Imperial College London

DrKatrinaLythgoe

Faculty of MedicineSchool of Public Health

Honorary Lecturer
 
 
 
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Contact

 

+44 (0)20 7594 3820k.lythgoe CV

 
 
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Location

 

Norfolk PlaceSt Mary's Campus

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Summary

 

Publications

Publication Type
Year
to

38 results found

Pellis L, Scarabel F, Stage HB, Overton CE, Chappell LHK, Fearon E, Bennett E, Lythgoe KA, House TA, Hall Iet al., 2021, Challenges in control of COVID-19: short doubling time and long delay to effect of interventions, PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol: 376, ISSN: 0962-8436

Journal article

Villabona-Arenas CJ, Hué S, Baxter J, Hall M, Lythgoe KA, Bradley J, Atkins KEet al., 2021, USING PHYLOGENETICS TO ACCURATELY INFER HIV-1 TRANSMISSION DIRECTION

<jats:title>Abstract</jats:title><jats:p>Inferring the direction of transmission between linked individuals living with HIV provides unparalleled power to understand the epidemiology that determines transmission. State-of-the-art approaches to infer directionality use phylogenetic ancestral state reconstruction to identify the individual in whom the most recent common ancestor of the virus populations originated. However, these methods vary in their accuracy when applied to different datasets and it is currently unclear under what circumstances inferring directionality is inaccurate and when bias is more likely. To evaluate the performance of phylogenetic ancestral state reconstruction, we inferred directionality for 112 HIV transmission pairs where the direction of transmission was known, and detailed additional information was available. Next, we fit a statistical model to evaluate the extent to which epidemiological, sampling, genetic and phylogenetic factors influenced the outcome of the inference. Third, we repeated the analysis under real-life conditions when only routinely collected data are available. We found that the inference of directionality depends principally on the topology class and branch length characteristics of the phylogeny. Specifically, directionality is most correctly inferred when the phylogenetic diversity and the minimum root-to-tip distance in the transmitter is greater than that of the recipient partner and when the minimum inter-host patristic distance is large. Similarly, under real-life conditions, the probability of identifying the correct transmitter increases from 52%—when a monophyletic-monophyletic or paraphyletic-polyphyletic tree topology is observed, when the sample size in both partners is small and when the tip closest to the root does not agree with the state at the root—to 93% when a paraphyletic-monophyletic topology is observed, when the sample size is large and when the tip closest to the

Journal article

Lythgoe KA, Hall M, Ferretti L, de Cesare M, MacIntyre-Cockett G, Trebes A, Andersson M, Otecko N, Wise EL, Moore N, Lynch J, Kidd S, Cortes N, Mori M, Williams R, Vernet G, Justice A, Green A, Nicholls SM, Ansari MA, Abeler-Dorner L, Moore CE, Peto TEA, Eyre DW, Shaw R, Simmonds P, Buck D, Todd JA, Connor TR, Ashraf S, Filipe ADS, Shepherd J, Thomson EC, Bonsall D, Fraser C, Golubchik Tet al., 2021, SARS-CoV-2 within-host diversity and transmission, SCIENCE, Vol: 372, Pages: 256-+, ISSN: 0036-8075

Journal article

Illingworth CJR, Raghwani J, Serwadda D, Sewankambo NK, Robb ML, Eller MA, Redd AR, Quinn TC, Lythgoe KAet al., 2020, A de novo approach to inferring within-host fitness effects during untreated HIV-1 infection, PLOS PATHOGENS, Vol: 16, ISSN: 1553-7366

Journal article

Lythgoe KA, Hall M, Ferretti L, de Cesare M, MacIntyre-Cockett G, Trebes A, Andersson M, Otecko N, Wise EL, Moore N, Lynch J, Kidd S, Cortes N, Mori M, Williams R, Vernet G, Justice A, Green A, Nicholls SM, Ansari MA, Abeler-Dörner L, Moore CE, Peto TEA, Eyre DW, Shaw R, Simmonds P, Buck D, Todd JA, Connor TR, da Silva Filipe A, Shepherd J, Thomson EC, Bonsall D, Fraser C, Golubchik Tet al., 2020, Within-host genomics of SARS-CoV-2

