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Journal articles on the topic 'Variants du SARS-CoV-2'

Author: Grafiati

Published: 1 February 2025

Last updated: 31 July 2025

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1

Huamán Saavedra, Juan Jorge. "SARS-COV-2 variants." Revista Médica de Trujillo 16, no. 1 (2021): 1–2. http://dx.doi.org/10.17268/rmt.2020.v16i01.01.

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Hassan, Dlshad Abdullah, Sazan Qadir Maulud, Rzgar Farooq Rashid, Jivan Qasim Ahmed, and Rezhna Khider Ali. "Molecular Epidemiology of SARS-CoV-2 Variants in Vaccinated and Non-Vaccinated Patients of Erbil Province, Kurdistan Region-Iraq." BioMed Target Journal 2, no. 1 (2024): 24–29. http://dx.doi.org/10.59786/bmtj.213.

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Multiple new SARS-CoV-2 variants of concern (VOC) have emerged globally since the onset of the COVID-19 pandemic. With the virus continuing to evolve, more are expected. This emphasizes the need for rapid diagnostic methods for the detection of circulating lineages. Variants-specific real-time reverse transcription (rRT)-PCR method can be used as an alternative to genome sequencing, which is expensive and labored for identifying these variants, especially in settings with limited resources. We assessed the prevalence of various SARS-CoV-2 variants spreading in the Erbil province using a diagno

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Liang, Hong-Yu, Yuyan Wu, Vicky Yau, et al. "SARS-CoV-2 Variants, Current Vaccines and Therapeutic Implications for COVID-19." Vaccines 10, no. 9 (2022): 1538. http://dx.doi.org/10.3390/vaccines10091538.

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Over the past two years, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused hundreds of millions of infections, resulting in an unprecedented pandemic of coronavirus disease 2019 (COVID-19). As the virus spreads through the population, ongoing mutations and adaptations are being discovered. There is now substantial clinical evidence that demonstrates the SARS-CoV-2 variants have stronger transmissibility and higher virulence compared to the wild-type strain of SARS-CoV-2. Hence, development of vaccines against SARS-CoV-2 variants to boost individual immunity has become

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4

Scarpa, Fabio, Francesco Branda, Nicola Petrosillo, and Massimo Ciccozzi. "On the SARS-CoV-2 Variants." Infectious Disease Reports 16, no. 2 (2024): 289–97. http://dx.doi.org/10.3390/idr16020024.

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The evolutionary dynamics of viruses, particularly exemplified by SARS-CoV-2 during the ongoing COVID-19 pandemic, underscore the intricate interplay between genetics, host adaptation, and viral spread. This paper delves into the genetic evolution of SARS-CoV-2, emphasizing the implications of viral variants on global health. Initially emerging from the Wuhan-Hu-1 lineage, SARS-CoV-2 rapidly diversified into numerous variants, each characterized by distinct mutations in the spike protein and other genomic regions. Notable variants such as B.1.1.7 (α), B.1.351 (β), P.1 (γ), B.1.617.2 (δ), and t

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Tang, Ziyang. "A Study on the Relationship between the 3-D Structure of Spike Proteins and Infectiousness of SARS-CoV-2 Delta Variant." Highlights in Science, Engineering and Technology 8 (August 17, 2022): 169–77. http://dx.doi.org/10.54097/hset.v8i.1124.

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Since the outbreak of novel coronavirus pneumonia in Wuhan in 2019, the SARS-CoV-2 epidemic has become a hot topic. Over time, SARS-CoV-2 has evolved many variants. The diversity of the 3-D structure of the variant’s proteins resulted in the difference in the binding ability and infectious differences between different virus variants and human angiotensin-converting enzyme 2 (ACE2) receptors. In 2020, an evolutionary analysis of the Delta and Delta Plus variants of SARS-CoV-2 provided a three-dimensional model of the protein of the delta variant. However, it only focused on the delta variant a

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Caputo, Emilia, and Luigi Mandrich. "SARS-CoV-2: Searching for the Missing Variants." Viruses 14, no. 11 (2022): 2364. http://dx.doi.org/10.3390/v14112364.

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Structural and phylogenetic analysis of the spike glycoprotein highlighted that the last variants, annotated as omicron, have about 30 mutations compared to the initial version reported in China, while the delta variant, supposed to be the omicron ancestor, shows only 7 mutations. Moreover, the five omicron variants were isolated between November 2021 and January 2022, and the last variant BA.2.75, unofficially named centaurus, was isolated in May 2022. It appears that, since the isolation of the delta variant (October 2020) to the omicron BA.1 (November 2021), there was an interval of one yea

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Mishra, Mitali, Aleena Zahra, Lokendra V. Chauhan, et al. "A Short Series of Case Reports of COVID-19 in Immunocompromised Patients." Viruses 14, no. 5 (2022): 934. http://dx.doi.org/10.3390/v14050934.

