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Article: Shared Common Ancestry of Rodent Alphacoronaviruses Sampled Globally

Tsoleridis, Theocharis / Chappell, Joseph / Fooks, Anthony / Monchatre-leroy, elodie / Drosten, Christian / McClure, Patrick / Holmes, Edward

Viruses, 11(2):125

2019

Abstract: The recent discovery of novel alphacoronaviruses (alpha-CoVs) in European and Asian rodents revealed that rodent coronaviruses (CoVs) sampled worldwide formed a discrete phylogenetic group within this genus. To determine the evolutionary history of ... ...

Institution	Charité - Universitätsmedizin Berlin
Abstract	The recent discovery of novel alphacoronaviruses (alpha-CoVs) in European and Asian rodents revealed that rodent coronaviruses (CoVs) sampled worldwide formed a discrete phylogenetic group within this genus. To determine the evolutionary history of rodent CoVs in more detail, particularly the relative frequencies of virus-host co-divergence and cross-species transmission, we recovered longer fragments of CoV genomes from previously discovered European rodent alpha-CoVs using a combination of PCR and high-throughput sequencing. Accordingly, the full genome sequence was retrieved from the UK rat coronavirus, along with partial genome sequences from the UK field vole and Poland-resident bank vole CoVs, and a short conserved ORF1b fragment from the French rabbit CoV. Genome and phylogenetic analysis showed that despite their diverse geographic origins, all rodent alpha-CoVs formed a single monophyletic group and shared similar features, such as the same gene constellations, a recombinant beta-CoV spike gene, and similar core transcriptional regulatory sequences (TRS). These data suggest that all rodent alpha CoVs sampled so far originate from a single common ancestor, and that there has likely been a long-term association between alpha CoVs and rodents. Despite this likely antiquity, the phylogenetic pattern of the alpha-CoVs was also suggestive of relatively frequent host-jumping among the different rodent species.
Keywords	COVID-19 ; Coronavirus ; ancestry ; alphacoronavirus ; evolution ; rodents ; recombination
Language	English
Document type	Article
Database	Repository for Life Sciences

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Article ; Online: Discovery of Novel Coronaviruses in Rodents.

Tsoleridis, Theocharis / Ball, Jonathan K

Methods in molecular biology (Clifton, N.J.)

2020 Volume 2203, Page(s) 33–40

Abstract: The recent emergence of SARS, SARS-CoV2 and MERS and the discovery of novel coronaviruses in animals and birds suggest that the Coronavirus family is far more diverse than previously thought. In the last decade, several new coronaviruses have been ... ...

Abstract	The recent emergence of SARS, SARS-CoV2 and MERS and the discovery of novel coronaviruses in animals and birds suggest that the Coronavirus family is far more diverse than previously thought. In the last decade, several new coronaviruses have been discovered in rodents around the globe, suggesting that they are the natural reservoirs of the virus. In this chapter we describe the process of screening rodent tissue for novel coronaviruses with PCR, a method that is easily adaptable for screening a range of animals.
MeSH term(s)	Animals ; Coronavirus/genetics ; Coronavirus/isolation & purification ; Coronavirus Infections/veterinary ; Coronavirus Infections/virology ; Polymerase Chain Reaction/methods ; Rodentia
Keywords	covid19
Language	English
Publishing date	2020-08-23
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-0900-2_2
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Discovery of Novel Coronaviruses in Rodents

Tsoleridis, Theocharis / Ball, Jonathan K

Methods Mol Biol

Abstract	The recent emergence of SARS, SARS-CoV2 and MERS and the discovery of novel coronaviruses in animals and birds suggest that the Coronavirus family is far more diverse than previously thought. In the last decade, several new coronaviruses have been discovered in rodents around the globe, suggesting that they are the natural reservoirs of the virus. In this chapter we describe the process of screening rodent tissue for novel coronaviruses with PCR, a method that is easily adaptable for screening a range of animals.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #728130
Database	COVID19

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Article ; Online: Revisiting the origins of the Sobemovirus genus: A case for ancient origins of plant viruses.

Ghafari, Mahan / Sõmera, Merike / Sarmiento, Cecilia / Niehl, Annette / Hébrard, Eugénie / Tsoleridis, Theocharis / Ball, Jonathan / Moury, Benoît / Lemey, Philippe / Katzourakis, Aris / Fargette, Denis

PLoS pathogens

2024 Volume 20, Issue 1, Page(s) e1011911

Abstract: The discrepancy between short- and long-term rate estimates, known as the time-dependent rate phenomenon (TDRP), poses a challenge to extrapolating evolutionary rates over time and reconstructing evolutionary history of viruses. The TDRP reveals a ... ...