<jats:title>Abstract</jats:title><jats:p>Extensive global sampling and whole genome sequencing of the pandemic virus SARS-CoV-2 have enabled researchers to characterise its spread, and to identify mutations that may increase transmission or enable the virus to escape therapies or vaccines. Two important components of viral spread are how frequently variants arise within individuals, and how likely they are to be transmitted. Here, we characterise the within-host diversity of SARS-CoV-2, and the extent to which genetic diversity is transmitted, by quantifying variant frequencies in 1390 clinical samples from the UK, many from individuals in known epidemiological clusters. We show that SARS-CoV-2 infections are characterised by low levels of within-host diversity across the entire viral genome, with evidence of strong evolutionary constraint in Spike, a key target of vaccines and antibody-based therapies. Although within-host variants can be observed in multiple individuals in the same phylogenetic or epidemiological cluster, highly infectious individuals with high viral load carry only a limited repertoire of viral diversity. Most viral variants are either lost, or occasionally fixed, at the point of transmission, consistent with a narrow transmission bottleneck. These results suggest potential vaccine-escape mutations are likely to be rare in infectious individuals. Nonetheless, we identified Spike variants present in multiple individuals that may affect receptor binding or neutralisation by antibodies. Since the fitness advantage of escape mutations in highly-vaccinated populations is likely to be substantial, resulting in rapid spread if and when they do emerge, these findings underline the need for continued vigilance and monitoring.</jats:p>

Journal article

Pellis L, Scarabel F, Stage HB, Overton CE, Chappell LHK, Lythgoe KA, Fearon E, Bennett E, Curran-Sebastian J, Das R, Fyles M, Lewkowicz H, Pang X, Vekaria B, Webb L, House TA, Hall Iet al., 2020, Challenges in control of COVID-19: short doubling times and long delay to effect of interventions

<jats:title>Abstract</jats:title><jats:p>The unconstrained growth rate of COVID-19 is crucial for measuring the impact of interventions, assessing worst-case scenarios, and calibrating mathematical models for policy planning. However, robust estimates are limited, with scientific focus on the time-insensitive basic reproduction number <jats:italic>R</jats:italic>0. Using multiple countries, data streams and methods, we consistently estimate that European COVID-19 cases doubled every three days when unconstrained, with the impact of physical distancing interventions typically seen about nine days after implementation, during which time cases grew eight-fold. The combination of fast growth and long detection delays explains the struggle in countries’ response better than large values of <jats:italic>R</jats:italic>0 alone, and warns against relaxing physical distancing measures too quickly. Testing and tracing are fundamental in shortening such delays, thus preventing cases from escalating unnoticed.</jats:p>

Journal article

Fryer HR, Raghwani J, Gill MJ, van Marle G, Golbchik T, Grove J, Lythgoe KAet al., 2020, Limited evolution despite years of measurable viremia in a cART-treated seronegative HIV-1 positive individual

<jats:title>Abstract</jats:title><jats:p>Understanding the role that antibodies play in controlling HIV-1 infection and in the dynamics that underpin the formation of the HIV-1 reservoir are important steps towards combatting this global disease. To address these gaps, we performed whole-genome, deep sequence analysis of longitudinal plasma HIV-1 samples from an individual who failed to develop detectable anti-HIV-1 antibodies for 4 years post infection. These analyses reveal limited evolution despite months of measurable viremia during treatment with cART. We used a mathematical model to simultaneously analyse the viral and evolutionary dynamics of this unique individual. We propose a role for antibodies in reducing viral infectivity and demonstrate how our data are consistent with a theory of rapid activation of latently infected cells prior to effective viral suppression. Our study supports and elucidates a recent finding that although the latent reservoir persists for years once virus is effectively suppressed, prior to suppression, viral strains within the reservoir turn over rapidly. The implications for a cure are significant.</jats:p>

