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1.
J Med Virol ; 93(9): 5630-5634, 2021 09.
Article in English | MEDLINE | ID: covidwho-1363678

ABSTRACT

Since the start of the coronavirus disease 2019 (COVID-19) pandemic, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly widespread worldwide becoming one of the major global public health issues of the last centuries. Currently, COVID-19 vaccine rollouts are finally upon us carrying the hope of herd immunity once a sufficient proportion of the population has been vaccinated or infected, as a new horizon. However, the emergence of SARS-CoV-2 variants brought concerns since, as the virus is exposed to environmental selection pressures, it can mutate and evolve, generating variants that may possess enhanced virulence. Codon usage analysis is a strategy to elucidate the evolutionary pressure of the viral genome suffered by different hosts, as possible cause of the emergence of new variants. Therefore, to get a better picture of the SARS-CoV-2 codon bias, we first identified the relative codon usage rate of all Betacoronaviruses lineages. Subsequently, we correlated putative cognate transfer ribonucleic acid (tRNAs) to reveal how those viruses adapt to hosts in relation to their preferred codon usage. Our analysis revealed seven preferred codons located in three different open reading frame which appear preferentially used by SARS-CoV-2. In addition, the tRNA adaptation analysis indicates a wide strategy of competition between the virus and mammalian as principal hosts highlighting the importance to reinforce the genomic monitoring to prompt identify any potential adaptation of the virus into new potential hosts which appear to be crucial to prevent and mitigate the pandemic.


Subject(s)
Betacoronavirus/genetics , Codon Usage , Coronavirus Infections/virology , Genome, Viral , Mammals , SARS-CoV-2/genetics , Animals , COVID-19 , COVID-19 Vaccines , Codon , Host-Pathogen Interactions , Humans , Mutation , Open Reading Frames , Phylogeny , RNA, Transfer
2.
Cell Discov ; 7(1): 44, 2021 Jun 15.
Article in English | MEDLINE | ID: covidwho-1269383

ABSTRACT

The presence of SARS-CoV-2 mutants, including the emerging variant B.1.1.7, has raised great concerns in terms of pathogenesis, transmission, and immune escape. Characterizing SARS-CoV-2 mutations, evolution, and effects on infectivity and pathogenicity is crucial to the design of antibody therapies and surveillance strategies. Here, we analyzed 454,443 SARS-CoV-2 spike genes/proteins and 14,427 whole-genome sequences. We demonstrated that the early variant B.1.1.7 may not have evolved spontaneously in the United Kingdom or within human populations. Our extensive analyses suggested that Canidae, Mustelidae or Felidae, especially the Canidae family (for example, dog) could be a possible host of the direct progenitor of variant B.1.1.7. An alternative hypothesis is that the variant was simply yet to be sampled. Notably, the SARS-CoV-2 whole-genome represents a large number of potential co-mutations. In addition, we used an experimental SARS-CoV-2 reporter replicon system to introduce the dominant co-mutations NSP12_c14408t, 5'UTR_c241t, and NSP3_c3037t into the viral genome, and to monitor the effect of the mutations on viral replication. Our experimental results demonstrated that the co-mutations significantly attenuated the viral replication. The study provides valuable clues for discovering the transmission chains of variant B.1.1.7 and understanding the evolutionary process of SARS-CoV-2.

