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Article ; Online: Author Correction: Epidemiological drivers of transmissibility and severity of SARS-CoV-2 in England.

Perez-Guzman, Pablo N / Knock, Edward / Imai, Natsuko / Rawson, Thomas / Elmaci, Yasin / Alcada, Joana / Whittles, Lilith K / Thekke Kanapram, Divya / Sonabend, Raphael / Gaythorpe, Katy A M / Hinsley, Wes / FitzJohn, Richard G / Volz, Erik / Verity, Robert / Ferguson, Neil M / Cori, Anne / Baguelin, Marc

Nature communications

2023 Volume 14, Issue 1, Page(s) 8099

Language	English
Publishing date	2023-12-07
Publishing country	England
Document type	Published Erratum
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-44062-9
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Article ; Online: Epidemiological drivers of transmissibility and severity of SARS-CoV-2 in England.

Nature communications

2023 Volume 14, Issue 1, Page(s) 4279

Abstract: As the SARS-CoV-2 pandemic progressed, distinct variants emerged and dominated in England. These variants, Wildtype, Alpha, Delta, and Omicron were characterized by variations in transmissibility and severity. We used a robust mathematical model and ... ...

Abstract	As the SARS-CoV-2 pandemic progressed, distinct variants emerged and dominated in England. These variants, Wildtype, Alpha, Delta, and Omicron were characterized by variations in transmissibility and severity. We used a robust mathematical model and Bayesian inference framework to analyse epidemiological surveillance data from England. We quantified the impact of non-pharmaceutical interventions (NPIs), therapeutics, and vaccination on virus transmission and severity. Each successive variant had a higher intrinsic transmissibility. Omicron (BA.1) had the highest basic reproduction number at 8.3 (95% credible interval (CrI) 7.7-8.8). Varying levels of NPIs were crucial in controlling virus transmission until population immunity accumulated. Immune escape properties of Omicron decreased effective levels of immunity in the population by a third. Furthermore, in contrast to previous studies, we found Alpha had the highest basic infection fatality ratio (2.9%, 95% CrI 2.7-3.2), followed by Delta (2.2%, 95% CrI 2.0-2.4), Wildtype (1.2%, 95% CrI 1.1-1.2), and Omicron (0.7%, 95% CrI 0.6-0.8). Our findings highlight the importance of continued surveillance. Long-term strategies for monitoring and maintaining effective immunity against SARS-CoV-2 are critical to inform the role of NPIs to effectively manage future variants with potentially higher intrinsic transmissibility and severe outcomes.
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; Bayes Theorem ; COVID-19/epidemiology ; England/epidemiology
Language	English
Publishing date	2023-07-17
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-39661-5
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Article ; Online: Factors associated with reattendance to emergency services following COVID-19 hospitalization.

Daunt, Anna / Perez-Guzman, Pablo N / Cafferkey, John / Manalan, Kavina / Cooke, Graham / White, Peter J / Hauck, Katharina / Mallia, Patrick / Nayagam, Shevanthi

Journal of medical virology

2020 Volume 93, Issue 3, Page(s) 1250–1252

MeSH term(s)	COVID-19 ; China ; Hospitalization ; Humans ; SARS-CoV-2
Keywords	covid19
Language	English
Publishing date	2020-10-30
Publishing country	United States
Document type	Letter ; Comment
ZDB-ID	752392-0
ISSN	1096-9071 ; 0146-6615
ISSN (online)	1096-9071
ISSN	0146-6615
DOI	10.1002/jmv.26594
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Article ; Online: Validity of the UK early access to medicines scheme criteria for Remdesivir use in patients with COVID-19 disease.

Daunt, Anna / Perez-Guzman, Pablo N / Liew, Felicity / Hauck, Katharina / Costelloe, Ceire E / Thursz, Mark R / Cooke, Graham / Nayagam, Shevanthi

The Journal of infection

2020 Volume 81, Issue 4, Page(s) 647–679

MeSH term(s)	Adenosine Monophosphate/analogs & derivatives ; Alanine/analogs & derivatives ; Betacoronavirus ; COVID-19 ; Coronavirus Infections/drug therapy ; Health Services Accessibility ; Humans ; London ; Pandemics ; Pneumonia, Viral ; Retrospective Studies ; SARS-CoV-2 ; State Medicine ; United Kingdom ; COVID-19 Drug Treatment
Chemical Substances	remdesivir (3QKI37EEHE) ; Adenosine Monophosphate (415SHH325A) ; Alanine (OF5P57N2ZX)
Keywords	covid19
Language	English
Publishing date	2020-06-21
Publishing country	England
Document type	Letter ; Comment
ZDB-ID	424417-5
ISSN	1532-2742 ; 0163-4453
ISSN (online)	1532-2742
ISSN	0163-4453
DOI	10.1016/j.jinf.2020.06.049
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Article ; Online: Correction to: Association between HIV infection and hypertension: a global systematic review and meta-analysis of cross-sectional studies.

