Endemic Scenario Research Articles

Estimating pathogen spread using structured coalescent and birth–death models: A quantitative comparison

Elucidating disease spread between subpopulations is crucial in guiding effective disease control efforts. Genomic epidemiology and phylodynamics have emerged as key principles to estimate such spread from pathogen phylogenies derived from molecular data. Two well-established structured phylodynamic methodologies – based on the coalescent and the birth–death model – are frequently employed to estimate viral spread between populations. Nonetheless, these methodologies operate under distinct assumptions whose impact on the accuracy of migration rate inference is yet to be thoroughly investigated.In this manuscript, we present a simulation study, contrasting the inferential outcomes of the structured coalescent model with constant population size and the multitype birth–death model with a constant rate. We explore this comparison across a range of migration rates in endemic diseases and epidemic outbreaks. The results of the epidemic outbreak analysis revealed that the birth–death model exhibits a superior ability to retrieve accurate migration rates compared to the coalescent model, regardless of the actual migration rate. Thus, to estimate accurate migration rates, the population dynamics have to be accounted for. On the other hand, for the endemic disease scenario, our investigation demonstrates that both models produce comparable coverage and accuracy of the migration rates, with the coalescent model generating more precise estimates. Regardless of the specific scenario, both models similarly estimated the source location of the disease.This research offers tangible modelling advice for infectious disease analysts, suggesting the use of either model for endemic diseases. For epidemic outbreaks, or scenarios with varying population size, structured phylodynamic models relying on the Kingman coalescent with constant population size should be avoided as they can lead to inaccurate estimates of the migration rate. Instead, coalescent models accounting for varying population size or birth–death models should be favoured. Importantly, our study emphasises the value of directly capturing exponential growth dynamics which could be a useful enhancement for structured coalescent models.

Spatiality of Human Visceral Leishmaniasis in Maranhão, Brazil

Objective: the study analyzed the spatio-temporal and epidemiological behavior of HVL in the state of Maranhão, between 2010 and 2020. Theoretical framework: In Brasil, HVL is one of several diseases with compulsory notification, and is registered in 21 Federation Units, establishing itself in the five Brasilian regions. The Northeast region has the highest number of recorded cases, considered a focus of transmission of the disease, with Maranhão being one of the states with the highest occurrence. Method: the study used secondary data from the Notifiable Diseases Information System. The incidence rate, lethality rate, mortality rate, Odds Ratio and Annual Increment Rate were calculated. Results and conclusions: pointed to an endemic scenario of the disease. The predominant profile was male, aged between 1 and 9 years old, brown color/race, primary education and urban residence area. It is necessary to monitor the environment where vectors are present to control them and reduce the possibility of illness. Implications: the study is relevant as it contributes with epidemiological data and health indicators from an endemic region, so that health authorities can implement surveillance actions, health education and carry out public health interventions respecting socioeconomic differences and local environmental. Novelty: the identification of areas at risk for the disease in a given region allows us to know their spatiality, the population's chances of becoming ill and the rate of increase in the disease.

Comparative analysis of antibody responses to BNT162b2, ChAdOx1, and CoronaVac vaccines in the Albanian population over the pandemic years 2021 to 2022.

This repeated cross-sectional study with two independent sample populations compared the antibody response to severe acute respiratory syndrome coronavirus 2 vaccines in Albania in July-August 2021 and 2022. In 2021, it found higher anti-spike-1 seropositivity and antibody levels in fully vaccinated individuals, especially with BNT162b2 and ChAdOx1 and to a lesser degree with CoronaVac. By 2022, all single-dose recipients showed high antibody responses, suggesting natural infection-enhanced immunity. The study indicates a significant evolution in the antibody response to different coronavirus disease 2019 vaccines and suggests that a single vaccine dose, coupled with natural infection, might suffice to maintain adequate immunity levels in an endemic scenario.

