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Article ; Online: Heterologous vaccination interventions to reduce pandemic morbidity and mortality: Modeling the US winter 2020 COVID-19 wave.

Hupert, Nathaniel / Marín-Hernández, Daniela / Gao, Bo / Águas, Ricardo / Nixon, Douglas F

Proceedings of the National Academy of Sciences of the United States of America

2022 Volume 119, Issue 3

Abstract: COVID-19 remains a stark health threat worldwide, in part because of minimal levels of targeted vaccination outside high-income countries and highly transmissible variants causing infection in vaccinated individuals. Decades of theoretical and ... ...

Abstract	COVID-19 remains a stark health threat worldwide, in part because of minimal levels of targeted vaccination outside high-income countries and highly transmissible variants causing infection in vaccinated individuals. Decades of theoretical and experimental data suggest that nonspecific effects of non-COVID-19 vaccines may help bolster population immunological resilience to new pathogens. These routine vaccinations can stimulate heterologous cross-protective effects, which modulate nontargeted infections. For example, immunization with
MeSH term(s)	Algorithms ; BCG Vaccine/administration & dosage ; BCG Vaccine/immunology ; COVID-19/epidemiology ; COVID-19/immunology ; COVID-19/virology ; COVID-19 Vaccines/administration & dosage ; COVID-19 Vaccines/immunology ; Hospital Mortality ; Hospitalization/statistics & numerical data ; Humans ; Intensive Care Units/statistics & numerical data ; Models, Theoretical ; Pandemics/prevention & control ; Patient Admission/statistics & numerical data ; SARS-CoV-2/immunology ; SARS-CoV-2/physiology ; Seasons ; Survival Rate ; United States/epidemiology ; Vaccination/methods ; Vaccination/statistics & numerical data
Chemical Substances	BCG Vaccine ; COVID-19 Vaccines
Language	English
Publishing date	2022-01-10
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2025448119
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Article ; Online: Author Correction: Potential health and economic impacts of dexamethasone treatment for patients with COVID-19.

Águas, Ricardo / Mahdi, Adam / Shretta, Rima / Horby, Peter / Landray, Martin / White, Lisa

Nature communications

2021 Volume 12, Issue 1, Page(s) 1596

Language	English
Publishing date	2021-03-05
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/s41467-021-22038-x
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Article ; Online: Potential health and economic impacts of dexamethasone treatment for patients with COVID-19.

Águas, Ricardo / Mahdi, Adam / Shretta, Rima / Horby, Peter / Landray, Martin / White, Lisa

Nature communications

2021 Volume 12, Issue 1, Page(s) 915

Abstract: Dexamethasone can reduce mortality in hospitalised COVID-19 patients needing oxygen and ventilation by 18% and 36%, respectively. Here, we estimate the potential number of lives saved and life years gained if this treatment were to be rolled out in the ... ...

Abstract	Dexamethasone can reduce mortality in hospitalised COVID-19 patients needing oxygen and ventilation by 18% and 36%, respectively. Here, we estimate the potential number of lives saved and life years gained if this treatment were to be rolled out in the UK and globally, as well as the cost-effectiveness of implementing this intervention. Assuming SARS-CoV-2 exposure levels of 5% to 15%, we estimate that, for the UK, approximately 12,000 (4,250 - 27,000) lives could be saved between July and December 2020. Assuming that dexamethasone has a similar effect size in settings where access to oxygen therapies is limited, this would translate into approximately 650,000 (240,000 - 1,400,000) lives saved globally over the same time period. If dexamethasone acts differently in these settings, the impact could be less than half of this value. To estimate the full potential of dexamethasone in the global fight against COVID-19, it is essential to perform clinical research in settings with limited access to oxygen and/or ventilators, for example in low- and middle-income countries.
MeSH term(s)	COVID-19/drug therapy ; COVID-19/economics ; COVID-19/mortality ; COVID-19/therapy ; Cost-Benefit Analysis ; Dexamethasone/economics ; Dexamethasone/therapeutic use ; Hospital Mortality ; Hospitalization ; Humans ; Quality-Adjusted Life Years ; Respiration, Artificial ; SARS-CoV-2 ; United Kingdom/epidemiology ; Ventilators, Mechanical
Chemical Substances	Dexamethasone (7S5I7G3JQL)
Language	English
Publishing date	2021-02-10
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/s41467-021-21134-2
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Article: Human movement patterns of farmers and forest workers from the Thailand-Myanmar border.