Davis, Katherine / Perez-Guzman, Pablo / Hoyer, Annika / Brinks, Ralph / Gregg, Edward / Althoff, Keri N / Justice, Amy C / Reiss, Peter / Gregson, Simon / Smit, Mikaela

BMC medicine

2021 Volume 19, Issue 1, Page(s) 228

Language	English
Publishing date	2021-09-08
Publishing country	England
Document type	Published Erratum
ZDB-ID	2131669-7
ISSN	1741-7015 ; 1741-7015
ISSN (online)	1741-7015
ISSN	1741-7015
DOI	10.1186/s12916-021-02112-3
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Article ; Online: Quantifying the effect of delaying the second COVID-19 vaccine dose in England: a mathematical modelling study.

The Lancet. Public health

2023 Volume 8, Issue 3, Page(s) e174–e183

Abstract: Background: The UK was the first country to start national COVID-19 vaccination programmes, initially administering doses 3 weeks apart. However, early evidence of high vaccine effectiveness after the first dose and the emergence of the SARS-CoV-2 alpha ...

Abstract	Background: The UK was the first country to start national COVID-19 vaccination programmes, initially administering doses 3 weeks apart. However, early evidence of high vaccine effectiveness after the first dose and the emergence of the SARS-CoV-2 alpha variant prompted the UK to extend the interval between doses to 12 weeks. In this study, we aimed to quantify the effect of delaying the second vaccine dose in England. Methods: We used a previously described model of SARS-CoV-2 transmission, calibrated to COVID-19 surveillance data from England, including hospital admissions, hospital occupancy, seroprevalence data, and population-level PCR testing data, using a Bayesian evidence-synthesis framework. We modelled and compared the epidemic trajectory in the counterfactual scenario in which vaccine doses were administered 3 weeks apart against the real reported vaccine roll-out schedule of 12 weeks. We estimated and compared the resulting numbers of daily infections, hospital admissions, and deaths. In sensitivity analyses, we investigated scenarios spanning a range of vaccine effectiveness and waning assumptions. Findings: In the period from Dec 8, 2020, to Sept 13, 2021, the number of individuals who received a first vaccine dose was higher under the 12-week strategy than the 3-week strategy. For this period, we estimated that delaying the interval between the first and second COVID-19 vaccine doses from 3 to 12 weeks averted a median (calculated as the median of the posterior sample) of 58 000 COVID-19 hospital admissions (291 000 cumulative hospitalisations [95% credible interval 275 000-319 000] under the 3-week strategy vs 233 000 [229 000-238 000] under the 12-week strategy) and 10 100 deaths (64 800 deaths [60 200-68 900] vs 54 700 [52 800-55 600]). Similarly, we estimated that the 3-week strategy would have resulted in more infections compared with the 12-week strategy. Across all sensitivity analyses the 3-week strategy resulted in a greater number of hospital admissions. In results by age group, the 12-week strategy led to more hospitalisations and deaths in older people in spring 2021, but fewer following the emergence of the delta variant during summer 2021. Interpretation: England's delayed-second-dose vaccination strategy was informed by early real-world data on vaccine effectiveness in the context of limited vaccine supplies in a growing epidemic. Our study shows that rapidly providing partial (single-dose) vaccine-induced protection to a larger proportion of the population was successful in reducing the burden of COVID-19 hospitalisations and deaths overall. Funding: UK National Institute for Health Research; UK Medical Research Council; Community Jameel; Wellcome Trust; UK Foreign, Commonwealth and Development Office; Australian National Health and Medical Research Council; and EU.
MeSH term(s)	Humans ; Aged ; Infant ; COVID-19 Vaccines ; COVID-19 ; Bayes Theorem ; Seroepidemiologic Studies ; Australia ; SARS-CoV-2 ; England
Chemical Substances	COVID-19 Vaccines
Language	English
Publishing date	2023-02-09
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2468-2667
ISSN (online)	2468-2667
DOI	10.1016/S2468-2667(22)00337-1
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Article ; Online: Characteristics and outcomes of clinically diagnosed RT-PCR swab negative COVID-19: a retrospective cohort study.

Middleton, Paul / Perez-Guzman, Pablo N / Cheng, Alexandra / Kumar, Naveenta / Kont, Mara D / Daunt, Anna / Mukherjee, Sujit / Cooke, Graham / Hallett, Timothy B / Hauck, Katharina / White, Peter J / Thursz, Mark R / Nayagam, Shevanthi

Scientific reports

2021 Volume 11, Issue 1, Page(s) 2455

Abstract: Patients with strong clinical features of COVID-19 with negative real time polymerase chain reaction (RT-PCR) SARS-CoV-2 testing are not currently included in official statistics. The scale, characteristics and clinical relevance of this group are not ... ...