Chagas Disease: Clinical and Epidemiological Aspects

Chagas disease is an infectious ailment classified among neglected diseases. Currently, it remains a significant contributor to endemic scenarios, acute and/or chronic complications, and mortality. The main objective of this study focuses on updating and reviewing the scientific literature on Chagas disease. Accordingly, 18 studies, including systematic reviews, mixed studies, and/or meta-analyses published between 2013 and 2023, were selected from the Scielo and PubMed research platforms. Among the findings, a notable challenge is highlighted in the early diagnosis of the disease, leading to a higher incidence of chronic complications. Additionally, the study emphasizes the importance of continuous education for healthcare professionals and the enhancement of promotion and prevention policies as less costly measures for managing the endemic scenario of the disease. Another crucial aspect in disease management involves raising awareness among the population regarding the clinical manifestations of Chagas disease and the identification of infestation sources of the transmitting agent. Therefore, progress in reducing and controlling the endemicity of Chagas disease can only be achieved through collaboration between healthcare institutions and the population.

Descriptive analysis to assess seasonal patterns of COVID-19 and influenza in low-income and middle-income countries in Asia, the Middle East and Latin America

ObjectivesUnderstanding disease seasonality can help predict the occurrence of outbreaks and inform public health planning. Respiratory diseases typically follow seasonal patterns; however, knowledge regarding the seasonality of COVID-19 and its...

Observatório Covid-19 Fiocruz - uma análise da evolução da pandemia de fevereiro de 2020 a abril de 2022

Abstract The COVID-19 pandemic had a significant impact on the living and working conditions of the entire population of Brazil, having a different and more intense effect on groups considered to be vulnerable. The objective of this article is to present an overview of the evolution of the pandemic in the country according to the bulletins of the Covid-19 Fiocruz Observatory in the period between the declarations of the beginning and end of the Public Health Emergency of National Concern (ESPIN, in Portuguese), February 2020 to April 2022. Several of the indicators adopted in the 69 bulletins published for the analysis of the pandemic were used, such as cases and deaths due to SARIs and COVID-19, age groups, % of occupancy of ICU beds, and vaccination, among others. The evolution analysis was organized between years and phases of the pandemic, seeking to highlight what characterized each moment. The closing statement of ESPIN in Brazil coincides with the discussions on the transition from a pandemic to an endemic scenario, without this representing the elimination of the virus, infections, and disease, posing the challenges of advances in vaccination processes in Brazil and around the world, as well as living with scenarios that may require the adoption of temporary protection measures in epidemic periods and periods of greater risk for vulnerable groups.

Covid-19 Fiocruz Observatory - an analysis of the evolution of the pandemic from February 2020 to April 2022.

The COVID-19 pandemic had a significant impact on the living and working conditions of the entire population of Brazil, having a different and more intense effect on groups considered to be vulnerable. The objective of this article is to present an overview of the evolution of the pandemic in the country according to the bulletins of the Covid-19 Fiocruz Observatory in the period between the declarations of the beginning and end of the Public Health Emergency of National Concern (ESPIN, in Portuguese), February 2020 to April 2022. Several of the indicators adopted in the 69 bulletins published for the analysis of the pandemic were used, such as cases and deaths due to SARIs and COVID-19, age groups, % of occupancy of ICU beds, and vaccination, among others. The evolution analysis was organized between years and phases of the pandemic, seeking to highlight what characterized each moment. The closing statement of ESPIN in Brazil coincides with the discussions on the transition from a pandemic to an endemic scenario, without this representing the elimination of the virus, infections, and disease, posing the challenges of advances in vaccination processes in Brazil and around the world, as well as living with scenarios that may require the adoption of temporary protection measures in epidemic periods and periods of greater risk for vulnerable groups.

