Molecular evolution of the human monkeypox virus.

Recently, in 2022, new cases of human monkeypox virus (hMPXV) occurred in Europe and North America. The first case was reported in Europe in May 2022, and subsequently, more than 50 000 new cases were confirmed in 100 countries. Currently, the classification of hMPXV according to the nextstrain occurs in five big clades (1A, A.1, A.2, A.1.1, and B.1). According to the resurgence of smallpox-like disease caused by hMPXV and the spread of the virus to the European and American continents, in the present study, we review and summarize the molecular evolution of the hMPXV, determining the molecular evolution of the main clades. A total of 442 hMPXV whole-genome sequences with available information from the country and sampling date (between October 2017 and 2022), were obtained and evaluated using the Bayesian method. The clade B.1 which is currently circulating was the most frequent (n = 415; 93.9%). The other clades presented the following frequencies: 1A (n = 13; 2.9%), A.1 (n = 10; 2.3%), A.2 (n = 3; 0.7%) and A.1.1 (n = 1; 0.2%) The overall nucleotide divergence of hMPXV was 5.590e-5. The 1A clade was detected between 2017 and 2020. A.1 was observed, and between 2019 and 2022 some A.2 sequences were detected. In 2022, the great predominance of B.1 was observed. The common ancestor of the hMPXV belongs to the clade 1A and the time to the Most Recent Common Ancestor (tMRCA) was 2017-04-04 (Highest Posterior Density 95% (HPD95%): 2017-03-09; 2017-08-04) on the West African continent. The tMRCA of A.1 was 2018-05-21 (HPD95%: 2018-05-20; 2018-07-04) with divergence of 6.885e-5 substitutions per site per year. This clade was of West African origin but was eventually detected in European countries. Also, A.2 was detected with sequences of North America and showed tMRCA of 2019-07-15 (HPD95%: 2018-11-18; 2020-02-24). A.1.1 showed tMRCA from 2021 to 06-05 (HPD95%: 2021-06-05; 2021-11-26) and this clade was detected in North America and was the precursor for the globally spreading B.1 which tMRCA was 2022-04-26 (HPD95%: 2022-02-27; 2022-04-26). hMPXV has been spread from West Africa to the United Kingdom, Israel, Singapore, the USA, Canada, Portugal, Spain, Ireland, France, Belgium, the Netherlands, Switzerland, Germany, Italy, Slovenia, Austria, the Republic Czech, Sweden, and Finland. hMPXV also reached countries such as Brazil, Mexico, Australia, and Taiwan. The common ancestor of the hMPXV belongs to the clade 1A with origin in the West African continent. Clade B.1 was responsible for the recent widespread worldwide. Immunization to prevent the spread of hMPXV is not yet available to the public, future studies should focus on the development of effective vaccines to contain the spread of this virus.

Molecular evolution of SARS-CoV-2 from December 2019 to August 2022.

