Biology subjects

Torres, C.

Publications and source records attributed to Torres, C..

26 records · Page 2Linked to original sources

bioRxiv2022

Evolution of SARS-CoV-2 during the first year of the COVID-19 pandemic in Northwestern Argentina

Studies about the evolution of SARS-CoV-2 lineages in different backgrounds such as naive populations, are still scarce, especially from South America. The aim of this work was to study the introduction and diversification pattern of SARS-CoV-2 during the first year of the COVID-19 pandemic in the Northwestern Argentina (NWA) region and to analyze the evolutionary dynamics of the main lineages found. In this study, we analyzed a total of 260 SARS-CoV-2 whole-genome sequences from Argentina, belonging to the Provinces of Jujuy, Salta and Tucuman, from March 31st, 2020, to May 22nd, 2021, which covered the full first wave and the early second wave of the COVID-19 pandemic in Argentina. In the first wave, eight lineages were identified: B.1.499 (76.9%), followed by N.5 (10.2%), B.1.1.274 (3.7%), B.1.1.348 (3.7%), B.1 (2.8%), B.1.600 (0.9%), B.1.1.33 (0.9%) and N.3 (0.9%). During the early second wave, the first-wave lineages were displaced by the introduction of variants of concern (VOC) (Alpha, Gamma), or variants of interest (VOI) (Lambda, Zeta, Epsilon) and other lineages with more limited distribution. Phylodynamic analyses of the B.1.499 and N.5, the two most prevalent lineages in NWA, revealed that the substitution rate of lineage N.5 (7.9 x 10-4 substitutions per site per year, s/s/y) was a [~]40% faster than that of lineage B.1.499 (5.9 x 10-4 s/s/y), although both are in the same order of magnitude than other non-VOC lineages. No mutations associated with a biological characteristic of importance were observed as signatures markers of the phylogenetic groups established in Northwestern Argentina, however, single sequences in non-VOC lineages did present mutations of biological importance or associated with VOCs as sporadic events, showing that many of these mutations could emerge from circulation in the general population. This study contributed to the knowledge about the evolution of SARS-CoV-2 in a pre-vaccination and without post-exposure immunization period.

bioinformatics↗

bioRxiv2022

Exploring Genomic Conservation in Actinobacteriophages with Small Genomes

Actinobacteriophages of a wide range of genome sizes continue to be isolated and characterized, but only a handful of these have atypically small genomes, defined in this work as genome sizes under 20,000 bp. These "small phages" are relatively rare and have received minimal study thus far. Of the actinobacteriophages published in PhagesDB.org, small phages have been isolated on Arthrobacter, Gordonia, Rhodococcus, and Microbacterium hosts. A previous study by Pope et al. showed that Gordonia small phages have similar gene products and amino acid sequences. Here, we set out to further examine relationships between small Gordonia phages as well as small phages that infect other hosts. Of the 3222 sequenced phages listed on PhagesDB, we identified 109 distinctly small phages with genome sizes under 20,000 bp. The majority of the small phages were isolated on Arthrobacter or Microbacterium hosts. Using comparative genomics, we searched for patterns of similarity among 34 cluster-representative small phages. Dot plot comparisons showed that there was more amino acid conservation than nucleotide identity amongst small phages. Gene content similarity (GCS) analysis revealed that the temperate Gordonia phages in Cluster CW share significant GCS values (over 35%) with the lytic Arthrobacter phages in Cluster AN, suggesting that some small phages have a considerable degree of genomic similarity with each other. SplitsTree analyses of shared phams (genes with substantial amino acid identity) supported the complexity of clustering criteria in small phages, given shuffling of genes across phages of different clusters and close relationships despite varied cluster membership. We observed this continuum of phage diversity through Rhodococcus phage RRH1s closer similarity to phages in Gordonia subcluster CW1 than CW1 is to Gordonia subcluster CW3. Finally, we were able to confirm the presence of conserved phams across not only small Gordonia phages but also within small phages from different clusters and hosts. Studying these genomic trends hidden in small phages allows us to better understand and appreciate the overall diversity of phages.