Abstract	The discrepancy between short- and long-term rate estimates, known as the time-dependent rate phenomenon (TDRP), poses a challenge to extrapolating evolutionary rates over time and reconstructing evolutionary history of viruses. The TDRP reveals a decline in evolutionary rate estimates with the measurement timescale, explained empirically by a power-law rate decay, notably observed in animal and human viruses. A mechanistic evolutionary model, the Prisoner of War (PoW) model, has been proposed to address TDRP in viruses. Although TDRP has been studied in animal viruses, its impact on plant virus evolutionary history remains largely unexplored. Here, we investigated the consequences of TDRP in plant viruses by applying the PoW model to reconstruct the evolutionary history of sobemoviruses, plant pathogens with significant importance due to their impact on agriculture and plant health. Our analysis showed that the Sobemovirus genus dates back over four million years, indicating an ancient origin. We found evidence that supports deep host jumps to Poaceae, Fabaceae, and Solanaceae occurring between tens to hundreds of thousand years ago, followed by specialization. Remarkably, the TDRP-corrected evolutionary history of sobemoviruses was extended far beyond previous estimates that had suggested their emergence nearly 9,000 years ago, a time coinciding with the Neolithic period in the Near East. By incorporating sequences collected through metagenomic analyses, the resulting phylogenetic tree showcases increased genetic diversity, reflecting a deep history of sobemovirus species. We identified major radiation events beginning between 4,600 to 2,000 years ago, which aligns with the Neolithic period in various regions, suggesting a period of rapid diversification from then to the present. Our findings make a case for the possibility of deep evolutionary origins of plant viruses.
MeSH term(s)	Animals ; Humans ; Phylogeny ; Biological Evolution ; RNA Viruses/genetics ; Plant Viruses/genetics ; Plants ; Evolution, Molecular
Language	English
Publishing date	2024-01-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	2205412-1
ISSN	1553-7374 ; 1553-7374
ISSN (online)	1553-7374
ISSN	1553-7374
DOI	10.1371/journal.ppat.1011911
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: SARS-CoV-2 proteins (version 2020.2) in the IUPHAR/BPS Guide to Pharmacology Database

Alexander, Stephen P.H. / Ball, Jonathan K. / Tsoleridis, Theocharis

IUPHAR/BPS Guide to Pharmacology CITE; Vol 2020 No; 2633-1020

2020 Volume 2

Abstract: CoronavirusesCoronaviruses are large, often spherical, enveloped, single-stranded positive-sense RNA viruses, ranging in size from 80-220 nm. Of the four structural proteins encoded in the viral genome, the RNA winds around the highly basic nucleocapsid ( ...

Abstract	CoronavirusesCoronaviruses are large, often spherical, enveloped, single-stranded positive-sense RNA viruses, ranging in size from 80-220 nm. Of the four structural proteins encoded in the viral genome, the RNA winds around the highly basic nucleocapsid (N) protein. The three other structural proteins, envelope (E), membrane (M) and spike (S), are transmembrane proteins. The E protein is a small (9-12 kDa) single transmembrane domain protein, which enables virus assembly with the M protein, a larger (23-35 kDa) 3TM protein. Coronaviruses are named for the crown-shaped appearance of the virus due to the large (120+ kDa) S spike 1TM glycoprotein, which forms extended homotrimers. The spike protein binds to the animal host cell by interacting with specific anchoring proteins, typically proteinases, such as angiotensin-converting enzyme 2 or aminopeptidase N. This binding facilitates viral entry into the cell and the release of the genome. Aside from the four structural proteins, the remainder of the genome encodes accessory or non-structural proteins and includes proteinases to cleave the two encoded polyproteins. The remainder of the genome encodes elements for viral replication, assembly and release, as well as proteins which manipulate the host's innate immune system.
Keywords	covid19
Subject code	612
Language	English
Publishing date	2020-04-20
Publisher	University of Edinburgh
Publishing country	uk
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Identification of Infectious Agents in High-Throughput Sequencing Data Sets Is Easily Achievable Using Free, Cloud-Based Bioinformatics Platforms.

Chappell, Joseph G / Byaruhanga, Timothy / Tsoleridis, Theocharis / Ball, Jonathan K / McClure, C Patrick

Journal of clinical microbiology

2019 Volume 57, Issue 12

MeSH term(s)	Cloud Computing ; Computational Biology ; Computer Simulation ; High-Throughput Nucleotide Sequencing ; Software
Language	English
Publishing date	2019-11-22
Publishing country	United States
Document type	Letter ; Research Support, Non-U.S. Gov't ; Comment
ZDB-ID	390499-4
ISSN	1098-660X ; 0095-1137
ISSN (online)	1098-660X
ISSN	0095-1137
DOI	10.1128/JCM.01386-19
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Article ; Online: Enterovirus D68 epidemic, UK, 2018, was caused by subclades B3 and D1, predominantly in children and adults, respectively, with both subclades exhibiting extensive genetic diversity.

