Corpus overview


MeSH Disease

HGNC Genes

SARS-CoV-2 proteins


SARS-CoV-2 Proteins
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    Codon pattern reveals SARS-CoV-2 to be a monomorphic strain that emerged through recombination of replicase and envelope alleles of bat and pangolin origin

    Authors: Kanika Bansal; Prabhu B Patil; Vyacheslav A. Dibrova; Yulia V. Dibrova; Volodymyr M. Vasylyk; Mykhailo Y. Novikov; Nataliia V. Shults; Sergiy G. Gychka; Scott Lee; Zhaohui Cui; Adebola Adebayo; Tiffiany Aholou; Minal Amin; Peter Aryee; Cindy Castaneda; Trudy Chambers; Amy Fleshman; Christin Goodman; Tony Holmes; Asha Ivey-Stephenson; Emiko Kamitani; Susan Katz; Jennifer Knapp; Maureen Kolasa; Maranda Lumsden; Erin Mayweather; Asfia Mohammed; Anne Moorman; Alpa Patel-Larson; Lara Perinet; Mark Pilgard; Deirdre Pratt; Shanica Railey; Jaina Shah; Dawn Tuckey; Emilio Dirlikov; Dale Rose; Julie Villanueva; Alicia Fry; Aron Hall; Hannah Kirking; Jacqueline Tate; Cherie Drenzek; Tatiana Lanzieri; Rebekah Stewart

    doi:10.1101/2020.10.12.335521 Date: 2020-10-12 Source: bioRxiv

    Viruses are dependent on the host tRNA pool, and an optimum codon usage pattern (CUP) is a driving force in its evolution. Systematic analysis of CUP of replicase ( rdrp PROTEIN), spike, envelope (E), membrane glycoprotein (M PROTEIN), and nucleocapsid (N PROTEIN) encoding genes of SARS-CoV-2 from reported diverse lineages to suggest one-time host jump of a SARS-CoV-2 isolate into the human host. In contrast to human isolates, a high degree of variation in CUP of these genes suggests that bats, pangolins, and dogs are natural reservoirs of diverse strains. At the same time, our analysis suggests that dogs are not a source of SARS-CoV-2. Interestingly, CUP of rdrp PROTEIN displays conservation with two bat SARS isolates RaTG13 and RmYN02. CUP of the SARS-CoV-2 E gene PROTEIN is also conserved with bat and pangolin isolates with variations for a few amino acids. This suggests role allele replacement in these two genes involving SARS strains of least two hosts. At the same time, a relatively conserved CUP pattern in replicase and envelope across hosts suggests them it to be an ideal target in antiviral development for SARS-CoV-2.

    Healthcare workers in elderly care: a source of silent SARS-CoV-2 transmission?

    Authors: Mirjam Jeanne Dorine Dautzenberg; Andrea Eikelenboom-Boskamp; Jacqueline Janssen; Miranda Drabbe; Ewoud de Jong; Eefke Weesendorp; Marion Koopmans; Andreas Voss

    doi:10.1101/2020.09.07.20178731 Date: 2020-09-09 Source: medRxiv

    Importance: Healthcare workers (HCWs), including those with mild symptoms, may be an important source of COVID-19 MESHD within elderly care. Objective: To gain insight into the spread of SARS-CoV-2 among HCWs working in elderly care settings. Design: Cross-sectional study among HCWs working in elderly care in the South-East of the Netherlands, testing for SARS-CoV-2, between March 31 and April 17, 2020. Setting: HCWs working in geriatric rehabilitation, somatic and psychogeriatric wards or small-scale living groups and district nursing, with a total of 5245 HCWs within 4 organisations. Participants: 621 HCWs with mild respiratory symptoms. Main Outcomes: Number of HCWs testing positive for SARS-CoV-2 in pharyngeal swabs, using real-time reverse-transcriptase PCR targeting the SARS-CoV-2 E-gene PROTEIN, N-gene PROTEIN, and RdRP PROTEIN. HCWs filled out a survey to collect information on symptoms and possible sources of infection. Results: 133/615 (21.6%) HCWs tested positive for SARS-CoV-2, ranging from 15.6 to 44.4% per elderly care organisation, and from 0 to 64.3% per separate location of the organizations, respectively. 74.6% of tested HCWs were nursing staff, 1.7% elderly care physicians, 20.3% other HCWs with patient contact and 3.4% HCWs without patient contact. In the univariate analysis, fever MESHD, runny or stuffy nose, anosmia MESHD, general malaise, myalgia MESHD, headache MESHD and ocular pain MESHD were associated with SARS-CoV-2 positivity, while gastro-intestinal symptoms and respiratory symptoms, other than runny or stuffy nose were not. Risk factors for SARS-CoV-2 positivity were contact with patients or colleagues with suspected or proven COVID-19 MESHD. Whole genome sequencing of 22 samples in 2 facilities strongly suggests spread within facilities. Conclusions and Relevance: We found a high SARS-CoV-2 prevalence among HCWs in nursing homes and district nursing, supporting the hypothesis of undetected spread within elderly care facilities. Structural testing of elderly care HCWs, including track and trace of contacts, should be performed to control this spread, even when only mild symptoms are present.