Willingness to pay for an annual vaccine in an endemic COVID-19 scenario: a contingent valuation study in Metro Manila, Philippines

Using the Contingent Valuation Method, this paper estimated willingness to pay (WTP) for annual COVID-19 booster vaccines for the endemic phase of the disease. The study found that, on the average, Metro Manila households would be WTP PhP2,199.71–2,410.50 (US$42.71–46.81) for a one-dose vaccine with 90% efficacy for one year. This WTP estimate is a measure of the perceived benefits from preventing COVID-19 infection, suggesting the potential for private markets to cater to those who prefer to obtain the annual booster COVID-19 vaccine privately, while a public vaccination program that subsidizes partially or fully the cost of the vaccine for those with lower capacity to pay is likely to pass a social cost–benefit assessment. Consistent with economic theory, WTP was found to significantly decrease with vaccine price and increase with income. Further, the study found general acceptance (measured in terms of the Health Benefit Model constructs) of COVID-19 vaccines among Metro Manila households despite the dengue vaccine controversy in the country immediately prior to the COVID-19 pandemic.

Social Inclusion of Persons with Disabilities into Mainstream Society: Using the Community Care Context

Social Inclusion is an important and extremely desirable phenomenon for persons with disabilities(PWDs). It is the gateway to creating the sense and opportunities for PWDs by recognizing being as integral and potential human resources and a responsible segment of society. In addition to the lack of research and policies that have been formulated from time to time to emphasize the concept and importance of the Social Inclusion of PWDs’, the traditional response of the community towards PWDs has deterred the social inclusion of PWDs. The basic theme of this research study was to explore the efforts made by community members for the social inclusion of PWDs in the Community Care context. A qualitative research method was used to conduct the study. At first, the document -analysis of previous research studies was made to explore the efforts made by the Government and policymakers for the social inclusion of PWDs in the COVID-19 endemic scenario. The open-ended interviews were conducted with the 20 professionals related to special education and social welfare fields to explore the efforts made by the community stakeholders as an element of community care to deal with social restrictions for PWDs and foster their social inclusion to make them productive members of society. The content -analysis reflected that no significant effort has been made at the governmental level for the social inclusion of PWDs d. Finally, the study suggested two Social Inclusion models; 1) Personal Social Services Model (PSSM) and 2) the Social-Ecological Model (SEM) of Social Inclusion which deals with the Individual, Interpersonal, Organizational, Community, and Socio-Political Factors of Society.

Analysis of optimal lockdown in integral economic-epidemic model.

We analyze the optimal lockdown in an economic-epidemic model with realistic infectiveness distribution. The model is described by Volterra integral equations and accurately depicts the COVID-19 infectivity pattern from clinical data. A maximum principle is derived, and a qualitative dynamic analysis of the optimal lockdown problem is provided over finite and infinite horizons. We analytically prove and economically justify the possibility of an endemic scenario when the infection rate begins to climb after the lockdown ends.

Exploring a COVID-19 Endemic Scenario: High-Resolution Agent-Based Modeling of Multiple Variants.

Ourefforts as a society to combat the ongoing COVID-19 pandemic are continuously challenged by the emergence of new variants. These variants can be more infectious than existing strains and many of them are also more resistant to available vaccines. The appearance of these new variants causenew surges of infections, exacerbated by infrastructural difficulties, such as shortages of medical personnel or test kits. In this work, a high-resolution computational framework for modeling the simultaneous spread of two COVID-19 variants: a widely spread base variant and a new one, is established. The computational framework consists of a detailed database of a representative U.S. town and a high-resolution agent-based model that uses the Omicron variant as the base variant and offers flexibility in the incorporation of new variants. The results suggest that the spread of new variants can be contained with highly efficacious tests and mild loss of vaccine protection. However, the aggressiveness of the ongoing Omicron variant and the current waning vaccine immunity point to an endemic phase of COVID-19, in which multiple variants will coexist and residents continue to suffer from infections.

Reducing infection risk in multiple sclerosis and neuromyelitis optica spectrum disorders: a Brazilian reference center's approach.

