Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil.
Published: April 2023
AI Article Synopsis
Article Abstract
Viral metagenomics has been extensively applied for the identification of emerging or poorly characterized viruses. In this study, we applied metagenomics for the identification of viral infections among pediatric patients with acute respiratory disease, but who tested negative for SARS-CoV-2. Twelve pools composed of eight nasopharyngeal specimens were submitted to viral metagenomics. Surprisingly, in two of the pools, we identified reads belonging to the poorly characterized Malawi polyomavirus (MWPyV). Then, the samples composing the positive pools were individually tested using quantitative polymerase chain reaction for identification of the MWPyV index cases. MWPyV-positive samples were also submitted to respiratory virus panel testing due to the metagenomic identification of different clinically important viruses. Of note, MWPyV-positive samples tested also positive for respiratory syncytial virus types A and B. In this study, we retrieved two complete MWPyV genome sequences from the index samples that were submitted to phylogenetic inference to investigate their viral origin. Our study represents the first molecular and genomic characterization of MWPyV obtained from pediatric patients in South America. The detection of MWPyV in acutely infected infants suggests that this virus might participate (coparticipate) in cases of respiratory symptoms. Nevertheless, future studies based on testing of a larger number of clinical samples and MWPyV complete genomes appear to be necessary to elucidate if this emerging polyomavirus might be clinically important.
Now that it has been realized that viruses are ubiquitous, questions have been raised on factors influencing their diversity and distribution. For phytoviruses, understanding the interplay between plant diversity and virus species richness and prevalence remains cardinal. As both the amplification and the dilution of viral species richness due to increasing host diversity have been theorized and observed, a deeper understanding of how plants and viruses interact in natural environments is needed to explore how host availability conditions viral diversity and distributions.
Objective: The aim of this study was to assess the clinical value of metagenomic next-generation sequencing (mNGS) of blood samples for the identification of disseminated tuberculosis (DTB).
Methods: A total of 48 individuals suspected of DTB were enrolled. All patients underwent mNGS of peripheral blood and conventional microbiological tests.
The prevalence of antibiotic resistance genes (ARGs) in agricultural soils has garnered significant attention. However, the long-term impacts of various nitroge (N)-substitution fertilization regimes on the distribution of soil ARGs and their dominant drivers in a subtropical triple-cropping system remain largely unexplored. This study employed a metagenomic approach to analyze soil ARGs, microbial communities, mobile genetic elements (MGEs), and viruses from a maize-maize-cabbage rotation field experiment with five different fertilization regimes.
Giant viruses are crucial for marine ecosystem dynamics because they regulate microeukaryotic community structure, accelerate carbon and nutrient cycles, and drive the evolution of their hosts through co-evolutionary processes. Previously reported long-term observations revealed that these viruses display seasonal fluctuations in abundance. However, the underlying genetic mechanisms driving such dynamics of these viruses remain largely unknown.