Abstract	Patients with strong clinical features of COVID-19 with negative real time polymerase chain reaction (RT-PCR) SARS-CoV-2 testing are not currently included in official statistics. The scale, characteristics and clinical relevance of this group are not well described. We performed a retrospective cohort study in two large London hospitals to characterize the demographic, clinical, and hospitalization outcome characteristics of swab-negative clinical COVID-19 patients. We found 1 in 5 patients with a negative swab and clinical suspicion of COVID-19 received a clinical diagnosis of COVID-19 within clinical documentation, discharge summary or death certificate. We compared this group to a similar swab positive cohort and found similar demographic composition, symptomology and laboratory findings. Swab-negative clinical COVID-19 patients had better outcomes, with shorter length of hospital stay, reduced need for > 60% supplementary oxygen and reduced mortality. Patients with strong clinical features of COVID-19 that are swab-negative are a common clinical challenge. Health systems must recognize and plan for the management of swab-negative patients in their COVID-19 clinical management, infection control policies and epidemiological assessments.
MeSH term(s)	Adult ; COVID-19/diagnosis ; COVID-19/epidemiology ; COVID-19/genetics ; COVID-19/virology ; COVID-19 Testing/methods ; COVID-19 Testing/trends ; Cohort Studies ; False Negative Reactions ; Female ; Hospitalization/statistics & numerical data ; Hospitals ; Humans ; London/epidemiology ; Male ; Middle Aged ; Real-Time Polymerase Chain Reaction ; Retrospective Studies ; Reverse Transcriptase Polymerase Chain Reaction/methods ; SARS-CoV-2/genetics ; SARS-CoV-2/isolation & purification ; Specimen Handling
Language	English
Publishing date	2021-01-28
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-81930-0
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Article ; Online: Mapping the Current and Future Noncommunicable Disease Burden in Kenya by Human Immunodeficiency Virus Status: A Modeling Study.

Smit, Mikaela / Perez-Guzman, Pablo N / Mutai, Kennedy K / Cassidy, Rachel / Kibachio, Joseph / Kilonzo, Nduku / Hallett, Timothy B

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

2019 Volume 71, Issue 8, Page(s) 1864–1873

Abstract: Background: The noncommunicable disease (NCD) burden in Kenya is not well characterized, despite estimates needed to identify future health priorities. We aimed to quantify current and future NCD burden in Kenya by human immunodeficiency virus (HIV) ... ...

Abstract	Background: The noncommunicable disease (NCD) burden in Kenya is not well characterized, despite estimates needed to identify future health priorities. We aimed to quantify current and future NCD burden in Kenya by human immunodeficiency virus (HIV) status. Methods: Original systematic reviews and meta-analyses of prevalence/incidence of cardiovascular disease (CVD), chronic kidney disease, depression, diabetes, high total cholesterol, hypertension, human papillomavirus infection, and related precancerous stages in Kenya were carried out. An individual-based model was developed, simulating births, deaths, HIV disease and treatment, aforementioned NCDs, and cancers. The model was parameterized using systematic reviews and epidemiological national and regional surveillance data. NCD burden was quantified for 2018-2035 by HIV status among adults. Results: Systematic reviews identified prevalence/incidence data for each NCD except ischemic heart disease. The model estimates that 51% of Kenyan adults currently suffer from ≥1 NCD, with a higher burden in people living with HIV (PLWH) compared to persons not living with HIV (62% vs 51%), driven by their higher age profile and partly by HIV-related risk for NCDs. Hypertension and high total cholesterol are the main NCD drivers (adult prevalence of 20.5% [5.3 million] and 9.0% [2.3 million]), with CVD and cancers the main causes of death. The burden is projected to increase by 2035 (56% in persons not living with HIV; 71% in PLWH), with population growth doubling the number of people needing services (15.4 million to 28.1 million) by 2035. Conclusions: NCD services will need to be expanded in Kenya. Guidelines in Kenya already support provision of these among both the general and populations living with HIV; however, coverage remains low.
MeSH term(s)	Adult ; Cardiovascular Diseases/epidemiology ; HIV ; HIV Infections/complications ; HIV Infections/epidemiology ; Humans ; Kenya/epidemiology ; Noncommunicable Diseases/epidemiology
Language	English
Publishing date	2019-11-13
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1099781-7
ISSN	1537-6591 ; 1058-4838
ISSN (online)	1537-6591
ISSN	1058-4838
DOI	10.1093/cid/ciz1103
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Article ; Online: Association between HIV infection and hypertension: a global systematic review and meta-analysis of cross-sectional studies.

