Clinical and epidemiological aspects of Delta and Gamma SARS-CoV-2 variant of concern from the western Brazilian Amazon

BACKGROUND The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants has become a major concern contributing to increased morbidity and mortality worldwide. OBJECTIVES Here we describe the replacement of the Gamma variant of concern (VOC) with Delta in the western Brazilian Amazon. METHODS In this study, we analysed 540 SARS-CoV-2 positive samples determined by qualitative real-time RT-PCR selected in the state of Rondônia between June and December 2021. The positive cohort was sequenced through next-generation sequencing (NGS) and each sample was quantified using real-time RT-qPCR, the whole genome sequence was obtained, SARS-CoV-2 lineages were classified using the system Pango and the maximum likelihood (ML) method was used to conduct phylogenetic analyses. FINDINGS A total of 540 high-quality genomes were obtained, where the Delta VOC showed the highest prevalence making up 72%, with strain AY.43 being the most abundant, while the Gamma VOC was present in 28%, where the P.1 strain was the most frequent. In this study population, only 32.96% (178/540) had completed the vaccination schedule. MAIN CONCLUSIONS This study highlighted the presence of Gamma and Delta variants of SARS-CoV-2 in RO. Furthermore, we observed the replacement of the Gamma VOC with the Delta VOC and its lineages.

Trypanosoma cruzi transcriptome during axenic epimastigote growth curve

BACKGROUND Trypanosoma cruzi is an important protozoan parasite and the causative agent of Chagas disease. A critical step in understanding T. cruzi biology is the study of cellular and molecular features exhibited during its growth curve. OBJECTIVES We aimed to acquire a global view of the gene expression profile of T. cruzi during epimastigote growth. METHODS RNA-Seq analysis of total and polysomal/granular RNA fractions was performed along the 10 days T. cruzi epimastigote growth curve in vitro, in addition to cell viability and cell cycle analyses. We also analysed the polysome profile and investigated the presence of granular RNA by FISH and western blotting. FINDINGS We identified 1082 differentially expressed genes (DEGs), of which 220 were modulated in both fractions. According to the modulation pattern, DEGs were grouped into 12 clusters and showed enrichment of important gene ontology (GO) terms. Moreover, we showed that by the sixth day of the growth curve, polysomal content declined greatly and the RNA granules content appeared to increase, suggesting that a portion of mRNAs isolated from the sucrose gradient during late growth stages was associated with RNA granules and not only polyribosomes. Furthermore, we discuss several modulated genes possibly involved in T. cruzi growth, mainly during the stationary phase, such as genes related to cell cycle, pathogenesis, metabolic processes and RNA-binding proteins.

The zinc finger protein TcZFP2 binds target mRNAs enriched during Trypanosoma cruzi metacyclogenesis

Trypanosomes are parasitic protozoa in which gene expression is primarily controlled through the regulation of mRNA stability and translation. This post-transcriptional control is mediated by various families of RNA-binding proteins, including those with zinc finger CCCH motifs. CCCH zinc finger proteins have been shown to be essential to differentiation events in trypanosomatid parasites. Here, we functionally characterise TcZFP2 as a predicted post-transcriptional regulator of differentiation in Trypanosoma cruzi. This protein was detected in cell culture-derived amastigotes and trypomastigotes, but it was present in smaller amounts in metacyclic trypomastigote forms of T. cruzi. We use an optimised recombinant RNA immunopreciptation followed by microarray analysis assay to identify TcZFP2 target mRNAs. We further demonstrate that TcZFP2 binds an A-rich sequence in which the adenosine residue repeats are essential for high-affinity recognition. An analysis of the expression profiles of the genes encoding the TcZFP2-associated mRNAs throughout the parasite life cycle by microarray hybridisation showed that most of the associated mRNAs were upregulated in the metacyclic trypomastigote forms, also suggesting a role for TcZFP2 in metacyclic trypomastigote differentiation. Knockdown of the orthologous Trypanosoma brucei protein levels showed ZFP2 to be a positive regulator of specific target mRNA abundance.

Yeasts and filamentous fungi in bottled mineral water and tap water from municipal supplies

The main objective of this study was to analyse the occurrence of yeasts and filamentous fungi in drinking water as well as to investigate their correlation with the indicator bacteria of faecal pollution. Yeasts were detected in 36.6 percent and 11.6 percent of the bottled mineral on water dispensers and tap water samples from municipal system, respectively. Twenty-one (35.0 percent) of bottled mineral water and two (3.3 percent) of tap water samples were positive for filamentous fungi. For bottled mineral water 12 (20.0 percent) of 60 samples were positive for total coliform, compared with 3(5.0 percent)out of 60 samples from tap water. The mineral water from dispensers was more contaminated than tap water. Strains belonging to the genera Candida identified to the species level were C. parapsilosis, C. glabrata and C. albicans. Thus, bottled mineral water from water dispensers and tap water could be considered a possible transmission route for filamentous fungi and yeasts, and could constitute a potential health hazard, mainly to immunocompromised indivuals.

O principal objetivo do presente estudo foi avaliar a prevalência de leveduras e fungos filamentosos em água potável, bem como investigar suas correlações com bactérias indicadoras de contaminação fecal. Leveduras foram detectadas em 36,6 por cento e 11,6 por cento das amostras de água mineral de garrafão em dispensadores de água e água de torneira do sistema municipal, respectivamente. Vinte e uma (35,5 por cento) das amostras de água mineral de garrafão e duas (3,3 por cento) das amostras de água de torneira foram positivas para fungos filamentosos. Para água mineral de garrafão, 12 (20.0 por cento) das 60 amostras foram positivas para coliforme total, comparado com 3 (5.0 por cento) das 60 amostras de água de torneira. A água coletada de garrafões de água mineral dos dispensadores foi marcadamente mais contaminada que as amostras de água de torneira. Candida spp identificadas ao nível de espécie foram C. parapsilosis, C. glabrata e C. albicans. Como está sendo reportado, água mineral de garrafão em dispensador e água de torneira pode ser considerada como possíveis vias de transmissão de fungos filamentosos e leveduras, e podem constituir um potencial risco para a saúde, principalmente de pessoas imunocomprometidas.

Utilização de um meio cromogênico e da técnica de semi-nested PCR para identificação de espécies de Candida / Use of chromogenic medium and semi-nested PCR-based assay to identify Candida species

Nesse trabalho, o meio cromogênico CHROMagar Candida e a técnica de semi-nested PCR (sn-PCR) foram comparados quanto a sua capacidade de identificar a espécie de 52 isolados clínicos de Candida sp. Com o emprego do meio cromogênico, 39 (75%) isolados foram identificados presuntivamente como C. albicans (n = 22), C. glabrata (n = 9), C. tropicalis (n = 5) e C. krusei (n = 3). Treze isolados (25%) não puderam ser identificados. Por meio da técnica de sn-PCR, que se baseia na amplificação de uma região do cluster gênico do RNA ribossomal (5.8S – 28S), 43 (83%) isolados foram identificados como C.albicans (n = 24), C. glabrata (n = 11), C. tropicalis (n = 5), C. parapsilosis (n = 3) e nove isolados não puderam ser identificados em nível de espécie. Entre os 52 isolados analisados, 34 (65,4%) apresentaram resultados concordantes pelos dois métodos, 12 (23,1%) apresentaram resultados discrepantes, e 6 (11,5%) não puderam ser identificadas por nenhuma das duas metodologias. Os resultados indicam que ambas as técnicas apresentam limitações, mas o método de sn-PCR é mais adequado que o meio cromogênico para a identificação de espécies do gênero Candida, devido ao menor número de isolados que não puderam ser identificados.