Characterization of Dengue Virus Type 2: New Insights on the 2010 Brazilian Epidemic

Dengue viruses (DENV) serotypes 1, 2, and 3 have been causing yearly outbreaks in Brazil. In this study, we report the re-introduction of DENV2 in the coast of São Paulo State. Partial envelope viral genes were sequenced from eighteen patients with dengue fever during the 2010 epidemic. Phylogenetic analysis showed this strain belongs to the American/Asian genotype and was closely related to the virus that circulated in Rio de Janeiro in 2007 and 2008. The phylogeny also showed no clustering by clinical presentation, suggesting that the disease severity could not be explained by distinct variants or genotypes. The time of the most recent common ancestor of American/Asian genotype and the São Paulo and Rio de Janeiro (SP/RJ) monophyletic cluster was estimated to be around 40 and 10 years, respectively. Since this virus was first identified in Brazil in 2007, we suggest that it was already circulating in the country before causing the first documented outbreak. This is the first description of the 2010 outbreak in the State of São Paulo, Brazil, and should contribute to efforts to control and monitor the spread of DENVs in endemic areas

Differential Diagnosis in the Management of Acute Respiratory Infections through Point-of-Care Rapid Testing in a Post-Pandemic Scenario in Latin America: Special Focus on COVID-19, Influenza, and Respiratory Syncytial Virus

This review provides a comprehensive summary of evidence to explore the role and value of differential diagnosis in the management of Acute Respiratory Infections (ARIs) through point-of-care (POC) rapid testing in a post-pandemic scenario, paying particular attention to coronavirus disease 2019 (COVID-19), influenza, and respiratory syncytial virus (RSV). The document builds on a review of literature and policies and a process of validation and feedback by a group of seven experts from Latin America (LATAM). Evidence was collected to understand scientific and policy perspectives on the differential diagnosis of ARIs and POC rapid testing, with a focus on seven countries: Argentina, Brazil, Chile, Colombia, Costa Rica, Mexico, and Peru. The evidence indicates that POC rapid testing can serve to improve ARI case management, epidemiological surveillance, research and innovation, and evidence-based decision-making. With multiple types of rapid tests available for POC, decisions regarding which tests to use require the consideration of the testing purpose, available resources, and test characteristics regarding accuracy, accessibility, affordability, and results turnaround time. Based on the understanding of the current situation, this document provides a set of recommendations for the implementation of POC rapid testing in LATAM, supporting decision-making and guiding efforts by a broad range of stakeholders

Inter- and Intra-Host Viral Diversity in a Large Seasonal DENV2 Outbreak

<div><p>Background</p><p>High genetic diversity at both inter- and intra-host level are hallmarks of RNA viruses due to the error-prone nature of their genome replication. Several groups have evaluated the extent of viral variability using different RNA virus deep sequencing methods. Although much of this effort has been dedicated to pathogens that cause chronic infections in humans, few studies investigated arthropod-borne, acute viral infections.</p><p>Methods and Principal Findings</p><p>We deep sequenced the complete genome of ten DENV2 isolates from representative classical and severe cases sampled in a large outbreak in Brazil using two different approaches. Analysis of the consensus genomes confirmed the larger extent of the 2010 epidemic in comparison to a previous epidemic caused by the same viruses in another city two years before (genetic distance = 0.002 and 0.0008 respectively). Analysis of viral populations within the host revealed a high level of conservation. After excluding homopolymer regions of 454/Roche generated sequences, we found 10 to 44 variable sites per genome population at a frequency of >1%, resulting in very low intra-host genetic diversity. While up to 60% of all variable sites at intra-host level were non-synonymous changes, only 10% of inter-host variability resulted from non-synonymous mutations, indicative of purifying selection at the population level.</p><p>Conclusions and Significance</p><p>Despite the error-prone nature of RNA-dependent RNA-polymerase, dengue viruses maintain low levels of intra-host variability.</p></div

Deep Sequence obtained results and Inter-host viral variability.

<p>All estimates were done after excluding homopolymer sites (HPs) from virus sequenced in 454.</p><p>The % <i>Variable sites/genome size</i> was calculated by dividing the <i>number of variable sites (SNP)</i> per <i># sites excluding HPs</i>. The <i>“# total of nt variants</i>” does consider the total amount of nucleotides (reads) that vary in such position. This number was used to calculate the overall genetic variability.</p

Bayesian phylogenetic tree of 124 DENV2 complete genomes.

<p>A-The tree shows the eleven Brazilian viruses sequenced in this study (two-color highlighted cluster at the top) and globally sampled DENV2 genomes. Blue branches represent Brazilian viruses sampled in previous epidemics. Posterior probability of all key nodes is depicted. B- Clusters of viruses sequenced during this study. The blue bar in the branch leading to clade 2 represents the amino acid change at position T180I in envelope gene.</p

Clinical and laboratorial information of DENV-2 samples.