3.
Nat Immunol ; 22(7): 820-828, 2021 07.
Article in English | MEDLINE | ID: covidwho-1225511

ABSTRACT

Efficient immune responses against viral infection are determined by sufficient activation of nucleic acid sensor-mediated innate immunity1,2. Coronavirus disease 2019, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), remains an ongoing global pandemic. It is an urgent challenge to clarify the innate recognition mechanism to control this virus. Here we show that retinoic acid-inducible gene-I (RIG-I) sufficiently restrains SARS-CoV-2 replication in human lung cells in a type I/III interferon (IFN)-independent manner. RIG-I recognizes the 3' untranslated region of the SARS-CoV-2 RNA genome via the helicase domains, but not the C-terminal domain. This new mode of RIG-I recognition does not stimulate its ATPase, thereby aborting the activation of the conventional mitochondrial antiviral-signaling protein-dependent pathways, which is in accordance with lack of cytokine induction. Nevertheless, the interaction of RIG-I with the viral genome directly abrogates viral RNA-dependent RNA polymerase mediation of the first step of replication. Consistently, genetic ablation of RIG-I allows lung cells to produce viral particles that expressed the viral spike protein. By contrast, the anti-SARS-CoV-2 activity was restored by all-trans retinoic acid treatment through upregulation of RIG-I protein expression in primary lung cells derived from patients with chronic obstructive pulmonary disease. Thus, our findings demonstrate the distinctive role of RIG-I as a restraining factor in the early phase of SARS-CoV-2 infection in human lung cells.


Subject(s)
COVID-19/immunology , DEAD Box Protein 58/immunology , Lung/immunology , Receptors, Immunologic/immunology , SARS-CoV-2/immunology , A549 Cells , Animals , Cell Line , Cell Line, Tumor , Chlorocebus aethiops , Dogs , HEK293 Cells , Humans , Interferon Type I/immunology , Interferons/immunology , Lung/virology , Madin Darby Canine Kidney Cells , Pulmonary Disease, Chronic Obstructive/immunology , RNA-Dependent RNA Polymerase/immunology , Sf9 Cells , Signal Transduction/immunology , Vero Cells , Viral Proteins/immunology
4.
Biochem Biophys Res Commun ; 557: 273-279, 2021 06 11.
Article in English | MEDLINE | ID: covidwho-1174101

ABSTRACT

Recently, the novel coronavirus (SARS-CoV-2), which has spread from China to the world, was declared a global public health emergency, which causes lethal respiratory infections. Acetylation of several proteins plays essential roles in various biological processes, such as viral infections. We reported that the nucleoproteins of influenza virus and Zaire Ebolavirus were acetylated, suggesting that these modifications contributed to the molecular events involved in viral replication. Similar to influenza virus and Ebolavirus, the coronavirus also contains single-stranded RNA, as its viral genome interacts with the nucleocapsid (N) proteins. In this study, we report that SARS-CoV and SARS-CoV-2 N proteins are strongly acetylated by human histone acetyltransferases, P300/CBP-associated factor (PCAF), and general control nonderepressible 5 (GCN5), but not by CREB-binding protein (CBP) in vitro. Liquid chromatography-mass spectrometry analyses identified 2 and 12 acetyl-lysine residues from SARS-CoV and SARS-CoV-2 N proteins, respectively. Particularly in the SARS-CoV-2 N proteins, the acetyl-lysine residues were localized in or close to several functional sites, such as the RNA interaction domains and the M-protein interacting site. These results suggest that acetylation of SARS-CoV-2 N proteins plays crucial roles in their functions.


Subject(s)
COVID-19/metabolism , Coronavirus Nucleocapsid Proteins/metabolism , Histone Acetyltransferases/metabolism , SARS Virus/metabolism , SARS-CoV-2/metabolism , Severe Acute Respiratory Syndrome/metabolism , p300-CBP Transcription Factors/metabolism , Acetylation , CREB-Binding Protein/metabolism , Coronavirus Nucleocapsid Proteins/chemistry , Humans , Models, Molecular , Phosphoproteins/chemistry , Phosphoproteins/metabolism , SARS Virus/chemistry , SARS-CoV-2/chemistry
5.
J Pharm Anal ; 11(3): 265-271, 2021 Jun.
Article in English | MEDLINE | ID: covidwho-1157542