    Retesting Positive for SARS-CoV-2 RNA in Recovered COVID-19 MESHD Patients Reveals Low Levels of Non-Replicating Virus

    Authors: Flora Marzia Liotti; Giulia Menchinelli; Simona Marchetti; Rosalba Ricci; Brunella Posteraro; Francesco Landi; Maurizio Sanguinetti; Paola Cattani

    doi:10.21203/ Date: 2020-08-14 Source: ResearchSquare

    Background: The follow-up of COVID-19 MESHD recovered patients is especially important to assess their infectivity and/or transmissibility statuses in order to maximize the COVID-19 MESHD management and containment. The aim of this study was to determine both total (genomic) and replicative (sub-genomic) SARS-CoV-2 RNA levels in nasal/oropharyngeal swab (NOS) samples from patients at follow-up times after COVID-19 MESHD recovering. Materials/methods: We tested 176 NOS samples of COVID-19 MESHD recovered patients who were followed up at the Fondazione Policlinico Universitario A. Gemelli IRCCS in Rome from 21 April to 18 June 2020, according to our COVID-19 MESHD care protocol. The RT-PCR tests were performed using the Allplex™ 2019-nCoV and the Quanty COVID-19 MESHD assays (for total RNA detection and quantification, respectively) and an in-house assay (for replicative RNA detection).  Results: Of 176 NOS samples studied, 32 (18.2%) tested positive for total RNA, with CT values ranging from 29.3 to 38.8 for E, RdRP PROTEIN, and N genes PROTEIN (9 samples), 32.2 to 39.3 for RdRP PROTEIN and N genes PROTEIN (7 samples) or 35.8 to 39.8 for the N gene PROTEIN (16 samples). Consistently, viral loads ranged from 1.6 × 101 to 1.3 × 104 RNA copies/mL. Interestingly, we found replicative RNA in only one of 32 positive samples based on the presence of E-gene PROTEIN sub-genomic RNA (CT value of 39.1). The CT value (29.3) of E-gene PROTEIN genomic RNA in this sample was the lowest among the CT values of all 9 samples in which the E gene PROTEIN was detected. Testing samples obtained from the 32 patients at the time of COVID-19 MESHD diagnosis showed that the CT values ranged from 17.1 to 38.1 for E, RdRP PROTEIN, and N genes PROTEIN. Of note, the mean CT value of E-gene PROTEIN sub-genomic RNA (34.9) in these samples differed of 9.0 ± 2.8 from the mean CT value of E-gene PROTEIN genomic RNA (25.9). Finally, all but one of the 32 patients had positive serology results against SARS-CoV-2. Conclusions: Our findings show that at least a proportion of COVID-19 MESHD recovered patients were still positive for SARS-CoV-2 RNA, despite to a lower extent, and that only a minority of them was likely to have actively replicating virus in the upper respiratory tract.

    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.

