Biology subjects

Sims, A.

Publications and source records attributed to Sims, A..

5 recordsLinked to original sources

bioRxiv2026

Viral dispersal drives changes in population composition

In an acute viral infection, a small seeding population expands rapidly over several orders of magnitude, then declines. This vast population growth is accompanied by spatial expansion as infection spreads to new anatomical sites within the host. Evolutionary theory predicts that spatially expanding populations experience more extreme stochastic losses of genetic diversity than spatially unstructured populations. To test this prediction in the context of viral dynamics, we evaluated the impact of spatial expansion on viral population genetic structure and assessed how modulators of viral dispersal affected this structure. To this end, we developed a means of implementing the spatial expansion of influenza A virus in cell culture and applied it to a viral population carrying a diverse genetic barcode. Across this simplified cellular landscape, we found that spatial expansion produces a patchwork of distinct viral subpopulations. We then evaluated the consequences for population structure of two modulators of viral dispersal: extracellular viscosity and a common polymorphism in the viral attachment protein. Both physical constraint and viral phenotype altered the extent of genetic bottlenecking and spatial heterogeneity that developed during expansion, indicating that environmental features and viral traits that modulate dispersal also modulate viral population composition, diversity and evolution.

microbiology↗

bioRxiv2025

SARS-CoV-2 cellular coinfection is limited by superinfection exclusion.

The coinfection of individual cells is a requirement for exchange between two or more virus genomes, which is a major mechanism driving virus evolution. Coinfection is restricted by a mechanism known as superinfection exclusion (SIE), which prohibits the infection of a previously infected cell by a related virus after a period of time. SIE regulates coinfection for many different viruses, but its relevance to the infection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) was unknown. In this study, we investigated this using a pair of SARS-CoV-2 variant viruses encoding distinct fluorescent reporter proteins. We show for the first time that SARS-CoV-2 coinfection of individual cells is limited temporally by SIE. We defined the kinetics of the onset of SIE for SARS-CoV-2 in this system, showing that the potential for coinfection starts to diminish within the first hour of primary infection, and then falls exponentially as the time between the two infection events is increased. We then asked how these kinetics would affect the potential for coinfection with viruses during a spreading infection. We used plaque assays to model the localised spread of SARS-CoV-2 observed in infected tissue, and showed that the kinetics of SIE restrict coinfection, and therefore sites of possible genetic exchange, to a small interface of infected cells between spreading viral infections. This indicates that SIE, by reducing the likelihood of coinfection of cells, likely reduces the opportunities for genetic exchange between different strains of SARS-CoV-2 and therefore is an underappreciated factor in shaping SARS-CoV-2 evolution.

microbiology↗

bioRxiv2022

Superinfection exclusion creates spatially distinct influenza virus populations

Influenza viruses can interact during coinfections, allowing viral fitness to be altered by genome complementation and competition, and increasing population diversity through reassortment. However, opportunities for these interactions are limited, as coinfection is blocked shortly after primary infection by a process known as superinfection exclusion (SIE). We asked whether SIE, which occurs at the level of individual cells, could limit within-host interactions between populations of influenza viruses as they spread across regions of cells. We first created a simplified model of within-host spread by infecting monolayers of cells with two isogenic influenza A viruses, each encoding a different fluorophore, and measuring the proportion of coinfected cells. In this system SIE begins within 2-4 hours of primary infection, with the kinetics of onset defined by the dose of primary virus. We then asked how SIE controls opportunities for coinfection as viruses spread across a monolayer of cells. We observed that viruses spreading from a single coinfected focus continued to coinfect cells as they spread, as all new infections were of cells that had not yet established SIE. In contrast, viruses spreading towards each other from separately infected foci could only establish minimal regions of coinfection before SIE blocked further coinfection. This patterning was recapitulated in the lungs of infected mice and is likely to apply to other viruses that exhibit SIE. It suggests that the kinetics of SIE onset separate a spreading infection into discrete regions, within which interactions between virus populations can occur freely, and between which they are blocked. ImportanceViral fitness and diversity are altered by genome interactions, which occur when multiple viruses coinfect a cell. This has been extensively studied for influenza A viruses (IAV), which use genome reassortment to adapt to new hosts and create pandemic strains, and whose replication can be compromised by the acquisition of defective-interfering RNAs. Coinfection of an individual cell by IAV is restricted by the gradual onset of superinfection exclusion (SIE). Replication of IAVs within host organisms involve the asynchronous replication of viruses as they spread to infect multiple cells. We found that under these circumstances, SIE creates spatially separated sub-populations of IAV, between which there are limited opportunities for genome interactions. Our work suggests SIE will cause many viruses to segregate into distinct subpopulations within their hosts, constraining the effects of genome interactions on their fitness and evolution.

microbiology↗

bioRxiv2019

A dormant sub-population expressing interleukin-1 receptor characterises anti-estrogen resistant ALDH+ breast cancer stem cells

Estrogen receptor-positive (ER+) breast tumours are often treated with anti-estrogen (AE) therapies but frequently develop resistance. Cancer Stem Cells (CSCs) with high aldehyde dehydrogenase (ALDH) activity (ALDH+ cells) are reported to be enriched following AE treatment. Here we perform in vitro and in vivo functional CSC assays and gene expression analysis to characterise the ALDH+ population in AE resistant metastatic patient samples and an ER+ cell line. We show that the IL1{beta} signalling pathway is activated in ALDH+ cells and data from single cells reveals that AE treatment selects for IL1R1-expressing ALDH+ cells. Importantly, we demonstrate that increased expression of IL1R1 is observed in the tumours of patients treated with AE therapy and predicts for treatment failure. Single-cell gene expression analysis revealed that at least 2 sub-populations exist within the ALDH+ population, one proliferative and one quiescent. Following AE therapy, the quiescent ALDH+IL1R1+ population is expanded, which suggests CSC dormancy as an adaptive strategy that facilitates treatment resistance. Supporting this, analysis of AE resistant dormant tumours reveals significantly increased expression of ALDH1A1, ALDH1A3 and IL1R1 genes. Thus, we propose that targeting of ALDH+IL1R1+ cells will reverse AE resistance, including in patients with minimal residual disease.

cancer biology↗

bioRxiv2019

Microtubules are necessary for proper Reticulon localization during mitosis

During mitosis, the structure of the Endoplasmic Reticulum (ER) displays a dramatic reorganization and remodeling event, however the mechanism driving these changes is poorly understood. Recently, the Reticulon family of ER shaping proteins has been identified as possible factors to promote these drastic changes in ER morphology. In addition, the Reticulons and other ER shaping proteins have been directly linked to several hereditary neurodegenerative disorders. Here, we provide key insight into the cytoskeletal factors involved in the Drosophila Reticulon, Reticulon-like 1 (Rtnl1) during mitosis in the early embryo. At prometaphase, Rtnl1 localizes at the spindle poles just prior to the bulk of ER localization suggesting a role in recruitment. Using precise temporal injections of cytoskeletal inhibitors in the early syncytial Drosophila embryo, we show that microtubules, not microfilaments are necessary for proper Rtnl1 localization and function during mitosis. Lastly, we show that astral microtubules are necessary for Rtnl1 localization at the spindle poles early in mitosis. This work highlights the role of the microtubule cytoskeleton in Rtnl1 localization and ER dynamics during mitosis and sheds light on a pathway towards inheritance of this major organelle.

cell biology↗