Multiple sclerosis (MS) and neuromyelitis optica spectrum disorders (NMOSD) are the most common autoimmune diseases of the central nervous system (CNS). They present chronic relapsing courses that demand treatment with disease-modifying drugs (DMDs) to prevent inflammatory activity. Disease-modifying drugs lead to immunomodulation or immunosuppression through diverse mechanisms (e.g., shifting lymphocyte and cytokine profile, suppressing specific lymphocyte subpopulations). Thus, patients are more prone to infectious complications and associated worsening of disease. To present feasible strategies for mitigating the infection risk of MS and NMOSD treated patients. Targeted literature review concerning the management of infection risk with an emphasis on vaccination, therapy-specific measures, and particularities of the Brazilian endemic infectious diseases' scenario. We propose a vaccination schedule, infectious screening routine, and prophylactic measures based on the current scientific evidence. Awareness of emergent tropical diseases is necessary due to evidence of demyelinating events and possible parainfectious cases of MS and NMOSD.

Tuberculosis/HIV co-infection in Northeastern Brazil: Prevalence trends, spatial distribution, and associated factors.

The objective was to analyze the prevalence trend, spatial distribution, and TB-HIV co-infection-associated factors in an endemic scenario for TB in Northeastern Brazil. An ecological and temporal series study was conducted based on secondary data obtained from the Brazilian Notifiable Diseases Information System between January 2008 and December 2019. The prevalence rates were determined for each year and the average for the period. Prais-Winsten regressions were used for temporal variation analysis, scanning techniques were used to detect spatial clusters, and the Poisson regression model was used to explore the factors associated with the outcome. A total of 947 TB cases were reported, of which 501 (52.9%) underwent HIV testing, and of these, 73 were positive. The average prevalence was 20.0%, ranging from 1.5% in 2018 to 44.4% in 2009. A decreasing trend was found. Sixty-seven cases (92%) were geocoded, and two statistically significant (p < 0.005) high relative risk (RR) spatial clusters were detected. Statistically significant associations (p < 0.05) between the co-infection and variables such as male gender, living in the urban area, entry due to relapse, and case closure due to loss to follow-up were evidenced, and these variables constituted risk factors. A decreasing prevalence of TB-HIV co-infection has been found, as well as a heterogeneous spatial distribution with the formation of spatial clusters in urban areas characterized by socio-spatial inequalities associated with clinical-epidemiological factors. Such findings provide subsidies for rethinking health care activities and improving public policies for vulnerable populations.

COVID-19 vaccine hesitancy in Sweden and Italy: The role of trust in authorities.

Background:The success of vaccination campaigns against COVID-19 infection is vital for moving from a COVID-19 pandemic to an endemic scenario. We aimed to unravel the influence of the risk perception of epidemics along with individual and contextual factors on adherence to COVID-19 vaccination campaigns in Italy and Sweden.Methods:We compared the results of two nationwide surveys carried out in August 2021 across four domains of epidemic risk perception: perceived likelihood, perceived impact on the individual and perceived individual and authority knowledge. The roles of individual and contextual determinants were also explored.Results:The survey included 2144 participants in Sweden (52.3% women) and 2010 in Italy (52.6% women). In both countries, we found that trust in authorities was one of the main drivers of this process, with two-fold increased odds of being vaccinated. Being highly educated and having a higher relative income were associated with a higher adherence to the vaccination campaign (for relative income OR = 1.44, 95% CI 1.23–1.67 in Sweden and OR = 1.18, 95% CI 1.04–1.34 in Italy; for education OR = 1.90, 95% CI 1.30–2.77 in Sweden and OR = 1.47, 95% CI 1.09–1.97 in Italy), whereas a right and centre-right compared with a left and centre-left political orientation was negatively related to vaccination adherence (OR = 0.41, 95% CI 0.25–0.67 in Sweden and OR = 0.47, 95% CI 0.33–0.68 in Italy).Conclusions:Increasing trust in authorities, along with an equal global distribution of vaccine doses, can contribute to accelerating vaccination campaigns around the world and, in turn, to move towards an endemic scenario.

Tuberculosis forecasting and temporal trends by sex and age in a high endemic city in northeastern Brazil: where were we before the Covid-19 pandemic?

