Respiratory Pathogens

Evaluating COVID-19 reporting data in the context of testing strategies across 31 LMICs

Background COVID-19 case counts are the predominant measure used to track epidemiological dynamics and inform policy decision-making. Case counts, however, are influenced by testing rates and strategies, which have varied over time and space. A method to consistently interpret COVID-19 case counts in the context of other surveillance data is needed, especially for data-limited settings…
Slight reduction in SARS-CoV-2 exposure viral load due to masking results in a significant reduction in transmission with widespread implementation

Masks are a vital tool for limiting SARS-CoV-2 spread in the population. Here we utilize a mathematical model to assess the impact of masking on transmission within individual transmission pairs and at the population level. Our model quantitatively links mask efficacy to reductions in viral load and subsequent transmission risk. Our results reinforce that the…
Evaluating COVID-19 reporting data in the context of testing strategies across 31 low- and middle-income countries

Background The case count for coronavirus disease 2019 (COVID-19) is the predominant measure used to track epidemiological dynamics and inform policy decision-making. Case counts, however, are influenced by testing rates and strategies, which have varied over time and space. A method to interpret COVID-19 case counts consistently in the context of other surveillance data is…
Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State

The rapid spread of SARS-CoV-2 has gravely impacted societies around the world. Outbreaks in different parts of the globe are shaped by repeated introductions of new lineages and subsequent local transmission of those lineages. Here, we sequenced 3940 SARS-CoV-2 viral genomes from Washington State to characterize how the spread of SARS-CoV-2 in Washington State (USA)…
Examination of scenarios introducing rubella vaccine in the Democratic Republic of the Congo

Background Rubella vaccine has yet to be introduced into the national immunization schedule of the Democratic Republic of the Congo (DRC); the current burden of congenital rubella syndrome (CRS) is unknown and likely to be high. An important consideration prior to introducing rubella containing vaccine (RCV) is the potential inverse relationship between RCV coverage and…
Insights into population behavior during the COVID-19 pandemic from cell phone mobility data and manifold learning

Understanding the complex interplay between human behavior, disease transmission and non-pharmaceutical interventions during the COVID-19 pandemic could provide valuable insights with which to focus future public health efforts. Cell phone mobility data offer a modern measurement instrument to investigate human mobility and behavior at an unprecedented scale. We investigate aggregated and anonymized mobility data, which…
Mathematical modelling of respiratory syncytial virus (RSV) in low- and middle-income countries: a systematic review

Background Due to high burden of respiratory syncytial virus (RSV) in low- and middle-income countries (LMIC), international funding organizations have prioritized the development of RSV vaccines. Mathematical models of RSV will play an important role in assessing the relative value of these interventions. Our objectives were to provide an overview of the existing RSV modelling…
Mechanistic modeling of SARS-CoV-2 immune memory, variants, and vaccines

Early waves of the SARS-CoV-2 pandemic were driven by importation events and subsequent policy responses. However, epidemic dynamics in 2021 are largely driven by the spread of more transmissible and/or immune-evading variants, which in turn are countered by vaccination programs. Here we describe updates to the methodology of Covasim (COVID-19 Agent-based Simulator) to account for…
Modelling the impact of reopening schools in the UK in early 2021 in the presence of the alpha variant and with roll-out of vaccination against SARS-CoV-2

Background Following the resurgence of the COVID-19 epidemic in the UK in late 2020 and the emergence of the alpha (also known as B117) variant of the SARS-CoV-2 virus, a third national lockdown was imposed from January 4, 2021. Following the decline of COVID-19 cases over the remainder of January 2021, the question of when…
Modelling the potential impact of mask use in schools and society on COVID-19 control in the UK

As the UK reopened after the first wave of the COVID-19 epidemic, crucial questions emerged around the role for ongoing interventions, including test-trace-isolate (TTI) strategies and mandatory masks. Here we assess the importance of masks in secondary schools by evaluating their impact over September 1–October 23, 2020. We show that, assuming TTI levels from August…