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1.
Front Med (Lausanne) ; 8: 765249, 2021.
Article in English | MEDLINE | ID: covidwho-1581291

ABSTRACT

Ending COVID-19 pandemic requires a collaborative understanding of SARS-CoV-2 and COVID-19 mechanisms. Yet, the evolving nature of coronaviruses results in a continuous emergence of new variants of the virus. Central to this is the need for a continuous monitoring system able to detect potentially harmful variants of the virus in real-time. In this manuscript, we present the International Database of SARS-CoV-2 Variations (IDbSV), the result of ongoing efforts in curating, analyzing, and sharing comprehensive interpretation of SARS-CoV-2's genetic variations and variants. Through user-friendly interactive data visualizations, we aim to provide a novel surveillance tool to the scientific and public health communities. The database is regularly updated with new records through a 4-step workflow (1-Quality control of curated sequences, 2-Call of variations, 3-Functional annotation, and 4-Metadata association). To the best of our knowledge, IDbSV provides access to the largest repository of SARS-CoV-2 variations and the largest analysis of SARS-CoV-2 genomes with over 60 thousand annotated variations curated from the 1,808,613 genomes alongside their functional annotations, first known appearance, and associated genetic lineages, enabling a robust interpretation tool for SARS-CoV-2 variations to help understanding SARS-CoV-2 dynamics across the world.

2.
SN Compr Clin Med ; : 1-4, 2021 Sep 08.
Article in English | MEDLINE | ID: covidwho-1568437

ABSTRACT

In the COVID-19 pandemic era, anti-SARS-CoV-2 vaccination is considered to be the most efficient way to overtake the COVID-19 scourge. Like all medicines, vaccines are not devoid of risks and can in rare cases cause some various side effects. The objective of this case report is to highlight this unusual presentation of Henoch-Schönlein purpura following an anti-COVID-19 vaccination in a 62-year-old adult. The 62-year-old patient admitted to the emergency room for a petechial purpuric rash, sloping, occurring within hours, involving both legs and ascending. The clinical signs also included polyarthralgia and hematuria. Reported in the history the notion of an anti-COVID-19 vaccination 8 days prior to the onset of symptomatology. In the case of our patient, we retain the diagnosis of rheumatoid purpura based on the EULAR/PRINTO/PReS diagnostic criteria. Corticosteroid therapy (prednisone) was started, resulting to a rapid regression of clinical and laboratory symptoms, few days after the treatment. Patient was asymptomatic on subsequent visits. The low number of published cases of post-vaccine vasculitis does not question the safety of vaccines, but knowledge of such complications deserves to be known in order to avoid new immunizations that could have more serious consequences, and to avoid aggravating or reactivating a pre-existing vasculitis.

3.
3 Biotech ; 10(11): 483, 2020 Nov.
Article in English | MEDLINE | ID: covidwho-1384661

ABSTRACT

SARS-CoV-2, which causes severe pneumonia epidemics, probably originated from Chinese horseshoe bats, but the intermediate and host range is still unknown. ACE2 is the entry receptor for SARS-CoV-2. The binding capacity of SARS-CoV-2 spike protein to ACE2 is the critical determinant of viral host range and cross-species infection. Here, we used an in silico approach to predict the potential animals range with high susceptibility to SARS-CoV-2 by modelling and studying the Spike-ACE2 interaction of 22 domestic and wild animals. Our results showed that all studied animals are potentially susceptible to SARS-CoV-2 infection with a slight difference in the binding affinity and stability of their ACE2-RBD complexes. Furthermore, we identified a specific substitution of tyrosine to histidine at position 41 in ACE2 that likely reduces the affinity to SARS-CoV-2 in horses and greater horseshoe bats. These results may help to provide important insights into SARS-CoV-2 host range which will make it possible to control the spread of the virus and identify animal models that could be used for screening antiviral drugs or vaccine candidates against SARS-CoV-2.

4.
Microbiol Resour Announc ; 10(16)2021 Apr 22.
Article in English | MEDLINE | ID: covidwho-1199753

ABSTRACT

Here, we report the near-complete genome sequence and the genetic variations of a clinical sample of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) harboring the N501Y mutation assigned to the B.1.1.7 lineage. The sample was collected from a nasopharyngeal swab of a female patient from Temara, Morocco, and the sequencing was done using Ion S5 technology.

5.
Microbiol Resour Announc ; 10(11)2021 Mar 18.
Article in English | MEDLINE | ID: covidwho-1143001

ABSTRACT

We report the nearly complete genome sequence and the genetic variations of a clinical sample of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) collected from a nasopharyngeal swab specimen from a male patient from Harhoura-Rabat, Morocco. The sequence, which was obtained using Ion Torrent technology, is valuable as it carries a recently described deletion (His69-Val70) and substitution (Asn439Lys).

