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Alphabaculoviruses are lethal dsDNA viruses of Lepidoptera that have high genetic diversity and are transmitted in aggregates within proteinaceous occlusion bodies. This mode of transmission has implications for their efficacy as biological insecticides. A Nicaraguan isolate of Spodoptera frugiperda multiple nucleopolyhedrovirus (SfMNPV-NIC) comprising nine genotypic variants has been the subject of considerable study due to the influence of variant interactions on the insecticidal properties of mixed-variant occlusion bodies. As part of a systematic study on the replication and transmission of variant mixtures, a tool for the accurate quantification of a selection of genotypic variants was developed based on the quantitative PCR technique (qPCR). First, primer pairs were designed around a region of high variability in four variants named SfNic-A, SfNic-B, SfNic-C and SfNic-E to produce amplicons of 103-150 bp. Then, using cloned purified amplicons as standards, amplification was demonstrated over a dynamic range of 108-101 copies of each target. The assay was efficient (mean ± SD: 98.5 ± 0.8%), reproducible, as shown by low inter- and intra-assay coefficients of variation (<5%), and specific to the target variants (99.7-100% specificity across variants). The quantification method was validated on mixtures of genotype-specific amplicons and demonstrated accurate quantification. Finally, mixtures of the four variants were quantified based on mixtures of budded virions and mixtures of DNA extracted from occlusion-derived virions. In both cases, mixed-variant preparations compared favorably to total viral genome numbers by quantification of the polyhedrin (polh) gene that is present in all variants. This technique should prove invaluable in elucidating the influence of variant diversity on the transmission and insecticidal characteristics of this pathogen.

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Candida glabrata (Nakaseomyces glabrata) is an emergent and opportunistic fungal pathogen that colonizes and persists in different niches within its human host. In this work, we studied five clinical isolates from one patient (P7), that have a clonal origin, and all of which come from blood cultures except one, P7-3, obtained from a urine culture. We found phenotypic variation such as sensitivity to high temperature, oxidative stress, susceptibility to two classes of antifungal agents, and cell wall porosity. Only isolate P7-3 is highly resistant to the echinocandin caspofungin while the other four isolates from P7 are sensitive. However, this same isolate P7-3, is the only one that displays susceptibility to fluconazole (FLC), while the rest of the isolates are resistant to this antifungal. We sequenced the PDR1 gene which encodes a transcription factor required to induce the expression of several genes involved in the resistance to FLC and found that all the isolates encode for the same Pdr1 amino acid sequence except for the last isolate P7-5, which contains a single amino acid change, G1099C in the putative Pdr1 transactivation domain. Consistent with the resistance to FLC, we found that the CDR1 gene, encoding the main drug efflux pump in C. glabrata, is highly overexpressed in the FLC-resistant isolates, but not in the FLC-sensitive P7-3. In addition, the resistance to FLC observed in these isolates is dependent on the PDR1 gene. Additionally, we found that all P7 isolates have a different proportion of cell wall carbohydrates compared to our standard strains CBS138 and BG14. In P7 isolates, mannan is the most abundant cell wall component, whereas ß-glucan is the most abundant component in our standard strains. Consistently, all P7 isolates have a relatively low cell wall porosity compared to our standard strains. These data show phenotypic and genotypic variability between clonal isolates from different niches within a single host, suggesting microevolution of C. glabrata during an infection.

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Hepatitis C virus (HCV) remains a significant global health challenge, affecting millions of people worldwide, with chronic infection a persistent threat. Despite the advent of direct-acting antivirals (DAAs), challenges in diagnosis and treatment remain, compounded by the lack of an effective vaccine. The HCV genome, characterized by high genetic variability, consists of eight distinct genotypes and over ninety subtypes, underscoring the complex dynamics of the virus within infected individuals. This study delves into the intriguing realm of HCV genetic diversity, specifically exploring the phenomenon of mixed infections and the subsequent detection of recombinant forms within the conserved internal ribosome entry site (IRES) region. Previous studies have identified recombination as a rare event in HCV. However, our findings challenge this notion by providing the first evidence of 1a/3a (and vice versa) inter-genotypic recombination within the conserved IRES region. Utilizing advanced sequencing methods, such as deep sequencing and molecular cloning, our study reveals mixed infections involving genotypes 1a and 3a. This comprehensive approach not only confirmed the presence of mixed infections, but also identified the existence of recombinant forms not previously seen in the IRES region. The recombinant sequences, although present as low-frequency variants, open new avenues for understanding HCV evolution and adaptation.

