scholarly journals Epidemiological Dynamics of SARS-CoV-2 VOC Gamma in Rio de Janeiro, Brazil

2021 ◽  
Author(s):  
Filipe Romero Rebello Moreira ◽  
Mirela D’arc ◽  
Diana Mariani ◽  
Alice Laschuk Herlinger ◽  
Francine Bittencourt Schiffler ◽  
...  
Keyword(s):  
Rio De Janeiro ◽  
Complex Dynamics ◽  
Global Public Health ◽  
Viral Loads ◽  
Genomic Epidemiology ◽  
Clock Analysis ◽  
Rapid Dissemination ◽  
Mechanistic Basis ◽  
Epidemiology Investigation ◽  
Rates Of Growth

Abstract The emergence and widespread circulation of SARS-CoV-2 variants of concern (VOC) or interest (VOI) imposes an enhanced threat to global public health. In Brazil, one of the countries most severely impacted throughout the pandemic, a complex dynamics involving variants co-circulation and turnover events has been recorded with the emergence and spread of VOC Gamma in Manaus in late 2020. In this context, we present a genomic epidemiology investigation based on samples collected between December 2020 and May 2021 in the second major Brazilian metropolis, Rio de Janeiro. By sequencing 244 novel genomes through all epidemiological weeks in this period, we were able to document the introduction and rapid dissemination of VOC Gamma in the city, driving the rise of the third local epidemic wave. Molecular clock analysis indicates this variant has circulated locally since the first weeks of 2021 and only seven weeks were necessary for it to achieve a frequency above 70%, consistent with rates of growth observed in Manaus and other states. Moreover, a Bayesian phylogeographic reconstruction indicates VOC Gamma spread throughout Brazil between December 2020 and January 2021, and that it was introduced in Rio de Janeiro through at least 13 events coming from nearly all regions of the country. Comparative analysis of RT-qPCR cycle threshold (Ct) values provides further evidence that VOC Gamma induces higher viral loads (N1 target; mean reduction of Ct: 2.7, 95% CI = ±0.7). This analysis corroborates the previously proposed mechanistic basis for this variant enhanced transmissibility and distinguished epidemiological behavior. Our results document the evolution of VOC Gamma and provide independent assessment of scenarios previously studied in Manaus, therefore contributing to the better understanding of the epidemiological dynamics currently being surveyed in other Brazilian regions.

scholarly journals Epidemiological dynamics of SARS-CoV-2 VOC Gamma in Rio de Janeiro, Brazil

2021 ◽  
Author(s):  
Filipe Romero Rebello Moreira ◽  
Mirela D'arc ◽  
Diana Mariani ◽  
Alice Laschuk Herlinger ◽  
Francine Bittencourt Schiffler ◽  
...  
Keyword(s):  
Rio De Janeiro ◽  
Complex Dynamics ◽  
Global Public Health ◽  
Viral Loads ◽  
Genomic Epidemiology ◽  
Clock Analysis ◽  
Rapid Dissemination ◽  
Mechanistic Basis ◽  
Epidemiology Investigation ◽  
Rates Of Growth

The emergence and widespread circulation of SARS-CoV-2 variants of concern (VOC) or interest (VOI) imposes an enhanced threat to global public health. In Brazil, one of the countries most severely impacted throughout the pandemic, a complex dynamics involving variants co-circulation and turnover events has been recorded with the emergence and spread of VOC Gamma in Manaus in late 2020. In this context, we present a genomic epidemiology investigation based on samples collected between December 2020 and May 2021 in the second major Brazilian metropolis, Rio de Janeiro. By sequencing 244 novel genomes through all epidemiological weeks in this period, we were able to document the introduction and rapid dissemination of VOC Gamma in the city, driving the rise of the third local epidemic wave. Molecular clock analysis indicates this variant has circulated locally since the first weeks of 2021 and only seven weeks were necessary for it to achieve a frequency above 70%, consistent with rates of growth observed in Manaus and other states. Moreover, a Bayesian phylogeographic reconstruction indicates VOC Gamma spread throughout Brazil between December 2020 and January 2021, and that it was introduced in Rio de Janeiro through at least 13 events coming from nearly all regions of the country. Comparative analysis of RT-qPCR cycle threshold (Ct) values provide further evidence that VOC Gamma induces higher viral loads (N1 target; mean reduction of Ct: 2.7, 95% CI = 2.0 - 3.4). This analysis corroborates the previously proposed mechanistic basis for this variant enhanced transmissibility and distinguished epidemiological behavior. Our results document the evolution of VOC Gamma and provide independent assessment of scenarios previously studied in Manaus, therefore contributing to the better understanding of the epidemiological dynamics currently being surveyed in other Brazilian regions.

