Biology subjects

Zaballos, A.

Publications and source records attributed to Zaballos, A..

4 recordsLinked to original sources

bioRxiv2022

Genomic accordions may hold the key to Monkeypox Clade IIb's increased transmissibility

The currently expanding monkeypox epidemic is caused by a subclade IIb descendant of a monkeypox virus (MPXV) lineage traced back to Nigeria in 1971. In contrast to monkeypox cases caused by clade I and subclade IIa MPXV, the prognosis of current cases is generally favorable, but person-to-person transmission is much more efficient. MPXV evolution is driven by selective pressure from hosts and loss of virus-host interacting genes. However, there is no satisfactory genetic explanation using single-nucleotide polymorphisms (SNPs) for the observed increased MPXV transmissibility. We hypothesized that key genomic changes may occur in the genomes low-complexity regions (LCRs), which are highly challenging to sequence and have been dismissed as uninformative. Using a combination of highly sensitive techniques, we determined a first high-quality MPXV genome sequence of a representative of the current epidemic with LCRs resolved at unprecedented accuracy. This effort revealed significant variation in short-tandem repeats within LCRs. We demonstrate that LCR entropy in the MPXV genome is significantly higher than that of SNPs and that LCRs are not randomly distributed. In silico analyses indicate that expression, translation, stability, or function of MPXV orthologous poxvirus genes (OPGs) 153, 204, and 208 could be affected in a manner consistent with the established "genomic accordion" evolutionary strategies of orthopoxviruses. Consequently, we posit that genomic studies focusing on phenotypic MPXV clade-/subclade-/lineage-/strain differences should change their focus to the study of LCR variability instead of SNP variability.

genomics↗

bioRxiv2022

Identification of β2 microglobulin, the product of B2M gene, as a Host Factor for Vaccinia Virus Infection by Genome-Wide CRISPR genetic screens

Genome-wide genetic screens are powerful tools to identify genes that act as host factors of viruses. We have applied this technique to the analyze the infection of HeLa cells by Vaccinia virus, in an attempt to find genes necessary for infection. Infection of cell populations harboring single gene inactivations resulted in no surviving cells, suggesting that no single gene knock-out was able to provide complete resistance to Vaccinia virus and thus allow cells to survive infection. In the absence of an absolute infection blockage, we explored if some gene inactivations could provide partial protection leading to a reduced probability of infection. Multiple experiments using modified screening procedures involving replication restricted viruses led to the identification of multiple genes whose inactivation potentially increase resistance to infection and therefore cell survival. As expected, significant gene hits were related to proteins known to act in virus entry, such as ITGB1 and AXL as well as genes belonging to their downstream related pathways. Additionally, we consistently found {beta}2-microglobulin, encoded by the B2M gene, among the screening top hits, a novel finding that was further explored. Inactivation of B2M resulted in 54% and 91% reduced VV infection efficiency in HeLa and HAP1 cell lines respectively. In the absence of B2M, while virus binding to the cells was unaffected, virus internalization and early gene expression were significantly diminished. These results point to {beta}2-microglobulin as a relevant factor in the Vaccinia virus entry process. Author summaryOrthopoxviruses, a genus belonging to the family Poxviridae, include human pathogens like Variola virus, the causative agent of the now eradicated Smallpox, and Monkeypox virus that cause human outbreaks of zoonotic origin. Being the prototype Poxvirus, Vaccinia virus has been extensively used as the ideal model to study infection. For Poxviruses, both fluid phase endocytosis and direct fusion at the plasma membrane have been described as modes of entry. To date, only a few cellular factors have been identified in the vaccinia virus entry pathway. In this study, we report that blind genome-wide genetic screens allowed us to identify several cellular factors involved in Vaccinia Virus infection, of which many could be related to known factors in virus entry. In addition, we found that {beta}2-microglobulin constitute a novel player for Poxvirus entry not related to previously described cellular pathways involved in the entry process. These findings add new information to the complex picture of Poxvirus entry and open the door to the discovery of new entry mechanisms used by Poxviruses.