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Wheat yellow (stripe) rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most devastating diseases of wheat worldwide. Pst populations are composed of multiple genetic groups, each carrying one or more races characterized by different avirulence/virulence combinations. Since the severe epidemics in 2017, yellow rust has become the most economically important wheat foliar disease in Uruguay. A set of 124 Pst isolates collected from wheat fields in Uruguay between 2017 and 2021 were characterized phenotypically, and 27 of those isolates were subsequently investigated in-depth by additional molecular genotyping and race phenotyping analyses. Three genetic groups were identified, PstS7, PstS10, and PstS13, with the latter being the most prevalent. Two races previously reported in Europe, Warrior (PstS7) and Benchmark (PstS10), were detected in four and two isolates, respectively. A third race, known as Triticale2015 (PstS13), that was first detected in Europe in 2015 and in Argentina in 2017 was detected at several locations. Additional virulence to Yr3, Yr17, Yr25, Yr27, or Yr32 was detected in three new race variants within PstS13. The identification of these new races, which have not been reported outside South America, provides strong evidence of the local evolution of virulence in Pst during the recent epidemic years.

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The adaptive potential of plants is commonly used as an indicator of genotypes with higher breeding program potential. However, the complexity and interaction of plant metabolic parameters pose a challenge to selection strategies. In this context, this study aimed to explore phenotypic plasticity within the germplasm of Hybrid Timor coffee. Additionally, we assessed the utility of the multivariate phenotypic plasticity index (MVPi) as a promising tool to predict genotype performance across diverse climatic conditions. To achieve this, we evaluated the performance of seven accessions from the Hybrid Timor germplasm in comparison to the Rubi and IPR 100 cultivars, known for their susceptibility and resistance to drought, respectively. The experiment took place in a greenhouse under two conditions: one with normal soil moisture levels near maximum capacity, and the other with a water deficit scenario involving a period of no irrigation followed by rehydration. Data on physiological and biochemical factors were collected at three stages: before applying the water deficit, during its imposition, and after rehydration. Growth data were obtained by the difference between the beginning and end of the experimental period Furthermore, field evaluations of the productivity of the same genotypes were carried out over two consecutive seasons. Based on physiological and biochemical assessments, the MVPi was computed, employing Euclidean distance between principal component multivariate analysis scores. Subsequently, this index was correlated with growth and productivity data through linear regressions. Our findings reveal that the plastic genotypes that are capable of significantly altering physiological and biochemical parameters in response to environmental stimuli exhibited reduced biomass loss in both aerial and root parts. As a result, this positively influenced their productivity. Enhanced plasticity was particularly prominent in accessions from the MG Germplasm Collection: MG 311-Hybrid Timor UFV 428-02, MG 270-Hybrid Timor UFV 377-21, and MG 279-Hybrid Timor UFV 376-31, alongside the Rubi MG 1192 cultivar. The MVPi emerged as a valuable instrument to assess genotype adaptability and predict their performance under varying climatic scenarios.

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Introduction: Antimicrobial resistance (AMR) is a major threat to animal and public health worldwide; consequently, several AMR surveillances programs have been implemented internationally in both human and veterinary medicine, including indicator bacteria such as Escherichia coli. However, companion animals are not typically included in these surveillance programs. Nevertheless, there have been reports of increasing levels of antimicrobial resistance in E. coli strains isolated from dogs worldwide. In Chile, there is limited information available on AMR in E. coli isolated from companion animals, which prevents the establishment of objective prevention and control measures. Methods: For this reason, the aim of this study was to characterize the phenotypic and genotypic AMR of E. coli strains isolated from healthy household dogs in Chile. For this purpose, a multi-stage sampling was carried out in the Metropolitan Region of Chile, obtaining samples from 600 healthy dogs. These samples were processed using traditional bacteriology and molecular techniques to isolate E. coli strains. We assessed the minimal inhibitory concentration of 17 antimicrobials and conducted a search of six antimicrobial resistance genes, as well as class 1 and 2 integrons, in the isolated strains. Results: Two-hundred and twenty-four strains of E. coli were recovered, and 96.9% (n = 217) showed resistance to at least one drug and only 3.1% (n = 7) were susceptible to all analyzed antimicrobials. Most strains were resistant to cefalexin (91.5%, n = 205, 1st-generation cephalosporin), followed by ampicillin (68.3%, n = 153) and cefpodoxime (31.3%, n = 70, 3rd-generation cephalosporin). Moreover, 24.1% (n = 54) tested positive for extended-spectrum-ß-lactamases and 34.4% (n = 77) were multidrug resistant. As for the AMR genes, the most detected was qnrB (28.1%, n = 63), followed by blaCTX-M (22.3%, n = 50), and blaTEM-1 (19.6%, n = 44). Additionally, 16.1% (n = 36) harbored class 1 integrons. Our study shows that E. coli strains isolated from healthy household dogs exhibit resistance to several relevant drugs and also antimicrobial resistance genes considered critical for human health. These results can be used as a starting point for the prevention and control of antimicrobial resistance from companion animals. This background should be considered when formulating future resistance surveillance programs or control plans in which companion animals must be included.

