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Department of Clinical Laboratory, National Clinical Research Center for Child Health, National Children's Regional Medical Center, the Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China.; Department of Clinical Laboratory, National Clinical Research Center for Child Health, National Children's Regional Medical Center, the Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China.; Department of Clinical Laboratory, National Clinical Research Center for Child Health, National Children's Regional Medical Center, the Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China.; Department of Clinical Laboratory, National Clinical Research Center for Child Health, National Children's Regional Medical Center, the Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China.

During the COVID-19 pandemic, genetic variants of SARS-CoV-2 have been emerging and spreading around the world. Several SARS-CoV-2 endemic variants were found in United Kingdom, South Africa, Japan, and India between 2020 and April 2021. Studies have shown that many SARS-CoV-2 variants are more infectious than early wild strain and produce immune escape. These SARS-CoV-2 variants have brought new challenges to the prevention and control of COVID-19. This review summarizes and analyzes the biological characteristics of different amino acid mutations and the epidemic characteristics and immune escape of different SARS-CoV-2 variants. We hope to provide scientific reference for the monitoring, prevention, and control measures of new SARS-CoV-2 variants and the development strategy of the second-generation vaccine.CI - © 2021 Wiley Periodicals LLC.

Biohazard Prevention Centre, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland.; Biohazard Prevention Centre, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland.; Biohazard Prevention Centre, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland.; Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, 90-419 Lodz, Poland.; Biohazard Prevention Centre, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) responsible for coronavirus disease 2019 (COVID-19) was discovered in December 2019 in Wuhan, China. Since that time, the virus has spread around the world, which resulted in an announcement of the World Health Organization (WHO), dated in March 2020, that COVID-19 was a worldwide pandemic, and since then, the world has been struggling with this disease. SARS-CoV-2, similar to other RNA viruses, continually mutates, and new variants are appearing. Among large numbers of detected SARS-CoV-2 variants, only an insignificant amount of them are able to pose a risk to public health, as they are more contagious and cause more severe conditions. The emerged variants were classified by the Centers for Disease Control and Prevention (CDC) in collaboration with SARS-CoV-2 Interagency Group (SIG) according to strictly defined pattern. Variants were classified as variants of concern, variants of interest, and variants of high

2021-05-02

Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.; Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.; Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.; Department of Systems Biology, Columbia University Medical Center, New York City, New York, USA.; Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.

The avalanche of genomic data generated from the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus requires the development of tools to detect and monitor its mutations across the world. Here, we present a webtool, coronapp, dedicated to easily processing user-provided SARS-CoV-2 genomic sequences and visualizing the current worldwide status of SARS-CoV-2 mutations. The webtool allows users to highlight mutations and categorize them by frequency, country, genomic location and effect on protein sequences, and to monitor their presence in the population over time. The tool is available at http://giorgilab.unibo.it/coronannotator/ for the annotation of user-provided sequences. The full code is freely shared at https://github.com/federicogiorgi/giorgilab/tree/master/coronannotator.CI - © 2020 Wiley Periodicals LLC.

2021-01-18

Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China.; Department of Biochemistry & Food Sciences, University of Kordofan, El-Obeid, 51111, Sudan.; Lab of Molecular Immunology, Virus Inspection Department, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, China.; Center for Medical Innovation, Nagasaki University, 1-7-1 Sakamoto, Nagasaki 852-8588, Japan.; Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China.

The outbreak of the coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The pandemic apparently started in December 2019 in Wuhan, China, and has since affected many countries worldwide, turning into a major global threat. Chinese researchers reported that SARS-CoV-2 could be classified into two major variants. They suggest that investigating the variations and characteristics of these variants might help assess risks and develop better treatment and prevention strategies. The two variants were named L-type and S-type, in which L-type was prevailed in an initial outbreak in Wuhan, Central China's Hubei Province, and S-type was phylogenetically older than L-type and less prevalent at an early stage, but with a later increase in frequency in Wuhan. There were 149 mutations in 103 sequenced SARS-CoV-2 genomes, 83 of which were nonsynonymous, leading to alteration in the amino acid sequence of proteins. Much effort is currently

College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia.; College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia.; College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia.; Department of Comparative Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11533, Saudi Arabia.; College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia.