Severe acute respiratorysyndrome coronavirus-2 (SARS-CoV-2) pandemic spread rapidly and this scenario is concerning worldwide, presenting more than 590 million coronavirus disease 2019 cases and 6.4 million deaths. The emergence of novel lineages carrying several mutations in the spike protein has raised additional public health concerns worldwide during the pandemic. The present study review and summarizes the temporal spreading and molecular evolution of SARS-CoV-2 clades and variants worldwide. The evaluation of these data is important for understanding the evolutionary histories of SARSCoV-2 lineages, allowing us to identify the origins of each lineage of this virus responsible for one of the biggest pandemics in history. A total of 2897 SARS-CoV-2 whole-genome sequences with available information from the country and sampling date (December 2019 to August 2022), were obtained and were evaluated by Bayesian approach. The results demonstrated that the SARS-CoV-2 the time to the most recent common ancestor (tMRCA) in Asia was 2019-12-26 (highest posterior density 95% [HPD95%]: 2019-12-18; 2019-12-29), in Oceania 2020-01-24 (HPD95%: 2020-01-15; 2020-01-30), in Africa 2020-02-27 (HPD95%: 2020-02-21; 2020-03-04), in Europe 2020-02-27 (HPD95%: 2020-02-20; 2020-03-06), in North America 2020-03-12 (HPD95%: 2020-03-05; 2020-03-18), and in South America 2020-03-15 (HPD95%: 2020-03-09; 2020-03-28). Between December 2019 and June 2020, 11 clades were detected (20I [Alpha] and 19A, 19B, 20B, 20C, 20A, 20D, 20E [EU1], 20F, 20H [Beta]). From July to December 2020, 4 clades were identified (20J [Gamma, V3], 21 C [Epsilon], 21D [Eta], and 21G [Lambda]). Between January and June 2021, 3 clades of the Delta variant were detected (21A, 21I, and 21J). Between July and December 2021, two variants were detected, Delta (21A, 21I, and 21J) and Omicron (21K, 21L, 22B, and 22C). Between January and June 2022, the Delta (21I and 21J) and Omicron (21K, 21L, and 22A) variants were detected. Finally, between July and August 2022, 3 clades of Omicron were detected (22B, 22C, and 22D). Clade 19A was first detected in the SARS-CoV-2 pandemic (Wuhan strain) with origin in 2019-12-16 (HPD95%: 2019-12-15; 2019-12-25); 20I (Alpha) in 2020-11-24 (HPD95%: 2020-11-15; 2021-12-02); 20H (Beta) in 2020-11-25 (HPD95%: 2020-11-13; 2020-11-29); 20J (Gamma) was 2020-12-21 (HPD95%: 2020-11-05; 2021-01-15); 21A (Delta) in 2020-09-20 (HPD95%: 2020-05-17; 2021-02-03); 21J (Delta) in 2021-02-26 (2020-11-02; 2021-04-24); 21M (Omicron) in 2021-01-25 (HPD95%: 2020-09-16; 2021-08-08); 21K (Omicron) in 2021-07-30 (HPD95%: 2021-05-30; 2021-10-19); 21L (Omicron) in 2021-10-03 (HPD95%: 2021-04-16; 2021-12-23); 22B (Omicron) in 2022-01-25 (HPD95%: 2022-01-10; 2022-02-05); 21L in 2021-12-20 (HPD95%: 2021-05-16; 2021-12-31). Currently, the Omicron variant predominates worldwide, with the 21L clade branching into 3 (22A, 22B, and 22C). Phylogeographic data showed that Alpha variant originated in the United Kingdom, Beta in South Africa, Gamma in Brazil, Delta in India, Omicron in South Africa, Mu in Colombia, Epsilon in the United States of America, and Lambda in Peru. The COVID-19 pandemic has had a significant impact on global health worldwide and the present study provides an overview of the molecular evolution of SARS-CoV-2 lineage clades (from the Wuhan strain to the currently circulating lineages of the Omicron).

COVID-19 pandemic in Southern Brazil: Hospitalizations, intensive care unit admissions, lethality rates, and length of stay between March 2020 and April 2022.

Coronavirus disease 2019 (COVID-19) pandemic spread rapidly with more than 515 million cases and 6.2 million deaths. Epidemiological factors are important for understanding the state of the pandemic. This study aims to evaluate the hospitalizations, intensive care unit (ICU) admissions, and lethality from March 2020 to April 2022. Data were collected from a hospital in Porto Alegre city, southern Brazil. The Mann-Whitney, analysis of variance, and Kruskal-Wallis tests were used to compare quantitative variables. Categorical variables were compared by Pearson's χ2 test. p values <0.05 for all tests were considered significant. Were observed 3784 hospitalizations. Males were 51.4% and the age was 60.4± 20.3. Intensive care unit (ICU) patients were 31.2%, the median length of stay (LOS) was 9.0 and lethality was 13.3%. ICU lethality was 34.5% versus 4.6% in other inpatients (p < 0.01). The LOS of ICU patients was 22.0 versus 7.0 in other inpatients (p < 0.01). The first peak (July-Novemebr 2020) showed ICU occupancy of 79.1%. The second peak (December 2020-June 2021) with 91.6% occupancy. The third peak January-March 2022 with 81.0% occupancy (p < 0.01). Lethality rates were 10.3% in 2020, 14.9% in 2021 and 15.4% in 2022 (p < 0.01). In conclusion, the ICU occupancy rate was higher in 2021 and the lethality rates of ICU patients were high during pandemic years (10.3% in 2020, 14.9% in 2021, and 15.2% in 2022). The lethality of these patients ranged from 25.0% in March to 21.8% in December 2020, from 20.9% in January 22.2% in Decemebr 2021, and 35.7% in January 2022 to 21.4% in April 2022. These data demonstrate that COVID-19 is a critical illness, even in a private hospital setting.

Temporal analysis of bovine pestivirus diversity in Brazil.

