161 results on '"Salje H"'
Search Results
2. Ongoing diphtheria outbreak in Yemen: a cross-sectional and genomic epidemiology study
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Badell, E., Alharazi, A., Criscuolo, A., Almoayed, K.A.A., Lefrancq, N., Bouchez, V., Guglielmini, J., Hennart, M., Carmi-Leroy, A., Zidane, N., Pascal-Perrigault, M., Lebreton, M., Martini, H., Salje, H., Toubiana, J., Dureab, F., Dhabaan, G., Brisse, S., Rawah, A.A., Aldawla, M.A., Al-Awdi, E.M., Al-Moalmy, N.M., Al-Shami, H.Z., Al-Somainy, A.A.
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- 2021
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3. Evaluating the impact of curfews and other measures on SARS-CoV-2 transmission in French Guiana
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Andronico A, Tran Kiem C, Paireau J, Succo T, Bosettit P, Lefrancq N, Nacher M, Djossou F, Sanna A, Flamand C, Salje H, Rousseau C, Cauchemez S
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- 2021
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4. SARS-CoV-2 transmission across age groups in France and implications for control
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Tran Kiem C, Bosetti P, Paireau J, Crepey P, Salje H, Lefrancq N, Fontanet A, Benamouzig D, Boelle PY, Desenclos JC, Opatowski L, Cauchemez S
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- 2021
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5. Monitoring the proportion of the population infected by SARS-CoV-2 using age-stratified hospitalization and serological data: a modelling study
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Hoze N, Paireau J, Lapidus N, Tran Kiem C, Salje H, Severi G, Touvier M, Zins M, de Lamballerie X, Lévy-Bruhl D, Carrat F, Cauchemez S
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- 2021
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6. Monitoring the proportion of the population infected by SARS-CoV-2 using age-stratified hospitalisation and serological data: a modelling study.
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Hozé, N, Paireau, J, Lapidus, N, Tran Kiem, C, Salje, H, Severi, G, Touvier, M, Zins, M, de Lamballerie, X, Lévy-Bruhl, D, Carrat, F, Cauchemez, S, Hozé, N, Paireau, J, Lapidus, N, Tran Kiem, C, Salje, H, Severi, G, Touvier, M, Zins, M, de Lamballerie, X, Lévy-Bruhl, D, Carrat, F, and Cauchemez, S
- Abstract
BACKGROUND: Regional monitoring of the proportion of the population who have been infected by SARS-CoV-2 is important to guide local management of the epidemic, but is difficult in the absence of regular nationwide serosurveys. We aimed to estimate in near real time the proportion of adults who have been infected by SARS-CoV-2. METHODS: In this modelling study, we developed a method to reconstruct the proportion of adults who have been infected by SARS-CoV-2 and the proportion of infections being detected, using the joint analysis of age-stratified seroprevalence, hospitalisation, and case data, with deconvolution methods. We developed our method on a dataset consisting of seroprevalence estimates from 9782 participants (aged ≥20 years) in the two worst affected regions of France in May, 2020, and applied our approach to the 13 French metropolitan regions over the period March, 2020, to January, 2021. We validated our method externally using data from a national seroprevalence study done between May and June, 2020. FINDINGS: We estimate that 5·7% (95% CI 5·1-6·4) of adults in metropolitan France had been infected with SARS-CoV-2 by May 11, 2020. This proportion remained stable until August, 2020, and increased to 14·9% (13·2-16·9) by Jan 15, 2021. With 26·5% (23·4-29·8) of adult residents having been infected in Île-de-France (Paris region) compared with 5·1% (4·5-5·8) in Brittany by January, 2021, regional variations remained large (coefficient of variation [CV] 0·50) although less so than in May, 2020 (CV 0·74). The proportion infected was twice as high (20·4%, 15·6-26·3) in 20-49-year-olds than in individuals aged 50 years or older (9·7%, 6·9-14·1). 40·2% (34·3-46·3) of infections in adults were detected in June to August, 2020, compared with 49·3% (42·9-55·9) in November, 2020, to January, 2021. Our regional estimates of seroprevalence were strongly correlated with the external validation dataset (coefficient of correlation 0·89). INTERPRETATION: Our simple appr
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- 2021
7. Reconstructing unseen transmission events to infer dengue dynamics from viral sequences
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Salje, H., Wesolowski, A., Brown, T.S., Kiang, M.V., Berry, I.M., Lefrancq, N., Fernandez, S., Jarman, R.G., Ruchusatsawat, K., Iamsirithaworn, S., Vandepitte, W.P., Suntarattiwong, P., Read, J.M., Klungthong, C., Thaisomboonsuk, B., Engø-Monsen, K., Buckee, C., Cauchemez, S., Cummings, D.A.T., Salje, H., Wesolowski, A., Brown, T.S., Kiang, M.V., Berry, I.M., Lefrancq, N., Fernandez, S., Jarman, R.G., Ruchusatsawat, K., Iamsirithaworn, S., Vandepitte, W.P., Suntarattiwong, P., Read, J.M., Klungthong, C., Thaisomboonsuk, B., Engø-Monsen, K., Buckee, C., Cauchemez, S., and Cummings, D.A.T.
- Abstract
For most pathogens, transmission is driven by interactions between the behaviours of infectious individuals, the behaviours of the wider population, the local environment, and immunity. Phylogeographic approaches are currently unable to disentangle the relative effects of these competing factors. We develop a spatiotemporally structured phylogenetic framework that addresses these limitations by considering individual transmission events, reconstructed across spatial scales. We apply it to geocoded dengue virus sequences from Thailand (N = 726 over 18 years). We find infected individuals spend 96% of their time in their home community compared to 76% for the susceptible population (mainly children) and 42% for adults. Dynamic pockets of local immunity make transmission more likely in places with high heterotypic immunity and less likely where high homotypic immunity exists. Age-dependent mixing of individuals and vector distributions are not important in determining spread. This approach provides previously unknown insights into one of the most complex disease systems known and will be applicable to other pathogens.
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- 2021
8. Impact of neighborhood biomass cooking patterns on episodic high indoor particulate matter concentrations in clean fuel homes in Dhaka, Bangladesh
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Salje, H., Gurley, E. S., Homaira, N., Ram, P. K., Haque, R., Petri, W., Moss, W. J., Luby, S. P., Breysse, P., and Azziz-Baumgartner, E.
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- 2014
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9. Comparing insights from clinic-based versus community-based outbreak investigations: a case study of chikungunya in Bangladesh
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Paul, KK, Salje, H, Rahman, MW, Rahman, M, Gurley, ES, Paul, KK, Salje, H, Rahman, MW, Rahman, M, and Gurley, ES
- Abstract
Background: Outbreak investigations typically focus their efforts on identifying cases that present at healthcare facilities. However, these cases rarely represent all cases in the wider community. In this context, community-based investigations may provide additional insight into key risk factors for infection, however, the benefits of these more laborious data collection strategies remains unclear. Methods: We used different subsets of the data from a comprehensive outbreak investigation to compare the inferences we make in alternative investigation strategies. Results: The outbreak investigation team interviewed 1,933 individuals from 460 homes. 364 (18%) of individuals had symptoms consistent with chikungunya. A theoretical clinic-based study would have identified 26% of the cases. Adding in community-based cases provided an overall estimate of the attack rate in the community. Comparison with controls from the same household revealed that those with at least secondary education had a reduced risk. Finally, enrolling residents from households across the community allowed us to characterize spatial heterogeneity of risk and identify the type of clothing usually worn and travel history as risk factors. This also revealed that household-level use of mosquito control was not associated with infection. Conclusions: These findings highlight that while clinic-based studies may be easier to conduct, they only provide limited insight into the burden and risk factors for disease. Enrolling people who escaped from infection, both in the household and in the community allows a step change in our understanding of the spread of a pathogen and maximizes opportunities for control.
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- 2020
10. Indoor exposure to particulate matter and the incidence of acute lower respiratory infections among children: A birth cohort study in urban Bangladesh
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Gurley, E. S., Homaira, N., Salje, H., Ram, P. K., Haque, R., Petri, W., Bresee, J., Moss, W. J., Breysse, P., Luby, S. P., and Azziz-Baumgartner, E.
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- 2013
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11. Nationally-representative serostudy of dengue in Bangladesh allows generalizable disease burden estimates
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Salje, H, Paul, KK, Paul, R, Rodriguez-Barraquer, I, Rahman, Z, Alam, MS, Rahman, M, Al-Amin, HM, Heffelfinger, J, Gurley, E, Salje, H, Paul, KK, Paul, R, Rodriguez-Barraquer, I, Rahman, Z, Alam, MS, Rahman, M, Al-Amin, HM, Heffelfinger, J, and Gurley, E
- Abstract
Serostudies are needed to answer generalizable questions on disease risk. However, recruitment is usually biased by age or location. We present a nationally-representative study for dengue from 70 communities in Bangladesh. We collected data on risk factors, trapped mosquitoes and tested serum for IgG. Out of 5866 individuals, 24% had evidence of historic infection, ranging from 3% in the north to >80% in Dhaka. Being male (aOR:1.8, [95%CI:1.5–2.0]) and recent travel (aOR:1.3, [1.1–1.8]) were linked to seropositivity. We estimate that 40 million [34.3–47.2] people have been infected nationally, with 2.4 million ([1.3–4.5]) annual infections. Had we visited only 20 communities, seropositivity estimates would have ranged from 13% to 37%, highlighting the lack of representativeness generated by small numbers of communities. Our findings have implications for both the design of serosurveys and tackling dengue in Bangladesh.
