scholarly journals Analysis of the SARS-CoV-2 envelope (E), nucleocapsid (N), and non-structural protein12 (nsp12) genes from COVID-19 patients in West Java

2021 ◽  
Vol 3 (1) ◽  
pp. 20-31
Author(s):  
Azzania Fibriani ◽  
Irin Annisa Evitayani ◽  
Gusti Ayu Prani Pradani ◽  
Rebecca Stephanie ◽  
Ema Rahmawati ◽  
...  
Keyword(s):  
Target Genes ◽  
Asian Country ◽  
World Health ◽  
Nasopharyngeal Swab ◽  
Envelope Gene ◽  
Structural Protein ◽  
Protein Structure Analysis ◽  
West Java ◽  
Stability Change ◽  
Health Organization

According to World Health Organization, as of January 2021, Indonesia is the only Southeast Asian country in which COVID-19 is still occurring in community transmission. West Java is one of the provinces holding the highest positive cases number. With the envelope (E), nucleocapsid (N), and non-structural protein 12 (nsp12) being the target genes of SARS-CoV-2 diagnostic kits and several antiviral drugs, the study of genetic variations has become relevant and greatly important. Out of 267 oro-nasopharyngeal swab specimens that were previously confirmed positive for COVID-19 in qPCR diagnostic test in Laboratorium Kesehatan Provinsi Jawa Barat, ten samples with acceptable qualities were selected and three samples were sequenced using Sanger sequencing. Nonsynonymous mutations were observed in the envelope gene (L21F) and in the nucleocapsid genes (R203K, G204R, A211S, and S193I). Phylogenetic analysis showed that samples were clustered with other sequences carrying identical mutations, but clustered non-discriminatively with all sequences when carrying no mutation. No pattern in geographical areas and clades, except for R203K-G204R for being a marker for the GR clade. Protein structure analysis showed that mutations observed did not change the hydrophobicity and the secondary structure of the nucleocapsid, while stability change (ΔΔG) showed that all mutations, aside from the R203K-G204R, have neutral effect on the protein stability. Therefore, it can be concluded that mutations observed in this experiment did not impart preference to disperse in certain geographical areas or cause any significant structural change in the protein.

scholarly journals The Central Role of Non-Structural Protein 1 (NS1) in Influenza Biology and Infection

2020 ◽  
Vol 21 (4) ◽  
pp. 1511 ◽  
Author(s):  
Nícia Rosário-Ferreira ◽  
António J. Preto ◽  
Rita Melo ◽  
Irina S. Moreira ◽  
Rui M. M. Brito
Keyword(s):  
Viral Disease ◽  
Influenza Viruses ◽  
World Health ◽  
World Population ◽  
Structural Protein ◽  
Human Respiratory Tract ◽  
Host Interactions ◽  
The World ◽  
Health Organization

Influenza (flu) is a contagious viral disease, which targets the human respiratory tract and spreads throughout the world each year. Every year, influenza infects around 10% of the world population and between 290,000 and 650,000 people die from it according to the World Health Organization (WHO). Influenza viruses belong to the Orthomyxoviridae family and have a negative sense eight-segment single-stranded RNA genome that encodes 11 different proteins. The only control over influenza seasonal epidemic outbreaks around the world are vaccines, annually updated according to viral strains in circulation, but, because of high rates of mutation and recurrent genetic assortment, new viral strains of influenza are constantly emerging, increasing the likelihood of pandemics. Vaccination effectiveness is limited, calling for new preventive and therapeutic approaches and a better understanding of the virus–host interactions. In particular, grasping the role of influenza non-structural protein 1 (NS1) and related known interactions in the host cell is pivotal to better understand the mechanisms of virus infection and replication, and thus propose more effective antiviral approaches. In this review, we assess the structure of NS1, its dynamics, and multiple functions and interactions, to highlight the central role of this protein in viral biology and its potential use as an effective therapeutic target to tackle seasonal and pandemic influenza.