In this study, phylogenetic and evolutionary analyses of cattle pestiviruses (BVDV-1, 2 and HoBiPeV) originating in Brazil were used to investigate the temporal diversification of subgenotypes in the country. Inferred dated phylogeny and time of the most recent common ancestor (tMRCA) demonstrated that some BVDV subgenotypes (1a, 1b, 1d, 1e, and 2b) and HoBi-like sequences clustered according to the region in which they were collected and that the diversification of subgenotypes appears to have occurred around the introduction of first Bos taurus and then Bos indicus, followed by expansion to form the adapted Brazilian breeds. The present results help to elucidate the temporal facts that led to diversification of ruminant pestiviruses in cattle in Brazil.

Infecção cervical e anal pelo HPV em mulheres vivendo com HIV/AIDS: uma série de casos / Cervical and anal HPV infection in women living with HIV/AIDS: a series of cases

Introdução: Mulheres que vivem com o vírus da imunodeficiência humana (MVHIV) possuem risco aumentado de coinfecção pelo papilomavírus humano (HPV). A infecção persistente pelo HPV nos órgãos genitais de MVHIV pode resultar em câncer cervical e/ou anal. O objetivo deste estudo foi determinar a frequência da infecção por HPV cervical e anal em MVHIV e estabelecer relações epidemiológicas com os genótipos virais e dados clínicos e sociodemográficos. Métodos: Vinte e três mulheres foram avaliadas. Amostras do colo do útero e do ânus foram coletadas e analisadas por citologia convencional e para detecção do tipo do HPV pela técnica de nested-PCR e sequenciamento. Resultados: O HPV foi detectado em 39,1% das amostras do colo uterino e 47,8% do ânus. Dez tipos de HPV foram identificados, sendo cinco de alto risco e cinco de baixo risco para câncer. O HPV 11 foi o mais prevalente em todas as amostras analisadas. A detecção do HPV foi associada com situação conjugal, níveis linfócitos TCD4+, carga do HIV, citologias cervical e anal anormais. Anormalidade cervical e anal foi observada em 43,5% e 17,4% das mulheres, respectivamente, sendo o genótipo 11 o mais encontrado nesses casos. Conclusão: Tipos de HPV de alto e baixo risco para câncer foram identificados nas amostras. Os resultados destacam a importância da triagem citológica e molecular em MVHIV, mesmo em casos com tipos de HPV de baixo risco.

Introduction: Women living with HIV (WLHIV) have an increased risk of co-infection with human papillomavirus (HPV). Persistent HPV infection in the genital organs of WLHIV may result in cervical and/or anal cancer. The objective of this study was to determine the frequency of cervical and anal HPV infection in WLHIV and establish epidemiological relationships with viral genotypes and clinical and sociodemographic data. Methods: Twenty-three women were evaluated. Cervical and anal samples were collected and analyzed using conventional cytology. HPV type was determined by nested polymerase chain reaction and sequencing. Results: HPV was detected in 39.1% and 47.8% of cervical and anal samples, respectively. Ten types of HPV were identified, of which 5 had high (16, 35, 45, 53, and 56) and 5 had low (11, 44, 61, 70, and 84) oncogenic risk. HPV-11 was the prevalent type among analyzed samples. HPV detection was associated with marital status, CD4+ T lymphocyte count, HIV burden, and abnormal cervical and anal cytology. Cervical and anal abnormalities were observed in 43.5% and 17.4% of women, respectively, with genotype 11 being the most common in these cases. Conclusions: High- and low-oncogenic risk HPV were identified in the samples. The results highlight the importance of cytological and molecular screening in WLHIV, even in cases of low-risk HPV types.

Molecular phylogenetic assessment of the canine parvovirus 2 worldwide and analysis of the genetic diversity and temporal spreading in Brazil.

Canine parvovirus type 2 (CPV-2) is a relevant pathogen for dogs and causes a severe disease in carnivore species. CPV-2 reached pandemic proportions after the 1970s with the worldwide dissemination, generating antigenic and genetic variants (CPV-2a, CPV-2b, and CPV-2c) with different pathobiology in comparison with the original type CPV-2. The present study aimed to assess the current global CPV-2 molecular phylogeny and to analyze genetic diversity and temporal spreading of variants from Brazil. A total of 284 CPV-2 whole-genome sequences (WGS) and 684 VP2 complete genes (including 23 obtained in the present study) were compared to analyze phylogenetic relationships. Bayesian coalescent analysis estimated the time to the most recent common ancestor (tMRCA) and the population dynamics of the different CPV-2 lineages in the last decades. The WGS phylogenetic tree demonstrated two main clades disseminated worldwide today. The VP2 gene tree showed a total of four well-defined clades distributed in different geographic regions, including one with CPV-2 sequences exclusive from Brazil. These clades do not have a relationship with the previous classification into CPV-2a, CPV-2b, and CPV-2c, despite some having a predominance of one or more antigenic types. Temporal analysis demonstrated that the main CPV-2 clades evolved within a few years (from the 1980s to 1990s) in North America and they spread worldwide afterwards. Population dynamics analysis demonstrated that CPV-2 presented a major dissemination increase at the end of the 1980s / beginning of the 1990s followed by a period of stability and a second minor increase from 2000 to 2004.