Tun, Sai Thein Than / Min, Myo Chit / Aguas, Ricardo / Fornace, Kimberly / Htoo, Gay Nay / White, Lisa J / Parker, Daniel M

Wellcome open research

2023 Volume 6, Page(s) 148

Abstract: ... ...

Abstract	Background
Language	English
Publishing date	2023-10-02
Publishing country	England
Document type	Journal Article
ISSN	2398-502X
ISSN	2398-502X
DOI	10.12688/wellcomeopenres.16784.2
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Article ; Online: Levels of SARS-CoV-2 population exposure are considerably higher than suggested by seroprevalence surveys.

Chen, Siyu / Flegg, Jennifer A / White, Lisa J / Aguas, Ricardo

PLoS computational biology

2021 Volume 17, Issue 9, Page(s) e1009436

Abstract: Accurate knowledge of prior population exposure has critical ramifications for preparedness plans for future SARS-CoV-2 epidemic waves and vaccine prioritization strategies. Serological studies can be used to estimate levels of past exposure and thus ... ...

Abstract	Accurate knowledge of prior population exposure has critical ramifications for preparedness plans for future SARS-CoV-2 epidemic waves and vaccine prioritization strategies. Serological studies can be used to estimate levels of past exposure and thus position populations in their epidemic timeline. To circumvent biases introduced by the decay in antibody titers over time, methods for estimating population exposure should account for seroreversion, to reflect that changes in seroprevalence measures over time are the net effect of increases due to recent transmission and decreases due to antibody waning. Here, we present a new method that combines multiple datasets (serology, mortality, and virus positivity ratios) to estimate seroreversion time and infection fatality ratios (IFR) and simultaneously infer population exposure levels. The results indicate that the average time to seroreversion is around six months, IFR is 0.54% to 1.3%, and true exposure may be more than double the current seroprevalence levels reported for several regions of England.
MeSH term(s)	COVID-19/epidemiology ; COVID-19/virology ; England/epidemiology ; Humans ; Pandemics ; SARS-CoV-2/physiology ; Seroepidemiologic Studies
Language	English
Publishing date	2021-09-20
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2193340-6
ISSN	1553-7358 ; 1553-734X
ISSN (online)	1553-7358
ISSN	1553-734X
DOI	10.1371/journal.pcbi.1009436
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Article ; Online: A simple polystyrene microfluidic device for sensitive and accurate SERS-based detection of infection by malaria parasites.

Oliveira, Maria João / Caetano, Soraia / Dalot, Ana / Sabino, Filipe / Calmeiro, Tomás R / Fortunato, Elvira / Martins, Rodrigo / Pereira, Eulália / Prudêncio, Miguel / Byrne, Hugh J / Franco, Ricardo / Águas, Hugo

The Analyst

2023 Volume 148, Issue 17, Page(s) 4053–4063

Abstract: Early and accurate detection of infection by pathogenic microorganisms, such as Plasmodium, the causative agent of malaria, is critical for clinical diagnosis and ultimately determines the patient's outcome. We have combined a polystyrene-based ... ...

Abstract	Early and accurate detection of infection by pathogenic microorganisms, such as Plasmodium, the causative agent of malaria, is critical for clinical diagnosis and ultimately determines the patient's outcome. We have combined a polystyrene-based microfluidic device with an immunoassay which utilises Surface-Enhanced Raman Spectroscopy (SERS) to detect malaria. The method can be easily translated to a point-of-care testing format and shows excellent sensitivity and specificity, when compared to the gold standard for laboratorial detection of Plasmodium infections. The device can be fabricated in less than 30 min by direct patterning on shrinkable polystyrene sheets of adaptable three-dimensional microfluidic chips. To validate the microfluidic system, samples of
MeSH term(s)	Humans ; Animals ; Parasites ; Polystyrenes ; Plasmodium falciparum ; Reproducibility of Results ; Malaria/diagnosis ; Malaria, Falciparum/diagnosis ; Plasmodium ; Sensitivity and Specificity ; Lab-On-A-Chip Devices
Chemical Substances	Polystyrenes
Language	English
Publishing date	2023-08-21
Publishing country	England
Document type	Journal Article
ZDB-ID	210747-8
ISSN	1364-5528 ; 0003-2654
ISSN (online)	1364-5528
ISSN	0003-2654
DOI	10.1039/d3an00971h
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Article ; Online: The assembly effect: the connectedness between populations is a double-edged sword for public health interventions.

