RESUMO
The second wave of COVID-19 occurred in South America in early 2021 and was mainly driven by Gamma and Lambda variants. In this study, we aimed to describe the emergence and local genomic diversity of the SARS-CoV-2 Lambda variant in Argentina, from its initial entry into the country until its detection ceased. Molecular surveillance was conducted on 9356 samples from Argentina between October 2020 and April 2022, and sequencing, phylogenetic, and phylogeographic analyses were performed. Our findings revealed that the Lambda variant was first detected in Argentina in January 2021 and steadily increased in frequency until it peaked in April 2021, with continued detection throughout the year. Phylodynamic analyses showed that at least 18 introductions of the Lambda variant into the country occurred, with nine of them having evidence of onward local transmission. The spatial--temporal reconstruction showed that Argentine clades were associated with Lambda sequences from Latin America and suggested an initial diversification in the Metropolitan Area of Buenos Aires before spreading to other regions in Argentina. Genetic analyses of genome sequences allowed us to describe the mutational patterns of the Argentine Lambda sequences and detect the emergence of rare mutations in an immunocompromised patient. Our study highlights the importance of genomic surveillance in identifying the introduction and geographical distribution of the SARS-CoV-2 Lambda variant, as well as in monitoring the emergence of mutations that could be involved in the evolutionary leaps that characterize variants of concern.
Assuntos
COVID-19 , SARS-CoV-2 , Humanos , Argentina/epidemiologia , SARS-CoV-2/genética , Filogenia , COVID-19/epidemiologia , MutaçãoRESUMO
The COVID-19 pandemic has lately been driven by Omicron. This work aimed to study the dynamics of SARS-CoV-2 Omicron lineages during the third and fourth waves of COVID-19 in Argentina. Molecular surveillance was performed on 3431 samples from Argentina, between EW44/2021 and EW31/2022. Sequencing, phylogenetic and phylodynamic analyses were performed. A differential dynamic between the Omicron waves was found. The third wave was associated with lineage BA.1, characterized by a high number of cases, very fast displacement of Delta, doubling times of 3.3 days and a low level of lineage diversity and clustering. In contrast, the fourth wave was longer but associated with a lower number of cases, initially caused by BA.2, and later by BA.4/BA.5, with doubling times of about 10 days. Several BA.2 and BA.4/BA.5 sublineages and introductions were detected, although very few clusters with a constrained geographical distribution were observed, suggesting limited transmission chains. The differential dynamic could be due to waning immunity and an increase in population gatherings in the BA.1 wave, and a boosted population (for vaccination or recent prior immunity for BA.1 infection) in the wave caused by BA2/BA.4/BA.5, which may have limited the establishment of the new lineages.
Assuntos
COVID-19 , SARS-CoV-2 , Humanos , SARS-CoV-2/genética , COVID-19/epidemiologia , Argentina/epidemiologia , Pandemias , FilogeniaRESUMO
INTRODUCTION: Coinfection with two SARS-CoV-2 viruses is still a very understudied phenomenon. Although next generation sequencing methods are very sensitive to detect heterogeneous viral populations in a sample, there is no standardized method for their characterization, so their clinical and epidemiological importance is unknown. MATERIAL AND METHODS: We developed VICOS (Viral COinfection Surveillance), a new bioinformatic algorithm for variant calling, filtering and statistical analysis to identify samples suspected of being mixed SARS-CoV-2 populations from a large dataset in the framework of a community genomic surveillance. VICOS was used to detect SARS-CoV-2 coinfections in a dataset of 1,097 complete genomes collected between March 2020 and August 2021 in Argentina. RESULTS: We detected 23 cases (2%) of SARS-CoV-2 coinfections. Detailed study of VICOS's results together with additional phylogenetic analysis revealed 3 cases of coinfections by two viruses of the same lineage, 2 cases by viruses of different genetic lineages, 13 were compatible with both coinfection and intra-host evolution, and 5 cases were likely a product of laboratory contamination. DISCUSSION: Intra-sample viral diversity provides important information to understand the transmission dynamics of SARS-CoV-2. Advanced bioinformatics tools, such as VICOS, are a necessary resource to help unveil the hidden diversity of SARS-CoV-2.