Journal article

Lythgoe KA, Lumley SF, Pellis L, McKeating JA, Matthews PCet al., 2020, Estimating hepatitis B virus cccDNA persistence in chronic infection

<jats:title>Abstract</jats:title><jats:p>Hepatitis B virus (HBV) infection is a major global health problem with over 240 million infected individuals at risk of developing progressive liver disease and hepatocellular carcinoma. HBV is an enveloped DNA virus that establishes its genome as an episomal, covalently closed circular DNA (cccDNA) in the nucleus of infected hepatocytes. Currently available standard-of-care treatments for chronic hepatitis B (CHB) include nucleos(t)ide analogues (NA) that suppress HBV replication but do not target the cccDNA and hence rarely cure infection. There is considerable interest in determining the lifespan of cccDNA molecules to design and evaluate new curative treatments. We took a novel approach to this problem by developing a new mathematical framework to model changes in evolutionary rates during infection which, combined with previously determined within-host evolutionary rates of HBV, we used to determine the lifespan of cccDNA. We estimate that during HBe-antigen positive (HBeAg<jats:sup>POS</jats:sup>) infection the cccDNA lifespan is 61 (36-236) days, whereas during the HBeAg<jats:sup>NEG</jats:sup> phase of infection it is only 26 (16-81) days. We found that cccDNA replicative capacity declined by an order of magnitude between HBeAg<jats:sup>POS</jats:sup> and HBeAg<jats:sup>NEG</jats:sup> phases of infection. Our estimated lifespan of cccDNA is too short to explain the long durations of chronic infection observed in patients on NA treatment, suggesting that either a sub-population of long-lived hepatocytes harbouring cccDNA molecules persists during therapy, or that NA therapy does not suppress all viral replication. These results provide a greater understanding of the biology of the cccDNA reservoir and can aid the development of new curative therapeutic strategies for treating CHB.</jats:p><jats:sec><jats:title>Author Summary</jats:t

Journal article

Downs LO, Vawda S, Bester PA, Lythgoe KA, Wang T, McNaughton AL, Smith DA, Maponga T, Freeman O, Várnai KA, Davies J, Woods K, Fraser C, Barnes E, Goedhals D, Matthews PCet al., 2020, Bimodal distribution and set point HBV DNA viral loads in chronic infection: retrospective analysis of cohorts from the UK and South Africa

<jats:title>Abstract</jats:title><jats:p>Hepatitis B virus (HBV) DNA viral loads (VL) show wide variation between individuals with chronic hepatitis B (CHB) infection, and are used to determine treatment eligibility. There are few refined descriptions of VL distribution in CHB, and limited understanding of the biology that underpins these patterns. We set out to describe the VL distribution in independent cohorts from the UK and South Africa, to identify associated host characteristics, and to compare with VL in HIV-1 and hepatitis C (HCV) infection. We show the presence of a set-point in chronic HBV infection and report significant differences in the viral load distribution of HBV when compared to HIV and HCV.</jats:p>

Journal article

Villabona-Arenas CJ, Hall M, Lythgoe KA, Gaffney SG, Regoes RR, Hué S, Atkins KEet al., 2019, HIV-1 founder variant multiplicity is determined by the infection stage of the source partner

<jats:title>Abstract</jats:title><jats:p>During sexual transmission, the large genetic diversity of HIV-1 within an individual is frequently reduced to one founder variant that initiates infection<jats:sup>1</jats:sup>. Understanding the drivers of this bottleneck is crucial to develop effective infection control strategies<jats:sup>2</jats:sup>. Genetic characteristics of the potential founder viruses and events in the recipient partner are both known to contribute to this bottleneck, but little is understood about the importance of the source partner<jats:sup>3</jats:sup>. To test the hypothesis that the source partner affects the multiplicity of HIV founder variants, we developed a phylodynamic model calibrated using genetic and epidemiological data on all existing transmission pairs for whom the direction of transmission and the infection stage of the source partner are known. Our results demonstrate the importance of infection stage of the source partner, and not exposure route, in determining founder variant multiplicity. Specifically, acquiring infection from someone in the acute (early) stage of infection increases the risk of multiple variant transmission when compared with someone in the chronic (later) stage of infection. This study provides the first direct test of source partner characteristics to explain the low frequency of multiple founder strain infections and can inform clinical intervention study design and interpretation.</jats:p>

