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Article ; Online: coiaf: Directly estimating complexity of infection with allele frequencies.

Paschalidis, Aris / Watson, Oliver J / Aydemir, Ozkan / Verity, Robert / Bailey, Jeffrey A

2023 Volume 19, Issue 6, Page(s) e1010247

Abstract: In malaria, individuals are often infected with different parasite strains. The complexity of infection (COI) is defined as the number of genetically distinct parasite strains in an individual. Changes in the mean COI in a population have been shown to ... ...

Abstract	In malaria, individuals are often infected with different parasite strains. The complexity of infection (COI) is defined as the number of genetically distinct parasite strains in an individual. Changes in the mean COI in a population have been shown to be informative of changes in transmission intensity with a number of probabilistic likelihood and Bayesian models now developed to estimate the COI. However, rapid, direct measures based on heterozygosity or FwS do not properly represent the COI. In this work, we present two new methods that use easily calculated measures to directly estimate the COI from allele frequency data. Using a simulation framework, we show that our methods are computationally efficient and comparably accurate to current approaches in the literature. Through a sensitivity analysis, we characterize how the distribution of parasite densities, the assumed sequencing depth, and the number of sampled loci impact the bias and accuracy of our two methods. Using our developed methods, we further estimate the COI globally from Plasmodium falciparum sequencing data and compare the results against the literature. We show significant differences in the estimated COI globally between continents and a weak relationship between malaria prevalence and COI.
MeSH term(s)	Humans ; Malaria, Falciparum/epidemiology ; Malaria, Falciparum/genetics ; Malaria, Falciparum/parasitology ; Bayes Theorem ; Plasmodium falciparum/genetics ; Gene Frequency/genetics ; Malaria/parasitology
Language	English
Publishing date	2023-06-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	2193340-6
ISSN	1553-7358 ; 1553-734X
ISSN (online)	1553-7358
ISSN	1553-734X
DOI	10.1371/journal.pcbi.1010247
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Article ; Online: A framework for reconstructing SARS-CoV-2 transmission dynamics using excess mortality data.

Ghafari, Mahan / Watson, Oliver J / Karlinsky, Ariel / Ferretti, Luca / Katzourakis, Aris

Nature communications

2022 Volume 13, Issue 1, Page(s) 3015

Abstract: The transmission dynamics and burden of SARS-CoV-2 in many regions of the world is still largely unknown due to the scarcity of epidemiological analyses and lack of testing to assess the prevalence of disease. In this work, we develop a quantitative ... ...

Abstract	The transmission dynamics and burden of SARS-CoV-2 in many regions of the world is still largely unknown due to the scarcity of epidemiological analyses and lack of testing to assess the prevalence of disease. In this work, we develop a quantitative framework based on excess mortality data to reconstruct SARS-CoV-2 transmission dynamics and assess the level of underreporting in infections and deaths. Using weekly all-cause mortality data from Iran, we are able to show a strong agreement between our attack rate estimates and seroprevalence measurements in each province and find significant heterogeneity in the level of exposure across the country with 11 provinces reaching near 100% attack rates. Despite having a young population, our analysis reveals that incorporating limited access to medical services in our model, coupled with undercounting of COVID-19-related deaths, leads to estimates of infection fatality rate in most provinces of Iran that are comparable to high-income countries.
MeSH term(s)	COVID-19/epidemiology ; Humans ; Iran/epidemiology ; SARS-CoV-2 ; Seroepidemiologic Studies
Language	English
Publishing date	2022-05-31
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/s41467-022-30711-y
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Article ; Online: Global impact of the first year of COVID-19 vaccination: a mathematical modelling study.

Watson, Oliver J / Barnsley, Gregory / Toor, Jaspreet / Hogan, Alexandra B / Winskill, Peter / Ghani, Azra C

The Lancet. Infectious diseases

2022 Volume 22, Issue 9, Page(s) 1293–1302

Abstract: Background: The first COVID-19 vaccine outside a clinical trial setting was administered on Dec 8, 2020. To ensure global vaccine equity, vaccine targets were set by the COVID-19 Vaccines Global Access (COVAX) Facility and WHO. However, due to vaccine ... ...