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- 2019
12. Spread of Yellow Fever Virus outbreak in Angola and the Democratic Republic Congo 2015-2016: a modelling study
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Kraemer, M, Faria, N, Reiner, R, Golding, N, Nikolay, B, Stasse, S, Johansson, M, Salje, H, Faye, O, Wint, G, Niedrig, M, Shearer, F, Hill, S, Thompson, R, Bisanzio, D, Taveira, N, Nax, H, Pradelski, B, Nsoesie, E, Murphy, N, Bogoch, I, Khan, K, Brownstein, J, Tatem, A, de Oliveira, T, Smith, D, Sall, A, Pybus, O, Hay, S, and Cauchemez, S
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Angola ,Yellow fever virus ,Democratic Republic of Congo - Abstract
This is an Open Access article under the CC BY license. BACKGROUND: Since late 2015, an epidemic of yellow fever has caused more than 7334 suspected cases in Angola and the Democratic Republic of the Congo, including 393 deaths. We sought to understand the spatial spread of this outbreak to optimise the use of the limited available vaccine stock. METHODS: We jointly analysed datasets describing the epidemic of yellow fever, vector suitability, human demography, and mobility in central Africa to understand and predict the spread of yellow fever virus. We used a standard logistic model to infer the district-specific yellow fever virus infection risk during the course of the epidemic in the region. FINDINGS: The early spread of yellow fever virus was characterised by fast exponential growth (doubling time of 5-7 days) and fast spatial expansion (49 districts reported cases after only 3 months) from Luanda, the capital of Angola. Early invasion was positively correlated with high population density (Pearson's r 0·52, 95% CI 0·34-0·66). The further away locations were from Luanda, the later the date of invasion (Pearson's r 0·60, 95% CI 0·52-0·66). In a Cox model, we noted that districts with higher population densities also had higher risks of sustained transmission (the hazard ratio for cases ceasing was 0·74, 95% CI 0·13-0·92 per log-unit increase in the population size of a district). A model that captured human mobility and vector suitability successfully discriminated districts with high risk of invasion from others with a lower risk (area under the curve 0·94, 95% CI 0·92-0·97). If at the start of the epidemic, sufficient vaccines had been available to target 50 out of 313 districts in the area, our model would have correctly identified 27 (84%) of the 32 districts that were eventually affected. INTERPRETATION: Our findings show the contributions of ecological and demographic factors to the ongoing spread of the yellow fever outbreak and provide estimates of the areas that could be prioritised for vaccination, although other constraints such as vaccine supply and delivery need to be accounted for before such insights can be translated into policy. info:eu-repo/semantics/publishedVersion
- Published
- 2017
13. Understanding dengue virus evolution to support epidemic surveillance and counter-measure development
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Pollett, S., primary, Melendrez, M.C., additional, Maljkovic Berry, I., additional, Duchêne, S., additional, Salje, H., additional, Cummings, D.A.T., additional, and Jarman, R.G., additional
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- 2018
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14. Evaluating Hospital-Based Surveillance for Outbreak Detection in Bangladesh: Analysis of Healthcare Utilization Data
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Nikolay, B, Salje, H, Sturm-Ramirez, K, Azziz-Baumgartner, E, Homaira, N, Ahmed, M, Luliano, AD, Paul, RC, Rahman, M, Hossain, MJ, Luby, SP, Cauchemez, S, Gurley, ES, Nikolay, B, Salje, H, Sturm-Ramirez, K, Azziz-Baumgartner, E, Homaira, N, Ahmed, M, Luliano, AD, Paul, RC, Rahman, M, Hossain, MJ, Luby, SP, Cauchemez, S, and Gurley, ES
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- 2017
15. Spread of yellow fever virus outbreak in Angola and the Democratic Republic of the Congo 2015-16: a modelling study
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Kraemer, MUG, Faria, NR, Reiner, RC, Golding, N, Nikolay, B, Stasse, S, Johansson, MA, Salje, H, Faye, O, Wint, GRW, Niedrig, M, Shearer, FM, Hill, SC, Thompson, RN, Bisanzio, D, Taveira, N, Nax, HH, Pradelski, BSR, Nsoesie, EO, Murphy, NR, Bogoch, II, Khan, K, Brownstein, JS, Tatem, AJ, de Oliveira, T, Smith, DL, Sall, AA, Pybus, OG, Hay, SI, Cauchemez, S, Kraemer, MUG, Faria, NR, Reiner, RC, Golding, N, Nikolay, B, Stasse, S, Johansson, MA, Salje, H, Faye, O, Wint, GRW, Niedrig, M, Shearer, FM, Hill, SC, Thompson, RN, Bisanzio, D, Taveira, N, Nax, HH, Pradelski, BSR, Nsoesie, EO, Murphy, NR, Bogoch, II, Khan, K, Brownstein, JS, Tatem, AJ, de Oliveira, T, Smith, DL, Sall, AA, Pybus, OG, Hay, SI, and Cauchemez, S
- Abstract
BACKGROUND: Since late 2015, an epidemic of yellow fever has caused more than 7334 suspected cases in Angola and the Democratic Republic of the Congo, including 393 deaths. We sought to understand the spatial spread of this outbreak to optimise the use of the limited available vaccine stock. METHODS: We jointly analysed datasets describing the epidemic of yellow fever, vector suitability, human demography, and mobility in central Africa to understand and predict the spread of yellow fever virus. We used a standard logistic model to infer the district-specific yellow fever virus infection risk during the course of the epidemic in the region. FINDINGS: The early spread of yellow fever virus was characterised by fast exponential growth (doubling time of 5-7 days) and fast spatial expansion (49 districts reported cases after only 3 months) from Luanda, the capital of Angola. Early invasion was positively correlated with high population density (Pearson's r 0·52, 95% CI 0·34-0·66). The further away locations were from Luanda, the later the date of invasion (Pearson's r 0·60, 95% CI 0·52-0·66). In a Cox model, we noted that districts with higher population densities also had higher risks of sustained transmission (the hazard ratio for cases ceasing was 0·74, 95% CI 0·13-0·92 per log-unit increase in the population size of a district). A model that captured human mobility and vector suitability successfully discriminated districts with high risk of invasion from others with a lower risk (area under the curve 0·94, 95% CI 0·92-0·97). If at the start of the epidemic, sufficient vaccines had been available to target 50 out of 313 districts in the area, our model would have correctly identified 27 (84%) of the 32 districts that were eventually affected. INTERPRETATION: Our findings show the contributions of ecological and demographic factors to the ongoing spread of the yellow fever outbreak and provide estimates of the areas that could be prioritised for vaccination, although
- Published
- 2017
16. Enquête de séroprévalence suite à un foyer de dengue, France métropolitaine, novembre 2015
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Rousseau, C., primary, Succo, T., additional, Nikolai, B., additional, Maquart, M., additional, De Crouy-Chanel, P., additional, Salje, H., additional, Leparc Goffart, I., additional, Cauchemez, S., additional, and Noël, H., additional
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- 2017
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17. Revealing the microscale spatial signature of dengue transmission and immunity in an urban population
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Salje, H, Lessler, J, Endy, TP, Curriero, FC, Gibbons, RV, Nisalak, A, Nimmannitya, S, Kalayanarooj, S, Jarman, RG, Thomas, SJ, Burke, DS, Cummings, DAT, Salje, H, Lessler, J, Endy, TP, Curriero, FC, Gibbons, RV, Nisalak, A, Nimmannitya, S, Kalayanarooj, S, Jarman, RG, Thomas, SJ, Burke, DS, and Cummings, DAT
- Abstract
It is well-known that the distribution of immunity in a population dictates the future incidence of infectious disease, but this process is generally understood at individual or macroscales. For example, herd immunity to multiple pathogens has been observed at national and city levels. However, the effects of population immunity have not previously been shown at scales smaller than the city (e.g., neighborhoods). In particular, no study has shownlong-termeffects of population immunity at scales consistent with the spatial scale of person-to-person transmission. Here, we use the location of dengue patients' homes in Bangkok with the serotype of the infecting pathogen to investigate the spatiotemporal distribution of disease risk at small spatial scales over a 5-y period. We find evidence for localized transmission at distances of under 1 km. We also observe patterns of spatiotemporal dependence consistent with the expected impacts of homotypic immunity, heterotypic immunity, and immune enhancement of disease at these distances. Our observations indicate that immunological memory of dengue serotypes occurs at the neighborhood level in this large urban setting. These methods have broad applications to studying the spatiotemporal structure of disease risk where pathogen serotype or genetic information is known.