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Immunocompromised individuals are at risk of prolonged SARS-CoV-2 infection due to weaker immunity, co-morbidities, and lowered vaccine effectiveness, which may evolve highly mutated variants of SARS-CoV-2. Nonetheless, limited data are available on the immune responses elicited by SARS-CoV-2 infection, reinfections, and vaccinations with emerging variants in immunocompromised patients. We analyzed clinical samples that were opportunistically collected from eight immunocompromised individuals for mutations in SARS-CoV-2 genomes, neutralizing antibody (NAb) titers against different SARS-CoV-2 v

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Lu, Yonghua, Tianfu Zhao, Ming Lu, et al. "The Analyses of High Infectivity Mechanism of SARS-CoV-2 and Its Variants." COVID 1, no. 4 (2021): 666–73. http://dx.doi.org/10.3390/covid1040054.

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SARS-CoV-2 has high infectivity and some of its variants have higher transmissibility. To explore the high infectivity mechanism, the charge distributions of SARS-CoV, SARS-CoV-2, and variants of concern were calculated through a series of net charge calculation formulas. The results showed that the SARS-CoV-2 spike protein had more positive charges than that of SARS-CoV. Further results showed that the variants had similar but higher positive charges than preexisting SARS-CoV-2. In particular, the Delta variant had the greatest increase in positive charges in S1 resulting in the highest infec

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9

De Pace, Vanessa, Bianca Bruzzone, Andrea Orsi, et al. "Comparative Analysis of Five Multiplex RT-PCR Assays in the Screening of SARS-CoV-2 Variants." Microorganisms 10, no. 2 (2022): 306. http://dx.doi.org/10.3390/microorganisms10020306.

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The rapid and presumptive detection of SARS-CoV-2 variants may be performed using multiplex RT-PCR assays. The aim of this study was to evaluate the diagnostic performance of five qualitative RT-PCR tests as compared with next-generation sequencing (NGS). We retrospectively examined a multi-variant panel (n = 72) of SARS-CoV-2-positive nasopharyngeal swabs categorized as variants of concern (Alpha, Beta, Gamma and Delta), variants under monitoring (Iota and Kappa) and wild-type strains circulating in Liguria (Italy) from January to August 2021. First, NGS libraries of study samples were prepar

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10

Lauring, Adam S., and Preeti N. Malani. "Variants of SARS-CoV-2." JAMA 326, no. 9 (2021): 880. http://dx.doi.org/10.1001/jama.2021.14181.

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11

Berche, Patrick. "Les variants SARS-CoV-2." Revue de biologie médicale 361, no. 4 (2021): 13–21. https://doi.org/10.3917/rbm.361.0013.

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Comme beaucoup d’autres virus à ARN, le coronavirus SARS-CoV-2 évolue par de multiples mutations au cours du temps. Ces mutations sont liées à des erreurs de lecture de l’ARN polymérase virale. La plupart sont silencieuses, c’est-à-dire qu’elles ne modifient pas ou peu la séquence peptidique des protéines et n’ont aucune conséquence virale. Cependant, certains mutants, surnommés « variants of concern », peuvent changer la structure tridimensionnelle de protéines impliquées dans la contagiosité ou la pathogénicité des virus. Cela concerne notamment de la protéine S (Spike) qui, en interagissant

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12

Huang, Junjie, Qianqian Ma, Zhengding Su, and Xiyao Cheng. "Advancements in the Development of Anti-SARS-CoV-2 Therapeutics." International Journal of Molecular Sciences 25, no. 19 (2024): 10820. http://dx.doi.org/10.3390/ijms251910820.

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus that causes COVID-19, and so far, it has occurred five noteworthy variants of concern (VOC). SARS-CoV-2 invades cells by contacting its Spike (S) protein to its receptor on the host cell, angiotensin-converting enzyme 2 (ACE2). However, the high frequency of mutations in the S protein has limited the effectiveness of existing drugs against SARS-CoV-2 variants, particularly the Omicron variant. Therefore, it is critical to develop drugs that have highly effective antiviral activity against both SARS-CoV-2 and its variants

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Rabaan, Ali A., Abbas Al Mutair, Khalid Hajissa, et al. "A Comprehensive Review on the Current Vaccines and Their Efficacies to Combat SARS-CoV-2 Variants." Vaccines 10, no. 10 (2022): 1655. http://dx.doi.org/10.3390/vaccines10101655.

