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1.
Food Environ Virol ; 14(2): 190-198, 2022 Jun.
Article in English | MEDLINE | ID: covidwho-1877973

ABSTRACT

Side by side air sampling was conducted using a PTFE filter membrane as dry sampler and an impinger containing a suitable culture medium as a wet sampler. Most of the samples were collected from two hospitals and few air samples were collected from private houses of non-hospitalized confirmed COVID-19 patients. The collected air samples were analyzed using RT-PCR. The results indicated that all air samples collected from the hospitals were PCR negative for SARS-CoV-2. While two of four air samples collected from the house of non-hospitalized patients were PCR positive. In this study, most of the hospitalized patients had oxygen mask and face mask, and hence this may be a reason for our negative results regarding the presence of SARS-CoV-2 in indoor air of the hospitals, while non-hospitalized patients did not wear oxygen and protective face masks in their houses. Moreover, a very high concentration of particles in the size range of droplet nuclei (< 5 µm) was identified compared to particles in the size range of respiratory droplets (> 5-10 µm) in the areas where patients were hospitalized. It can be concluded that using face mask by patients can prevent the release of viruses into the indoor air, even in hospitals with a high density of patients.


Subject(s)
Air Pollution, Indoor , COVID-19 , Hospitals , Humans , Oxygen , SARS-CoV-2
2.
Cells ; 11(6)2022 03 15.
Article in English | MEDLINE | ID: covidwho-1742343

ABSTRACT

Viruses are one of the most important concerns for human health, and overcoming viral infections is a worldwide challenge. However, researchers have been trying to manipulate viral genomes to overcome various disorders, including cancer, for vaccine development purposes. CRISPR (clustered regularly interspaced short palindromic repeats) is becoming one of the most functional and widely used tools for RNA and DNA manipulation in multiple organisms. This approach has provided an unprecedented opportunity for creating simple, inexpensive, specific, targeted, accurate, and practical manipulations of viruses, such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), human immunodeficiency virus-1 (HIV-1), and vaccinia virus. Furthermore, this method can be used to make an effective and precise diagnosis of viral infections. Nevertheless, a valid and scientifically designed CRISPR system is critical to make more effective and accurate changes in viruses. In this review, we have focused on the best and the most effective ways to design sgRNA, gene knock-in(s), and gene knock-out(s) for virus-targeted manipulation. Furthermore, we have emphasized the application of CRISPR technology in virus diagnosis and in finding significant genes involved in virus-host interactions.


Subject(s)
COVID-19 , Virus Diseases , Viruses , COVID-19/diagnosis , CRISPR-Cas Systems/genetics , Clustered Regularly Interspaced Short Palindromic Repeats/genetics , DNA Viruses , Host Microbial Interactions , Humans , SARS-CoV-2/genetics , Virus Diseases/diagnosis , Virus Diseases/genetics , Viruses/genetics
3.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-317470

ABSTRACT

Background: The widespread outbreak of SARS-CoV-2 has become a deal threat for human health. This new emerged virus coupled with severe acute respiratory syndrome (SARS) and middle east respiratory syndrome (MERS) viruses belong to coronoviridae family, which develop SARS in human being. However, prior to the emergence of virulent viruses, the coronaviruses were known as the leading causes of mild common cold. Getting more knowledge about the genome organization of different strains can conduct us how these viruses evolve and become a virulent strain. Here, we reported the difference of oligonucleotide distribution contributing in genome of two groups of coronaviruses, SARS related viruses versa common cold coronaviruses, by employing weighting algorithms approaches. Results: In this study, we found a few oligonucleotides, which significantly distinguish two viral groups. Among dinucleotide’s features, the discrepancy of TC and CC between SARS related viruses and common cold coronaviruses was quite considerable. Furthermore, CC dinucleotide was sequentially repeated in a few multinucleotide patterns including CCA, CCAC, ACCAC, and CACCAC motifs with the highest values, which also discriminated two viral groups. Conclusions: Theses remarkable oligonucleotides might point towards the existence of some particular RNA elements that might be involved in viral infectivity.

