Using excess deaths and testing statistics to improve estimates of COVID-19 mortalities

Böttcher, Lucas; D’Orsogna, Maria R.; Chou, Tom

doi:10.1101/2021.01.10.21249524

Cited by 5 publications

(7 citation statements)

References 29 publications

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“…Previous studies have positively associated neuroticism, extroversion, and kindness with the perceived cost of complying with preventive measures, while awareness showed a negative association [59]. It has been proposed that, in countries where there are no reliable indicators to measure the number of people infected and dead by COVID-19, as is the case in many Latin American countries, the relative excess of deaths over the time period should be used as a more reliable indicator of the development of the disease [5].…”

Section: Discussionmentioning

confidence: 99%

“…Latin America has overcome major recent health challenges such as Zika, but they were not as lethal as the current COVID-19, the Coronavirus Disease 2019 caused by SARS-CoV-2, with high rates of subclinical infections and inconsistent and insufficient diagnostic tests detected, making it difficult to know the actual number of people infected [4]. Analyzing deaths during 2020 in Peru, Ecuador, Mexico, and Spain, there were significantly greater excess deaths than the ones recorded for COVID-19, something that has not happened in Denmark, Germany, or Norway [5]. By the end of February 2020, Brazil became the first Latin American country to report the first case of COVID-19, followed by Ecuador, Argentina, and Chile.…”

Section: Introductionmentioning

confidence: 99%

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Effects of the COVID-19 Pandemic on Mental Health in Peru: Psychological Distress

et al. 2021

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This pandemic has been classified as a “psychological pandemic” that produces anxiety, depression, post-traumatic stress disorder, and sleep disorders. As the mental health effects of the Coronavirus Disease 2019 (COVID-19), caused by SARS-CoV-2, continue to unfold, there are still large knowledge gaps about the variables that predispose individuals to, or protect individuals against the disease. However, there are few publications on the effects of the COVID-19 pandemic on the mental health of citizens in Latin American countries. In this study, the effects that COVID-19 had on citizens of Peru have been described. For this, 1699 questionnaires, collected between 2 April and 2 September 2020, were analyzed. Descriptive, bivariate analysis was performed with odds ratio (OR) calculations and a data mining methodology. Sociodemographic variables (from the General Health Questionnaire), health conditions and perception, symptoms, and variables related to contact and preventive measures regarding COVID-19 were analyzed. As compared to other countries, less affectation of mental health and increased use of preventive measures were observed. It has been suggested that the country’s precarious health system and poverty rates prior to the pandemic may justify higher mortality figures in Peru than in other Latin American countries, despite prompt action for its containment and compliance with the protective measures. Psychological distress had a greater incidence in women, young people, people without a partner, and people without university studies. The most significant conditioning variables were self-perceived health status, headache or muscle pain over the past 14 days, level of studies, and age. The extensive use of preventive measures against COVID-19 is in line with the strict legislative measures taken, and this is, in turn, in line with other countries when looking at the lower effect on mental health, but contrary when focusing on the high lethality identified. The need to include the economy or availability and quality of healthcare in future studies arises, as well as the suitability to analyze the cause for differences between countries.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Effects of the COVID-19 Pandemic on Mental Health in Peru: Psychological Distress

et al. 2021

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“…For each infected compartment I, I , and I , we calculate the infection fatality ratios (IFRs) [3] by dividing the associated cumulative number of deaths by the total number of infections in the unvaccinated, prime-vaccinated, and prime-boost-vaccinated compartments, respectively. The IFR of the unvaccinated pool of individuals is…”

Section: Data and Code Availabilitymentioning

confidence: 99%

“…As of June 28, 2021, the number of confirmed COVID-19 cases exceeded 180 million and more than 3.9 million COVID-19 deaths in more than 219 countries were reported [2]. Large differences between excess deaths and reported COVID-19 deaths across different countries suggest that the actual death toll associated with COVID-19 is even higher [3].…”

Section: Introductionmentioning

confidence: 99%

Decisive Conditions for Strategic Vaccination against SARS-CoV-2

Böttcher

Nagler

2021

Preprint

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While vaccines that protect against SARS-CoV-2 are being approved, the number of available doses remains limited. As it may take months until the production of vaccines can meet the actual demand, the majority of available SARS-CoV-2 vaccines elicits strong immune responses when administered as prime-boost regimens. Since the immunological response to the first ('prime') injection may provide already a substantial degree of protection against infection, it may be more effective---under certain conditions---to vaccinate as many people as possible with only one shot, instead of administering a person a second ('boost') shot. Such a strategic vaccination campaign may help to more effectively slow down the spread of SARS-CoV-2, reduce hospitalizations, and reduce deaths. Yet, the conditions which make single-dose vaccination favourable over prime-boost administrations are not well understood. Here, we formulate a model that helps explore these decisive conditions as a function of the various time scales and epidemiological mechanisms at work. We study how these conditions arise from disease prevalence, vaccination rates, basic reproduction number, prime and prime-boost efficacies, prime-boost intervals, and waning rates. By combining epidemiological modeling, random sampling techniques, and decision tree learning, we find that prime-first vaccination is robustly favored over prime-boost vaccination campaigns, even for high vaccination rates, high disease prevalence, and a relatively low single-dose efficacy.

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“…Estimates of disease prevalence and other surveillance metrics [14,15] need to account for FPRs and FNRs, in particular if reported positive-testing rates [16] are in the few percent range and potentially dominated by type I errors. In addition to type-I/II testing errors, another confounding effect is biased testing [17], that is, preferential testing of individuals that are expected to carry a high viral load ( e.g ., symptomatic and hospitalized individuals).…”

Section: Introductionmentioning

confidence: 99%

A statistical model of COVID-19 testing in populations: effects of sampling bias and testing errors

Böttcher

D’Orsogna

Chou

2021

Preprint

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We develop a statistical model for the testing of disease prevalence in a population. The model assumes a binary test result, positive or negative, but allows for biases in sample selection and both type I (false positive) and type II (false negative) testing errors. Our model also incorporates multiple test types and is able to distinguish between retesting and exclusion after testing. Our quantitative framework allows us to directly interpret testing results as a function of errors and biases. By applying our testing model to COVID-19 testing data and actual case data from specific jurisdictions, we are able to estimate and provide uncertainty quantification of indices that are crucial in a pandemic, such as disease prevalence and fatality ratios.

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Using excess deaths and testing statistics to improve estimates of COVID-19 mortalities

Cited by 5 publications

References 29 publications

Effects of the COVID-19 Pandemic on Mental Health in Peru: Psychological Distress

Effects of the COVID-19 Pandemic on Mental Health in Peru: Psychological Distress

Decisive Conditions for Strategic Vaccination against SARS-CoV-2

A statistical model of COVID-19 testing in populations: effects of sampling bias and testing errors

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