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Since the first case of Coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 2019, SARS-CoV-2 infection has affected many individuals worldwide. Eventually, some highly infectious mutants—caused by frequent genetic recombination—have been reported for SARS-CoV-2 that can potentially escape from the immune responses and induce long-term immunity, linked with a high mortality rate. In addition, several reports stated that vaccines designed for the SARS-CoV-2 wild-type variant have mixed responses against the variants of concern (VOCs) and varia

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So, Min-Kyung, Sholhui Park, Kyunghoon Lee, Soo-Kyung Kim, Hae-Sun Chung, and Miae Lee. "Variant Prediction by Analyzing RdRp/S Gene Double or Low Amplification Pattern in Allplex SARS-CoV-2 Assay." Diagnostics 11, no. 10 (2021): 1854. http://dx.doi.org/10.3390/diagnostics11101854.

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The spread of delta variants (B.1.671.2) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a severe global threat. Multiplex real-time PCR is a common method for confirming SARS-CoV-2 infection, however, additional tests, such as whole genomic sequencing, are required to reveal the presence or type of viral mutation. Moreover, applying whole genomic sequencing to all SARS-CoV-2 positive samples is challenging due to time and cost constraints. Here, we report that the double or low amplification curve observed during RNA-dependent RNA polymerase (RdRp) gene/S gene amplification

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Hemanth, Kumar Kandikattu, Sekhar Yadavalli Chandra, Sathisha Upparahalli Venkateshaiah †, and Mishrs Anil. "Vaccine efficacy in mutant SARS-CoV-2 variants." Internationa J Cell Biol Physiol 4, no. 1-2 (2021): 1–14. https://doi.org/10.264195/IJCBP.ISP.

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of the SARS-CoV-2 virus remain poorly understood, including its rapid mutation and its effects on populations of different ages. The present literature of review is focused on the effectiveness of current available vaccines in view of immerging several SARS-CoV-2 variants. The most dangerous and infectious SARS-CoV-2 strain, B117, was recently discovered in the United Kingdom, and another new variant, 501.V2, was discovered in South Africa. In countries such as the United States, Japan, India, and Brazil, the variant B117 spread far more quickly than the original strain. The new SARS-CoV-2 mut

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Tulimilli, SubbaRao V., Siva Dallavalasa, Chaithanya G. Basavaraju, et al. "Variants of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and Vaccine effectiveness." Vaccines 10, no. 10 (2022): 1751. http://dx.doi.org/10.3390/vaccines10101751.

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The incidence and death toll due to SARS-CoV-2 infection varied time-to-time; and depended on several factors, including severity (viral load), immune status, age, gender, vaccination status, and presence of comorbidities. The RNA genome of SARS-CoV-2 has mutated and produced several variants, which were classified by the SARS-CoV-2 Interagency Group (SIG) into four major categories. The first category; “Variant Being Monitored (VBM)”, consists of Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), Epsilon (B.1.427, B.1.429), Eta (B.1.525), Iota (B.1.526), Kappa (B.1.617.1), Mu (B

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17

Miao, Miao, Erik De Clercq, and Guangdi Li. "Genetic Diversity of SARS-CoV-2 over a One-Year Period of the COVID-19 Pandemic: A Global Perspective." Biomedicines 9, no. 4 (2021): 412. http://dx.doi.org/10.3390/biomedicines9040412.

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused a global pandemic of coronavirus disease in 2019 (COVID-19). Genome surveillance is a key method to track the spread of SARS-CoV-2 variants. Genetic diversity and evolution of SARS-CoV-2 were analyzed based on 260,673 whole-genome sequences, which were sampled from 62 countries between 24 December 2019 and 12 January 2021. We found that amino acid (AA) substitutions were observed in all SARS-CoV-2 proteins, and the top six proteins with the highest substitution rates were ORF10, nucleocapsid, ORF3a, spike glycoprotein, RNA-dep

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Costa, Sara Mesquita, Maria Clara da Costa Simas, Luciana Jesus da Costa, and Rosane Silva. "Dynamics of SARS-CoV-2 Mutations in Wastewater Provide Insights into the Circulation of Virus Variants in the Population." International Journal of Molecular Sciences 26, no. 9 (2025): 4324. https://doi.org/10.3390/ijms26094324.

