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Article: Evolution of the SARS-CoV-2 genome and emergence of variants of concern

Safari, Iman / Elahi, Elahe

Archives of virology. 2022 Feb., v. 167, no. 2

2022

Abstract: The high transmission and mortality rates associated with SARS-CoV-2 have led to tragic consequences worldwide. Large-scale whole-genome sequencing of the SARS-CoV-2 genome since its identification in late 2019 has identified many sequence changes and ... ...

Abstract	The high transmission and mortality rates associated with SARS-CoV-2 have led to tragic consequences worldwide. Large-scale whole-genome sequencing of the SARS-CoV-2 genome since its identification in late 2019 has identified many sequence changes and the emergence of novel strains, each described by co-segregation of a particular set of sequence variations. Variants designated G, alpha (B.1.1.7), beta (B.1.351), gamma (P.1), and delta (B.1.617.2) are important lineages that emerged sequentially and are considered variants of concern. A notable feature of the last four, each of which ultimately evolved from clade G, is the large number (≥ 20) of co-segregating sequence variations associated with them. Several variations are in the spike gene, and some variations are shared among or between strains. Meanwhile, observation of recurrent infections with the same or different SARS-CoV-2 lineages has raised concerns about the duration of the immune responses induced by the initial infection or the vaccine that was administered. While the alpha strain is sensitive to immune responses induced by earlier strains, the beta, gamma, and delta strains can escape antibody neutralization. Apart from random replication errors, intra-host RNA editing, chronic infections, and recombination are processes that may promote the accumulation of sequence changes in the SARS-CoV-2 genome. The known contribution of recombination to coronavirus evolution and recent data pertaining to SARS-CoV-2 suggest that recombination may be particularly important. Continued surveillance of the SARS-CoV-2 genome is imperative.
Keywords	RNA ; Severe acute respiratory syndrome coronavirus 2 ; antibodies ; evolution ; genes ; monitoring ; mortality ; neutralization ; vaccines ; virology
Language	English
Dates of publication	2022-02
Size	p. 293-305.
Publishing place	Springer Vienna
Document type	Article
Note	Review
ZDB-ID	7491-3
ISSN	1432-8798 ; 0304-8608
ISSN (online)	1432-8798
ISSN	0304-8608
DOI	10.1007/s00705-021-05295-5
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Article ; Online: Evolution of the SARS-CoV-2 genome and emergence of variants of concern.

Safari, Iman / Elahi, Elahe

Archives of virology

2021 Volume 167, Issue 2, Page(s) 293–305

Abstract	The high transmission and mortality rates associated with SARS-CoV-2 have led to tragic consequences worldwide. Large-scale whole-genome sequencing of the SARS-CoV-2 genome since its identification in late 2019 has identified many sequence changes and the emergence of novel strains, each described by co-segregation of a particular set of sequence variations. Variants designated G, alpha (B.1.1.7), beta (B.1.351), gamma (P.1), and delta (B.1.617.2) are important lineages that emerged sequentially and are considered variants of concern. A notable feature of the last four, each of which ultimately evolved from clade G, is the large number (≥ 20) of co-segregating sequence variations associated with them. Several variations are in the spike gene, and some variations are shared among or between strains. Meanwhile, observation of recurrent infections with the same or different SARS-CoV-2 lineages has raised concerns about the duration of the immune responses induced by the initial infection or the vaccine that was administered. While the alpha strain is sensitive to immune responses induced by earlier strains, the beta, gamma, and delta strains can escape antibody neutralization. Apart from random replication errors, intra-host RNA editing, chronic infections, and recombination are processes that may promote the accumulation of sequence changes in the SARS-CoV-2 genome. The known contribution of recombination to coronavirus evolution and recent data pertaining to SARS-CoV-2 suggest that recombination may be particularly important. Continued surveillance of the SARS-CoV-2 genome is imperative.
MeSH term(s)	COVID-19 ; Humans ; Neutralization Tests ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus
Chemical Substances	Spike Glycoprotein, Coronavirus
Language	English
Publishing date	2021-11-30
Publishing country	Austria
Document type	Journal Article ; Review
ZDB-ID	7491-3
ISSN	1432-8798 ; 0304-8608
ISSN (online)	1432-8798
ISSN	0304-8608
DOI	10.1007/s00705-021-05295-5
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Article ; Online: Combination of mesenchymal stem cells and nicorandil: an emerging therapeutic challenge against COVID-19 infection-induced multiple organ dysfunction.

