COVID-19 deaths detected in a systematic post-mortem surveillance study in Africa

Mwananyanda, Lawrence; Gill, Christopher J.; MacLeod, W. Bentley; Kwenda, Geoffrey; Pieciak, Rachel; Mupila, Zachariah; Mupeta, Francis; Forman, Leah S; Ziko, Luunga; Etter, Lauren; Thea, Donald M

doi:10.1101/2020.12.22.20248327

Cited by 22 publications

(27 citation statements)

References 27 publications

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“…Countries in Africa also appeared to have a delayed first wave [ 26 ], with younger age, cross-reactive immunity, previous vaccinations or experience with prior epidemics all invoked as possible causes. However, several studies indicate that insufficient data represent a major explanation [ 27 , 28 , 29 ], with data on excess mortality from funeral houses or burials demonstrating the significant under-ascertainment of deaths. In Venezuela, official data are hard to come by.…”

Section: Discussionmentioning

confidence: 99%

Signatures of the Venezuelan Humanitarian Crisis in the First Wave of COVID-19: Fuel Shortages and Border Migration

et al. 2021

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Testing and isolation have been crucial for controlling the COVID-19 pandemic. Venezuela has one of the weakest testing infrastructures in Latin America and the low number of reported cases in the country has been attributed to substantial underreporting. However, the Venezuelan epidemic seems to have lagged behind other countries in the region, with most cases occurring within the capital region and four border states. Here, we describe the spatial epidemiology of COVID-19 in Venezuela and its relation to the population mobility, migration patterns, non-pharmaceutical interventions and fuel availability that impact population movement. Using a metapopulation model of SARS-CoV-2 transmission dynamics, we explore how movement patterns could have driven the observed distribution of cases. Low within-country connectivity most likely delayed the onset of the epidemic in most states, except for those bordering Colombia and Brazil, where high immigration seeded outbreaks. NPIs slowed early epidemic growth and subsequent fuel shortages appeared to be responsible for limiting the spread of COVID-19 across the country.

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Section: Discussionmentioning

confidence: 99%

Signatures of the Venezuelan Humanitarian Crisis in the First Wave of COVID-19: Fuel Shortages and Border Migration

et al. 2021

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“…The population prevalence of infectious SARS-CoV-2 is estimated as the average reported number of daily new cases of COVID-19 multiplied by the average duration of the infectious period (in days) divided by the adult population size. While new daily cases are likely to be under-reported [16] leading to an under-estimate of new COVID-19 cases, we also calculate the COVID-19 mortality rate from the reported COVID-19 cases and deaths so that the two measures will be consistent.…”

Section: Contact Modelmentioning

confidence: 99%

The Risks and Benefits of Providing HIV Services during the COVID-19 Pandemic

Stover

Kelly

Mudimu

et al. 2021

Preprint

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Introduction The COVID-19 pandemic has caused widespread disruptions including to health services. In the early response to the pandemic many countries restricted population movements and some health services were suspended or limited. In late 2020 and early 2021 some countries re-imposed restrictions. Health authorities need to balance the potential harms of additional SARS-CoV-2 transmission due to contacts associated with health services against the benefits of those services, including fewer new HIV infections and deaths. This paper examines these trade-offs for select HIV services. Methods We used four HIV simulation models (Goals, HIV Synthesis, Optima HIV and EMOD) to estimate the benefits of continuing HIV services in terms of fewer new HIV infections and deaths. We used three COVID-19 transmission models (Covasim, Cooper/Smith and a simple contact model) to estimate the additional deaths due to SARS-CoV-2 transmission among health workers and clients. We examined four HIV services: voluntary medical male circumcision, HIV diagnostic testing, viral load testing and programs to prevent mother-to-child transmission. We compared COVID-19 deaths in 2020 and 2021 with HIV deaths occurring now and over the next 50 years discounted to present value. The models were applied to countries with a range of HIV and COVID-19 epidemics. Results Maintaining these HIV services could lead to additional COVID-19 deaths of 0.002 to 0.15 per 10,000 clients. HIV-related deaths averted are estimated to be much larger, 19 - 146 discounted deaths per 10,000 clients. Discussion While there is some additional short-term risk of SARS-CoV-2 transmission associated with providing HIV services, the risk of additional COVID-19 deaths is at least 100 times less than the HIV deaths averted by those services. Ministries of Health need to take into account many factors in deciding when and how to offer essential health services during the COVID-19 pandemic. This work shows that the benefits of continuing key HIV services are far larger than the risks of additional SARS-CoV-2 transmission.

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“…While some of this difference can be potentially explained by a lower infection fatality ratio (IFR) for the entire population due to a lower median age (2)(3)(4), evidence suggests that at least critically ill COVID-19 African patients experience higher, not lower mortality than elsewhere (5), as plausibly expected due to weaker health infrastructure (6). News reports (7), studies using seroprevalence (8,9), PCR testing in morgues (10), as well as indirect data sources such as obituaries on social media (11) point to substantial under-ascertainment of cases and deaths in low-income countries, potentially ten-fold (suggested by excess mortality data from Egypt (12)) or even nearly hundred-fold (13) in crisis-ridden regions. While in high income countries (12) confirmed COVID-19 deaths are approximately in line with excess death statistics, in many African countries there are no reliable mortality statistics, precluding the use of excess deaths to infer the true scale of the pandemic.…”

Section: Introductionmentioning

confidence: 99%

Date of introduction and epidemiologic patterns of SARS-CoV-2 in Mogadishu, Somalia: estimates from transmission modelling of 2020 excess mortality data

Koltai

Warsame

Bashiir

et al. 2021

Preprint

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Introduction In countries with weak surveillance systems confirmed COVID-19 deaths are likely to underestimate the death toll of the pandemic. Many countries also have incomplete vital registration systems, hampering excess mortality estimation. Here, we fitted a dynamic transmission model to satellite imagery data on burial patterns in Mogadishu, Somalia during 2020 to estimate the date of introduction, transmissibility and other epidemiologic characteristics of 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 (R0) and the effect of non-pharmaceutical interventions in Mogadishu up to September 2020. Results Under the assumption that excess deaths in Mogadishu February-September 2020 were directly attributable to SARS-CoV-2 infection we arrived at median estimates of October-November 2019 for the date of introduction and low R0 estimates (1.3-1.5) stemming from the early and slow rise of excess deaths. The effect of control measures on transmissibility appeared small. Conclusion Subject to study assumptions, a very early SARS-CoV-2 introduction event may have occurred in Somalia. Estimated transmissibility in the first epidemic wave was lower than observed in European settings.

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COVID-19 deaths detected in a systematic post-mortem surveillance study in Africa

Cited by 22 publications

References 27 publications

Signatures of the Venezuelan Humanitarian Crisis in the First Wave of COVID-19: Fuel Shortages and Border Migration

Signatures of the Venezuelan Humanitarian Crisis in the First Wave of COVID-19: Fuel Shortages and Border Migration

The Risks and Benefits of Providing HIV Services during the COVID-19 Pandemic

Date of introduction and epidemiologic patterns of SARS-CoV-2 in Mogadishu, Somalia: estimates from transmission modelling of 2020 excess mortality data

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