Assuntos
COVID-19 , Coinfecção , Humanos , SARS-CoV-2/genética , Filogenia , Genoma Viral , Biologia Computacional , Sequência ConsensoRESUMO
This work aimed to evaluate the whole-organism and cellular level responses to different combinations of water temperature and salinity of the notothenioid Patagonotothen cornucola at the end of the yolk-sac larval stage. Egg masses of the species were collected in the wild and then maintained at natural water conditions (4 °C and 30 PSU). Newly hatched larvae were placed in aquaria with different combinations of water temperature (4 °C, 12 °C, and 16 °C) and salinity (15 and 30 PSU) during four days before yolk sac absorption. Larvae exposed to 12 °C grew more in length than those exposed to 16 °C, but yolk volume was more reduced in larvae exposed to 16 °C than those exposed to 4 °C and 30 PSU than of 15 PSU. In addition, a higher proportion of larvae exposed to 12 °C and 15 PSU completely absorbed their yolk. Whereas the more tolerant larvae to high temperatures were those exposed to 16 °C and 30 PSU, lipid peroxidation and protein oxidation were highest at natural and at 12 °C and 30 PSU conditions, respectively. The nutritional status (as standardized DNA/RNA index-sRD -) was low in all cases, even at natural conditions (average sRD ~ 1). Our study suggests that, in the context of climate change, the mortality rate of yolk-sac larvae of P. cornucola would not increase due to temperature or salinity stress. However, indirect effects (such as habitat degradation or changes in food availability) would be critical after complete absorption of the yolk.
Assuntos
Perciformes , Salinidade , Animais , Peixes , Larva , Perciformes/fisiologia , Temperatura , Água , Saco VitelinoRESUMO
Due to its organoleptic and nutraceutical qualities, strawberry fruit (Fragaria x ananassa, Duch) is a worldwide important commodity. The role of ethylene in the regulation of strawberry cell wall metabolism was studied in fruit from Toyonoka cultivar harvested at white stage, when most changes associated with fruit ripening have begun. Fruit were treated with ethephon, an ethylene-releasing reagent, or with 1-methylcyclopropene (1-MCP), a competitive inhibitor of ethylene action, maintaining a set of non-treated fruit as controls for each condition. Ethephon treated-fruit showed higher contents of hemicelluloses, cellulose and neutral sugars regarding controls, while 1-MCP-treated fruit showed a lower amount of those fractions. On the other hand, ethephon-treated fruit presented a lower quantity of galacturonic acid from ionically and covalently bound pectins regarding controls, while 1-MCP-treated fruit showed higher contents of those components. We also explored the ethylene effect over the mRNA accumulation of genes related to pectins and hemicelluloses metabolism, and a relationship between gene expression patterns and cell wall polysaccharides contents was shown. Moreover, we detected that strawberry necrotrophic pathogens growth more easily on plates containing cell walls from ethephon-treated fruit regarding controls, while a lower growth rate was observed when cell walls from 1-MCP treated fruit were used as the only carbon source, suggesting an effect of ethylene on cell wall structure. Around 60% of strawberry cell wall is made up of pectins, which in turns is 70% made by homogalacturonans. Our findings support the idea of a central role for pectins on strawberry fruit softening and a participation of ethylene in the regulation of this process.
Assuntos
Parede Celular/metabolismo , Etilenos/farmacologia , Fragaria/metabolismo , Reguladores de Crescimento de Plantas/farmacologia , Metabolismo dos Carboidratos/efeitos dos fármacos , Celulose/metabolismo , Etilenos/metabolismo , Fragaria/microbiologia , Fragaria/ultraestrutura , Frutas/genética , Frutas/crescimento & desenvolvimento , Frutas/ultraestrutura , Interações Hospedeiro-Patógeno/efeitos dos fármacos , Pectinas/genética , Pectinas/metabolismo , Reguladores de Crescimento de Plantas/metabolismo , Polissacarídeos/metabolismo , RNA Mensageiro/metabolismoRESUMO
Several cell wall enzymes are carbohydrate active enzymes that contain a putative Carbohydrate Binding Module (CBM) in their structures. The main function of these non-catalitic modules is to facilitate the interaction between the enzyme and its substrate. Expansins are non-hydrolytic proteins present in the cell wall, and their structure includes a CBM in the C-terminal that bind to cell wall polymers such as cellulose, hemicelluloses and pectins. We studied the ability of the Expansin2 CBM (CBMFaEXP2) from strawberry (Fragaria x ananassa, Duch) to modify the cell wall of Arabidopsis thaliana. Plants overexpressing CBMFaEXP2 were characterized phenotypically and biochemically. Transgenic plants were taller than wild type, possibly owing to a faster growth of the main stem. Cell walls of CBMFaEXP2-expressing plants were thicker and contained higher amount of pectins. Lower activity of a set of enzymes involved in cell wall degradation (PG, ß-Gal, ß-Xyl) was found, and the expression of the corresponding genes (AtPG, Atß-Gal, Atß-Xyl5) was reduced also. In addition, a decrease in the expression of two A. thaliana Expansin genes (AtEXP5 and AtEXP8) was observed. Transgenic plants were more resistant to Botrytis cinerea infection than wild type, possibly as a consequence of higher cell wall integrity. Our results support the hypothesis that the overexpression of a putative CBM is able to modify plant cell wall structure leading to modulation of wall loosening and plant growth. These findings might offer a tool to controlling physiological processes where cell wall disassembly is relevant, such as fruit softening.