scholarly journals Co-Circulation of Two Independent Clades and Persistence of CHIKV-ECSA Genotype during Epidemic Waves in Rio de Janeiro, Southeast Brazil

Pathogens ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 984
Author(s):  
Allison Araújo Fabri ◽  
Cintia Damasceno dos Santos Rodrigues ◽  
Carolina Cardoso dos Santos ◽  
Flávia Löwen Levy Chalhoub ◽  
Simone Alves Sampaio ◽  
...  
Keyword(s):  
Rio De Janeiro ◽  
Chikungunya Virus ◽  
Structural Proteins ◽  
Clinical Samples ◽  
Limited Information ◽  
Surveillance Studies ◽  
Genomic Epidemiology ◽  
Clinical Complications ◽  
Phylogenetic Reconstructions ◽  
Rapid Dissemination

The Chikungunya virus infection in Brazil has raised several concerns due to the rapid dissemination of the virus and its association with several clinical complications. Nevertheless, there is limited information about the genomic epidemiology of CHIKV circulating in Brazil from surveillance studies. Thus, to better understand its dispersion dynamics in Rio de Janeiro (RJ), one of the most affected states during the 2016–2019 epidemic waves, we generated 23 near-complete genomes of CHIKV isolates from two main cities located in the metropolitan mesoregion, obtained directly from clinical samples. Our phylogenetic reconstructions suggest the 2019-CHIKV-ECSA epidemic in RJ state was characterized by the co-circulation of multiple clade (clade A and B), highlighting that two independent introduction events of CHIKV-ECSA into RJ state have occurred between 2016–2019, both mediated from the northeastern region. Interestingly, we identified that the two-clade displaying eighteen characteristic amino acids changes among structural and non-structural proteins. Our findings reinforce that genomic data can provide information about virus genetic diversity and transmission dynamics, which might assist in the arbovirus epidemics establishing of an effective surveillance framework.

Perceived Experiences of Community Violence Among Adolescents: A School Survey From Rio de Janeiro, Brazil

2021 ◽  
pp. 088626052110051
Author(s):  
Claudia L. de Moraes ◽  
Érika B. dos Santos ◽  
Michael E. Reichenheim ◽  
Stella R. Taquette ◽  
Luciane Stochero ◽  
...  
Keyword(s):  
Public Schools ◽  
Community Violence ◽  
Rio De Janeiro ◽  
Public Health Problem ◽  
Cross Sectional Study ◽  
Global Public Health ◽  
Cross Sectional ◽  
Interpersonal Aggression ◽  
Adolescent Students ◽  
Management Actions

Community violence (CV) is a global public health problem due to its high frequency and severe consequences. Although CV is one of the leading causes of death among adolescents, little is known about the everyday CV situations that do not lead to death. This study aimed to estimate the frequency of exposure to and involvement in CV situations among adolescent students from public and private schools in the city of Rio de Janeiro, Brazil. This was a cross-sectional study of 693 individuals in their second year of high school selected through stratified multistage random sampling. Information about their exposure to and involvement in CV was collected through a self-completed multidimensional questionnaire in the classrooms. For approximately 30% of the adolescents, someone close to them had been murdered, and 40% had already seen the corpse of a victim of homicide. Seventeen percent reported having been directly involved in CV situations. Approximately 38%, 13%, and 25% had been victims of robberies, interpersonal aggression, and death threats to either themselves or their relatives, respectively. Many of these situations occurred more than once. In general, CV was more frequently reported by boys and by those who did not live with both parents. Adolescents from higher economic classes experienced more interpersonal aggression and felt a greater need to carry a gun. Those who belonged to the lower economic classes and studied in public schools were more exposed to lethal violence than other students. The results call attention to the very high percentage of adolescent students that are involved in CV situations as well as to the differences in violence rates among population subgroups. Such findings should be considered when planning CV prevention and management actions in schools and other socialization spaces for adolescents.