Changes in Gene Expression in PBMCs Profiles of PPARα Target Genes in Obese and Non-Obese Individuals During Fasting

2014 ◽  
Vol 66 (1) ◽  
pp. 19-25 ◽  
Author(s):  
Ingrid Felicidade ◽  
Juliana Cristina Marcarini ◽  
Clísia Mara Carreira ◽  
Marla Karine Amarante ◽  
Lydia A. Afman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Target Genes ◽  
Mononuclear Cells ◽  
Human Peripheral Blood ◽  
Obese Group ◽  
World Health ◽  
Peripheral Blood Mononuclear ◽  
Expression Levels ◽  
Patients With Diabetes ◽  
Health Organization

Background: The prevalence of obesity has risen dramatically and the World Health Organization estimates that 700 million people will be obese worldwide by 2015. Approximately, 50% of the Brazilian population above 20 years of age is overweight, and 16% is obese. Aim: This study aimed to evaluate the differences in the expression of PPARα target genes in human peripheral blood mononuclear cells (PBMCs) and free fatty acids (FFA) in obese and non-obese individuals after 24 h of fasting. We first presented evidence that Brazilian people exhibit expression changes in PPARα target genes in PBMCs under fasting conditions. Methods: Q-PCR was utilized to assess the mRNA expression levels of target genes. Results: In both groups, the FFA concentrations increased significantly after 24 h of fasting. The basal FFA mean concentration was two-fold higher in the obese group compared with the non-obese group. After fasting, all genes evaluated in this study showed increased expression levels compared with basal expression in both groups. Conclusion: However, our results reveal no differences in gene expression between the obese and non-obese, more studies are necessary to precisely delineate the associated mechanisms, particularly those that include groups with different degrees of obesity and patients with diabetes mellitus type 2 because the expression of the main genes that are involved in β-oxidation and glucose level maintenance are affected by these factors. © 2014 S. Karger AG, Basel

scholarly journals A novel point mutation in the N gene of SARS-CoV-2 may affect the detection of the virus by RT-qPCR

2021 ◽  
Author(s):  
Mohammad Rubayet Hasan ◽  
Sathyavathi Sundararaju ◽  
Chidambaram Manickam ◽  
Faheem Mirza ◽  
Hamad Al-Hail ◽  
...  
Keyword(s):  
Viral Genome ◽  
Large Scale ◽  
Target Genes ◽  
Cytidine Deaminase ◽  
World Health ◽  
N Gene ◽  
Single Nucleotide ◽  
E Gene ◽  
Reverse Transcription Pcr ◽  
Health Organization

Since the beginning of the coronavirus disease 2019 (COVID-19) pandemic, laboratory testing to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by real-time reverse transcription PCR (RT-qPCR) has played a central role in mitigating the spread of the virus (1). Soon after the viral genome sequences were available, several RT-qPCR assays were developed and made available by World Health Organization (WHO) for public use (https://www.who.int/docs/default-source/coronaviruse/whoinhouseassays.pdf). The primer and probe sequences for these assays were chosen from multiple target genes within the viral genome such as the E gene, RdRp gene, ORF1ab and N gene. Many commercial and laboratory-developed assays were developed for SARS-CoV-2 detection based on these primer and probe sequences. The large-scale sustained person-to-person transmission of SARS-CoV-2 has led to many mutational events, some of which may affect the sensitivity and specificity of available PCR assays (2). Recently, mutations in the E gene (C26340T) and N gene (C29200T) were reported affecting the detection of target genes by two commercial assays in 8 and 1 patients, respectively. Interestingly, both mutations are of C>T type, a common single nucleotide polymorphism (SNP) that may be associated with strong host cell mRNA editing mechanisms known as APOBEC cytidine deaminase (3, 4). Another study found a G to U substitution in position 29140 that affected the sensitivity of detection of N gene-based assays (5). Here we report a novel N gene mutation (C29200A) seen in 3 patients, which affected the detection of SARS-CoV-2 N gene by a commercial assay.

scholarly journals Una presentación infrecuente de COVID-19, con diarrea como síntoma inicial, el primer caso diagnosticado en Cartagena, Colombia.