ABSTRACT

Since the World Health Organization (WHO) declared COVID-19, the disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as a pandemic in March 2020, and more than 117 million people worldwide have been confirmed to have been infected. Scientists, medical professionals, and other stakeholders are racing against time to find and develop effective medicines for COVID-19. However, no drug with high efficacy to treat SARS-CoV-2 infection has been approved. With the increasing popularity of gene therapy, scientists have explored the utilization of small RNAs such as microRNAs (miRNAs) as therapeutics. miRNAs are non-coding RNAs with high affinity for the 3'-UTRs of targeted messenger RNAs (mRNAs). Interactions between host cells and viral genomes may induce the upregulation or downregulation of various miRNAs. Therefore, understanding the expression patterns of these miRNAs and their functions will provide insights into potential miRNA-based therapies. This review systematically summarizes the potential targets of miRNA-based therapies for SARS-CoV-2 infection and examines the viability of possible transfection methods.

6.
Gene Rep ; 23: 101055, 2021 Jun.
Article in English | MEDLINE | ID: covidwho-1086939

ABSTRACT

The novel corona virus disease or COVID-19 caused by a positive strand RNA virus (PRV) called SARS-CoV-2 is plaguing the entire planet as we conduct this study. In this study a multifaceted analysis was carried out employing dinucleotide signature, codon usage and codon context to compare and unravel the genomic as well as genic characteristics of the SARS-CoV-2 isolates and how they compare to other PRVs which represents some of the most pathogenic human viruses. The main emphasis of this study was to comprehend the codon biology of the SARS-CoV-2 in the backdrop of the other PRVs like Poliovirus, Japanese encephalitis virus, Hepatitis C virus, Norovirus, Rubella virus, Semliki Forest virus, Zika virus, Dengue virus, Human rhinoviruses and the Betacoronaviruses since codon usage pattern along with the nucleotide composition prevalent within the viral genome helps to understand the biology and evolution of viruses. Our results suggest discrete genomic dinucleotide signature within the PRVs. Some of the genes from the different SARS-CoV-2 isolates were also found to demonstrate heterogeneity in terms of their dinucleotide signature. The SARS-CoV-2 isolates also demonstrated a codon context trend characteristically dissimilar to the other PRVs. The findings of this study are expected to contribute to the developing global knowledge base in countering COVID-19.

7.
Environ Res ; 195: 110863, 2021 04.
Article in English | MEDLINE | ID: covidwho-1086923

ABSTRACT

BACKGROUND: Previous studies described the presence of SARS-CoV-2 in outdoor air particulate matter (PM) in urban areas of northern Italy and USA. The city of Madrid was heavily affected by COVID-19 during March-June 2020. Also, this city usually displays high concentrations of PM under several atmospheric situations. This is mandatory to assess the presence of viral RNA in PM, as an indicator of epidemic recurrence. Our study was aimed at investigating the presence of SARS-CoV-2 RNA in outdoor air samples (on PM10, PM2.5 and PM1). METHODS: Six samples of PM10, PM2.5 and PM1 were collected between the May 4th and 22nd 2020 in Madrid, on quartz fiber filters by using MCV high volume samplers (30 m3 h-1 flow) with three inlets (Digitel DHA-80) for sampling PM10, PM2.5 and PM1. RNA extraction and amplification was performed according to the protocol recently set by Setti et al.2020c in Italy. Up to three highly specific molecular marker genes (N1, N2, and RP) were used to test the presence of SARS-CoV-2 RNA. RESULTS: After RNA extraction and expression measurements of N1, N2 and RP genes from all the collected filters, no presence of SARS-CoV-2 RNA was observed. Control tests to exclude false positive results were successfully accomplished. CONCLUSIONS: No presence of SARS-CoV-2 in quartz fiber filters samplers for PM10, PM2.5 and PM1 fractions was observed in our study carried out in Madrid during the month of May 2020. Nevertheless, the absence of viral genomes could be due to different factors including: limited social interactions and economic activities resulting in reduced circulation of the coronavirus, lower daily PM concentration in outdoor air, as well as to meteorological stability and higher temperature that characterize spring season. Further research should be carried out during winter, in presence of higher viral circulation and daily PM exceedances.