Safari, Anahid / Lionetti, Vicenzo / Razeghian-Jahromi, Iman

Stem cell research & therapy

2021 Volume 12, Issue 1, Page(s) 404

Abstract: The recent COronaVIrus Disease (COVID)-19 pandemic has placed an unprecedented burden on the drug development opportunity to prevent the onset of multi-organ failure.Emerging experimental reports have highlighted the beneficial effects of mesenchymal ... ...

Abstract	The recent COronaVIrus Disease (COVID)-19 pandemic has placed an unprecedented burden on the drug development opportunity to prevent the onset of multi-organ failure.Emerging experimental reports have highlighted the beneficial effects of mesenchymal stem cell (MSC) administration against COVID-19. MSCs and their derived exosomes may attenuate SARS-CoV-2-induced inflammatory response through managing the immune cell function and cytokine expression. Although these are promising results, the exposure of MSCs to chemical compounds with pharmacological activities may further improve their homing, survival, and paracrine machinery.Nicorandil (N-[2-hydroxyethyl]-nicotinamide nitrate), an established adenosine triphosphate-sensitive potassium channel opener, is recently hypothesized to modulate inflammation as well as cell injury and death in COVID-19-affected lungs through inhibiting reactive oxygen species levels and apoptosis. Since it also exerts protective effects against hypoxia-induced MSC apoptosis, we assumed that transplanted MSCs combined to long-term nicorandil administration may survive longer in a severely inflamed microenvironment and have more beneficial effects in the treatment of SARS-CoV-2 infection than MSCs alone.
MeSH term(s)	COVID-19 ; Humans ; Mesenchymal Stem Cell Transplantation ; Mesenchymal Stem Cells ; Multiple Organ Failure ; Nicorandil/pharmacology ; SARS-CoV-2
Chemical Substances	Nicorandil (260456HAM0)
Language	English
Publishing date	2021-07-15
Publishing country	England
Document type	Letter
ZDB-ID	2548671-8
ISSN	1757-6512 ; 1757-6512
ISSN (online)	1757-6512
ISSN	1757-6512
DOI	10.1186/s13287-021-02482-8
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Article ; Online: World-wide tracking of major SARS-CoV-2 genome haplotypes in sequences of June 1 to November 15, 2020 and discovery of rapid expansion of a new haplotype.

Safari, Iman / InanlooRahatloo, Kolsoum / Elahi, Elahe

Journal of medical virology

2021 Volume 93, Issue 5, Page(s) 3251–3256

Abstract: Earlier, 13 haplotype groups defined by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome sequence variations were identified in 2790 sequences available in March 2020. Also, 23403A>G that causes p. Asp614Gly in the spike protein and is ...