6.
Pan Afr Med J ; 38: 34, 2021.
Article in English | MEDLINE | ID: covidwho-1110742

ABSTRACT

Since December 2019, the world has experienced the emergence in China of a new infection called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This infection quickly has progressed to a global pandemic since March 2020, with very high human-to-human transmission rate. Besides lung injury, COVID-19 is also associated with cardio and neurovascular complications. Herein, we report the case of a 77-year-old female who presented with non-severe COVID-19 and multiple ischemic strokes secondary to an extensive carotid thrombosis. The ischemic stroke was supposed to have been caused by the cytokine storm related to COVID-19. The possibility of hemorrhagic transformation, based on the assessment of bleeding score, limited the use of anticoagulation, and probably explained the stroke recurrence and poor outcome in our patient. The pathogenic mechanism and the management of this complex situation are still lacking and further studies are needed.


Subject(s)
COVID-19/complications , Carotid Artery Thrombosis/etiology , Cytokine Release Syndrome/virology , Ischemic Stroke/etiology , Aged , Cytokine Release Syndrome/physiopathology , Female , Humans , Recurrence
7.
PLoS One ; 16(2): e0246295, 2021.
Article in English | MEDLINE | ID: covidwho-1063220

ABSTRACT

Since December 2019, the coronavirus disease (COVID-19) pandemic has catapulted the world into a marked health crisis, with over 29 million cases and >930,000 deaths. To better detect affected individuals at an early stage and stop disease progression to an advanced stage, several studies have been conducted to identify the clinical, biological, and radiological characteristics of COVID-19. This study aimed to enrich the literature by critically analyzing the clinical and biological characteristics of 134 patients from the North African Mediterranean region, including numerous genetic, epigenetic, and environmental factors that may influence disease evolution. This single-center retrospective study included all patients older than 18 years confirmed to have COVID-19 and hospitalized at the Cheikh Khalifa University Hospital affiliated with Mohammed VI University of Health Sciences, Casablanca, Morocco. Clinical, demographic, and biological data were analyzed in a cohort of severe and non-severe patients. Univariate analysis was performed to identify factors predictive of severity. There were 134 patients: the median age was 53 years, and 54.5% were male. Of these, 89 had mild to moderate disease; 45 had severe to critical disease, of which 14 died and 31 survived. Advanced age, presence of comorbidities, male sex, and infection in ethnic or family groups were risk factors for progression to severe disease. The presence of abnormalities in the following parameters were strongly associated with progression to severe disease: white blood cells (WBC), neutrophils, lymphocytes, C-reactive protein (CRP), procalcitonin, D-dimers, lactate dehydrogenase (LDH), ferritin, creatinine, aspartate aminotransferase (ASAT), and alanine aminotransferase (ALAT) during both admission and hospitalization. Based on these results and an extensive literature review, we recommend that clinicians closely monitor the biological parameters identified herein and perform immunological and genetic studies.


Subject(s)
COVID-19/blood , SARS-CoV-2/isolation & purification , Adult , Aged , COVID-19/diagnosis , COVID-19/epidemiology , Female , Humans , Male , Middle Aged , Morocco/epidemiology , Retrospective Studies , Severity of Illness Index
8.
Heliyon ; 6(12): e05739, 2020 Dec.
Article in English | MEDLINE | ID: covidwho-974077

ABSTRACT

The coronavirus disease 19 (COVID-19) is a highly contagious and rapidly spreading infection caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In some cases, the disease can be fatal which resulted in more than one million deaths worldwide according the WHO. Currently, there is no effective vaccine or treatment for COVID-19, however many small-molecule inhibitors have shown potent antiviral activity against SARS-CoV-2 and some of them are now under clinical trials. Despite their promising activities, the development of these small molecules for the clinical use can be limited by many factors like the off-target effect, the poor stability, and the low bioavailability. The clusters of differentiation CD147, CD209, CD299 have been identified as essential entry co-receptors for SARS-CoV-2 species specificity to humans, although the underlying mechanisms are yet to be fully elucidated. In this paper, protein-protein docking was utilized for identifying the critical epitopes in CD147, CD209 and CD299 which are involved in the binding with SARS-CoV-2 Spike receptor binding domain (RBD). The results of binding free energies showed a high affinity of SARS-CoV-2 RBD to CD299 receptor which was used as a reference to derive hypothetical peptide sequences with specific binding activities to SARS-CoV-2 RBD. Molecular docking and molecular dynamics simulations of the newly designed peptides showed favorable binding features and stability with SARS-CoV-2 RBD and therefore can be further considered as potential candidates in future anti-SARS CoV-2 drug discovery studies.

