Phylogeographic Analysis of HIV-1 Subtype C Dissemination in Southern Brazil

The HIV-1 subtype C has spread efficiently in the southern states of Brazil (Rio Grande do Sul, Santa Catarina and Paraná). Phylogeographic studies indicate that the subtype C epidemic in southern Brazil was initiated by the introduction of a single founder virus population at some time point between 1960 and 1980, but little is known about the spatial dynamics of viral spread. A total of 135 Brazilian HIV-1 subtype C pol sequences collected from 1992 to 2009 at the three southern state capitals (Porto Alegre, Florianópolis and Curitiba) were analyzed. Maximum-likelihood and Bayesian methods were used to explore the degree of phylogenetic mixing of subtype C sequences from different cities and to reconstruct the geographical pattern of viral spread in this country region. Phylogeographic analyses supported the monophyletic origin of the HIV-1 subtype C clade circulating in southern Brazil and placed the root of that clade in Curitiba (Paraná state). This analysis further suggested that Florianópolis (Santa Catarina state) is an important staging post in the subtype C dissemination displaying high viral migration rates from and to the other cities, while viral flux between Curitiba and Porto Alegre (Rio Grande do Sul state) is very low. We found a positive correlation (r2 = 0.64) between routine travel and viral migration rates among localities. Despite the intense viral movement, phylogenetic intermixing of subtype C sequences from different Brazilian cities is lower than expected by chance. Notably, a high proportion (67%) of subtype C sequences from Porto Alegre branched within a single local monophyletic sub-cluster. These results suggest that the HIV-1 subtype C epidemic in southern Brazil has been shaped by both frequent viral migration among states and in situ dissemination of local clades

Early mobilisation in critically ill COVID-19 patients: a subanalysis of the ESICM-initiated UNITE-COVID observational study

Background Early mobilisation (EM) is an intervention that may improve the outcome of critically ill patients. There is limited data on EM in COVID-19 patients and its use during the first pandemic wave. Methods This is a pre-planned subanalysis of the ESICM UNITE-COVID, an international multicenter observational study involving critically ill COVID-19 patients in the ICU between February 15th and May 15th, 2020. We analysed variables associated with the initiation of EM (within 72 h of ICU admission) and explored the impact of EM on mortality, ICU and hospital length of stay, as well as discharge location. Statistical analyses were done using (generalised) linear mixed-effect models and ANOVAs. Results Mobilisation data from 4190 patients from 280 ICUs in 45 countries were analysed. 1114 (26.6%) of these patients received mobilisation within 72 h after ICU admission; 3076 (73.4%) did not. In our analysis of factors associated with EM, mechanical ventilation at admission (OR 0.29; 95% CI 0.25, 0.35; p = 0.001), higher age (OR 0.99; 95% CI 0.98, 1.00; p ≤ 0.001), pre-existing asthma (OR 0.84; 95% CI 0.73, 0.98; p = 0.028), and pre-existing kidney disease (OR 0.84; 95% CI 0.71, 0.99; p = 0.036) were negatively associated with the initiation of EM. EM was associated with a higher chance of being discharged home (OR 1.31; 95% CI 1.08, 1.58; p = 0.007) but was not associated with length of stay in ICU (adj. difference 0.91 days; 95% CI − 0.47, 1.37, p = 0.34) and hospital (adj. difference 1.4 days; 95% CI − 0.62, 2.35, p = 0.24) or mortality (OR 0.88; 95% CI 0.7, 1.09, p = 0.24) when adjusted for covariates. Conclusions Our findings demonstrate that a quarter of COVID-19 patients received EM. There was no association found between EM in COVID-19 patients' ICU and hospital length of stay or mortality. However, EM in COVID-19 patients was associated with increased odds of being discharged home rather than to a care facility. Trial registration ClinicalTrials.gov: NCT04836065 (retrospectively registered April 8th 2021)

Reluctance to start medication for Parkinson's disease: a mutual misunderstanding by patients and physicians