- Published
- 2012
18. Impact of neighborhood biomass cooking patterns on episodic high indoor particulate matter concentrations in clean fuel homes in Dhaka, Bangladesh
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Salje, H., primary, Gurley, E. S., additional, Homaira, N., additional, Ram, P. K., additional, Haque, R., additional, Petri, W., additional, Moss, W. J., additional, Luby, S. P., additional, Breysse, P., additional, and Azziz-Baumgartner, E., additional
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- 2013
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19. Synchrony of Dengue Incidence in Ho Chi Minh City and Bangkok.
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Cuong Hoang Quoc, Salje Henrik, Rodriguez-Barraquer Isabel, Yoon In-Kyu, Nguyen Van Vinh Chau, Nguyen Thanh Hung, Ha Manh Tuan, Phan Trong Lan, Bridget Willis, Ananda Nisalak, Siripen Kalayanarooj, Derek A T Cummings, and Cameron P Simmons
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Arctic medicine. Tropical medicine ,RC955-962 ,Public aspects of medicine ,RA1-1270 - Abstract
BACKGROUND:Ho Chi Minh City and Bangkok are highly dengue endemic. The extent to which disease patterns are attributable to local versus regional dynamics remains unclear. To address this gap we compared key transmission parameters across the locations. METHODS AND PRINCIPAL FINDINGS:We used 2003-2009 age-stratified case data to inform catalytic transmission models. Further, we compared the spatial clustering of serotypes within each city. We found that annual case numbers were highly consistent across the two cities (correlation of 0.77, 95% CI: 0.74-0.79) as was the annual force of infection (correlation of 0.57, 95% CI: 0.46-0.68). Serotypes were less similar with serotype-specific correlations ranging from 0.65 for DENV1 to -0.14 for DENV4. Significant spatial clustering of serotypes was observed in HCMC at distances
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- 2016
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20. Quantifying the effect of vector targeted interventions to control dengue.
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Salje H
- Abstract
Competing Interests: I declare no competing interests.
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- 2024
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21. Reconciling heterogeneous dengue virus infection risk estimates from different study designs.
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Huang AT, Buddhari D, Kaewhiran S, Iamsirithaworn S, Khampaen D, Farmer A, Fernandez S, Thomas SJ, Barraquer IR, Hunsawong T, Srikiatkhachorn A, Dos Santos GR, O'Driscoll M, Hamins-Puertolas M, Endy T, Rothman AL, Cummings DAT, Anderson K, and Salje H
- Abstract
Uncovering rates at which susceptible individuals become infected with a pathogen, i.e. the force of infection (FOI), is essential for assessing transmission risk and reconstructing distribution of immunity in a population. For dengue, reconstructing exposure and susceptibility statuses from the measured FOI is of particular significance as prior exposure is a strong risk factor for severe disease. FOI can be measured via many study designs. Longitudinal serology are considered gold standard measurements, as they directly track the transition of seronegative individuals to seropositive due to incident infections (seroincidence). Cross-sectional serology can provide estimates of FOI by contrasting seroprevalence across ages. Age of reported cases can also be used to infer FOI. Agreement of these measurements, however, have not been assessed. Using 26 years of data from cohort studies and hospital-attended cases from Kamphaeng Phet province, Thailand, we found FOI estimates from the three sources to be highly inconsistent. Annual FOI estimates from seroincidence was 2.46 to 4.33-times higher than case-derived FOI. Correlation between seroprevalence-derived and case-derived FOI was moderate (correlation coefficient=0.46) and no systematic bias. Through extensive simulations and theoretical analysis, we show that incongruences between methods can result from failing to account for dengue antibody kinetics, assay noise, and heterogeneity in FOI across ages. Extending standard inference models to include these processes reconciled the FOI and susceptibility estimates. Our results highlight the importance of comparing inferences across multiple data types to uncover additional insights not attainable through a single data type/analysis.
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- 2024
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22. Challenges and Approaches to Establishing Multi-Pathogen Serosurveillance: Findings from the 2023 Serosurveillance Summit.
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Carcelen AC, Kong AC, Takahashi S, Hegde S, Jaenisch T, Chu M, Rochford R, Kostandova N, Gurley ES, Wesolowski A, Azman AS, van der Klis FRM, den Hartog G, Drakeley C, Heaney C, Winter AK, Salje H, Rodriguez-Barraquer I, Leung DT, Njenga SM, Kagucia EW, Jambo KC, Wolter N, Charles RC, Saboyá-Díaz MI, Martin DL, and Moss WJ
- Abstract
Multiplex-based serological surveillance is a valuable but underutilized tool to understand gaps in population-level exposure, susceptibility, and immunity to infectious diseases. Assays for which blood samples can be tested for antibodies against several pathogens simultaneously, such as multiplex bead immunoassays, can more efficiently integrate public health surveillance in low- and middle-income countries. On March 7-8, 2023 a group of experts representing research institutions, multilateral organizations, private industry, and country partners met to discuss experiences, identify challenges and solutions, and create a community of practice for integrated, multi-pathogen serosurveillance using multiplex bead assay technologies. Participants were divided into six working groups: 1) supply chain; 2) laboratory assays; 3) seroepidemiology; 4) data analytics; 5) sustainable implementation; and 6) use case scenarios. These working groups discussed experiences, challenges, solutions, and research needs to facilitate integrated, multi-pathogen serosurveillance for public health. Several solutions were proposed to address challenges that cut across working groups.
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- 2024
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23. Informing an investment case for Japanese encephalitis vaccine introduction in Bangladesh.
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Duque MP, Naser AM, Dos Santos GR, O'Driscoll M, Paul KK, Rahman M, Alam MS, Al-Amin HM, Rahman MZ, Hossain ME, Paul RC, Luby SP, Cauchemez S, Vanhomwegen J, Gurley ES, and Salje H
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- Bangladesh epidemiology, Humans, Animals, Seroepidemiologic Studies, Adolescent, Adult, Antibodies, Viral immunology, Antibodies, Viral blood, Child, Male, Female, Young Adult, Child, Preschool, Middle Aged, Culicidae virology, Mosquito Vectors virology, Encephalitis, Japanese epidemiology, Encephalitis, Japanese prevention & control, Encephalitis, Japanese transmission, Japanese Encephalitis Vaccines immunology, Encephalitis Virus, Japanese immunology
- Abstract
Japanese encephalitis virus (JEV) is a major threat to human health. Bangladesh is considering introducing a JEV vaccine; however, the investment case is hampered by a limited understanding of key aspects of JEV ecology. We conducted a seroprevalence study in a high-incidence region using an assay that limits cross-reactivity with dengue virus. We also trapped mosquitoes and collected information about potential host species. We used mathematical models to recover risk factors for infection and underlying probabilities of severe disease and death. We observed 19.0% [95% confidence interval (CI):17.1 to 21.1] of JEV antibodies. On average, 0.7% (95% CI: 0.2 to 2.0) of the susceptible population gets infected yearly, with pig proximity being the main human infection risk factor. Our traps captured 10 different mosquito species that have been linked with JEV transmission. We estimated that 1 in 1000 infections results in severe disease, 1 in 10,000 results in death, and 76% of severe cases are missed by surveillance.
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- 2024
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24. Risks of releasing imperfect Wolbachia strains for arbovirus control.
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Salje H and Jiggins FM
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- Animals, Humans, Mosquito Vectors microbiology, Mosquito Vectors virology, Wolbachia genetics, Arboviruses, Arbovirus Infections transmission, Arbovirus Infections prevention & control
- Abstract
Competing Interests: We declare no competing interests.
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- 2024
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25. Dynamics of measles immunity from birth and following vaccination.
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Wang W, O'Driscoll M, Wang Q, Zhao S, Salje H, and Yu H
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- Humans, Female, Infant, Child, Preschool, Infant, Newborn, Child, Male, Immunity, Maternally-Acquired immunology, Adult, Cohort Studies, Measles virus immunology, Pregnancy, Antibodies, Viral blood, Antibodies, Viral immunology, Measles Vaccine immunology, Measles Vaccine administration & dosage, Measles immunology, Measles prevention & control, Vaccination
- Abstract
Measles remains a major threat to human health despite widespread vaccination. While we know that maternal antibodies can impair vaccine-induced immunity, the relative contributions of pre-existing immunity levels, maternal and infant characteristics on vaccine responses remain unclear, hampering evidence-based vaccination policy development. Here we combine serological data from 1,505 individuals (aged 0-12 years) in a mother-infant cohort and in a child cohort with empirical models to reconstruct antibody trajectories from birth. We show that while highly heterogeneous across a population, measles antibody evolution is strongly predictive from birth at the individual level, including following vaccination. Further, we find that caesarean section births were linked with 2.56 (95% confidence interval: 1.06-6.37) increased odds of primary vaccine failure, highlighting the long-term immunological consequences of birth route. Finally, we use our new understanding of antibody evolution to critically assess the population-level consequences of different vaccination schedules, the results of which will allow country-level evaluations of vaccine policy., (© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)
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- 2024
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26. Geographical migration and fitness dynamics of Streptococcus pneumoniae.