    Epidemiological description and analysis of RdRp PROTEIN, E and N genes PROTEIN dynamic by RT-PCR of SARS-CoV-2 in Moroccan population: Experience of the National Reference Laboratory (LNR)-UM6SS

    Authors: Houda Benrahma; Idrissa Diawara; Imane Smyej; Jalila Rahoui; Nida Meskaouni; Rachid Benmessaoud; Khadija Arouro; Khadija Jaras; Zahra Adam; Salma Nahir; Zineb Aouzal; Hajar Elguazzar; Leila Jeddane; Fadwa Ousti; Jalila Elbakkouri; Chakib Nejjari

    doi:10.1101/2020.06.18.20135137 Date: 2020-06-20 Source: medRxiv

    The coronavirus disease 2019 MESHD ( COVID-19 MESHD), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a new infectious disease MESHD that first emerged in Hubei province, China, in December 2019. On 2 March 2020, the Moroccan Ministry of Health confirmed the first COVID-19 MESHD case in Morocco. The new virus SARS-CoV-2 was identified in the sample of a Moroccan expatriate residing in Italy. Without a therapeutic vaccine or specific antiviral drugs, early detection and isolation become essential against novel Coronavirus. This study aims to analyze the epidemiological profile of the SARS-CoV-2 in Moroccan cases and to investigate the dynamic of RdRp PROTEIN gene, N PROTEIN gene, and E PROTEIN gene in patients from diagnosis until the recovery. Among 859 Covid-19 MESHD RT-PCR tests realized for 285 patients, 133 cases had positive results Covid-19 MESHD. 9 % of these cases present the 3 genes RdRp PROTEIN, N, and E, 47% only the RdRp PROTEIN gene, 2% with RdRp PROTEIN and N gene PROTEIN, 26% cases are positives with N gene PROTEIN, and 16 % with N and E gene PROTEIN. The analysis of the Covid-19 MESHD genes ( RdRp PROTEIN, N, and E) dynamic reveal that more than 6% stay positive with detection of the N and E gene PROTEIN, and 14% with the N gene PROTEIN after 12 days of treatment. The median period from positive to the first negative Covid-19 MESHD RT-PCR tests was 6.8{+/-}2.24 days for 44% cases, 14.31 {+/-} 2.4 days for 30%, and 22.67 {+/-} 1.21 days for 4%. This a first description of the Moroccan COVID-19 MESHD cases and the analysis of the dynamic of the 3 genes RdRp PROTEIN, N, and E. The analysis of our population can help to involved in the care of patients.

    Sewage surveillance for the presence of SARS-CoV-2 genome as a useful wastewater based epidemiology (WBE) tracking tool in India

    Authors: Sudipti Arora; Aditi Nag; Jasmine Sethi; Jayana Rajvanshi; Sonika Saxena; Sandeep Kumar Shrivastava; Akhilendra Bhushan Gupta

    doi:10.1101/2020.06.18.20135277 Date: 2020-06-20 Source: medRxiv

    The infection with SARS-CoV-2 is reported to be accompanied by the shedding of the virus in stool samples of infected MESHD patients. Earlier reports have suggested that COVID-19 MESHD agents can be present in the fecal and sewage samples and thus it can be a good indication of the pandemic extent in a community. However, no such studies have been reported in the Indian context so far. Since, several factors like local population physiology, the climatic conditions, sewage composition, and processing of samples could possibly affect the detection of the viral genome, it becomes absolutely necessary to check for the presence of the SARS-CoV-2 in the wastewater samples from wastewater treatment plants (WWTPs) serving different localities of Jaipur city, which has been under red zone (pandemic hotspots) since early April 2020. Samples from different local municipal WWTPs and hospital wastewater samples were collected and wastewater based epidemiology (WBE) studies for the presence of SARS-CoV-2 were carried out using the RT-PCR technique to confirm the presence of different COVID-19 MESHD target genes namely S gene, E PROTEIN gene, ORF1ab PROTEIN gene, RdRp PROTEIN gene and N PROTEIN gene in the viral load of wastewater samples. In the present study, the untreated wastewater samples from the municipal WWTPs and hospital wastewater samples showed the presence of SARS-CoV-2 viral genome, which was correlated with the increased number of COVID-19 MESHD positive patients from the concerned areas, as per reported in the publically available health data. This is the first study that investigated the presence of SARS-CoV-2 viral genome in wastewater, at higher ambient temperature (above 40{degrees}C), further validating WBE as a potential tool in predicting and mitigating outbreaks.