Journal article

Illingworth CJR, Raghwani J, Serwadda D, Sewankambo NK, Robb ML, Eller MA, Redd AR, Quinn TC, Lythgoe KAet al., 2019, A de novo approach to inferring within-host fitness effects during untreated HIV-1 infection

<jats:title>Abstract</jats:title><jats:p>In the absence of effective antiviral therapy, HIV-1 evolves in response to the within-host environment, of which the immune system is an important aspect. During the earliest stages of infection, this process of evolution is very rapid, driven by a small number of CTL escape mechanisms. As the infection progresses, immune escape variants evolve under reduced magnitudes of selection, while competition between an increasing number of polymorphic alleles (i.e., clonal interference) makes it difficult to quantify the magnitude of selection acting upon specific variant alleles. To tackle this complex problem, we developed a novel multi-locus inference method to evaluate the role of selection during the chronic stage of within-host infection. We applied this method to targeted sequence data from the p24 and gp41 regions of HIV-1 collected from 34 patients with long-term untreated HIV-1 infection. We identify a broad distribution of beneficial fitness effects during infection, with a small number of variants evolving under strong selection and very many variants evolving under weaker selection. The uniquely large number of infections analysed granted a previously unparalleled statistical power to identify loci at which selection could be inferred to act with statistical confidence. Our model makes no prior assumptions about the nature of alleles under selection, such that any synonymous or non-synonymous variant may be inferred to evolve under selection. However, the majority of variants inferred with confidence to be under selection were non-synonymous in nature, and in nearly all cases were associated with either CTL escape in p24 or neutralising antibody escape in gp41. Sites inferred to be under selection in multiple hosts have high within-host and between-host diversity albeit not all sites with high between-host diversity were inferred to be under selection at the within-host level. Our identification of sel

Journal article

Caudill VR, Qin S, Winstead R, Kaur J, Tisthammer K, Pineda EG, Carja O, Eggo RM, Koelle K, Lythgoe K, Roy S, Allen N, Aviles M, Baker BA, Bauer W, Bermudez S, Carlson C, Catalan FL, Chemel AK, Evans D, Fiutek N, Fryer E, Goodfellow SM, Hecht M, Hopp K, Hopson ED, Jaberi A, Kinney C, Lao D, Le A, Lo J, Lopez AG, López A, Lorenzo FG, Luu GT, Mahoney AR, Melton RL, Nascimento GD, Pradhananga A, Rodrigues NS, Shieh A, Sims J, Singh R, Sulaeman H, Thu R, Tran K, Tran L, Winters EJ, Wong A, Pennings PSet al., 2019, CpG-creating Mutations are Costly in Many Human Viruses

<jats:title>Abstract</jats:title><jats:p>Mutations can occur throughout the virus genome and may be beneficial or deleterious. We are interested in mutations that yield a C next to a G, producing CpG sites. CpG sites are rare in eukaryotic and viral genomes. For the eukaryotes, it is thought that CpG sites are rare because they are prone to mutation when methylated. In viruses, we know less about why CpG sites are rare. A previous study in HIV suggested that CpG-creating transition mutations are more costly that similar non-CpG-creating mutations. To determine if this is the case in other viruses, we analyzed the allele frequencies of CpG-creating and non-CpG-creating mutations across various strains, subtypes, and genes of viruses using existing data obtained from Genbank, HIV Databases, and Virus Pathogen Resource. Our results suggest that CpG sites are costly for most viruses. By understanding the cost of CpG sites, we can obtain further insights into the evolution and adaptation of viruses.</jats:p>