Abstract	Background: The first COVID-19 vaccine outside a clinical trial setting was administered on Dec 8, 2020. To ensure global vaccine equity, vaccine targets were set by the COVID-19 Vaccines Global Access (COVAX) Facility and WHO. However, due to vaccine shortfalls, these targets were not achieved by the end of 2021. We aimed to quantify the global impact of the first year of COVID-19 vaccination programmes. Methods: A mathematical model of COVID-19 transmission and vaccination was separately fit to reported COVID-19 mortality and all-cause excess mortality in 185 countries and territories. The impact of COVID-19 vaccination programmes was determined by estimating the additional lives lost if no vaccines had been distributed. We also estimated the additional deaths that would have been averted had the vaccination coverage targets of 20% set by COVAX and 40% set by WHO been achieved by the end of 2021. Findings: Based on official reported COVID-19 deaths, we estimated that vaccinations prevented 14·4 million (95% credible interval [Crl] 13·7-15·9) deaths from COVID-19 in 185 countries and territories between Dec 8, 2020, and Dec 8, 2021. This estimate rose to 19·8 million (95% Crl 19·1-20·4) deaths from COVID-19 averted when we used excess deaths as an estimate of the true extent of the pandemic, representing a global reduction of 63% in total deaths (19·8 million of 31·4 million) during the first year of COVID-19 vaccination. In COVAX Advance Market Commitment countries, we estimated that 41% of excess mortality (7·4 million [95% Crl 6·8-7·7] of 17·9 million deaths) was averted. In low-income countries, we estimated that an additional 45% (95% CrI 42-49) of deaths could have been averted had the 20% vaccination coverage target set by COVAX been met by each country, and that an additional 111% (105-118) of deaths could have been averted had the 40% target set by WHO been met by each country by the end of 2021. Interpretation: COVID-19 vaccination has substantially altered the course of the pandemic, saving tens of millions of lives globally. However, inadequate access to vaccines in low-income countries has limited the impact in these settings, reinforcing the need for global vaccine equity and coverage. Funding: Schmidt Science Fellowship in partnership with the Rhodes Trust; WHO; UK Medical Research Council; Gavi, the Vaccine Alliance; Bill & Melinda Gates Foundation; National Institute for Health Research; and Community Jameel.
MeSH term(s)	COVID-19 ; COVID-19 Vaccines ; Global Health ; Humans ; Models, Theoretical ; Vaccination ; Vaccines
Chemical Substances	COVID-19 Vaccines ; Vaccines
Language	English
Publishing date	2022-06-23
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2061641-7
ISSN	1474-4457 ; 1473-3099
ISSN (online)	1474-4457
ISSN	1473-3099
DOI	10.1016/S1473-3099(22)00320-6
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Zs.A 5743: Show issues

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Article: Selection of artemisinin partial resistance Kelch13 mutations in Uganda in 2016-22 was at a rate comparable to that seen previously in South-East Asia.

Meier-Scherling, Cecile P G / Watson, Oliver J / Asua, Victor / Ghinai, Isaac / Katairo, Thomas / Garg, Shreeya / Conrad, Melissa / Rosenthal, Philip J / Okell, Lucy C / Bailey, Jeffrey A

medRxiv : the preprint server for health sciences

2024

Abstract: Background: Artemisinin partial resistance, mediated by mutations in the : Methods: We investigated K13 mutation prevalence at 16 sites in Uganda (2016-2022, 6586 samples), and five sites in SEA (2003-2018, 5465 samples) by calculating selection ... ...