SARS-CoV-2 causes severe acute respiratory syndrome, which has led to significant morbidity and mortality around the world. Since its emergence, extensive prophylactic and therapeutic countermeasures have been employed to successfully prevent the spread of COVID-19. Extensive work has been undertaken on using monoclonal antibody therapies, mass vaccination programs, and antiviral drugs to prevent and treat COVID-19. However, since antiviral drugs could take years to become widely available, immunotherapy and vaccines currently appear to be the most feasible option. In December 2020, the first vaccine against SARS-CoV-2 was approved by the World Health Organization (WHO) and, subsequently, many other vaccines were approved for use by different international regulators in different countries. Most monoclonal antibodies (mAbs) and vaccines target the SARS-CoV-2 surface spike (S) protein. Recently, mutant (or variant) SARS-CoV-2 strains with increased infectivity and virulence that evade

National Clinical Research Center for Child Health, National Children's Regional Medical Center, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China.; National Clinical Research Center for Child Health, National Children's Regional Medical Center, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China.; National Clinical Research Center for Child Health, National Children's Regional Medical Center, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China.; National Clinical Research Center for Child Health, National Children's Regional Medical Center, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China.

During the COVID-19 pandemic, SARS-CoV-2 variants have emerged and spread worldwide. The Delta (B.1.617.2) variant was first reported in India in October 2020 and was classified as a "variant of concern (VOC)" by the WHO on 11 May, 2021. Compared to the wild-type strain, several studies have shown that the Delta variant is more transmissible and has higher viral loads in infected samples. COVID-19 patients infected with the Delta variant have a higher risk of hospitalization, intensive care unit (ICU) admission, and mortality. The Delta variant is becoming the dominant strain in many countries around the world. This review summarizes and analyses the biological characteristics of key amino acid mutations, the epidemic characteristics, and the immune escape of the Delta variant. We hope to provide scientific reference for the monitoring and prevention measures of the SARS-CoV-2 Delta variant and the development strategy of a second-generation vaccine.CI - Copyright © 2021 Tian, Sun

2021-08-04

Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, India.; Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, West Bengal, India.; Laboratório de Genética Celular e Molecular, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.; Laboratório de Bioinformática e Química Computacional, Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia (UESB), Jequié, Brazil.; Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, India.; Laboratório de Genética Celular e Molecular, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.; Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, India.; Laboratório de Genética Celular e Molecular, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.; Laboratório de Genética Celular e Molecular, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.; Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia.; Laboratório de Biologia Molecular e Computacional de Fungos, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil.; Clinical Research Center, Oftalmic, CRO, Moscow, Russia.; Department of Computer Science, Virginia Commonwealth University, Richmond, VA, United States.; Laboratório de Genética Celular e Molecular, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.

The Spike (S) protein of the SARS-CoV-2 virus is critical for its ability to attach and fuse into the host cells, leading to infection, and transmission. In this review, we have initially performed a meta-analysis of keywords associated with the S protein to frame the outline of important research findings and directions related to it. Based on this outline, we have reviewed the structure, uniqueness, and origin of the S protein of SARS-CoV-2. Furthermore, the interactions of the Spike protein with host and its implications in COVID-19 pathogenesis, as well as drug and vaccine development, are discussed. We have also summarized the recent advances in detection methods using S protein-based RT-PCR, ELISA, point-of-care lateral flow immunoassay, and graphene-based field-effect transistor (FET) biosensors. Finally, we have also discussed the emerging Spike mutants and the efficacy of the Spike-based vaccines against those strains. Overall, we have covered most of the recent advances on

2021-05-16

Department of Immunology, Victor Babes National Institute of Pathology, Bucharest, Romania.; Department of Pathology, Colentina Clinical Hospital, Bucharest, Romania.; Doctoral School, University of Bucharest, Bucharest, Romania.; Department of Clinical Pharmacy, University of Medicine and Pharmacy of Craiova, Craiova, Romania.; Department of Toxicology, University of Medicine and Pharmacy of Craiova, Craiova, Romania.; Department of Immunology, Victor Babes National Institute of Pathology, Bucharest, Romania.; Department of Pathology, Colentina Clinical Hospital, Bucharest, Romania.; Section of Public Health, Department of Biomedical, Metabolic and Neural Sciences, Environmental, Genetic and Nutritional Epidemiology Research Center (CREAGEN), University of Modena and Reggio Emilia, Modena, Italy.; Section of Public Health, Department of Biomedical, Metabolic and Neural Sciences, Environmental, Genetic and Nutritional Epidemiology Research Center (CREAGEN), University of Modena and Reggio Emilia, Modena, Italy.; Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA.; Research Group of Clinical Pharmacology and Pharmacogenomics, Faculty of Phrarmacy, School of Health Sciences, National and Kapodistrian University of Athens, Athens, Greece.; Department of Pharmacy, Laboratory of Molecular Biology and Immunology, University of Patras, Patras, Greece.; Department of Forensic Sciences and Toxicology, Faculty of Medicine, University of Crete, Heraklion, Greece.; Laboratory of Clinical Virology, Medical School, University of Crete, Heraklion, Greece.; Department of Forensic Sciences and Toxicology, Faculty of Medicine, University of Crete, Heraklion, Greece.; Department of Analytical and Forensic Medical Toxicology, Sechenov University, Moscow, Russia.