9.
PLoS One ; 15(11): e0240345, 2020.
Article in English | MEDLINE | ID: covidwho-917985

ABSTRACT

In late December 2019, an emerging viral infection COVID-19 was identified in Wuhan, China, and became a global pandemic. Characterization of the genetic variants of SARS-CoV-2 is crucial in following and evaluating it spread across countries. In this study, we collected and analyzed 3,067 SARS-CoV-2 genomes isolated from 55 countries during the first three months after the onset of this virus. Using comparative genomics analysis, we traced the profiles of the whole-genome mutations and compared the frequency of each mutation in the studied population. The accumulation of mutations during the epidemic period with their geographic locations was also monitored. The results showed 782 variants sites, of which 512 (65.47%) had a non-synonymous effect. Frequencies of mutated alleles revealed the presence of 68 recurrent mutations, including ten hotspot non-synonymous mutations with a prevalence higher than 0.10 in this population and distributed in six SARS-CoV-2 genes. The distribution of these recurrent mutations on the world map revealed that certain genotypes are specific to geographic locations. We also identified co-occurring mutations resulting in the presence of several haplotypes. Moreover, evolution over time has shown a mechanism of mutation co-accumulation which might affect the severity and spread of the SARS-CoV-2. The phylogentic analysis identified two major Clades C1 and C2 harboring mutations L3606F and G614D, respectively and both emerging for the first time in China. On the other hand, analysis of the selective pressure revealed the presence of negatively selected residues that could be taken into considerations as therapeutic targets. We have also created an inclusive unified database (http://covid-19.medbiotech.ma) that lists all of the genetic variants of the SARS-CoV-2 genomes found in this study with phylogeographic analysis around the world.


Subject(s)
Betacoronavirus/genetics , Genetic Variation , Genome, Viral , Betacoronavirus/classification , Betacoronavirus/isolation & purification , COVID-19 , China , Coronavirus Infections/pathology , Coronavirus Infections/virology , Evolution, Molecular , Humans , Pandemics , Phylogeny , Pneumonia, Viral/pathology , Pneumonia, Viral/virology , Polyproteins , Protein Structure, Tertiary , SARS-CoV-2 , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/genetics , Viral Proteins/chemistry , Viral Proteins/genetics
10.
Pathogens ; 9(10)2020 Oct 10.
Article in English | MEDLINE | ID: covidwho-904960

ABSTRACT

The COVID-19 pandemic has been ongoing since its onset in late November 2019 in Wuhan, China. Understanding and monitoring the genetic evolution of the virus, its geographical characteristics, and its stability are particularly important for controlling the spread of the disease and especially for the development of a universal vaccine covering all circulating strains. From this perspective, we analyzed 30,983 complete SARS-CoV-2 genomes from 79 countries located in the six continents and collected from 24 December 2019, to 13 May 2020, according to the GISAID database. Our analysis revealed the presence of 3206 variant sites, with a uniform distribution of mutation types in different geographic areas. Remarkably, a low frequency of recurrent mutations has been observed; only 169 mutations (5.27%) had a prevalence greater than 1% of genomes. Nevertheless, fourteen non-synonymous hotspot mutations (>10%) have been identified at different locations along the viral genome; eight in ORF1ab polyprotein (in nsp2, nsp3, transmembrane domain, RdRp, helicase, exonuclease, and endoribonuclease), three in nucleocapsid protein, and one in each of three proteins: Spike, ORF3a, and ORF8. Moreover, 36 non-synonymous mutations were identified in the receptor-binding domain (RBD) of the spike protein with a low prevalence (<1%) across all genomes, of which only four could potentially enhance the binding of the SARS-CoV-2 spike protein to the human ACE2 receptor. These results along with intra-genomic divergence of SARS-CoV-2 could indicate that unlike the influenza virus or HIV viruses, SARS-CoV-2 has a low mutation rate which makes the development of an effective global vaccine very likely.