Abstract	Background: Artemisinin partial resistance, mediated by mutations in the Methods: We investigated K13 mutation prevalence at 16 sites in Uganda (2016-2022, 6586 samples), and five sites in SEA (2003-2018, 5465 samples) by calculating selection coefficients using Bayesian mixed-effect linear models. We then tested whether SEA K13 mutation prevalence could have been forecast accurately using up to the first five years of available data and forecast future K13 mutation prevalence in Uganda. Findings: The selection coefficient for the prevalence of relevant K13 mutations (441L, 469F/Y, 561H, 675V) was estimated at s=0·383 (95% CrI: 0·247 - 0·528) per year, a 38% relative prevalence increase. Selection coefficients across Uganda were s=0·968 (0·463 - 1·569) for 441L, s=0·153 (-0·445 - 0·727) for 469F, s=0·222 (-0·011 - 0·398) for 469Y, and s=0·152 (-0·023 - 0·312) for 675V. In SEA, the selection coefficient was s=-0·005 (-0·852 - 0·814) for 539T, s=0·574 (-0·092 - 1·201) for 580Y, and s=0·308 (0·089 - 0·536) for all validated K13 mutations. Forecast prevalences for Uganda assuming constant selection neared fixation (>95% prevalence) within a decade (2028-2033) for combined K13 mutations. Interpretation: The selection of K13 mutations in Uganda was at a comparable rate to that observed in SEA, suggesting K13 mutations may continue to increase quickly in Uganda. Funding: NIH R01AI156267, R01AI075045, and R01AI089674.
Language	English
Publishing date	2024-02-04
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.02.03.24302209
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Article ; Online: Country differences in transmissibility, age distribution and case-fatality of SARS-CoV-2: a global ecological analysis.

Favas, Caroline / Jarrett, Prudence / Ratnayake, Ruwan / Watson, Oliver J / Checchi, Francesco

International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases

2021 Volume 114, Page(s) 210–218

Abstract: Objectives The first COVID-19 pandemic waves in many low-income countries appeared milder than initially forecasted. We conducted a country-level ecological study to describe patterns in key SARS-CoV-2 outcomes by country and region and explore ... ...

Abstract	Objectives The first COVID-19 pandemic waves in many low-income countries appeared milder than initially forecasted. We conducted a country-level ecological study to describe patterns in key SARS-CoV-2 outcomes by country and region and explore associations with potential explanatory factors, including population age structure and prior exposure to endemic parasitic infections. Methods We collected publicly available data and compared them using standardisation techniques. We then explored the association between exposures and outcomes using random forest and linear regression. We adjusted for potential confounders and plausible effect modifications. Results While mean time-varying reproduction number was highest in the European and Americas regions, median age of death was lower in the Africa region, with a broadly similar case-fatality ratio. Population age was strongly associated with mean (β=0.01, 95% CI, 0.005, 0.011) and median age of cases (β=-0.40, 95% CI, -0.53, -0.26) and deaths (β= 0.40, 95% CI, 0.17, 0.62). Conclusions Population age seems an important country-level factor explaining both transmissibility and age distribution of observed cases and deaths. Endemic infections seem unlikely, from this analysis, to be key drivers of the variation in observed epidemic trends. Our study was limited by the availability of outcome data and its causally uncertain ecological design.
MeSH term(s)	Age Distribution ; Americas ; COVID-19 ; Humans ; Pandemics ; SARS-CoV-2 ; United States
Language	English
Publishing date	2021-11-06
Publishing country	Canada
Document type	Journal Article
ZDB-ID	1331197-9
ISSN	1878-3511 ; 1201-9712
ISSN (online)	1878-3511
ISSN	1201-9712
DOI	10.1016/j.ijid.2021.11.004
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Zs.A 4516: Show issues

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Article ; Online: Modelling the impact of vaccine hesitancy in prolonging the need for Non-Pharmaceutical Interventions to control the COVID-19 pandemic.

Olivera Mesa, Daniela / Hogan, Alexandra B / Watson, Oliver J / Charles, Giovanni D / Hauck, Katharina / Ghani, Azra C / Winskill, Peter

Communications medicine

2022 Volume 2, Page(s) 14

Abstract: Background: Vaccine hesitancy - a delay in acceptance or refusal of vaccines despite availability - has the potential to threaten the successful roll-out of SARS-CoV-2 vaccines globally. In this study, we aim to understand the likely impact of vaccine ... ...