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SARS-CoV-2 high transmission and genomic mutations result in the emergence of new variants that impact COVID-19 vaccine efficacy and virus transmission by evading the host immune system. Wastewater-based epidemiology is an effective approach to monitor SARS-CoV-2 variants circulation in the population but is a challenge due to the presence of reaction inhibitors and the low concentrations of SARS-CoV-2 in this environment. Here, we aim to improve SARS-CoV-2 variant detection in wastewater by employing nested PCR followed by next-generation sequencing (NGS) of small amplicons of the S gene. Eig

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Nas, Farouk S., Eka Ekanem, Muhammad Ali, and Muhammad S. Abdallah. "Review on SARS-CoV-2 Variants of Concern (VOC)." SAR Journal of Pathology and Microbiology 3, no. 2 (2022): 18–23. http://dx.doi.org/10.36346/sarjpm.2022.v03i02.003.

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Nearly two years since the start of the SARS-CoV-2 pandemic, which has caused over 5 million deaths, the world continues to be on high COVID-19 alert. The World Health Organization (WHO), in collaboration with national authorities, public health institutions and scientists have been closely monitoring and assessing the evolution of SARS-CoV-2 since January 2020. The emergences of specific SARS-CoV-2 variants were characterized as Variant of Interest (VOI) and Variant of Concern (VOC), to prioritize global monitoring and research, and to inform the ongoing global response to the COVID-19 pandem

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Umunnakwe, Chijioke N., Zinhle N. Makatini, Mathapelo Maphanga, et al. "Evaluation of a commercial SARS-CoV-2 multiplex PCR genotyping assay for variant identification in resource-scarce settings." PLOS ONE 17, no. 6 (2022): e0269071. http://dx.doi.org/10.1371/journal.pone.0269071.

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The rapid emergence and spread of numerous severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants across the globe underscores the crucial need for continuous SARS-CoV-2 surveillance to ensure that potentially more pathogenic variants are detected early and contained. Whole genome sequencing (WGS) is currently the gold standard for COVID-19 surveillance; however, it remains cost-prohibitive and requires specialized technical skills. To increase surveillance capacity, especially in resource-scarce settings, supplementary methods that are cost- and time-effective are needed. Real-

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Tangwangvivat, Ratanaporn, Supaporn Wacharapluesadee, Papassorn Pinyopornpanish, et al. "SARS-CoV-2 Variants Detection Strategies in Wastewater Samples Collected in the Bangkok Metropolitan Region." Viruses 15, no. 4 (2023): 876. http://dx.doi.org/10.3390/v15040876.

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Wastewater surveillance is considered a promising approach for COVID-19 surveillance in communities. In this study, we collected wastewater samples between November 2020 and February 2022 from twenty-three sites in the Bangkok Metropolitan Region to detect the presence of SARS-CoV-2 and its variants for comparison to standard clinical sampling. A total of 215 wastewater samples were collected and tested for SARS-CoV-2 RNA by real-time PCR with three targeted genes (N, E, and ORF1ab); 102 samples were positive (42.5%). The SARS-CoV-2 variants were determined by a multiplex PCR MassARRAY assay t

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Ramasamy, Santhamani, Abhinay Gontu, Sabarinath Neerukonda, et al. "SARS-CoV-2 Prevalence and Variant Surveillance among Cats in Pittsburgh, Pennsylvania, USA." Viruses 15, no. 7 (2023): 1493. http://dx.doi.org/10.3390/v15071493.

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Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infects many mammals, and SARS-CoV-2 circulation in nonhuman animals may increase the risk of novel variant emergence. Cats are highly susceptible to SARS-CoV-2 infection, and there were cases of virus transmission between cats and humans. The objective of this study was to assess the prevalence of SARS-CoV-2 variant infection of cats in an urban setting. We investigated the prevalence of SARS-CoV-2 variant infections in domestic and community cats in the city of Pittsburgh (n = 272). While no cats tested positive for SARS-CoV-2 vira

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Avgeris, Margaritis, Panagiotis G. Adamopoulos, Aikaterini Galani, et al. "Novel Nested-Seq Approach for SARS-CoV-2 Real-Time Epidemiology and In-Depth Mutational Profiling in Wastewater." International Journal of Molecular Sciences 22, no. 16 (2021): 8498. http://dx.doi.org/10.3390/ijms22168498.