Copyright © 2014 Published by Elsevier Ltd.Reluctance to start medication has never been investigated before in PD. We studied reluctance to start medication for PD motor symptoms, namely its prevalence, underlying reasons, drug-specificity, and associated delay in the start of PD medication. A cross-sectional observational international study was conducted. Patients with a clinical diagnosis of PD advised to start antiparkinsonian medication in the previous 5 years were invited to complete a questionnaire in three centers located in North America and Europe. An electronic online survey was sent to physicians through the mailing list of the Movement Disorder Society. 469 participants (201 PD patients, 268 physicians). 40.2% (n = 82) of the patients reported reluctance to start medication, but 88.6% (n = 234/264) of the physicians estimated that ≤20% of their patients with PD had been reluctant to start medication. The most common reasons reported by patients were the fear of side effects (n = 35, 55.6%), followed by non-acceptance of diagnosis (n = 23, 36.5%); fear of a temporally limited benefit was more commonly selected by physicians (n = 92/267, 34.5%). Patients indicated reluctance to start DAs more frequently compared with L-DOPA (OR: 2.22, 95% CI: 1.30, 9.03; p = 0.013) while physicians perceived L-DOPA to be associated with more reluctance (OR: 4.7, 95% CI: 3.41; 6.59; p < 0.0001). Patients with PD and physicians have a different perspective on the issue of reluctance to start medication. There is a need to bring physicians and patients with PD closer to a shared vision of the problem reluctance to start medication.info:eu-repo/semantics/publishedVersio

Detection of the B"-GWGR variant in the southernmost region of Brazil: unveiling the complexity of the human immunodeficiency virus-1 subtype B epidemic

Typical human immunodeficiency virus-1 subtype B (HIV-1B) sequences present a GPGR signature at the tip of the variable region 3 (V3) loop; however, unusual motifs harbouring a GWGR signature have also been isolated. Although epidemiological studies have detected this variant in approximately 17-50% of the total infections in Brazil, the prevalence of B"-GWGR in the southernmost region of Brazil is not yet clear. This study aimed to investigate the C2-V3 molecular diversity of the HIV-1B epidemic in southernmost Brazil. HIV-1 seropositive patients were ana-lysed at two distinct time points in the state of Rio Grande do Sul (RS98 and RS08) and at one time point in the state of Santa Catarina (SC08). Phylogenetic analysis classified 46 individuals in the RS98 group as HIV-1B and their molecular signatures were as follows: 26% B"-GWGR, 54% B-GPGR and 20% other motifs. In the RS08 group, HIV-1B was present in 32 samples: 22% B"-GWGR, 59% B-GPGR and 19% other motifs. In the SC08 group, 32 HIV-1B samples were found: 28% B"-GWGR, 59% B-GPGR and 13% other motifs. No association could be established between the HIV-1B V3 signatures and exposure categories in the HIV-1B epidemic in RS. However, B-GPGR seemed to be related to heterosexual individuals in the SC08 group. Our results suggest that the established B"-GWGR epidemics in both cities have similar patterns, which is likely due to their geographical proximity and cultural relationship

Phylogenetic-based inference reveals distinct transmission dynamics of SARS-CoV-2 lineages Gamma and P.2 in Brazil