Journal article

Pike VL, Lythgoe KA, King KC, 2019, On the diverse and opposing effects of nutrition on pathogen virulence, PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol: 286, ISSN: 0962-8452

Journal article

Raghwani J, Wu C-H, Ho CKY, De Jong M, Molenkamp R, Schinkel J, Pybus OG, Lythgoe KAet al., 2019, High-Resolution Evolutionary Analysis of Within-Host Hepatitis C Virus Infection, JOURNAL OF INFECTIOUS DISEASES, Vol: 219, Pages: 1722-1729, ISSN: 0022-1899

Journal article

Thompson RN, Wymant C, Spriggs RA, Raghwani J, Fraser C, Lythgoe KAet al., 2019, Link between the numbers of particles and variants founding new HIV-1 infections depends on the timing of transmission, Virus Evolution, Vol: 5, ISSN: 2057-1577

Understanding which HIV-1 variants are most likely to be transmitted is important for vaccine design and predicting virus evolution. Since most infections are founded by single variants, it has been suggested that selection at transmission has a key role in governing which variants are transmitted. We show that the composition of the viral population within the donor at the time of transmission is also important. To support this argument, we developed a probabilistic model describing HIV-1 transmission in an untreated population, and parameterised the model using both within-host next generation sequencing data and population-level epidemiological data on heterosexual transmission. The most basic HIV-1 transmission models cannot explain simultaneously the low probability of transmission and the non-negligible proportion of infections founded by multiple variants. In our model, transmission can only occur when environmental conditions are appropriate (e.g. abrasions are present in the genital tract of the potential recipient), allowing these observations to be reconciled. As well as reproducing features of transmission in real populations, our model demonstrates that, contrary to expectation, there is not a simple link between the number of viral variants and the number of viral particles founding each new infection. These quantities depend on the timing of transmission, and infections can be founded with small numbers of variants yet large numbers of particles. Including selection, or a bias towards early transmission (e.g. due to treatment), acts to enhance this conclusion. In addition, we find that infections initiated by multiple variants are most likely to have derived from donors with intermediate set-point viral loads, and not from individuals with high set-point viral loads as might be expected. We therefore emphasise the importance of considering viral diversity in donors, and the timings of transmissions, when trying to discern the complex factors governing

Journal article

Abdullah N, Kelly JT, Graham SC, Birch J, Goncalves-Carneiro D, Mitchell T, Thompson RN, Lythgoe KA, Logan N, Hosie MJ, Bavro VN, Willett BJ, Heaton MP, Bailey Det al., 2018, Structure-Guided Identification of a Nonhuman Morbillivirus with Zoonotic Potential, JOURNAL OF VIROLOGY, Vol: 92, ISSN: 0022-538X

Journal article

Thompson RN, Wymant C, Spriggs RA, Raghwani J, Fraser C, Lythgoe KAet al., 2018, Link between the numbers of particles and variants founding new HIV-1 infections depends on the timing of transmission

<jats:title>ABSTRACT</jats:title><jats:p>Understanding which HIV-1 variants are most likely to be transmitted is important for vaccine design and predicting virus evolution. Since most infections are founded by single variants, it has been suggested that selection at transmission has a key role in governing which variants are transmitted. We show that the composition of the viral population within the donor at the time of transmission is also important. To support this argument, we developed a probabilistic model describing HIV-1 transmission in an untreated population, and parameterised the model using both within-host next generation sequencing data and population-level epidemiological data on heterosexual transmission. The most basic HIV-1 transmission models cannot explain simultaneously the low probability of transmission and the non-negligible proportion of infections founded by multiple variants. In our model, transmission can only occur when environmental conditions are appropriate (e.g. abrasions are present in the genital tract of the potential recipient), allowing these observations to be reconciled. As well as reproducing features of transmission in real populations, our model demonstrates that, contrary to expectation, there is not a simple link between the number of viral variants and the number of viral particles founding each new infection. These quantities depend on the timing of transmission, and infections can be founded with small numbers of variants yet large numbers of particles. Including selection, or a bias towards early transmission (e.g. due to treatment) acts to enhance this conclusion. In addition, we find that infections initiated by multiple variants are most likely to have derived from donors with intermediate set-point viral loads, and not from individuals with high set-point viral loads as might be expected. We therefore emphasise the importance of considering viral diversity in donors, and the timings of transmiss

