Incipient parallel evolution of SARS-CoV-2 Deltacron variant in South Brazil

With the coexistence of multiple lineages and increased international travel, recombination and gene flow are likely to become increasingly important in the adaptive evolution of SARS-CoV-2. These processes could result in genetic introgression and the incipient parallel evolution of multiple recombinant lineages. However, identifying recombinant lineages is challenging, and the true extent of recombinant evolution in SARS-CoV-2 may be underestimated. This study describes the first SARS-CoV-2 Deltacron recombinant case identified in Brazil. We demonstrate that the recombination breakpoint is at the beginning of the Spike gene. The 5′ genome portion (circa 22 kb) resembles the AY.101 (Delta), and the 3′ genome portion (circa 8 kb nucleotides) is most similar to the BA.1.1 (Omicron). Furthermore, evolutionary genomic analyses indicate that the new strain emerged after a single recombination event between lineages of diverse geographical locations in December 2021 in South Brazil. This Deltacron, AYBA-RS, is one of the dozens of recombinants described in 2022. The submission of only four sequences in the GISAID database suggests that this lineage had a minor epidemiological impact. However, the recent emergence of this and other Deltacron recombinant lineages (XD, XF, and XS) suggests that gene flow and recombination may play an increasingly important role in the COVID-19 pandemic. We explain the evolutionary and population genetic theory that supports this assertion, concluding that this stresses the need for continued genomic surveillance. This monitoring is vital for countries where multiple variants are present, as well as for countries that receive significant inbound international travel

Physicochemical and microbiological characterization of buffalo milk intended for dairy products in RS, with emphasis on the phenotypic and genotypic identification of Staphylococcus spp

A ascenção do mercado de derivados de leite bubalino no Rio Grande do Sul (RS) enfatiza a necessidade da caracterização e regulamentação desse produto. Visando atender esse objetivo, foram coletadas ao longo de um ano 69 amostras de leite de búfala a granel dos três produtores do RS. As médias dos resultados foram: 5,5g/100g para gordura, 4,06g/100g para proteína, 5,07g/100g para lactose, 15,5g/100g para sólidos totais, 9,96g/100g para sólidos não gordurosos, 0,161g/100g para cálcio, 1,034 g/mL para densidade, -0,527°C para índice crioscópico, 16°D para acidez, 95x10³ cél/mL para contagem de células somáticas, 9,0x104 UFC/mL para contagem padrão em placas, 1,6x10²MPN/mL para Escherichia coli e 6,3x103 UFC/mL para Staphylococcus spp. Verificou-se a ausência de Salmonella spp., Listeria monocytogenes e resíduos de antimicrobianos nas amostras. O teor de ácidos graxos desejáveis das amostras mostrou relação com o manejo e alimentação dos animais. A biodiversidade de Staphylococcus spp. revelou 11 espécies, sendo S. aureus frequente em 36 (52%, n=69) amostras de leite. Além disso, 50 (47,62%, n=105) dos S. aureus isolados apresentaram potencial enterotoxigênico carreando sea (42,85%; n=45) e/ou sed (6,67%; n=7). Entre as 50 cepas com potencial enterotoxigênico, 11 (22%) foram sensíveis a todos os antimicrobianos e 15 (30%) foram classificadas como multirresistentes. O leite de búfala a granel no RS apresentou características físico-químicas e microbiológicas satisfatórias. A presença de cepas de S. aureus enterotoxigênicas e multirresistentes, importante do ponto de vista epidemiológico e sanitário, requer a redução das fontes de contaminação e a manutenção de baixas temperaturas durante o armazenamento e processamento desta matéria-prima.The rise of the buffalo milk derivatives market in Rio Grande do Sul (RS) emphasizes the need for characterization and regulation of this product. In order to meet this objective, 69 samples of bulk buffalo milk were collected over the course of a year from the three producers in RS. The mean results were: 5.5g/100g for fat, 4.06g/100g for protein, 5.07g/100g for lactose, 15.5g/100g for total solids, 9.96g/100g for non-fat solids, 0.161 g/100g for calcium, 1.034 g/mL for density, -0.527°C for freezing point, 16°D for acidity, 95x10³ cell/mL for somatic cell count, 9.0x104 CFU/mL for standard plate count, 1 .6x10²MPN/mL for Escherichia coli and 6.3x103 CFU/mL for Staphylococcus spp. Salmonella spp., Listeria monocytogenes and antimicrobial residues were not detected in the samples. The lipid profile showed a relationship between the desirable fatty acid content for human nutrition and the handling and feeding of the animals. Biodiversity of Staphylococcus spp. revealed 11 different species, with S. aureus frequent in 36 (52%, n=69) of the milk samples. Furthermore, 50 (47.62%, n=105) of the S. aureus isolated showed enterotoxigenic potential harbouring sea (42.85%; n=45) and/or sed (6.67%; n=7). Among the 50 strains with enterotoxigenic potential, 11 (22%) were sensitive to all antimicrobials and 15 (30%) were classified as multiresistant. Bulk buffalo milk in RS demonstrated satisfactory physicochemical and microbiological characteristics. The presence of enterotoxigenic and multiresistant strains of S. aureus, important from an epidemiological and sanitary point of view, it requires the reduction of contamination sources and the maintenance of low temperatures during the storage and processing of this raw material

Análise molecular dos genes SMN1 e SMN2 em pacientes com suspeita clínica de atrofia muscular espinal

