7 research outputs found

    Phylogenetic Classification of Feline Immunodeficiency Virus

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    Background: The feline immunodeficiency virus (FIV) is responsible for a retroviral disease that affects domestic and wild cats worldwide, causing Feline Acquired Immunodeficiency Syndrome (FAIDS). FIV is a lentivirus from the family Retroviridae and its genome has 3 main structural genes: gag, pol and env. Phylogenetic studies have classified FIV into 7 subtypes according to the diversity among strains from the World, mainly in the env gene. Epidemiological analyses have demonstrated the high predominance of FIV-A and FIV-B. This in silico study aimed to perform a phylogenetic analysis to study FIV diversity worldwide. Materials, Methods & Results: A total of 60 whole genome sequences (WGS) and 122 FIV env gene sequences were included in 2 datasets, which were aligned using MAFFT version 7. Recombination among genomes and/or env genes was analyzed with RDP5 software. Phylogenetic analyses with both datasets were performed, after removing the recombinant sequences, by the W-IQ-TREE and constructed and edited by the FigTree. A total of 12 recombination events involving 19 WGS were detected. In addition, 27 recombination events involving 49 sequences were observed in the env gene. A high rate of recombinants was observed inter-subtypes (A/B and B/D) and intra-subtypes (A/A). All recombinants were removed from the subsequent phylogenetic analyses. Phylogenies demonstrated 6 distinct main clades, 5 from domestic cats (A, B, C, E, U) and 1 from wild cat sequences (W) in the WGS, as well as in the specific env gene analyses. Most clustered with subtype B sequences. In the WGS analysis, clade B had a prevalence of 65.9% Brazilian sequences (27/41) and 2.4% Japanese sequences (1/41). In the env gene analyses, clade B showed a prevalence of 43.8% of Brazilian sequences (32/73) and 20.5% of USA sequences (15/73). The results of both analyses also confirm the FIV-wide geographical distribution around the world. In the phylogenetic analyses carried out with WGS, sequences from China (1/41; 2.4%), Colombia (1/41; 2.4%) and the USA (1/41; 2.4%) were identified in clade A; sequence from Canada in clade C (1/41; 2.4%); sequence from Botswana belonged to clade E (1/41; 2.4%); sequences from Brazil clustered into clade U (2/41; 5% - data not yet published); and sequences belonging to the clade W were from Canada (1/41; 2.4%) and the USA (5/41; 12.3%). Specific env gene phylogenetic analyses showed sequences from Colombia (1/73; 1.4%), France (2/73; 2.7%), the Netherlands (3/73; 4.1%), Switzerland (2/73; 2.7%), EUA (6/73; 8.3%), belonging to clade A; sequence from Canada belonging to clade C (1/73; 1.4%); sequences from Brazil belonging to clade U (2/73; 5% - data not yet published); and sequences belonging to clade W from the USA (6/73; 8.3%). Discussion: The results presented here demonstrate that FIV has a rapid viral evolution due to recombination and mutation events, more specifically in the env gene, which is highly variable. Currently, this retrovirus is classified into 7 subtypes (A, B, C, D, E, F and U-NZenv) according to their high genomic diversity. It also highlighted the importance of in silico sequence and phylogeny studies to demonstrate evolutionary processes. This was the first study to address the WGS FIV diversity with a phylogenetic approach. Keywords: FIV, in silico, phylogeny, subtypes, recombination.

    Perfil do engenheiro de produção do Vale do Taquari

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    Atualmente existe uma demanda pela renovação dos conteúdos ministrados nas universidades, de modo a condicionar o alinhamento às conveniências mercadológicas das instituições. Neste trabalho, é realizada uma pesquisa para verificar o perfil do Engenheiro de Produção graduado na Univates e atuante no Vale do Taquari aliada ao estudo de materiais, máquinas e softwares presentes nos laboratórios da Univates. O objetivo é verificar se o perfil do Engenheiro de Produção do Vale do Taquari está em consonância com a expectativa dos empresários, além da averiguação dos equipamentos dos laboratórios da Instituição. A revisão bibliográfica do estudo traz temas como a evolução do profissional da engenharia, o perfil do Engenheiro, o perfil do Engenheiro de Produção e os laboratórios recomendados para a formação do Engenheiro de Produção. Também é realizada a descrição dos laboratórios da Univates. Para fazer a avaliação do perfil do Engenheiro de Produção, questionários foram respondidos por vinte egressos da Univates e por vinte empresários do Vale do Taquari. Os resultados demonstram que o perfil do Engenheiro de Produção formado pela Univates está de acordo com o requerido pelos empresários. As competências determinadas como as mais importantes foram a utilização de indicadores de desempenho e o melhoramento de processos. As principais habilidades elencadas foram a identificação e a resolução de problemas e o trabalho em equipe. Os conhecimentos básicos considerados como essenciais foram a matemática e a expressão oral. O conhecimento específico tido como o mais importante foi a gerência da produção. Além disso, os entrevistados sugerem a implantação de softwares que contribuam para o desenvolvimento das competências e conhecimentos específicos do profissional em questão. Verificou-se ainda que os laboratórios da Univates estão, em sua maioria, de acordo com a recomendação de órgãos fiscalizadores. Não obstante, o perfil do egresso que está sendo formado está em sintonia com o que consta no projeto pedagógico do curso. Em síntese, os resultados são consideráveis e podem contribuir para o aperfeiçoamento da qualidade profissional

