RESUMEN
The novel coronavirus SARS-CoV-2, which emerged in late 2019, has since spread around the world and infected hundreds of millions of people with coronavirus disease 2019 (COVID-19). While this viral species was unknown prior to January 2020, its similarity to other coronaviruses that infect humans has allowed for rapid insight into the mechanisms that it uses to infect human hosts, as well as the ways in which the human immune system can respond. Here, we contextualize SARS-CoV-2 among other coronaviruses and identify what is known and what can be inferred about its behavior once inside a human host. Because the genomic content of coronaviruses, which specifies the virus's structure, is highly conserved, early genomic analysis provided a significant head start in predicting viral pathogenesis and in understanding potential differences among variants. The pathogenesis of the virus offers insights into symptomatology, transmission, and individual susceptibility. Additionally, prior research into interactions between the human immune system and coronaviruses has identified how these viruses can evade the immune system's protective mechanisms. We also explore systems-level research into the regulatory and proteomic effects of SARS-CoV-2 infection and the immune response. Understanding the structure and behavior of the virus serves to contextualize the many facets of the COVID-19 pandemic and can influence efforts to control the virus and treat the disease. IMPORTANCE COVID-19 involves a number of organ systems and can present with a wide range of symptoms. From how the virus infects cells to how it spreads between people, the available research suggests that these patterns are very similar to those seen in the closely related viruses SARS-CoV-1 and possibly Middle East respiratory syndrome-related CoV (MERS-CoV). Understanding the pathogenesis of the SARS-CoV-2 virus also contextualizes how the different biological systems affected by COVID-19 connect. Exploring the structure, phylogeny, and pathogenesis of the virus therefore helps to guide interpretation of the broader impacts of the virus on the human body and on human populations. For this reason, an in-depth exploration of viral mechanisms is critical to a robust understanding of SARS-CoV-2 and, potentially, future emergent human CoVs (HCoVs).Copyright © 2021 Rando et al.
RESUMEN
The OBO Foundry ontologies are outstanding resources for classifying and curating concepts in the life sciences. However, the use of annotated texts, figures, and data is far from widespread. In this work, I curated 360 cell type mentions in five different single-cell RNA-seq, COVID-19 related scientific articles. These mentions were gathered from the main figures, alongside mentions of tissue, taxon, life stage, and gender of the samples. I manually matched the terms used to NCBITaxon, UBERON, MMUSDV, HSAPDV, PATO, UBERON, and CL ontologies where appropriate. Only 130/360 cell type mentions (36%) could be matched (based on synonyms) to UBERON and CL. Strikingly, none of the 360 mentions cell types could be completely described by OBO ontologies. These results provide evidence that there is an urgent need to improve the reporting of cell-type-related results and enhance ontology generation systems to facilitate completeness in the light of the rise of novel definitions. Copyright © 2020 for this paper by its authors.