The HIV-1 epidemic in Brazil has spread towards the Northern country region, but little is known about HIV-1 subtypes and prevalence of HIV strains with resistance mutations to antiretrovirals in ...some of the Northern states. HIV-1 protease (PR) and reverse transcriptase (RT) sequences were obtained from 73 treatment-naive and -experienced subjects followed between 2013 and 2014 at a public health reference unit from Roraima, the northernmost Brazilian state. The most prevalent HIV-1 clade observed in the study population was the subtype B (91%), followed by subtype C (9%). Among 12 HIV-1 strains from treatment-naïve patients, only one had a transmitted drug resistance mutation for NNRTI. Among 59 treatment-experienced patients, 12 (20%) harbored HIV-1 strains with acquired drug resistance mutations (ADRM) that reduce the susceptibility to two classes of antiretroviral drugs (NRTI and NNRTI or NRTI and PI), and five (8%) harbored HIV-1 strains with ADRM that reduced susceptibility to only one class of antiretroviral drugs (NNRTI or PI). No patients harboring HIV strains with reduced susceptibility to all three classes of antiretroviral drugs were detected. A substantial fraction of treatment-experienced patients with (63%) and without (70%) ADRM had undetectable plasma viral loads (<40 copies/ml) at the time of sampling. Among treatment-experienced with plasma viral loads above 2,000 copies/ml, 44% displayed no ADRM. This data showed that the HIV-1 epidemic in Roraima displayed a much lower level of genetic diversity and a lower prevalence of ADRM than that described in other Brazilian states.
The Human immunodeficiency virus type-1 (HIV-1) epidemic in Brazil is mainly driven by the subtype B pandemic lineage (BPANDEMIC), while Caribbean non-pandemic subtype B clades (BCAR) seem to account ...for a very low fraction of HIV-infections in this country. The molecular characteristics of the HIV-1 subtype B strains disseminated in the Northern and Northeastern Brazilian regions, however, have not been explored so far. In this study, we estimate the prevalence of the HIV-1 BPANDEMIC and BCAR clades across different Brazilian regions and we reconstruct the spatiotemporal dynamics of dissemination of the major Brazilian BCAR clades. A total of 2,682 HIV-1 subtype B pol sequences collected from 21 different Brazilian states from the five country regions between 1998 and 2013 were analyzed. Maximum Likelihood phylogenetic analyses revealed that the BCAR strains reached 16 out 21 Brazilian states here analyzed. The BCAR clades comprise a low fraction (<10%) of subtype B infections in most Brazilian states analyzed, with exception of Roraima (41%), Amazonas (14%) and Maranhão (14%). Bayesian phylogeographic analyses indicate that BCAR strains originally from the Hispaniola and Trinidad and Tobago were introduced at multiple times into different states from all Brazilian regions and a few of those strains, probably introduced into Roraima, Maranhão and São Paulo between the late 1970s and the early 1980s, established secondary outbreaks in the Brazilian population. These results support that the HIV-1 subtype B epidemics in some Brazilian states from the Northern and Northeastern regions display a unique molecular pattern characterized by the high prevalence of BCAR lineages, which probably reflects a strong epidemiological link with the HIV-1 epidemics in the Caribbean region.
A new coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is currently causing a life-threatening pandemic. In this study, we report the complete genome sequencing and genetic ...characterisation of a SARS-CoV-2 detected in Manaus, Amazonas, Brazil, and the protocol we designed to generate high-quality SARS-CoV-2 full genome data. The isolate was obtained from an asymptomatic carrier returning from Madrid, Spain. Nucleotide sequence analysis showed a total of nine mutations in comparison with the original human case in Wuhan, China, and support this case as belonging to the recently proposed lineage A.2. Phylogeographic analysis further confirmed the likely European origin of this case. To our knowledge, this is the first SARS-CoV-2 genome obtained from the North Brazilian Region. We believe that the information generated in this study may contribute to the ongoing efforts toward the SARS-CoV-2 emergence.