Cardiogenic shock treated with temporary mechanical circulatory support in Brazil: The effect of learning curve.

AIMS: Treatment with mechanical circulatory support (MCS) has been proposed to mitigate mortality in cardiogenic shock (CS). However, there is a lack of data on MCS programs implementation and the effect of the learning curve on its outcomes in limited resources countries such as Brazil. METHODS: Prospective cohort of patients with CS admitted in four tertiary-care centers treated with Impella CP or veno-arterial extracorporeal membrane oxygenation (VA-ECMO). Clinical outcomes were peri-procedural complications, short-term mortality rate, and the centers' learning curve. The cohort was divided into two periods: from April 2017 to July 2018 (n = 24), and from August 2018 to December 2020 (n = 25). RESULTS: The study enrolled 49 patients [age 59 (43-63) years; 34 (70%) males]. The most common causes for CS were acute myocardial infarction in 22 (45%) and acute decompensation of chronic heart failure in 10 (20%). VA-ECMO was employed in 35 (71%) and Impella CP in 14 (29%) of patients. Overall complications occurred in 37 (76%) of patients, where major bleeding in 19 (38%) was the most common. The overall mortality rate was 61%, but it was lower in the second period (40%) in comparison to the first period (83%), p = 0.002. The learning curve analysis showed a decrease in the mortality rate after 40 consecutive cases. CONCLUSIONS: Implementation of a temporary MCS program for refractory CS in a limited resource country is feasible. The learning curve effect might have played a role on survival rate since high morbimortality has decreased within time reaching optimal results by the end of the study.

Recent molecular evolution of hepatitis B virus genotype F in Latin America.

The evolution of hepatitis B virus genotype F (HBV-F) in Latin America is not completely understood. The aim of this study was to evaluate the molecular evolution of HBV-F in Latin America by comparing 224 whole-genome sequences. Bayesian coalescent analysis was performed to estimate the time to the most recent common ancestor. Four main clades were found, dating from between 1245 and 1730. In addition, four subclades were identified, dating to between 1705 and 1801. The overall effective population size of HBV-F grew in the 18th century and showed an initial expansion outward from Venezuela to other countries from Latin America. Although HBV-F originated thousands of years ago, circulating strains of HBV-F appear to have spread in recent centuries, particularly in the 18th and 19th centuries. The new molecular data provide valuable information for characterizing the evolution of Native American HBV-F in recent centuries.

COVID-19: hypernatremia is a significant predictor of mortality

Introduction: Coronavirus disease 2019 (COVID-19) pandemic spread rapidly, creating a worrisome scenario worldwide. In hospitalized patients, dysnatremia (hyponatremia and/or hypernatremia) is the most common electrolyte disturbance, reported in 30­40% of cases and associated with a poor prognosis. This study aimed to evaluate the association between dysnatremia and mortality in hospitalized patients infected with SARS-COV-2. Methods: Retrospective longitudinal study that analyzed data from hospital records of 1,000 patients with COVID-19 (median age, 62.5 years; 57.1% men), including 109 (10.9%) deaths. Kaplan-Meier survival curves and Cox proportional hazard models with Hazard Ratio (HR) with 95% confidence intervals (95%CI) were applied to confirm the association between dysnatremia (hyponatremia and/or hypernatremia) and death. Results: Hypernatremia was detected in 83 (76.1%) of the patients who died, with a cumulative reduction in survival (p < 0.01) and a 2.42-fold increased mortality risk (95%CI: 1.45­2.91). In the multivariable analysis, hypernatremia was the main factor associated with increased mortality (HR: 1.50; 95%CI: 1.23­1.81). Long length of stay (LOS) (HR: 1.54; 95%CI: 1.21­1.78), old age (HR: 1.63; 95%CI: 1.28­1.88), and chronic kidney disease (HR: 1.77; 95%CI: 1.21­3.30) were also associated with death. Conclusion: Hypernatremia during hospitalization is an important risk factor for poor prognosis and an increased mortality risk. LOS, old age, and chronic kidney disease could also be used for risk stratification in patients with COVID-19.