Davis, Katherine / Perez-Guzman, Pablo / Hoyer, Annika / Brinks, Ralph / Gregg, Edward / Althoff, Keri N / Justice, Amy C / Reiss, Peter / Gregson, Simon / Smit, Mikaela

BMC medicine

2021 Volume 19, Issue 1, Page(s) 105

Abstract: Background: Improved access to effective antiretroviral therapy has meant that people living with HIV (PLHIV) are surviving to older ages. However, PLHIV may be ageing differently to HIV-negative individuals, with dissimilar burdens of non-communicable ... ...

Abstract	Background: Improved access to effective antiretroviral therapy has meant that people living with HIV (PLHIV) are surviving to older ages. However, PLHIV may be ageing differently to HIV-negative individuals, with dissimilar burdens of non-communicable diseases, such as hypertension. While some observational studies have reported a higher risk of prevalent hypertension among PLHIV compared to HIV-negative individuals, others have found a reduced burden. To clarify the relationship between HIV and hypertension, we identified observational studies and pooled their results to assess whether there is a difference in hypertension risk by HIV status. Methods: We performed a global systematic review and meta-analysis of published cross-sectional studies that examined hypertension risk by HIV status among adults aged > 15 (PROSPERO: CRD42019151359). We searched MEDLINE, EMBASE, Global Health and Cochrane CENTRAL to August 23, 2020, and checked reference lists of included articles. Our main outcome was the risk ratio for prevalent hypertension in PLHIV compared to HIV-negative individuals. Summary estimates were pooled with a random effects model and meta-regression explored whether any difference was associated with study-level factors. Results: Of 21,527 identified studies, 59 were eligible (11,101,581 participants). Crude global hypertension risk was lower among PLHIV than HIV-negative individuals (risk ratio 0.90, 95% CI 0.85-0.96), although heterogeneity between studies was high (I Conclusions: Our findings suggest that the relationship between HIV status and prevalent hypertension differs by region. The results highlight the need to tailor hypertension prevention and care to local contexts and underscore the importance of rapidly optimising integration of services for HIV and hypertension in the worst affected regions. The role of different risk factors for hypertension in driving context-specific trends remains unclear, so development of further cohorts of PLHIV and HIV-negative controls focused on this would also be valuable.
MeSH term(s)	Adult ; Aged ; Cross-Sectional Studies ; Global Health ; HIV Infections/complications ; HIV Infections/epidemiology ; Humans ; Hypertension/epidemiology ; Middle Aged ; Risk Factors
Language	English
Publishing date	2021-05-13
Publishing country	England
Document type	Journal Article ; Meta-Analysis ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Systematic Review
ISSN	1741-7015
ISSN (online)	1741-7015
DOI	10.1186/s12916-021-01978-7
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Article: Reproducible parallel inference and simulation of stochastic state space models using odin, dust, and mcstate.

FitzJohn, Richard G / Knock, Edward S / Whittles, Lilith K / Perez-Guzman, Pablo N / Bhatia, Sangeeta / Guntoro, Fernando / Watson, Oliver J / Whittaker, Charles / Ferguson, Neil M / Cori, Anne / Baguelin, Marc / Lees, John A

Wellcome open research

2021 Volume 5, Page(s) 288

Abstract: State space models, including compartmental models, are used to model physical, biological and social phenomena in a broad range of scientific fields. A common way of representing the underlying processes in these models is as a system of stochastic ... ...

Abstract	State space models, including compartmental models, are used to model physical, biological and social phenomena in a broad range of scientific fields. A common way of representing the underlying processes in these models is as a system of stochastic processes which can be simulated forwards in time. Inference of model parameters based on observed time-series data can then be performed using sequential Monte Carlo techniques. However, using these methods for routine inference problems can be made difficult due to various engineering considerations: allowing model design to change in response to new data and ideas, writing model code which is highly performant, and incorporating all of this with up-to-date statistical techniques. Here, we describe a suite of packages in the R programming language designed to streamline the design and deployment of state space models, targeted at infectious disease modellers but suitable for other domains. Users describe their model in a familiar domain-specific language, which is converted into parallelised C++ code. A fast, parallel, reproducible random number generator is then used to run large numbers of model simulations in an efficient manner. We also provide standard inference and prediction routines, though the model simulator can be used directly if these do not meet the user's needs. These packages provide guarantees on reproducibility and performance, allowing the user to focus on the model itself, rather than the underlying computation. The ability to automatically generate high-performance code that would be tedious and time-consuming to write and verify manually, particularly when adding further structure to compartments, is crucial for infectious disease modellers. Our packages have been critical to the development cycle of our ongoing real-time modelling efforts in the COVID-19 pandemic, and have the potential to do the same for models used in a number of different domains.
Language	English
Publishing date	2021-06-10
Publishing country	England
Document type	Journal Article
ISSN	2398-502X
ISSN	2398-502X
DOI	10.12688/wellcomeopenres.16466.2
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