We present postmortem evidence of invasive pulmonary aspergillosis (IPA) in a patient with severe COVID-19. Autopsies of COVID-19 confirmed cases were performed. The patient died despite ...antimicrobials, mechanical ventilation, and vasopressor support. Histopathology and peripheral blood galactomannan antigen testing confirmed IPA. Aspergillus penicillioides infection was confirmed by nucleotide sequencing and BLAST analysis. Further reports are needed to assess the occurrence and frequency of IPA in SARS-CoV-2 infections, and how they interact clinically.
Measles is a human infectious disease of global concern that is caused by the measles virus. In this study, we report the complete genome sequencing of one measles virus isolate, genotype D8, that ...was obtained directly from a urine sample in Boa Vista city, the capital of Roraima state in Brazil. Phylogenetic reconstruction grouped the genome described in this study with that of samples from Australia, South Korea, and Italy. To our knowledge, this is the first complete genome sequence of a wild-type measles virus reported from Latin America. Therefore, the present data strengthen the current knowledge on the molecular epidemiology of measles worldwide.
The rapid spread of the SARS-CoV-2 Variant of Concern (VOC) Gamma in Amazonas during early 2021 fueled a second large COVID-19 epidemic wave and raised concern about the potential role of ...reinfections. Very few cases of reinfection associated with the VOC Gamma have been reported to date, and their potential impact on clinical, immunological, and virological parameters remains largely unexplored. Here we describe 25 cases of SARS-CoV-2 reinfection in Brazil. SARS-CoV-2 genomic analysis confirmed that individuals were primo-infected with distinct viral lineages between March and December 2020 (B.1.1, B.1.1.28, B.1.1.33, B.1.195, and P.2) and reinfected with the VOC Gamma between 3 to 12 months after primo-infection. We found a similar mean cycle threshold (Ct) value and limited intra-host viral diversity in both primo-infection and reinfection samples. Sera of 14 patients tested 10-75 days after reinfection displayed detectable neutralizing antibodies (NAb) titers against SARS-CoV-2 variants that circulated before (B.1.*), during (Gamma), and after (Delta and Omicron) the second epidemic wave in Brazil. All individuals had milder or no symptoms after reinfection, and none required hospitalization. These findings demonstrate that individuals reinfected with the VOC Gamma may display relatively high RNA viral loads at the upper respiratory tract after reinfection, thus contributing to onward viral transmissions. Despite this, our study points to a low overall risk of severe Gamma reinfections, supporting that the abrupt increase in hospital admissions and deaths observed in Amazonas and other Brazilian states during the Gamma wave was mostly driven by primary infections. Our findings also indicate that most individuals analyzed developed a high anti-SARS-CoV-2 NAb response after reinfection that may provide some protection against reinfection or disease by different SARS-CoV-2 variants.
The 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.