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Considering the lack of effective treatments against COVID-19, wastewater-based epidemiology (WBE) is emerging as a cost-effective approach for real-time population-wide SARS-CoV-2 monitoring. Here, we report novel molecular assays for sensitive detection and mutational/variant analysis of SARS-CoV-2 in wastewater. Highly stable regions of SARS-CoV-2 RNA were identified by RNA stability analysis and targeted for the development of novel nested PCR assays. Targeted DNA sequencing (DNA-seq) was applied for the analysis and quantification of SARS-CoV-2 mutations/variants, following hexamers-based

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Aboagye, Frank T., Lawrence Annison, Henry Kwadwo Hackman, et al. "Molecular Epidemiology of SARS-CoV-2 within Accra Metropolis Postlockdown." Advances in Virology 2024 (March 29, 2024): 1–12. http://dx.doi.org/10.1155/2024/2993144.

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Introduction. Currently, sequencing has been the only tool for the identification of circulating severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants. However, it is known to be an expensive and laborious approach involving high technical expertise. Considering the reduced adherence to preventive measures postlockdown in Accra, this study presents an alternative method that leverages polymerase chain reaction (PCR) to identify circulating SARS-CoV-2 variants in the Accra Metropolis postlockdown. Methods. This prospective cross-sectional study was conducted between July and Dec

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Medel-Martinez, Ana, Cristina Paules, María Peran, et al. "Placental Infection Associated with SARS-CoV-2 Wildtype Variant and Variants of Concern." Viruses 15, no. 9 (2023): 1918. http://dx.doi.org/10.3390/v15091918.

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The original SARS-CoV-2 lineages have been replaced by successive variants of concern (VOCs) over time. The aim of this study was to perform an assessment of the placental infection by SARS-CoV-2 according to the predominant variant at the moment of COVID-19 diagnosis. This was a prospective study of SARS-CoV-2-positive pregnant women between March 2020 and March 2022. The population was divided into pregnancies affected by COVID-19 disease during 2020 (Pre-VOC group) and pregnancies affected after December 2020 by SARS-CoV-2 variants of concern (VOC group). The presence of virus was assessed

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Pennisi, Rosamaria, Davide Gentile, Paola Trischitta, et al. "Selective Control by Pistacia vera L. and Its Carotenoid Zeaxanthin on SARS-CoV-2 Virus." International Journal of Molecular Sciences 26, no. 4 (2025): 1667. https://doi.org/10.3390/ijms26041667.

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Since the onset of the COVID-19 (COronaVIrus Disease 19) pandemic, SARS-CoV-2 has exhibited a high transmission rate, further enhanced by new variants able to better adapt to humans. Addressing this issue has been challenging due to viral resistance and side effects associated with antiviral drugs and vaccines. As a result, there has been a growing interest in plant-derived compounds with antiviral properties. Our study revealed that pistachio extracts significantly inhibited SARS-CoV-2 viral entry. Employing pseudotyped particles bearing the S protein of SARS-CoV-2, we demonstrated that treat

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Arakawa, Hiroshi. "The Natural Evolution of RNA Viruses Provides Important Clues about the Origin of SARS-CoV-2 Variants." SynBio 2, no. 3 (2024): 285–97. http://dx.doi.org/10.3390/synbio2030017.

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Despite the recent pandemic, the origin of its causative agent, SARS-CoV-2, remains controversial. This study identifies several prototype SARS-CoV-2 variants (proto-variants) that are descendants of the Wuhan variant. A thorough evaluation of the evolutionary histories of the genomes of these proto-variants reveals that most mutations in proto-variants were biased toward mutations that change the amino acid sequence. While these nonsynonymous substitutions (N mutations) were common in SARS-CoV-2 proto-variants, nucleotide changes that do not result in an amino acid change, termed synonymous s

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Shy, Cherng-Gueih, Jian-He Lu, Hui-Chen Lin, et al. "Rapid Control of a SARS-CoV-2 B.1.617.2 (Delta) Variant COVID-19 Community Outbreak: The Successful Experience in Pingtung County of Taiwan." International Journal of Environmental Research and Public Health 19, no. 3 (2022): 1421. http://dx.doi.org/10.3390/ijerph19031421.

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The Severe Acute Respiratory Syndrome-associated Coronavirus 2 (SARS-CoV-2) was an outbreak in December, 2019 and rapidly spread to the world. All variants of SARS-CoV-2, including the globally and currently dominant Delta variant (Delta-SARS-CoV-2), caused severe disease and mortality. Among all variants, Delta-SARS-CoV-2 had the highest transmissibility, growth rate, and secondary attack rate than other variants except for the new variant of Omicron that still exists with many unknown effects. In Taiwan, the pandemic Delta-SARS-CoV-2 began in Pingtung from 14 June 2021 and ceased at 11 July

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Tilak, Rina. "Evolving Faces of SARS-CoV-2 with the Emergence of Diverse Variants." Journal of Communicable Diseases 54, no. 1 (2022): 141–49. http://dx.doi.org/10.24321/0019.5138.202260.