Subject(s)
Air Pollutants , Air Pollution , COVID-19 , Air Pollutants/analysis , Air Pollution/analysis , Cities , Communicable Disease Control , Environmental Monitoring , Humans , Italy , Particulate Matter/analysis , RNA, Viral , SARS-CoV-2
8.
Emerg Microbes Infect ; 10(1): 51-65, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1066197

ABSTRACT

COVID-19 is a respiratory illness caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and declared by the World Health Organization a global public health emergency. Among the severe outbreaks across South America, Uruguay has become known for curtailing SARS-CoV-2 exceptionally well. To understand the SARS-CoV-2 introductions, local transmissions, and associations with genomic and clinical parameters in Uruguay, we sequenced the viral genomes of 44 outpatients and inpatients in a private healthcare system in its capital, Montevideo, from March to May 2020. We performed a phylogeographic analysis using sequences from our cohort and other studies that indicate a minimum of 23 independent introductions into Uruguay, resulting in five major transmission clusters. Our data suggest that most introductions resulting in chains of transmission originate from other South American countries, with the earliest seeding of the virus in late February 2020, weeks before the borders were closed to all non-citizens and a partial lockdown implemented. Genetic analyses suggest a dominance of S and G clades (G, GH, GR) that make up >90% of the viral strains in our study. In our cohort, lethal outcome of SARS-CoV-2 infection significantly correlated with arterial hypertension, kidney failure, and ICU admission (FDR < 0.01), but not with any mutation in a structural or non-structural protein, such as the spike D614G mutation. Our study contributes genetic, phylodynamic, and clinical correlation data about the exceptionally well-curbed SARS-CoV-2 outbreak in Uruguay, which furthers the understanding of disease patterns and regional aspects of the pandemic in Latin America.


Subject(s)
COVID-19/complications , Mutation , SARS-CoV-2/genetics , Adolescent , Adult , Aged , Aged, 80 and over , COVID-19/epidemiology , COVID-19/virology , Disease Outbreaks , Female , Humans , Male , Middle Aged , Phylogeny , Polymorphism, Single Nucleotide , SARS-CoV-2/classification , SARS-CoV-2/isolation & purification , Uruguay/epidemiology , Young Adult
9.
Eur J Ophthalmol ; 31(1): 138-143, 2021 Jan.
Article in English | MEDLINE | ID: covidwho-1052384

ABSTRACT

PURPOSE: To evaluate the role of viral infections in the pathogenesis of primary acquired nasolacrimal duct obstruction. METHODS: The study included 48 patients diagnosed with primary acquired nasolacrimal duct obstruction undergoing dacryocystorhinostomy surgery. Prior to dacryocystorhinostomy surgery, nasal swab sample was taken from the inferior meatus at the same side. During dacryocystorhinostomy, tissue biopsy sample (2 × 2 mm) was taken from the junction area of the lacrimal sac and nasolacrimal duct. Following nucleic acid extraction, polymerase chain reaction was performed. RESULTS: The patients consisted of 9 (18.8%) men and 39 (81.2%) women with a mean age of 51.0 ± 14.3 years. Qualitative polymerase chain reaction showed viral genome in the nasal swabs of 10 (20.8%) patients, including coronavirus 229E (three cases), coronavirus HKU1 (two cases), respiratory syncytial virus (two cases), coronavirus OC43 (one case), coronavirus NL63 (one case), and adenovirus (one case). In the dacryocystorhinostomy samples, viral genomes were detected in four (8.3%) cases, including respiratory syncytial virus (two cases), coronavirus HKU1 (one case), and adenovirus (one case). There was a statistically significant agreement between nasal mucosal swab and dacryocystorhinostomy biopsy samples in terms of respiratory syncytial virus positivity (kappa = 1.000, p = 0.001). CONCLUSION: Although the viral genome was detected in the samples, a direct relationship between viruses and pathogenesis of primary acquired nasolacrimal duct obstruction could not be revealed because of the low number of positive results. However, considering the profibrotic characteristics of specific viruses such as respiratory syncytial virus and adenovirus, viral infections may be one of the many predisposing factors of primary acquired nasolacrimal duct obstruction.


