are well-known to be unstable due to putative RNA recombination events that excise inserted nucleic acids. RNA recombination has been demonstrated to be co-regulated with replication fidelity in alphaviruses, but it is ... ...

Abstract	Reporter genes for RNA viruses are well-known to be unstable due to putative RNA recombination events that excise inserted nucleic acids. RNA recombination has been demonstrated to be co-regulated with replication fidelity in alphaviruses, but it is unknown how recombination events at the minority variant level act, which is important for vaccine and trans-gene delivery design. Therefore, we sought to characterize the removal of a reporter gene by a low-fidelity alphavirus mutant over multiple replication cycles. To examine this, GFP was inserted into TC-83, a live-attenuated vaccine for the alphavirus Venezuelan equine encephalitis virus, as well as a low-fidelity variant of TC-83, and passaged until fluorescence was no longer observed. Short-read RNA sequencing using ClickSeq was performed to determine which regions of the viral genome underwent recombination and how this changed over multiple replication cycles. A rapid removal of the GFP gene was observed, where minority variants in the virus population accumulated small deletions that increased in size over the course of passaging. Eventually, these small deletions merged to fully remove the GFP gene. The removal was significantly enhanced during the passaging of low-fidelity TC-83, suggesting that increased levels of recombination are a defining characteristic of this mutant.
MeSH term(s)	Animals ; Cell Line ; Chlorocebus aethiops ; Click Chemistry/methods ; Encephalitis Virus, Venezuelan Equine/genetics ; Gene Deletion ; Genes, Reporter/genetics ; Genome, Viral/genetics ; Green Fluorescent Proteins/genetics ; Horses ; RNA/genetics ; RNA, Viral/genetics ; Recombination, Genetic/genetics ; Sequence Analysis, RNA ; Vaccines, Attenuated ; Vero Cells
Chemical Substances	RNA, Viral ; RNA, recombinant ; Vaccines, Attenuated ; Green Fluorescent Proteins (147336-22-9) ; RNA (63231-63-0)
Keywords	covid19
Language	English
Publishing date	2020-06-19
Publishing country	Switzerland
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v12060660
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Article: A Low Fidelity Virus Shows Increased Recombination during the Removal of an Alphavirus Reporter Gene

Kautz, Tiffany F / Jaworski, Elizabeth / Routh, Andrew / Forrester, Naomi L

Viruses. 2020 June 19, v. 12, no. 6

2020

Abstract	Reporter genes for RNA viruses are well-known to be unstable due to putative RNA recombination events that excise inserted nucleic acids. RNA recombination has been demonstrated to be co-regulated with replication fidelity in alphaviruses, but it is unknown how recombination events at the minority variant level act, which is important for vaccine and trans-gene delivery design. Therefore, we sought to characterize the removal of a reporter gene by a low-fidelity alphavirus mutant over multiple replication cycles. To examine this, GFP was inserted into TC-83, a live-attenuated vaccine for the alphavirus Venezuelan equine encephalitis virus, as well as a low-fidelity variant of TC-83, and passaged until fluorescence was no longer observed. Short-read RNA sequencing using ClickSeq was performed to determine which regions of the viral genome underwent recombination and how this changed over multiple replication cycles. A rapid removal of the GFP gene was observed, where minority variants in the virus population accumulated small deletions that increased in size over the course of passaging. Eventually, these small deletions merged to fully remove the GFP gene. The removal was significantly enhanced during the passaging of low-fidelity TC-83, suggesting that increased levels of recombination are a defining characteristic of this mutant.
Keywords	RNA ; Venezuelan equine encephalitis virus ; fluorescence ; live vaccines ; mutants ; reporter genes ; sequence analysis ; viruses
Language	English
Dates of publication	2020-0619
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2516098-9
ISSN	1999-4915
ISSN	1999-4915
DOI	10.3390/v12060660
Database	NAL-Catalogue (AGRICOLA)

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Article: Venezuelan Equine Encephalitis Virus V3526 Vaccine RNA-Dependent RNA Polymerase Mutants Increase Vaccine Safety Through Restricted Tissue Tropism in a Murine Model.

Haines, Clint A / Campos, Rafael K / Azar, Sasha R / Warmbrod, K Lane / Kautz, Tiffany F / Forrester, Naomi L / Rossi, Shannan L

Zoonoses (Burlington, Mass.)