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Introducción: La resistencia del HIV a los antirretrovirales (ARVs) es una de las principales causas de fallo terapéutico en niños, niñas y adolescentes que conviven con el virus. Desde el año 2006, el Laboratorio de Biología Celular y Retrovirus del Hospital Garrahan realiza el estudio genotípico de resistencia (ER) del HIV-1 a los ARVs a fin de identificar mutaciones que disminuyen la susceptibilidad del virus a los fármacos que componen el tratamiento ARV. Objetivos: El objetivo del trabajo fue estudiar el tipo y frecuencia de resistencia del HIV a los ARVs, a través de un análisis de 371 ER realizados entre los años 2006 y 2021 en niños, niñas y adolescentes con HIV-1 adquirido por transmisión vertical y con solicitud médica de ER por presentar fallo terapéutico. Resultados: Entre los años 2006 y 2013 la proporción de casos con resistencia a al menos una clase de fármaco ARV fue mayor al 90%, sugiriendo una asociación directa entre el fallo virológico y la disminución en la susceptibilidad del HIV-1 a uno o más componentes del TARV. A partir del año 2012, se observa una disminución progresiva del nivel de resistencia de HIV-1, llegando al 50% en 2021 (p<0.0001). La frecuencia de mutaciones de resistencia fue diferente para cada una de las clases de ARVs. Mientras que la resistencia a INNTR no sufrió cambios significativos a lo largo del período de estudio, oscilando entre 27% y 75%. La proporción de mutaciones a IPs en pacientes con fallo virológico disminuyó de 87% en 2006 a 17% en 2021 y para los INTR, disminuyó de 79% en 2006 a 45% en 2021. Conclusión: El nivel de resistencia a los ARVs ha disminuido de manera sustancial a lo largo de los últimos 16 años, probablemente por el uso de nuevos fármacos ARV con alta potencia que posibilitaron la intensificación de los tratamientos ARV y la implementación de criterios de fallo terapéutico más estrictos tanto a nivel clínico como virológico (AU)

Introduction: HIV resistance to antiretroviral (ARV) drugs is one of the main causes of therapeutic failure in children and adolescents living with the virus. Since 2006, the Cell Biology and Retrovirus Laboratory of the Garrahan Hospital has been performing the genotypic study of HIV-1 resistance to ARV drugs in order to identify mutations that reduce the susceptibility of the virus to the drugs that constitute ARV treatment. Objectives: The aim of this study was to assess the type and frequency of HIV resistance to ARV drugs through an analysis of 371 genotype studies performed between 2006 and 2021 in children and adolescents with HIV-1 acquired through motherto-child transmission and with medical request for genotype study due to therapeutic failure. Results: Between 2006 and 2013, the proportion of cases with resistance to at least one ARV drug class was greater than 90%, suggesting a direct association between virologic failure and decreased susceptibility of HIV-1 to one or more components of ART. From 2012 onwards, a progressive decrease in the level of HIV-1 resistance was observed, reaching 50% in 2021 (p<0.0001). The frequency of resistant mutations was different for each of the ARV classes, while resistance to non-nucleoside reverse transcriptase inhibitors (NNRTIs) did not change significantly over the study period, ranging from 27% to 75%. The proportion of drug-resistant mutations to protease inhibitors (PI) in patients with virologic failure decreased from 87% in 2006 to 17% in 2021 and for NNRTIs from 79% in 2006 to 45% in 2021. Conclusion: The level of resistance to ARV drugs has decreased substantially over the last 16 years, probably due to the use of new ARV drugs with high potency that allowed the intensification of ARV treatments and the implementation of stricter criteria for therapeutic failure both clinically and virologically (AU)

