Respiratory Pathogens

Clinical management and mortality among COVID-19 cases in sub-Saharan Africa: A retrospective study from Burkina Faso and simulated case analysis

Background Absolute numbers of COVID-19 cases and deaths reported to date in the sub-Saharan Africa (SSA) region have been significantly lower than those across the Americas, Asia and Europe. As a result, there has been limited information about the demographic and clinical characteristics of deceased cases in the region, as well as the impacts of…
Modelling the impact of relaxing COVID-19 control measures during a period of low viral transmission

Objectives To assess the risks associated with relaxing coronavirus disease 2019 (COVID-19)-related physical distancing restrictions and lockdown policies during a period of low viral transmission. Design Network-based viral transmission risks in households, schools, workplaces, and a variety of community spaces and activities were simulated in an agent-based model, Covasim. Setting The model was calibrated for…
Modeling the economic impact of different vial-opening thresholds for measles-containing vaccines

Introduction: The lack of specific policies on how many children must be present at a vaccinating location before a healthcare worker can open a measles-containing vaccine (MCV) – i.e. the vial-opening threshold – has led to inconsistent practices, which can have wide-ranging systems effects. Methods: Using HERMES-generated simulation models of the routine immunization supply chains…
Identifying transmission routes of Streptococcus pneumoniae and sources of acquisitions in high transmission communities

Identifying the transmission sources and reservoirs of Streptococcus pneumoniae (SP) is a long-standing question for pneumococcal epidemiology, transmission dynamics, and vaccine policy. Here we use serotype to identify SP transmission and examine acquisitions (in the same household, local community, and county, or of unidentified origin) in a longitudinal cohort of children and adults from the…
Epidemiological and Economic Effects of Priming With the Whole-Cell Bordetella pertussis Vaccine

Importance: Current acellular pertussis vaccines may not protect against transmission of Bordetella pertussis. Objective: To assess whether a priming dose of whole-cell pertussis (wP) vaccine is cost-effective at reducing pertussis infection in infants. Design, Setting, and Participants: Mathematical model of pertussis transmission fit to US incidence data in a simulation of the US population. In…
Extracting transmission networks from phylogeographic data for epidemic and endemic diseases: Ebola virus in Sierra Leone, 2009 H1N1 pandemic influenza and polio in Nigeria

Background Phylogeography improves our understanding of spatial epidemiology. However, application to practical problems requires choices among computational tools to balance statistical rigor, computational complexity, sensitivity to sampling strategy and interpretability. Methods We introduce a fast, heuristic algorithm to reconstruct partially-observed transmission networks (POTN) that combines features of phylogenetic and transmission tree approaches. We compare the…
Asymptomatic transmission and the resurgence of Bordetella pertussis

Background The recent increase in whooping cough incidence (primarily caused by Bordetella pertussis) presents a challenge to both public health practitioners and scientists trying to understand the mechanisms behind its resurgence. Three main hypotheses have been proposed to explain the resurgence: 1) waning of protective immunity from vaccination or natural infection over time, 2) evolution…

Respiratory Pathogens

Clinical management and mortality among COVID-19 cases in sub-Saharan Africa: A retrospective study from Burkina Faso and simulated case analysis

Modelling the impact of relaxing COVID-19 control measures during a period of low viral transmission

Modeling the economic impact of different vial-opening thresholds for measles-containing vaccines

Identifying transmission routes of Streptococcus pneumoniae and sources of acquisitions in high transmission communities

Epidemiological and Economic Effects of Priming With the Whole-Cell Bordetella pertussis Vaccine

Extracting transmission networks from phylogeographic data for epidemic and endemic diseases: Ebola virus in Sierra Leone, 2009 H1N1 pandemic influenza and polio in Nigeria

Asymptomatic transmission and the resurgence of Bordetella pertussis