    Evolution and Epidemic Spread of the Avian Infectious Bronchitis Virus (IBV) GI-23 in Brazil

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    Infectious bronchitis virus (IBV) is a pathogen affecting poultry flocks worldwide. GI-23 is an IBV lineage with a rapid spread into different continents of the world, and it was reported for the first time in South American/Brazilian broiler farms last year. This study aimed to investigate the recent introduction and epidemic spread of IBV GI-23 in Brazil. Ninety-four broiler flocks infected with this lineage were evaluated from October 2021 to January 2023. IBV GI-23 was detected using real-time RT-qPCR, and the S1 gene hypervariable regions 1 and 2 (HVR1/2) were sequenced. S1 complete and HVR1/2 nucleotide sequence datasets were used to carry out phylogenetic and phylodynamic analyses. Brazilian IBV GI-23 strains clustered into two specific subclades (SA.1 and SA.2), both in tree branches with IBV GI-23 from Eastern European poultry-producing countries, suggesting two independent and recent introductions (around 2018). Viral phylodynamic analysis showed that the IBV GI-23 population increased from 2020 to 2021, remaining constant for one year and declining in 2022. S1 amino acid sequences from Brazilian IBV GI-23 presented specific and characteristic substitutions in the HVR1/2 for subclades IBV GI-23 SA.1 and SA.2. This study brings new insights into the introduction and recent epidemiology of IBV GI-23 in Brazil

    Rapid DNA Detection of <i>Salmonella enterica</i> Typhimurium and Heidelberg from Poultry Samples

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    The Salmonella enterica serovars Typhimurium (S. Typhimurium), Heidelberg (S. Heidelberg), and their monophasic variants (S. 1,4,[5],12:i:-, S. 1,4,[5],12:r:- and S. 1,4,[5],12:-:1,2) are highly disseminated in poultry farming and can contaminate chicken meat, eggs, and other foods of avian origin. A time-consuming bacteriological and serological analysis is usually required to identify serovars by traditional methods. Incomplete and inconclusive serological results are frequent in routine analysis, mainly due to the occurrence of bacterial isolates presenting similar antigenic profiles. Molecular biology assays have been developed to improve the detection of specific Salmonella serovars and strains. This study aimed to develop a multiplex real-time PCR (SHTAmp) for the rapid DNA detection of S. Typhimurium, S. Heidelberg, and their monophasic variants from poultry samples. The methodology was used in the analysis of 147 field isolates from Brazilian poultry flocks previously evaluated with serological analysis. The results demonstrated that it was able to specifically and rapidly detect 21 S. Typhimurium and 57 S. Heidelberg isolates with complete antigenic formulae. Furthermore, SHTAmp was able to differentiate nine S. Typhimurium and 44 S. Heidelberg isolates with incomplete serological formulae (monophasic and aphasic variants). The complete methodology was also successfully used to detect these bacteria directly from 34 poultry samples after pre-enrichment in buffered peptone water (BPW). In conclusion, SHTAmp is a fast and accurate method to detect the two frequent and concerning serovars S. Typhimurium and S. Heidelberg directly from poultry samples