Tun, Sai Thein Than / Parker, Daniel M / Aguas, Ricardo / White, Lisa J

Malaria journal

2021 Volume 20, Issue 1, Page(s) 189

Abstract: Background: Many public health interventions lead to disruption or decrease of transmission, providing a beneficial effect for people in the population regardless of whether or not they individually participate in the intervention. This protective ... ...

Abstract	Background: Many public health interventions lead to disruption or decrease of transmission, providing a beneficial effect for people in the population regardless of whether or not they individually participate in the intervention. This protective benefit has been referred to as a herd or community effect and is dependent on sufficient population participation. In practice, public health interventions are implemented at different spatial scales (i.e., at the village, district, or provincial level). Populations, however defined (i.e., neighbourhoods, villages, districts) are frequently connected to other populations through human movement or travel, and this connectedness can influence potential herd effects. Methods: The impact of a public health intervention (mass drug administration for malaria) was modelled, for different levels of connectedness between populations that have similar disease epidemiology (e.g., two nearby villages which have similar baseline malaria incidences and similar malaria intervention measures), or between populations of varying disease epidemiology (e.g., two nearby villages which have different baseline malaria incidences and/or malaria intervention measures). Results: The overall impact of the interventions deployed could be influenced either positively (adding value to the intervention) or negatively (reducing the impact of the intervention) by how much the intervention units are connected with each other (e.g., how frequent people go to the other village or town) and how different the disease intensity between them are. This phenomenon is termed the "assembly effect", and it is a meta-population version of the more commonly understood "herd effect". Conclusions: The connectedness of intervention units or populations is an important factor to be considered to achieve success in public health interventions that could provide herd effects. Appreciating the assembly effect can improve the cost-effective strategies for global disease elimination projects.
MeSH term(s)	Disease Eradication/statistics & numerical data ; Humans ; Malaria/prevention & control ; Mass Drug Administration/statistics & numerical data ; Rural Population/statistics & numerical data ; Travel/statistics & numerical data
Language	English
Publishing date	2021-04-17
Publishing country	England
Document type	Journal Article
ISSN	1475-2875
ISSN (online)	1475-2875
DOI	10.1186/s12936-021-03726-x
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Article ; Online: Levels of SARS-CoV-2 population exposure are considerably higher than suggested by seroprevalence surveys.

Siyu Chen / Jennifer A Flegg / Lisa J White / Ricardo Aguas

PLoS Computational Biology, Vol 17, Iss 9, p e

2021 Volume 1009436

Abstract	Accurate knowledge of prior population exposure has critical ramifications for preparedness plans for future SARS-CoV-2 epidemic waves and vaccine prioritization strategies. Serological studies can be used to estimate levels of past exposure and thus position populations in their epidemic timeline. To circumvent biases introduced by the decay in antibody titers over time, methods for estimating population exposure should account for seroreversion, to reflect that changes in seroprevalence measures over time are the net effect of increases due to recent transmission and decreases due to antibody waning. Here, we present a new method that combines multiple datasets (serology, mortality, and virus positivity ratios) to estimate seroreversion time and infection fatality ratios (IFR) and simultaneously infer population exposure levels. The results indicate that the average time to seroreversion is around six months, IFR is 0.54% to 1.3%, and true exposure may be more than double the current seroprevalence levels reported for several regions of England.
Keywords	Biology (General) ; QH301-705.5
Subject code	333
Language	English
Publishing date	2021-09-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: How many human pathogens are there in Laos? An estimate of national human pathogen diversity and analysis of historical trends.

Clarkson, Madeleine Claire / Aguas, Ricardo / Sweet, Kathryn / Roberts, Tamalee / Strobel, Michel / Newton, Paul N

BMJ global health

2021 Volume 5, Issue 10

Abstract: Objective: The emergence of infectious diseases pose major global health threats. Estimates of total in-country human pathogen diversity, and insights as to how and when species were described through history, could be used to estimate the probability ... ...