Abstract	Background: Vaccine hesitancy - a delay in acceptance or refusal of vaccines despite availability - has the potential to threaten the successful roll-out of SARS-CoV-2 vaccines globally. In this study, we aim to understand the likely impact of vaccine hesitancy on the control of the COVID-19 pandemic. Methods: We modelled the potential impact of vaccine hesitancy on the control of the pandemic and the relaxation of non-pharmaceutical interventions (NPIs) by combining an epidemiological model of SARS-CoV-2 transmission with data on vaccine hesitancy from population surveys. Results: Our simulations suggest that the mortality over a 2-year period could be up to 7.6 times higher in countries with high vaccine hesitancy compared to an ideal vaccination uptake if NPIs are relaxed. Alternatively, high vaccine hesitancy could prolong the need for NPIs to remain in place. Conclusions: While vaccination is an individual choice, vaccine-hesitant individuals have a substantial impact on the pandemic trajectory, which may challenge current efforts to control COVID-19. In order to prevent such outcomes, addressing vaccine hesitancy with behavioural interventions is an important priority in the control of the COVID-19 pandemic.
Language	English
Publishing date	2022-02-10
Publishing country	England
Document type	Journal Article
ISSN	2730-664X
ISSN (online)	2730-664X
DOI	10.1038/s43856-022-00075-x
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Article ; Online: Reassessing Reported Deaths and Estimated Infection Attack Rate during the First 6 Months of the COVID-19 Epidemic, Delhi, India.

Pons-Salort, Margarita / John, Jacob / Watson, Oliver J / Brazeau, Nicholas F / Verity, Robert / Kang, Gagandeep / Grassly, Nicholas C

Emerging infectious diseases

2022 Volume 28, Issue 4, Page(s) 759–766

Abstract: India reported >10 million coronavirus disease (COVID-19) cases and 149,000 deaths in 2020. To reassess reported deaths and estimate incidence rates during the first 6 months of the epidemic, we used a severe acute respiratory syndrome coronavirus 2 ... ...

Abstract	India reported >10 million coronavirus disease (COVID-19) cases and 149,000 deaths in 2020. To reassess reported deaths and estimate incidence rates during the first 6 months of the epidemic, we used a severe acute respiratory syndrome coronavirus 2 transmission model fit to data from 3 serosurveys in Delhi and time-series documentation of reported deaths. We estimated 48.7% (95% credible interval 22.1%-76.8%) cumulative infection in the population through the end of September 2020. Using an age-adjusted overall infection fatality ratio based on age-specific estimates from mostly high-income countries, we estimated that just 15.0% (95% credible interval 9.3%-34.0%) of COVID-19 deaths had been reported, indicating either substantial underreporting or lower age-specific infection-fatality ratios in India than in high-income countries. Despite the estimated high attack rate, additional epidemic waves occurred in late 2020 and April-May 2021. Future dynamics will depend on the duration of natural and vaccine-induced immunity and their effectiveness against new variants.
MeSH term(s)	COVID-19 ; Epidemics ; Humans ; Incidence ; India/epidemiology ; SARS-CoV-2
Language	English
Publishing date	2022-02-25
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1380686-5
ISSN	1080-6059 ; 1080-6040
ISSN (online)	1080-6059
ISSN	1080-6040
DOI	10.3201/eid2804.210879
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Zs.A 4778: Show issues

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Article ; Online: Estimating long-term vaccine effectiveness against SARS-CoV-2 variants: a model-based approach.

Hogan, Alexandra B / Doohan, Patrick / Wu, Sean L / Mesa, Daniela Olivera / Toor, Jaspreet / Watson, Oliver J / Winskill, Peter / Charles, Giovanni / Barnsley, Gregory / Riley, Eleanor M / Khoury, David S / Ferguson, Neil M / Ghani, Azra C

Nature communications

2023 Volume 14, Issue 1, Page(s) 4325

Abstract: With the ongoing evolution of the SARS-CoV-2 virus updated vaccines may be needed. We fitted a model linking immunity levels and protection to vaccine effectiveness data from England for three vaccines (Oxford/AstraZeneca AZD1222, Pfizer-BioNTech ... ...

