Biology subjects

Kemp, S. A.

Publications and source records attributed to Kemp, S. A..

5 recordsLinked to original sources

bioRxiv2026

Identification and Masking of Artefactual and Misleading Within-Host Variants in Deep-Sequencing SARS-CoV-2 Data

Deep sequencing data are increasingly used to study within-host viral diversity and to inform evolutionary inference. For SARS-CoV-2, analyses based on intra-host single-nucleotide variants (iSNVs) have been widely applied to quantify within-host diversity and infer transmission dynamics. However, these applications critically depend on the reliable identification of low-frequency variants, which remain vulnerable to systematic and technical artefacts. In this study, we show that recurrent artefactual iSNVs are common in large-scale SARS-CoV-2 sequencing data and can persist even under conservative minor allele frequency (MAF) thresholds. Using data from the UKs Office for National Statistics COVID-19 Infection Survey, we demonstrate that such artefacts are predominantly sequencing centre-rather than protocol-specific. Each centre exhibits a modest, distinct set of recurrent artefactual variants showing little overlap with sites routinely masked at the consensus level. To address this, we developed a systematic, dataset-aware framework that uses recurrence within sequencing datasets to identify small, noise-adapted sets of artefactual iSNVs to mask. Applying this framework reduces spurious sharing of low-frequency variants between samples and qualitatively alters downstream inferences, including estimates of within-host diversity and transmission bottleneck sizes. Together, these findings highlight the importance of explicit, dataset-aware artefact control for robust inference from within-host variation, particularly as genomic studies increasingly seek to exploit sub-consensus diversity in rapidly evolving pathogens such as SARS-CoV-2.

genomics↗

bioRxiv2024

Cortical contributions to attentional orienting and response cancellation in action stopping

Action cancellation involves the termination of planned or initiated movement. Contemporary models of action cancellation, such as the Pause-then-Cancel model, propose that this occurs via a two-stage process, initiated in the cortex by the pre-supplementary motor area (preSMA) and inferior frontal gyrus (IFG). Previous experimental work using electromyography (EMG) has identified that the cancellation of actions can involve the partial activation of the responding muscles, which does not result in an overt behavioural response. In this study, we used functional near-infrared spectroscropy (fNIRS) to investigate the neural correlates of these partial responses in a modified stopping task (a response- and stimulus-selective stop-signal task), controlling for the attentional effects that have long confounded action cancellation research by comparing responses to stop stimuli with those to ignore stimuli. We identified stopping-related activity in the preSMA but not the IFG, consistent with predictions of the Pause-then-Cancel model. Additionally, we observed increased preSMA activity in trials where no partial responses occurred, potentially due to the cumulative effect of different inhibitory processes in those trials. This study also highlights the utility of combining fNIRS and EMG in examining the cortical correlates and dynamic processes involved in action cancellation.

neuroscience↗

bioRxiv2024

Nasopharyngeal specific selection and emergence of SARS-CoV-2 spike fusion peptide mutation P812S during chronic infection

Omicron emergence represented a seismic event in the COVID-19 pandemic, demonstrating what was essentially antigenic shift in a virus that cannot reassort its genome as influenza can. Understanding the success of Omicron is essential, and yet we have little understanding of the biological underpinnings of its ability to accommodate diverse mutations and bring together deleterious mutations to generate a highly successful new serotype. Persistent SARS-CoV-2 infections are a likely source of new variants and may provide valuable insight into past and future evolutionary trajectories, in particular those involving allosteric interactions that defy genotype to phenotype prediction. Here we observe upper airway specific evolution of SARS-CoV-2 demonstrating fusion peptide (FP) domain mutation S:P812S adjacent to the S2 cleavage site that emerged during a chronic infection in an immunocompromised individual. Indeed, this mutation had previously emerged in an ancestral B lineage as well as the delta variant lineage and transmitted successfully in populations globally, though remains uncharacterised. P812S in spike pseudotyped virus particles did not impact entry efficiency across cell lines expressing endogenous ACE2 and TMPRSS2. However, efficiency of spike cleavage at S1/S2 was reduced and molecular dynamics simulation demonstrated altered S1/S2 loop conformations that possibly impacted furin mediated cleavage. Consistent with impaired S1/S2 cleavage, and reminiscent of Omicron BA.1, cell-cell fusogenicity was severely impaired by introduction of P812S. The mutation also introduced significant perturbations to the FP region and also affected protomer-protomer packing. P812S conferred evasion of a neutralising monoclonal antibody targeting the fusion peptide, consistent with significant structural rearrangements in the FP region. Finally, P812S bearing viruses showed evasion of polyclonal neutralising antibodies in sera from vaccinated individuals at 32{degrees}C (simulating upper respiratory tract) and to a lesser extent at 37{degrees}C. Thus we report a novel mutational adaptation to the upper airway allowing enhanced immune evasion to fusion peptide targeting neutralising antibodies that also incurs a defect in ability to induce syncytia. These data shed light on the balance between upper airway adaptation/immune evasion by SARS-CoV-2, ability to induce syncytia formation, and disease severity given the established link between syncytia and severe COVID-19.