microbiology↗

bioRxiv2021

Comprehensive evolutionary analysis of complete Epstein Barr virus genomes from Argentina and other geographies

Epstein Barr virus sequence variability has been deeply studied throughout the past years in isolates from various geographic regions and consequent geographic variation at both genetic and genomic levels has been described. However, isolates from South America have been underrepresented in these studies. Here, we sequenced 15 complete EBV genomes that we analyzed, by means of a custom-built bioinformatic pipeline, together with publicly available raw NGS data for 199 EBV isolates from other parts of the globe. Phylogenetic relations of the genomes, geographic structure and variability of the data set, and evolution rates for the whole genome and each gene were assessed. The present study contributes to overcome the scarcity of EBV complete genomes from South America, and hence, achieves the most comprehensive geography-related variability study by determining the actual contribution of each EBV gene to the geographic segregation of the entire genomes. Moreover, to the best of our knowledge, we established for the first time the evolution rate for the entire EBV genome, on a host-virus codivergence-independent assumption, and statistically demonstrate that evolution rates, on a gene-by-gene basis, are related to the encoded protein function. Considering evolution of dsDNA viruses with a codivergence-independent approach, may lay the basis for future research on EBV evolution. Additionally, this work also expands the sampling-time lapse of available complete genomes derived from different EBV-related conditions, a matter that until today, prevents for detailed phylogeographic analysis.

evolutionary biology↗

bioRxiv2020

Complete Genome Sequences of Nine Cluster A Mycobacteriophages: AgentM, Ajay, Aragog, Archetta, ForGetIt, Koko, Ph8s, Phlorence, and Wilkins

BackgroundBacteriophages are ubiquitous, highly diverse, and relatively understudied. Growing interest in phage therapy has underscored the importance of isolating and characterizing novel bacteriophages. The Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) program aims to address this need by involving undergraduates around the world in authentic research. Materials and MethodsNine novel mycobacteriophages - AgentM, Ajay, Aragog, Archetta, ForGetIt, Koko, Ph8s, Phlorence, and Wilkins - were isolated from soil samples in southern California using host Mycobacterium smegmatis mc2155. Each purified phage was characterized using transmission electron microscopy and genome sequencing and annotation. ResultsAll nine bacteriophages were placed into mycobacteriophage Cluster A based on nucleotide similarity with other phages. The average genome length of all nine phages was 50,706 bp. On average, each phage had 87 total coding genes and GC content between 60-63%, consistent with that of other Cluster A phages. Transmission electron microscopy of phage particles revealed they had icosahedral heads and long, flexible tails, consistent with that of the Siphoviridae family. Plaque morphology and genome analysis confirms the nine novel phages are temperate as expected of Cluster A phages. ConclusionsAgentM, Ajay, Aragog, Archetta, ForGetIt, Koko, Ph8s, Phlorence, and Wilkins are all mycobacteriophages that belong to the Siphoviridae family. Comparative genomic analyses revealed genetic mosaicism and diversity among these Cluster A phages. The discovery of these novel phages expands on the existing library of mycobacteriophage genomes.

microbiology↗

bioRxiv2020

Novel Cluster AZ Arthrobacter phages Powerpuff, Lego, and YesChef exhibit close functional relationships with Microbacterium phages

Bacteriophages exhibit a vast spectrum of relatedness and there is increasing evidence of close genomic relationships independent of host genus. The variability in phage similarity at the nucleotide, amino acid, and gene content levels confounds attempts at quantifying phage relatedness, especially as more novel phages are isolated. This study describes three highly similar novel Arthrobacter globiformis phages-Powerpuff, Lego, and YesChef-which were assigned to Cluster AZ using a nucleotide-based clustering parameter. Phages in Cluster AZ and Microbacterium Cluster EH, as well as the former Microbacterium singleton Zeta1847, exhibited low nucleotide similarity but gene content similarity in excess of the recently adopted Microbacterium clustering parameter, which resulted in the reassignment of Zeta1847 to Cluster EH. Additionally, Clusters AZ and EH phages encode a shared integrase indicative of a lysogenic life cycle; in the first experimental verification of a Cluster AZ phages life cycle, we show that phage Powerpuff is a true temperate phage and forms stable lysogens that exhibit immunity to superinfection by related phages, despite lacking identifiable repressors typically required for lysogenic maintenance and superinfection immunity. The ability of phage Powerpuff to undergo and maintain lysogeny suggests that other closely related phages encoding an integrase but lacking an identified repressor may be temperate as well. Our findings further highlight the importance of using multiple metrics to capture phage relatedness, provide additional evidence of significant shared phage genomic content spanning multiple actinobacterial host genera, and demonstrate the continued need for verification and characterization of life cycles in newly isolated phages.