Abstract	With the ongoing evolution of the SARS-CoV-2 virus updated vaccines may be needed. We fitted a model linking immunity levels and protection to vaccine effectiveness data from England for three vaccines (Oxford/AstraZeneca AZD1222, Pfizer-BioNTech BNT162b2, Moderna mRNA-1273) and two variants (Delta, Omicron). Our model reproduces the observed sustained protection against hospitalisation and death from the Omicron variant over the first six months following dose 3 with the ancestral vaccines but projects a gradual waning to moderate protection after 1 year. Switching the fourth dose to a variant-matched vaccine against Omicron BA.1/2 is projected to prevent nearly twice as many hospitalisations and deaths over a 1-year period compared to administering the ancestral vaccine. This result is sensitive to the degree to which immunogenicity data can be used to predict vaccine effectiveness and uncertainty regarding the impact that infection-induced immunity (not captured here) may play in modifying future vaccine effectiveness.
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; BNT162 Vaccine ; COVID-19/prevention & control ; ChAdOx1 nCoV-19 ; Vaccine Efficacy ; COVID-19 Vaccines
Chemical Substances	BNT162 Vaccine ; ChAdOx1 nCoV-19 (B5S3K2V0G8) ; COVID-19 Vaccines
Language	English
Publishing date	2023-07-19
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/s41467-023-39736-3
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Article ; Online: Long-term vaccination strategies to mitigate the impact of SARS-CoV-2 transmission: A modelling study.

Hogan, Alexandra B / Wu, Sean L / Toor, Jaspreet / Olivera Mesa, Daniela / Doohan, Patrick / Watson, Oliver J / Winskill, Peter / Charles, Giovanni / Barnsley, Gregory / Riley, Eleanor M / Khoury, David S / Ferguson, Neil M / Ghani, Azra C

PLoS medicine

2023 Volume 20, Issue 11, Page(s) e1004195

Abstract: Background: Vaccines have reduced severe disease and death from Coronavirus Disease 2019 (COVID-19). However, with evidence of waning efficacy coupled with continued evolution of the virus, health programmes need to evaluate the requirement for regular ... ...

Abstract	Background: Vaccines have reduced severe disease and death from Coronavirus Disease 2019 (COVID-19). However, with evidence of waning efficacy coupled with continued evolution of the virus, health programmes need to evaluate the requirement for regular booster doses, considering their impact and cost-effectiveness in the face of ongoing transmission and substantial infection-induced immunity. Methods and findings: We developed a combined immunological-transmission model parameterised with data on transmissibility, severity, and vaccine effectiveness. We simulated Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) transmission and vaccine rollout in characteristic global settings with different population age-structures, contact patterns, health system capacities, prior transmission, and vaccine uptake. We quantified the impact of future vaccine booster dose strategies with both ancestral and variant-adapted vaccine products, while considering the potential future emergence of new variants with modified transmission, immune escape, and severity properties. We found that regular boosting of the oldest age group (75+) is an efficient strategy, although large numbers of hospitalisations and deaths could be averted by extending vaccination to younger age groups. In countries with low vaccine coverage and high infection-derived immunity, boosting older at-risk groups was more effective than continuing primary vaccination into younger ages in our model. Our study is limited by uncertainty in key parameters, including the long-term durability of vaccine and infection-induced immunity as well as uncertainty in the future evolution of the virus. Conclusions: Our modelling suggests that regular boosting of the high-risk population remains an important tool to reduce morbidity and mortality from current and future SARS-CoV-2 variants. Our results suggest that focusing vaccination in the highest-risk cohorts will be the most efficient (and hence cost-effective) strategy to reduce morbidity and mortality.
MeSH term(s)	Humans ; SARS-CoV-2 ; COVID-19/prevention & control ; Vaccination ; Vaccines
Chemical Substances	Vaccines
Language	English
Publishing date	2023-11-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	2185925-5
ISSN	1549-1676 ; 1549-1277
ISSN (online)	1549-1676
ISSN	1549-1277
DOI	10.1371/journal.pmed.1004195
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Zs.A 6042: Show issues

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Article: Global risk of selection and spread of

Watson, Oliver J / Tran, Thu Nguyen-Anh / Zupko, Robert J / Symons, Tasmin / Thomson, Rebecca / Visser, Theodoor / Rumisha, Susan / Dzianach, Paulina A / Hathaway, Nicholas / Kim, Isaac / Juliano, Jonathan J / Bailey, Jeffrey A / Slater, Hannah / Okell, Lucy / Gething, Peter / Ghani, Azra / Boni, Maciej F / Parr, Jonathan B / Cunningham, Jane

medRxiv : the preprint server for health sciences

2024

Abstract: In the thirteen years since the first report ... ...

Abstract	In the thirteen years since the first report of
Language	English
Publishing date	2024-01-01
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.10.21.23297352
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