Subject(s)
Adenoviruses, Human/genetics , Coronavirus/genetics , Genome, Viral/genetics , Lacrimal Duct Obstruction/virology , Nasal Mucosa/virology , Nasolacrimal Duct/virology , Respiratory Syncytial Viruses/genetics , Adenoviruses, Human/isolation & purification , Adult , Aged , Aged, 80 and over , Biopsy , Coronavirus/isolation & purification , Dacryocystorhinostomy , Female , Humans , Lacrimal Duct Obstruction/therapy , Male , Middle Aged , Nasolacrimal Duct/surgery , Prospective Studies , Real-Time Polymerase Chain Reaction , Respiratory Syncytial Viruses/isolation & purification , Young Adult
10.
Med Sci Monit ; 27: e930886, 2021 Jan 25.
Article in English | MEDLINE | ID: covidwho-1045272

ABSTRACT

Alterations in brain functioning, especially in regions associated with cognition, can result from infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and are predicted to result in various psychiatric diseases. Recent studies have shown that SARS-CoV-2 infection and coronavirus disease 2019 (COVID-19) can directly or indirectly affect the central nervous system (CNS). Therefore, diseases associated with sequelae of COVID-19, or 'long COVID', also include serious long-term mental and cognitive changes, including the condition recently termed 'brain fog'. Hypoxia in the microenvironment of select brain areas may benefit the reproductive capacity of the virus. It is possible that in areas of cerebral hypoxia, neuronal cell energy metabolism may become compromised after integration of the viral genome, resulting in mitochondrial dysfunction. Because of their need for constant high metabolism, cerebral tissues require an immediate and constant supply of oxygen. In hypoxic conditions, neurons with the highest oxygen demand become dysfunctional. The resulting cognitive impairment benefits viral spread, as infected individuals exhibit behaviors that reduce protection against infection. The effects of compromised mitochondrial function may also be an evolutionary advantage for SARS-CoV-2 in terms of host interaction. A high viral load in patients with COVID-19 that involves the CNS results in the compromise of neurons with high-level energy metabolism. Therefore, we propose that selective neuronal mitochondrial targeting in SARS-CoV-2 infection affects cognitive processes to induce 'brain fog' and results in behavioral changes that favor viral propagation. Cognitive changes associated with COVID-19 will have increasing significance for patient diagnosis, prognosis, and long-term care.


Subject(s)
COVID-19/metabolism , Cognitive Dysfunction/metabolism , Health Behavior , Hypoxia, Brain/metabolism , Mitochondria/metabolism , Neurons/metabolism , SARS-CoV-2/physiology , COVID-19/complications , COVID-19/physiopathology , COVID-19/psychology , COVID-19/transmission , Cognitive Dysfunction/physiopathology , Cognitive Dysfunction/psychology , Energy Metabolism , Humans , Hypoxia, Brain/physiopathology , Hypoxia, Brain/psychology , Microbial Viability , Viral Load , Virus Replication
11.
J Clin Med ; 9(12)2020 Dec 07.
Article in English | MEDLINE | ID: covidwho-967778