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Belman S, Lefrancq N, Nzenze S, Downs S, du Plessis M, Lo SW, McGee L, Madhi SA, von Gottberg A, Bentley SD, and Salje H
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- Humans, Genome, Bacterial genetics, Penicillin Resistance drug effects, Penicillin Resistance genetics, Penicillins pharmacology, Pneumococcal Infections epidemiology, Pneumococcal Infections immunology, Pneumococcal Infections microbiology, Pneumococcal Infections transmission, Pneumococcal Vaccines immunology, Serogroup, South Africa epidemiology, Vaccines, Conjugate immunology, Heptavalent Pneumococcal Conjugate Vaccine immunology, Locomotion, Genetic Fitness drug effects, Genetic Fitness genetics, Streptococcus pneumoniae drug effects, Streptococcus pneumoniae genetics, Streptococcus pneumoniae immunology, Streptococcus pneumoniae isolation & purification, Geographic Mapping
- Abstract
Streptococcus pneumoniae is a leading cause of pneumonia and meningitis worldwide. Many different serotypes co-circulate endemically in any one location
1,2 . The extent and mechanisms of spread and vaccine-driven changes in fitness and antimicrobial resistance remain largely unquantified. Here using geolocated genome sequences from South Africa (n = 6,910, collected from 2000 to 2014), we developed models to reconstruct spread, pairing detailed human mobility data and genomic data. Separately, we estimated the population-level changes in fitness of strains that are included (vaccine type (VT)) and not included (non-vaccine type (NVT)) in pneumococcal conjugate vaccines, first implemented in South Africa in 2009. Differences in strain fitness between those that are and are not resistant to penicillin were also evaluated. We found that pneumococci only become homogenously mixed across South Africa after 50 years of transmission, with the slow spread driven by the focal nature of human mobility. Furthermore, in the years following vaccine implementation, the relative fitness of NVT compared with VT strains increased (relative risk of 1.68; 95% confidence interval of 1.59-1.77), with an increasing proportion of these NVT strains becoming resistant to penicillin. Our findings point to highly entrenched, slow transmission and indicate that initial vaccine-linked decreases in antimicrobial resistance may be transient., (© 2024. The Author(s).)- Published
- 2024
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27. Results of a nationally representative seroprevalence survey of chikungunya virus in Bangladesh.
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Allen SW, Ribeiro Dos Santos G, Paul KK, Paul R, Rahman MZ, Alam MS, Rahman M, Al-Amin HM, Vanhomwegen J, Weaver SC, Smull T, Lee KH, Gurley ES, and Salje H
- Abstract
There is an increasing global burden from chikungunya virus (CHIKV). Bangladesh reported a major epidemic in 2017, however, it was unclear if there had been prior widespread transmission. We conducted a nationally representative seroprevalence survey in 70 randomly selected communities immediately prior to the epidemic. We found 69/2,938 (2.4%) of sampled individuals were seropositive to CHIKV. Being seropositive to dengue virus (aOR 3.13 [95% CIs: 1.86-5.27]), male sex (aOR 0.59 [95% CIs: 0.36-0.99]), and community presence of Aedes aegypti mosquitoes (aOR: 1.80, 95% CI: 1.05-3.07) were significantly associated with CHIKV seropositivity. Using a spatial prediction model, we estimated that across the country, 4.99 (95% CI: 4.89 - 5.08) million people had been previously infected. These findings highlight high population susceptibility prior to the major outbreak and that previous outbreaks must have been spatially isolated., (© The Author(s) 2024. Published by Oxford University Press on behalf of Infectious Diseases Society of America.)
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- 2024
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28. Estimating geographical spread of Streptococcus pneumoniae within Israel using genomic data.
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Cheng HR, Belman S, Salje H, Dagan R, and Bentley SD
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- Israel epidemiology, Humans, Whole Genome Sequencing methods, Phylogeny, Genomics, Streptococcus pneumoniae genetics, Streptococcus pneumoniae classification, Streptococcus pneumoniae isolation & purification, Pneumococcal Infections microbiology, Pneumococcal Infections epidemiology, Genome, Bacterial
- Abstract
Understanding how pathogens spread across geographical space is fundamental for control measures such as vaccination. Streptococcus pneumoniae (the pneumococcus) is a respiratory bacterium responsible for a large proportion of infectious disease morbidity and mortality globally. Even in the post-vaccination era, the rates of invasive pneumococcal disease (IPD) remain stable in most countries, including Israel. To understand the geographical spread of the pneumococcus in Israel, we analysed 1174 pneumococcal genomes from patients with IPD across multiple regions. We included the evolutionary distance between pairs of isolates inferred using whole-genome data within a relative risk (RR) ratio framework to capture the geographical structure of S. pneumoniae . While we could not find geographical structure at the overall lineage level, the extra granularity provided by whole-genome sequence data showed that it takes approximately 5 years for invasive pneumococcal isolates to become fully mixed across the country.This article contains data hosted by Microreact.
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- 2024
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29. The deadly potential of chikungunya virus.
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Salje H and Cortés Azuero O
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- Humans, Animals, Chikungunya virus, Chikungunya Fever
- Abstract
Competing Interests: We declare no competing interests.
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- 2024
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30. Chikungunya seroprevalence, force of infection, and prevalence of chronic disability after infection in endemic and epidemic settings: a systematic review, meta-analysis, and modelling study.
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Kang H, Auzenbergs M, Clapham H, Maure C, Kim JH, Salje H, Taylor CG, Lim A, Clark A, Edmunds WJ, Sahastrabuddhe S, Brady OJ, and Abbas K
- Subjects
- Humans, Seroepidemiologic Studies, Chikungunya virus immunology, Prevalence, Epidemics, Endemic Diseases, Adult, Disabled Persons statistics & numerical data, Male, Female, Chikungunya Fever epidemiology
- Abstract
Background: Chikungunya is an arboviral disease transmitted by Aedes aegypti and Aedes albopictus mosquitoes with a growing global burden linked to climate change and globalisation. We aimed to estimate chikungunya seroprevalence, force of infection (FOI), and prevalence of related chronic disability and hospital admissions in endemic and epidemic settings., Methods: In this systematic review, meta-analysis, and modelling study, we searched PubMed, Ovid, and Web of Science for articles published from database inception until Sept 26, 2022, for prospective and retrospective cross-sectional studies that addressed serological chikungunya virus infection in any geographical region, age group, and population subgroup and for longitudinal prospective and retrospective cohort studies with data on chronic chikungunya or hospital admissions in people with chikungunya. We did a systematic review of studies on chikungunya seroprevalence and fitted catalytic models to each survey to estimate location-specific FOI (ie, the rate at which susceptible individuals acquire chikungunya infection). We performed a meta-analysis to estimate the proportion of symptomatic patients with laboratory-confirmed chikungunya who had chronic chikungunya or were admitted to hospital following infection. We used a random-effects model to assess the relationship between chronic sequelae and follow-up length using linear regression. The systematic review protocol is registered online on PROSPERO, CRD42022363102., Findings: We identified 60 studies with data on seroprevalence and chronic chikungunya symptoms done across 76 locations in 38 countries, and classified 17 (22%) of 76 locations as endemic settings and 59 (78%) as epidemic settings. The global long-term median annual FOI was 0·007 (95% uncertainty interval [UI] 0·003-0·010) and varied from 0·0001 (0·00004-0·0002) to 0·113 (0·07-0·20). The highest estimated median seroprevalence at age 10 years was in south Asia (8·0% [95% UI 6·5-9·6]), followed by Latin America and the Caribbean (7·8% [4·9-14·6]), whereas median seroprevalence was lowest in the Middle East (1·0% [0·5-1·9]). We estimated that 51% (95% CI 45-58) of people with laboratory-confirmed symptomatic chikungunya had chronic disability after infection and 4% (3-5) were admitted to hospital following infection., Interpretation: We inferred subnational heterogeneity in long-term average annual FOI and transmission dynamics and identified both endemic and epidemic settings across different countries. Brazil, Ethiopia, Malaysia, and India included both endemic and epidemic settings. Long-term average annual FOI was higher in epidemic settings than endemic settings. However, long-term cumulative incidence of chikungunya can be similar between large outbreaks in epidemic settings with a high FOI and endemic settings with a relatively low FOI., Funding: International Vaccine Institute., Competing Interests: Declaration of interests We declare no competing interests., (Copyright © 2024 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license. Published by Elsevier Ltd.. All rights reserved.)