4.
Infect Genet Evol ; 97: 105188, 2022 01.
Article in English | MEDLINE | ID: covidwho-1568934

ABSTRACT

The best and most effective way to combat pandemics is to use effective vaccines and live attenuated vaccines are among the most effective vaccines. However, one of the major problems is the length of time it takes to get the attenuated vaccines. Today, the CRISPR toolkit (Clustered Regularly Inerspaced Short Palindromic Repeats) has made it possible to make changes with high efficiency and speed. Using this toolkit to make point mutations on the RNA virus's genome in a coculture of permissive and nonpermissive cells and under controlled conditions can accelerate changes in the genome and accelerate natural selection to obtain live attenuated vaccines.


Subject(s)
COVID-19 Vaccines/genetics , COVID-19/prevention & control , CRISPR-Cas Systems , Gene Editing/methods , Mutation Rate , SARS-CoV-2/genetics , Viral Proteins/genetics , APOBEC Deaminases/genetics , APOBEC Deaminases/immunology , Adenosine Deaminase/genetics , Adenosine Deaminase/immunology , Bacterial Proteins/genetics , Bacterial Proteins/immunology , COVID-19/immunology , COVID-19 Vaccines/biosynthesis , Endonucleases/genetics , Endonucleases/immunology , Gene Expression , Genome, Viral , Humans , RNA-Binding Proteins/genetics , RNA-Binding Proteins/immunology , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/immunology , SARS-CoV-2/immunology , Selection, Genetic , Vaccines, Attenuated , Viral Proteins/immunology
5.
Rev Med Virol ; : e2305, 2021 Oct 26.
Article in English | MEDLINE | ID: covidwho-1482169

ABSTRACT

The development of effective and safe COVID-19 vaccines is a major move forward in our global effort to control the SARS-CoV-2 pandemic. The aims of this study were (1) to develop an inactivated whole-virus SARS-CoV-2 candidate vaccine named BIV1-CovIran and (2) to determine the safety and potency of BIV1-CovIran inactivated vaccine candidate against SARS-CoV-2. Infectious virus was isolated from nasopharyngeal swab specimen and propagated in Vero cells with clear cytopathic effects in a biosafety level-3 facility using the World Health Organization's laboratory biosafety guidance related to COVID-19. After characterisation of viral seed stocks, the virus working seed was scaled-up in Vero cells. After chemical inactivation and purification, it was formulated with alum adjuvant. Finally, different animal species were used to determine the toxicity and immunogenicity of the vaccine candidate. The study showed the safety profile in studied animals including guinea pig, rabbit, mice and monkeys. Immunisation at two different doses (3 or 5 µg per dose) elicited a high level of SARS-CoV-2 specific and neutralising antibodies in mice, rabbits and nonhuman primates. Rhesus macaques were immunised with the two-dose schedule of 5 or 3 µg of the BIV1-CovIran vaccine and showed highly efficient protection against 104 TCID50 of SARS-CoV-2 intratracheal challenge compared with the control group. These results highlight the BIV1-CovIran vaccine as a potential candidate to induce a strong and potent immune response that may be a promising and feasible vaccine to protect against SARS-CoV-2 infection.

6.
Future Microbiol ; 15: 1747-1758, 2020 12.
Article in English | MEDLINE | ID: covidwho-1011368

ABSTRACT

COVID-19 caused by SARS-CoV-2, is an international concern. This infection requires urgent efforts to develop new antiviral compounds. To date, no specific drug in controlling this disease has been identified. Developing the new treatment is usually time consuming, therefore using the repurposing broad-spectrum antiviral drugs could be an effective strategy to respond immediately. In this review, a number of broad-spectrum antivirals with potential efficacy to inhibit the virus replication via targeting the virus spike protein (S protein), RNA-dependent RNA polymerase (RdRp), 3-chymotrypsin-like protease (3CLpro) and papain-like protease (PLpro) that are critical in the pathogenesis and life cycle of coronavirus, have been evaluated as possible treatment options against SARS-CoV-2 in COVID-19 patients.


