An indirect method to monitor the fraction of people ever infected with COVID-19: An application to the United States

Accounting for assay performance when estimating the temporal dynamics in SARS-CoV-2 seroprevalence in the U.S

Reconstructing the incidence of SARS-CoV-2 infection is central to understanding the state of the pandemic. Seroprevalence studies are often used to assess cumulative infections as they can identify asymptomatic infection. Since July 2020, commercial laboratories have conducted nationwide serosurveys for the U.S. CDC. They employed three assays, with different sensitivities and specificities, potentially introducing biases in seroprevalence estimates. Using models, we show that accounting for assays explains some of the observed state-to-state variation in seroprevalence, and when integrating case and death surveillance data, we show that when using the Abbott assay, estimates of proportions infected can differ substantially from seroprevalence estimates. We also found that states with higher proportions infected (before or after vaccination) had lower vaccination coverages, a pattern corroborated using a separate dataset. Finally, to understand vaccination rates relative to the increase in cases, we estimated the proportions of the population that received a vaccine prior to infection.

Evolution of the lethality due to SARS-CoV-2 in Spain according to age group and sex

The emergence of SARS-CoV-2 in China in December 2019 has posed a major challenge to health systems in all countries around the world. One of the most relevant epidemiological measures to consider during the course of a pandemic is the proportion of cases that eventually die from the disease (case fatality ratio, CFR). Monitoring the evolution of this indicator is of paramount importance because it allows for the assessment of both variations in the lethality of the virus and the effectiveness of the control measures implemented by health authorities. One of the problems with estimating the CFR in practice is that the available data only show daily or weekly counts of new cases and deaths; there is no information on when each deceased patient was infected and therefore it is not possible to know exactly how many cases there were at the time the patient became infected. Various approaches have been proposed for calculating the CFR by correcting for the time lag between infection and death. In this paper, we present a novel methodology to perform a non-parametric estimation of the evolution of the CFR by initially identifying an optimal time lag between infections and deaths. The goodness of this procedure is assessed by means of a simulation study and the method is applied to the estimation of the CFR in Spain in the period from July 2020 to March 2022.

The impact of COVID-19 vaccines on the Case Fatality Rate: The importance of monitoring breakthrough infections

Objectives

This study aimed to test the behavior of the case fatality rate (CFR) in a mixed population of vaccinated and unvaccinated individuals by illustrating the role of both the effectiveness of vaccines in preventing deaths and the detection of infections among both the vaccinated (breakthrough infections) and unvaccinated individuals.

Methods

We simulated three hypothetical CFR scenarios that resulted from a different combination of vaccine effectiveness in preventing deaths and the efforts in detecting infections among both the vaccinated and unvaccinated individuals.

Results

In the presence of vaccines, the CFR depends not only on the effectiveness of vaccines in preventing deaths but also on the detection of breakthrough infections. As a result, a decline in the CFR may not imply that vaccines are effective in reducing deaths. Likewise, a constant CFR can still mean that vaccines are effective in reducing deaths.

Conclusions

Unless vaccinated people are also tested for COVID-19 infection, the CFR loses its meaning in tracking the pandemic. This shows that unless efforts are directed at detecting breakthrough infections, it is hard to disentangle the effect of vaccines in reducing deaths from the probability of detecting infections on the CFR.

Model based estimation of the SARS-CoV-2 immunization level in austria and consequences for herd immunity effects

Several systemic factors indicate that worldwide herd immunity against COVID-19 will probably not be achieved in 2021. On the one hand, vaccination programs are limited by availability of doses and on the other hand, the number of people already infected is still too low to have a disease preventing impact and new emerging variants of the virus seem to partially neglect developed antibodies from previous infections. Nevertheless, by February 2021 after one year of observing high numbers of reported COVID-19 cases in most European countries, we might expect that the immunization level should have an impact on the spread of SARS-CoV-2. Here we present an approach for estimating the immunization of the Austrian population and discuss potential consequences on herd immunity effects. To estimate immunization we use a calibrated agent-based simulation model that reproduces the actual COVID-19 pandemic in Austria. From the resulting synthetic individual-based data we can extract the number of immunized persons. We then extrapolate the progression of the epidemic by varying the obtained level of immunization in simulations of an hypothetical uncontrolled epidemic wave indicating potential effects on the effective reproduction number. We compared our theoretical findings with results derived from a classic differential equation SIR-model. As of February 2021, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$14.7\%$$\end{document}14.7% of the Austrian population has been affected by a SARS-CoV-2 infection which causes a \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$9\%$$\end{document}9% reduction of the effective reproduction number and a \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$24.7\%$$\end{document}24.7% reduction of the prevalence peak compared to a fully susceptible population. This estimation is now recomputed on a regular basis to publish model based analysis of immunization level in Austria also including the fast growing effects of vaccination programs. This provides substantial information for decision makers to evaluate the necessity of non pharmaceutical intervention measures based on the estimated impact of natural and vaccinated immunization.