microbiology↗

bioRxiv2019

Phylodynamics of sunflower chlorotic mottle virus, a re-emerging pathosystem

Distribution and epidemiological patterns of sunflower chlorotic mottle virus (SCMoV) in sunflower (Helianthus annuus L.) growing areas in Argentina were studied from 2006 to 2017. The virus was detected exclusively in the Pampas region (Entre Rios, Santa Fe, Cordoba, La Pampa and Buenos Aires provinces). Phylodynamic analyses performed using the coat protein gene of SCMoV isolates from sunflower and weeds dated the most recent common ancestor (MRCA) back to 1887 (HPD95% = 1572-1971), which coincides with the dates of sunflower introduction in Argentina. The MRCA was located in the south of Buenos Aires province and was associated with sunflower host (posterior probability for the ancestral host, ppah= 0.98). The Bayesian phylodynamic analyses revealed the dispersal patterns of SCMoV, suggesting a link between natural host diversity, crop displacement by human activities and virus spread.

plant biology↗

bioRxiv2019

Integrating natural history-derived phenomics with comparative genomics to study the genetic architecture of convergent evolution

Evolutionary convergence has been long considered primary evidence of adaptation driven by natural selection and provides opportunities to explore evolutionary repeatability and predictability. In recent years, there has been increased interest in exploring the genetic mechanisms underlying convergent evolution, in part due to the advent of genomic techniques. However, the current genomics gold rush in studies of convergence has overshadowed the reality that most trait classifications are quite broadly defined, resulting in incomplete or potentially biased interpretations of results. Genomic studies of convergence would be greatly improved by integrating deep vertical, natural history knowledge with horizontal knowledge focusing on the breadth of taxonomic diversity. Natural history collections have and continue to be best positioned for increasing our comprehensive understanding of phenotypic diversity, with modern practices of digitization and databasing of morphological traits providing exciting improvements in our ability to evaluate the degree of morphological convergence. Combining more detailed phenotypic data with the well-established field of genomics will enable scientists to make progress on an important goal in biology: to understand the degree to which genetic or molecular convergence is associated with phenotypic convergence. Although the fields of comparative biology or comparative genomics alone can separately reveal important insights into convergent evolution, here we suggest that the synergistic and complementary roles of natural history collection-derived phenomic data and comparative genomics methods can be particularly powerful in together elucidating the genomic basis of convergent evolution among higher taxa.

evolutionary biology↗

bioRxiv2018

KRASG12D and TP53R167H Cooperate to Induce Pancreatic Ductal Adenocarcinoma in Sus Scrofa Pigs

Although survival has improved in recent years, the prognosis of patients with advanced pancreatic ductal adenocarcinoma (PDAC) remains poor. Despite substantial differences in anatomy, physiology, genetics, and metabolism, the overwhelming majority of preclinical testing relies on transgenic mice. Hence, while mice have allowed for tremendous advances in cancer biology, they have been a poor predictor of drug performance/toxicity in the clinic. Given the greater similarity of sus scrofa pigs to humans, we engineered transgenic sus scrofa expressing a LSL-KRASG12D-TP53R167H cassette. By applying Adeno-Cre to pancreatic duct cells in vitro, cells self-immortalized and established tumors in immunocompromised mice. When Adeno-Cre was administered to the main pancreaticduct in vivo, pigs developed extensive PDAC at the injection site hallmarked by excessive proliferation and desmoplastic stroma. This serves as the first large animal model of pancreatic carcinogenesis, and may allow for insight into new avenues of translational research not before possible in rodents.

cancer biology↗