Biology subjects

Pereson, M. J.

Publications and source records attributed to Pereson, M. J..

3 recordsLinked to original sources

bioRxiv2021

TNF-α levels in respiratory samples are associated with SARS-CoV-2 infection.

PurposeThe aim of this study was to measure levels of IL-6 and TNF- in respiratory samples from individuals with symptoms compatible with COVID-19 and analyze their association with SARS-CoV-2 presence. MethodsSARS-CoV-2 detection was performed using the CDC (USA) real-time RT-PCR primers, probes and protocols. Cytokine concentrations were measured using commercial reagents based on enzyme linked immunosorbent assay (ELISA). ResultsTNF- median levels were greater in COVID19 (+) symptomatic group (5.88 (1.36 - 172.1) pg/ml) compared to COVID19 (-) symptomatic individuals (2.87 (1.45 - 69.9) pg/ml) (p=0.0003). No significant differences were shown in IL-6 median values between COVID-19 (+) and (-) symptomatic patients (5.40 (1.7 - 467) pg/ml and 6.07 (1.57 - 466.6) pg/ml respectively). In addition, increased TNF- levels (greater than 10 pg/ml), but not IL-6, were associated with SARS-CoV-2 presence (OR= 5.7; p=0.006; 95% CI= 1,551 to 19,11). ConclusionsWe found a statistically significant association between the production of local TNF- and the presence of the virus in early stages of infection. IL-6 showed high levels in swabs from some symptomatic patients but independent from SARS-CoV-2 presence and viral load, individuals age and gender. On the contrary, TNF- evaluation confirmed the presence of inflammatory response but mostly related to COVID-19. More studies are required in order to characterize the cytokine profile expressed at the site of infection of SARS-CoV-2 and its implications in disease outcomes.

immunology↗

bioRxiv2020

Evolutionary analysis of SARS-CoV-2 spike protein for its different clades

ObjectiveThe spike protein of SARS-CoV-2 has become the main target for antiviral and vaccine development. Despite its relevance, there is scarce information about its evolutionary traces. The aim of this study was to investigate the diversification patterns of the spike for each clade of SARS-CoV-2 through different approaches. MethodsTwo thousand and one hundred sequences representing the seven clades of the SARS-CoV-2 were included. Patterns of genetic diversifications and nucleotide evolutionary rate were estimated for the spike genomic region. ResultsThe haplotype networks showed a star shape, where multiple haplotypes with few nucleotide differences diverge from a common ancestor. Four hundred seventy nine different haplotypes were defined in the seven analyzed clades. The main haplotype, named Hap-1, was the most frequent for clades G (54%), GH (54%), and GR (56%) and a different haplotype (named Hap-252) was the most important for clades L (63.3%), O (39.7%), S (51.7%), and V (70%). The evolutionary rate for the spike protein was estimated as 1.08 x 10-3 nucleotide substitutions/site/year. Moreover, the nucleotide evolutionary rate after nine months of pandemic was similar for each clade. ConclusionsIn conclusion, the present evolutionary analysis is relevant since the spike protein of SARS-CoV-2 is the target for most therapeutic candidates; besides, changes in this protein could have consequences on viral transmission, response to antivirals and efficacy of vaccines. Moreover, the evolutionary characterization of clades improves knowledge of SARS-CoV-2 and deserves to be assessed in more detail since re-infection by different phylogenetic clades has been reported.

evolutionary biology↗

bioRxiv2020

THE ORIGIN OF A NEW HUMAN VIRUS: PHYLOGENETIC ANALYSIS OF THE EVOLUTION OF SARS-COV-2

During the first months of SARS-CoV-2 evolution in a new host, contrasting hypotheses have been proposed about the way the virus has evolved and diversified worldwide. The aim of this study was to perform a comprehensive evolutionary analysis to describe the human outbreak and the evolutionary rate of different genomic regions of SARS-CoV-2. The molecular evolution in nine genomic regions of SARS-CoV-2 was analyzed using three different approaches: phylogenetic signal assessment, emergence of amino acid substitutions, and Bayesian evolutionary rate estimation in eight successive fortnights since the virus emergence. All observed phylogenetic signals were very low and trees topologies were in agreement with those signals. However, after four months of evolution, it was possible to identify regions revealing an incipient viral lineages formation despite the low phylogenetic signal, since fortnight 3. Finally, the SARS-CoV-2 evolutionary rate for regions nsp3 and S, the ones presenting greater variability, was estimated to values of 1.37 x 10-3 and 2.19 x 10-3 substitution/site/year, respectively. In conclusion, results obtained in this work about the variable diversity of crucial viral regions and the determination of the evolutionary rate are consequently decisive to understand essential feature of viral emergence. In turn, findings may allow characterizing for the first time, the evolutionary rate of S protein that is crucial for vaccines development.

evolutionary biology↗