scholarly journals High diversity in Delta variant across countries revealed via genome-wide analysis of SARS-CoV-2 beyond the Spike protein

2021 ◽  
Author(s):  
Pritha Ghosh ◽  
Rohit Suratekar ◽  
Michiel J.M. Niesen ◽  
Praveen Anand ◽  
Gregory Donadio ◽  
...  
Keyword(s):  
Amino Acid ◽  
Spike Protein ◽  
P Value ◽  
Missense Mutations ◽  
Systematic Analysis ◽  
Viral Loads ◽  
Amino Acid Mutations ◽  
Mechanistic Basis ◽  
Alpha Variant ◽  
High Diversity

The highly contagious Delta variant of SARS-CoV-2 has emerged as the new dominant global strain, and reports of reduced effectiveness of COVID-19 vaccines against the Delta variant are highly concerning. While there has been extensive focus on understanding the amino acid mutations in the Delta variant's Spike protein, the mutational landscape of the rest of the SARS-CoV-2 proteome (25 proteins) remains poorly understood. To this end, we performed a systematic analysis of mutations in all the SARS-CoV-2 proteins from nearly 2 million SARS-CoV-2 genomes from 176 countries/territories. Six highly-prevalent missense mutations in the viral life cycle-associated Membrane (I82T), Nucleocapsid (R203M, D377Y), NS3 (S26L), and NS7a (V82A, T120I) proteins are almost exclusive to the Delta variant compared to other variants of concern (mean prevalence across genomes: Delta = 99.74%, Alpha = 0.06%, Beta = 0.09%, Gamma = 0.22%). Furthermore, we find that the Delta variant harbors a more diverse repertoire of mutations across countries compared to the previously dominant Alpha variant (cosine similarity: meanAlpha = 0.94, S.D.Alpha = 0.05; meanDelta = 0.86, S.D.Delta = 0.1; Cohen's dAlpha-Delta = 1.17, p-value < 0.001). Overall, our study underscores the high diversity of the Delta variant between countries and identifies a list of targetable amino acid mutations in the Delta variant's proteome for probing the mechanistic basis of pathogenic features such as high viral loads, high transmissibility, and reduced susceptibility against neutralization by vaccines.

Factors predicting the severity of dengue in patients with warning signs in Rio de Janeiro, Brazil (1986–2012)

2019 ◽  
Vol 113 (11) ◽  
pp. 670-677 ◽  
Author(s):  
Bianca De Santis Gonçalves ◽  
Rita Maria Ribeiro Nogueira ◽  
Ana Maria Bispo de Filippis ◽  
Marco Aurélio Pereira Horta
Keyword(s):  
Rio De Janeiro ◽  
Dengue Infection ◽  
Warning Signs ◽  
Severe Dengue ◽  
Enzyme Linked Immunosorbent Assay ◽  
Infection Status ◽  
Viral Loads ◽  
Dengue Virus Type 3 ◽  
Dengue With Warning Signs ◽  
Type 3

AbstractBackgroundSince 1981, >12 million cases of dengue have been reported in Brazil. Early prediction of severe dengue with no warning signs is crucial to avoid progression to severe dengue. Here we aimed to identify early markers of dengue severity and characterize dengue infection in patients in Rio de Janeiro.MethodsWe evaluated early severity markers, serotypes, infection status, number of days of illness and viral loads associated with dengue fever in patients from Rio de Janeiro, Brazil through an observational retrospective study (1986–2012). We compared dengue without warning signs and dengue with warning signs/severe dengue (DWWS/SD). Infection status was classified by enzyme-linked immunosorbent assay and viraemia was quantified by quantitative real-time reverse transcription polymerase chain reaction.ResultsThe presence of DWWS/ SD was significantly associated with younger age; patients 13–19 y of age had a significantly greater chance of presenting warning signs. Dengue virus type 3 (DENV3) was more likely to induce DWWS/SD, which was more frequent on days 4–5 of illness.ConclusionsDENV3, 4–5 d of illness and 13–19 y of age were early biomarkers of dengue severity. To our knowledge, this was the first study to analyse the characteristics of dengue severity in the state of Rio de Janeiro over 27 y of epidemics since the introduction of DENV.

