Publications
Results
- Showing results for:
- Reset all filters
Search results
-
Journal articleVieira A, Wan Y, Ryan Y, et al., 2024,
Rapid expansion and international spread of M1UK in the post-pandemic UK upsurge of Streptococcus pyogenes
, Nature Communications, Vol: 15, ISSN: 2041-1723The UK observed a marked increase in scarlet fever and invasive group A streptococcal infection in 2022 with severe outcomes in children and similar trends worldwide. Here we report lineage M1UK to be the dominant source of invasive infections in this upsurge. Compared with ancestral M1global strains, invasive M1UK strains exhibit reduced genomic diversity and fewer mutations in two-component regulator genes covRS. The emergence of M1UK is dated to 2008. Following a bottleneck coinciding with the COVID-19 pandemic, three emergent M1UK clades underwent rapid nationwide expansion, despite lack of detection in previous years. All M1UK isolates thus-far sequenced globally have a phylogenetic origin in the UK, with dispersal of the new clades in Europe. While waning immunity may promote streptococcal epidemics, the genetic features of M1UK point to a fitness advantage in pathogenicity, and a striking ability to persist through population bottlenecks.
-
Journal articleSubissi L, Otieno JR, Worp N, et al., 2024,
An updated framework for SARS-CoV-2 variants reflects the unpredictability of viral evolution
, NATURE MEDICINE, ISSN: 1078-8956 -
Journal articleWardle J, Bhatia S, Cori A, et al., 2024,
Temporal variations in international air travel: implications for modelling the spread of infectious diseases
, JOURNAL OF TRAVEL MEDICINE, Vol: 31, ISSN: 1195-1982 -
Journal articleMaddren R, Collyer B, Phillips AE, et al., 2024,
Patterns of individual compliance with anthelmintic treatment for soil-transmitted helminth infections in southern Ethiopia over six rounds of community-wide mass drug administration
, TRANSACTIONS OF THE ROYAL SOCIETY OF TROPICAL MEDICINE AND HYGIENE, Vol: 118, Pages: 304-312, ISSN: 0035-9203 -
Journal articleMutono N, Basáñez M-G, James A, et al., 2024,
Elimination of transmission of onchocerciasis (river blindness) with long-term ivermectin mass drug administration with or without vector control in sub-Saharan Africa: a systematic review and meta-analysis
, The Lancet Global Health, Vol: 12, Pages: e771-e782, ISSN: 2214-109XBACKGROUND: WHO has proposed elimination of transmission of onchocerciasis (river blindness) by 2030. More than 99% of cases of onchocerciasis are in sub-Saharan Africa. Vector control and mass drug administration of ivermectin have been the main interventions for many years, with varying success. We aimed to identify factors associated with elimination of onchocerciasis transmission in sub-Saharan Africa. METHODS: For this systematic review and meta-analysis we searched for published articles reporting epidemiological or entomological assessments of onchocerciasis transmission status in sub-Saharan Africa, with or without vector control. We searched MEDLINE, PubMed, Web of Science, Embase, Cochrane Central Register of Controlled Trials, African Index Medicus, and Google Scholar databases for all articles published from database inception to Aug 19, 2023, without language restrictions. The search terms used were "onchocerciasis" AND "ivermectin" AND "mass drug administration". The three inclusion criteria were (1) focus or foci located in Africa, (2) reporting of elimination of transmission or at least 10 years of ivermectin mass drug administration in the focus or foci, and (3) inclusion of at least one of the following assessments: microfilarial prevalence, nodule prevalence, Ov16 antibody seroprevalence, and blackfly infectivity prevalence. Epidemiological modelling studies and reviews were excluded. Four reviewers (NM, AJ, AM, and TNK) extracted data in duplicate from the full-text articles using a data extraction tool developed in Excel with columns recording the data of interest to be extracted, and a column where important comments for each study could be highlighted. We did not request any individual-level data from authors. Foci were classified as achieving elimination of transmission, being close to elimination of transmission, or with ongoing transmission. We used mixed-effects meta-regression models to identify factors assoc
-