Howson-Wells, Hannah C / Tsoleridis, Theocharis / Zainuddin, Izzah / Tarr, Alexander W / Irving, William L / Ball, Jonathan K / Berry, Louise / Clark, Gemma / McClure, C Patrick

Microbial genomics

2022 Volume 8, Issue 5

Abstract: Enterovirus D68 (EV-D68) has recently been identified in biennial epidemics coinciding with diagnoses of non-polio acute flaccid paralysis/myelitis (AFP/AFM). We investigated the prevalence, genetic relatedness and associated clinical features of EV-D68 ... ...

Abstract	Enterovirus D68 (EV-D68) has recently been identified in biennial epidemics coinciding with diagnoses of non-polio acute flaccid paralysis/myelitis (AFP/AFM). We investigated the prevalence, genetic relatedness and associated clinical features of EV-D68 in 193 EV-positive samples from 193 patients in late 2018, UK. EV-D68 was detected in 83 (58 %) of 143 confirmed EV-positive samples. Sequencing and phylogenetic analysis revealed extensive genetic diversity, split between subclades B3 (
MeSH term(s)	Aged ; Central Nervous System Viral Diseases ; Child ; Enterovirus D, Human/genetics ; Enterovirus Infections/diagnosis ; Enterovirus Infections/epidemiology ; Epidemics ; Genetic Variation ; Humans ; Myelitis ; Neuromuscular Diseases ; Phylogeny ; United Kingdom/epidemiology
Language	English
Publishing date	2022-05-09
Publishing country	England
Document type	Journal Article
ZDB-ID	2835258-0
ISSN	2057-5858 ; 2057-5858
ISSN (online)	2057-5858
ISSN	2057-5858
DOI	10.1099/mgen.0.000825
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Article ; Online: Hepatitis C subtyping assay failure in UK patients born in sub-Saharan Africa: Implications for global treatment and elimination.

Adeboyejo, Kazeem / King, Barnabas J / Tsoleridis, Theocharis / Tarr, Alexander W / McLauchlan, John / Irving, William L / Ball, Jonathan K / McClure, C Patrick

Journal of medical virology

2022 Volume 95, Issue 1, Page(s) e28178

Abstract: BACKGROUND AND AIMS: The newly developed direct-acting antivirals have revolutionized the treatment of chronic hepatitis C virus (HCV), with cure rates as high as 98% in some cohorts. Although genome sequencing has demonstrated that some subtypes of HCV ... ...

Abstract	BACKGROUND AND AIMS: The newly developed direct-acting antivirals have revolutionized the treatment of chronic hepatitis C virus (HCV), with cure rates as high as 98% in some cohorts. Although genome sequencing has demonstrated that some subtypes of HCV naturally harbor drug resistance associated substitutions (RAS), these are often overlooked as "rarities." Furthermore, commercial subtyping assays and associated epidemiological findings are skewed towards Western cohorts and whole-genome sequencing can be problematic to deploy without significant infrastructure and training support. We thus aimed to develop a simple, robust and accurate HCV subtyping pipeline, to optimize and streamline molecular detection and sequence-based typing of diverse RAS-containing subtypes. Methods: HCV serum derived from 146 individuals, whose likely source of infection was from sub-Saharan Africa (SSA) was investigated with a novel panel of single round polymerase chain reaction (PCR) assays targeting NS5B and NS5A genomic regions. Virus subtype assignments were determined by pairwise-distance analysis and compared to both diagnostic laboratory assignments and free-to-use online typing tools. Results: Partial NS5A and NS5B sequences were respectively obtained from 131 to 135 HCV-positive patients born in 19 different countries from SSA but attending clinics in the UK. We determined that routine clinical diagnostic methods incorrectly subtyped 59.0% of samples, with a further 6.8% incorrectly genotyped. Of five commonly used online tools, Geno2Pheno performed most effectively in determining a subtype in agreement with pairwise distance analysis. Conclusion: This study provides a simple low-cost pathway to accurately subtype in SSA, guide regional therapeutic choice and assist global surveillance and elimination initiatives.
MeSH term(s)	Humans ; Hepatitis C, Chronic/diagnosis ; Hepatitis C, Chronic/drug therapy ; Hepatitis C, Chronic/epidemiology ; Antiviral Agents/therapeutic use ; Antiviral Agents/pharmacology ; Viral Nonstructural Proteins/genetics ; Hepatitis C/diagnosis ; Hepatitis C/drug therapy ; Hepatitis C/epidemiology ; Hepacivirus/genetics ; Genotype ; Africa South of the Sahara/epidemiology ; United Kingdom/epidemiology ; Drug Resistance, Viral/genetics
Chemical Substances	Antiviral Agents ; Viral Nonstructural Proteins
Language	English
Publishing date	2022-10-08
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	752392-0
ISSN	1096-9071 ; 0146-6615
ISSN (online)	1096-9071
ISSN	0146-6615
DOI	10.1002/jmv.28178
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Article ; Online: The Impact of Real-Time Whole-Genome Sequencing in Controlling Healthcare-Associated SARS-CoV-2 Outbreaks.