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Turkish White Cheese is a brined (or pickled) cheese with a salty, acidic flavor and a soft or semi-hard texture. It is the most produced and consumed type of cheese in Turkey. The purpose of this study was to determine the non-starter lactic acid bacteria and yeast microbiota of traditionally produced Turkish White Cheese and analyze the chemical properties and the aroma profile of the cheese. The results of the study identified 27 distinct strains belonging to 14 the non-starter lactic acid bacteria species and 49 different strains belonging to 11 yeast species. Lactobacillus plantarum was found to be the dominant species among the lactic acid bacteria, while Candida zeylanoides was the dominant yeast species in the White Cheese samples. In addition, Kluyveromyces lactis and Debaryomyces hansenii were prominent yeast species in cheese samples. Turkish White Cheese samples had different aromatic properties. The study is highly significant as it anaylzed both non-starter lactic acid bacteria and yeast microbiota of traditionally produced Turkish White Cheese through molecular methods. It also determined and analyzed a number of chemical and aromatic properties of White Cheese.

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Antimicrobial resistance is a threat to public health. The emergence of antibiotic-resistant Staphylococcus aureus represents a priority for the implementation of preventive measures. The objective was to isolate S. aureus in humans, animals, and animal health care environment, and to characterize the genotypic and phenotypic profile of antimicrobial resistance in these isolates. We isolated S. aureus from staff, animals, and environment of a veterinary hospital, and identified their antimicrobial resistance profiles. Samples were collected from 20 humans, 13 animals, 14 surfaces, 8 mobile phones, and 7 veterinarians' stethoscopes by using sterile swabs. S. aureus was isolated by culturing on mannitol salt agar and preliminary identification was done by Gram staining and catalase test. Subsequently, a polymerase chain reaction was performed for species confirmation and investigating their antimicrobial-resistant genotypic profiles. Phenotypic profiles of resistant isolates were determined using the disk-diffusion technique. Ten S. aureus isolates were recovered from 5/20 humans (25%), it was also recovered from 2/13 animals (15.38%), including 1 dog and 1 cat, and from 1/14 of surfaces (7.14%). The oxacillin-susceptible mecA-positive Staphylococcus aureus phenotype was identified in a feline. Most of the isolates carried at least two resistance genes of different antimicrobial classes, with 90% (9/10) presenting the gene blaZ, with 10% (1/10) presenting the gene mecA, 20% (2/10) presenting tet38, 10% (1/10) presenting tetM, 90% (9/10) presenting norA, 50% (5/10) presenting norC, 10% (1/10) presenting ermA, and 60% (6/10) presenting ermB. In antibiograms, resistance to penicillin was identified in all the isolates, resistance to erythromycin was identified in 80% (8/10), and all the isolate's resistance to erythromycin presented erythromycin-induced resistance to clindamycin. Antimicrobial resistance in the veterinary hospital requires attention due to the risk of interspecies transmission, gene transfer between bacteria that colonize companion animals and humans and, can make antimicrobial therapy difficult.

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When a seed produced by a single-cross (SC) maize hybrid is sown, the resulting grain yield is usually lower than that of the hybrid due to the inbreeding generated. However, if a seed from a mixture of s hybrids were sown instead, the synthetic variety thus formed (SynSC) would have a lower inbreeding coefficient (FSynSC) and a higher grain yield. The grain yield s, the finite number of representatives of each parent SC (m) and the inbreeding coefficient of the parent lines of the SCs (F) are related to the FSynSC. In addition, randomness and the finite size of m can cause the loss of genes and genotypes and increase the FSynSC. The objectives of this study were to derive formulas for (1) expressing FSynSC in terms of m, F, and s, and (2) calculating the probability of the occurrence of gene and genotype loss. It was found that for the probability of no genotype being missing from the progeny representing a parent to be at least 0.95, it is necessary that m ≥ 15. It was also found that a sample size of 7 is sufficient for FSynSC to stabilize, more visibly as F is larger, and for the probability of the occurrence of erosion to be practically zero.

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ABSTRACT: Canonical correlation analysis based on genotypic correlations allows determining the associations between groups of traits and carrying out the direct or indirect selection of superior genotypes. This study investigated the existence of linear and multivariate relationships between high and low heritability traits via canonical correlation analysis based on genotypic correlations. The experiment was conducted at the Professor Diogo Alves de Melo Experimental Field at the Universidade Federal de Viçosa, in Viçosa, MG. 90 wheat cultivars were evaluated under a 9 × 10 alpha-lattice design, with three replications and plots consisting of four rows of three meters spaced at 0.20 meters. Canonical groups were established between spike height and plant height, days for heading, number of spikelets per spike, and number of grains per spike (Group I) and, spike weight, spike grain mass, 100-grain mass, hectoliter weight, and grain yield (Group II). There was dependence between the established groups, which allowed the investigation of the relationships between traits based on their genotypic values. The traits cycle and plant height can be used for indirect selection of genotypes superior in hectoliter weight and grain yield, which are important factors for industries and farmers.