Fundação de Amparo à Pesquisa do Estado do Amazonas (PCTI-EmergeSaude/AM call 005/2020 and Rede Genômica de Vigilância em Saúde-REGESAM); Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) (grant 402457/2020–0); CNPq/Ministério da Ciência, Tecnologia, Inovação e Comunicação/Ministério da Saúde (MS/FNDCT/ SCTIE/Decit) (grant 403276/2020-9); Departamento da Ciência e Tecnologia (DECIT), Ministério da Saúde; Inova Fiocruz/Fundação Oswaldo Cruz (Grants VPPCB-007-FIO-18–2–30 and VPPCB-005-FIO-20–2–87), INCT-FCx (465259/2014–6) and Fundação Carlos Chagas Filho de Amparo a` Pesquisa do Estado do Rio de Janeiro (26/210.196/2020). CNPq (306146/2017–7, 303902/2019–1, 302317/2017–1 and 313403/2018-0, respectively). FAPERJ (Grant number E-26/202.896/2018).Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Salvador, BA, BrazilFundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de AIDS e Imunologia Molecular. Rio de Janeiro, RJ, BrazilFundação Oswaldo Cruz. Leônidas e Maria Deane Institute. Laboratório de Ecologia de Doenças Transmissíveis na Amazônia. Manaus, AM, BrazilFundação Oswaldo Cruz. Programa de Computação Científica. Grupo de Métodos Analíticos em Vigilância Epidemiológica. Rio de Janeiro, RJ, BrazilFundação Oswaldo Cruz. Instituto Gonçalo Moniz. Salvador, BA, BrazilFundação Oswaldo Cruz. Instituto Aggeu Magalhães. Recife, PE, BrazilFundação Oswaldo Cruz. Instituto Aggeu Magalhães. Recife, PE, BrazilMinistério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, BrasilInstituto Adolfo Lutz. São Paulo, SP, BrazilSecretaria de Saúde de Aparecida de Goiânia. Goiás, GO, BrazilSecretaria de Saúde de Aparecida de Goiânia. Goiás, GO, BrazilLaboratório HLAGYN. Goiânia, GO, BrazilFundação Oswaldo Cruz . Fortaleza, CE, BrazilFundação Oswaldo Cruz. Instituto Carlos Chagas. Curitiba, PR, BrazilFundação Oswaldo Cruz. Instituto Gonçalo Moniz. Salvador, BA, BrazilFundação Oswaldo Cruz. Instituto Aggeu Magalhães. Recife, PE, BrazilUniversidade Federal do Espirito Santo. Departamento de Biologia. Centro de Ciências Exatas, Naturais e da Saude. Espirito Santo, ES, BrazilOswaldo Cruz Foundation. Oswaldo Cruz Institute. Laboratory of Respiratory Viruses and Measles. Rio de Janeiro, RJ, BrazilOswaldo Cruz Foundation. Oswaldo Cruz Institute. Laboratory of Respiratory Viruses and Measles. Rio de Janeiro, RJ, BrazilThe COVID-19 epidemic in Brazil experienced two major lineage replacements until mid-2021. The first was driven by lineage P.2, in late 2020, and the second by lineage Gamma, in early 2021. To understand how these SARS-CoV-2 lineages spread in Brazil, we analyzed 11,724 genomes collected throughout the country between September 2020 and April 2021. Our findings indicate that lineage P.2 probably emerged in July 2020 in the Rio de Janeiro state and Gamma in November 2020 in the Amazonas state. Both states were the main hubs of viral disseminations to other Brazilian locations. We estimate that Gamma was 1.56-3.06 times more transmissible than P.2 in Rio de Janeiro and that the median effective reproductive number (Re) of Gamma varied according to the geographic context (Re = 1.59-3.55). In summary, our findings support that lineage Gamma was more transmissible and spread faster than P.2 in Brazil

Reemergence of Dengue Virus serotype 3, Brazil, 2023

Fundação Oswaldo Cruz. Rio de Janeiro, RJ, Brazil / Fundação Oswaldo Cruz. Manaus, AM, Brazil.Centers for Disease Control and Prevention. San Juan, PR, USA.Laboratório Central de Saúde Pública de Roraima. Boa Vista, RR, Brazil.Laboratório Central de Saúde Pública de Roraima. Boa Vista, RR, Brazil.Fundação Oswaldo Cruz. Manaus, AM, Brazil.Fundação Oswaldo Cruz. Manaus, AM, Brazil.Fundação Oswaldo Cruz. Manaus, AM, Brazil.Fundação Oswaldo Cruz. Manaus, AM, Brazil.Fundação Oswaldo Cruz. Manaus, AM, Brazil.Fundação de Vigilância em Saúde Dra. Rosemary Costa Pinto. Manaus, AM, Brazil.Fundação de Medicina Tropical Dr Heitor Vieira Dourado. Manaus, AM, Brazil.Ministério da Saúde. Secretaria de Vigilância em Saúde e Ambiente. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde e Ambiente. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Laboratório Central de Saúde Pública do Paraná. Curitiba, PR, Brazil.Laboratório Central de Saúde Pública do Paraná. Curitiba, PR, Brazil.Laboratório Central de Saúde Pública do Paraná. Curitiba, PR, Brazil.Fundação Oswaldo Cruz. Rio de Janeiro, RJ, Brazil.Fundação Oswaldo Cruz. Rio de Janeiro, RJ, Brazil.Fundação Oswaldo Cruz. Rio de Janeiro, RJ, BrazilFundação Oswaldo Cruz. Rio de Janeiro, RJ, Brazil.Fundação Oswaldo Cruz. Rio de Janeiro, RJ, Brazil.Fundação Oswaldo Cruz. Recife, PE, Brazil.Fundação Oswaldo Cruz. Recife, PE, Brazil.Fundação Oswaldo Cruz. Curitiba, PR, Brazil.Universidade Federal do Espírito Santo. Alegre, ES, Brazil.Florida Department of Health. Tampa, FL, USA.Florida Department of Health. Tampa, FL, USA.Centers for Disease Control and Prevention. San Juan, PR, USA.Fundação Oswaldo Cruz. Rio de Janeiro, RJ, Brazil.We characterized 3 autochthonous dengue virus serotype 3 cases and 1 imported case from 2 states in the North and South Regions of Brazil, 15 years after Brazil’s last outbreak involving this serotype. We also identified a new Asian lineage recently introduced into the Americas, raising concerns about future outbreaks