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Since the emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in December 2019, scientists have tracked five variants of concern (VOC) of SARS-CoV-2. The variants such as B.1.1.7 and B.1.617.2 primarily originated independently from the United Kingdom and India, respectively, and subsequently became dominant across the globe. The adaptability of these variants depends on their relative survival fitness to the positive selection pressure acting on them. Antiviral drugs and vaccine usage might act as a selective environment, thus, facilitating the positive selection resulti

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Zhao, Gan, Zhiyu Zhang, Yuan Ding, et al. "A DNA Vaccine Encoding the Full-Length Spike Protein of Beta Variant (B.1.351) Elicited Broader Cross-Reactive Immune Responses against Other SARS-CoV-2 Variants." Vaccines 11, no. 3 (2023): 513. http://dx.doi.org/10.3390/vaccines11030513.

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The SARS-CoV-2 pandemic remains an ongoing threat to global health with emerging variants, especially the Omicron variant and its sub-lineages. Although large-scale vaccination worldwide has delivered outstanding achievements for COVID-19 prevention, a declining effectiveness to a different extent in emerging SARS-CoV-2 variants was observed in the vaccinated population. Vaccines eliciting broader spectrum neutralizing antibodies and cellular immune responses are urgently needed and important. To achieve this goal, rational vaccine design, including antigen modeling, screening and combination,

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Ozverel, Cenk Serhan, Pinar Tulay, Mahmut Cerkez Ergoren, et al. "SARS-CoV-2 Alpha Variant Infection of a Patient Immunized by Inactive Sinovac (CoronaVac) Vaccine." EuroBiotech Journal 6, no. 1 (2022): 27–31. http://dx.doi.org/10.2478/ebtj-2022-0003.

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Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first detected in December 2019, and shortly after pandemic has been declared by the World Health Organization (WHO) due to its unstoppable global spread. Considerable amount of effort has beenput around the World in order to develop a safe and effective vaccine against SARS-CoV-2. Inactivated and RNA vaccines have already passed phase three studies showing sufficient efficacy and safety, respectively. Nowadays, there is a noticeable dominance of SARS-CoV-2 variants with various mutations over the wild type SARS-CoV-2. H

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Guan, Xiaoqing, Abhishek K. Verma, Gang Wang, Abhijeet Roy, Stanley Perlman, and Lanying Du. "A Unique mRNA Vaccine Elicits Protective Efficacy against the SARS-CoV-2 Omicron Variant and SARS-CoV." Vaccines 12, no. 6 (2024): 605. http://dx.doi.org/10.3390/vaccines12060605.

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The highly pathogenic coronaviruses SARS-CoV-2 and SARS-CoV have led to the COVID-19 pandemic and SARS outbreak, respectively. The receptor-binding domain (RBD) of the spike (S) protein of SARS-CoV-2, particularly the Omicron variant, has frequent mutations, resulting in the reduced efficiency of current COVID-19 vaccines against new variants. Here, we designed two lipid nanoparticle-encapsulated mRNA vaccines by deleting the mutant RBD of the SARS-CoV-2 Omicron variant (SARS2-S (RBD-del)) or by replacing this mutant RBD with the conserved and potent RBD of SARS-CoV (SARS2-S (SARS-RBD)). Both

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Feldberg, Liron, Anat Zvi, Yfat Yahalom-Ronen, and Ofir Schuster. "Discriminative Identification of SARS-CoV-2 Variants Based on Mass-Spectrometry Analysis." Biomedicines 11, no. 9 (2023): 2373. http://dx.doi.org/10.3390/biomedicines11092373.

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The spread of SARS-CoV-2 variants of concern (VOCs) is of great importance since genetic changes may increase transmissibility, disease severity and reduce vaccine effectiveness. Moreover, these changes may lead to failure of diagnostic measures. Therefore, variant-specific diagnostic methods are essential. To date, genetic sequencing is the gold-standard method to discriminate between variants. However, it is time-consuming (taking several days) and expensive. Therefore, the development of rapid diagnostic methods for SARS-CoV-2 in accordance with its genetic modification is of great importan

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Myasoedov, V. V., P. V. Nartov, K. V. Yurko, et al. "SARS-COV-2 genetic variability in the inter-peak period." Annals of Mechnikov Institute, no. 1 (March 13, 2022): 42–45. https://doi.org/10.5281/zenodo.6350409.

