Joanna Warwick-Dugdale's research while affiliated with University of Exeter and other places

Publications (23)

Article
Full-text available
Whole genome sequencing of SARS-CoV-2 has occurred at an unprecedented scale, and can be exploited for characterising outbreak risks at the fine-scale needed to inform control strategies. One setting at continued risk of COVID-19 outbreaks are higher education institutions, associated with student movements at the start of term, close living condit...
Article
Full-text available
Vaccines based on the spike protein of SARS-CoV-2 are a cornerstone of the public health response to COVID-19. The emergence of hypermutated, increasingly transmissible variants of concern (VOCs) threaten this strategy. Omicron (B.1.1.529), the fifth VOC to be described, harbours multiple amino acid mutations in spike, half of which lie within the...
Article
Full-text available
Background: Since the emergence of SARS-CoV-2, evolutionary pressure has driven large increases in the transmissibility of the virus. However, with increasing levels of immunity through vaccination and natural infection the evolutionary pressure will switch towards immune escape. Genomic surveillance in regions of high immunity is crucial in detec...
Article
Full-text available
The Delta (B.1.617.2) variant was the predominant UK circulating SARS-CoV-2 strain between May and December 2021. How Delta infection compares with previous variants is unknown. This prospective observational cohort study assessed symptomatic adults participating in the app-based COVID Symptom Study who tested positive for SARS-CoV-2 from May 26 to...
Article
Full-text available
Mitigation of SARS-CoV-2 transmission from international travel is a priority. We evaluated the effectiveness of travellers being required to quarantine for 14-days on return to England in Summer 2020. We identified 4,207 travel-related SARS-CoV-2 cases and their contacts, and identified 827 associated SARS-CoV-2 genomes. Overall, quarantine was as...
Article
Full-text available
Mitigation of SARS-CoV-2 transmission from international travel is a priority. We evaluated the effectiveness of travellers being required to quarantine for 14-days on return to England in Summer 2020. We identified 4,207 travel-related SARS-CoV-2 cases and their contacts, and identified 827 associated SARS-CoV-2 genomes. Overall, quarantine was as...
Article
Full-text available
Understanding SARS-CoV-2 transmission in higher education settings is important to limit spread between students, and into at-risk populations. In this study, we sequenced 482 SARS-CoV-2 isolates from the University of Cambridge from 5 October to 6 December 2020. We perform a detailed phylogenetic comparison with 972 isolates from the surrounding c...
Article
Full-text available
Understanding SARS-CoV-2 transmission in higher education settings is important to limit spread between students, and into at-risk populations. In this study, we sequenced 482 SARS-CoV-2 isolates from the University of Cambridge from 5 October to 6 December 2020. We perform a detailed phylogenetic comparison with 972 isolates from the surrounding c...
Article
The evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus leads to new variants that warrant timely epidemiological characterization. Here we use the dense genomic surveillance data generated by the COVID-19 Genomics UK Consortium to reconstruct the dynamics of 71 different lineages in each of 315 English local authori...
Article
Vaccination and disease The United Kingdom has high rates of vaccination for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), exceeding 80% of adults. As immunity wanes and social distancing is relaxed, how are rates of illness and severe disease affected by more infectious variants? Elliott et al . used reverse transcription PCR data...
Article
Full-text available
Background The SARS-CoV-2 variant B.1.1.7 was first identified in December, 2020, in England. We aimed to investigate whether increases in the proportion of infections with this variant are associated with differences in symptoms or disease course, reinfection rates, or transmissibility. Methods We did an ecological study to examine the associatio...
Article
Full-text available
Microbes play fundamental roles in shaping natural ecosystem properties and functions, but do so under constraints imposed by their viral predators. However, studying viruses in nature can be challenging due to low biomass and the lack of universal gene markers. Though metagenomic short-read sequencing has greatly improved our virus ecology toolkit...
Preprint
Full-text available
Background Whole-genome sequencing has been used successfully to provide additional information for transmission pathways in infectious spread. We report and interpret genomic sequencing results in clinical context from a large outbreak of COVID-19 with 46 cases across staff and patients in a community hospital in the UK. Methods Following multiple...
Article
Full-text available
Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability o...
Preprint
Full-text available
Microbes play fundamental roles in shaping natural ecosystem properties and functions, but do so under constraints imposed by their viral predators. However, studying viruses in nature can be challenging due to low biomass and the lack of universal gene markers. Though metagenomic short-read sequencing has greatly improved our virus ecology toolkit...
Article
Full-text available
Marine viruses impact global biogeochemical cycles via their influence on host community structure and function, yet our understanding of viral ecology is constrained by limitations in host culturing and a lack of reference genomes and 'universal' gene markers to facilitate community surveys. Short-read viral metagenomic studies have provided clues...
Article
Full-text available
Microbial communities living in the oceans are major drivers of global biogeochemical cycles. With nutrients limited across vast swathes of the ocean, marine microbes eke out a living under constant assault from predatory viruses. Viral concentrations exceed those of their bacterial prey by an order of magnitude in surface water, making these oblig...
Preprint
Full-text available
Marine bacteriophages impact global biogeochemical cycles via their influence on host community structure and function, yet our understanding of viral ecology is constrained by limitations in culturing of important hosts and the lack of a 'universal' gene to facilitate community surveys. While recent advances in short-read viral metagenomics offer...
Preprint
This protocol describes a generalizable, long-read, low-input metagenomic sequencing approach ('VirION') for the survey of viral communities. A significant obstacle in adopting long-read technology for viral metagenomics lies in obtaining the amount of DNA required; e.g. viral DNA extraction from 20 L of seawater yields far less than the micrograms...