Journal article

Raghwani J, Wu C-H, Ho CKY, de Jong M, Molenkamp R, Schinkel J, Pybus OG, Lythgoe KAet al., 2018, High resolution evolutionary analysis of within-host hepatitis C virus infection

<jats:title>ABSTRACT</jats:title><jats:p>Despite the breakthroughs in the treatment of HCV infection in recent years, we have a limited understanding of how virus diversity generated within individuals impacts the evolution and spread of HCV variants at the population scale. Addressing this gap will be important for building models for molecular epidemiology, which can identify main sources of disease transmission and evaluate the risks of drug-resistance mutations emerging and disseminating in a population. Here, we have undertaken a high-resolution analysis of HCV within-host evolution from four individuals co-infected with HIV. Specifically, we used long-read, deep-sequenced data of the full-length HCV envelope glycoprotein, longitudinally sampled from acute to chronic HCV infection to investigate the underlying viral evolutionary dynamics. In three individuals we found strong statistical support for population structure maintaining within-host HCV genetic diversity. Furthermore, we found significant variation in rates of molecular evolution among different regions of the HCV envelope region, both within and between individuals. Lastly, we report the first estimate of the within-host population genetic rate of recombination for HCV (0.28 x 10<jats:sup>-7</jats:sup> recombinations per site per day; interquartile range: 0.13-1.05 x 10<jats:sup>-7</jats:sup>), which is two orders of magnitude lower than that estimated for HIV-1, and four orders of magnitude lower than the nucleotide substitution rate of the HCV envelope gene. Together, these observations indicate that population structure and strong genetic linkage shapes within-host HCV evolutionary dynamics. These results will guide the future investigation of potential HCV drug resistance adaptation during infection, and at the population scale.</jats:p>

Journal article

Lumley SF, McNaughton AL, Klenerman P, Lythgoe KA, Matthews PCet al., 2018, Hepatitis B virus Adaptation to the CD8+T Cell Response: Consequences for Host and Pathogen, FRONTIERS IN IMMUNOLOGY, Vol: 9, ISSN: 1664-3224

Journal article

Raghwani J, Redd AD, Longosz AF, Wu C-H, Serwadda D, Martens C, Kagaayi J, Sewankambo N, Porcella SF, Grabowski MK, Quinn TC, Eller MA, Eller LA, Wabwire-Mangen F, Robb ML, Fraser C, Lythgoe KAet al., 2018, Evolution of HIV-1 within untreated individuals and at the population scale in Uganda, PLOS PATHOGENS, Vol: 14, ISSN: 1553-7366

Journal article

Lythgoe KA, Gardner A, Pybus OG, Grove Jet al., 2017, Short-sighted virus evolution and a germline hypothesis for chronic viral infections., Trends in Microbiology, Vol: 25, Pages: 336-348, ISSN: 0966-842X

With extremely short generation times and high mutability, many viruses can rapidly evolve and adapt to changing environments. This ability is generally beneficial to viruses as it allows them to evade host immune responses, evolve new behaviours, and exploit ecological niches. However, natural selection typically generates adaptation in response to the immediate selection pressures that a virus experiences in its current host. Consequently, we argue that some viruses, particularly those characterised by long durations of infection and ongoing replication, may be susceptible to short-sighted evolution, whereby a virus' adaptation to its current host will be detrimental to its onward transmission within the host population. Here we outline the concept of short-sighted viral evolution and provide examples of how it may negatively impact viral transmission among hosts. We also propose that viruses that are vulnerable to short-sighted evolution may exhibit strategies that minimise its effects. We speculate on the various mechanisms by which this may be achieved, including viral life history strategies that result in low rates of within-host evolution, or the establishment of a 'germline' lineage of viruses that avoids short-sighted evolution. These concepts provide a new perspective on the way in which some viruses have been able to establish and maintain global pandemics.

