Biology subjects

Orton, R. J.

Publications and source records attributed to Orton, R. J..

6 recordsLinked to original sources

bioRxiv2024

Diversity and evolution of the human anellome

Anelloviruses are a group of small, circular, single-stranded DNA viruses that are found ubiquitously across mammalian hosts. Here, we explored a large number of publicly available human microbiome datasets and retrieved a total of 829 anellovirus genomes, substantially expanding the known diversity of these viruses. The majority of new genomes fall within the three major human anellovirus genera: Alphatorquevirus, Betatorquevirus and Gammatorquevirus, while we also present one new genome of the under-sampled Hetorquevirus genus. The phylogeny reconstructed from the conserved ORF1 gene reveals three additional, previously undescribed, human anellovirus clades. We performed recombination analysis and show evidence of extensive recombination across all human anelloviruses. Interestingly, more than 95% of the detected events are between members of the same clade and only 15 inter-clade recombination events were detected. The breakpoints of recombination cluster in hotspots at the ends and outside of the ORF1 gene, while a recombination coldspot was detected within the gene. Our analysis suggests that anellovirus evolution is governed by homologous recombination, however events between distant viruses or ones producing chimaeric ORF1s likely lead to non-viable recombinants. The large number of genomes further allowed us to examine how essential genomic features vary across anelloviruses. These include functional domains in the ORF1 protein and the nucleotide motif of the replication loop region, required for the viruses rolling-circle replication. A subset of the genomes assembled in both this and previous studies are completely lacking these essential elements, opening up the possibility that anellovirus intracellular populations contain defective virus genomes (DVGs). Overall, our study highlights key features of anellovirus genomics and evolution, a largely understudied group of viruses whose potential in virus-based therapeutics is recently being explored.

evolutionary biology↗

bioRxiv2022

Selection analysis identifies unusual clustered mutational changes in Omicron lineage BA.1 that likely impact Spike function

Among the 30 non-synonymous nucleotide substitutions in the Omicron S-gene are 13 that have only rarely been seen in other SARS-CoV-2 sequences. These mutations cluster within three functionally important regions of the S-gene at sites that will likely impact (i) interactions between subunits of the Spike trimer and the predisposition of subunits to shift from down to up configurations, (ii) interactions of Spike with ACE2 receptors, and (iii) the priming of Spike for membrane fusion. We show here that, based on both the rarity of these 13 mutations in intrapatient sequencing reads and patterns of selection at the codon sites where the mutations occur in SARS-CoV-2 and related sarbecoviruses, prior to the emergence of Omicron the mutations would have been predicted to decrease the fitness of any genomes within which they occurred. We further propose that the mutations in each of the three clusters therefore cooperatively interact to both mitigate their individual fitness costs, and adaptively alter the function of Spike. Given the evident epidemic growth advantages of Omicron over all previously known SARS-CoV-2 lineages, it is crucial to determine both how such complex and highly adaptive mutation constellations were assembled within the Omicron S-gene, and why, despite unprecedented global genomic surveillance efforts, the early stages of this assembly process went completely undetected.

evolutionary biology↗

bioRxiv2021

In vitro evolution of Remdesivir resistance reveals genome plasticity of SARS-CoV-2

Remdesivir (RDV) is used widely for COVID-19 patients despite varying results in recent clinical trials. Here, we show how serially passaging SARS-CoV-2 in vitro in the presence of RDV selected for drug-resistant viral populations. We determined that the E802D mutation in the RNA-dependent RNA polymerase was sufficient to confer decreased RDV sensitivity without affecting viral fitness. Analysis of more than 200,000 sequences of globally circulating SARS-CoV-2 variants show no evidence of widespread transmission of RDV-resistant mutants. Surprisingly, we also observed changes in the Spike (i.e., H69 E484, N501, H655) corresponding to mutations identified in emerging SARS-CoV-2 variants indicating that they can arise in vitro in the absence of immune selection. This study illustrates SARS-CoV-2 genome plasticity and offers new perspectives on surveillance of viral variants. One Sentence SummarySARS-CoV-2 drug resistance & genome plasticity