Caracterização epidemiológica das neoplasias do sistema nervoso central em pacientes da região Norte do Brasil / Epidemiological characterization of central nervous system tumors in patients from Northern Brazil

Introdução: A incidência de neoplasias que acometem o Sistema Nervoso Central (SNC) tem aumentado gradativamente no mundo. No Brasil, as neoplasias encefálicas primárias são classificadas como a sétima causa de morte entre as neoplasias malignas. O objetivo do presente estudo foi caracterizar o perfil epidemiológico dos pacientes acometidos por neoplasias do SNC em um estado do Norte do Brasil.Métodos: Estudo retrospectivo, onde 196 prontuários, entre 2012 e 2016, de dois hospitais na região Norte do Brasil foram analisados.Resultados: O glioblastoma multiforme foi predominante (30,6%) entre as neoplasias primárias, seguido pelo astrocitoma (12,2%). As neoplasias secundárias, identificadas como metástases encefálicas, corresponderam a 29,9% da amostra, principalmente derivadas de neoplasias do pulmão e mama. A gravidade histológica das lesões neoplásicas foi mais frequente nos homens (p= 0,01). Foi observado que as neoplasias ocorreram com maior frequência a partir da 4º década de vida, exceto nos casos de astrocitoma e meduloblastoma, que foram detectadas principalmente em crianças e adultos jovens.Conclusão: A caracterização dos casos de neoplasias do SNC é de importante para a compreensão da situação atual deste problema de saúde pública na região norte do Brasil.

Introduction: The incidence of central nervous system (CNS) cancer has gradually increased worldwide. In Brazil, primary brain tumors are the seventh leading cause of death among malignant tumors. The objective of the present study was to characterize the epidemiological profile of patients with CNS cancer from a state in northern Brazil.Methods: This retrospective study analyzed 196 medical records between 2012 and 2016 from two hospitals in northern Brazil.Results: Glioblastoma multiforme was predominant (30.6%) among primary tumors, followed by astrocytoma (12.2%). Secondary cancer, defined as brain metastases, accounted for 29.9% of the sample and was mostly associated with lung and breast cancer. The histological severity of neoplastic lesions was more frequent in men (p = 0.01). Cancer occurred more frequently after the fourth decade of life, except in cases of astrocytoma and medulloblastoma, which mostly affected children and young adults.Conclusion: The characterization of CNS tumors is important for understanding the current situation of this public health problem in northern Brazil.

Incidência e fatores de risco associados à falha na ventilação não invasiva em pacientes pediátricos / Incidence and risk factors associated with noninvasive ventilation failure in pediatric patients

Introdução: O suporte ventilatório é usado para o tratamento de pacientes com insuficiência respiratória aguda (IRpA) ou crônica agudizada. A ventilação não-invasiva (VNI) na IRpA pediátrica é amplamente usada em bebês prematuros e crianças, porém até a data atual os estudos têm sido escassos. Portanto, o objetivo do presente estudo foi determinar os fatores de risco associados à falha na VNI em uma unidade de terapia intensiva pediátrica.Métodos: Coorte retrospectiva a partir de prontuários de pacientes admitidos na unidade de terapia intensiva (UTI) Pediátrica de um Hospital de Caxias do Sul, entre maio de 2017 e outubro de 2019, que utilizaram VNI.Resultados: A incidência de falha na VNI foi de 33%. Asma (RR = 1,36; IC95% = 1,08-1,72), uso de VNI em pacientes pós-extubação (RR = 1,97; IC95% = 1,17-3,29), uso contínuo da VNI (RR = 2,44; IC95% = 1,18-5,05), encerramento à noite (RR = 2,52; IC95% = 1,53-4,14), modalidade final ventilação mandatória intermitente sincronizada (SIMV) (RR = 4,20; IC95% = 2,20-7,90), pressão expiratória positiva final (PEEP) no início da ventilação (6,8 ± 1,1; p < 0,01) e fração inspiratória de O2 (FIO2) final (53,10 ± 18,50; p < 0,01) foram associados à falha. Adicionalmente, a pressão arterial sistólica (PAS) inicial (118,68 ± 18,68 mmHg; p = 0,02), a frequência respiratória inicial (FR) (47,69 ± 14,76; p = 0,28) e final (47,54 ± 14,76; p < 0,01) foram associados a falha.Conclusão: A modalidade ventilatória final SIMV, demostra ser o melhor preditor de risco de falha, seguido do turno em que a VNI é finalizada, onde à noite existe maior risco de falha. Além disso, foram preditores de falha, porém com menor robustez, a pressão positiva inspiratória (PIP) final e a FR final.