Journal article

Doekes HM, Fraser C, Lythgoe KA, 2017, Effect of the latent reservoir on the evolution of HIV at the within- and between-host Levels, PLoS Computational Biology, Vol: 13, Pages: 1-27, ISSN: 1553-734X

The existence of long-lived reservoirs of latently infected CD4+ T cells is the major barrier to curing HIV, and has been extensively studied in this light. However, the effect of these reservoirs on the evolutionary dynamics of the virus has received little attention. Here, we present a within-host quasispecies model that incorporates a long-lived reservoir, which we then nest into an epidemiological model of HIV dynamics. For biologically plausible parameter values, we find that the presence of a latent reservoir can severely delay evolutionary dynamics within a single host, with longer delays associated with larger relative reservoir sizes and/or homeostatic proliferation of cells within the reservoir. These delays can fundamentally change the dynamics of the virus at the epidemiological scale. In particular, the delay in within-host evolutionary dynamics can be sufficient for the virus to evolve intermediate viral loads consistent with maximising transmission, as is observed, and not the very high viral loads that previous models have predicted, an effect that can be further enhanced if viruses similar to those that initiate infection are preferentially transmitted. These results depend strongly on within-host characteristics such as the relative reservoir size, with the evolution of intermediate viral loads observed only when the within-host dynamics are sufficiently delayed. In conclusion, we argue that the latent reservoir has important, and hitherto under-appreciated, roles in both within- and between-host viral evolution.

Journal article

Blanquart F, Grabowski MK, Herbeck J, Nalugoda F, Serwadda D, Eller MA, Robb ML, Gray R, Kigozi G, Laeyendecker O, Lythgoe KA, Nakigozi G, Quinn TC, Reynolds SJ, Wawer MJ, Fraser Cet al., 2016, A transmission-virulence evolutionary trade-off explains attenuation of HIV-1 in Uganda, eLife, Vol: 5, ISSN: 2050-084X

Evolutionary theory hypothesizes that intermediate virulence maximizes pathogenfitness as a result of a trade-off between virulence and transmission, but empirical evidenceremains scarce. We bridge this gap using data from a large and long-standing HIV-1 prospectivecohort, in Uganda. We use an epidemiological-evolutionary model parameterised with this data toderive evolutionary predictions based on analysis and detailed individual-based simulations. Werobustly predict stabilising selection towards a low level of virulence, and rapid attenuation of thevirus. Accordingly, set-point viral load, the most common measure of virulence, has declined in thelast 20 years. Our model also predicts that subtype A is slowly outcompeting subtype D, with bothsubtypes becoming less virulent, as observed in the data. Reduction of set-point viral loads shouldhave resulted in a 20% reduction in incidence, and a three years extension of untreatedasymptomatic infection, increasing opportunities for timely treatment of infected individuals.

Journal article

Lythgoe KA, Blanquart F, Pellis L, Fraser Cet al., 2016, Large Variations in HIV-1 Viral Load Explained by Shifting-Mosaic Metapopulation Dynamics, PLOS Biology, Vol: 14, ISSN: 1545-7885

The viral population of HIV-1, like many pathogens that cause systemic infection, is structured and differentiated within the body. The dynamics of cellular immune trafficking through the blood and within compartments of the body has also received wide attention. Despite these advances, mathematical models, which are widely used to interpret and predict viral and immune dynamics in infection, typically treat the infected host as a well-mixed homogeneous environment. Here, we present mathematical, analytical, and computational results that demonstrate that consideration of the spatial structure of the viral population within the host radically alters predictions of previous models. We study the dynamics of virus replication and cytotoxic T lymphocytes (CTLs) within a metapopulation of spatially segregated patches, representing T cell areas connected by circulating blood and lymph. The dynamics of the system depend critically on the interaction between CTLs and infected cells at the within-patch level. We show that for a wide range of parameters, the system admits an unexpected outcome called the shifting-mosaic steady state. In this state, the whole body's viral population is stable over time, but the equilibrium results from an underlying, highly dynamic process of local infection and clearance within T-cell centers. Notably, and in contrast to previous models, this new model can explain the large differences in set-point viral load (SPVL) observed between patients and their distribution, as well as the relatively low proportion of cells infected at any one time, and alters the predicted determinants of viral load variation.

