detecting-sars-cov-2-virus-reverse-transcription-loop-mediated

Detecting SARS-CoV-2 Virus by Reverse Transcription-Loop-Mediated Isothermal Amplification

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus has dramatically impacted human health. It continues to be a threat to modern ...

Universidad Icesi

Tropical ecosystems hold an extremely diverse array of endophytic fungi, but their potential use still remains to be explored. In this study, we isolated an endophytic fungus from the leaves of Otoba gracilipes, a medicinal tree from a tropical rainforest in Colombia. Following isolation and cultivation, we evaluated its extracellular crude extract for antioxidant activity. Using traditional and molecular methods (ITS1, NL1 regions), the endophyte was identified as Fusarium oxysporum. Fresh spores from the fungal isolate were inoculated in liquid media (potato dextrose broth [PDB] and potato dextrose-yeast extract broth [PDYB]) and centrifuged for recovering extracellular polysaccharides from the exhausted medium after 30 days of cultivation. Crude extracts were recovered, purified, lyophilized, and evaluated for their ability to inactivate the free radical 2,2-diphenyl-1-picrylhydrazyl (DPPH). The extracts obtained from PDB culture media had a 51.5% of scavenging effect on DPPH after 5 min of reaction compared with the extracts from PDBY (26.4%), which suggests a high antioxidant potential of these fungal extracts. Thus, our results suggest other fungi from tropical ecosystems should be explored as potential sources of novel enzymes and other metabolites with bioactivity.

Antioxidant activity of exo-metabolites produced by Fusarium oxysporum: An endophytic fungus isolated from leaves of Otoba gracilipes.

Forty percent of the world's population live in areas where they are at risk from dengue fever, dengue hemorrhagic fever, and dengue shock syndrome. Dengue viruses are transmitted primarily by the mosquito Aedes aegypti. In Cali, Colombia, approximately 30% of field collected Ae. aegypti are naturally refractory to all four dengue serotypes.

Transcriptome comparison of dengue-susceptible and -resistant field derived strains of Colombian Aedes aegypti using RNA-sequencing.

As the world enters its second year of the pandemic caused by SARS-CoV-2, intense efforts have been directed to develop an effective diagnosis, prevention, and treatment strategies. One promising drug target to design COVID-19 treatments is the SARS-CoV-2 M. To date, a comparative understanding of M dynamic stereoelectronic interactions with either covalent or non-covalent inhibitors (depending on their interaction with a pocket called S1' or oxyanion hole) has not been still achieved. In this study, we seek to fill this knowledge gap using a cascade in silico protocol of docking, molecular dynamics simulations, and MM/PBSA in order to elucidate pharmacophore models for both types of inhibitors. After docking and MD analysis, a set of complex-based pharmacophore models was elucidated for covalent and non-covalent categories making use of the residue bonding point feature. The highest ranked models exhibited ROC-AUC values of 0.93 and 0.73, respectively for each category. Interestingly, we observed that the active site region of M protein-ligand complex undergoes large conformational changes, especially within the S2 and S4 subsites. The results reported in this article may be helpful in virtual screening (VS) campaigns to guide the design and discovery of novel small-molecule therapeutic agents against SARS-CoV-2 M protein.

Novel covalent and non-covalent complex-based pharmacophore models of SARS-CoV-2 main protease (M) elucidated by microsecond MD simulations.

Aedes aegypti is the primary vector of dengue, Zika, and chikungunya viruses. Studies have shown that insecticide resistance affects vector competence (VC) of some mosquito species. This study evaluates the effect of resistance to lambda-cyhalothrin and kdr V1016I mutation genotypes on the VC of Ae. aegypti strains for DENV-2, ZIKV, and CHIKV. Three Ae. aegypti strains with gradual lambda-cyhalothrin resistance (susceptible, resistant, and highly resistant) were infected with DENV-2, ZIKV, and CHIKV. Individual mosquitoes were tested to detect virus infection in the abdomen and head-salivary glands, using RT-PCR, and genotypes for V1016I mutations using allele-specific PCR. Recorded VC variables were midgut infection rate (MIR), dissemination rate (DIR), and dissemination efficiency (DIE). Lambda-cyhalothrin resistance affects differentially VC variables for ZIKV, DENV-2, and CHIKV. For ZIKV, an apparent gradual increase in DIR and DIE with the increase in insecticide resistance was observed. For DENV-2 the MIR and DIE were higher in insecticide resistant strains. For CHIKV, only MIR could be evaluated, this variable was higher in insecticide resistance strains. The presence of kdr V1016I mutation on mosquito resistant strains did not affect VC variables for three study viruses.

Vector competence of lambda-cyhalothrin resistant Aedes aegypti strains for dengue-2, Zika and chikungunya viruses in Colombia.

Viruses are constantly changing as a result of mutations, and new viral variants are expected to appear over time. The virus that causes coronavirus disease 2019, severe acute respiratory syndrome coronavirus 2, is not excluded from this condition. Patients with some types of immunodeficiency have been reported to experience symptoms that vary from mild to severe, or even death, after being infected with severe acute respiratory syndrome coronavirus 2. We report a case of a woman with severe hypogammaglobulinemia who developed a prolonged and fatal severe acute respiratory syndrome coronavirus 2 infection.

Article	Year
Antioxidant activity of exo-metabolites produced by Fusarium oxysporum: An endophytic fungus isolated from leaves of Otoba gracilipes. MicrobiologyOpen\| PubMed ID: 31297981	2019
Transcriptome comparison of dengue-susceptible and -resistant field derived strains of Colombian Aedes aegypti using RNA-sequencing. Memorias do Instituto Oswaldo Cruz\| PubMed ID: 34076041	2021
Novel covalent and non-covalent complex-based pharmacophore models of SARS-CoV-2 main protease (M) elucidated by microsecond MD simulations. Scientific reports\| PubMed ID: 35982147	2022
Vector competence of lambda-cyhalothrin resistant Aedes aegypti strains for dengue-2, Zika and chikungunya viruses in Colombia. PloS one\| PubMed ID: 36282839	2022
Persistent and fatal severe acute respiratory syndrome coronavirus 2 infection in a patient with severe hypogammaglobulinemia: a case report. Journal of medical case reports\| PubMed ID: 37173711	2023

Paola A. Caicedo

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