Introduction: Ventilatory support is used for the treatment of patients with acutely chronic or acute respiratory failure (ARF). Noninvasive ventilation (NIV) in pediatric ARF is widely used in preterm infants and children, but studies to date have been limited. Therefore, the aim of the present study was to determine the risk factors associated with NIV failure in a pediatric intensive care unit.Methods: This retrospective cohort study was based on medical records of patients admitted to the pediatric intensive care unit of a hospital in Caxias do Sul, southern Brazil, between May 2017 and October 2019, who used NIV.Results: The incidence of NIV failure was 33%. Asthma (relative risk [RR] = 1.36; 95% confidence interval [CI] = 1.08-1.72), post-extubation use of NIV (RR = 1.97; 95% CI = 1.17-3.29), continuous use of NIV (RR = 2.44; 95% CI = 1.18-5.05), completion at night (RR = 2.52; 95% CI = 1.53-4.14), final mode synchronized intermittent mandatory ventilation (SIMV) (RR = 4.20; 95% CI = 2.20-7.90), positive end-expiratory pressure at the beginning of ventilation (6.8 ± 1.1; p < 0.01), and final fraction of inspired oxygen (53.10 ± 18.50; p < 0.01) were associated with failure. Additionally, initial systolic blood pressure (118.68 ± 18.68 mmHg; p = 0.02), initial respiratory rate (IRR) (47.69 ± 14.76; p = 0.28), and final respiratory rate (47.54 ± 14.76; p < 0.01) were associated with failure.Conclusion: The final ventilatory mode SIMV proves to be the best failure risk predictor, followed by the shift in which NIV is completed, as there is a greater risk of failure at night. In addition, final positive inspiratory pressure and final respiratory rate were less robust predictors of failure.

Temporal and geographic spreading of hepatitis B virus genotype A (HBV-A) in Brazil and the Americas.

Hepatitis B virus genotype A (HBV-A) is disseminated in different countries around the world. It presents a high genetic diversity and is classified into seven subgenotypes (A1-A7). HBV-A1 and HBV-A2 are the most frequent and spread in almost all American countries. This study aimed to evaluate the molecular epidemiology of these two subgenotypes, with a special focus on the temporal and geographic spreading in the Americas and Brazil. Bayesian coalescent analyses with HBV-A1 and HBV-A2 whole-genome sequences were performed to study viral phylodynamic and phylogeography. HBV-A1 evolutionary history demonstrated that it was initially disseminated from Africa to other continents probably after the 1400s and mainly in the 17th-18th centuries. The whole viral population grew between the 1700s-1900s and then reached a stationary phase. In Brazil, HBV-A1 common ancestors dated back to the 1600s with successive introductions between the 17th-18th centuries. In contrast, HBV-A2 spread from Europe to other continents after the 1800s, with an increase in the viral population over decades. It was introduced in the 20th century in America and between the 1950s-1970s in Brazil, presenting a high increase in the viral population from the 1970s to the 1980s. The circulation continents for HBV-A1 are Africa and America, while for HBV-A2 are Europe and America. HBV-A is one of the predominant genotypes in America (including Brazil) because of the early introduction by human migration processes of the subgenotypes A1 and A2 between the 16th and 20th centuries and the continuous spreading inside the continent over time.

Hepatitis B virus genotypes in Brazil: Introduction and dissemination.

Hepatitis B is a viral infectious disease highly spread worldwide with a long evolutionary history associated with human migrations through the continents and countries. Hepatitis B virus (HBV) was disseminated probably from Africa and diverged into ten genotypes (HBV-A to HBV-J) distributed around the world. In Brazil, almost all HBV genotypes were already reported, with a predominance of three ones: A (52.1%), D (36.8%), and F (7.7%). This review aimed to evaluate the introduction and dissemination of the main HBV genotypes and subgenotypes in Brazil over the last centuries to explain the current epidemic scenario. The highest frequency of HBV-A is a consequence of the introduction and spreading of HBV-A1 in the 16th to 19th centuries due to the African slave trade, but the more recent introduction of HBV-A2 from Europe also contributed to the current situation. HBV-D is the second most frequent genotype because it was consecutively introduced by migrations from Europe (mainly subgenotype D3, but also D2) and the Middle East (D1) in the 19th to 20th centuries. On contrary, HBV-F (F1a, F1b, F2a, F2b, F3, and F4) was disseminated by the Amerindians in all South American countries, including Brazil, by migrations inside the continent for more than three centuries ago. Other HBV genotypes are rare and eventually frequent in some human groups because of the dissemination by very specific epidemiological routes. In conclusion, the current scenario of the HBV epidemics is a consequence of the introduction and dissemination of some subgenotypes from the three main genotypes A, D, and F over the last five centuries.

