Xiaoyue Xi
A5036440835- COVID-19 epidemiological studies
- COVID-19 Pandemic Impacts
- HIV/AIDS Research and Interventions
- HIV, Drug Use, Sexual Risk
- COVID-19 and Mental Health
- SARS-CoV-2 and COVID-19 Research
- COVID-19 Clinical Research Studies
- HIV Research and Treatment
- Vaccine Coverage and Hesitancy
- Viral Infections and Outbreaks Research
- Data-Driven Disease Surveillance
- HIV/AIDS Impact and Responses
- COVID-19 and healthcare impacts
- COVID-19 Digital Contact Tracing
- Probabilistic and Robust Engineering Design
- Adolescent Sexual and Reproductive Health
- Gaussian Processes and Bayesian Inference
- Bayesian Modeling and Causal Inference
- Bioinformatics and Genomic Networks
- SARS-CoV-2 detection and testing
- Advanced Multi-Objective Optimization Algorithms
- Influenza Virus Research Studies
- Statistical Methods and Inference
- Healthcare Systems and Reforms
- Evolution and Genetic Dynamics
Imperial College London
2018-2025
University of Cambridge
2020-2025
MRC Biostatistics Unit
2020-2025
Medical Research Council
2020-2025
London Centre for Neglected Tropical Disease Research
2020-2021
National University of Singapore
2020
Emodo (United States)
2020
Novartis (Switzerland)
2020
University of Oxford
2020
Brown University
2020
BackgroundIn the face of rapidly changing data, a range case fatality ratio estimates for coronavirus disease 2019 (COVID-19) have been produced that differ substantially in magnitude. We aimed to provide robust estimates, accounting censoring and ascertainment biases.MethodsWe collected individual-case data patients who died from COVID-19 Hubei, mainland China (reported by national provincial health commissions Feb 8, 2020), cases outside (from government or ministry websites media reports...
Global prospects for COVID-19 control Lower-income countries have recognized the potential impact of coronavirus disease 2019 (COVID-19) from observing ongoing epidemics. Many intervened quickly and early with measures to slow viral transmission, which may partly explain low rates observed so far in these countries. Walker et al. calibrated a global model country-specific data (see Perspective by Metcalf ). Despite potentially protective effects younger demographics, closer intergenerational...
SummaryBackgroundCOVID-19 has the potential to cause substantial disruptions health services, due cases overburdening system or response measures limiting usual programmatic activities. We aimed quantify extent which services for HIV, tuberculosis, and malaria in low-income middle-income countries with high burdens of these diseases could lead additional loss life over next 5 years.MethodsAssuming a basic reproduction number 3·0, we constructed four scenarios possible responses COVID-19...
In response to the COVID-19 pandemic, countries have sought control SARS-CoV-2 transmission by restricting population movement through social distancing interventions, thus reducing number of contacts. Mobility data represent an important proxy measure distancing, and here, we characterise relationship between mobility for 52 around world. Transmission significantly decreased with initial reduction in 73% analysed, but found evidence decoupling following relaxation strict measures 80%...
Age-specific contact How can the resurgent epidemics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during 2020 be explained? Are they a result students going back to school? To address this question, Monod et al. created matrix for infection based on data collected in Europe and China extended it United States. Early pandemic, before interventions were widely implemented, contacts concentrated among individuals similar age highest school-aged children, between children...
Summary Background A range of case fatality ratio (CFR) estimates for COVID-19 have been produced that differ substantially in magnitude. Methods We used individual-case data from mainland China and cases detected outside to estimate the time between onset symptoms outcome (death or discharge hospital). next obtained age-stratified CFR by relating aggregate distribution dates observed cumulative deaths China, assuming a constant attack rate age adjusting demography population, age-...
WHO has called for increased testing in response to the COVID-19 pandemic, but countries have taken different approaches and effectiveness of alternative strategies is unknown. We aimed investigate potential impact isolation on transmission severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
Abstract As of 1st June 2020, the US Centres for Disease Control and Prevention reported 104,232 confirmed or probable COVID-19-related deaths in US. This was more than twice number next most severely impacted country. We jointly model epidemic at state-level, using publicly available death data within a Bayesian hierarchical semi-mechanistic framework. For each state, we estimate individuals that have been infected, are currently infectious time-varying reproduction (the average secondary...
A SARS-CoV-2 transmission model fitted to surveillance data estimates virus transmissibility, infection severity, and the impact of interventions.
<ns4:p><ns4:bold>Background</ns4:bold>: The COVID-19 epidemic was declared a Global Pandemic by WHO on 11 March 2020. By 24 2020, over 440,000 cases and almost 20,000 deaths had been reported worldwide. In response to the fast-growing epidemic, which began in Chinese city of Wuhan, Hubei, China imposed strict social distancing Wuhan 23 January 2020 followed closely similar measures other provinces. These interventions have impacted economic productivity China, ability economy resume without...
Following the emergence of a novel coronavirus (SARS-CoV-2) and its spread outside China, Europe has experienced large epidemics. In response, many European countries have implemented unprecedented non-pharmaceutical interventions including case isolation, closure schools universities, banning mass gatherings and/or public events, most recently, wide-scale social distancing local national lockdowns. this technical update, we extend semi-mechanistic Bayesian hierarchical model that infers...