    Temporal evolution and adaptation of SARS-COV 2 codon usage

    Authors: Maddalena Dilucca; Sergio Forcelloni; Andrea Giansanti; Alexandros Georgakilas; Athanasia Pavlopoulou

    doi:10.1101/2020.05.29.123976 Date: 2020-06-03 Source: bioRxiv

    The outbreak of severe acute respiratory syndrome-coronavirus-2 MESHD (SARS-CoV-2) has caused an unprecedented pandemic. Since the first sequenced whole-genome of SARS-CoV-2 on January 2020, the identification of its genetic variants has become crucial in tracking and evaluating their spread across the globe. In this study, we compared 15,259 SARS-CoV-2 genomes isolated from 60 countries since the outbreak of this novel coronavirus with the first sequenced genome in Wuhan to quantify the evolutionary divergence of SARS-CoV-2. Thus, we compared the codon usage patterns, every two weeks, of 13 of SARS-CoV-2 genes encoding for the membrane protein (M PROTEIN), envelope (E), spike surface glycoprotein (S PROTEIN), nucleoprotein (N PROTEIN), non-structural 3C-like proteinase ( 3CLpro PROTEIN), ssRNA-binding protein ( RBP HGNC), 2-O-ribose methyltransferase (OMT), endoRNase (RNase), helicase HGNC, RNA-dependent RNA polymerase PROTEIN ( RdRp PROTEIN), Nsp7, Nsp8, and exonuclease ExoN. As a general rule, we find that SARS-CoV-2 genome tends to diverge over time by accumulating mutations on its genome and, specifically, on the coding sequences for proteins N PROTEIN and S. Interestingly, different patterns of codon usage were observed among these genes. Genes S, Nsp7, NSp8, tend to use a norrower set of synonymous codons that are better optimized to the human host. Conversely, genes E PROTEIN and M consistently use a broader set of synonymous codons, which does not vary with respect to the reference genome. We identified key SARS-CoV-2 genes (S, N, ExoN, RNase, RdRp PROTEIN, Nsp7 and Nsp8) suggested to be causally implicated in the virus adaptation to the human host.

    In silico Proteome analysis of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)

    Authors: Chittaranjan Baruah; Papari Devi; Dhirendra K Sharma

    doi:10.1101/2020.05.23.104919 Date: 2020-05-24 Source: bioRxiv

    Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (2019-nCoV), is a positive-sense, single-stranded RNA coronavirus. The virus is the causative agent of coronavirus disease 2019 MESHD ( COVID-19 MESHD) and is contagious through human-to-human transmission. The present study reports sequence analysis, complete coordinate tertiary structure prediction and in silico sequence-based and structure-based functional characterization of full SARS-CoV-2 proteome based on the NCBI reference sequence NC_045512 (29903 bp ss-RNA) which is identical to GenBank entry MN908947 and MT415321. The proteome includes 12 major proteins namely orf1ab polyprotein (includes 15 proteins), surface glycoprotein, ORF3a PROTEIN protein, envelope PROTEIN envelope protein HGNC, membrane glycoprotein PROTEIN, ORF6 PROTEIN protein, ORF7a PROTEIN protein, orf7b, ORF8 PROTEIN, Nucleocapsid phosphoprotein and ORF10 PROTEIN protein. Each protein of orf1ab polyprotein group has been studied separately. A total of 25 polypeptides have been analyzed out of which 15 proteins are not yet having experimental structures and only 10 are having experimental structures with known PDB IDs MESHD. Out of 15 newly predicted structures six (6) were predicted using comparative modeling and nine (09) proteins having no significant similarity with so far available PDB structures were modeled using ab-initio modeling. Structure verification using recent tools QMEANDisCo 4.0.0 and ProQ3 for global and local (per-residue) quality estimates indicate that the all-atom model of tertiary structure of high quality and may be useful for structure-based drug designing targets. The study has identified nine major targets ( spike protein PROTEIN, envelop protein, membrane protein, nucleocapsid PROTEIN protein, 2-O-ribose methyltransferase, endoRNAse, 3-to-5 exonuclease, RNA-dependent RNA polymerase PROTEIN and helicase HGNC) for which drug design targets could be considered. There are other 16 nonstructural proteins PROTEIN (NSPs), which may also be percieved from the drug design angle. The protein structures have been deposited to ModelArchive. Tunnel analysis revealed the presence of large number of tunnels in NSP3 HGNC NSP3 PROTEIN, ORF 6 protein and membrane glycoprotein PROTEIN indicating a large number of transport pathways for small ligands influencing their reactivity.

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins

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