Subject(s)
Antiviral Agents/therapeutic use , COVID-19/drug therapy , SARS-CoV-2/drug effects , Virus Replication/drug effects , Chymases/drug effects , Coronavirus Papain-Like Proteases/drug effects , Coronavirus RNA-Dependent RNA Polymerase/drug effects , Drug Repositioning , Humans , Virus Internalization/drug effects
7.
IUBMB Life ; 72(10): 2097-2111, 2020 10.
Article in English | MEDLINE | ID: covidwho-696287

ABSTRACT

The pandemic coronavirus disease 2019 (COVID-19), caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has affected millions of people worldwide. To date, there are no proven effective therapies for this virus. Efforts made to develop antiviral strategies for the treatment of COVID-19 are underway. Respiratory viral infections, such as influenza, predispose patients to co-infections and these lead to increased disease severity and mortality. Numerous types of antibiotics such as azithromycin have been employed for the prevention and treatment of bacterial co-infection and secondary bacterial infections in patients with a viral respiratory infection (e.g., SARS-CoV-2). Although antibiotics do not directly affect SARS-CoV-2, viral respiratory infections often result in bacterial pneumonia. It is possible that some patients die from bacterial co-infection rather than virus itself. To date, a considerable number of bacterial strains have been resistant to various antibiotics such as azithromycin, and the overuse could render those or other antibiotics even less effective. Therefore, bacterial co-infection and secondary bacterial infection are considered critical risk factors for the severity and mortality rates of COVID-19. Also, the antibiotic-resistant as a result of overusing must be considered. In this review, we will summarize the bacterial co-infection and secondary bacterial infection in some featured respiratory viral infections, especially COVID-19.


Subject(s)
Anti-Bacterial Agents/therapeutic use , Antiviral Agents/therapeutic use , Bacterial Infections/epidemiology , COVID-19/epidemiology , Pandemics , Pneumonia, Bacterial/epidemiology , Acinetobacter baumannii/drug effects , Acinetobacter baumannii/pathogenicity , Bacterial Infections/drug therapy , Bacterial Infections/microbiology , Bacterial Infections/virology , COVID-19/drug therapy , COVID-19/microbiology , COVID-19/virology , Coinfection , Haemophilus influenzae/drug effects , Haemophilus influenzae/pathogenicity , Host-Pathogen Interactions/immunology , Humans , Immunity, Innate/drug effects , Klebsiella pneumoniae/drug effects , Klebsiella pneumoniae/pathogenicity , Legionella pneumophila/drug effects , Legionella pneumophila/pathogenicity , Methicillin-Resistant Staphylococcus aureus/drug effects , Methicillin-Resistant Staphylococcus aureus/pathogenicity , Pneumonia, Bacterial/drug therapy , Pneumonia, Bacterial/microbiology , Pneumonia, Bacterial/virology , Pseudomonas aeruginosa/drug effects , Pseudomonas aeruginosa/pathogenicity , Respiratory System/drug effects , Respiratory System/microbiology , Respiratory System/pathology , Respiratory System/virology , SARS-CoV-2/drug effects , SARS-CoV-2/pathogenicity , Streptococcus pneumoniae/drug effects , Streptococcus pneumoniae/pathogenicity , Streptococcus pyogenes/drug effects , Streptococcus pyogenes/pathogenicity
8.
Future Virol. ; 5(15): 317-323, 20200501.
Article in English | WHO COVID, ELSEVIER | ID: covidwho-681938

ABSTRACT

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was first identified in several patients who traveled to Wuhan or went to a seafood wholesale market in Wuhan. The phylogenetic tree showed that SARS-CoV-2 was 96.2% identical to bat β-coronaviruses from lineage B. Also, several studies reported that SARS-CoV-2 uses the SARS-CoV receptor, angiotensin-converting enzyme 2, for entry to target cells. Lung alveolar and small intestine are potential targets for SARS-CoV-2 due to the high expression of the angiotensin-converting enzyme 2 receptor. In this review, we focused on the zoonotic β-coronaviruses and given there is no specific drug or vaccine for coronavirus disease 2019, we reviewed the literature on the therapy options for SARS and Middle East respiratory syndrome coronavirus infection, in order to discover their possible use in the treatment of SARS-CoV-2 infections.

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