Abstract	Earlier, 13 haplotype groups defined by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome sequence variations were identified in 2790 sequences available in March 2020. Also, 23403A>G that causes p. Asp614Gly in the spike protein and is one of the defining variations of the haplotype group H1, was becoming increasingly prevalent. As a follow-up, 74922 SARS-CoV-2 sequences retrieved from individuals infected in June 1 to November 15 were analyzed. Consistent with the reports on 23403A>G, H1 haplotype frequency increased world-wide; among August to November sequences, only 0.3% were associated with non-H1 haplotypes. This finding prompted assessment of H1 sub-haplotypes among the sequences of the later stage of the coronavirus disease 2019 pandemic. The distribution of the sub-haplotypes differed in different regions, but 98.4% of the sequences were associated with five H1 sub-haplotypes. One of these had not been previously observed and had emerged in Europe by June 2020. The most important finding of the present study is identification of this new sub-haplotype (H1r) and finding evidence that suggest it may have a high potential for expansion. Its frequency had reached 10%-90% in various countries/territories of Europe by the end of September. The new sub-haplotype is defined by seven sequence variations, one of which causes Ala222Val in the spike protein.
MeSH term(s)	COVID-19/epidemiology ; COVID-19/virology ; Genetic Variation ; Genome, Viral ; Global Health ; Haplotypes ; Humans ; SARS-CoV-2/genetics ; Spike Glycoprotein, Coronavirus/genetics
Chemical Substances	Spike Glycoprotein, Coronavirus
Language	English
Publishing date	2021-02-15
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	752392-0
ISSN	1096-9071 ; 0146-6615
ISSN (online)	1096-9071
ISSN	0146-6615
DOI	10.1002/jmv.26802
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Article ; Online: Wound Healing Activities of

Javanmardi, Setareh / Safari, Iman / Aghaz, Faranak / Khazaei, Mozafar

The international journal of lower extremity wounds

2020 Volume 20, Issue 3, Page(s) 272–281

Abstract: Skin burn is a major health problem in the community and seeking new and suitable treatment is suggested. In this regard, traditional remedies were consider in many countries. Regarding clinical application of herbal medicine in the healing of burn ... ...

Abstract	Skin burn is a major health problem in the community and seeking new and suitable treatment is suggested. In this regard, traditional remedies were consider in many countries. Regarding clinical application of herbal medicine in the healing of burn wounds, the present study was designed to evaluate the effect of
MeSH term(s)	Animals ; Burns/drug therapy ; Male ; Milk ; Ointments ; Plant Extracts/pharmacology ; Rats ; Rats, Wistar ; Wound Healing
Chemical Substances	Ointments ; Plant Extracts
Language	English
Publishing date	2020-06-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	2171119-7
ISSN	1552-6941 ; 1534-7346
ISSN (online)	1552-6941
ISSN	1534-7346
DOI	10.1177/1534734620921589
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Article: Characterization, in vitro antibacterial activity, and toxicity for rat of tetracycline in a nanocomposite hydrogel based on PEG and cellulose

Iman, Maryam / Barati, Aboulfazl / Safari, Saeed

Cellulose. 2020 Jan., v. 27, no. 1

2020

Abstract: Hydrogels are among the drug delivery systems that are used to modify drug release by the oral route. Inclusion of porous nanoparticles and cellulose nanofibers (CNF) in a hydrogel matrix structure improves the mechanical strength of the hydrogel and ... ...

Abstract	Hydrogels are among the drug delivery systems that are used to modify drug release by the oral route. Inclusion of porous nanoparticles and cellulose nanofibers (CNF) in a hydrogel matrix structure improves the mechanical strength of the hydrogel and modifies drug release. CNF have been widely used for the preparation of biomedical systems because of low toxicity, biodegradability, and biocompatibility. Besides, a positive influence on mechanical and physical resistance is shown. In this study, nanocomposite hydrogels containing polyethylene glycol, Acrylamide, N, N′-methylene bis-acrylamide, and CNF are formulated, and then tetracycline was loaded into the hydrogels. Tetracycline release was measured using UV spectrometer. Morphology and microscopic structure of synthesized nanocomposites are studied using FE-SEM, XRD, and FTIR analyses. Moreover, the antibacterial activity of tetracycline nanocomposite hydrogels against Staphylococcus aureus and Escherichia coli was tested. Nanocomposite hydrogel oral toxicity test was performed in adult male Wistar rats. The results showed that the formulation has no significant statistical effect on the behavioral pattern, body weight, and clinical parameters of the experimental animals. Furthermore, pathological examination showed the normal structure of stomach and intestine. Antibacterial activity study showed that Staphylococcus aureus and E. Coli are sensitive to the formulated compound 3. Therefore, these formulations can be considered for future as oral drug delivery systems.
Keywords	Escherichia coli ; Fourier transform infrared spectroscopy ; Staphylococcus aureus ; X-ray diffraction ; acrylamides ; adults ; antibacterial properties ; biocompatibility ; biodegradability ; body weight ; cellulose ; cellulose nanofibers ; drug delivery systems ; drugs ; hydrogels ; intestines ; laboratory animals ; males ; nanocomposites ; nanoparticles ; polyethylene glycol ; rats ; scanning electron microscopy ; spectrometers ; stomach ; strength (mechanics) ; tetracycline ; toxicity ; toxicity testing
Language	English
Dates of publication	2020-01
Size	p. 347-356.
Publishing place	Springer Netherlands
Document type	Article
ZDB-ID	1496831-9
ISSN	1572-882X ; 0969-0239
ISSN (online)	1572-882X
ISSN	0969-0239
DOI	10.1007/s10570-019-02783-5
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Article ; Online: Response to Mungmunpuntipantip and Wiwanitkit.