Dissemination and evolution of SARS-CoV-2 in the early pandemic phase in South America.

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic spread rapidly and this scenario is concerning in South America, mainly in Brazil with more than seven million cases of infection. Three major pandemic lineages/clades could be identified along with SARS-CoV-2 dissemination (G, GR, and GH) in the Americas. These clades differ according to their genomic characteristics, virulence, and spreading times. The present study describes the main clades and the respective temporal spreading analyses based on SARS-CoV-2 whole-genome sequences (WGS) from South America, obtained in the early pandemic phase (from March 1 to May 31 in 2020). SARS-CoV-2 WGSs with available information from country and year of sampling were obtained from different countries and the main clades were identified and analyzed independently with a Bayesian approach. The results demonstrated the prevalence of clades GR (n = 842; 54.6%), G (n = 529; 34.3%), and GH (n = 171; 11.1%). The frequencies of the clades were significantly different between South American countries. Clade G was the most prevalent in Ecuador, Suriname, and Uruguay, clade GR in Argentina, Brazil, and Peru, and clade GH in Colombia. The phylodynamic analysis indicated that all these main lineages increased viral spreading from February to early March and after an evolutionary stationary phase was observed. The decrease observed in the virus dissemination was directly associated to the reduction of social movement after March. In conclusion, these data demonstrated the current predominance of clades G, GR, and GH in South America because of the early dissemination of them in the first pandemic phase in South America.

Temporal evolution and global spread of hepatitis B virus genotype G.

Hepatitis B virus (HBV) infection is considered a major health problem in the world. HBV is classified into genotypes A to J disseminated worldwide. Genotypes A, D and F are the most frequent in the Western World, B and C are predominant in the East, and E, F, H and J are infrequent and restricted to specific regions. HBV-G is a rare genotype, but it has been detected in different continents. This study aimed to report the temporal evolution and global spread of HBV-G comparing whole-genome sequences of this genotype from different regions in the world. Bayesian coalescent analysis was performed to estimate the time to the most recent common ancestor (tMRCA) and the population dynamics in the last decades. The results demonstrated that tMRCA of all HBV-Gs dated back to 1855 (95% highest posterior density interval [HPD 95%]: 1778 - 1931). This genotype has a possible origin in North America and it was disseminated to other continents (South and Central America, Europe, Asia and Africa) more than one century later (around the 1970s). The viral population demonstrated constant spreading from 1855 to the 1980s, followed by an increase in the 1990s and reached a plateau after the 2000s. Wide spreading at the beginning of the 1990s was probably associated with the dissemination by highly sexual active groups and injecting drug users. In conclusion, the present study demonstrated that HBV-G was originated in the 19th century with main events of spread at the end of the 20th century.

Evolutionary history of hepatitis B virus genotype H.

Hepatitis B virus genotype H (HBV-H) molecular evolution was studied by comparing all published whole-genome sequences. Bayesian coalescent analysis was performed to estimate phylogenetic relationships, time to the most recent common ancestor (tMRCA), and viral population dynamics along the time. Phylogenetic tree demonstrated two main clades or lineages: HBV-H I (with sequences from Central and North America) and HBV-H II (with sequences from North and South America, and Asia). HBV-H II had more genome sequences (n = 26; 83.9%), including one specific subclade with all sequences outside of the Americas. Overall HBV-H tMRCA dated back to 1933 (95% highest posterior density interval [HPD 95%]: 1875-1957) with a very probable origin in Mexico and posterior dissemination to other American and Asian countries. The temporal analysis demonstrated that HBV-H I spread only in Mexico and the neighbor country of Nicaragua probably in the 1960s to the 1970s (1968; HPD 95%: 1908-1981), while HBV-II disseminated to other American and Asian countries around one decade later (1977; HPD 95%: 1925-1985). The phylogeographic analysis reinforced the Mexican origin of this genotype. The whole HBV-H population increased from the 1980s to the 2000s. In conclusion, HBV-H has two main lineages with a common origin in Mexico approximately nine decades ago.