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- 2024
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31. The genetic diversity of Nipah virus across spatial scales.
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Cortes-Azuero O, Lefrancq N, Nikolay B, McKee C, Cappelle J, Hul V, Ou TP, Hoem T, Lemey P, Rahman MZ, Islam A, Gurley ES, Duong V, and Salje H
- Abstract
Background: Nipah virus (NiV), a highly lethal virus in humans, circulates in Pteropus bats throughout South and Southeast Asia. Difficulty in obtaining viral genomes from bats means we have a poor understanding of NiV diversity., Methods: We develop phylogenetic approaches applied to the most comprehensive collection of genomes to date (N=257, 175 from bats, 73 from humans) from six countries over 22 years (1999-2020). We divide the four major NiV sublineages into 15 genetic clusters. Using Approximate Bayesian Computation fit to a spatial signature of viral diversity, we estimate the presence and the average size of genetic clusters per area., Results: We find that, within any bat roost, there are an average of 2.4 co-circulating genetic clusters, rising to 5.5 clusters at areas of 1500-2000km2. We estimate that each genetic cluster occupies an average area of 1.3million km2 (95%CI: 0.6-2.3 million), with 14 clusters in an area of 100,000km2 (95%CI: 6-24). In the few sites in Bangladesh and Cambodia where genomic surveillance has been concentrated, we estimate that most clusters have been identified, but only ∼15% of overall NiV diversity has been uncovered., Conclusion: Our findings are consistent with entrenched co-circulation of distinct lineages, even within roosts, coupled with slow migration over larger spatial scales., (© The Author(s) 2024. Published by Oxford University Press on behalf of Infectious Diseases Society of America.)
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- 2024
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32. Antigenic distance between primary and secondary dengue infections correlates with disease risk.
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Wang L, Huang AT, Katzelnick LC, Lefrancq N, Escoto AC, Duret L, Chowdhury N, Jarman R, Conte MA, Berry IM, Fernandez S, Klungthong C, Thaisomboonsuk B, Suntarattiwong P, Vandepitte W, Whitehead SS, Cauchemez S, Cummings DAT, and Salje H
- Subjects
- Humans, Thailand epidemiology, Risk Factors, Hospitalization, Dengue immunology, Dengue epidemiology, Dengue virology, Dengue Virus immunology, Antigens, Viral immunology
- Abstract
Many pathogens continuously change their protein structure in response to immune-driven selection, resulting in weakened protection even in previously exposed individuals. In addition, for some pathogens, such as dengue virus, poorly targeted immunity is associated with increased risk of severe disease through a mechanism known as antibody-dependent enhancement. However, it remains unclear whether the antigenic distances between an individual's first infection and subsequent exposures dictate disease risk, explaining the observed large-scale differences in dengue hospitalizations across years. Here, we develop a framework that combines detailed antigenic and genetic characterization of viruses with details on hospitalized cases from 21 years of dengue surveillance in Bangkok, Thailand, to identify the role of the antigenic profile of circulating viruses in determining disease risk. We found that the risk of hospitalization depended on both the specific order of infecting serotypes and the antigenic distance between an individual's primary and secondary infections, with risk maximized at intermediate antigenic distances. These findings suggest that immune imprinting helps determine dengue disease risk and provide a pathway to monitor the changing risk profile of populations and to quantifying risk profiles of candidate vaccines.
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- 2024
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33. Protective Role of NS1-Specific Antibodies in the Immune Response to Dengue Virus through Antibody-Dependent Cellular Cytotoxicity.
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Sanchez-Vargas LA, Mathew A, Salje H, Sousa D, Casale NA, Farmer A, Buddhari D, Anderson K, Iamsirithaworn S, Kaewhiran S, Friberg H, Currier JR, and Rothman AL
- Abstract
Background: Dengue virus (DENV) non-structural protein 1 (NS1) has multiple functions within infected cells, on the cell surface, and in secreted form, and is highly immunogenic. Immunity from previous DENV infections is known to exert both positive and negative effects on subsequent DENV infections, but the contribution of NS1-specific antibodies to these effects is incompletely understood., Methods: We investigated the functions of NS1-specific antibodies and their significance in DENV infection. We analyzed plasma samples collected in a prospective cohort study prior to symptomatic or subclinical secondary DENV infection. We measured binding to purified recombinant NS1 protein and to NS1-expressing CEM cells, antibody-mediated NK cell activation by plate-bound NS1 protein, and antibody-dependent cellular cytotoxicity (ADCC) of NS1-expressing target cells., Results: We found that antibody responses to NS1 were highly serotype-cross-reactive and that subjects who experienced subclinical DENV infection had significantly higher antibody responses to NS1 in pre-infection plasma than subjects who experienced symptomatic infection. We observed strong positive correlations between antibody binding and NK activation., Conclusions: These findings demonstrate the involvement of NS1-specific antibodies in ADCC and provide evidence for a protective effect of NS1-specific antibodies in secondary DENV infection., (© The Author(s) 2024. Published by Oxford University Press on behalf of Infectious Diseases Society of America. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)
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- 2024
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34. Integration of population-level data sources into an individual-level clinical prediction model for dengue virus test positivity.
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Williams RJ, Brintz BJ, Ribeiro Dos Santos G, Huang AT, Buddhari D, Kaewhiran S, Iamsirithaworn S, Rothman AL, Thomas S, Farmer A, Fernandez S, Cummings DAT, Anderson KB, Salje H, and Leung DT
- Subjects
- Humans, Models, Statistical, Prognosis, Climate, Fever, Dengue Virus, Dengue diagnosis, Dengue epidemiology
- Abstract
The differentiation of dengue virus (DENV) infection, a major cause of acute febrile illness in tropical regions, from other etiologies, may help prioritize laboratory testing and limit the inappropriate use of antibiotics. While traditional clinical prediction models focus on individual patient-level parameters, we hypothesize that for infectious diseases, population-level data sources may improve predictive ability. To create a clinical prediction model that integrates patient-extrinsic data for identifying DENV among febrile patients presenting to a hospital in Thailand, we fit random forest classifiers combining clinical data with climate and population-level epidemiologic data. In cross-validation, compared to a parsimonious model with the top clinical predictors, a model with the addition of climate data, reconstructed susceptibility estimates, force of infection estimates, and a recent case clustering metric significantly improved model performance.
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- 2024
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35. Comparing the Performance of Three Models Incorporating Weather Data to Forecast Dengue Epidemics in Reunion Island, 2018-2019.
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Andronico A, Menudier L, Salje H, Vincent M, Paireau J, de Valk H, Gallian P, Pastorino B, Brady O, de Lamballerie X, Lazarus C, Paty MC, Vilain P, Noel H, and Cauchemez S
- Subjects
- Animals, Humans, Reunion epidemiology, Weather, Dengue, Dengue Virus, Aedes, Epidemics
- Abstract
We developed mathematical models to analyze a large dengue virus (DENV) epidemic in Reunion Island in 2018-2019. Our models captured major drivers of uncertainty including the complex relationship between climate and DENV transmission, temperature trends, and underreporting. Early assessment correctly concluded that persistence of DENV transmission during the austral winter 2018 was likely and that the second epidemic wave would be larger than the first one. From November 2018, the detection probability was estimated at 10%-20% and, for this range of values, our projections were found to be remarkably accurate. Overall, we estimated that 8% and 18% of the population were infected during the first and second wave, respectively. Out of the 3 models considered, the best-fitting one was calibrated to laboratory entomological data, and accounted for temperature but not precipitation. This study showcases the contribution of modeling to strengthen risk assessments and planning of national and local authorities., Competing Interests: Potential conflicts of interest. All authors: No reported conflicts. All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest. Conflicts that the editors consider relevant to the content of the manuscript have been disclosed., (© The Author(s) 2023. Published by Oxford University Press on behalf of Infectious Diseases Society of America.)
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- 2024
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36. Achieving zero deaths from dengue virus under evolving population immunity.
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Salje H
- Subjects
- Humans, Immunity, Herd, Dengue Virus, Dengue epidemiology, Dengue prevention & control, Zika Virus
- Abstract
Competing Interests: I declare no competing interests.
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- 2024
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37. Household immunity and individual risk of infection with dengue virus in a prospective, longitudinal cohort study.
