Molecular Characterization of Whole-Genome SARS-CoV-2 from the First Suspected Cases of the XE Variant in the Lazio Region, Italy DOI Creative Commons
Martina Rueca, Emanuela Giombini,

Giulia Gramigna

et al.

Diagnostics, Journal Year: 2022, Volume and Issue: 12(9), P. 2219 - 2219

Published: Sept. 14, 2022

We report two cases of SARS-CoV-2 recombinant variant XE detected in nasopharyngeal swabs (NPS) hospitalized patients with no evident epidemiological link Lazio, Central Italy. Whole-Genome Sequencing (WGS) performed on an Ion Torrent GSS5 platform according to Italian flash surveys showed genomes corresponding the PANGOLIN unclassified lineage and Nextclade clade. Further analyses were then carried out investigate more deeply genetic characteristics these XE-like sequences. When phylogenetic trees, by using IQ-TREE, built splitting genome into regions putative recombination site, upstream downstream seen be clustered near BA.1 BA.2 sequences, respectively. However, our sequences separately, a significant bootstrap, from classified European strains, although site between was identified at nucleotide 11556 RDP4 software, consistent breakpoint. These findings show risk introduction novel variants existence phylogenetically separated, that could make their exact taxonomy difficult. It follows need for continued surveillance WGS.

Language: Английский

Evolution of SARS-CoV-2 Variants: Implications on Immune Escape, Vaccination, Therapeutic and Diagnostic Strategies DOI Creative Commons
Nur Zawanah Zabidi, Hern Liang Liew, Isra Ahmad Farouk

et al.

Viruses, Journal Year: 2023, Volume and Issue: 15(4), P. 944 - 944

Published: April 10, 2023

The COVID-19 pandemic caused by SARS-CoV-2 is associated with a lower fatality rate than its SARS and MERS counterparts. However, the rapid evolution of has given rise to multiple variants varying pathogenicity transmissibility, such as Delta Omicron variants. Individuals advanced age or underlying comorbidities, including hypertension, diabetes cardiovascular diseases, are at higher risk increased disease severity. Hence, this resulted in an urgent need for development better therapeutic preventive approaches. This review describes origin human coronaviruses, particularly well sub-variants. Risk factors that contribute severity implications co-infections also considered. In addition, various antiviral strategies against COVID-19, novel repurposed drugs targeting viral host proteins, immunotherapeutic strategies, discussed. We critically evaluate current emerging vaccines their efficacy, immune evasion new impact on diagnostic testing examined. Collectively, global research public health authorities, along all sectors society, prepare upcoming future coronavirus outbreaks.

Language: Английский

Citations

70
Targetable elements in SARS-CoV-2 S2 subunit for the design of pan-coronavirus fusion inhibitors and vaccines DOI Creative Commons

Liyan Guo,

Sheng Lin, Zimin Chen

et al.

Signal Transduction and Targeted Therapy, Journal Year: 2023, Volume and Issue: 8(1)

Published: May 10, 2023

Abstract The ongoing global pandemic of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome 2 (SARS‐CoV‐2), has devastating impacts on the public health and economy. Rapid viral antigenic evolution led to continual generation new variants. Of special note is recently expanding Omicron subvariants that are capable immune evasion from most existing neutralizing antibodies (nAbs). This posed challenges for prevention treatment COVID-19. Therefore, exploring broad-spectrum antiviral agents combat emerging variants imperative. In sharp contrast massive accumulation mutations within SARS-CoV-2 receptor-binding domain (RBD), S2 fusion subunit remained highly conserved among Hence, S2-based therapeutics may provide effective cross-protection against Here, we summarize developed inhibitors (e.g., nAbs, peptides, proteins, small-molecule compounds) candidate vaccines targeting elements in subunit. main focus includes all targetable elements, namely, peptide, stem helix, heptad repeats 1 (HR1-HR2) bundle. Moreover, a detailed summary characteristics action-mechanisms each class cross-reactive inhibitors, which should guide promote future design coronaviruses.

Language: Английский

Citations

48
Molecular evolution of SARS‐CoV‐2 from December 2019 to August 2022 DOI
Jonas Michel Wolf, Lucas Wolf, Graziele Lima Bello

et al.

Journal of Medical Virology, Journal Year: 2022, Volume and Issue: 95(1)

