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Article
Open AccessThe P323L substitution in the SARS-CoV-2 polymerase (NSP12) confers a selective advantage during infection
The mutational landscape of SARS-CoV-2 varies at the dominant viral genome sequence and minor genomic variant population. During the COVID-19 pandemic, an early substitution in the genome was the D614G change ...
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Article
Open AccessVoluntary risk mitigation behaviour can reduce impact of SARS-CoV-2: a real-time modelling study of the January 2022 Omicron wave in England
Predicting the likely size of future SARS-CoV-2 waves is necessary for public health planning. In England, voluntary “plan B” mitigation measures were introduced in December 2021 including increased home worki...
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Article
Open AccessStructural insights in cell-type specific evolution of intra-host diversity by SARS-CoV-2
As the global burden of SARS-CoV-2 infections escalates, so does the evolution of viral variants with increased transmissibility and pathology. In addition to this entrenched diversity, RNA viruses can also di...
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Article
The furin cleavage site in the SARS-CoV-2 spike protein is required for transmission in ferrets
SARS-CoV-2 entry requires sequential cleavage of the spike glycoprotein at the S1/S2 and the S2ʹ cleavage sites to mediate membrane fusion. SARS-CoV-2 has a polybasic insertion (PRRAR) at the S1/S2 cleavage si...
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Article
Open AccessSARS-CoV-2 vaccine ChAdOx1 nCoV-19 infection of human cell lines reveals low levels of viral backbone gene transcription alongside very high levels of SARS-CoV-2 S glycoprotein gene transcription
ChAdOx1 nCoV-19 is a recombinant adenovirus vaccine against SARS-CoV-2 that has passed phase III clinical trials and is now in use across the globe. Although replication-defective in normal cells, 28 kbp of ad...
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Article
Open AccessAnalysis of an Ebola virus disease survivor whose host and viral markers were predictive of death indicates the effectiveness of medical countermeasures and supportive care
Ebola virus disease (EVD) is an often-fatal infection where the effectiveness of medical countermeasures is uncertain. During the West African outbreak (2013–2016), several patients were treated with different...
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Article
Open AccessVariation around the dominant viral genome sequence contributes to viral load and outcome in patients with Ebola virus disease
Viral load is a major contributor to outcome in patients with Ebola virus disease (EVD), with high values leading to a fatal outcome. Evidence from the 2013–2016 Ebola virus (EBOV) outbreak indicated that diff...
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Article
Open AccessCharacterisation of the transcriptome and proteome of SARS-CoV-2 reveals a cell passage induced in-frame deletion of the furin-like cleavage site from the spike glycoprotein
SARS-CoV-2 is a recently emerged respiratory pathogen that has significantly impacted global human health. We wanted to rapidly characterise the transcriptomic, proteomic and phosphoproteomic landscape of this...
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Article
Open AccessDeep splicing plasticity of the human adenovirus type 5 transcriptome drives virus evolution
Viral genomes have high gene densities and complex transcription strategies rendering transcriptome analysis through short-read RNA-seq approaches problematic. Adenovirus transcription and splicing is especial...
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Article
Open AccessProteomics informed by transcriptomics for characterising differential cellular susceptibility to Nelson Bay orthoreovirus infection
Nelson Bay orthoreovirus (NBV) is a fusogenic bat borne virus with an unknown zoonotic potential. Previous studies have shown that NBV can infect and replicate in a wide variety of cell types derived from thei...
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Article
Virus genomes reveal factors that spread and sustained the Ebola epidemic
The 2013–2016 West African epidemic caused by the Ebola virus was of unprecedented magnitude, duration and impact. Here we reconstruct the dispersal, proliferation and decline of Ebola virus throughout the reg...
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Article
Open AccessA comparison of host gene expression signatures associated with infection in vitro by the Makona and Ecran (Mayinga) variants of Ebola virus
The Ebola virus (EBOV) variant Makona (which emerged in 2013) was the causative agent of the largest outbreak of Ebola Virus Disease recorded. Differences in virus-host interactions between viral variants have...
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Article
Open AccessTranscriptomic signatures differentiate survival from fatal outcomes in humans infected with Ebola virus
In 2014, Western Africa experienced an unanticipated explosion of Ebola virus infections. What distinguishes fatal from non-fatal outcomes remains largely unknown, yet is key to optimising personalised treatme...
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Article
Open AccessProteomics informed by transcriptomics for characterising active transposable elements and genome annotation in Aedes aegypti
Aedes aegypti is a vector for the (re-)emerging human pathogens dengue, chikungunya, yellow fever and Zika viruses. Almost half of the Ae. aegypti genome is comprised of transposable e...
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Article
Real-time, portable genome sequencing for Ebola surveillance
A nanopore DNA sequencer is used for real-time genomic surveillance of the Ebola virus epidemic in the field in Guinea; the authors demonstrate that it is possible to pack a genomic surveillance laboratory in ...
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Article
Open AccessTemporal and spatial analysis of the 2014–2015 Ebola virus outbreak in West Africa
Analysis of 179 new Ebola virus sequences from patient samples collected in Guinea between March 2014 and January 2015 shows how different lineages evolved and spread in West Africa.
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Article
Open AccessElucidating variations in the nucleotide sequence of Ebola virus associated with increasing pathogenicity
Ebolaviruses cause a severe and often fatal haemorrhagic fever in humans, with some species such as Ebola virus having case fatality rates approaching 90%. Currently, the worst Ebola virus outbreak since the d...
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Article
De novo derivation of proteomes from transcriptomes for transcript and protein identification
Integration of transcriptomic and proteomic data allows more detailed annotation of proteomes of model and non-model species.
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Protocol
Study of Nucleolar Localization of Adenovirus Core Proteins
This chapter describes the techniques used to study nucleolar-localized proteins. The chapter starts with cloning of viral proteins for expression in mammalian cells as fusion proteins to well-characterized ta...
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Article
An Upwelling Event at Onondaga Lake, NY: Characterization, Impact and Recurrence*
The occurrence, features and impacts on oxygen resources of an upwelling event in culturally eutrophic Onondaga Lake, NY, are documented, and recurrence is investigated, based on data collected as part of long...