2021 ◽  
Vol 10 (1) ◽  
pp. 65-74
Author(s):  
Germán Enrique Arenas ◽  
Jesús De León Martínez ◽  
Marcela Negrete Vasquez ◽  
Mario Lora ◽  
Martín Carvajal ◽  
...  
Keyword(s):  
World Health ◽  
Nasopharyngeal Swab ◽  
Imaging Data ◽  
Rt Pcr ◽  
Global Pandemic ◽  
First Case ◽  
Initial Symptoms ◽  
The Common ◽  
Severity Of The Disease ◽  
Health Organization

Introduction: the Coronavirus disease 2019 (COVID-19) was declared as a global pandemic by the World Health Organization on March 11, 2020. The clinical presentation and severity of the disease has been described from its most typical symptoms, the common cold, pneumonia and respiratory distress syndrome, to the involvement of other organs and systems such such as the gastrointestinal, renal and cardiovascular. Case report: we describe the first case of COVID-19 diagnosed in Cartagena, Colombia, on March 11, 2020, and its uncommon clinic presentation, which was almost unknown at the time. An 85-year-old woman with week-long initial symptoms of nausea and occasional vomiting, with progression to diarrhea and a 38.5 oC fever during the last three days. The patient came from Oxford, UK, and she had been on a Caribbean cruise excursion since the end of February, 2020. Chest computed tomography showed ground glass opacities in both peripheral and central lung fields, multilobar and predominantly subpleural; without evidence of consolidation or pleural effusion. COVID-19 was confirmed three days after admission, when a RT-PCR molecular test performed on a nasopharyngeal swab sample tested positive for SARS-Cov-2 Conclusion: this first case of COVID-19 diagnosed in Cartagena occurred at a time when our health system was not prepared to face the pandemic. However, despite having manifested with a clinical that had not been described at the time, and thanks to the epidemiological, clinical and imaging data, the case could be adequately approached, diagnosed and treated according to the necessary and recommended measures at the time.

scholarly journals A multisystem inflammatory syndrome in children associated with COVID-19 in a 11-years-old girl

2021 ◽  
pp. 78-78
Author(s):  
Milena Bjelica ◽  
Gordana Vilotijevic-Dautovic ◽  
Andrea Djuretic ◽  
Slobodan Spasojevic
Keyword(s):  
Gastrointestinal Symptoms ◽  
World Health ◽  
Nasopharyngeal Swab ◽  
First Case ◽  
Control And Prevention ◽  
Inflammatory State ◽  
Life Threatening ◽  
History Of ◽  
Health Organization ◽  
Inflammatory Syndrome

Introduction. Multisystem inflammatory syndrome in children (MIS-C) is a post-viral, life-threatening, inflammatory state with multisystem involvement that typically manifests 3-4 weeks after SARS-CoV-2 infection. In this article, we present the first case of MIS-C in the Institute for Child and Youth Health Care of Vojvodina at the beginning of the COVID-19 pandemic. Case outline. A previously 11-years-old healthy girl got sick two days before admission to the hospital with a fever, headache, vomiting, abdominal pain, and fatigue. She was tested positive for COVID-19 by nasopharyngeal swab PCR with positive IgM and IgG antibodies. In the further course the illness presented with prolonged fever, laboratory evidence of inflammation, multiorgan involvement such as respiratory, gastrointestinal, cardiovascular, and dermatologic. Based on Centers for Disease Control and Prevention and World Health Organization criteria the diagnosis of MIS-C was made and IVIG and methylprednisolone were introduced with favorable clinical course. Conclusion. Every prolonged and unusual febrile state, especially if it is accompanied by gastrointestinal symptoms, in a school-age child, should be investigated in the direction of recent COVID-19 infection or exposure. In a case of a positive COVID-19 history or history of exposure, the MIS-C diagnosis should be considered.

scholarly journals Rapid COVID-19 Screening Based on Self-Reported Symptoms: Psychometric Assessment and Validation of the EPICOVID19 Short Diagnostic Scale

10.2196/23897 ◽  
2021 ◽  
Vol 23 (1) ◽  
pp. e23897 ◽  
Author(s):  
Luca Bastiani ◽  
Loredana Fortunato ◽  
Stefania Pieroni ◽  
Fabrizio Bianchi ◽  
Fulvio Adorni ◽  
...  
Keyword(s):  
Phase Ii ◽  
Immunoglobulin M ◽  
World Health ◽  
Nasopharyngeal Swab ◽  
Cutoff Score ◽  
Serological Tests ◽  
Convenience Sample ◽  
Respiratory Problems ◽  
Health Organization ◽  
Taste And Smell

