Biology subjects

Bare, P.

Publications and source records attributed to Bare, P..

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↗

bioRxiv2017

Case-control study highlights a different gut microbiome in cirrhotic patients with and without hepatocellular carcinoma

BackgroundNo specific microbiome in patients with hepatocellular carcinoma (HCC) has been reported to date.\n\nAimTo compare the gut microbiome found in cirrhotic patients with and without HCC.\n\nMethodsFrom 407 patients with Child Pugh A/B cirrhosis prospectively followed, 25 with HCC (cases) were matched with 25 without HCC (wo-HCC) in a 1:1 ratio according to age, gender, etiology, Child Pugh and severity of portal hypertension. In addition results were also compared with 25 healthy subjects. Faecal stool samples were collected noninvasively, aliquoted for DNA extraction and sequenced for the V3-V4 region of the microbial 16S rRNA (Illumina MiSeq Platform).\n\nResultsThere were no significant clinical differences among cases and controls. We found a differential abundance in family members of Firmicutes with a 3-fold increased of Erysipelotrichaceae and a 5-fold decrease in family Leuconostocaceae in HCC when compared to wo-HCC controls. Genus Fusobacterium was found 5-fold decreased in HCC versus wo-HCC. The ratio bacteriodes/prevotella was increased in HCC due to the significant decrease in the genus prevotella. Genus Odoribacter and Butyricimonas were more differentialy abundant in HCC. This pattern has been previously associated with an inflammatory milieu with a putative increased activation of NOD-like receptor signalling pathways. A Random Forest model trained with differential abundant taxa correctly classifyed HCC individuals with an error of 22%.\n\nConclusionsA pattern of microbiome linked to inflammation was observed in cirrhotic patients with HCC. These findings open the discussion whether or not microbiota has a physiopathologic role in HCC development in cirrhosis.

cancer biology↗