scholarly journals Earlier In Vitro Viral Production With SARS-CoV-2 Alpha Than With Beta, Gamma, B, or A.27 Variants

2021 ◽  
Vol 11 ◽  
Author(s):  
Samuel Lebourgeois ◽  
Houssem Redha Chenane ◽  
Nadhira Houhou-Fidouh ◽  
Reyene Menidjel ◽  
Valentine Marie Ferré ◽  
...  
Keyword(s):  
A549 Cells ◽  
Public Health Emergency ◽  
Global Public Health ◽  
Viral Production ◽  
Viral Loads ◽  
The World ◽  
Alpha Variant ◽  
Culture Supernatants ◽  
Similar Kinetic

Since its emergence in China at the end of 2019, SARS-CoV-2 has rapidly spread across the world to become a global public health emergency. Since then, the pandemic has evolved with the large worldwide emergence of new variants, such as the Alpha (B.1.1.7 variant), Beta (B.1.351 variant), and Gamma (P.1 variant), and some other under investigation such as the A.27 in France. Many studies are focusing on antibody neutralisation changes according to the spike mutations, but to date, little is known regarding their respective replication capacities. In this work, we demonstrate that the Alpha variant provides an earlier replication in vitro, on Vero E6 and A549 cells, than Beta, Gamma, A.27, and historical lineages. This earlier replication was associated with higher infectious titres in cell-culture supernatants, in line with the higher viral loads observed among Alpha-infected patients. Interestingly, Beta and Gamma variants presented similar kinetic and viral load than the other non-Alpha-tested variants.

scholarly journals SARS-CoV-2 Mpro inhibitors with antiviral activity in a transgenic mouse model

Science ◽  
2021 ◽  
pp. eabf1611
Author(s):  
Jingxin Qiao ◽  
Yue-Shan Li ◽  
Rui Zeng ◽  
Feng-Liang Liu ◽  
Rong-Hua Luo ◽  
...  
Keyword(s):  
Antiviral Activity ◽  
Mouse Model ◽  
Transgenic Mouse ◽  
Transgenic Mouse Model ◽  
Global Public Health ◽  
Viral Loads ◽  
Main Protease ◽  
Pharmacokinetic Properties ◽  
Intraperitoneal Treatment

The COVID-19 pandemic caused by the SARS-CoV-2 virus continually poses serious threats to global public health. The main protease (Mpro) of SARS-CoV-2 plays a central role in viral replication. We designed and synthesized 32 new bicycloproline-containing Mpro inhibitors derived from either Boceprevir or Telaprevir, both of which are approved antivirals. All compounds inhibited SARS-CoV-2 Mpro activity in vitro with IC50 values ranging from 7.6 to 748.5 nM. The co-crystal structure of Mpro in complex with MI-23, one of the most potent compounds, revealed its interaction mode. Two compounds (MI-09 and MI-30) showed excellent antiviral activity in cell-based assays. In a SARS-CoV-2 infection transgenic mouse model, oral or intraperitoneal treatment with MI-09 or MI-30 significantly reduced lung viral loads and lung lesions. Both also displayed good pharmacokinetic properties and safety in rats.

scholarly journals Unveiling the Gut Microbiota and Resistome of Wild Cotton Mice, Peromyscus gossypinus , from Heavy Metal- and Radionuclide-Contaminated Sites in the Southeastern United States