$<p>supernatant of sample ACS46 cultured viruses in C6/36 (1week).</p>&<p>Although the low platelets number, the patient had no additional evidence of severity.</p>*<p>Days after the onset.</p><p>VL- viral load in copy number/ml.</p><p>Nd- not done.</p

Inter-host variability.

<p>A- The line graph summarizes the level of accumulated variability per genome region across the Santos consensus viruses. B- Variability (synonymous changes) among consensus sequences sampled in Santos (light blue squares) compared to the variability among viruses from previous epidemics in 2008 in Ribeirão Preto, SP (green squares). Non-synonymous changes are represented in dark blue in both populations.</p

Hepatitis C: sexual or intrafamilial transmission? Epidemiological and phylogenetic analysis of hepatitis C virus in 24 infected couples Hepatite C: transmissão sexual ou intrafamiliar? Análise epidemiológica e filogenética do vírus da hepatite C em 24 casais infectados

The role of sexual or intrafamilial transmission of hepatitis C is controversial. A phylogenetic analysis was performed on the non-structural region 5B of the hepatitis C virus (NS5B-HCV). High percentages of homology (mean of 98.3%) were shown between the couples. Twenty (83.3%) of the 24 men but only two of the women (8.3%) reported having had sexually transmitted diseases during their lives. The risk factors for HCV acquisition were blood transfusion (10 couples), use of illegal injected drugs (17), use of inhalants (15), acupuncture (5) and tattoos (5). The shared use of personal hygiene items included toothbrushes between six couples (25%), razor blades between 16 (66.7%), nail clippers between 21 (87.5%) and manicure pliers between 14 (58.3%). The high degree of similarity of the hepatitis C virus genome supports the hypothesis of hepatitis C virus transmission between these couples. The shared use of personal hygiene items suggests the possibility of intrafamilial transmission of infection.<br>O papel da transmissão sexual ou intrafamiliar da hepatite C é controverso. Foi feita análise filogenética, região não estrutural 5B do vírus da hepatite C (NS5B-HCV). Altas percentagens de homologia com média de 98,3% foi revelada entre os casais. Vinte (83,3%) de 24 homens, contra apenas duas (8,3%) mulheres reportaram doença sexualmente transmisível durante suas vidas. Os fatores de risco para aquisição da doença foram: transfusão de sangue para 10 casais, uso de drogas ilícitas injetáveis para 17, inalatórias para 15, acupuntura em 5 e tatuagens para 5. O compartilhamento de utensílios de higiene pessoal incluem: escova de dente para seis (25%) dos casais, lâmina de barbear para 16 (66,7%), cortador de unhas para 21 (87,5%) e alicate de manicure para 14 (58,3%). O alto grau de similaridade genômica entre os vírus da hepatite C suporta a hipótese de transmissão entre os casais. O uso compartilhado de utensílios de higiene pessoal sugere a possibilidade de transmissão intrafamiliar

Hepatitis C viral load does not predict disease outcome: going beyond numbers A carga viral do vírus da hepatite C não prediz a evolução: indo além dos números

The analysis of 58 patients with chronic hepatitis C without cirrhosis and treated with interferon-alpha demonstrated that hepatitis C viral (HCV) load does not correlate with the histological evolution of the disease (p = 0.6559 for architectural alterations and p = 0.6271 for the histological activity index). Therefore, the use of viral RNA quantification as an evolutive predictor or determinant of the severity of hepatitis C is incorrect and of relative value. A review of the literature provided fundamental and interdependent HCV (genotype, heterogeneity and mutants, specific proteins), host (sex, age, weight, etc) and treatment variables (dosage, time of treatment, type of interferon) within the broader context of viral kinetics, interferon-mediated immunological response (in addition to natural immunity against HCV) and the role of interferon as a modulator of fibrogenesis. Therefore, viral load implies much more than numbers and the correct interpretation of these data should consider a broader context depending on multiple factors that are more complex than the simple value obtained upon quantification.<br>Através da análise de 58 pacientes tratados com Interferon Alfa em função de hepatite C crônica e sem cirrose, demonstramos que a carga viral do Vírus da Hepatite C (VHC) não se correlacionou com a evolução histológica da doença (p = 0,6559 para alterações arquiteturais e p = 0,6271 para o Índice de Atividade Histológica-IAH). Assim a utilização da quantificação do RNA viral como preditor evolutivo ou determinante da gravidade da hepatite C é incorreto e de valor relativo. Revisando o tema encontramos variáveis do VHC (genótipo, heterogeneidade e mutantes, proteínas específicas), do hospedeiro (sexo, idade, peso, etc) e dos medicamentos (posologia, tempo de tratamento, tipo de Interferon) fundamentais e interdependentes, inseridas no contexto mais amplo da cinética viral, da resposta imunológica mediada pelo Interferon (além da imunidade natural em resposta ao VHC) e do papel do Interferon como modulador da fibrogênese. Assim, há muito mais que números por trás da Carga Viral e sua correta interpretação deve ser feita considerando-se um horizonte mais amplo dependente de múltiplos fatores mais complexos que o simples valor obtido na quantificaçã