A atrofia muscular espinal (AME) é uma das doenças de herança autossômica recessiva mais frequentes, com uma incidência estimada de 1 em cada 10.000 nascidos vivos. A AME se caracteriza por degeneração de neurônios motores na medula espinal, causando fraqueza progressiva de membros e tronco, seguida de atrofia muscular. Os pacientes são classificados em AME tipo I, AME tipo II e AME tipo III, baseado na idade de início dos sintomas e na evolução clínica. As três formas clínicas são causadas por alterações no gene de sobrevivência do neurônio motor (SMN1), que apresenta uma cópia homóloga (SMN2). Em torno de 95% dos pacientes com AME são homozigotos para ausência do exon 7 do gene SMN1, devido a uma deleção desse gene ou à uma conversão para SMN2. A ausência de SMN2 não tem consequências clínicas e é encontrada em aproximadamente 5% dos indivíduos normais, mas o número de cópias de SMN2 modula o fenótipo de pacientes com AME. Devido a este espectro uniforme de mutação, a análise molecular realizada mais frequentemente é a detecção de deleções e conversões dos éxons 7 e/ou 8 dos genes SMN1 e SMN2 nos pacientes com suspeita clínica de AME. Neste trabalho, um protocolo baseado no sistema TaqMan® foi desenvolvido e comparado com a metodologia de PCR-RFLP (restriction fragment length polymorfism) utilizada no laboratório, avaliando o potencial de aplicação no diagnóstico molecular de pacientes com AME. Amostras de DNA de 100 indivíduos com suspeita clínica de AME foram analisadas pelos dois métodos. Amostras suspeitas de apresentar conversão foram analisadas por sequenciamento direto de DNA. Homozigotos para a ausência do exon 7 do gene SMN1 foram identificados em 58 casos (58%), sendo a maioria devido à deleção desse gene. Destes pacientes, 56 foram classificados, de acordo com os critérios diagnósticos revisados para AME, e distribuídos da seguinte forma: 26 (46,4%) do tipo I, 16 (28,6%) tipo II e 14 (25,0%) tipo III. Oito casos de conversão do gene SMN1 para SMN2 foram encontradas entre os pacientes e a distribuição desses casos entre as três formas clínicas foi a seguinte: 4 pacientes do tipo III, 3 do tipo II e 1 do tipo I. Cinco casos de homozigotos para ausência do gene SMN2 foram identificados entre os demais indivíduos. A comparação do método PCR-RFLP com o método baseado no sistema TaqMan® descrito neste estudo mostrou que ambos foram específicos e precisos para essas análises. No entanto, o ensaio TaqMan® foi mais sensível e mais rápido e parece ser um método adequado para o diagnóstico de AME.Spinal muscular atrophy (SMA) is one of the most frequent autosomal recessive disorder with an estimated incidence of 1 case in each 10,000 live-births. SMA is characterized by degeneration of motor neurons in the spinal cord, causing progressive weakness of the limbs and trunk, followed by muscle atrophy. Patients have been classified in type I–III SMA based on age at onset and clinical course. All three types of SMA are caused by alterations in the survival motor neuron gene (SMN1) that also have a homologous copy named SMN2. About 95% of SMA patients show homozygous absence of SMN1 exon 7 due a deletion of this gene or a conversion into SMN2. The absence of SMN2 is found in about 5% of individuals with no clinical phenotype, but number of SMN2 copies modulates the phenotype of SMA patients. Considering this uniform mutation spectrum, direct molecular genetic testing consists basically of detecting deletions and conversions of exons 7 and 8 of these genes in SMA patients. In this work, we develop a real time PCR TaqMan® method and compared with the most commonly used PCR restriction fragment length polymorphism (PCR-RFLP) assay, evaluating the potential application of molecular diagnosis of SMA patients. DNA samples from 100 individuals with clinical features of SMA were analyzed by both methods. Besides, patients DNA samples carrying a conversion event were analysed by direct DNA sequencing. Homozygous for SMN1 exon 7 absence were identified in 58 cases (58%) being the majority due to gene deletion and eight cases of gene conversion. From those, 56 were classified, according to the revised diagnostic criteria, and distributed as follows: 26 (46.4%) SMA type I, 16 (28.6%) SMA type II and 14 (25.0%) SMA type III. In addition, gene conversion was observed in 4 SMA type I patients, 3 SMA type II and 1 SMA type III patient. Among the remaining individuals five samples were found to be homozygous for absence of SMN2 gene. Comparing PCR-RFLP method and the method based on the TaqMan® system describe in this study, we verify that both were precise and specific for these analyses. However, the TaqMan® assay was faster and more sensitive than PCR-RFLP and was shown to be a suitable method for the diagnosis of SMA

Caracterização molecular de pacientes com atrofia muscular espinhal : resultados preliminares

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Caracterização molecular de pacientes com atrofia muscular espinhal : resultados preliminares

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Molecular analysis of spinal muscular atrophy : a genotyping protocol based on TaqMan(®) real-time PCR

Spinal muscular atrophy (SMA) is an autosomal recessive inherited disorder caused by alterations in the survival motor neuron I (SMN1) gene. SMA patients are classified as type I-IV based on severity of symptoms and age of onset. About 95% of SMA cases are caused by the homozygous absence of SMN1 due to gene deletion or conversion into SMN2. PCR-based methods have been widely used in genetic testing for SMA. In this work, we introduce a new approach based on TaqMan® real-time PCR for research and diagnostic settings. DNA samples from 100 individuals with clinical signs and symptoms suggestive of SMA were analyzed. Mutant DNA samples as well as controls were confirmed by DNA sequencing. We detected 58 SMA cases (58.0%) by showing deletion of SMN1 exon 7. Considering clinical information available from 56 of them, the patient distribution was 26 (46.4%) SMA type I, 16 (28.6%) SMA type II and 14 (25.0%) SMA type III. Results generated by the new method was confirmed by PCR-RFLP and by DNA sequencing when required. In conclusion, a protocol based on real-time PCR was shown to be effective and specific for molecular analysis of SMA patients