Inferring the number of COVID-19 cases from recently reported deaths

Jombart, Thibaut; Zandvoort, Kevin van; Russell, Tim; Jarvis, Christopher I; Gimma, Amy; Abbott, Sam; Clifford, Samuel; Funk, Sebastian; Gibbs, Hamish; Liu, Yang; Pearson, Carl A. B.; Bosse, Nikos I.; Eggo, Rosalind M; Kucharski, Adam J.; Edmunds, W. John

doi:10.12688/wellcomeopenres.15786.1

Cited by 36 publications

(48 citation statements)

References 8 publications

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“…Assuming an 18 days delay from the onset of illness to death [14; 18; 19], we also estimate the number of deaths across the country and compare those to the reported numbers from the ministry of health (see Figure D.4b). This results shows that by the time the first death is reported in Iran, hundreds to perhaps thousands of cases could have been present in the population [20].…”

Section: Epidemiological Analysismentioning

confidence: 71%

Ongoing outbreak of COVID-19 in Iran: challenges and signs of concern with under-reporting of prevalence and deaths

Ghafari

Hejazi

Karshenas

et al. 2020

Preprint

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Iran was among the first group of countries with a major outbreak of COVID-19 in Asia. With nearly 100 exported cases to various other countries by Feb 25, 2020 it has since been the epicentre of the outbreak in the Middle East. By examining the age- and gender-stratified national data taken from PCR-confirmed cases and deaths related to COVID-19 on Mar 13 (reported by the Iranian ministry of health) and those taken from hospitalised patients in 14 university hospitals across Tehran on Apr 4 (reported by Tehran University of Medical Sciences), we find that the crude case fatality ratio of the two reports in those aged 60 and younger are identical and are almost 10 times higher than those reported from China, Italy, Spain and several other European countries (reported from government or ministry of health websites). Assuming a constant attack rate across all age-groups, we adjust for demography, delay from confirmation to death, and under-ascertainment of cases, to estimate the infection fatality ratio based on the reports from Mar 13. We find that our estimates are aligned with reports from China and the UK for those aged 60 and above [n=4609], but are 2-3 times higher in younger age-groups [n=6756] suggesting that only less than 10% of symptomatic cases were detected across the country at the time. Using inbound travel data (from China to Iran) and matching the dates of the flights with prevalence of cases in China from Jan to Mar 2020, we assess the risk of importation of active cases into the country. Further, using outbound travel data, based on detected cases exported from Iran to several other countries, we estimate the size of the outbreak in the country on Feb 25 and Mar 6 to be 13,700 (95% CI: 7,600 - 33,300) and 60,500 (43,200 - 209,200), respectively. We next estimate the start of the outbreak using 18 whole-genome sequences obtained from cases with a travel history to Iran and the first sequence obtained from inside the country. Finally, we use a mathematical model to predict the evolution of the epidemic and assess its burden on the healthcare system. Our modelling analysis suggests the first peak of the epidemic was on Apr 5 and the next one likely follows within the next 6-10 weeks with approximately 30,000 ICU beds required (IQR: 12K - 60K) and over 1 million active cases (IQR: 740K - 3.7M) during the peak weeks. We caution that relaxed, stringent intervention measures, during a period of highly under-reported spread, would result in misinformed public health decisions and a significant burden on the hospitals in the coming weeks.

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Section: Epidemiological Analysismentioning

confidence: 71%

Ongoing outbreak of COVID-19 in Iran: challenges and signs of concern with under-reporting of prevalence and deaths

Ghafari

Hejazi

Karshenas

et al. 2020

Preprint

View full text Add to dashboard Cite

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“…We therefore cannot assume the number of infectious cases to be directly observed: rather, we estimate it from the death count D t (see also Jombart et al [26]). Let C t be the cumulative number of (symptomatic) infectious cases.…”

Section: Observable Quantitiesmentioning

confidence: 99%

Modelling COVID-19 Contagion: Risk Assessment and Targeted Mitigation Policies

Cont

Kotlicki

2020

SSRN Journal

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We use a spatial epidemic model with demographic and geographic heterogeneity to study the regional dynamics of COVID-19 across 133 regions in England. Our model emphasises the role of variability of regional outcomes and heterogeneity across age groups and geographic locations, and provides a framework for assessing the impact of policies targeted towards sub-populations or regions. We define a concept of efficiency for comparative analysis of epidemic control policies and show targeted mitigation policies based on local monitoring to be more efficient than country-level or non-targeted measures. In particular, our results emphasise the importance of shielding vulnerable sub-populations and show that targeted policies based on local monitoring can considerably lower fatality forecasts and, in many cases, prevent the emergence of second waves which may occur under centralised policies.

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“…The authorities should have reliable estimations of the number of SARS-CoV-2 infected individuals. However, there are few attempts to estimate the total amount of infections (1)(2)(3)(4)(5). Consequently, health systems face enormous challenges since an unknown and probably a high proportion of all SARS-CoV-2 infections remains undetected.…”

Section: Introductionmentioning

confidence: 99%

“…In an attempt to solve the mentioned problem, we anchor our analysis in the cumulative number of deaths, which is a statistic much more difficult to alter, in free societies, than the number of SARS-CoV-2 tests 2 .…”

Section: Introductionmentioning

confidence: 99%

SARS-CoV-2 Infections in the World: An Estimation of the Infected Population and a Measure of How Higher Detection Rates Save Lives

Villalobos

2020

Front. Public Health

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This paper provides an estimation of the accumulated detection rates and the accumulated number of infected individuals by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Worldwide, on July 20, it has been estimated above 160 million individuals infected by SARS-CoV-2. Moreover, it is found that only about 1 out of 11 infected individuals are detected. In an information context in which population-based seroepidemiological studies are not frequently available, this study shows a parsimonious alternative to provide estimates of the number of SARS-CoV-2 infected individuals. By comparing our estimates with those provided by the populationbased seroepidemiological ENE-COVID study in Spain, we confirm the utility of our approach. Then, using a crosscountry regression, we investigated if differences in detection rates are associated with differences in the cumulative number of deaths. The hypothesis investigated in this study is that higher levels of detection of SARS-CoV-2 infections can reduce the risk exposure of the susceptible population with a relatively higher risk of death. Our results show that, on average, detecting 5 instead of 35 percent of the infections is associated with multiplying the number of deaths by a factor of about 6. Using this result, we estimated that 120 days after the pandemic outbreak, if the US would have tested with the same intensity as South Korea, about 85,000 out of their 126,000 reported deaths could have been avoided.

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Inferring the number of COVID-19 cases from recently reported deaths

Cited by 36 publications

References 8 publications

Ongoing outbreak of COVID-19 in Iran: challenges and signs of concern with under-reporting of prevalence and deaths

Ongoing outbreak of COVID-19 in Iran: challenges and signs of concern with under-reporting of prevalence and deaths

Modelling COVID-19 Contagion: Risk Assessment and Targeted Mitigation Policies

SARS-CoV-2 Infections in the World: An Estimation of the Infected Population and a Measure of How Higher Detection Rates Save Lives

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