Published: Dec. 2, 2022

Severe acute respiratorysyndrome coronavirus-2 (SARS-CoV-2) pandemic spread rapidly and this scenario is concerning worldwide, presenting more than 590 million coronavirus disease 2019 cases 6.4 deaths. The emergence of novel lineages carrying several mutations in the spike protein has raised additional public health concerns worldwide during pandemic. present study review summarizes temporal spreading molecular evolution SARS-CoV-2 clades variants worldwide. evaluation these data important for understanding evolutionary histories SARSCoV-2 lineages, allowing us to identify origins each lineage virus responsible one biggest pandemics history. A total 2897 whole-genome sequences with available information from country sampling date (December August 2022), were obtained evaluated by Bayesian approach. results demonstrated that time most recent common ancestor (tMRCA) Asia was 2019-12-26 (highest posterior density 95% [HPD95%]: 2019-12-18; 2019-12-29), Oceania 2020-01-24 (HPD95%: 2020-01-15; 2020-01-30), Africa 2020-02-27 2020-02-21; 2020-03-04), Europe 2020-02-20; 2020-03-06), North America 2020-03-12 2020-03-05; 2020-03-18), South 2020-03-15 2020-03-09; 2020-03-28). Between December June 2020, 11 detected (20I [Alpha] 19A, 19B, 20B, 20C, 20A, 20D, 20E [EU1], 20F, 20H [Beta]). From July 4 identified (20J [Gamma, V3], 21 C [Epsilon], 21D [Eta], 21G [Lambda]). January 2021, 3 Delta variant (21A, 21I, 21J). two detected, 21J) Omicron (21K, 21L, 22B, 22C). 2022, (21I 22A) detected. Finally, between (22B, 22C, 22D). Clade 19A first (Wuhan strain) origin 2019-12-16 2019-12-15; 2019-12-25); 20I (Alpha) 2020-11-24 2020-11-15; 2021-12-02); (Beta) 2020-11-25 2020-11-13; 2020-11-29); 20J (Gamma) 2020-12-21 2020-11-05; 2021-01-15); 21A (Delta) 2020-09-20 2020-05-17; 2021-02-03); 21J 2021-02-26 (2020-11-02; 2021-04-24); 21M (Omicron) 2021-01-25 2020-09-16; 2021-08-08); 21K 2021-07-30 2021-05-30; 2021-10-19); 21L 2021-10-03 2021-04-16; 2021-12-23); 22B 2022-01-25 2022-01-10; 2022-02-05); 2021-12-20 2021-05-16; 2021-12-31). Currently, predominates clade branching into (22A, Phylogeographic showed Alpha originated United Kingdom, Beta Africa, Gamma Brazil, India, Mu Colombia, Epsilon States America, Lambda Peru. COVID-19 had a significant impact on global provides an overview (from Wuhan strain currently circulating Omicron).

Language: Английский

Citations

57
Carrimycin inhibits coronavirus replication by decreasing the efficiency of programmed –1 ribosomal frameshifting through directly binding to the RNA pseudoknot of viral frameshift-stimulatory element DOI Creative Commons
Hongying Li, Jianrui Li, Jiayu Li

et al.

Acta Pharmaceutica Sinica B, Journal Year: 2024, Volume and Issue: 14(6), P. 2567 - 2580

Published: March 3, 2024

The pandemic of SARS-CoV-2 worldwide with successive emerging variants urgently calls for small-molecule oral drugs broad-spectrum antiviral activity. Here, we show that carrimycin, a new macrolide antibiotic in the clinic and an candidate phase III trials, decreases efficiency programmed –1 ribosomal frameshifting coronaviruses thus impedes viral replication fashion. Carrimycin binds directly to coronaviral frameshift-stimulatory element (FSE) RNA pseudoknot, interrupting protein translation switch from ORF1a ORF1b thereby reducing level core components transcription complexes. Combined carrimycin known replicase inhibitors yielded synergistic inhibitory effect on coronaviruses. Because FSE mechanism is essential all coronaviruses, could be drug human by targeting conserved RNA. This finding may open direction discovery coronavirus variants.

Language: Английский

Citations

6
Molecular aspects of Omicron, vaccine development, and recombinant strain XE: A review DOI

K. Akash,

Avinash Sharma, Deepak Kumar

et al.

Journal of Medical Virology, Journal Year: 2022, Volume and Issue: 94(10), P. 4628 - 4643

Published: June 16, 2022

The global pandemic of COVID-19 began in December 2019 and is still continuing. past 2 years have seen the emergence several variants that were more vicious than each other. Omicron (B.1.1.529) proved to be a huge epidemiological concern as rate infection this particular strain was enormous. identified South Africa on November 24, 2021 classified "Variant Concern" 26, 2021. variant possessed mutations key RBD region, S thereby increasing affinity ACE2 for better transmission virus. Antibody resistance found it able reduce vaccine efficiency vaccines. need booster brought forth due prevalence and, subsequently, led targeted research development variant-specific vaccines dosage. This review discusses broadly genomic characters features along with its specific mutations, evolution, antibody resistance, evasion, utilization CRISPR-Cas12a assay detection, T-cell immunity elicited by against Omicron, strategies decrease also XE recombinant infectivity BA.2 subvariant Omicron.

Language: Английский

Citations

22
Development of variant‐proof severe acute respiratory syndrome coronavirus 2, pan‐sarbecovirus, and pan‐β‐coronavirus vaccines DOI
Jie Zhou, Zezhong Liu, Guangxu Zhang

et al.