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Hamins-Puértolas M, Buddhari D, Salje H, Cummings DAT, Fernandez S, Farmer A, Kaewhiran S, Khampaen D, Iamsirithaworn S, Srikiatkhachorn A, Waickman A, Thomas SJ, Rothman AL, Endy T, Rodriguez-Barraquer I, and Anderson KB
- Subjects
- Adult, Humans, Child, Prospective Studies, Cohort Studies, Longitudinal Studies, Thailand epidemiology, Dengue Virus, Dengue
- Abstract
Although it is known that household infections drive the transmission of dengue virus (DENV), it is unclear how household composition and the immune status of inhabitants affect the individual risk of infection. Most population-based studies to date have focused on paediatric cohorts because more severe forms of dengue mainly occur in children, and the role of adults in dengue transmission is understudied. Here we analysed data from a multigenerational cohort study of 470 households, comprising 2,860 individuals, in Kamphaeng Phet, Thailand, to evaluate risk factors for DENV infection. Using a gradient-boosted regression model trained on annual haemagglutination inhibition antibody titre inputs, we identified 1,049 infections, 90% of which were subclinical. By analysing imputed infections, we found that individual antibody titres, household composition and antibody titres of other members in the same household affect an individual's risk of DENV infection. Those individuals living in households with high average antibody titres, or households with more adults, had a reduced risk of infection. We propose that herd immunity to dengue acts at the household level and may provide insight into the drivers of the recent change in the shifting age distribution of dengue cases in Thailand., (© 2023. The Author(s), under exclusive licence to Springer Nature Limited.)
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- 2024
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38. Transplacental transfer efficiency of maternal antibodies against influenza A(H1N1)pdm09 virus and dynamics of naturally acquired antibodies in Chinese children: a longitudinal, paired mother-neonate cohort study.
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Li M, Wang W, Chen J, Zhan Z, Xu M, Liu N, Ren L, You L, Zheng W, Shi H, Zhao Z, Huang C, Chen X, Zheng N, Lu W, Zhou X, Zhou J, Liao Q, Yang J, Jit M, Salje H, and Yu H
- Subjects
- Adult, Female, Humans, Infant, Infant, Newborn, Male, Pregnancy, Young Adult, Antibodies, Viral, Cohort Studies, East Asian People, Longitudinal Studies, Mothers, Retrospective Studies, Seroepidemiologic Studies, Influenza A Virus, H1N1 Subtype, Influenza, Human epidemiology, Influenza, Human prevention & control
- Abstract
Background: The 2009 pandemic H1N1 influenza A virus (A(H1N1)pdm09 virus) evolves rapidly and has continued to cause severe infections in children since its emergence in 2009. We aimed to characterise the kinetics of maternally and naturally acquired antibodies against historical A(H1N1)pdm09 strains and to assess the extent to which the response to heterologous strains following infection or vaccination affects observed A(H1N1)pdm09 strain-specific antibody titres in a Chinese paediatric population., Methods: In this retrospective study, we used residual serum samples from 528 mother-neonate pairs from a non-interventional, longitudinal cohort study in southern China conducted from Sept 20, 2013, to Aug 24, 2018, from six local hospitals in Anhua County, Hunan Province, China. Mother-neonate pairs were eligible for inclusion if the neonates were born after Sept 20, 2013, and their mothers had resided in the study sites for at least 3 months. We tested samples with a haemagglutination inhibition (HAI) assay to measure antibody levels against three historical A(H1N1)pdm09 strains that were antigenically similar to the strains that circulated during the 2009 pandemic (A/Hunan-Kaifu/SWL4204/2009 [SWL4204/09 strain], A/Hunan-Daxiang/SWL1277/2016 [SWL1277/16 strain], and A/Hunan-Yanfeng/SWL185/2018 [SWL185/18 strain]). We also determined the seroprevalence, geometric mean titres (GMTs), transfer ratio of maternal antibodies, and the dynamics of maternally and naturally acquired antibodies in children, from birth to 3 years of age., Findings: 1066 mother-neonate pairs were enrolled in the original cohort between Sept 20, 2013, and Oct 14, 2015. Of these, 528 pairs (523 mothers, 528 neonates) were selected for the present study. The median age of the mothers was 25 years (IQR 23 to 29). 291 (55%) of 528 children were boys and 237 (45%) were girls, and most children (452 [86%]) were breastfed before the age of 6 months. The GMTs and the seroprevalence for the SWL4204/09 strain were higher than those for the SWL1277/16 and SWL185/18 strains among mothers (GMTs: 10·4 [95% CI 9·8 to 11·1] vs 9·3 [8·7 to 9·8] vs 8·0 [7·5 to 8·4], p<0·0001; seroprevalence: 11·1% [95% CI 8·5 to 14·1] vs 6·9% [4·9 to 9·4] vs 4·6% [3·0 to 6·8], p=0·0003) and among neonates (GMTs: 10·7 [10·0 to 11·5] vs 9·4 [8·8 to 10·0] vs 8·1 [7·6 to 8·6], p<0·0001; seroprevalence: 13·4% [10·7 to 16·7] vs 8·7% [6·5 to 11·5] vs 6·1% [4·2 to 8·5], p=0·0002). Regardless of the A(H1N1)pdm09-specific strain, maternal antibodies could be transferred efficiently via the placenta (mean transfer ratios: 1·10 for SWL4204/09 vs 1·09 for SWL1277/16 vs 1·06 for SWL185/18; p=0·93). The A(H1N1)pdm09 strain-specific antibodies waned below the protective threshold of 1:40 within 2 months after birth. After maternal antibody waning, there were periodic increases and decreases in HAI antibody titres against three A(H1N1)pdm09 strains, and such increases were all significantly associated with a higher immune response to heterologous strains. Vaccination against the SWL4204/09 strain was associated with a poor response to the SWL185/18 strain (β-0·20, 95% CI -0·28 to -0·13; p<0·0001)., Interpretation: Our findings suggest low pre-existing immunity against influenza A(H1N1)pdm09 virus among unvaccinated Chinese adult female and paediatric populations. This evidence, together with the rapid decay of maternal antibodies and the observed cross-reactivity among different A(H1N1)pdm09 strains, highlights the importance of accelerating maternal and paediatric influenza vaccination in China., Funding: The Key Program of the National Natural Science Foundation of China., Translation: For the Chinese translation of the abstract see Supplementary Materials section., Competing Interests: Declaration of interests HY has received research funding from Sanofi Pasteur, GlaxoSmithKline, Yichang HEC Changjiang Pharmaceutical Company, Shanghai Roche Pharmaceutical Company, and SINOVAC Biotech Ltd. All other authors declare no competing interests., (Copyright © 2023 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY-NC-ND 4.0 license. Published by Elsevier Ltd.. All rights reserved.)
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- 2023
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39. A systematic review of the data, methods and environmental covariates used to map Aedes-borne arbovirus transmission risk.
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Lim AY, Jafari Y, Caldwell JM, Clapham HE, Gaythorpe KAM, Hussain-Alkhateeb L, Johansson MA, Kraemer MUG, Maude RJ, McCormack CP, Messina JP, Mordecai EA, Rabe IB, Reiner RC Jr, Ryan SJ, Salje H, Semenza JC, Rojas DP, and Brady OJ
- Subjects
- Animals, Humans, Mosquito Vectors, Arboviruses, Aedes, Arbovirus Infections epidemiology, Yellow Fever epidemiology, Zika Virus Infection, Chikungunya Fever, Zika Virus, Dengue epidemiology
- Abstract
Background: Aedes (Stegomyia)-borne diseases are an expanding global threat, but gaps in surveillance make comprehensive and comparable risk assessments challenging. Geostatistical models combine data from multiple locations and use links with environmental and socioeconomic factors to make predictive risk maps. Here we systematically review past approaches to map risk for different Aedes-borne arboviruses from local to global scales, identifying differences and similarities in the data types, covariates, and modelling approaches used., Methods: We searched on-line databases for predictive risk mapping studies for dengue, Zika, chikungunya, and yellow fever with no geographical or date restrictions. We included studies that needed to parameterise or fit their model to real-world epidemiological data and make predictions to new spatial locations of some measure of population-level risk of viral transmission (e.g. incidence, occurrence, suitability, etc.)., Results: We found a growing number of arbovirus risk mapping studies across all endemic regions and arboviral diseases, with a total of 176 papers published 2002-2022 with the largest increases shortly following major epidemics. Three dominant use cases emerged: (i) global maps to identify limits of transmission, estimate burden and assess impacts of future global change, (ii) regional models used to predict the spread of major epidemics between countries and (iii) national and sub-national models that use local datasets to better understand transmission dynamics to improve outbreak detection and response. Temperature and rainfall were the most popular choice of covariates (included in 50% and 40% of studies respectively) but variables such as human mobility are increasingly being included. Surprisingly, few studies (22%, 31/144) robustly tested combinations of covariates from different domains (e.g. climatic, sociodemographic, ecological, etc.) and only 49% of studies assessed predictive performance via out-of-sample validation procedures., Conclusions: Here we show that approaches to map risk for different arboviruses have diversified in response to changing use cases, epidemiology and data availability. We identify key differences in mapping approaches between different arboviral diseases, discuss future research needs and outline specific recommendations for future arbovirus mapping., (© 2023. BioMed Central Ltd., part of Springer Nature.)
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- 2023
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40. Maternally derived antibody titer dynamics and risk of hospitalized infant dengue disease.