Journal article

Fraser C, Lythgoe K, Leventhal GE, Shirreff G, Hollingsworth TD, Alizon S, Bonhoeffer Set al., 2014, Virulence and Pathogenesis of HIV-1 Infection: An Evolutionary Perspective, SCIENCE, Vol: 343, Pages: 1328-+, ISSN: 0036-8075

Journal article

van de Vijver DA, Nichols BE, Abbas UL, Boucher CA, Cambiano V, Eaton JW, Glaubius R, Lythgoe K, Mellors J, Phillips A, Sigaloff KC, Hallett TBet al., 2013, Pre-exposure prophylaxis (PrEP) will have a limited impact on the prevalence of HIV-1 drug resistance in sub-Saharan Africa: comparison of mathematical models, AIDS, Vol: 27, Pages: 2943-2951, ISSN: 0269-9370

BACKGROUND: Preexposure prophylaxis (PrEP) with tenofovir and emtricitabine can prevent new HIV-1 infections, but there is a concern that use of PrEP could increase HIV drug resistance resulting in loss of treatment options. We compared standardized outcomes from three independent mathematical models simulating the impact of PrEP on HIV transmission and drug resistance in sub-Saharan African countries.METHODS: All models assume that people using PrEP receive an HIV test every 3-6 months. The models vary in structure and parameter choices for PrEP coverage, effectiveness of PrEP (at different adherence levels) and the rate with which HIV drug resistance emerges and is transmitted.RESULTS: The models predict that the use of PrEP in conjunction with antiretroviral therapy will result in a lower prevalence of HIV than when only antiretroviral therapy is used. With or without PrEP, all models suggest that HIV drug resistance will increase over the next 20 years due to antiretroviral therapy. PrEP will increase the absolute prevalence of drug resistance in the total population by less than 0.5% and amongst infected individuals by at most 7%. Twenty years after the introduction of PrEP, the majority of drug-resistant infections is due to antiretroviral therapy (50-63% across models), whereas 40-50% will be due to transmission of drug resistance, and less than 4% to the use of PrEP.CONCLUSION: HIV drug resistance resulting from antiretroviral therapy is predicted to far exceed that resulting from PrEP. Concern over drug resistance should not be a reason to limit the use of PrEP.

Journal article

van de Vijver DAMC, Nichols BE, Abbas UL, Boucher CAB, Cambiano V, Eaton JW, Glaubius R, Lythgoe K, Mellors J, Phillips A, Sigaloff KC, Hallett TBet al., 2013, Preexposure prophylaxis will have a limited impact on HIV-1 drug resistance in sub-Saharan Africa: a comparison of mathematical models, AIDS, Vol: 27, Pages: 2943-2951, ISSN: 0269-9370

Journal article

Lythgoe KA, Pellis L, Fraser C, 2013, IS HIV SHORT-SIGHTED? INSIGHTS FROM A MULTISTRAIN NESTED MODEL, EVOLUTION, Vol: 67, Pages: 2769-2782, ISSN: 0014-3820

Journal article

Lythgoe K, 2013, Invisible foes, Current Biology, Vol: 23, Pages: R548-R549, ISSN: 0960-9822

Journal article

Lythgoe KA, Fraser C, 2012, New insights into the evolutionary rate of HIV-1 at the within-host and epidemiological levels, PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol: 279, Pages: 3367-3375, ISSN: 0962-8452

Journal article

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