2022 Volume 2

Abstract: Background: Venezuelan equine encephalitis virus (VEEV) is an arbovirus endemic to the Americas. There are no approved vaccines or antivirals. TC-83 and V3526 are the best-characterized vaccine candidates for VEEV. Both are live-attenuated vaccines and ... ...

Abstract	Background: Venezuelan equine encephalitis virus (VEEV) is an arbovirus endemic to the Americas. There are no approved vaccines or antivirals. TC-83 and V3526 are the best-characterized vaccine candidates for VEEV. Both are live-attenuated vaccines and have been associated with safety concerns, albeit less so for V3526. A previous attempt to improve the TC-83 vaccine focused on further attenuating the vaccine by adding mutations that altered the error incorporation rate of the RNA-dependent RNA polymerase (RdRp). Methods: The research presented here examines the impact of these RdRp mutations in V3526 by cloning the 3X and 4X strains, assessing vaccine efficacy against challenge in adult female CD-1 mice, examining neutralizing antibody titers, investigating vaccine tissue tropism, and testing the stability of the mutant strains. Results: Our results show that the V3526 RdRp mutants exhibited reduced tissue tropism in the spleen and kidney compared to wild-type V3526, while maintaining vaccine efficacy. Illumina sequencing showed that the RdRp mutations could revert to wild-type V3526. Conclusions: The observed genotypic reversion is likely of limited concern because wild-type V3526 is still an effective vaccine capable of providing protection. Our results indicate that the V3526 RdRp mutants may be a safer vaccine design than the original V3526.
Language	English
Publishing date	2022-01-13
Publishing country	United States
Document type	Journal Article
DOI	10.15212/zoonoses-2021-0016
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Article ; Online: Chikungunya: Evolutionary history and recent epidemic spread.

Weaver, Scott C / Forrester, Naomi L

Antiviral research

2015 Volume 120, Page(s) 32–39

Abstract: Chikungunya virus (CHIKV) has a long history of emergence into urban transmission cycles from its ancestral, enzootic, sylvatic foci in Sub-Saharan Africa, most recently spreading to the Americas beginning in 2013. Since 2004, reemergence has resulted in ...

Abstract	Chikungunya virus (CHIKV) has a long history of emergence into urban transmission cycles from its ancestral, enzootic, sylvatic foci in Sub-Saharan Africa, most recently spreading to the Americas beginning in 2013. Since 2004, reemergence has resulted in millions of cases of severe, debilitating and often chronic arthralgia on five continents. Here, we review this history based on phylogenetic studies, and discuss probable future spread and disease in the Americas. We also discuss a series of mutations in the recently emerged Indian Ocean Lineage that has adapted the virus for transmission for the first time by the Aedes albopictus urban mosquito vector, and compare CHIKV to other arboviruses with and without similar histories of urbanization. This article forms part of a symposium in Antiviral Research on "Chikungunya discovers the New World."
MeSH term(s)	Chikungunya Fever/epidemiology ; Chikungunya Fever/virology ; Chikungunya virus/classification ; Chikungunya virus/genetics ; Epidemics ; Evolution, Molecular ; Global Health ; Humans ; Molecular Epidemiology ; Phylogeny ; Rural Population ; Urban Population
Language	English
Publishing date	2015-08
Publishing country	Netherlands
Document type	Journal Article ; Review
ZDB-ID	306628-9
ISSN	1872-9096 ; 0166-3542
ISSN (online)	1872-9096
ISSN	0166-3542
DOI	10.1016/j.antiviral.2015.04.016
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Zs.A 1627: Show issues

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Article: Variable changes in nematode infection prevalence and intensity after Rabbit Haemorrhagic Disease Virus emerged in wild rabbits in Scotland and New Zealand.

Hernandez, Alexander D / Boag, Brian / Neilson, Roy / Forrester, Naomi L

International journal for parasitology. Parasites and wildlife

2018 Volume 7, Issue 2, Page(s) 187–195

Abstract: The myxoma virus (a microparasite) reduced wild rabbit numbers worldwide when introduced in the 1950s, and is known to interact with co-infecting helminths (macroparasites) causing both increases and decreases in macroparasite population size. In the ... ...