Background Confirmed COVID-19 cases have been registered in more than 200 countries, and as of July 28, 2020, over 16 million cases have been reported to the World Health Organization. This study was conducted during the epidemic peak of COVID-19 in Italy. The early identification of individuals with suspected COVID-19 is critical in immediately quarantining such individuals. Although surveys are widely used for identifying COVID-19 cases, outcomes, and associated risks, no validated epidemiological tool exists for surveying SARS-CoV-2 infection in the general population. Objective We evaluated the capability of self-reported symptoms in discriminating COVID-19 to identify individuals who need to undergo instrumental measurements. We defined and validated a method for identifying a cutoff score. Methods Our study is phase II of the EPICOVID19 Italian national survey, which launched in April 2020 and included a convenience sample of 201,121 adults who completed the EPICOVID19 questionnaire. The Phase II questionnaire, which focused on the results of nasopharyngeal swab (NPS) and serological tests, was mailed to all subjects who previously underwent NPS tests. Results Of 2703 subjects who completed the Phase II questionnaire, 694 (25.7%) were NPS positive. Of the 472 subjects who underwent the immunoglobulin G (IgG) test and 421 who underwent the immunoglobulin M test, 22.9% (108/472) and 11.6% (49/421) tested positive, respectively. Compared to NPS-negative subjects, NPS-positive subjects had a higher incidence of fever (421/694, 60.7% vs 391/2009, 19.5%; P<.001), loss of taste and smell (365/694, 52.6% vs 239/2009, 11.9%; P<.001), and cough (352/694, 50.7% vs 580/2009, 28.9%; P<.001). With regard to subjects who underwent serological tests, IgG-positive subjects had a higher incidence of fever (65/108, 60.2% vs 43/364, 11.8%; P<.001) and pain in muscles/bones/joints (73/108, 67.6% vs 71/364, 19.5%; P<.001) than IgG-negative subjects. An analysis of self-reported COVID-19 symptom items revealed a 1-factor solution, the EPICOVID19 diagnostic scale. The following optimal scores were identified: 1.03 for respiratory problems, 1.07 for chest pain, 0.97 for loss of taste and smell 0.97, and 1.05 for tachycardia (ie, heart palpitations). These were the most important symptoms. For adults aged 18-84 years, the cutoff score was 2.56 (sensitivity: 76.56%; specificity: 68.24%) for NPS-positive subjects and 2.59 (sensitivity: 80.37%; specificity: 80.17%) for IgG-positive subjects. For subjects aged ≥60 years, the cutoff score was 1.28, and accuracy based on the presence of IgG antibodies improved (sensitivity: 88.00%; specificity: 89.58%). Conclusions We developed a short diagnostic scale to detect subjects with symptoms that were potentially associated with COVID-19 from a wide population. Our results support the potential of self-reported symptoms in identifying individuals who require immediate clinical evaluations. Although these results come from the Italian pandemic period, this short diagnostic scale could be optimized and tested as a screening tool for future similar pandemics.

Anti-SARS and anti-HCV drugs repurposing against the Papain-like protease of the newly emerged coronavirus (2019-nCoV)

2020 ◽  
Author(s):  
Abdo Elfiky ◽  
Noha S Ibrahim
Keyword(s):  
Middle East ◽  
Human Infection ◽  
Central China ◽  
World Health ◽  
Chinese Government ◽  
Structural Protein ◽  
East Region ◽  
Starting Point ◽  
Human Coronaviruses ◽  
Health Organization