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<strong>The aim of the study</strong> – to determine the variants of SARS-CoV-2 virus in the inter-peak period (before the beginning of the new wave) in patients of Kharkiv and Kharkiv region with confirmed SARS-CoV-2 infection. <strong>Materials and methods.</strong> The smears (40 nasopharyngeal samples) from patients with symptoms of ARVI or suspected COVID-19, who were hospitalized to MNE KRC "Regional clinical infectious diseases hospital" in June 2021 and who were identified as positive for SARS-CoV-2 were used study for research conducting.  Cross-sectiona

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Alexiev, Ivailo, Ivan Ivanov, Marta Giovanetti, et al. "Early Detection of the Recombinant SARS-CoV-2 XAN Variant in Bulgaria: Initial Genomic Insights into Yet Another Piece of the Growing Puzzle of Recombinant Clades." Microorganisms 11, no. 8 (2023): 2041. http://dx.doi.org/10.3390/microorganisms11082041.

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The first recombinant SARS-CoV-2 variants were identified in 2022, causing public health concerns. The importance of recombinant variants has increased especially since the WHO designated the recombinant variant XBB and its lineages as subvariants that require monitoring on 20 November 2022. In this study, we provide the first insights into the new SARS-CoV-2 variant named XAN, a recombinant composed of Omicron sub-lineages BA.2 and BA.5. To our knowledge, this is the first report on the recombinant SARS-CoV-2 XAN variant identified in Bulgaria.

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Konishi, Tomokazu, and Toa Takahashi. "Mutation Trajectory of Omicron SARS-CoV-2 Virus, Measured by Principal Component Analysis." COVID 4, no. 4 (2024): 571–81. http://dx.doi.org/10.3390/covid4040038.

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Since 2019, the SARS-CoV-2 virus has caused a global pandemic, resulting in widespread infections and ongoing mutations. Analyzing these mutations is essential for predicting future impacts. Unlike influenza mutations, SARS-CoV-2 mutations displayed distinct selective patterns that were concentrated in the spike protein and small ORFs. In contrast to the gradual accumulation seen in influenza mutations, SARS-CoV-2 mutations lead to the abrupt emergence of new variants and subsequent outbreaks. This phenomenon may be attributed to their targeted cellular substances; unlike the influenza virus,

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Naji, Hassan. "Notable Variants of SARS-CoV-2." European Journal of Medical and Health Sciences 3, no. 2 (2021): 44–47. http://dx.doi.org/10.24018/ejmed.2021.3.2.742.

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The current coronavirus pandemic has brought many deaths and affected economies around the world. The causative agent of COVID-19 is identified as SARS-CoV-2, a close relative to SARS-CoV that caused an outbreak of severe acute respiratory distress in 2002-2003. During the course of the pandemic, there has been many reports of mutations that occurred to SARS-CoV-2 with several lineages that has been identified around the globe. In this paper, a summary of the notable variants of SARS-CoV-2 is discussed.

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Unselt, Desiree, Katherine Knudsen, Christopher Rounds, et al. "Abstract 437: Characterization of SARS-CoV-2 using the Ion AmpliSeq SARS-CoV-2 research panel." Cancer Research 82, no. 12_Supplement (2022): 437. http://dx.doi.org/10.1158/1538-7445.am2022-437.

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Abstract Background: The rapid spread of COVID-19 has resulted in an urgent need for effective diagnostic and therapeutic strategies against SARS-CoV-2. Next-generation sequencing (NGS) is a powerful tool in the identification and characterization of this pathogen and genomic information may aid in understanding the mechanisms of therapeutic resistance, vaccine escape, virulence, and pathogenicity. The Ion AmpliSeq SARS-CoV-2 Research Panel is a targeted NGS solution that facilitates sequence analysis of the SARS-CoV-2 genome. Paired with a bioinformatics assembly and variant calling pipelines

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Musa-Booth, T. O., B. Adegboro, and N. Medugu. "Evolution of SARS-CoV-2 variants: a mini-review." African Journal of Clinical and Experimental Microbiology 23, no. 3 (2022): 221–26. http://dx.doi.org/10.4314/ajcem.v23i3.1.