BackgroundInternational and global organisations advocate targeting interventions to areas of high HIV prevalence (ie, hotspots). To better understand the potential benefits geo-targeted control, we assessed extent which hotspots along Lake Victoria sustain transmission in neighbouring populations south-central Uganda.MethodsWe did a population-based survey Rakai, Uganda, using data from Rakai Community Cohort Study. The study surveyed all individuals aged 15–49 years four high-prevalence...
<ns4:p><ns4:bold>Background</ns4:bold>: The COVID-19 epidemic was declared a Global Pandemic by WHO on 11 March 2020. By 24 2020, over 440,000 cases and almost 20,000 deaths had been reported worldwide. In response to the fast-growing epidemic, which began in Chinese city of Wuhan, Hubei, China imposed strict social distancing Wuhan 23 January 2020 followed closely similar measures other provinces. These interventions have impacted economic productivity China, ability economy resume without...
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Gamma variant of concern has spread rapidly across Brazil since late 2020, causing substantial infection and death waves. Here we used individual-level patient records after hospitalization with suspected or confirmed disease 2019 (COVID-19) between 20 January 2020 26 July 2021 to document temporary, sweeping shocks in hospital fatality rates that followed the 14 state capitals, during which typically more than half...
Italy was the first European country to experience sustained local transmission of COVID-19. As 1st May 2020, Italian health authorities reported 28,238 deaths nationally. To control epidemic, government implemented a suite non-pharmaceutical interventions (NPIs), including school and university closures, social distancing full lockdown involving banning public gatherings non essential movement. In this report, we model effect NPIs on using data average mobility. We estimate that...
Abstract As of 1st June 2020, the US Centers for Disease Control and Prevention reported 104,232 confirmed or probable COVID-19-related deaths in US. This was more than twice number next most severely impacted country. We jointly modelled epidemic at state-level, using publicly available death data within a Bayesian hierarchical semi-mechanistic framework. For each state, we estimate individuals that have been infected, are currently infectious time-varying reproduction (the average...
Abstract HIV incidence in eastern and southern Africa has historically been concentrated among girls women aged 15–24 years. As new cases decline with interventions, population-level infection dynamics may shift by age gender. Here, we integrated population-based surveillance of 38,749 participants the Rakai Community Cohort Study longitudinal deep-sequence viral phylogenetics to assess how population groups driving transmission have changed from 2003 2018 Uganda. We observed 1,117...
People living with HIV can acquire secondary infections through a process called superinfection, giving rise to simultaneous infection genetically distinct variants (multiple infection). Multiple provides the necessary conditions for generation of novel recombinant forms and may worsen clinical outcomes increase rate transmission seronegative sexual partners. To date, studies multiple have relied on insensitive bulk-sequencing, labor intensive single genome amplification protocols, or...
1 Abstract Brazil is currently reporting the second highest number of COVID-19 deaths in world. Here we characterise initial dynamics across country and assess impact non-pharmaceutical interventions (NPIs) that were implemented using a semi-mechanistic Bayesian hierarchical modelling approach. Our results highlight significant these NPIs had states, reducing an average R t > 3 to 1.5 by 9-May-2020, but failed reduce < 1, congruent with worsening epidemic has experienced since. We...
Abstract HIV incidence in eastern and southern Africa has historically been concentrated among girls women aged 15-24 years. As new cases decline with interventions, population-level infection dynamics may shift by age gender. Here, we integrated population-based surveillance of 38,749 participants the Rakai Community Cohort Study longitudinal deep sequence viral phylogenetics to assess how population groups driving transmission have changed from 2003 2018 Uganda. We observed 1,117...
Analysis of genetic sequence data from the SARS-CoV-2 pandemic can provide insights into epidemic origins, worldwide dispersal, and epidemiological history. With few exceptions, genomic analysis has focused on geographically distributed sets with isolates in any given location. Here, we report an 20 whole SARS- CoV-2 genomes a single relatively small constrained outbreak Weifang, People's Republic China. Using Bayesian model-based phylodynamic methods, estimate mean basic reproduction number (
Abstract We fitted a model of SARS-CoV-2 transmission in care homes and the community to regional surveillance data for England. Among control measures implemented, only national lockdown brought reproduction number below 1 consistently; introduced one week earlier it could have reduced first wave deaths from 36,700 15,700 (95%CrI: 8,900–26,800). Improved clinical infection fatality ratio 1.25% 1.18%–1.33%) 0.77% 0.71%–0.84%). The was higher elderly residing (35.9%, 95%CrI: 29.1%–43.4%) than...
Across sub-Saharan Africa, key populations with elevated HIV-1 incidence and/or prevalence have been identified, but their contribution to disease spread remains unclear. We performed viral deep-sequence phylogenetic analyses quantify transmission dynamics between the general population (GP), fisherfolk communities (FF), and women at high risk of infection clients (WHR) in central southwestern Uganda. Between August 2014 2017, 6185 positive individuals were enrolled 3 GP 10 FF communities,...