microbiology↗

bioRxiv2021

Quantifying and cataloguing unknown sequences within human microbiomes

Advances in genome sequencing technologies and lower costs have enabled the exploration of a multitude of known and novel environments and microbiomes. This has led to an exponential growth in the raw sequence data that is deposited in online repositories. Metagenomic and metatranscriptomic data sets are typically analysed with regards to a specific biological question. However, it is widely acknowledged that these data sets are comprised of a proportion of sequences that bear no similarity to any currently known biological sequence, and this so-called dark matter is often excluded from downstream analyses. In this study, a systematic framework was developed to assemble, identify, and measure the proportion of unknown sequences present in distinct human microbiomes. This framework was applied to forty distinct studies, comprising 963 samples, and covering ten different human microbiomes including fecal, oral, lung, skin and circulatory system microbiomes. The framework was used to determine the proportion of taxonomically unknown sequences present within samples, and to compare such sequences both within and across assembled metagenomes. We found that whilst the human microbiome is one of the most extensively studied, on average 2% of assembled sequences have not yet been taxonomically defined. However, this proportion varied extensively among different microbiomes and was as high as 25% for skin and oral microbiomes that have more interactions with the environment. The publicly available data sets used have not previously been systematically mined to quantify and compare such dark matter. Typically, these unknown sequences are found in several microbiomes and potentially belong to unidentified novel microbes that we interact with on a daily basis. A cross-study comparison led to the identification of similar unknown sequences in different samples and/or microbiomes. A rate of taxonomic characterisation of 1.64% of unknown sequences being characterised per month was calculated from these taxonomically unknown sequences discovered in this study. Additionally, the approach led to the discovery of several potentially novel viral genomes that bear no similarity to sequences in the public databases. Both our computational framework and the novel unknown sequences produced are publicly available for future cross-referencing.

bioinformatics↗

bioRxiv2020

Population genomics of louping ill virus provide new insights into the evolution of tick-borne flaviviruses

BackgroundThe emergence and spread of tick-borne arboviruses pose an increased challenge to human and animal health. In Europe this is demonstrated by the increasingly wide distribution of tick-borne encephalitis virus (TBEV, Flavivirus, Flaviviridae), which has recently been found in the UK. However, much less is known about other tick-borne flaviviruses (TBFV), such as the closely related louping ill virus (LIV), an animal pathogen which is endemic to the UK and Ireland but which has been detected in other parts of Europe including Scandinavia and Russia. The emergence and potential spatial overlap of these viruses necessitates improved understanding of LIV genomic diversity, geographic spread and evolutionary history. Methodology/principal findingsWe sequenced a virus archive composed of 22 LIV isolates which had been sampled throughout the UK over a period of over 80 years. Combining this dataset with published virus sequences, we detected no sign of recombination and found low diversity and limited evidence for positive selection in the LIV genome. Phylogenetic analysis provided evidence of geographic clustering as well as long-distance movement, including movement events that appear recent. However, despite genomic data and an 80-year time span, we found that the data contained insufficient temporal signal to reliably estimate a molecular clock rate for LIV. Additional analyses revealed that this also applied to TBEV, albeit to a lesser extent, pointing to a general problem with phylogenetic dating for TBFV. Conclusions/significanceThe 22 LIV genomes generated during this study provide a more reliable LIV phylogeny, improving our knowledge of the evolution of tick-borne flaviviruses. Our inability to estimate a molecular clock rate for both LIV and TBEV suggests that temporal calibration of tick-borne flavivirus evolution should be interpreted with caution and highlight a unique aspect of these viruses which may be explained by their reliance on tick vectors. Author SummaryTick-borne pathogens represent a major emerging threat to public health and in recent years have been expanding into new areas. LIV is a neglected virus endemic to the UK and Ireland (though it has been detected in Scandinavia and Russia) which is closely related to the major human pathogen TBEV, but predominantly causes disease in sheep and grouse. The recent detection of TBEV in the UK, which has also emerged elsewhere in Europe, requires more detailed understanding of the spread and sequence diversity of LIV. This could be important for diagnosis and vaccination, but also to improve our understanding of the evolution and emergence of these tick-borne viruses. Here we describe the sequencing of 22 LIV isolates which have been sampled from several host species across the past century. We have utilised this dataset to investigate the evolutionary pressures that LIV is subjected to and have explored the evolution of LIV using phylogenetic analysis. Crucially we were unable to estimate a reliable molecular clock rate for LIV and found that this problem also extends to a larger phylogeny of TBEV sequences. This work highlights a previously unknown caveat of tick-borne flavivirus evolutionary analysis which may be important for understanding the evolution of these important pathogens.

evolutionary biology↗

bioRxiv2019

Spatiotemporal dynamics of RNA virus diversity in a phyllosphere microbial community

Although metagenomics reveals that natural virus communities harbor vast genetic diversity, the spatiotemporal dynamics of viral diversity in the wild are seldom tested, especially across small geographic scales. This problem is usefully examined in the above-ground phyllosphere, because terrestrial plants are frequently infected by taxonomically-diverse RNA viruses, whose elevated mutation rates generate abundant allele diversity. Here, we studied the problem by comparative analysis of RNA virus samples over time from three spatially-separated patches of a common perennial legume, white clover (Trifolium repens L.), growing in a grassy lawn in Woods Hole Village (Falmouth, MA, USA). We predicted that clover samples would show similarly high levels of virus species (alpha) diversity across space, but differing among-patch diversity of non-dominant virus taxa over time (4 samples spanning 6 weeks). Results showed that recognizable alpha diversity in clover patches was consistently dominated by RNA virus family Alphaflexiviridae across space, but that all patches showed inconsistent spatiotemporal presence of a diversity of minority virus families. Also, we observed that white clover mosaic virus (WClMV) dominated all patches across space and time. The high coverage of WClMV fostered an haplotype analysis, which revealed that two strains of the virus consistently infected clover plants during the 6-week period.

microbiology↗