Foroughinia, Farzaneh / Morovati, Najmeh / Safari, Anahid / Dianatpour, Mehdi / Jamhiri, Iman / Heydari, Seyed Taghi / Hooshmandi, Sedighe / Borhani-Haghighi, Afshin

Journal of clinical neuroscience : official journal of the Neurosurgical Society of Australasia

2022 Volume 99, Page(s) 393

Language	English
Publishing date	2022-03-31
Publishing country	Scotland
Document type	Letter ; Comment
ZDB-ID	1193674-5
ISSN	1532-2653 ; 0967-5868
ISSN (online)	1532-2653
ISSN	0967-5868
DOI	10.1016/j.jocn.2022.03.041
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Article ; Online: Evolution of SARS-CoV-2 genome from December 2019 to late March 2020: Emerged haplotypes and informative Tag nucleotide variations.

Safari, Iman / InanlooRahatloo, Kolsoum / Elahi, Elahe

Journal of medical virology

2020 Volume 93, Issue 4, Page(s) 2010–2020

Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes serious disease in humans. First identified in November/December 2019 in China, it has rapidly spread worldwide. We analyzed 2790 SARS-CoV-2 genome sequences from 56 countries that were ... ...

Abstract	Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes serious disease in humans. First identified in November/December 2019 in China, it has rapidly spread worldwide. We analyzed 2790 SARS-CoV-2 genome sequences from 56 countries that were available on April 2, 2020, to assess the evolution of the virus during this early phase of its expansion. We aimed to assess sequence variations that had evolved in virus genomes, giving the greatest attention to the S gene. We also aimed to identify haplotypes that the variations may define and consider their geographic and chronologic distribution. Variations at 1930 positions that together cause 1203 amino acid changes were identified. The frequencies of changes normalized to the lengths of genes and encoded proteins were relatively high in ORF3a and relatively low in M. A variation that causes an Asp614Gly near the receptor-binding domain of S were found at a high frequency, and it was considered that this may contribute to the rapid spread of viruses with this variation. Our most important findings relate to haplotypes. Sixty-six haplotypes that constitute thirteen haplotype groups (H1-H13) were identified, and 84.6% of the 2790 sequences analyzed were associated with these haplotypes. The majority of the sequences (75.1%) were associated with haplotype groups H1-H3. The distribution pattern of the haplotype groups differed in various geographic regions. A few were country/territory specific. The location and time of emergence of some haplotypes are discussed. Importantly, nucleotide variations that define the various haplotypes and Tag/signature variations for most of the haplotypes are reported. The practical applications of these variations are discussed.
MeSH term(s)	COVID-19/virology ; Evolution, Molecular ; Genetic Variation ; Genome, Viral ; Haplotypes ; Humans ; Phylogeography ; SARS-CoV-2/genetics ; Spike Glycoprotein, Coronavirus/genetics
Chemical Substances	Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Keywords	covid19
Language	English
Publishing date	2020-11-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	752392-0
ISSN	1096-9071 ; 0146-6615
ISSN (online)	1096-9071
ISSN	0146-6615
DOI	10.1002/jmv.26553
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Article ; Online: On the Capacity of Amplitude Modulated Soliton Communication over Long Haul Fibers.

