Date of introduction and epidemiologic patterns of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Mogadishu, Somalia: estimates from transmission modelling of satellite-based excess mortality data in 2020
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Abstract
Background: In countries with weak surveillance systems, confirmed coronavirus disease 2019 (COVID-19) deaths are likely to underestimate the pandemic’s death toll. Many countries also have incomplete vital registration systems, hampering excess mortality estimation. Here, we fitted a dynamic transmission model to satellite imagery data of cemeteries in Mogadishu, Somalia during 2020 to estimate the date of introduction and other epidemiologic parameters of the early spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in this low-income, crisis-affected setting.
Methods: We performed Markov chain Monte Carlo (MCMC) fitting with an age-structured compartmental COVID-19 model to provide median estimates and credible intervals for the date of introduction, the basic reproduction number ( R 0 ) and the effect of non-pharmaceutical interventions (NPIs) up to August 2020.
Results: Under the assumption that excess deaths in Mogadishu March-August 2020 were attributable to SARS-CoV-2 infections, we arrived at median estimates of November-December 2019 for the date of introduction and low R 0 estimates (1.4-1.7) reflecting the slow and early rise and long plateau of excess deaths. The date of introduction, the amount of external seeding, the infection fatality rate (IFR) and the effectiveness of NPIs are correlated parameters and not separately identifiable in a narrow range from deaths data. Nevertheless, to obtain introduction dates no earlier than November 2019 a higher population-wide IFR (≥0.7%) had to be assumed than obtained by applying age-specific IFRs from high-income countries to Somalia’s age structure.
Conclusions: Model fitting of excess mortality data across a range of plausible values of the IFR and the amount of external seeding suggests an early SARS-CoV-2 introduction event may have occurred in Somalia in November-December 2019. Transmissibility in the first epidemic wave was estimated to be lower than in European settings. Alternatively, there was another, unidentified source of sustained excess mortality in Mogadishu from March to August 2020.
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SciScore for 10.1101/2021.06.15.21258924: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources To compute the baseline (pre-pandemic) crude death rate (CDR), population denominators for Mogadishu (Banadir region) were estimated using the WorldPop project’s database (19), using either the 2015 or 2019 estimates, while also adjusting for in- and out-displacement to/from the city (20). WorldPopsuggested: NoneResults from OddPub: Thank you for sharing your code and data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:This study has several limitations. Our model fitting of excess deaths is predicated on the strong assumption …
SciScore for 10.1101/2021.06.15.21258924: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources To compute the baseline (pre-pandemic) crude death rate (CDR), population denominators for Mogadishu (Banadir region) were estimated using the WorldPop project’s database (19), using either the 2015 or 2019 estimates, while also adjusting for in- and out-displacement to/from the city (20). WorldPopsuggested: NoneResults from OddPub: Thank you for sharing your code and data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:This study has several limitations. Our model fitting of excess deaths is predicated on the strong assumption that the unexplained rise in burials from late January 2020 was due to deaths caused by SARS-CoV-2 infection. We investigated a number of alternative hypotheses other than COVID-19 that could explain the observed excess mortality. There was an ongoing cholera epidemic in Somalia following floods since 2017 (28), resulting in 19 confirmed deaths in Banadir (mostly children) from January to October 2020. In the four weeks of 20 January to 06 February, approximately coinciding with the first transient increase of excess burials in our dataset, there were four confirmed cholera deaths in the whole of Somalia, after a preceding period of no reported deaths. In the period from 16 February to 12 April there were 8 further cholera deaths reported Somalia-wide, and another 12 deaths in June-July. These numbers are much lower than the observed increase of burials between February and October 2020: approximately 1500 excess burials were directly identified from satellite imagery and we estimated total excess deaths in Banadir to be between four and twelve thousand. While some underestimation of cholera-related deaths is possible, due to its well-identifiable pathology we consider it unlikely that a major cholera outbreak was almost entirely missed and could explain a substantial proportion of the excess mortality. The very early date of introduction estimates are due both to the...
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