Corpus overview


MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinN (3)

ComplexRdRp (3)

NSP6 (1)

NSP12 (1)

ORF3a (1)


SARS-CoV-2 Proteins
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    Concentration of the cellular material in the nasopharyngeal swabs increases the clinical sensitivity of SARS-CoV2 RT-PCR

    Authors: Priya Kannian; Pasuvaraj Mahanathi; Veeraraghavan Ashwini

    doi:10.1101/2020.10.31.20218958 Date: 2020-11-04 Source: medRxiv

    Severe acute respiratory syndrome MESHD - coronavirus 2 (SARS-CoV2) is detected by a highly sensitive molecular method, reverse transcriptase-polymerase chain reaction (RT-PCR) from nasopharyngeal swab (NPS) samples collected in 2-3ml of viral transport medium (VTM). Unlike body fluids, NPS samples are undermined by high variability in the amount of cells that get suspended into the VTM. Hence, the cell density used for RNA extraction becomes an important analytical variable that contributes to the overall sensitivity of the RT-PCR. In this study, we compared the sensitivity of SARS-CoV2 RT-PCR in 50 NPS samples collected from in-patients of the COVID wards using the concentration and direct methods. The concentration method detected the viral RNA in all 50 samples, while the direct method was positive in only 41 (82%) samples (p=0.003). Additionally, the Ct values were lower in the direct method compared to concentration method among the 41 positive samples (p=0.03 for N gene PROTEIN and p=0.04 for RdRp PROTEIN gene). The mean CV% was also greater than or equal to 10%. Thus, the concentration of the cells prior to RNA extraction drastically improves the sensitivity of detection of SARS-CoV2 in NPS samples.

    Global variation in the SARS-CoV-2 proteome reveals the mutational hotspots in the drug and vaccine candidates

    Authors: L Ponoop Prasad Patro; Chakkarai Sathyaseelan; Patil Pranita Uttamrao; Thenmalarchelvi Rathinavelan

    doi:10.1101/2020.07.31.230987 Date: 2020-07-31 Source: bioRxiv

    To accelerate the drug and vaccine development against the severe acute respiratory syndrome MESHD virus 2 (SARS-CoV-2), a comparative analysis of SARS-CoV-2 proteome has been performed in two phases by considering manually curated 31389 whole genome sequences from 84 countries. Among the 9 mutations that occur at a high significance (T85I-NPS2, L37F- NSP6 PROTEIN, P323L- NSP12 PROTEIN, D614G-spike, Q57H- ORF3a PROTEIN, G251V- ORF3a PROTEIN, L84S- ORF8 PROTEIN, R203K-nucleocapsid and G204R-nucleocapsid), R203K-nucleocapsid and G204R-nucleocapsid are co-occurring (dependent) mutations and P323L- NSP12 PROTEIN and D614G-spike often appear simultaneously. Other notable variations that appear with a moderate to low significance are, M85- NSP1 HGNC deletion, D268- NSP2 HGNC NSP2 PROTEIN deletion, 112 amino acids deletion in ORF8 PROTEIN, a phenylalanine insertion amidst F34-F36 ( NSP6 PROTEIN) and several co-existing (dependent) substitution/deletion (I559V & P585S in NSP2 HGNC NSP2 PROTEIN, P504L & Y541C in NSP13 PROTEIN, G82 & H83 deletions in NSP1 HGNC and K141, S142 & F143 deletions in NSP2 HGNC NSP2 PROTEIN) mutations. P323L- NSP12 PROTEIN, D614G-spike, L37F- NSP6 PROTEIN, L84S- ORF8 PROTEIN and the sequences deficient of the high significant mutations have led to 4 major SARS-CoV-2 clades. The top 5 countries bearing all the high significant and majority of the moderate significant mutations are: USA, England, Wales, Australia and Scotland. Further, the majority of the significant mutations have evolved in the first phase and have already transmitted around the globe indicating the positive selection pressure. Among the 26 SARS-CoV-2 proteins, nucleocapsid PROTEIN protein, ORF3a PROTEIN, ORF8 PROTEIN, RNA dependent RNA polymerase PROTEIN and spike exhibit a higher heterogeneity compared with the rest of the proteins. However, NSP9 PROTEIN, NSP10 PROTEIN, NSP8 PROTEIN, the envelope protein PROTEIN and NSP4 HGNC NSP4 PROTEIN are highly resistant to mutations and can be exploited for drug/vaccine development.

    Prediction of SARS-CoV interaction with host proteins during lung aging reveals a potential role for TRIB3 HGNC in COVID-19 MESHD.

    Authors: Diogo de Moraes; Brunno Vivone Buquete Paiva; Sarah Santiloni Cury; Joao Pessoa Araujo Jr.; Marcelo Alves da Silva Mori; Robson Francisco Carvalho

    doi:10.1101/2020.04.07.030767 Date: 2020-04-09 Source: bioRxiv

    COVID-19 MESHD is prevalent in the elderly. Old individuals are more likely to develop pneumonia MESHD and respiratory failure MESHD due to alveolar damage MESHD, suggesting that lung senescence may increase the susceptibility to SARS-CoV-2 infection MESHD and replication. Considering that human coronavirus (HCoVs; SARS-CoV-2 and SARS-CoV) require host cellular factors for infection and replication, we analyzed Genotype-Tissue Expression (GTEx) data to test whether lung aging is associated with transcriptional changes in human protein-coding genes that potentially interact with these viruses. We found decreased expression of the gene tribbles homolog 3 ( TRIB3 HGNC) during aging in male individuals, and its protein was predicted to interact with HCoVs nucleocapsid protein PROTEIN and RNA-dependent RNA polymerase PROTEIN. Using publicly available lung single-cell data, we found TRIB3 HGNC expressed mainly in alveolar MESHD epithelial cells that express SARS-CoV-2 receptor ACE2 HGNC. Functional enrichment analysis of age-related genes, in common with SARS-CoV-induced perturbations, revealed genes associated with the mitotic cell cycle and surfactant metabolism. Given that TRIB3 HGNC was previously reported to decrease virus infection MESHD and replication, the decreased expression of TRIB3 HGNC in aged lungs may help explain why older male patients are related to more severe cases of the COVID-19 MESHD. Thus, drugs that stimulate TRIB3 HGNC expression should be evaluated as a potential therapy for the disease.

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins

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