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•Lineages P.2 and Gamma probably emerged around July and November 2020, respectively•Lineages P.2 and Gamma mostly spread from Rio de Janeiro and Amazonas, respectively•Gamma was locally transmitted in most Brazilian states by December 2020•Gamma spread faster and was more transmissible than P.2
Biological sciences; Viral microbiology; Phylogeny
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Previous issue date: 2014-09-23
CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
The study of genetic diversity and detection of mutations to antiretroviral therapy is crucial for epidemiological surveillance of HIV-1, because it can provide information about the viral biology, guiding policies for prevention and treatment. From 2007 to 2012, Roraima ranks among the top five states with the highest incidence rates, from 2008 to 2010 occupied the second position. Likewise, the capital of Boa Vista in 2007 until 2011 also ranks among the five capitals with highest incidence rate. Data related to HIV-1 genotyping or related data on resistance mutations in the state are of fundamental importance to understand the local epidemic. In this context, this work has identified circulating HIV-1 subtypes; evaluated primary and secondary resistance in patients with HIV and described the frequency of the CCR5 gene polymorphism (rs333) in patients treated at the Central Laboratory of the State of Roraima / HIV Lab. A total of 121 samples were collected and regions of the proviral DNA of RT / PR, integrase and envelope genes were amplified and subjected to nucleotide sequencing. Human genomic DNA was only amplified and compared by electrophoresis. Demographic data were analyzed using descriptive statistics, while the genetic data were evaluated by several bioinformatics tools for analyzing: resistance, genotyping, phylogenetic reconstruction and viral tropism. A frequency of 9.17% for the human CCR5 genotype / CCR5Δ32 and 90.83% in relation to CCR5 / CCR5 was observed. With respect to the viral subtype, the highest prevalence was found for subtype B (Integrase) and Pol gene, followed by subtype F1 and recombinant forms of B / F (Integrase) and B / D (Pol). Only one case of primary resistance was detected (7.69%), however, in patients receiving therapy this number achieved 30,7%. Phylogenetic analysis showed that the Roraima's samples grouped into different clades with Uruguayan, Brazilian, Venezuelan and Guyanese samples, which probably reflects distinct events of viral entry. Around 25% of X4 samples were found, which affects the possibility of administering the fusion Maraviroc inhibitors for these patients. We believe that the data obtained in this study will contribute to a better understanding of the HIV / AIDS epidemiology of in the state of Roraima. Besides the scientific return, we believe that the results will indirectly contribute to improving patient care in this population
O estudo da diversidade genética e da presença de mutações de resistências aos antirretrovirais é de fundamental importância para a vigilância epidemiológica do HIV-1, pois pode fornecer informações sobre a biologia do vírus e orientar as políticas de prevenção e tratamento. De 2007 a 2012, dentre todos os estados da federação, Roraima figura entre os cinco primeiros estados com as maiores taxas de incidências, sendo que de 2008 a 2010 ocupou a segunda posição. Da mesma maneira, a capital Boa Vista de 2007 até 2011 também se posiciona entre as cinco capitais com maior taxa de incidência. Dados relacionados a genotipagem do HIV-1 circulante ou dados relacionados sobre mutações de resistência no estado são de fundamental importância para compreender a epidemia local. Nesse contexto, este trabalho identificou os subtipos do HIV-1 circulante, avaliou a resistência primária e secundária nos pacientes portadores de HIV e descreveu a frequência do polimorfismo rs333 no gene CCR5, em pacientes atendidos no Laboratório Central do Estado de Roraima/Laboratório de HIV. Para isso foram coletadas 121 amostras e as regiões do DNA proviral da RT/PR, Integrase e Envelope foram amplificadas e submetidas ao sequeciamento nucleotídico. O DNA genômico humano foi apenas amplificado e comparado por eletroforese. Os dados demográficos foram analisados por estatística descritiva, enquanto que os dados genéticos foram avaliados por diversas ferramentas de bioinformática para análise de resistência, genotigem, reconstrução filogenética e tropismo viral. Foi observada uma freqüência de 9,17% para o genótipo humano CCR5/CCR5Δ32 e 90,83% em relação ao CCR5/CCR5. Com relação ao subtipo viral, a maior prevalência encontrada foi para o subtipo B (Integrase) e gene Pol, seguido do subtipo F1 e de formas recombinantes B/F (Integrase) e B/D ( Pol). Somente um caso de resistência primária foi detectado (7,69%), no entanto em pacientes em tratamento esse número atingiu 30,7% . A análise filogenética mostrou que as amostras de Roraima se agrupam em diferentes clados com amostras brasileiras, venezuelanas, uruguaias e guianenses, o que provalvelmente reflete eventos distintos de introdução viral. Foram encontradas 25% de amostras com tropismo X4, o que afeta a possibilidade de administração do inibidor de fusão Maroviroque em parte dos pacientes avaliados. Acreditamos que os dados obtidos no presente estudo contribuirão para um melhor entendimento da epidemiologia do HIV/AIDS no estado de Roraima. Além do retorno científico, acreditamos que os resultados contribuirão indiretamente para a melhoria do atendimento desta população de pacientes.
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