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O'Driscoll M, Buddhari D, Huang AT, Waickman A, Kaewhirun S, Iamsirithaworn S, Khampaen D, Farmer A, Fernandez S, Rodriguez-Barraquer I, Srikiatkhachorn A, Thomas S, Endy T, Rothman AL, Anderson K, Cummings DAT, and Salje H
- Subjects
- Humans, Infant, Infant, Newborn, Antibodies, Viral, Antibodies, Neutralizing, Antibody-Dependent Enhancement, Dengue, Dengue Virus, Severe Dengue
- Abstract
Infants less than 1 y of age experience high rates of dengue disease in dengue virus (DENV) endemic countries. This burden is commonly attributed to antibody-dependent enhancement (ADE), whereby concentrations of maternally derived DENV antibodies become subneutralizing, and infection-enhancing. Understanding antibody-related mechanisms of enhanced infant dengue disease risk represents a significant challenge due to the dynamic nature of antibodies and their imperfect measurement processes. Further, key uncertainties exist regarding the impact of long-term shifts in birth rates, population-level infection risks, and maternal ages on the DENV immune landscape of newborns and their subsequent risks of severe dengue disease in infancy. Here, we analyze DENV antibody data from two infant cohorts (N = 142 infants with 605 blood draws) and 40 y of infant dengue hospitalization data from Thailand. We use mathematical models to reconstruct maternally derived antibody dynamics, accounting for discretized measurement processes and limits of assay detection. We then explore possible antibody-related mechanisms of enhanced infant dengue disease risk and their ability to reconstruct the observed age distribution of hospitalized infant dengue cases. We find that ADE mechanisms are best able to reconstruct the observed data. Finally, we describe how the shifting epidemiology of dengue in Thailand, combined with declining birth rates, have decreased the absolute risk of infant dengue disease by 88% over a 40-y period while having minimal impact on the mean age of infant hospitalized dengue disease.
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- 2023
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41. The genetic diversity of Nipah virus across spatial scales.
- Author
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Azuero OC, Lefrancq N, Nikolay B, McKee C, Cappelle J, Hul V, Ou TP, Hoem T, Lemey P, Rahman MZ, Islam A, Gurley ES, Duong V, and Salje H
- Abstract
Nipah virus (NiV), a highly lethal virus in humans, circulates silently in Pteropus bats throughout South and Southeast Asia. Difficulty in obtaining genomes from bats means we have a poor understanding of NiV diversity, including how many lineages circulate within a roost and the spread of NiV over increasing spatial scales. Here we develop phylogenetic approaches applied to the most comprehensive collection of genomes to date (N=257, 175 from bats, 73 from humans) from six countries over 22 years (1999-2020). In Bangladesh, where most human infections occur, we find evidence of increased spillover risk from one of the two co-circulating sublineages. We divide the four major NiV sublineages into 15 genetic clusters (emerged 20-44 years ago). Within any bat roost, there are an average of 2.4 co-circulating genetic clusters, rising to 5.5 clusters at areas of 1,500-2,000 km
2 . Using Approximate Bayesian Computation fit to a spatial signature of viral diversity, we estimate that each genetic cluster occupies an average area of 1.3 million km2 (95%CI: 0.6-2.3 million), with 14 clusters in an area of 100,000 km2 (95%CI: 6-24). In the few sites in Bangladesh and Cambodia where genomic surveillance has been concentrated, we estimate that most of the genetic clusters have been identified, but only ~15% of overall NiV diversity has been uncovered. Our findings are consistent with entrenched co-circulation of distinct lineages, even within individual roosts, coupled with slow migration over larger spatial scales.- Published
- 2023
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42. Marginal effects of public health measures and COVID-19 disease burden in China: A large-scale modelling study.
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Wang Z, Wu P, Wang L, Li B, Liu Y, Ge Y, Wang R, Wang L, Tan H, Wu CH, Laine M, Salje H, and Song H
- Subjects
- Humans, SARS-CoV-2, Public Health, China epidemiology, COVID-19 epidemiology, COVID-19 prevention & control, Epidemics prevention & control
- Abstract
China had conducted some of the most stringent public health measures to control the spread of successive SARS-CoV-2 variants. However, the effectiveness of these measures and their impacts on the associated disease burden have rarely been quantitatively assessed at the national level. To address this gap, we developed a stochastic age-stratified metapopulation model that incorporates testing, contact tracing and isolation, based on 419 million travel movements among 366 Chinese cities. The study period for this model began from September 2022. The COVID-19 disease burden was evaluated, considering 8 types of underlying health conditions in the Chinese population. We identified the marginal effects between the testing speed and reduction in the epidemic duration. The findings suggest that assuming a vaccine coverage of 89%, the Omicron-like wave could be suppressed by 3-day interval population-level testing (PLT), while it would become endemic with 4-day interval PLT, and without testing, it would result in an epidemic. PLT conducted every 3 days would not only eliminate infections but also keep hospital bed occupancy at less than 29.46% (95% CI, 22.73-38.68%) of capacity for respiratory illness and ICU bed occupancy at less than 58.94% (95% CI, 45.70-76.90%) during an outbreak. Furthermore, the underlying health conditions would lead to an extra 2.35 (95% CI, 1.89-2.92) million hospital admissions and 0.16 (95% CI, 0.13-0.2) million ICU admissions. Our study provides insights into health preparedness to balance the disease burden and sustainability for a country with a population of billions., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Wang et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
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- 2023
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43. Integration of population-level data sources into an individual-level clinical prediction model for dengue virus test positivity.
- Author
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Williams RJ, Brintz BJ, Santos GRD, Huang A, Buddhari D, Kaewhiran S, Iamsirithaworn S, Rothman AL, Thomas S, Farmer A, Fernandez S, Cummings DAT, Anderson KB, Salje H, and Leung DT
- Abstract
The differentiation of dengue virus (DENV) infection, a major cause of acute febrile illness in tropical regions, from other etiologies, may help prioritize laboratory testing and limit the inappropriate use of antibiotics. While traditional clinical prediction models focus on individual patient-level parameters, we hypothesize that for infectious diseases, population-level data sources may improve predictive ability. To create a clinical prediction model that integrates patient-extrinsic data for identifying DENV among febrile patients presenting to a hospital in Thailand, we fit random forest classifiers combining clinical data with climate and population-level epidemiologic data. In cross validation, compared to a parsimonious model with the top clinical predictors, a model with the addition of climate data, reconstructed susceptibility estimates, force of infection estimates, and a recent case clustering metric, significantly improved model performance., Competing Interests: Conflicts of Interest: The authors have declared no conflicts of interest.
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- 2023
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44. Antigenic diversity and dengue disease risk.
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Wang L, Huang AT, Katzelnick LC, Lefrancq N, Escoto AC, Duret L, Chowdhury N, Jarman R, Conte MA, Berry IM, Fernandez S, Klungthong C, Thaisomboonsuk B, Suntarattiwong P, Vandepitte W, Whitehead S, Cauchemez S, Cummings DAT, and Salje H
- Abstract
Many pathogens continuously change their protein structure in response to immune-driven selection, resulting in weakened protection. In addition, for some pathogens such as dengue virus, poorly targeted immunity is associated with increased risk of severe disease, through a mechanism known as antibody-dependent enhancement. However, it remains a mystery whether the antigenic distance between an individual's first infection and subsequent exposures dictate disease risk, explaining the observed large-scale differences in dengue hospitalisations across years. Here we develop an inferential framework that combines detailed antigenic and genetic characterisation of viruses, and hospitalised cases from 21 years of surveillance in Bangkok, Thailand to identify the role of the antigenic profile of circulating viruses in determining disease risk. We find that the risk of hospitalisation depends on both the specific order of infecting serotypes and the antigenic distance between an individual's primary and secondary infections, with risk maximised at intermediate antigenic distances. These findings suggest immune imprinting helps determine dengue disease risk, and provides a pathway to monitor the changing risk profile of populations and to quantifying risk profiles of candidate vaccines., Competing Interests: Competing interests Material has been reviewed by the Walter Reed Army Institute of Research. There is no objection to its presentation and publication. The views expressed are those of the authors, and do not necessarily reflect the official views of the National Institutes of Health, the U.S. Departments of the Army, Navy, or Air Force, the U.S. Department of Defense, or the U.S. Government.
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- 2023
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45. Household Transmission Dynamics of Seasonal Human Coronaviruses.