Abstract	The myxoma virus (a microparasite) reduced wild rabbit numbers worldwide when introduced in the 1950s, and is known to interact with co-infecting helminths (macroparasites) causing both increases and decreases in macroparasite population size. In the 1990s Rabbit Haemorrhagic Disease Virus (RHDV) infected rabbits and also significantly reduced rabbit numbers in several countries. However, not much is known about RHDV interactions with macroparasites. In this study, we compare prevalence and intensity of infection for three gastrointestinal nematode species (
Language	English
Publishing date	2018-05-17
Publishing country	England
Document type	Journal Article
ZDB-ID	2715239-X
ISSN	2213-2244
ISSN	2213-2244
DOI	10.1016/j.ijppaw.2018.05.002
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Article ; Online: Evaluation of the inactivation of Venezuelan equine encephalitis virus by several common methods.

Patterson, Edward I / Warmbrod, Kelsey L / Bouyer, Donald H / Forrester, Naomi L

Journal of virological methods

2018 Volume 254, Page(s) 31–34

Abstract: Working with virological samples requires validated inactivation protocols for safe handling and disposal. Although many techniques exist to inactivate samples containing viruses, not all procedures have been properly validated or are compatible with ... ...

Abstract	Working with virological samples requires validated inactivation protocols for safe handling and disposal. Although many techniques exist to inactivate samples containing viruses, not all procedures have been properly validated or are compatible with subsequent assays. To aid in the development of inactivation protocols for Alphaviruses, and specifically Venezuelan equine encephalitis virus (VEEV), a variety of methods were evaluated for their ability to completely inactivate a high titer sample of the vaccine strain VEEV TC-83. The methods evaluated include reagents used in RNA extraction, fixation, treatment with a detergent, and heat inactivation. Most methods were successful at inactivating the sample; however, treatment with only Buffer AVL, SDS, and heat inactivation at 58 °C for one hour were not capable of complete inactivation of the virus in the sample. These results provide a substantial framework for identifying techniques that are safe for complete inactivation of Alphaviruses and to advise protocol implementation.
MeSH term(s)	Animals ; Cell Line ; Chlorocebus aethiops ; Cytopathogenic Effect, Viral/drug effects ; Cytopathogenic Effect, Viral/radiation effects ; Disinfectants/pharmacology ; Disinfection/methods ; Encephalitis Virus, Venezuelan Equine/drug effects ; Encephalitis Virus, Venezuelan Equine/radiation effects ; Hot Temperature ; Vero Cells
Chemical Substances	Disinfectants
Language	English
Publishing date	2018-01-28
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	8013-5
ISSN	1879-0984 ; 0166-0934
ISSN (online)	1879-0984
ISSN	0166-0934
DOI	10.1016/j.jviromet.2018.01.009
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Zs.A 1565: Show issues

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Article ; Online: Negeviruses Reduce Replication of Alphaviruses during Coinfection.

Patterson, Edward I / Kautz, Tiffany F / Contreras-Gutierrez, Maria A / Guzman, Hilda / Tesh, Robert B / Hughes, Grant L / Forrester, Naomi L

Journal of virology

2021 Volume 95, Issue 14, Page(s) e0043321

Abstract: Negeviruses are a group of insect-specific viruses (ISVs) that have been found in many arthropods. Their presence in important vector species led us to examine their interactions with arboviruses during coinfections. Wild-type negeviruses reduced the ... ...

Abstract	Negeviruses are a group of insect-specific viruses (ISVs) that have been found in many arthropods. Their presence in important vector species led us to examine their interactions with arboviruses during coinfections. Wild-type negeviruses reduced the replication of several alphaviruses during coinfections in mosquito cells. Negev virus (NEGV) isolates were also used to express green fluorescent protein (GFP) and anti-chikungunya virus (CHIKV) antibody fragments during coinfections with CHIKV. NEGV expressing anti-CHIKV antibody fragments was able to further reduce replication of CHIKV during coinfections, while reductions of CHIKV with NEGV expressing GFP were similar to titers with wild-type NEGV alone. These results are the first to show that negeviruses induce superinfection exclusion of arboviruses and to demonstrate a novel approach to deliver antiviral antibody fragments with paratransgenic ISVs. The ability to inhibit arbovirus replication and express exogenous proteins in mosquito cells makes negeviruses a promising platform for control of arthropod-borne pathogens.
MeSH term(s)	Aedes/virology ; Alphavirus/physiology ; Animals ; Cells, Cultured ; Chikungunya virus/physiology ; Chlorocebus aethiops ; Culex/virology ; Insect Viruses/physiology ; O'nyong-nyong Virus/physiology ; Semliki forest virus/physiology ; Vero Cells ; Virus Replication
Language	English
Publishing date	2021-06-24
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/JVI.00433-21
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