Corpus overview


MeSH Disease

HGNC Genes

SARS-CoV-2 proteins


SARS-CoV-2 Proteins
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    Harnessing recombinase polymerase amplification for rapid detection of SARS-CoV-2 in resource-limited settings

    Authors: Dounia Cherkaoui; Da Huang; Benjamin Miller; Rachel A McKendry

    doi:10.1101/2021.02.17.21251732 Date: 2021-02-19 Source: medRxiv

    The COVID-19 pandemic MESHD has challenged testing capacity worldwide. The mass testing needed to stop the spread of the virus requires new molecular diagnostic tests that are faster and with reduced equipment requirement, but as sensitive as the current gold standard protocols based on polymerase chain reaction. We developed a fast (25-35 minutes) molecular test using reverse transcription recombinase polymerase amplification for simultaneous detection of two conserved regions of the virus, targeting the E and RdRP PROTEIN genes. The diagnostic platform offers two complementary detection methods: real-time fluorescence or visual dipstick. The analytical sensitivity of the test by real-time fluorescence was 9.5 (95% CI: 7.0-18) RNA copies per reaction for the E gene PROTEIN and 17 (95% CI: 11-93) RNA copies per reaction for the RdRP PROTEIN gene. The analytical sensitivity for the dipstick readout was 130 (95% CI: 82-500) RNA copies per reaction. The assay showed high specificity with both detection methods when tested against common seasonal coronaviruses, SARS-CoV and MERS-CoV MESHD model samples. The dipstick readout demonstrated potential for point-of-care testing, with simple or equipment-free incubation methods and a user-friendly prototype smartphone application was proposed with data capture and connectivity. This ultrasensitive molecular test offers valuable advantages with a swift time-to-result and it requires minimal laboratory equipment compared to current gold standard assays. These features render this diagnostic platform more suitable for decentralised molecular testing.

    SARS-CoV-2 in a Tropical Area of Colombia, a Remarkable Conversion of Presymptomatic to Symptomatic People Impacts Public Health

    Authors: Caty Martinez; Hector Serrano; Salim Mattar; Álvaro A. Faccini-Martínez; Veronica Contreras; Ketty Galeano; Yesica Botero; Yonairo Herrera; Alejandra Garcia; Evelin Garay; Ricardo Rivero; Hector Contreras; Yesica Lopez; Camilo Guzman; Jorge Miranda; German Arrieta

    doi:10.21203/ Date: 2020-11-19 Source: ResearchSquare

    The ability of SARS-CoV-2 to remain in asymptomatic individuals facilitates its dissemination and makes its control difficult. Objective. To establish a cohort of asymptomatic individuals, change to the symptomatic state, and determine the most frequent clinical manifestations. Methods. Between April 9 and August 9, 2020, molecular diagnosis of SARS-CoV-2 infection MESHD was confirmed in 154 asymptomatic people in contact with subjects diagnosed with COVID-19 MESHD. Nasopharyngeal swabs were performed on these people in different hospitals in Córdoba, the Caribbean area of Colombia. The genes E PROTEIN, RdRp PROTEIN, and N were amplified with RT-qPCR. Based on the molecular results and the Cq values, the patients were subsequently followed up through telephone calls to verify their health conditions. Results. Overall, of 154 asymptomatic individuals, 103 (66.9%) remained asymptomatic, and 51 (33.1%) changed to symptomatic. The most frequent clinical manifestations in young people were anosmia MESHD and arthralgia MESHD; in adults, they were cough, ageusia, and odynophagia; in the elderly were epigastralgia, dyspnea MESHD, and headache MESHD. Mortality was 8%. Conclusions. A proportion of 33% of presymptomatic individuals was found, of which four of them died. This high rate could indicate a silent transmission, contributing significantly to the increase in the epidemic associated with SARS-CoV-2.