BackgroundThe aim of this study was to describe the temporal trend of tuberculosis cases according to sex and age group and evidence the level of disease before the Covid-19 pandemic in a TB high endemic city.MethodsThis was a time series study carried out in a city in northeast Brazil. The population was composed of cases of tuberculosis, excluding those with HIV-positive status, reported between the years 2002 and 2018. An exploratory analysis of the monthly rates of tuberculosis detection, smoothed according to sex and age group, was performed. Subsequently, the progression of the trend and prediction of the disease were also characterized according to these aspects. For the trends forecast, the seasonal autoregressive linear integrated moving average (ARIMA) model and the usual Box-Jenkins method were used to choose the most appropriate models.ResultsA total of 1620 cases of tuberculosis were reported, with an incidence of 49.7 cases per 100,000 inhabitants in men and 34.0 per 100,000 in women. Regarding the incidence for both sexes, there was a decreasing trend, which was similar for age. Evidence resulting from the application of the time series shows a decreasing trend in the years 2002–2018, with a trend of stability.ConclusionsThe study evidenced a decreasing trend in tuberculosis, even before the Covid-19 pandemic, for both sex and age; however, in a step really slow from that recommended by the World Health Organization. According to the results, the disease would have achieved a level of stability in the city next years, however it might have been aggravated by the pandemic. These findings are relevant to evidence the serious behavior and trends of TB in a high endemic scenario considering a context prior to the Covid-19 pandemic.

Genome-wide estimation of recombination, mutation and positive selection enlightens diversification drivers of Mycobacterium bovis

Genome sequencing has reinvigorated the infectious disease research field, shedding light on disease epidemiology, pathogenesis, host–pathogen interactions and also evolutionary processes exerted upon pathogens. Mycobacterium tuberculosis complex (MTBC), enclosing M. bovis as one of its animal-adapted members causing tuberculosis (TB) in terrestrial mammals, is a paradigmatic model of bacterial evolution. As other MTBC members, M. bovis is postulated as a strictly clonal, slowly evolving pathogen, with apparently no signs of recombination or horizontal gene transfer. In this work, we applied comparative genomics to a whole genome sequence (WGS) dataset composed by 70 M. bovis from different lineages (European and African) to gain insights into the evolutionary forces that shape genetic diversification in M. bovis. Three distinct approaches were used to estimate signs of recombination. Globally, a small number of recombinant events was identified and confirmed by two independent methods with solid support. Still, recombination reveals a weaker effect on M. bovis diversity compared with mutation (overall r/m = 0.037). The differential r/m average values obtained across the clonal complexes of M. bovis in our dataset are consistent with the general notion that the extent of recombination may vary widely among lineages assigned to the same taxonomical species. Based on this work, recombination in M. bovis cannot be excluded and should thus be a topic of further effort in future comparative genomics studies for which WGS of large datasets from different epidemiological scenarios across the world is crucial. A smaller M. bovis dataset (n = 42) from a multi-host TB endemic scenario was then subjected to additional analyses, with the identification of more than 1,800 sites wherein at least one strain showed a single nucleotide polymorphism (SNP). The majority (87.1%) was located in coding regions, with the global ratio of non-synonymous upon synonymous alterations (dN/dS) exceeding 1.5, suggesting that positive selection is an important evolutionary force exerted upon M. bovis. A higher percentage of SNPs was detected in genes enriched into “lipid metabolism”, “cell wall and cell processes” and “intermediary metabolism and respiration” functional categories, revealing their underlying importance in M. bovis biology and evolution. A closer look on genes prone to horizontal gene transfer in the MTBC ancestor and included in the 3R (DNA repair, replication and recombination) system revealed a global average negative value for Taijima’s D neutrality test, suggesting that past selective sweeps and population expansion after a recent bottleneck remain as major evolutionary drivers of the obligatory pathogen M. bovis in its struggle with the host.

Toward the Next-Generation COVID-19 Vaccines That Circumvent Antigenic Drift while Defusing Viral Infection

The emergence of vaccine-resistant variants suggests a complicated endemic scenario in the vaccination aftermath for COVID-19. The situation prompts us to enquire whether the antigen adopted by extant vaccines, the trimeric spike (S) protein, is the optimal in the sense of inducing an immunity that leaves the virus with no evolutionary route of evasion. The patterns of glycosylation camouflage suggest that the answer is negative while also suggesting an alternative antigen that appears to be better optimized, eliciting an additional immune attack as the virus gets primed for cell penetration. This type of vaccine is expected to induce antibodies capable of defusing the virus during the priming phase while also circumventing antigenic drift.