microbiology↗

bioRxiv2020

Phylodynamics of SARS-CoV-2 transmission in Spain

ObjectivesSARS-CoV-2 whole-genome analysis has identified three large clades spreading worldwide, designated G, V and S. This study aims to analyze the diffusion of SARS-CoV-2 in Spain/Europe. MethodsMaximum likelihood phylogenetic and Bayesian phylodynamic analyses have been performed to estimate the most probable temporal and geographic origin of different phylogenetic clusters and the diffusion pathways of SARS-CoV-2. ResultsPhylogenetic analyses of the first 28 SARS-CoV-2 whole genome sequences obtained from patients in Spain revealed that most of them are distributed in G and S clades (13 sequences in each) with the remaining two sequences branching in the V clade. Eleven of the Spanish viruses of the S clade and six of the G clade grouped in two different monophyletic clusters (S-Spain and G-Spain, respectively), with the S-Spain cluster also comprising 8 sequences from 6 other countries from Europe and the Americas. The most recent common ancestor (MRCA) of the SARS-CoV-2 pandemic was estimated in the city of Wuhan, China, around November 24, 2019, with a 95% highest posterior density (HPD) interval from October 30-December 17, 2019. The origin of S-Spain and G-Spain clusters were estimated in Spain around February 14 and 18, 2020, respectively, with a possible ancestry of S-Spain in Shanghai. ConclusionsMultiple SARS-CoV-2 introductions have been detected in Spain and at least two resulted in the emergence of locally transmitted clusters, with further dissemination of one of them to at least 6 other countries. These results highlight the extraordinary potential of SARS-CoV-2 for rapid and widespread geographic dissemination.

microbiology↗

bioRxiv2017

Cryptococcus neoformans can form titan-like cells in vitro in response to multiple signals that require the activation of several transduction pathways

Cryptococcus neoformans is an encapsulated pathogenic yeast that can change the size of the cells during infection. In particular, this process can occur by enlarging the size of the capsule without modifying the size of the cell body, or by increasing the diameter of the cell body, which is normally accompanied by an increase of the capsule too. This last process leads to the formation of cells of an abnormal enlarged size denominated titan cells. Previous works characterized titan cell formation during pulmonary infection but research on this topic has been hampered due to the difficulty to obtain them in vitro. In this work, we describe in vitro conditions (low nutrient, serum supplemented medium at neutral pH) that promote the transition from regular to titan-like cells. Moreover, addition of azide and static incubation of the cultures in a CO2 enriched atmosphere favored cellular enlargement. This transition occurred at low cell densities, suggesting that the process was regulated by quorum sensing molecules and was independent of the cryptococcal serotype/species. Transition to titan-like cell formation was impaired by pharmacological inhibition of PKC and TOR signaling pathways. Mutants affected in capsule synthesis did not form titan-like cells. Analysis of the gene expression profile in titan-like cells indicated that they overexpressed membrane proteins and transporters, being the gene encoding the Cig1 mannoprotein involved in iron uptake from heme groups the gene most differentially expressed compared to cells of regular size. We also investigated the gene expression profile of titan-like cells isolated from mice, and observed that during infection these cells mainly overexpressed genes related to metabolism and respiration. In summary, our work provides a new alternative method to investigate titan cell formation devoid the bioethical problems that involve animal experimentation.\n\nAUTHOR SUMMARYCryptococcus neoformans is a fungal pathogen that has a significant incidence in HIV+ patients in particular, in Subsaharian Africa, Asia and South America. This yeast poses an excellent model to investigate fungal virulence because it develops many strategies to adapt to the host and evade the immune response. One of the adaptation mechanisms involves the formation of Titan Cells, which are yeast of an abnormal large size. However, research on these cells has been limited to in vivo studies (mainly in mice) because they were not reproducibly found in vitro. In this work, we describe several conditions that induce the appearance of cells that mimic titan cells, and that we denominated as titan-like cells. The main factor that induced titan-like cells was the addition of serum to nutrient limited media. This has allowed to easily performing new approaches to characterize several signaling pathways involved in their development. We found that the formation of these cells is regulated by quorum sensing molecules, and that pathways such as PKC and TOR kinases regulate the process of cellular enlargement. We have also to perform transcriptomic analysis, which led to the identification of new genes that could be involved in the process. This work will open different research lines that will contribute to the elucidation of the role of these cells during infection and on the development of cryptococcal disease.

microbiology↗