Abstract	Objective: The emergence of infectious diseases pose major global health threats. Estimates of total in-country human pathogen diversity, and insights as to how and when species were described through history, could be used to estimate the probability of new pathogen discoveries. Data from the Lao People's Democratic Republic (Laos) were used in this proof-of-concept study to estimate national human pathogen diversity and to examine historical discovery rate drivers. Methods: A systematic survey of the French and English scientific and grey literature of pathogen description in Laos between 1874 and 2017 was conducted. The first descriptions of each known human pathogen in Laos were coded according to the diagnostic evidence available. Cumulative frequency of discovery across time informed the rate of discovery. Four distinct periods of health systems development in Laos were identified prospectively and juxtaposed to the unmodelled rate of discovery. A model with a time-varying rate of discovery was fitted to these data using a Markov-Chain- Monte-Carlo technique. Results: From 6456 pathogen descriptions, 245 discoveries of known human pathogens in Laos, including repeat discoveries using different grades of evidence, were identified. The models estimate that the Laos human pathogen species diversity in 2017 is between 169 and 206. During the last decade, there has been a 33-fold increase in the discovery rate coinciding with the strengthening of medical research and microbiology. Conclusion: Discovery curves can be used to model and estimate country-level human pathogen diversity present in a territory. Combining this with historical assessment improves the understanding of the factors affecting local pathogen discovery. Prospero registration number: A protocol of this work was registered on PROSPERO (ID:CRD42016046728).
MeSH term(s)	Forecasting ; Humans ; Infections/epidemiology ; Infections/microbiology ; Infections/parasitology ; Infections/virology ; Laos/epidemiology
Language	English
Publishing date	2021-03-25
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2059-7908
ISSN	2059-7908
DOI	10.1136/bmjgh-2020-002972
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Article ; Online: Percolation across households in mechanistic models of non-pharmaceutical interventions in SARS-CoV-2 disease dynamics.

Franco, Caroline / Ferreira, Leonardo Souto / Sudbrack, Vítor / Borges, Marcelo Eduardo / Poloni, Silas / Prado, Paulo Inácio / White, Lisa J / Águas, Ricardo / Kraenkel, Roberto André / Coutinho, Renato Mendes

Epidemics

2022 Volume 39, Page(s) 100551

Abstract: Since the emergence of the novel coronavirus disease 2019 (COVID-19), mathematical modelling has become an important tool for planning strategies to combat the pandemic by supporting decision-making and public policies, as well as allowing an assessment ... ...

Abstract	Since the emergence of the novel coronavirus disease 2019 (COVID-19), mathematical modelling has become an important tool for planning strategies to combat the pandemic by supporting decision-making and public policies, as well as allowing an assessment of the effect of different intervention scenarios. A proliferation of compartmental models were developed by the mathematical modelling community in order to understand and make predictions about the spread of COVID-19. While compartmental models are suitable for simulating large populations, the underlying assumption of a well-mixed population might be problematic when considering non-pharmaceutical interventions (NPIs) which have a major impact on the connectivity between individuals in a population. Here we propose a modification to an extended age-structured SEIR (susceptible-exposed-infected-recovered) framework, with dynamic transmission modelled using contact matrices for various settings in Brazil. By assuming that the mitigation strategies for COVID-19 affect the connections among different households, network percolation theory predicts that the connectivity among all households decreases drastically above a certain threshold of removed connections. We incorporated this emergent effect at population level by modulating home contact matrices through a percolation correction function, with the few additional parameters fitted to hospitalisation and mortality data from the city of São Paulo. Our model with percolation effects was better supported by the data than the same model without such effects. By allowing a more reliable assessment of the impact of NPIs, our improved model provides a better description of the epidemiological dynamics and, consequently, better policy recommendations.
MeSH term(s)	Brazil ; COVID-19/epidemiology ; Communicable Disease Control ; Humans ; Models, Theoretical ; Pandemics/prevention & control ; SARS-CoV-2
Language	English
Publishing date	2022-03-12
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2467993-8
ISSN	1878-0067 ; 1755-4365
ISSN (online)	1878-0067
ISSN	1755-4365
DOI	10.1016/j.epidem.2022.100551
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