Evolutionary dynamics and dissemination pattern of the SARS-CoV-2 lineage B.1.1.33 during the early pandemic phase in Brazil

We would like to thank the funding support from CGLab/MoH (General Laboratories Coordination of Brazilian Ministry of Health), CVSLR/FIOCRUZ (Coordination of Health Surveillance and Reference Laboratories of Oswaldo Cruz Foundation), CNPq COVID-19 MCTI 402457/2020-0, and INOVA VPPCB-005-FIO20-2Oswaldo Cruz Foundation. Oswaldo Cruz Institute. Laboratory of Respiratory Viruses and Measles. Rio de Janeiro, RJ, Brasil / Brazilian Ministry of Health. Pan-American Health Organization. SARS-CoV-2 National Reference Laboratory. Regional Reference Laboratory in Americas. Rio de Janeiro, RJ, Brazil.Universidade Federal do Espírito Santo - Campus de Alegre. Centro de Ciências Exatas, Naturais e da Saude. Departamento de Biologia. Vitória, ES, Brazil.Fundação Oswaldo Cruz. Gonçalo Moniz. Salvador, BA, Brazil.Universidad de la Republica. Centro Universitario Regional del Litoral Norte. Unidad de Genomica y Bioinformatica. Salto, Uruguay.Oswaldo Cruz Foundation. Oswaldo Cruz Institute. Laboratory of Respiratory Viruses and Measles. Rio de Janeiro, RJ, Brasil / Brazilian Ministry of Health. Pan-American Health Organization. SARS-CoV-2 National Reference Laboratory. Regional Reference Laboratory in Americas. Rio de Janeiro, RJ, Brazil.Oswaldo Cruz Foundation. Oswaldo Cruz Institute. Laboratory of Respiratory Viruses and Measles. Rio de Janeiro, RJ, Brasil / Brazilian Ministry of Health. Pan-American Health Organization. SARS-CoV-2 National Reference Laboratory. Regional Reference Laboratory in Americas. Rio de Janeiro, RJ, Brazil.Oswaldo Cruz Foundation. Oswaldo Cruz Institute. Laboratory of Respiratory Viruses and Measles. Rio de Janeiro, RJ, Brasil / Brazilian Ministry of Health. Pan-American Health Organization. SARS-CoV-2 National Reference Laboratory. Regional Reference Laboratory in Americas. Rio de Janeiro, RJ, Brazil.Oswaldo Cruz Foundation. Oswaldo Cruz Institute. Laboratory of Respiratory Viruses and Measles. Rio de Janeiro, RJ, Brasil / Brazilian Ministry of Health. Pan-American Health Organization. SARS-CoV-2 National Reference Laboratory. Regional Reference Laboratory in Americas. Rio de Janeiro, RJ, Brazil.Oswaldo Cruz Foundation. Oswaldo Cruz Institute. Laboratory of Respiratory Viruses and Measles. Rio de Janeiro, RJ, Brasil / Brazilian Ministry of Health. Pan-American Health Organization. SARS-CoV-2 National Reference Laboratory. Regional Reference Laboratory in Americas. Rio de Janeiro, RJ, Brazil.Oswaldo Cruz Foundation. Oswaldo Cruz Institute. Laboratory of Respiratory Viruses and Measles. Rio de Janeiro, RJ, Brasil / Brazilian Ministry of Health. Pan-American Health Organization. SARS-CoV-2 National Reference Laboratory. Regional Reference Laboratory in Americas. Rio de Janeiro, RJ, Brazil.Fundação Oswaldo Cruz. Instituto Aggeu Magalhaes. Recife, PE, Brazil.Fundação Oswaldo Cruz. Instituto Aggeu Magalhaes. Recife, PE, Brazil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Laboratorio Central de Saude Publica do Estado de Santa Catarina. Florianopolis, SC, Brazil.Laboratorio Central de Saude Publica do Estado Espirito Santo. Vitoria, ES, Brazil.Laboratorio Central de Saude Publica do Distrito Federal. Brasília, DF, Brazil.Laboratorio Central de Saude Publica de Alagoas. Maceio, AL, Brazil.Laboratorio Central de Saude Publica da Bahia. Salvador, BA, Brazil.Laboratorio Central de Saude Publica de Sergipe. Aracaju, SE, Brazil.Laboratorio Central de Saude Publica de Parana. Curitiba, PR, Brazil.Laboratorio Central de Saude Publica de Parana. Curitiba, PR, Brazil.Fundação Oswaldo Cuz - Mato Grosso do