Citations

... The receptor-binding domain was responsible for impaired cell fusion, while the S2 domain was important for endosomal fusion. The fast global spread and increased virulence of the Omicron variant may be attributable to changes in vaccines and antigenicity 35 . Studies have indicated that the R 0 of the Omicron variant reaches 8.2, and the transmission ability is exceedingly high, which is greater than the assumed transmissibility in our simulation 36 . ...
... In February 2021 the alpha variant was detected in Kenya [18]. The alpha variant has been reported to be less transmissible than other variants such as the delta variant but associated with a higher risk of acute respiratory distress syndrome [19,20]. ...
... Maximumlikelihood evolutionary analysis revealed some evidence of local clustering, which is to be expected given the small size of the country (Figs 1 and S1). Phylogenetic analysis of Alpha-variant genomes revealed considerable diversity, suggesting over 40 independent importations (Figs 1 and 3b), although this is likely to be a substantial underestimate [33]. ...
... Variants of Interest (VOI) of the virus, driving global infection. The diversity of such variants and emerging lineages [1][2][3][4][5] potentially shapes transmissibility, disease severity, and immune escape mechanisms that ultimately impact public health. Tracking the emergence and spread of SARS-CoV-2 lineages 1-6 using phylogenetics has been critical to informing the timing and stringency of COVID-19 public health interventions [7][8][9][10][11] . ...
... Up to this time, rates among individuals aged under 60 years were generally increasing across England [8] but in Cambridge local authority these case rates were stable [9]. UK Health Security Agency (UKHSA), a statutory body tasked with outbreak surveillance, became aware of increased incidence in a number of UoC Colleges, identified through both the national symptom-derived SARS-CoV-2 testing and through the work of the UoC asymptomatic screening programme which screened asymptomatic students weekly [7,10]. UKHSA conducted an analytical epidemiological survey into the determinants of SARS-CoV-2 incidence, results of which we present and discuss here. ...
... Another genomic analysis of the B.1.177 lineage in England showed it had a small advantage relative to the other lineages in September 2020 [51], although the advantage was not seen in all of the sublineages of B.1.177. However, almost 80% of all the B.1.177 ...
... The Delta variant was identified in India's Maharashtra state in Spring 2021. It had additional mutations that increased the ability of the spike protein to infect cells, resulting in increased transmissibility, disease severity, and breakthrough infections in vaccinated individuals (5,6). A notable example is the P681R mutation, located at a furin cleavage site that separates the spike protein into S1 and S2 subunits (7). ...
... Comparisons of the variations in transmissibility, clinical characteristics, severity, and outcomes between patients infected with early and late variants were examined in a few previous studies. In particular, studies have shown that late variants are characterized by higher transmissibility (delta: 43-68% more transmissible than previously circulating variants [1], omicron: 36.5% more transmissible than delta [2]) compared to early variants (alpha and beta: 40-70% more transmissible compared to the original virus [3]). Although the transmissibility rate of COVID-19 late variants is considered to be higher than the original virus and early circulating variants, the severity of symptoms and clinical outcomes among variants has also changed slightly. ...
... Attempts to recover these other viral genome types and replication stages have been made via bioinformatic mining of metatranscriptomes and total metagenomes (Al-Shayeb et al. 2020;Emerson et al. 2018;Starr et al. 2019). Together with long-read sequencing approaches that can recover more complete regions of viral genomes in a single sequence without reliance on de novo metagenomic assembly (Zablocki et al. 2021), ongoing validation of and improvements in laboratory and bioinformatics approaches are allowing us to gain a more complete understanding of viral diversity and viral predation of bacteria in soil. ...
... One study using cryo-electron microscopy confirms that p.D614G disrupts an interprotomer contact, thus facilitating the spike "open conformation" (Yurkovetskiy et al., 2020). This mutation is estimated to increase the transmissibility of SARS-CoV-2 by 20% (Volz et al., 2021), thus explaining why it had become the dominant strain by February 2021 (second Thai outbreak), similarly to what was observed in other Southeast Asian countries (Mat Yassim et al., 2021;Nyunt et al., 2021). ...