Ruminant pestiviruses in North Africa

Ruminant pestiviruses are widely distributed worldwide, causing congenital disease and massive economic losses. Although ruminant production is an important economic sector in North Africa, the knowledge about pestiviruses is scarce. The present study aimed at assessing the presence of Pestivirus in cattle in Algeria, and to review the data available on ruminant pestiviruses in North Africa. A cross-sectional study was conducted on dairy farms from North-Western Algeria. Blood samples from 234 dairy cattle from 31 herds were collected. All sera were analysed for the presence of antibodies using a commercial iELISA. The presence of Pestivirus RNA was also assessed by using a Reverse Transcription-PCR, and PCR-positive samples were sequenced. Risk factors related to Pestivirus infection were also analysed. The review of the presence of ruminant pestiviruses in North Africa was performed using a systematic search and compilation methodology of the peer-reviewed literature available in order to identify gaps of knowledge for future research. The seroprevalence at population and farm levels obtained in the present study (59.9% and 93.5%, respectively) concur with data reported in neighbouring countries. Risk factors associated with Pestivirus infection in cattle were the presence of sheep in the herd and the animal category (cow vs heifer). Furthermore, we confirmed the presence of BVDV-1a in Algeria. The scarce data suggest an endemic epidemiological scenario of pestivirus in livestock. The lack of studies about the epidemiology and molecular variability of ruminant pestiviruses in livestock and wildlife in North Africa is of concern for animal health and wildlife conservation, and needs to be addressed.

A model for the assessment of bluetongue virus serotype 1 persistence in Spain.

Bluetongue virus (BTV) is an arbovirus of ruminants that has been circulating in Europe continuously for more than two decades and has become endemic in some countries such as Spain. Spain is ideal for BTV epidemiological studies since BTV outbreaks from different sources and serotypes have occurred continuously there since 2000; BTV-1 has been reported there from 2007 to 2017. Here we develop a model for BTV-1 endemic scenario to estimate the risk of an area becoming endemic, as well as to identify the most influential factors for BTV-1 persistence. We created abundance maps at 1-km2 spatial resolution for the main vectors in Spain, Culicoides imicola and Obsoletus and Pulicaris complexes, by combining environmental satellite data with occurrence models and a random forest machine learning algorithm. The endemic model included vector abundance and host-related variables (farm density). The three most relevant variables in the endemic model were the abundance of C. imicola and Obsoletus complex and density of goat farms (AUC 0.86); this model suggests that BTV-1 is more likely to become endemic in central and southwestern regions of Spain. It only requires host- and vector-related variables to identify areas at greater risk of becoming endemic for bluetongue. Our results highlight the importance of suitable Culicoides spp. prediction maps for bluetongue epidemiological studies and decision-making about control and eradication measures.

Prevalence and spatial distribution of Mycobacterium leprae infection in a medium endemicity municipality

Objective: analyze serological profile and spatial distribution of Mycobacterium leprae infection and disease. Methods: cross-sectional study with cases of leprosy (n=42), household contacts (n=81) and school contacts (n=358). Interviews, dermato-neurological examination, serological and georeferencing made. Results: all seropositive cases lived in rural areas, more than two people per household, 50.0% had alteration of foot strength. 75.0% were elderly and married participants. Among seropositive schoolchildren, 75.0% female, 69.4% lived with more than four people 80.6% slept in the bedroom with someone. It was possible to observe hyper endemic areas of cases in the studied municipality and spatial-temporal relation among them (p=0.010). In addition, concentration of cases and schoolchildren in sectors of lower family income per capita was found. Conclusion: the serological analysis revealed that the cohabitation condition was related to the Mycobacterium leprae infection, and the spatial analysis showed a hidden endemic scenario.