Abstract A new mysterious coronavirus outbreak started last month in China. The World Health Organization (WHO) termed the new virus strain 2019-nCoV to be the seventh reported human coronaviruses (HCoV). A seafood market in Wuhan city, central China was the starting point of the emergence with unknown animal causes the first animal to human infection. Until today 904 confirmed deaths and more than 40000 cases confirmed in China and 28 countries. There is a massive fear of the human to human transmission of 2019-nCoV that reported last week by the Chinese government. The most famous two strains of HCoV are the Severe Acute Respiratory Syndrome coronavirus (SARS CoV) and the Middle East Respiratory Syndrome coronavirus (MERS CoV). The former had emerged in China in 2002 while the latter emerged in the Middle East region in 2012 and south Korea in 2015. In this study, the newly emerged 2019-nCoV papain-like protease (PLpro) is targeted by anti-SARS PLpro drugs and the anti-Hepatitis C Virus (HCV) Non-structural protein 3 (NS3) serine protease drugs. Sequence analysis, modeling, and docking are used to get a valid model for 2019-nCoV PLpro. The results suggest the effectiveness of the anti-SARS drugs (GRL-0667, GRL-0617, and Mycophenolic acid) and the anti-HCV drugs (Grazoprevir, Telaprevir, and Boceprevir) as potent inhibitors against the newly emerged coronavirus.

scholarly journals Do We Really Need Hazard Prevention at the Expense of Safeguarding Death Dignity in COVID-19?

Diagnostics ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 1913
Author(s):  
Cristoforo Pomara ◽  
Francesco Sessa ◽  
Domenico Galante ◽  
Lorenzo Pace ◽  
Antonio Fasanella ◽  
...  
Keyword(s):  
Cytopathic Effect ◽  
World Health ◽  
Replication Capacity ◽  
Nasopharyngeal Swab ◽  
Time Of Death ◽  
Rt Pcr ◽  
Viral Culture ◽  
The World ◽  
Health Organization ◽  
Test Objective

To date, little is known regarding the transmission risks of SARS-CoV-2 infection for subjects involved in handling, transporting, and examining deceased persons with known or suspected COVID-19 positivity at the time of death. This experimental study aims to define if and/or how long SARS-CoV-2 persists with replication capacity in the tissues of individuals who died with/from COVID-19, thereby generating infectious hazards. Sixteen patients who died with/from COVID-19 who underwent autopsy between April 2020 and April 2021 were included in this study. Based on PMI, all samples were subdivided into two groups: ‘short PMI’ group (eight subjects who were autopsied between 12 to 72 h after death); ‘long PMI’ (eight subjects who were autopsied between 24 to 78 days after death). All patients tested positive for RT-PCR at nasopharyngeal swab both before death and on samples collected during post-mortem investigation. Moreover, a lung specimen was collected and frozen at −80 °C in order to perform viral culture. The result was defined based on the cytopathic effect (subjective reading) combined with the positivity of the RT-PCR test (objective reading) in the supernatant. Only in one sample (PMI 12 h), virus vitality was demonstrated. This study, supported by a literature review, suggests that the risk of cadaveric infection in cases of a person who died from/with COVID-19 is extremely low in the first hours after death, becoming null after 12 h after death, confirming the World Health Organization (WHO) assumed in March 2020 and suggesting that the corpse of a subject who died from/with COVID-19 should be generally considered not infectious.

scholarly journals Rapid COVID-19 Screening Based on Self-Reported Symptoms: Psychometric Assessment and Validation of the EPICOVID19 Short Diagnostic Scale (Preprint)

2020 ◽  
Author(s):  
Luca Bastiani ◽  
Loredana Fortunato ◽  
Stefania Pieroni ◽  
Fabrizio Bianchi ◽  
Fulvio Adorni ◽  
...  
Keyword(s):  
Phase Ii ◽  
Immunoglobulin M ◽  
World Health ◽  
Nasopharyngeal Swab ◽  
Cutoff Score ◽  
Serological Tests ◽  
Convenience Sample ◽  
Respiratory Problems ◽  
Health Organization ◽  
Taste And Smell