ABSTRACT

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has rapidly evolved into a global pandemic. The hyperglycemia in patients with diabetes mellitus (DM) substantially compromises their innate immune system. SARS-CoV-2 uses human angiotensin-converting enzyme 2 (ACE2) receptors to enter the affected cell. Uncontrolled hyperglycemia-induced glycosylation of ACE2 and the S protein of SARS-CoV-2 could facilitate the binding of S protein to ACE2, enabling viral entry. Downregulation of ACE2 activity secondary to SARS-CoV-2 infection, with consequent accumulation of angiotensin II and metabolites, eventually leads to poor outcomes. The altered binding of ACE2 with SARS-CoV-2 and the compromised innate immunity of patients with DM increase their susceptibility to COVID-19; COVID-19 induces pancreatic ß-cell injury and poor glycemic control, which further compromises the immune response and aggravates hyperglycemia and COVID-19 progression, forming a vicious cycle. Sequential cleavage of viral S protein by furin and transmembrane serine protease 2 (TMPRSS2) triggers viral entry to release the viral genome into the target cell. Hence, TMPRSS2 and furin are possible drug targets. As type 1 DM exhibits a Th1-driven autoimmune process, the relatively lower mortality of COVID-19 in type 1 DM compared to type 2 DM might be attributed to an imbalance between Th1 and Th2 immunity. The anti-inflammatory effects of dipeptidyl peptidase-4 inhibitor may benefit patients with DM and COVID-19. The potential protective effects of sodium-glucose cotransporter-2 inhibitor (SGLT2i), including reduction in lactate level, prevention of lowering of cytosolic pH and reduction in pro-inflammatory cytokine levels may justify the provision of SGLT2i to patients with DM and mild or asymptomatic COVID-19. For patients with DM and COVID-19 who require hospitalization, insulin-based treatment is recommended with cessation of metformin and SGLT2i. Further evidence from randomized or case-control clinical trials is necessary to elucidate the effectiveness and pitfalls of different types of medication for DM.

12.
Viruses ; 12(12)2020 12 01.
Article in English | MEDLINE | ID: covidwho-954243

ABSTRACT

The emergence of SARS-CoV-2 in 2019 has caused a major health and economic crisis around the globe. Gaining knowledge about its attributes and interactions with human host cells is crucial. Non-coding RNAs (ncRNAs) are involved in the host cells' innate antiviral immune response. In RNA interference, microRNAs (miRNAs) may bind to complementary sequences of the viral RNA strand, forming an miRNA-induced silencing complex, which destroys the viral RNA, thereby inhibiting viral protein expression. There are several targets for human miRNAs on SARS-CoV-2's RNA, most of which are in the 5' and 3' untranslated regions. Mutations of the viral genome causing the creation or loss of miRNA binding sites may have crucial effects on SARS-CoV-2 pathogenicity. In addition to mediating immunity, the ncRNA landscape of host cells further influences their susceptibility to virus infection, as certain miRNAs are essential in the regulation of cellular receptors that are necessary for virus invasion. Conversely, virus infection also changes the host ncRNA expression patterns, possibly augmenting conditions for viral replication and dissemination. Hence, ncRNAs typically upregulated in SARS-CoV-2 infection could be useful biomarkers for disease progression and severity. Understanding these mechanisms could provide further insight into the pathogenesis and possible treatment options against COVID-19.


Subject(s)
Coronavirus Infections/immunology , Coronavirus Infections/virology , Coronavirus/pathogenicity , RNA, Untranslated/metabolism , Animals , Antiviral Agents/metabolism , Antiviral Agents/therapeutic use , Coronavirus/genetics , Coronavirus Infections/drug therapy , Coronavirus Infections/genetics , Humans , Immune Evasion/genetics , Mutation , RNA Interference , RNA, Untranslated/genetics , RNA, Untranslated/therapeutic use , RNA, Viral/genetics
13.
Microorganisms ; 8(8)2020 Aug 18.
Article in English | MEDLINE | ID: covidwho-854167