RESUMO: As análises de correlações canônicas baseadas nas correlações genotípicas, permitem determinar associações entre grupos de caracteres e realizar a seleção direta ou indireta de genótipos superiores. Objetivou-se com este trabalho investigar a existência de relações lineares e multivariadas entre caracteres de alta e baixa herdabilidade via análise de correlações canônicas com base nas correlações genotípicas. O experimento foi conduzido no Campo Experimental Professor Diogo Alves de Melo da Universidade Federal de Viçosa, em Viçosa, Minas Gerais. 90 cultivares de trigo foram avaliadas sob o delineamento alpha-lattice 9 × 10, com três repetições e parcelas constituídas por quatro linhas de três metros espaçadas a 0.20 metros. Os grupos canônicos foram estabelecidos entre altura de espiga e planta, dias para o espigamento, número de espiguetas por espiga e número de grãos por espiga (Grupo I) e, peso de espiga, massa de grãos da espiga, massa de 100 grãos, peso hectolitro e produtividade de grãos (Grupo II). Houve dependência entre os grupos estabelecidos, o que permitiu a investigação das relações entre os caracteres com base em seus valores genotípicos. Os caracteres ciclo e altura de plantas podem ser utilizados para a seleção indireta de genótipos superiores em peso hectolitro e produtividade, fatores estes importantes para indústrias e produtores.

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Canonical correlation analysis based on genotypic correlations allows determining the associations between groups of traits and carrying out the direct or indirect selection of superior genotypes. This study investigated the existence of linear and multivariate relationships between high and low heritability traits via canonical correlation analysis based on genotypic correlations. The experiment was conducted at the Professor Diogo Alves de Melo Experimental Field at the Universidade Federal de Viçosa, in Viçosa, MG. 90 wheat cultivars were evaluated under a 9 × 10 alpha-lattice design, with three replications and plots consisting of four rows of three meters spaced at 0.20 meters. Canonical groups were established between spike height and plant height, days for heading, number of spikelets per spike, and number of grains per spike (Group I) and, spike weight, spike grain mass, 100-grain mass, hectoliter weight, and grain yield (Group II). There was dependence between the established groups, which allowed the investigation of the relationships between traits based on their genotypic values. The traits cycle and plant height can be used for indirect selection of genotypes superior in hectoliter weight and grain yield, which are important factors for industries and farmers.

As análises de correlações canônicas baseadas nas correlações genotípicas, permitem determinar associações entre grupos de caracteres e realizar a seleção direta ou indireta de genótipos superiores. Objetivou-se com este trabalho investigar a existência de relações lineares e multivariadas entre caracteres de alta e baixa herdabilidade via análise de correlações canônicas com base nas correlações genotípicas. O experimento foi conduzido no Campo Experimental Professor Diogo Alves de Melo da Universidade Federal de Viçosa, em Viçosa, Minas Gerais. 90 cultivares de trigo foram avaliadas sob o delineamento alpha-lattice 9 × 10, com três repetições e parcelas constituídas por quatro linhas de três metros espaçadas a 0.20 metros. Os grupos canônicos foram estabelecidos entre altura de espiga e planta, dias para o espigamento, número de espiguetas por espiga e número de grãos por espiga (Grupo I) e, peso de espiga, massa de grãos da espiga, massa de 100 grãos, peso hectolitro e produtividade de grãos (Grupo II). Houve dependência entre os grupos estabelecidos, o que permitiu a investigação das relações entre os caracteres com base em seus valores genotípicos. Os caracteres ciclo e altura de plantas podem ser utilizados para a seleção indireta de genótipos superiores em peso hectolitro e produtividade, fatores estes importantes para indústrias e produtores.