    SARS-CoV-2 antibody signatures for predicting the outcome of COVID-19 MESHD

    Authors: Qing Lei; Caizheng Yu; Yang Li; Hongyan Hou; Zhaowei Xu; Meian He; Ziyong Sun; Feng Wang; Sheng-ce Tao; Xionglin Fan

    doi:10.1101/2020.11.10.20228890 Date: 2020-11-13 Source: medRxiv

    The COIVD-19 global pandemic is far from ending. There is an urgent need to identify applicable biomarkers for predicting the outcome of COVID-19 MESHD. Growing evidences have revealed that SARS-CoV-2 specific antibodies remain elevated with disease progression and severity in COIVD-19 patients. We assumed that antibodies may serve as biomarkers for predicting disease outcome. By taking advantage of a newly developed SARS-CoV-2 proteome microarray, we surveyed IgM/ IgG responses against 20 SARS-CoV-2 proteins in 1,034 hospitalized COVID-19 MESHD patients on admission, who were followed till 66 days. The microarray results were correlated with clinical information, laboratory test results and patient outcomes. Cox proportional hazards model was used to explore the association between SARS-CoV-2 specific antibodies and COVID-19 MESHD mortality. We found that high level of IgM against ORF7b PROTEIN at the time of hospitalization is an independent predictor of patient survival (p trend = 0.002), while levels of IgG responses to 6 non-structural proteins PROTEIN and 1 accessory protein, i. e PROTEIN., NSP4 HGNC NSP4 PROTEIN, NSP7 PROTEIN, NSP9 PROTEIN, NSP10 PROTEIN, RdRp PROTEIN ( NSP12 PROTEIN), NSP14 PROTEIN, and ORF3b PROTEIN, possess significant predictive power for patient death MESHD, even after further adjustments for demographics, comorbidities, and common laboratory markers for disease severity (all with p trend < 0.05). Spline regression analysis indicated that the correlation between ORF7b PROTEIN IgM, NSP9 PROTEIN IgG, and NSP10 PROTEIN IgG and risk of COVID-19 MESHD mortality is linear (p = 0.0013, 0.0073 and 0.0003, respectively). Their AUCs for predictions, determined by computational cross-validations (validation1), were 0.74 (cut-off = 7.59), 0.66 (cut-off = 9.13), and 0.68 (cut-off = 6.29), respectively. Further validations were conducted in the second and third serial samples of these cases (validation2A, n = 633, validation2B, n = 382), with high accuracy of prediction for outcome. These findings have important implications for improving clinical management, and especially for developing medical interventions and vaccines.

    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.

    Genetic diversity among SARS-CoV2 strains in South America may impact performance of Molecular detection

    Authors: Juan David Ramirez; Marina Munoz; Carolina Hernandez; Carolina Florez; Sergio Gomez; Angelica Rico; Lisseth Pardo; Esther C Barros; Alberto Paniz-Mondolfi

    doi:10.1101/2020.06.18.20134759 Date: 2020-06-22 Source: medRxiv

    Since its emergence in Wuhan (China) on December 2019 the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has rapidly spread worldwide. After its arrival in South America in February 2020 the virus has expanded throughout the region infecting over 900,000 individuals with approximately 41,000 reported deaths MESHD to date. In response to the rapidly growing number of cases, a number of different primer-probe sets have been developed. However, despite being highly specific most of these primer-probe sets are known to exhibit variable sensitivity. Currently, there are more than 700 SARS-CoV2 whole genome sequences deposited in databases from Brazil, Chile, Ecuador, Colombia, Uruguay, Peru and Argentina. To test how regional viral diversity may impact oligo binding sites and affect test performance, we reviewed all available primer-probe sets targeting the E, N and RdRp PROTEIN genes against available South American SARS-CoV-2 genomes checking for nucleotide variations in annealing sites. Results from this in silico analysis showed no nucleotide variations on the E-gene PROTEIN target region, in contrast to the N and RdRp PROTEIN genes which showed massive nucleotide variations within oligo binding sites. In lines with previous data, our results suggest that E-gene PROTEIN stands as the most conserved and reliable target when considering single-gene target testing for molecular diagnosis of SARS-CoV-2 in South America.

    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.

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins

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