11.
Bioinform Biol Insights ; 14: 1177932220965505, 2020.
Article in English | MEDLINE | ID: covidwho-892352

ABSTRACT

The global burden of infections and the rapid spread of viral diseases show the need for new approaches in the prevention and development of effective therapies. To this end, we aimed to explore novel inhibitor compounds that can stop replication or decrease the viral load of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), for which there is currently no approved treatment. Besides using the angiotensin-converting enzyme (ACE2) receptor as a main gate, the CoV-2 can bind to the glucose-regulating protein 78 (GRP78) receptor to get into the cells to start an infection. Here, we report potential inhibitors comprising small molecules and peptides that could interfere with the interaction of SARS-CoV-2 and its target cells by blocking the recognition of the GRP78 cellular receptor by the viral Spike protein. These inhibitors were discovered through an approach of in silico screening of available databases of bioactive peptides and polyphenolic compounds and the analysis of their docking modes. This process led to the selection of 9 compounds with optimal binding affinities to the target sites. The peptides (satpdb18674, satpdb18446, satpdb12488, satpdb14438, and satpdb28899) act on regions III and IV of the viral Spike protein and on its binding sites in GRP78. However, 4 polyphenols such as epigallocatechin gallate (EGCG), homoeriodictyol, isorhamnetin, and curcumin interact, in addition to the Spike protein and its binding sites in GRP78, with the ATPase domain of GRP78. Our work demonstrates that there are at least 2 approaches to block the spread of SARS-CoV-2 by preventing its fusion with the host cells via GRP78.

12.
Pathogens ; 9(10):829, 2020.
Article in English | MDPI | ID: covidwho-842870

ABSTRACT

The COVID-19 pandemic has been ongoing since its onset in late November 2019 in Wuhan, China. Understanding and monitoring the genetic evolution of the virus, its geographical characteristics, and its stability are particularly important for controlling the spread of the disease and especially for the development of a universal vaccine covering all circulating strains. From this perspective, we analyzed 30,983 complete SARS-CoV-2 genomes from 79 countries located in the six continents and collected from 24 December 2019, to 13 May 2020, according to the GISAID database. Our analysis revealed the presence of 3206 variant sites, with a uniform distribution of mutation types in different geographic areas. Remarkably, a low frequency of recurrent mutations has been observed;only 169 mutations (5.27%) had a prevalence greater than 1% of genomes. Nevertheless, fourteen non-synonymous hotspot mutations (>10%) have been identified at different locations along the viral genome;eight in ORF1ab polyprotein (in nsp2, nsp3, transmembrane domain, RdRp, helicase, exonuclease, and endoribonuclease), three in nucleocapsid protein, and one in each of three proteins: Spike, ORF3a, and ORF8. Moreover, 36 non-synonymous mutations were identified in the receptor-binding domain (RBD) of the spike protein with a low prevalence (<1%) across all genomes, of which only four could potentially enhance the binding of the SARS-CoV-2 spike protein to the human ACE2 receptor. These results along with intra-genomic divergence of SARS-CoV-2 could indicate that unlike the influenza virus or HIV viruses, SARS-CoV-2 has a low mutation rate which makes the development of an effective global vaccine very likely.

13.
J Biomol Struct Dyn ; : 1-12, 2020 Oct 07.
Article in English | MEDLINE | ID: covidwho-842248

ABSTRACT

The novel coronavirus, SARS-CoV-2, has infected more than 10 million people and caused more than 502,539 deaths worldwide as of June 2020. The explosive spread of the virus and the rapid increase in the number of cases require the immediate development of effective therapies and vaccines as well as accurate diagnosis tools. The pathogenesis of the disease is triggered by the entry of SARS-CoV-2 via its spike protein into ACE2-bearing host cells, particularly pneumocytes, resulting in overactivation of the immune system, which attacks the infected cells and damages the lung tissue. The interaction of the SARS-CoV-2 receptor binding domain (RBD) with host cells is primarily mediated by the N-terminal helix of ACE2; thus, inhibition of the spike-ACE2 interaction may be a promising therapeutic strategy for blocking the virus entry into host cells. In this paper, we used an in-silico approach to explore small-molecule α-helix mimetics as inhibitors that may disrupt the attachment of SARS-CoV-2 to ACE2. First, the RBD-ACE2 interface in the 6M0J structure was studied by the MM-GBSA decomposition module of the HawkDock server, which led to the identification of two critical target regions in the RBD. Next, two virtual screening experiments of 7236 α-helix mimetics from ASINEX were conducted on the above regions using the iDock tool, which resulted in 10 candidates with favorable binding affinities. Finally, the stability of RBD complexes with the top-two ranked compounds was further validated by 100 ns of molecular dynamics simulations.Communicated by Ramaswamy H. Sarma.

14.
Microbiol Resour Announc ; 9(32)2020 Aug 06.
Article in English | MEDLINE | ID: covidwho-696037

ABSTRACT

Here, we report the draft genome sequences of six severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains. SARS-CoV-2 is responsible for the COVID-19 pandemic, which started at the end of 2019 in Wuhan, China. The isolates were obtained from nasopharyngeal swabs from Moroccan patients with COVID-19. Mutation analysis revealed the presence of the spike D614G mutation in all six genomes, which is widely present in several genomes around the world.

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