immunology↗

bioRxiv2024

The ageing stopping network: Regional and network changes in the IFG, preSMA, and STN across the adult lifespan

Response inhibition, the cancellation of planned movement, is essential for everyday motor control. Extensive fMRI and brain stimulation research provides evidence for the crucial role of a number of cortical and subcortical regions in response inhibition, including the subthalamic nucleus (STN), pre-supplementary motor area (preSMA), and the inferior frontal gyrus (IFG). Current models assume that these regions operate as a network, with action cancellation originating in the cortical areas and then executed rapidly via the subcortex. Response inhibition slows in older age, a change that has been attributed to deterioration or changes in the connectivity and integrity of this network. However, previous research has mainly used whole-brain approaches when investigating changes in structural connectivity across the lifespan, or have used simpler measures to investigate structural ageing. Here, we used high-resolution quantitative and diffusion MRI to extensively examine the anatomical changes that occur in this network across the lifespan. We found substantial changes in iron concentration in these tracts, increases in the apparent diffusion coefficient, and some evidence for demyelination. Conversely, we found very little evidence for age-related anatomical changes in the regions themselves. We propose that some of the functional changes observed in these regions in older adult populations (e.g., increased BOLD recruitment) are a reflection of alterations to the connectivity between the regions, rather than localised regional change.

neuroscience↗

bioRxiv2021

SARS-CoV-2 Omicron spike mediated immune escape, infectivity and cell-cell fusion

The SARS-CoV-2 Omicron BA.1 variant emerged in late 2021 and is characterised by multiple spike mutations across all spike domains. Here we show that Omicron BA.1 has higher affinity for ACE2 compared to Delta, and confers very significant evasion of therapeutic monoclonal and vaccine-elicited polyclonal neutralising antibodies after two doses. mRNA vaccination as a third vaccine dose rescues and broadens neutralisation. Importantly, antiviral drugs remdesevir and molnupiravir retain efficacy against Omicron BA.1. We found that in human nasal epithelial 3D cultures replication was similar for both Omicron and Delta. However, in lower airway organoids, Calu-3 lung cells and gut adenocarcinoma cell lines live Omicron virus demonstrated significantly lower replication in comparison to Delta. We noted that despite presence of mutations predicted to favour spike S1/S2 cleavage, the spike protein is less efficiently cleaved in live Omicron virions compared to Delta virions. We mapped the replication differences between the variants to entry efficiency using spike pseudotyped virus (PV) entry assays. The defect for Omicron PV in specific cell types correlated with higher cellular RNA expression of TMPRSS2, and accordingly knock down of TMPRSS2 impacted Delta entry to a greater extent as compared to Omicron. Furthermore, drug inhibitors targeting specific entry pathways demonstrated that the Omicron spike inefficiently utilises the cellular protease TMPRSS2 that mediates cell entry via plasma membrane fusion. Instead, we demonstrate that Omicron spike has greater dependency on cell entry via the endocytic pathway requiring the activity of endosomal cathepsins to cleave spike. Consistent with suboptimal S1/S2 cleavage and inability to utilise TMPRSS2, syncytium formation by the Omicron spike was dramatically impaired compared to the Delta spike. Overall, Omicron appears to have gained significant evasion from neutralising antibodies whilst maintaining sensitivity to antiviral drugs targeting the polymerase. Omicron has shifted cellular tropism away from TMPRSS2 expressing cells that are enriched in cells found in the lower respiratory and GI tracts, with implications for altered pathogenesis.

microbiology↗