Introduction: COVID-19-associated mortality remains difficult to estimate in sub-Saharan Africa because of the lack of comprehensive systems of death registration. Based on death registers referring to the capital city of Madagascar, we sought to estimate the excess mortality during the COVID-19 pandemic and calculate the loss of life expectancy.
Methods: Death records between 2016 and 2021 were used to estimate weekly excess mortality during the pandemic period.
As the national reference laboratory for febrile illness in Madagascar, we processed samples from the first epidemic wave of COVID-19, between March and September 2020. We fit generalized additive models to cycle threshold (C) value data from our RT-qPCR platform, demonstrating a peak in high viral load, low-C value infections temporally coincident with peak epidemic growth rates estimated in real time from publicly-reported incidence data and retrospectively from our own laboratory testing data across three administrative regions. We additionally demonstrate a statistically significant effect of duration of time since infection onset on C value, suggesting that C value can be used as a biomarker of the stage at which an individual is sampled in the course of an infection trajectory.
View Article and Find Full Text PDFAs the national reference laboratory for febrile illness in Madagascar, we processed samples from the first epidemic wave of COVID-19, between March and September 2020. We fit generalized additive models to cycle threshold (C ) value data from our RT-qPCR platform, demonstrating a peak in high viral load, low-C value infections temporally coincident with peak epidemic growth rates estimated in real time from publicly-reported incidence data and retrospectively from our own laboratory testing data across three administrative regions. We additionally demonstrate a statistically significant effect of duration of time since infection onset on C value, suggesting that C value can be used as a biomarker of the stage at which an individual is sampled in the course of an infection trajectory.
View Article and Find Full Text PDFInfluenza Other Respir Viruses
July 2021
Background: Following the first detection of SARS-CoV-2 in passengers arriving from Europe on 19 March 2020, Madagascar took several mitigation measures to limit the spread of the virus in the country.
Methods: Nasopharyngeal and/or oropharyngeal swabs were collected from travellers to Madagascar, suspected SARS-CoV-2 cases and contact of confirmed cases. Swabs were tested at the national reference laboratory using real-time RT-PCR.
Objectives: Quantitative estimates of the impact of infectious disease outbreaks are required to develop measured policy responses. In many low- and middle-income countries, inadequate surveillance and incompleteness of death registration are important barriers.
Design: Here, we characterize how large an impact on mortality would have to be for being detectable using the uniquely detailed mortality notification data from the city of Antananarivo, Madagascar, with application to a recent measles outbreak.