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Introduction: Staphylococcus aureus is an important pathogen that can form biofilms on food contact surfaces (FCS) in the dairy industry, posing a serious food safety, and quality concern. Biofilm is a complex system, influenced by nutritional-related factors that regulate the synthesis of the components of the biofilm matrix. This study determines the prevalence of biofilm-associated genes and evaluates the development under different growth conditions and compositions of biofilms produced by S. aureus. Methods: Biofilms were developed in TSB, TSBG, TSBNaCl, and TSBGNaCl on stainless-steel (SS), with enumeration at 24 and 192 h visualized by epifluorescence and scanning electron microscopy (SEM). The composition of biofilms was determined using enzymatic and chemical treatments and confocal laser scanning microscopy (CLSM). Results and discussion: A total of 84 S. aureus (SA1-SA84) strains were collected from 293 dairy industry FCS (FCS-stainless steel [n = 183] and FCS-polypropylene [n = 110]) for this study. The isolates harbored the genes sigB (66%), sar (53%), agrD (52%), clfB/clfA (38%), fnbA/fnbB (20%), and bap (9.5%). 99. In particular, the biofilm formed by bap-positive S. aureus onto SS showed a high cell density in all culture media at 192 h in comparison with the biofilms formed at 24 h (p < 0.05). Epifluorescence microscopy and SEM revealed the metabolically active cells and the different stages of biofilm formation. CLSM analysis detected extracellular polymeric of S. aureus biofilms on SS, such as eDNA, proteins, and polysaccharides. Finally, the level of detachment on being treated with DNase I (44.7%) and NaIO 4(42.4%) was greater in the biofilms developed in TSB compared to culture medium supplemented with NaCl at 24 h; however, there was no significant difference when the culture medium was supplemented with glucose. In addition, after treatment with proteinase K, there was a lower level of biomass detachment (17.7%) of the biofilm developed in TSBNaCl (p < 0.05 at 24 h) compared to that in TSB, TSBG, and TSBGNaCl (33.6, 36.9, and 37.8%, respectively). These results represent a deep insight into the composition of S. aureus biofilms present in the dairy industry, which promotes the development of more efficient composition-specific disinfection strategies.

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Late blight disease, caused by the plant pathogen Phytophthora infestans, is one of the major threats for tomato and potato crops. Monitoring the populations of P. infestans is important to determine if there are changes in the sensitivity to fungicides and host preference. In this study, microsatellite markers and mitochondrial haplotypes were used to assess the genotype of isolates of P. infestans collected from tomato and potato plants in Colombia. Furthermore, sensitivity to the three fungicides cymoxanil (penetrant fungicide), mefenoxam, and fluopicolide (systemic fungicides), and tomato-potato host preference, were evaluated. Mitochondrial haplotyping showed that isolates collected on tomato were from the genetic groups Ia and Ib, while isolates collected on potatoes belonged to group IIa. Microsatellite analyses showed that isolates from tomato form two groups, including the Ib mitochondrial haplotype (which is genetically close to the US-1 clonal lineage) and the Ia haplotype (related to the EC-3 lineage), whereas Colombian isolates from potato formed a separate group. Furthermore, differences in sensitivity to fungicides were observed. Eighty-one percent of the isolates tested were resistant to mefenoxam with an EC50 >10 µg ml-1. Forty-two percent of the isolates showed an intermediate resistance to cymoxanil. The EC50 values ranged between 1 and 10 µg ml-1. For fluopicolide, 90% of the isolates were sensitive, with EC50 <1 µg ml-1. Host preference assays showed that potato isolates infected both host species. Thus, isolates that infect potatoes may pose a risk for tomato crops nearby.

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Genomic selection has been promising in situations where phenotypic assessments are expensive, laborious, and/or inefficient. This work evaluated the efficiency of genomic prediction methods combined with genetic models in clone and parent selection with the goal of increasing fresh root yield, dry root yield, as well as dry matter content in cassava roots. The bias and predictive ability of the combinations of prediction methods Genomic Best Linear Unbiased Prediction (G-BLUP), Bayes B, Bayes Cπ, and Reproducing Kernel Hilbert Spaces with additive and additive-dominant genetic models were estimated. Fresh and dry root yield exhibited predominantly dominant heritability, while dry matter content exhibited predominantly additive heritability. The combination of prediction methods and genetic models did not show significant differences in the predictive ability for dry matter content. On the other hand, the prediction methods with additive-dominant genetic models had significantly higher predictive ability than the additive genetic models for fresh and dry root yield, allowing higher genetic gains in clone selection. However, higher predictive ability for genotypic values did not result in differences in breeding value predictions between additive and additive-dominant genetic models. G-BLUP with the classical additive-dominant genetic model had the best predictive ability and bias estimates for fresh and dry root yield. For dry matter content, the highest predictive ability was obtained by G-BLUP with the additive genetic model. Dry matter content exhibited the highest heritability, predictive ability, and bias estimates compared with other traits. The prediction methods showed similar selection gains with approximately 67% of the phenotypic selection gain. By shortening the breeding cycle time by 40%, genomic selection may overcome phenotypic selection by 10%, 13%, and 18% for fresh root yield, dry root yield, and dry matter content, respectively, with a selection proportion of 15%. The most suitable genetic model for each trait allows for genomic selection optimization in cassava with high selection gains, thereby accelerating the release of new varieties.