Desfecho da aplicação da ventilação mecânica não invasiva na bronquiolite / Outcome of the application of noninvasive mechanical ventilation in bronchiolitis

A bronquiolite é uma infecção viral que pode levar a insuficiência ventilatória, nestes casos a aplicação de ventilação não invasiva é uma opção ao tratamento convencional. O objetivo deste estudo é identificar o desfecho da aplicação de ventilação não invasiva em crianças com bronquiolite. Trata-se de uma revisão da literatura, com busca de artigos nas bases de dados Biblioteca Virtual em Saúde, Cochrane Library, PEDro, Pubmed, Scielo e Science Direct, sem restrição de período, a partir das palavras chave Noninvasive ventilation AND Bronchiolitis. De um total de 1.192 artigos encontrados, 11 foram inclusos no presente estudo, quatro abordaram o desfecho relacionado à aspectos clínicos gerais (aumento no uso de VNI; menor tempo de internação; redução da frequência respiratória e fração inspirada de oxigênio) e sete relataram o índice de sucesso ou falha, e apesar da diferença entre as médias (sucesso 88,5 versus falha 15,1) não houve diferença significativa. Conclui-se que o desfecho de falha tem alta prevalência (11,5%), apesar disso, os estudos encontraram diferentes benefícios advindos do incremento na aplicação de VNI (redução da necessidade de ventilação mecânica invasiva, menor tempo de permanência em UTI, redução da mortalidade, melhora da frequência respiratória e da fração inspirada de oxigênio). (AU)

Bronchiolitis is a viral infection that can lead to ventilatory failure. In such cases, the application of noninvasive ventilation (NIV) is an alternative to conventional treatment. The aim of this study is to identify the outcome of the application of NIV in children with bronchiolitis. This is a literature review whose search for articles included the Virtual Health Library, Cochrane Library, PEDro, PubMed, SciELO, and Science Direct databases, with no date restriction, based on the keywords Noninvasive ventilation AND Bronchiolitis. Of a total of 1192 articles found, 11 were included in the present study. Four addressed the outcome related to general clinical aspects (increased use of NIV, shorter hospital stay, and reduced respiratory rate and inspired oxygen fraction) and seven reported the success or failure rate. Despite the difference between the means (success 88.5 versus failure 15.1) there was no significant difference. In conclusion, the failure outcome has a high prevalence (11.5%); however, studies have found different benefits arising from the increased application of NIV (reduced need for invasive mechanical ventilation, shorter intensive care unit stay, reduced mortality, and improved respiratory rate and inspired oxygen fraction). (AU)

Improvement of Mycobacterium tuberculosis detection in sputum using DNA extracted by sonication

Abstract Tuberculosis (TB) is one of the infectious diseases with high mortality in the world. DNA amplification techniques have been used to overcome barriers to the diagnosis of this disease. However, the success of these methodologies is highly dependent on the DNA obtained from the sample. This study was carried out to verify whether the DNA extracted by sonication (in house method) could yield suitable DNA for amplification by real-time PCR (qPCR). Sixty sputum samples were submitted to DNA extraction using sonication compared to a commercial method (Detect-TB kit, Labtest/MG-Brazil). All DNA samples were amplified by qPCR for IS6110 region (IS6110-qPCR/SYBR Green assay). Out of 60 samples, 40 were positive for TB; of these, all had positive results when extracted by sonication (100%) and 80% when extracted by the commercial method. The limit of detection (LOD) of Mycobacterium tuberculosis (H37Rv strain) by qPCR was 14CFU/mL when the DNA was extracted by sonication, compared to countless colonies when extracted by commercial kit. In conclusion, the sonication protocol (without purification step) proved to be a simple, fast, and suitable method for obtaining DNA for use in qPCR from sputum samples.

Improvement of Mycobacterium tuberculosis detection in sputum using DNA extracted by sonication.

Tuberculosis (TB) is one of the infectious diseases with high mortality in the world. DNA amplification techniques have been used to overcome barriers to the diagnosis of this disease. However, the success of these methodologies is highly dependent on the DNA obtained from the sample. This study was carried out to verify whether the DNA extracted by sonication (in house method) could yield suitable DNA for amplification by real-time PCR (qPCR). Sixty sputum samples were submitted to DNA extraction using sonication compared to a commercial method (Detect-TB kit, Labtest/MG-Brazil). All DNA samples were amplified by qPCR for IS6110 region (IS6110-qPCR/SYBR Green assay). Out of 60 samples, 40 were positive for TB; of these, all had positive results when extracted by sonication (100%) and 80% when extracted by the commercial method. The limit of detection (LOD) of Mycobacterium tuberculosis (H37Rv strain) by qPCR was 14 CFU/mL when the DNA was extracted by sonication, compared to countless colonies when extracted by commercial kit. In conclusion, the sonication protocol (without purification step) proved to be a simple, fast, and suitable method for obtaining DNA for use in qPCR from sputum samples.