Three waves changes, new variant strains, and vaccination effect against COVID-19 pandemic

It has been more than one year since the first case of the coronaviruses was infected by COVID-19 in China. The world witnessed three waves of the corona virus till now, and more upcoming is expected, whereas several challenges are presented. Empirical data displayed that the features of the virus effects do vary between the three periods. The severity of the disease, differences in symptoms, attitudes of the people have been reported, although the comparative characteristics of the three waves still keep essentially indefinite. In contrast, the sense of danger toward the cries gradually decreases in most countries. This may be due to some factors, including the approved vaccines, introducing alternative plans from politicians to control and deal with the epidemic, and decreasing the mortality rates. However, the alarm voice started to rise again with the appearance of new variant strains with several mutations in the virus. Several more questions began to be asked without sufficient answers. Mutations in COVID-19 have introduced an extreme challenge in preventing and treating SARS-COV-2. The essential feature for mutations is producing new variants known by high tensmibility, disturbing the viral fitness, and enhancing the virus replication. One of the variants that has emerged recently is the Delta variant (B.1.617.2), which was firstly detected in India. In November 2021, a more ferocious mutant appeared in South Africa, also called omicron (B.1.1.529). These mutants grabbed world attention because of their higher transmissibility than the progenitor variants and spread rapidly. Several information about the virus are still confusing and remains secret. There are eight approved vaccines in the market; however, the investigation race about their effect against reinfection and their role against the new variants is still under investigation. Furthermore, this is the first time vaccinating against COVID-19, so the question remains: Will we need an annual dose of the corona vaccines, and the side effects don't been observed till now?

SARS-CoV-2 infections in 165 countries over time

BACKGROUND

Understanding the dynamics of the COVID-19 pandemic and evaluating the efficacy of control measures requires knowledge of the number of infections over time. This number, however, often differs from the number of confirmed cases because of a large fraction of asymptomatic infections and different testing strategies.

METHODS

This study uses death count statistics, age-dependent infection fatality risks, and stochastic modeling to estimate the prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections among adults (aged 20 years or older) in 165 countries over time, from early 2020 until June 25, 2021. The accuracy of the approach is confirmed through comparison with previous nationwide seroprevalence surveys.

RESULTS

The estimates presented reveal that the fraction of infections that are detected vary widely over time and between countries, and hence confirmed cases alone often yield a false picture of the pandemic. As of June 25, 2021, the nationwide cumulative fraction of SARS-CoV-2 infections (cumulative infections relative to population size) was estimated as 98% (95% confidence interval [CI] 93-100%) for Peru, 83% (95% CI 61-94%) for Brazil, and 36% (95% CI 23-61%) for the United States.

CONCLUSIONS

The time-resolved estimates presented expand the possibilities to study the factors that influenced and still influence the pandemic's progression in 165 countries.

Underdetection in a stochastic SIR model for the analysis of the COVID-19 Italian epidemic

We propose a way to model the underdetection of infected and removed individuals in a compartmental model for estimating the COVID-19 epidemic. The proposed approach is demonstrated on a stochastic SIR model, specified as a system of stochastic differential equations, to analyse data from the Italian COVID-19 epidemic. We find that a correct assessment of the amount of underdetection is important to obtain reliable estimates of the critical model parameters. The adaptation of the model in each time interval between relevant government decrees implementing contagion mitigation measures provides short-term predictions and a continuously updated assessment of the basic reproduction number.

Reducing COVID-19 Cases and Deaths by Applying Blockchain in Vaccination Rollout Management

Goal: Because a fast vaccination rollout against coronavirus disease 2019 (COVID-19) is critical to restore daily life and avoid virus mutations, it is tempting to have a relaxed vaccination-administration management system. However, a rigorous management system can support the enforcement of preventive measures, and in turn, reduce incidence and deaths. Here, we model a trustable and reliable management system based on blockchain for vaccine distribution by extending the Susceptible-Exposed-Infected-Recovery (SEIR) model. The model includes prevention measures such as mask-wearing, social distancing, vaccination rate, and vaccination efficiency. It also considers negative social behavior, such as violations of social distance and attempts of using illegitimate vaccination proofs. By evaluating the model, we show that the proposed system can reduce up to 2.5 million cases and half a million deaths in the most demanding scenarios.

Detectable SARS-CoV-2 RNAemia in Critically Ill Patients, but Not in Mild and Asymptomatic Infections

Background

The SARS-CoV-2 pandemic has challenged many of our current routine practices in the treatment and care of patients. Given the critical importance of blood donation and transfusion we analyzed 92 blood samples of individuals infected with SARS-CoV-2 stratified by symptoms.

Study Design and Methods

We therefore tested blood samples for SARS-CoV-2 via RT-PCR targeting the E gene. In addition, we tested each blood sample for anti-SARS-CoV-2 IgG antibodies via ELISA and performed plaque reduction neutralization tests.

Results

SARS-CoV-2 RNA was absent in the blood of mild to asymptomatic patients (57 individuals) and only detectable in individuals with severe COVID-19 who were admitted to the intensive care unit (35 individuals) (n = 6/92 [6.5%]; p = 0.023 Fisher's exact test). Interestingly, anti-spike IgG antibodies were not significantly higher in intensive care unit patients compared to mild patients, but we found that their neutralizing capacity was disproportionately increased (p < 0.001).

Conclusion

Our observations support the hypothesis that there are no potential hazards from blood or plasma transfusion of SARS-CoV-2-positive individuals with mild flu-like symptoms and more importantly of asymptomatic individuals.