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The second wave of COVID-19 caused by severe acute respiratory syndrome virus (SARS-CoV-2) is rapidly spreading over the world. Mechanisms behind the flee from current antivirals are still unclear due to the continuous occurrence of SARS-CoV-2 genetic variants. Brazil is the world's second-most COVID-19 affected country. In the present study, we identified the genomic and proteomic variants of Brazilian SARS-CoV-2 isolates. We identified 16 different genotypic variants were found among the 27 isolates. The genotypes of three isolates such as Bra/1236/2021 (G15), Bra/MASP2C844R2/2020 (G11), and Bra/RJ-DCVN5/2020 (G9) have a unique mutant in NSP4 (S184N), 2'O-Mutase (R216N), membrane protein (A2V) and Envelope protein (V5A). A mutation in RdRp of SARS-CoV-2, particularly the change of Pro-to Leu-at 323 resulted in the stabilization of the structure in BRA/CD1739-P4/2020. NSP4, NSP5 protein mutants are more virulent in genotype 15 and 16. A fast protein folding rate changes the structural stability and leads to escape for current antivirals. Thus, our findings help researchers to develop the best potent antivirals based on the new mutant of Brazilian isolates.

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We compared viral suppression rates between patients who continued tenofovir disoproxil fumarate (TDF)/lamivudine (3TC) vs switched to zidovudine (ZDV)/3TC in combination with a boosted protease inhibitor after failure of first-line efavirenz/TDF/3TC. We found higher rates of viral suppression with continued TDF/3TC compared with switching to ZDV/3TC.

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Fascioliasis is a disease caused by Fasciola hepatica worldwide transmitted by lymnaeid snails mainly of the Galba/Fossaria group and F. gigantica restricted to parts of Africa and Asia and transmitted by Radix lymnaeids. Concern has recently risen regarding the high pathogenicity and human infection capacity of F. gigantica. Abnormally big-sized fasciolids were found infecting sheep in Ecuador, the only South American country where F. gigantica has been reported. Their phenotypic comparison with F. hepatica infecting sheep from Peru, Bolivia and Spain, and F. gigantica from Egypt and Vietnam demonstrated the Ecuadorian fasciolids to have size-linked parameters of F. gigantica. Genotyping of these big-sized fasciolids by rDNA ITS-2 and ITS-1 and mtDNA cox1 and nad1 and their comparison with other countries proved the big-sized fasciolids to belong to F. hepatica. Neither heterozygotic ITS position differentiated the two species, and no introgressed fragments and heteroplasmic positions in mtDNA were found. The haplotype diversity indicates introductions mainly from other South American countries, Europe and North America. Big-sized fasciolids from Ecuador and USA are considered to be consequences of F.gigantica introductions by past livestock importations. The vector specificity filter due to Radix absence should act as driving force in the evolution in such lineages.