Chen, Yu / Tavakkolnia, Iman / Alvarado, Alex / Safari, Majid

Entropy (Basel, Switzerland)

2020 Volume 22, Issue 8

Abstract: The capacity limits of fiber-optic communication systems in the nonlinear regime are not yet well understood. In this paper, we study the capacity of amplitude modulated first-order soliton transmission, defined as the maximum of the so-called time- ... ...

Abstract	The capacity limits of fiber-optic communication systems in the nonlinear regime are not yet well understood. In this paper, we study the capacity of amplitude modulated first-order soliton transmission, defined as the maximum of the so-called time-scaled mutual information. Such definition allows us to directly incorporate the dependence of soliton pulse width to its amplitude into capacity formulation. The commonly used memoryless channel model based on noncentral chi-squared distribution is initially considered. Applying a variance normalizing transform, this channel is approximated by a unit-variance additive white Gaussian noise (AWGN) model. Based on a numerical capacity analysis of the approximated AWGN channel, a general form of capacity-approaching input distributions is determined. These optimal distributions are discrete comprising a mass point at zero (off symbol) and a finite number of mass points almost uniformly distributed away from zero. Using this general form of input distributions, a novel closed-form approximation of the capacity is determined showing a good match to numerical results. Finally, mismatch capacity bounds are developed based on split-step simulations of the nonlinear Schro¨dinger equation considering both single soliton and soliton sequence transmissions. This relaxes the initial assumption of memoryless channel to show the impact of both inter-soliton interaction and Gordon-Haus effects. Our results show that the inter-soliton interaction effect becomes increasingly significant at higher soliton amplitudes and would be the dominant impairment compared to the timing jitter induced by the Gordon-Haus effect.
Language	English
Publishing date	2020-08-15
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2014734-X
ISSN	1099-4300 ; 1099-4300
ISSN (online)	1099-4300
ISSN	1099-4300
DOI	10.3390/e22080899
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Article ; Online: Genetic screening of

Jozaei, Roxanne / Javadi, Mohammad-Ali / Safari, Iman / Moghaddasi, Afrooz / Feizi, Sepehr / Kanavi, Mozhgan Rezaei / Najafi, Sajad / Safdari, Bahareh / Salahshourifar, Iman / Elahi, Elahe / Suri, Fatemeh

Ophthalmic genetics

2022 Volume 43, Issue 4, Page(s) 496–499

Abstract: Purpose: Transforming growth factor beta-induced (: Methods: Twenty-four : Results: Twenty-two out of 24 patients had mutations in exons 4 or 12 of : Conclusion: ... ...

Abstract	Purpose: Transforming growth factor beta-induced ( Methods: Twenty-four Results: Twenty-two out of 24 patients had mutations in exons 4 or 12 of Conclusion: TGFBI
MeSH term(s)	Corneal Dystrophies, Hereditary/diagnosis ; Corneal Dystrophies, Hereditary/genetics ; DNA Mutational Analysis ; Extracellular Matrix Proteins/genetics ; Genetic Testing ; Humans ; Iran/epidemiology ; Mutation ; Pedigree ; Phenotype ; Transforming Growth Factor beta/genetics
Chemical Substances	Extracellular Matrix Proteins ; Transforming Growth Factor beta ; betaIG-H3 protein (148710-76-3)
Language	English
Publishing date	2022-04-26
Publishing country	England
Document type	Journal Article ; Meta-Analysis
ZDB-ID	1199279-7
ISSN	1744-5094 ; 0167-6784 ; 1381-6810
ISSN (online)	1744-5094
ISSN	0167-6784 ; 1381-6810
DOI	10.1080/13816810.2022.2068040
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