    Phylogenetic Classification of Feline Immunodeficiency Virus

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    Background: The feline immunodeficiency virus (FIV) is responsible for a retroviral disease that affects domestic and wild cats worldwide, causing Feline Acquired Immunodeficiency Syndrome (FAIDS). FIV is a lentivirus from the family Retroviridae and its genome has 3 main structural genes: gag, pol and env. Phylogenetic studies have classified FIV into 7 subtypes according to the diversity among strains from the World, mainly in the env gene. Epidemiological analyses have demonstrated the high predominance of FIV-A and FIV-B. This in silico study aimed to perform a phylogenetic analysis to study FIV diversity worldwide. Materials, Methods &amp; Results: A total of 60 whole genome sequences (WGS) and 122 FIV env gene sequences were included in 2 datasets, which were aligned using MAFFT version 7. Recombination among genomes and/or env genes was analyzed with RDP5 software. Phylogenetic analyses with both datasets were performed, after removing the recombinant sequences, by the W-IQ-TREE and constructed and edited by the FigTree. A total of 12 recombination events involving 19 WGS were detected. In addition, 27 recombination events involving 49 sequences were observed in the env gene. A high rate of recombinants was observed inter-subtypes (A/B and B/D) and intra-subtypes (A/A). All recombinants were removed from the subsequent phylogenetic analyses. Phylogenies demonstrated 6 distinct main clades, 5 from domestic cats (A, B, C, E, U) and 1 from wild cat sequences (W) in the WGS, as well as in the specific env gene analyses. Most clustered with subtype B sequences. In the WGS analysis, clade B had a prevalence of 65.9% Brazilian sequences (27/41) and 2.4% Japanese sequences (1/41). In the env gene analyses, clade B showed a prevalence of 43.8% of Brazilian sequences (32/73) and 20.5% of USA sequences (15/73). The results of both analyses also confirm the FIV-wide geographical distribution around the world. In the phylogenetic analyses carried out with WGS, sequences from China (1/41; 2.4%), Colombia (1/41; 2.4%) and the USA (1/41; 2.4%) were identified in clade A; sequence from Canada in clade C (1/41; 2.4%); sequence from Botswana belonged to clade E (1/41; 2.4%); sequences from Brazil clustered into clade U (2/41; 5% - data not yet published); and sequences belonging to the clade W were from Canada (1/41; 2.4%) and the USA (5/41; 12.3%). Specific env gene phylogenetic analyses showed sequences from Colombia (1/73; 1.4%), France (2/73; 2.7%), the Netherlands (3/73; 4.1%), Switzerland (2/73; 2.7%), EUA (6/73; 8.3%), belonging to clade A; sequence from Canada belonging to clade C (1/73; 1.4%); sequences from Brazil belonging to clade U (2/73; 5% - data not yet published); and sequences belonging to clade W from the USA (6/73; 8.3%). Discussion: The results presented here demonstrate that FIV has a rapid viral evolution due to recombination and mutation events, more specifically in the env gene, which is highly variable. Currently, this retrovirus is classified into 7 subtypes (A, B, C, D, E, F and U-NZenv) according to their high genomic diversity. It also highlighted the importance of in silico sequence and phylogeny studies to demonstrate evolutionary processes. This was the first study to address the WGS FIV diversity with a phylogenetic approach. Keywords: FIV, in silico, phylogeny, subtypes, recombination.

    Emergence, Dissemination and Antimicrobial Resistance of the Main Poultry-Associated Salmonella Serovars in Brazil

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    Salmonella infects poultry, and it is also a human foodborne pathogen. This bacterial genus is classified into several serovars/lineages, some of them showing high antimicrobial resistance (AMR). The ease of Salmonella transmission in farms, slaughterhouses, and eggs industries has made controlling it a real challenge in the poultry-production chains. This review describes the emergence, dissemination, and AMR of the main Salmonella serovars and lineages detected in Brazilian poultry. It is reported that few serovars emerged and have been more widely disseminated in breeders, broilers, and layers in the last 70 years. Salmonella Gallinarum was the first to spread on the farms, remaining as a concerning poultry pathogen. Salmonella Typhimurium and Enteritidis were also largely detected in poultry and foods (eggs, chicken, turkey), being associated with several human foodborne outbreaks. Salmonella Heidelberg and Minnesota have been more widely spread in recent years, resulting in frequent chicken/turkey meat contamination. A few more serovars (Infantis, Newport, Hadar, Senftenberg, Schwarzengrund, and Mbandaka, among others) were also detected, but less frequently and usually in specific poultry-production regions. AMR has been identified in most isolates, highlighting multi-drug resistance in specific poultry lineages from the serovars Typhimurium, Heidelberg, and Minnesota. Epidemiological studies are necessary to trace and control this pathogen in Brazilian commercial poultry production chains

    Epidemiological Insights into Feline Leukemia Virus Infections in an Urban Cat (<i>Felis catus</i>) Population from Brazil

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    Feline leukemia virus (FeLV) is a retrovirus distributed worldwide in domestic cats and with different outcomes (progressive, regressive, abortive, focal). The present study reports an epidemiological survey of FeLV frequency and the evaluation of some risk factors and the two main disease outcomes (progressive and regressive) in an urban cat population from Brazil. A total of 366 cats with sociodemographic information and p27 FeLV antigen test performed were included in the study. FeLV DNA (provirus) in the blood samples of all cats was detected via real-time polymerase chain reaction (qPCR). Plasma samples from 109 FeLV-positive and FeLV-negative cats were also submitted to reverse transcription (RT-qPCR) to determine the FeLV viral load. The results demonstrated that 112 (30.6%) cats were positive through the p27 antigen and/or qPCR. A risk factor analysis demonstrated that cats without vaccination against FeLV (OR 9.9, p p p p p p = 0.001). A comparative analysis of the different detection methods in a subset of 109 animals confirmed FeLV infection in 58 cats, including 38 (65.5%) with progressive, 16 (27.6%) with regressive, and 4 (6.9%) with probably focal outcome diseases. In conclusion, this study demonstrates a high prevalence of FeLV in this urban cat population from Brazil and highlights the need to establish more effective prevention strategies (such as viral testing, vaccination programs, specific care for FeLV-positive cats) to reduce diseases associated with this virus in Brazil
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