Journal articleNascimento FF, Mehta SR, Little SJ, et al., 2024,
Assessing transmission attribution risk from simulated sequencing data in HIV molecular epidemiology
, AIDS, Vol: 38, Pages: 865-873, ISSN: 0269-9370BACKGROUND: HIV molecular epidemiology (ME) is the analysis of sequence data together with individual-level clinical, demographic, and behavioral data to understand HIV epidemiology. The use of ME has raised concerns regarding identification of the putative source in direct transmission events. This could result in harm ranging from stigma to criminal prosecution in some jurisdictions. Here we assessed the risks of ME using simulated HIV genetic sequencing data. METHODS: We simulated social networks of men-who-have-sex-with-men, calibrating the simulations to data from San Diego. We used these networks to simulate consensus and next-generation sequence (NGS) data to evaluate the risks of identifying direct transmissions using different HIV sequence lengths, and population sampling depths. To identify the source of transmissions, we calculated infector probability and used phyloscanner software for the analysis of consensus and NGS data, respectively. RESULTS: Consensus sequence analyses showed that the risk of correctly inferring the source (direct transmission) within identified transmission pairs was very small and independent of sampling depth. Alternatively, NGS analyses showed that identification of the source of a transmission was very accurate, but only for 6.5% of inferred pairs. False positive transmissions were also observed, where one or more unobserved intermediaries were present when compared to the true network. CONCLUSION: Source attribution using consensus sequences rarely infers direct transmission pairs with high confidence but is still useful for population studies. In contrast, source attribution using NGS data was much more accurate in identifying direct transmission pairs, but for only a small percentage of transmission pairs analyzed.
-
Journal articleSchmit N, Topazian HM, Natama HM, et al., 2024,
The public health impact and cost-effectiveness of the R21/Matrix-M malaria vaccine: a mathematical modelling study
, Lancet Infectious Diseases, Vol: 24, Pages: 465-475, ISSN: 1473-3099BACKGROUND: The R21/Matrix-M vaccine has demonstrated high efficacy against Plasmodium falciparum clinical malaria in children in sub-Saharan Africa. Using trial data, we aimed to estimate the public health impact and cost-effectiveness of vaccine introduction across sub-Saharan Africa. METHODS: We fitted a semi-mechanistic model of the relationship between anti-circumsporozoite protein antibody titres and vaccine efficacy to data from 3 years of follow-up in the phase 2b trial of R21/Matrix-M in Nanoro, Burkina Faso. We validated the model by comparing predicted vaccine efficacy to that observed over 12-18 months in the phase 3 trial. Integrating this framework within a mathematical transmission model, we estimated the cases, malaria deaths, and disability-adjusted life-years (DALYs) averted and cost-effectiveness over a 15-year time horizon across a range of transmission settings in sub-Saharan Africa. Cost-effectiveness was estimated incorporating the cost of vaccine introduction (dose, consumables, and delivery) relative to existing interventions at baseline. We report estimates at a median of 20% parasite prevalence in children aged 2-10 years (PfPR2-10) and ranges from 3% to 65% PfPR2-10. FINDINGS: Anti-circumsporozoite protein antibody titres were found to satisfy the criteria for a surrogate of protection for vaccine efficacy against clinical malaria. Age-based implementation of a four-dose regimen of R21/Matrix-M vaccine was estimated to avert 181 825 (range 38 815-333 491) clinical cases per 100 000 fully vaccinated children in perennial settings and 202 017 (29 868-405 702) clinical cases per 100 000 fully vaccinated children in seasonal settings. Similar estimates were obtained for seasonal or hybrid implementation. Under an assumed vaccine dose price of US$3, the incremental cost per clinical case averted was $7 (range 4-48) in perennial settings and $6 (3-63) in seasonal settings and the incremental cost per DALY averted was $34 (29-139) in perennial s
-
Journal articleBandyopadhyay AS, Lopez Cavestany R, Blake IM, et al., 2024,
Use of inactivated poliovirus vaccine for poliovirus outbreak response.