BACKGROUND Confirmed COVID-19 cases have been registered in more than 200 countries, and as of July 28, 2020, over 16 million cases have been reported to the World Health Organization. This study was conducted during the epidemic peak of COVID-19 in Italy. The early identification of individuals with suspected COVID-19 is critical in immediately quarantining such individuals. Although surveys are widely used for identifying COVID-19 cases, outcomes, and associated risks, no validated epidemiological tool exists for surveying SARS-CoV-2 infection in the general population. OBJECTIVE We evaluated the capability of self-reported symptoms in discriminating COVID-19 to identify individuals who need to undergo instrumental measurements. We defined and validated a method for identifying a cutoff score. METHODS Our study is phase II of the EPICOVID19 Italian national survey, which launched in April 2020 and included a convenience sample of 201,121 adults who completed the EPICOVID19 questionnaire. The Phase II questionnaire, which focused on the results of nasopharyngeal swab (NPS) and serological tests, was mailed to all subjects who previously underwent NPS tests. RESULTS Of 2703 subjects who completed the Phase II questionnaire, 694 (25.7%) were NPS positive. Of the 472 subjects who underwent the immunoglobulin G (IgG) test and 421 who underwent the immunoglobulin M test, 22.9% (108/472) and 11.6% (49/421) tested positive, respectively. Compared to NPS-negative subjects, NPS-positive subjects had a higher incidence of fever (421/694, 60.7% vs 391/2009, 19.5%; <i>P</i>&lt;.001), loss of taste and smell (365/694, 52.6% vs 239/2009, 11.9%; <i>P</i>&lt;.001), and cough (352/694, 50.7% vs 580/2009, 28.9%; <i>P</i>&lt;.001). With regard to subjects who underwent serological tests, IgG-positive subjects had a higher incidence of fever (65/108, 60.2% vs 43/364, 11.8%; <i>P</i>&lt;.001) and pain in muscles/bones/joints (73/108, 67.6% vs 71/364, 19.5%; <i>P</i>&lt;.001) than IgG-negative subjects. An analysis of self-reported COVID-19 symptom items revealed a 1-factor solution, the EPICOVID19 diagnostic scale. The following optimal scores were identified: 1.03 for respiratory problems, 1.07 for chest pain, 0.97 for loss of taste and smell 0.97, and 1.05 for tachycardia (ie, heart palpitations). These were the most important symptoms. For adults aged 18-84 years, the cutoff score was 2.56 (sensitivity: 76.56%; specificity: 68.24%) for NPS-positive subjects and 2.59 (sensitivity: 80.37%; specificity: 80.17%) for IgG-positive subjects. For subjects aged ≥60 years, the cutoff score was 1.28, and accuracy based on the presence of IgG antibodies improved (sensitivity: 88.00%; specificity: 89.58%). CONCLUSIONS We developed a short diagnostic scale to detect subjects with symptoms that were potentially associated with COVID-19 from a wide population. Our results support the potential of self-reported symptoms in identifying individuals who require immediate clinical evaluations. Although these results come from the Italian pandemic period, this short diagnostic scale could be optimized and tested as a screening tool for future similar pandemics.

scholarly journals Saliva as a Potential Diagnostic Tool for SARS–CoV-2

2021 ◽  
Vol 10 (27) ◽  
pp. 2029-2033
Author(s):  
Aakriti Khemka ◽  
Manpreet Arora ◽  
Aparna Dave ◽  
Pulin Saluja ◽  
Radhika Rai
Keyword(s):  
Health Sector ◽  
World Health ◽  
Nasopharyngeal Swab ◽  
Antibody Testing ◽  
Diagnostic Modality ◽  
Health Authorities ◽  
Public Health Authorities ◽  
Potential Risk Factors ◽  
Novel Coronavirus ◽  
Health Organization

BACKGROUND COVID 19 has been labelled as a global pandemic by the World Health Organization (WHO). The sudden rise in death toll and devastation associated with it has put the entire infrastructure, economy and health sector to test. The only way for the prevention and control of this infectious disease is rapid and accurate screening of masses. Public Health Authorities mainly use antibody testing in hot spots using a mix of RT-PCR and antibody testing nasopharyngeal and orpharyngeal swabs. Considering the potential risk factors, constraints of time, cost and manpower, mass screening for COVID is not possible through nasopharyngeal and oropharyngeal swabs alone. Hence, to search an alternate method to diagnose for the initial screening of patients is the need of the hour globally. Saliva can also be used as one of the diagnostic modalities for coronavirus, helping in the rapid testing of individuals at home or at hospital. The article intends to explain the evidence regarding the reliability of saliva as a diagnostic specimen in COVID-19 patients and demonstrates the association and potential of detecting novel coronavirus in saliva of patients and how its implication in future can aid in diagnosis as a non - invasive diagnostic modality. KEY WORDS COVID 19, Throat Swab, Nasopharyngeal Swab, Saliva, Diagnostic Fluid

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