ABSTRACT

Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The viral outbreak started in late 2019 and rapidly became a serious health threat to the global population. COVID-19 was declared a pandemic by the World Health Organization in March 2020. Several therapeutic options have been adopted to prevent the spread of the virus. Although vaccines have been developed, antivirals are still needed to combat the infection of this virus. SARS-CoV-2 is an enveloped virus, and its genome encodes polyproteins that can be processed into structural and nonstructural proteins. Maturation of viral proteins requires cleavages by proteases. Therefore, the main protease (3 chymotrypsin-like protease (3CLpro) or Mpro) encoded by the viral genome is an attractive drug target because it plays an important role in cleaving viral polyproteins into functional proteins. Inhibiting this enzyme is an efficient strategy to block viral replication. Structural studies provide valuable insight into the function of this protease and structural basis for rational inhibitor design. In this review, we describe structural studies on the main protease of SARS-CoV-2. The strategies applied in developing inhibitors of the main protease of SARS-CoV-2 and currently available protein inhibitors are summarized. Due to the availability of high-resolution structures, structure-guided drug design will play an important role in developing antivirals. The availability of high-resolution structures, potent peptidic inhibitors, and diverse compound scaffolds indicate the feasibility of developing potent protease inhibitors as antivirals for COVID-19.

14.
PLoS One ; 15(8): e0237559, 2020.
Article in English | MEDLINE | ID: covidwho-840723

ABSTRACT

BACKGROUND: The world is going through the critical phase of COVID-19 pandemic, caused by human coronavirus, SARS-CoV-2. Worldwide concerted effort to identify viral genomic changes across different sub-types has identified several strong changes in the coding region. However, there have not been many studies focusing on the variations in the 5' and 3' untranslated regions and their consequences. Considering the possible importance of these regions in host mediated regulation of viral RNA genome, we wanted to explore the phenomenon. METHODS: To have an idea of the global changes in 5' and 3'-UTR sequences, we downloaded 8595 complete and high-coverage SARS-CoV-2 genome sequence information from human host in FASTA format from Global Initiative on Sharing All Influenza Data (GISAID) from 15 different geographical regions. Next, we aligned them using Clustal Omega software and investigated the UTR variants. We also looked at the putative host RNA binding protein (RBP) and microRNA binding sites in these regions by 'RBPmap' and 'RNA22 v2' respectively. Expression status of selected RBPs and microRNAs were checked in lungs tissue. RESULTS: We identified 28 unique variants in SARS-CoV-2 UTR region based on a minimum variant percentage cut-off of 0.5. Along with 241C>T change the important 5'-UTR change identified was 187A>G, while 29734G>C, 29742G>A/T and 29774C>T were the most familiar variants of 3'UTR among most of the continents. Furthermore, we found that despite the variations in the UTR regions, binding of host RBP to them remains mostly unaltered, which further influenced the functioning of specific miRNAs. CONCLUSION: Our results, shows for the first time in SARS-Cov-2 infection, a possible cross-talk between host RBPs-miRNAs and viral UTR variants, which ultimately could explain the mechanism of escaping host RNA decay machinery by the virus. The knowledge might be helpful in developing anti-viral compounds in future.


Subject(s)
3' Untranslated Regions/genetics , 5' Untranslated Regions/genetics , Betacoronavirus/genetics , Coronavirus Infections/metabolism , Genome, Viral/genetics , Genomic Instability/genetics , Host-Pathogen Interactions/genetics , MicroRNAs/metabolism , Pneumonia, Viral/metabolism , RNA, Viral/metabolism , RNA-Binding Proteins/metabolism , Base Sequence , Binding Sites , COVID-19 , Coronavirus Infections/virology , Humans , Open Reading Frames/genetics , Pandemics , Pneumonia, Viral/virology , Protein Binding/genetics , SARS-CoV-2
15.
Emerg Microbes Infect ; 9(1): 1474-1488, 2020 Dec.
Article in English | MEDLINE | ID: covidwho-599992