2021 ◽  
Author(s):  
Jesse C. Thomas ◽  
Troy J. Kieran ◽  
John W. Finger ◽  
Natalia J. Bayona-Vásquez ◽  
Adelumola Oladeinde ◽  
...  
Keyword(s):  
Public Health ◽  
Southeastern United States ◽  
Antibiotic Resistance Genes ◽  
Health Concern ◽  
Contaminated Sites ◽  
Global Public Health ◽  
Public Health Concern ◽  
Peromyscus Gossypinus ◽  
Wild Cotton ◽  
Rapid Dissemination

Antimicrobial resistance is a serious global public health concern because of its prevalence and ubiquitous distribution. The rapid dissemination of antibiotic resistance genes is thought to be the result of the massive overuse of antibiotics in agriculture and therapeutics.

scholarly journals Turnover of SARS-CoV-2 lineages shaped the pandemic and enabled the emergence of new variants in the state of Rio de Janeiro, Brazil

2021 ◽  
Author(s):  
Ronaldo da Silva Francisco Junior ◽  
Alessandra Pavan Lamarca ◽  
Luiz G P de Almeida ◽  
Liliane Cavalcante ◽  
Douglas Terra Machado ◽  
...  
Keyword(s):  
Public Health ◽  
Rio De Janeiro ◽  
Health Management ◽  
The State ◽  
Lessons Learned ◽  
Overwhelming Majority ◽  
Social Distancing ◽  
Genomic Epidemiology ◽  
Strong Potential ◽  
Two Phases

In the present study, we provide a retrospective genomic epidemiology analysis of the SARS-CoV-2 pandemic in the state of Rio de Janeiro, Brazil. We gathered publicly available data from GISAD and sequenced more 1,927 new genomes sampled periodically from March 2021 to June 2021 from 91 out of the 92 cities of the state. Our results showed that the pandemic was characterized by three different phases driven by a successive replacement of lineages. All stages occurred in distinct mortality and mobility contexts, with higher evidence of social distancing measures being observed in early pandemic and relaxed in the last two phases. Interestingly, we noticed that viral supercarriers accounted for the overwhelming majority of the circulating virus (> 90%) among symptomatic individuals in the state. Moreover, SARS-CoV-2 genomic surveillance also revealed the emergence and spread of two new variants (P.5 and P.1.2) firstly reported in this study. Altogether, our findings provided important lessons learned from the different epidemiological aspects of the SARS-CoV-2 dynamic in the state of Rio de Janeiro that have a strong potential to shape future decisions aiming to improve public health management and understanding mechanisms underlying virus dispersion.

EPIDEMIOLOGY AND SURVIVAL ANALYSIS OF MOUTH AND OROPHARYNGEAL CANCER PATIENTS TREATED AT A PUBLIC HOSPITAL IN RIO DE JANEIRO, BRAZIL

2020 ◽  
Author(s):  
Jackeline Nogueira de Paula Barros
Keyword(s):  
Survival Rate ◽  
Rio De Janeiro ◽  
Survival Curve ◽  
Survival Rates ◽  
Rank Test ◽  
Anatomical Location ◽  
Anatomical Site ◽  
Global Public Health ◽  
Oral Neoplasms ◽  
Epidemiological Profile

AbstractMouth and oropharyngeal cancers (CAs) are considered to be global public health problems, with high psychosocial impacts and high costs. Developing an epidemiological profile and examining the survival rate among patients with CAs of the mouth and oropharynx are important for the development of public policy. Therefore, this retrospective study aimed to evaluate mouth and oropharyngeal CA patients treated at the Municipal Hospital Salgado Filho in Rio de Janeiro, Brazil between 2007 and 2017. Patient data regarding gender, age, ethnicity, diagnosis, anatomical site affected by the tumor, and habits were obtained from patient records and reports, and data regarding the deaths of patients were obtained from records and the Mortality Information System. After tabulation, data were descriptively analyzed using the Kaplan-Meier survival curve, and the log-rank test was used for the comparison of variables. Survival rates at 5 and 8 years were 71.1% and 48.8%, respectively. There were no significant differences among survival rates according to age, sex, ethnicity, or the anatomical location of tumors. The survival rates among mouth and oropharyngeal CA patients in this study were comparable with the results reported in developed countries.Keywords: Oral neoplasms, epidemiology, survival rate;

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