Francis, Rodric V / Billam, Harriet / Clarke, Mitch / Yates, Carl / Tsoleridis, Theocharis / Berry, Louise / Mahida, Nikunj / Irving, William L / Moore, Christopher / Holmes, Nadine / Ball, Jonathan K / Loose, Matthew / McClure, C Patrick

The Journal of infectious diseases

2021 Volume 225, Issue 1, Page(s) 10–18

Abstract: Nosocomial severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections have severely affected bed capacity and patient flow. We utilized whole-genome sequencing (WGS) to identify outbreaks and focus infection control resources and ... ...

Abstract	Nosocomial severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections have severely affected bed capacity and patient flow. We utilized whole-genome sequencing (WGS) to identify outbreaks and focus infection control resources and intervention during the United Kingdom's second pandemic wave in late 2020. Phylogenetic analysis of WGS and epidemiological data pinpointed an initial transmission event to an admission ward, with immediate prior community infection linkage documented. High incidence of asymptomatic staff infection with genetically identical viral sequences was also observed, which may have contributed to the propagation of the outbreak. WGS allowed timely nosocomial transmission intervention measures, including admissions ward point-of-care testing and introduction of portable HEPA14 filters. Conversely, WGS excluded nosocomial transmission in 2 instances with temporospatial linkage, conserving time and resources. In summary, WGS significantly enhanced understanding of SARS-CoV-2 clusters in a hospital setting, both identifying high-risk areas and conversely validating existing control measures in other units, maintaining clinical service overall.
MeSH term(s)	Asymptomatic Infections ; COVID-19 ; Cross Infection/epidemiology ; Delivery of Health Care ; Disease Outbreaks/prevention & control ; Health Personnel ; Humans ; Personal Protective Equipment ; Phylogeny ; Reverse Transcriptase Polymerase Chain Reaction/methods ; SARS-CoV-2 ; Whole Genome Sequencing
Language	English
Publishing date	2021-09-23
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	3019-3
ISSN	1537-6613 ; 0022-1899
ISSN (online)	1537-6613
ISSN	0022-1899
DOI	10.1093/infdis/jiab483
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Article ; Online: Retrieval of the Complete Coding Sequence of the UK-Endemic Tatenale Orthohantavirus Reveals Extensive Strain Variation and Supports Its Classification as a Novel Species.

Chappell, Joseph G / Tsoleridis, Theocharis / Onianwa, Okechukwu / Drake, Gabby / Ashpole, Ian / Dobbs, Phillipa / Edema, William / Kumi-Ansah, Frederick / Bennett, Malcolm / Tarlinton, Rachael E / Ball, Jonathan K / McClure, C Patrick

Viruses

2020 Volume 12, Issue 4

Abstract: Orthohantaviruses are globally distributed viruses, associated with rodents and other small mammals. However, data on the circulation of orthohantaviruses within the UK, particularly the UK-endemic Tatenale virus, is sparse. In this study, 531 animals ... ...

Abstract	Orthohantaviruses are globally distributed viruses, associated with rodents and other small mammals. However, data on the circulation of orthohantaviruses within the UK, particularly the UK-endemic Tatenale virus, is sparse. In this study, 531 animals from five rodent species were collected from two locations in northern and central England and screened using a degenerate, pan- orthohantavirus RT-PCR assay. Tatenale virus was detected in a single field vole (
MeSH term(s)	Genetic Variation ; Orthohantavirus/classification ; Orthohantavirus/genetics ; High-Throughput Nucleotide Sequencing ; Open Reading Frames ; Phylogeny ; RNA, Viral ; Sequence Analysis, RNA ; United Kingdom
Chemical Substances	RNA, Viral
Language	English
Publishing date	2020-04-17
Publishing country	Switzerland
Document type	Journal Article ; 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/v12040454
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