Assuntos
Arabidopsis/citologia , Arabidopsis/crescimento & desenvolvimento , Carboidratos/química , Parede Celular/metabolismo , Fragaria/metabolismo , Desenvolvimento Vegetal , Proteínas de Plantas/metabolismo , Arabidopsis/genética , Arabidopsis/microbiologia , Botrytis/fisiologia , Tamanho Celular , Parede Celular/genética , Regulação da Expressão Gênica de Plantas , Proteínas de Fluorescência Verde/metabolismo , Inflorescência/metabolismo , Fenótipo , Desenvolvimento Vegetal/genética , Doenças das Plantas/genética , Doenças das Plantas/microbiologia , Folhas de Planta/metabolismo , Proteínas de Plantas/química , Raízes de Plantas/metabolismo , Plantas Geneticamente Modificadas , Transporte Proteico , Proteínas Recombinantes de Fusão/metabolismo , Sementes/metabolismo , Frações Subcelulares/metabolismo , Transformação GenéticaRESUMO
Protein ubiquitination leading to degradation by the proteasome is an important mechanism in regulating key cellular functions. Protein ubiquitination is carried out by a three step process involving ubiquitin (Ub) activation by a E1 enzyme, the transfer of Ub to a protein E2, finally an ubiquitin ligase E3 catalyzes the transfer of the Ub peptide to an acceptor protein. The E3 component is responsible for the specific recognition of the target, making the unveiling of E3 components essential to understand the mechanisms regulating fundamental cell processes through the protein degradation pathways. The Arabidopsis thaliana seven in absentia-like 7 (AtSINAL7) gene encodes for a protein with characteristics from a C3HC4-type E3 ubiquitin ligase. We demonstrate here that AtSINAL7 protein is indeed an E3 protein ligase based on the self-ubiquitination in vitro assay. This activity is dependent of the presence of a Lys residue in position 124. We also found that higher AtSINAL7 transcript levels are present in tissues undergoing active cell division during floral development. An interesting observation is the circadian expression pattern of AtSINAL7 mRNA in floral buds. Furthermore, UV-B irradiation induces the expression of this transcript indicating that AtSINAL7 may be involved in a wide range of different cell processes.
Assuntos
Proteínas de Arabidopsis/metabolismo , Arabidopsis/enzimologia , Regulação Enzimológica da Expressão Gênica/efeitos da radiação , Regulação da Expressão Gênica de Plantas/efeitos da radiação , Ubiquitina-Proteína Ligases/biossíntese , Ubiquitinação/efeitos da radiação , Raios Ultravioleta , Arabidopsis/genética , Proteínas de Arabidopsis/genética , Regulação Enzimológica da Expressão Gênica/fisiologia , Regulação da Expressão Gênica de Plantas/fisiologia , Ubiquitina/genética , Ubiquitina/metabolismo , Ubiquitina-Proteína Ligases/genética , Ubiquitinação/fisiologiaRESUMO
A putative carbohydrate binding module (CBM) from strawberry (Fragaria × ananassa Duch.) expansin 2 (CBM-FaExp2) was cloned and the encoding protein was over-expressed in Escherichia coli and purified in order to evaluate its capacity to bind different cell wall polysaccharides "in vitro". The protein CBM-FaExp2 bound to microcrystalline cellulose, xylan and pectin with different affinities (K(ad) = 33.6 ± 0.44 mL g(-1), K(ad) = 11.37 ± 0.87 mL g(-1), K(ad) = 10.4 ± 0.19 mL g(-1), respectively). According to "in vitro" enzyme assays, this CBM is able to decrease the activity of cell wall degrading enzymes such as polygalacturonase, endo-glucanase, pectinase and xylanase, probably because the binding of CBM-FaExp2 to the different substrates interferes with enzyme activity. The results suggest that expansins would bind not only cellulose but also a wide range of cell wall polymers.