Sul. Campo Grande, MT, Brazil / Universidade Federal de Mato Grosso do Sul. Campo Grande, MT, Brazil.Ministério da Defesa. Hospital das Forças Armadas. Brasília, DF, Brazil.Ministério da Saude. Coordenadoria Geral de Laboratorios. Brasília, DF, Brazil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratorio de AIDS e Imunologia Molecular. Rio de Janeiro, RJ, Brazil.Oswaldo Cruz Foundation. Oswaldo Cruz Institute. Laboratory of Respiratory Viruses and Measles. Rio de Janeiro, RJ, Brasil / Brazilian Ministry of Health. Pan-American Health Organization. SARS-CoV-2 National Reference Laboratory. Regional Reference Laboratory in Americas. Rio de Janeiro, RJ, Brazil.A previous study demonstrates that most of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) Brazilian strains fell in three local clades that were introduced from Europe around late February 2020. Here we investigated in more detail the origin of the major and most widely disseminated SARS-CoV-2 Brazilian lineage B.1.1.33. We recovered 190 whole viral genomes collected from 13 Brazilian states from February 29 to April 31, 2020 and combined them with other B.1.1 genomes collected globally. Our genomic survey confirms that lineage B.1.1.33 is responsible for a variable fraction of the community viral transmissions in Brazilian states, ranging from 2% of all SARS-CoV-2 genomes from Pernambuco to 80% of those from Rio de Janeiro. We detected a moderate prevalence (5-18%) of lineage B.1.1.33 in some South American countries and a very low prevalence (<1%) in North America, Europe, and Oceania. Our study reveals that lineage B.1.1.33 evolved from an ancestral clade, here designated B.1.1.33-like, that carries one of the two B.1.1.33 synapomorphic mutations. The B.1.1.33-like lineage may have been introduced from Europe or arose in Brazil in early February 2020 and a few weeks later gave origin to the lineage B.1.1.33. These SARS-CoV-2 lineages probably circulated during February 2020 and reached all Brazilian regions and multiple countries around the world by mid-March, before the implementation of air travel restrictions in Brazil. Our phylodynamic analysis also indicates that public health interventions were partially effective to control the expansion of lineage B.1.1.33 in Rio de Janeiro because its median effective reproductive number (R e ) was drastically reduced by about 66% during March 2020, but failed to bring it to below one. Continuous genomic surveillance of lineage B.1.1.33 might provide valuable information about epidemic dynamics and the effectiveness of public health interventions in some Brazilian states

Genomic and Epidemiological Surveillance of Zika Virus in the Amazon Region

Zika virus (ZIKV) has caused an explosive epidemic linked to severe clinical outcomes in the Americas. As of June 2018, 4,929 ZIKV suspected infections and 46 congenital syndrome cases had been reported in Manaus, Amazonas, Brazil. Although Manaus is a key demographic hub in the Amazon region, little is known about the ZIKV epidemic there, in terms of both transmission and viral genetic diversity. Using portable virus genome sequencing, we generated 59 ZIKV genomes in Manaus. Phylogenetic analyses indicated multiple introductions of ZIKV from northeastern Brazil to Manaus. Spatial genomic analysis of virus movement among six areas in Manaus suggested that populous northern neighborhoods acted as sources of virus transmission to other neighborhoods. Our study revealed how the ZIKV epidemic was ignited and maintained within the largest urban metropolis in the Amazon. These results might contribute to improving the public health response to outbreaks in Brazil.status: publishe