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Quandelacy TM, Hitchings MDT, Lessler J, Read JM, Vukotich C, Azman AS, Salje H, Zimmer S, Gao H, Zheteyeva Y, Uzicanin A, and Cummings DAT
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- Child, Adult, Humans, Seasons, Respiratory Tract Infections, Coronavirus Infections, Coronavirus 229E, Human, Viruses, Coronavirus OC43, Human, Coronavirus NL63, Human
- Abstract
Background: Household transmission studies inform how viruses spread among close contacts, but few characterize household transmission of endemic coronaviruses., Methods: We used data collected from 223 households with school-age children participating in weekly disease surveillance over 2 respiratory virus seasons (December 2015 to May 2017), to describe clinical characteristics of endemic human coronaviruses (HCoV-229E, HcoV-HKU1, HcoV-NL63, HcoV-OC43) infections, and community and household transmission probabilities using a chain-binomial model correcting for missing data from untested households., Results: Among 947 participants in 223 households, we observed 121 infections during the study, most commonly subtype HCoV-OC43. Higher proportions of infected children (<19 years) displayed influenza-like illness symptoms than infected adults (relative risk, 3.0; 95% credible interval [CrI], 1.5-6.9). The estimated weekly household transmission probability was 9% (95% CrI, 6-13) and weekly community acquisition probability was 7% (95% CrI, 5-10). We found no evidence for differences in community or household transmission probabilities by age or symptom status. Simulations suggest that our study was underpowered to detect such differences., Conclusions: Our study highlights the need for large household studies to inform household transmission, the challenges in estimating household transmission probabilities from asymptomatic individuals, and implications for controlling endemic CoVs., Competing Interests: Potential conflicts of interest. T. M. Q. received honoraria for and served on the MEICHV COVID-19 Health Equity Community Advisory Board. M. D. T. H. and D. A. T. C. reports contract from Merck (to the University of Florida) for research unrelated to this manuscript. All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest. Conflicts that the editors consider relevant to the content of the manuscript have been disclosed., (© The Author(s) 2022. Published by Oxford University Press on behalf of Infectious Diseases Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
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- 2023
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46. Accounting for assay performance when estimating the temporal dynamics in SARS-CoV-2 seroprevalence in the U.S.
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García-Carreras B, Hitchings MDT, Johansson MA, Biggerstaff M, Slayton RB, Healy JM, Lessler J, Quandelacy T, Salje H, Huang AT, and Cummings DAT
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- Humans, Seroepidemiologic Studies, Asymptomatic Infections, Biological Assay, Antibodies, Viral, SARS-CoV-2, COVID-19 epidemiology
- Abstract
Reconstructing the incidence of SARS-CoV-2 infection is central to understanding the state of the pandemic. Seroprevalence studies are often used to assess cumulative infections as they can identify asymptomatic infection. Since July 2020, commercial laboratories have conducted nationwide serosurveys for the U.S. CDC. They employed three assays, with different sensitivities and specificities, potentially introducing biases in seroprevalence estimates. Using models, we show that accounting for assays explains some of the observed state-to-state variation in seroprevalence, and when integrating case and death surveillance data, we show that when using the Abbott assay, estimates of proportions infected can differ substantially from seroprevalence estimates. We also found that states with higher proportions infected (before or after vaccination) had lower vaccination coverages, a pattern corroborated using a separate dataset. Finally, to understand vaccination rates relative to the increase in cases, we estimated the proportions of the population that received a vaccine prior to infection., (© 2023. The Author(s).)
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- 2023
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47. The spatial signature of Plasmodium vivax and Plasmodium falciparum infections: quantifying the clustering of infections in cross-sectional surveys and cohort studies.
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Sandfort M, Monteiro W, Lacerda M, Nguitragool W, Sattabongkot J, Waltmann A, Salje H, Vantaux A, Witkowski B, Robinson LJ, Mueller I, and White M
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- Humans, Plasmodium vivax, Cross-Sectional Studies, Plasmodium falciparum, Cluster Analysis, Cohort Studies, Malaria, Falciparum, Malaria, Vivax
- Abstract
Background: Over the last decades, enormous successes have been achieved in reducing malaria burden globally. In Latin America, South East Asia, and the Western Pacific, many countries now pursue the goal of malaria elimination by 2030. It is widely acknowledged that Plasmodium spp. infections cluster spatially so that interventions need to be spatially informed, e.g. spatially targeted reactive case detection strategies. Here, the spatial signature method is introduced as a tool to quantify the distance around an index infection within which other infections significantly cluster., Methods: Data were considered from cross-sectional surveys from Brazil, Thailand, Cambodia, and Solomon Islands, conducted between 2012 and 2018. Household locations were recorded by GPS and finger-prick blood samples from participants were tested for Plasmodium infection by PCR. Cohort studies from Brazil and Thailand with monthly sampling over a year from 2013 until 2014 were also included. The prevalence of PCR-confirmed infections was calculated at increasing distance around index infections (and growing time intervals in the cohort studies). Statistical significance was defined as prevalence outside of a 95%-quantile interval of a bootstrap null distribution after random re-allocation of locations of infections., Results: Prevalence of Plasmodium vivax and Plasmodium falciparum infections was elevated in close proximity around index infections and decreased with distance in most study sites, e.g. from 21.3% at 0 km to the global study prevalence of 6.4% for P. vivax in the Cambodian survey. In the cohort studies, the clustering decreased with longer time windows. The distance from index infections to a 50% reduction of prevalence ranged from 25 m to 3175 m, tending to shorter distances at lower global study prevalence., Conclusions: The spatial signatures of P. vivax and P. falciparum infections demonstrate spatial clustering across a diverse set of study sites, quantifying the distance within which the clustering occurs. The method offers a novel tool in malaria epidemiology, potentially informing reactive intervention strategies regarding radius choices of operations around detected infections and thus strengthening malaria elimination endeavours., (© 2023. The Author(s).)
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- 2023
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48. Author Correction: Reconstructing Mayaro virus circulation in French Guiana shows frequent spillovers.
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Hozé N, Salje H, Rousset D, Fritzell C, Vanhomwegen J, Bailly S, Najm M, Enfissi A, Manuguerra JC, Flamand C, and Cauchemez S
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- 2023
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49. Geographic migration and vaccine-induced fitness changes of Streptococcus pneumoniae .
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Belman S, Lefrancq N, Nzenze S, Downs S, du Plessis M, Lo S, McGee L, Madhi SA, von Gottberg A, Bentley SD, and Salje H
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Streptococcus pneumoniae is a leading cause of pneumonia and meningitis worldwide. Many different serotypes co-circulate endemically in any one location. The extent and mechanisms of spread, and vaccine-driven changes in fitness and antimicrobial resistance (AMR), remain largely unquantified. Using geolocated genome sequences from South Africa (N=6910, 2000-2014) we developed models to reconstruct spread, pairing detailed human mobility data and genomic data. Separately we estimated the population level changes in fitness of strains that are (vaccine type, VT) and are not (non-vaccine type, NVT) included in the vaccine, first implemented in 2009, as well as differences in strain fitness between those that are and are not resistant to penicillin. We estimated that pneumococci only become homogenously mixed across South Africa after about 50 years of transmission, with the slow spread driven by the focal nature of human mobility. Further, in the years following vaccine implementation the relative fitness of NVT compared to VT strains increased (RR: 1.29 [95% CI 1.20-1.37]) - with an increasing proportion of these NVT strains becoming penicillin resistant. Our findings point to highly entrenched, slow transmission and indicate that initial vaccine-linked decreases in AMR may be transient., Competing Interests: Competing interests: Authors declare that they have no competing interests.
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- 2023
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50. Seroepidemiological Reconstruction of Long-term Chikungunya Virus Circulation in Burkina Faso and Gabon.
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Lim JK, Ridde V, Agnandji ST, Lell B, Yaro S, Yang JS, Hoinard D, Weaver SC, Vanhomwegen J, Salje H, and Yoon IK
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- Humans, Infant, Child, Preschool, Child, Adolescent, Young Adult, Adult, Middle Aged, Gabon epidemiology, Burkina Faso epidemiology, Disease Outbreaks, Chikungunya virus, Chikungunya Fever epidemiology
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Chikungunya virus (CHIKV) is a major public health concern worldwide. However, infection levels are rarely known, especially in Africa. We recruited individuals from Ouagadougou, Burkina Faso and Lambaréné, Gabon (age range, 1-55 years), tested their blood for CHIKV antibodies, and used serocatalytic models to reconstruct epidemiological histories. In Ouagadougou, 291 of 999 (29.1%) individuals were seropositive, ranging from 2% among those aged <10 years to 66% in those aged 40-55 years. We estimated there were 7 outbreaks since the 1970s but none since 2001, resulting in 600 000 infections in the city, none of which were reported. However, we could not definitively conclude whether infections were due to CHIKV or o'nyong-nyong, another alphavirus. In Lambaréné, 117 of 427 (27%) participants were seropositive. Our model identified a single outbreak sometime since 2007, consistent with the only reported CHIKV outbreak in the country. These findings suggest sporadic outbreaks in these settings and that the burden remains undetected or incorrectly attributed., Competing Interests: Potential conflicts of interest. H. S. reports being a paid consultant to Gavi, the Vaccine Alliance, for work understanding the potential of chikungunya vaccines. All other authors report no potential conflicts. Funding to pay the Open Access publication charges for this article was provided by the University of Cambridge. All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest. Conflicts that the editors consider relevant to the content of the manuscript have been disclosed., (© The Author(s) 2022. Published by Oxford University Press on behalf of Infectious Diseases Society of America.)
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- 2023
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