The outbreak of the coronavirus disease 2019 (COVID-19) has gathered 1 year of scientific/clinical information. This informational asset should be thoroughly and wisely used in the coming year colliding in a global task force to control this infection. Epidemiology of this infection shows that the available estimates of SARS-CoV-2 infection prevalence largely depended on the availability of molecular testing and the extent of tested population. Within molecular diagnosis, the viability and infectiousness of the virus in the tested samples should be further investigated. Moreover, SARS-CoV-2 has a genetic normal evolution that is a dynamic process. The immune system participates to the counterattack of the viral infection by pathogen elimination, cellular homoeostasis, tissue repair and generation of memory cells that would be reactivated upon a second encounter with the same virus. In all these stages, we still have knowledge to be gathered regarding antibody persistence, protective

2021-04-20

Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh.; Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh.; Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh.; Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh.; Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh.; Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh.; Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh.; Department of Biomedical Engineering, Jashore University of Science and Technology, Jashore, Bangladesh.; Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh.; Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh.; Department of Microbiology, University of Dhaka, Dhaka, Bangladesh.

Tracing the globally circulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) phylogenetic clades by high-throughput sequencing is costly, time-consuming, and labor-intensive. We here propose a rapid, simple, and cost-effective amplification refractory mutation system (ARMS)-based multiplex reverse-transcription polymerase chain reaction (PCR) assay to identify six distinct phylogenetic clades: S, L, V, G, GH, and GR. Our multiplex PCR is designed in a mutually exclusive way to identify V-S and G-GH-GR clade variants separately. The pentaplex assay included all five variants and the quadruplex comprised of the triplex variants alongside either V or S clade mutations that created two separate subsets. The procedure was optimized with 0.2-0.6 µM primer concentration, 56-60°C annealing temperature, and 3-5 ng/µl complementary DNA to validate on 24 COVID-19-positive samples. Targeted Sanger sequencing further confirmed the presence of the clade-featured mutations with

Department of Drug Discovery and Development, Auburn University Harrison School of Pharmacy, Auburn, AL 36849, USA.; Department of Drug Discovery and Development, Auburn University Harrison School of Pharmacy, Auburn, AL 36849, USA.; Department of Drug Discovery and Development, Auburn University Harrison School of Pharmacy, Auburn, AL 36849, USA.; Department of Drug Discovery and Development, Auburn University Harrison School of Pharmacy, Auburn, AL 36849, USA.; Department of Internal Medicine, Ramaiah Medical College and Hospital, Bengaluru 560054, Karnataka, India.; Department of Neuroscience, Middlebury College, Middlebury, VT 05753, USA.; Department of Drug Discovery and Development, Auburn University Harrison School of Pharmacy, Auburn, AL 36849, USA.; Department of Drug Discovery and Development, Auburn University Harrison School of Pharmacy, Auburn, AL 36849, USA.; Department of Drug Discovery and Development, Auburn University Harrison School of Pharmacy, Auburn, AL 36849, USA.; Department of Drug Discovery and Development, Auburn University Harrison School of Pharmacy, Auburn, AL 36849, USA.

The widespread increase in multiple severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants is causing a significant health concern in the United States and worldwide. These variants exhibit increased transmissibility, cause more severe disease, exhibit evasive immune properties, impair neutralization by antibodies from vaccinated individuals or convalescence sera, and reinfection. The Centers for Disease Control and Prevention (CDC) has classified SARS-CoV-2 variants into variants of interest, variants of concern, and variants of high consequence. Currently, four variants of concern (B.1.1.7, B.1.351, P.1, and B.1.617.2) and several variants of interests (B.1.526, B.1.525, and P.2) are characterized and are essential for close monitoring. In this review, we discuss the different SARS-CoV-2 variants, emphasizing variants of concern circulating the world and highlight the various mutations and how these mutations affect the characteristics of the virus. In addition, we