ABSTRACT

The mutations in the SARS-CoV-2 virus genome during COVID-19 dissemination are unclear. In 788 COVID-19 patients from Zhejiang province, we observed decreased rate of severe/critical cases compared with patients in Wuhan. For mechanisms exploration, we isolated one strain of SARS-CoV-2 (ZJ01) from a mild COVID-19 patient. Thirty-five specific gene mutations were identified. Phylogenetic and relative synonymous codon usage analysis suggested that ZJ01 may be a potential evolutionary branch of SARS-CoV-2. We classified 54 global virus strains based on the base (C or T) at positions 8824 and 28247 while ZJ01 has T at both sites. The prediction of the Furin cleavage site (FCS) and sequence alignment indicated that the FCS may be an important site of coronavirus evolution. ZJ01 mutations identified near the FCS (F1-2) caused changes in the structure and electrostatic distribution of the S surface protein, further affecting the binding capacity of Furin. Single-cell sequencing and ACE2-Furin co-expression results confirmed that the Furin expression was especially higher in glands, liver, kidneys, and colon. The evolutionary pattern of SARS-CoV-2 towards FCS formation may result in its clinical symptom becoming closer to HKU-1 and OC43 caused mild flu-like symptoms, further showing its potential in differentiating into mild COVID-19 subtypes.


Subject(s)
Betacoronavirus/isolation & purification , Coronavirus Infections/virology , Furin/metabolism , Pneumonia, Viral/virology , Adult , Betacoronavirus/genetics , COVID-19 , China/epidemiology , Codon , Coronavirus Infections/complications , Coronavirus Infections/epidemiology , Disease Progression , Evolution, Molecular , Female , Humans , Male , Middle Aged , Mutation , Pandemics , Phylogeny , Pneumonia, Viral/complications , Pneumonia, Viral/epidemiology , Retrospective Studies , SARS-CoV-2 , Sequence Analysis, RNA
16.
ESC Heart Fail ; 7(5): 2440-2447, 2020 10.
Article in English | MEDLINE | ID: covidwho-596164

ABSTRACT

AIMS: Since December 2019, the novel coronavirus SARS-CoV-2 has spread rapidly throughout China and keeps the world in suspense. Cardiovascular complications with myocarditis and embolism due to COVID-19 have been reported. SARS-CoV-2 genome detection in the heart muscle has not been demonstrated so far, and the underlying pathophysiological mechanisms remain to be investigated. METHODS AND RESULTS: Endomyocardial biopsies (EMBs) of 104 patients (mean age: 57.90 ± 16.37 years; left ventricular ejection fraction: 33.7 ± 14.6%, sex: n = 79 male/25 female) with suspected myocarditis or unexplained heart failure were analysed. EMB analysis included histology, immunohistochemistry, and detection of SARS-CoV-2 genomes by real-time reverse transcription polymerase chain reaction in the IKDT Berlin, Germany. Among 104 EMBs investigated, five were confirmed with SARS-CoV-2 infected by reverse real-time transcriptase polymerase chain reaction. We describe patients of different history of symptoms and time duration. Additionally, we investigated histopathological changes in myocardial tissue showing that the inflammatory process in EMBs seemed to permeate vascular wall leading to small arterial obliteration and damage. CONCLUSIONS: This is the first report that established the evidence of SARS-CoV-2 genomes detection in EMBs. In these patients, myocardial injury ischaemia may play a role, which could explain the ubiquitous troponin increases. EMB-based identification of the cause of myocardial injury may contribute to explain the different evolution of complicated SARS-CoV-2-infection and to design future specific and personalized treatment strategies.


Subject(s)
Coronavirus Infections/epidemiology , Gene Expression Regulation , Heart Failure/virology , Myocarditis/pathology , Pneumonia, Viral/epidemiology , SARS Virus/genetics , Adult , Age Factors , Aged , Biopsy, Needle , COVID-19 , Cohort Studies , Communicable Diseases, Emerging/epidemiology , Disease Outbreaks/statistics & numerical data , Endocardium/pathology , Female , Genomics , Germany/epidemiology , Heart Failure/genetics , Humans , Immunohistochemistry , Incidence , Male , Middle Aged , Myocarditis/genetics , Myocarditis/virology , Pandemics/statistics & numerical data , Real-Time Polymerase Chain Reaction/methods , Retrospective Studies , Sex Factors , Survival Analysis
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