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Resumen Objetivo: Determinar el impacto del uso de la prueba genotípica de resistencia en la respuesta y supervivencia a largo plazo de los pacientes infectados con el VIH-1 que presentaron fracaso a la terapia antirretroviral. Métodos: Se realizó un estudio de cohorte, retrospectivo, se definieron dos grupos basados en la forma de selección de la terapia de rescate utilizada: en base al resultado de la prueba genotípica de resistencia (grupo A) y en base al criterio de expertos (grupo B). Los pacientes fueron evaluados antes del cambio de la terapia de rescate según variables demográficas, clínicas y de laboratorio y evaluados a los 6, 12, 18, y 24 meses del cambio de tratamiento según respuesta virológica, respuesta de células CD4+, incidencia de enfermedades oportunistas y supervivencia. La información fue obtenida de las actas de la Comisión Nacional de Terapia Antirretroviral, la base de datos del IPK y las Historias Clínicas. Se utilizaron números absolutos y porcentajes, media y mediana, con sus respectivas desviaciones estándares (DE), Chi2, se aplicó el Riesgo Relativo (RR), prueba U de Mann-Whitney, y el método de Kaplan-Meier. Resultados: Los pacientes de grupo A tuvieron 1,44 veces mayor probabilidad de alcanzar supresión virológica completa que los pacientes del grupo B a los 6 meses, RR 1,44 (1,046- 2,054) p=0,017. El incremento promedio de Linfocitos T CD4+ fue de 117,40 células/mm3 en pacientes del grupo A y de 30,04 células/mm3 en pacientes del grupo B, p<0,005 a los 12 meses de iniciado el tratamiento. La incidencia de enfermedades oportunistas fue de 25,7% en el grupo B y de 5,6% en grupo A. El mayor porcentaje de sobrevida acumulada se observó en el grupo el grupo A (98,1%), en comparación con el grupo B (79%). Conclusiones: Los pacientes en los cuales el tratamiento de rescate se escogió basado en una prueba genotípica de resistencia tuvieron una mejor respuesta virológica, un mayor incremento de Linfocitos T CD4+ y una mayor supervivencia que aquellos en los que el tratamiento se eligió basado en el criterio de expertos.

Abstract Objective: To determine the impact of the use of genotypic resistance testing on the response and long-term survival of HIV-1 infected patients who have failed antiretroviral therapy. Methods: A retrospective cohort study was carried out; two groups were defined based on the method of selection of the rescue therapy used: based on the result of the genotypic resistance test (group A) and based on the criteria of experts (group B). The patients were evaluated before the change of rescue therapy according to demographic, clinical and laboratory variables and evaluated at 6, 12, 18, and 24 months after the change of treatment according to virological response, CD4 + cell response, incidence of opportunistic diseases. and survival. The information was obtained from the minutes of the National Commission for Antiretroviral Therapy, the IPK database and the Medical Records. Absolute numbers and percentages, mean and median, with their respective standard deviations (SD), Chi2, were used, the Relative Risk (RR), the Mann-Whitney U test, and the Kaplan-Meier method were applied. Results: Group A patients were 1.44 times more likely to achieve complete virological suppression than group B patients at 6 months, RR 1.44 (1.046-2.054) p = 0.017. The average increase in CD4 + T lymphocytes was 117.40 cells / mm3 in group A patients and 30.04 cells / mm3 in group B patients, p <0.005 12 months after startin treatment. The incidence of opportunistic diseases was 25.7% in group B and 5.6% in group A. The highest percentage of cumulative survival was observed in group A (98.1%), compared to the group B (79%). Conclusions: Patients in whom salvage treatment was chosen based on a genotypic resistance test had a better virological response, a greater increase in CD4 + T lymphocytes, and a longer survival than those in whom treatment was chosen based on expert judgment.

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Trichosporon spp. are widely distributed in the nature, comprising species that inhabit different ecological niches and can be found in the water, soil, and body surface of animals and humans. Such microorganisms have been classically associated with superficial infections; however, in the last decades, they have also been related to disseminated infections in immunocompromised patients, behaving as opportunistic agents, which demands rapid and accurate species identification for efficient therapy. Concordance level between the traditional phenotypic method and the molecular technique (gold standard) in the identification of all 59 Trichosporon samples was 59.3%. Identification concordance between MALDI-TOF spectrometry and the molecular technique was 71.2%. No isolate of environmental origin was identifiable by MALDI-TOF mass spectrometry (MS), and 100% of such environmental isolates were discordant for IGS region sequencing and phenotypic characterization. Both comparisons evidenced greatest concordance in the identification of T. asahii. The species T. debeurmannianum, T. dermatis, T. venhuisii and T. insectorum were not properly identified by both MALDI-TOF MS and the phenotypic technique. MALDI-TOF MS, in particular, seems to be appropriate to investigate yeasts of the genus Trichosporon; however, database updates are still necessary, especially for species that are not common in the clinical routine. With the aim of helping understand the aspects involved in early and accurate diagnosis of infections caused by this opportunistic agent, the present study compared the phenotypic, molecular (IGS region) and mass-spectrometry (MALDI-TOF) identification of 59 yeasts of the genus Trichosporon which had clinical and environmental origin and were kept in a mycology collection.

The present study compared the phenotypic, genotypic, and mass-spectrometry (MALDI-TOF) identification of 59 yeasts of the genus Trichosporon. MALDI-TOF MS, in particular, seems to be appropriate to investigate this yeasts when compared to a molecular technique (gold standard).

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