Journal of Medical Virology, Journal Year: 2022, Volume and Issue: 95(1)

Published: Sept. 26, 2022

Abstract The newly emerged severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) variants with high transmission rates and striking immune evasion have posed a serious challenge to the application of current first‐generation SARS‐CoV‐2 vaccines. Other sarbecoviruses, such as SARS‐CoV SARS‐related coronaviruses (SARSr‐CoVs), potential cause outbreaks in future. These facts call for development variant‐proof SARS‐CoV‐2, pan‐sarbecovirus or pan‐β‐CoV Several novel vaccine platforms been used develop vaccines broad‐spectrum neutralizing antibody responses protective immunity combat its variants, other well β‐CoVs, In this review, we discussed major target antigens efficacy summarized recent advances against sarbecoviruses β‐CoVs.

Language: Английский

Citations

22
Identification of key mutations responsible for the enhancement of receptor-binding affinity and immune escape of SARS-CoV-2 Omicron variant DOI Open Access
Wei Bu Wang,

Bo Yi,

Ze Hua Lei

et al.

Journal of Molecular Graphics and Modelling, Journal Year: 2023, Volume and Issue: 124, P. 108540 - 108540

Published: June 10, 2023

Language: Английский

Citations

11
Enhancing Public Health Outcomes with AI-Powered Clinical Surveillance: Precise Detection of COVID-19 Variants using qPCR and Nanopore Sequencing DOI Creative Commons
Hsing‐Yi Chung, Ming‐Jr Jian,

Chih-Kai Chang

et al.

Journal of Infection and Public Health, Journal Year: 2025, Volume and Issue: 18(3), P. 102663 - 102663

Published: Jan. 10, 2025

Language: Английский

Citations

0
Microalgae as an Efficient Vehicle for the Production and Targeted Delivery of Therapeutic Glycoproteins against SARS-CoV-2 Variants DOI Creative Commons
Jaber Dehghani, Ali Movafeghi, Elodie Mathieu‐Rivet

et al.

Marine Drugs, Journal Year: 2022, Volume and Issue: 20(11), P. 657 - 657

Published: Oct. 23, 2022

Severe acute respiratory syndrome–Coronavirus 2 (SARS-CoV-2) can infect various human organs, including the respiratory, circulatory, nervous, and gastrointestinal ones. The virus is internalized into cells by binding to angiotensin-converting enzyme (ACE2) receptor through its spike protein (S-glycoprotein). As S-glycoprotein required for attachment entry target cells, it primary mediator of SARS-CoV-2 infectivity. Currently, this glycoprotein has received considerable attention as a key component development antiviral vaccines or biologics against SARS-CoV-2. Moreover, since ACE2 constitutes main route virus, soluble form could be considered promising approach treatment coronavirus disease 2019 infection (COVID-19). Both are highly glycosylated molecules containing 22 7 consensus N-glycosylation sites, respectively. N-glycan structures attached these specific sites folding, conformation, recycling, biological activity both glycoproteins. Thus far, recombinant have been produced primarily in mammalian which an expensive process. Therefore, benefiting from cheaper cell-based biofactory would good value added cost-effective biopharmaceuticals directed COVID-19. To end, efficient synthesis machinery ability properly impose post-translational modifications make microalgae eco-friendly platform production pharmaceutical Notably, several (e.g., Chlamydomonas reinhardtii, Dunaliella bardawil, Chlorella species) already approved U.S. Food Drug Administration (FDA) safe food. Because microalgal contain rigid cell wall that act natural encapsulation protect proteins aggressive environment stomach, feature used rapid edible targeted delivery treatment/inhibition Herein, we reviewed pathogenesis mechanism then highlighted potential COVID-19 infection.

Language: Английский

Citations

18
Investigation of the N-Glycosylation of the SARS-CoV-2 S Protein Contained in VLPs Produced in Nicotiana benthamiana DOI Creative Commons

Juliette Balieu,

Jae-Wan Jung,

Philippe Chan

et al.

Molecules, Journal Year: 2022, Volume and Issue: 27(16), P. 5119 - 5119

Published: Aug. 11, 2022

The emergence of the SARS-CoV-2 coronavirus pandemic in China late 2019 led to fast development efficient therapeutics. Of major structural proteins encoded by genome, SPIKE (S) protein has attracted considerable research interest because central role it plays virus entry into host cells. Therefore, date, most immunization strategies aim at inducing neutralizing antibodies against surface viral S protein. is heavily glycosylated with 22 predicted N-glycosylation consensus sites as well numerous mucin-type O-glycosylation sites. As a consequence, O- and N-glycosylations this have received particular attention. Glycans N-linked are mainly exposed form shield-masking specific epitope escape antigenic recognition. In work, status within virus-like particles (VLPs) produced Nicotiana benthamiana (N. benthamiana) was investigated using glycoproteomic approach. We show that 20 among dominated complex plant N-glycans one carries oligomannoses. This suggests N. adopts an overall 3D structure similar recombinant homologues mammalian

Language: Английский

Citations

17