, Lancet Infect Dis, Vol: 24, Pages: e328-e342With continued wild poliovirus transmission in Afghanistan and Pakistan and circulating vaccine-derived poliovirus in certain countries, there exists an ongoing risk of importation of polioviruses into other countries, including those that have been polio-free for decades. Diversifying the poliovirus outbreak response toolkit is essential to account for different public health and epidemiological contexts. In this Personal View, we discuss data on intestinal and pharyngeal mucosal immunity induced by inactivated poliovirus vaccine (IPV), previous programmatic experience of poliovirus outbreak response with IPV, and outbreak response guidelines in countries that exclusively use IPV. With recent reports of poliovirus detection in polio-free countries such as the USA and the UK, it is important to assess the interplay of virus transmission dynamics, vaccine impact on preventing paralysis and virus spread, and regulatory complexities of using oral poliovirus vaccine (OPV) and IPV options for outbreak response. As the global eradication programme navigates through cessation of routine OPV use with replacement by IPV and stockpiling of novel OPVs, clarity on the impact of IPV use will be important for informed decision making by global, regional, and national policy makers.
-
Journal articleCuomo-Dannenburg G, McCain K, McCabe R, et al., 2024,
Marburg virus disease outbreaks, mathematical models, and disease parameters: a systematic review
, Lancet Infectious Diseases, Vol: 24, Pages: e307-e317, ISSN: 1473-3099Recent Marburg virus disease (MVD) outbreaks in Equatorial Guinea and Tanzania highlighted the importance of better understanding this highly lethal infectious pathogen. We conducted a systematic review (PROSPERO CRD42023393345), reported according to PRISMA guidelines, of peer-reviewed papers reporting historical outbreaks, modelling studies and epidemiological parameters focused on MVD. We searched PubMed and Web of Science until 31/03/2023. Two reviewers evaluated all titles and abstracts, with consensus-based decision-making. To ensure agreement, 31% (13/42) of studies were double-extracted and a custom-designed quality assessment questionnaire was used for risk of bias assessment. We present detailed information on 478 reported cases and 385 deaths from MVD. Analysis of historical outbreaks and seroprevalence estimates suggests the possibility of undetected MVD outbreaks, asymptomatic transmission and/or cross-reactivity with other pathogens. Only one study presented a mathematical model of MVD transmission. We estimate an unadjusted, pooled total random effect case fatality ratio for MVD of 61.9% (95% CI: 38.8-80.6%, I^2=93%). We identify important epidemiological parameters relating to transmission and natural history for which there are few estimates. This review and the accompanying database provide a comprehensive overview of MVD epidemiology, and identify key knowledge gaps, contributing crucial information for mathematical models to support future MVD epidemic responses.
-
Journal articleRawson T, Hinsley W, Sonabend R, et al., 2024,
The impact of health inequity on spatial variation of COVID-19 transmission in England
, PLoS Computational Biology, Vol: 20, ISSN: 1553-734XConsiderable spatial heterogeneity has been observed in COVID-19 transmission across administrative areas of England throughout the pandemic. This study investigates what drives these differences. We constructed a probabilistic case count model for 306 administrative areas of England across 95 weeks, fit using a Bayesian evidence synthesis framework. We incorporate the impact of acquired immunity, of spatial exportation of cases, and 16 spatially-varying socio-economic, socio-demographic, health, and mobility variables. Model comparison assesses the relative contributions of these respective mechanisms. We find that spatially-varying and time-varying differences in week-to-week transmission were definitively associated with differences in: time spent at home, variant-of-concern proportion, and adult social care funding. However, model comparison demonstrates that the impact of these terms is negligible compared to the role of spatial exportation between administrative areas. While these results confirm the impact of some, but not all, static measures of spatially-varying inequity in England, our work corroborates the finding that observed differences in disease transmission during the pandemic were predominantly driven by underlying epidemiological factors rather than aggregated metrics of demography and health inequity between areas. Further work is required to assess how health inequity more broadly contributes to these epidemiological factors.
This data is extracted from the Web of Science and reproduced under a licence from Thomson Reuters. You may not copy or re-distribute this data in whole or in part without the written consent of the Science business of Thomson Reuters.