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SARS-CoV-2 has evolved over time with several mutations, especially on the spike protein, which has led to emergence of various variants. With the evolution of SARS-CoV-2 come new challenges in surveillance, effectiveness of preventive and treatment strategies, and outcome of the disease. Despite the lockdowns, mask mandates and other preventive measures put in place, in addition to over 10 million vaccine doses that have been administered globally as of February 2022, COVID-19 cases have risen to over 435 million and resulted in over 5.9 million deaths, largely as a result of the evolution of

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Venkatakrishnan, A. J., Praveen Anand, Patrick J. Lenehan, et al. "On the Origins of Omicron’s Unique Spike Gene Insertion." Vaccines 10, no. 9 (2022): 1509. http://dx.doi.org/10.3390/vaccines10091509.

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The emergence of a heavily mutated SARS-CoV-2 variant (Omicron; Pango lineage B.1.1.529 and BA sublineages) and its rapid spread to over 75 countries raised a global public health alarm. Characterizing the mutational profile of Omicron is necessary to interpret its clinical phenotypes which are shared with or distinctive from those of other SARS-CoV-2 variants. We compared the mutations of the initially circulating Omicron variant (now known as BA.1) with prior variants of concern (Alpha, Beta, Gamma, and Delta), variants of interest (Lambda, Mu, Eta, Iota, and Kappa), and ~1500 SARS-CoV-2 lin

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Sammartino, Josè Camilla, Irene Cassaniti, Alessandro Ferrari, et al. "Evaluation of the Neutralizing Antibodies Response against 14 SARS-CoV-2 Variants in BNT162b2 Vaccinated Naïve and COVID-19 Positive Healthcare Workers from a Northern Italian Hospital." Vaccines 10, no. 5 (2022): 703. http://dx.doi.org/10.3390/vaccines10050703.

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SARS-CoV-2 still represents a global health burden, causing more than six million deaths worldwide. Moreover, the emergence of new variants has posed new issues in terms of vaccine efficacy and immunogenicity. In this study, we aimed to evaluate the neutralizing antibody response against SARS-CoV-2 variants in different cohorts of vaccinated and unvaccinated subjects. Four-fold diluted sera from SARS-CoV-2 naïve and recovered subjects vaccinated with two or three doses of the BNT162b2 vaccine were challenged against 14 SARS-CoV-2 variants, and the SARS-CoV-2 neutralizing antibody titer was mea

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Cocherie, Théophile, Karen Zafilaza, Valentin Leducq, et al. "Epidemiology and Characteristics of SARS-CoV-2 Variants of Concern: The Impacts of the Spike Mutations." Microorganisms 11, no. 1 (2022): 30. http://dx.doi.org/10.3390/microorganisms11010030.

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SARS-CoV-2 expresses on its surface the Spike protein responsible for binding with the ACE2 receptor and which carries the majority of immunodominant epitopes. Mutations mainly affect this protein and can modify characteristics of the virus, giving each variant a unique profile concerning its transmissibility, virulence, and immune escape. The first lineage selected is the B.1 lineage characterized by the D614G substitution and from which all SARS-CoV-2 variants of concern have emerged. The first three variants of concern Alpha, Beta, and Gamma spread in early 2021: all shared the N501Y substi

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Boshah, Hattan, Faris Samkari, Alexander U. Valle-Pérez, et al. "Evaluation of Potential Peptide-Based Inhibitors against SARS-CoV-2 and Variants of Concern." BioMed Research International 2023 (October 13, 2023): 1–17. http://dx.doi.org/10.1155/2023/3892370.

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The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has greatly affected all aspect of life. Although several vaccines and pharmaceuticals have been developed against SARS-CoV-2, the emergence of mutated variants has raised several concerns. The angiotensin-converting enzyme (ACE2) receptor cell entry mechanism of this virus has not changed despite the vast mutation in emerging variants. Inhibiting the spike protein by which the virus identifies the host ACE2 receptor is a promising therapeutic countermeasure to keep pace with rapidly emerging variants. Here, we synthesiz

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Tiacharoen, Vichapon, Thammanitchpol Denpetkul, Nathamon Kosoltanapiwat, et al. "Detection of SARS-CoV-2 and Variants in Hospital Wastewater in a Developing Country." Water 14, no. 23 (2022): 3798. http://dx.doi.org/10.3390/w14233798.

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Wastewater-based epidemiology (WBE) is a beneficial tool for comprehensive health information on communities, especially during the COVID-19 pandemic. In developing countries, including Thailand, the application of WBE is limited. Few SARS-CoV-2 detections and variants have been monitored in wastewater in these countries. This is because of the time-consuming, low recovery of viruses in the concentration techniques and difficulties in finding the proper primers and amplification kits. Therefore, this study aimed to quantify SARS-CoV-2 RNA concentration using a commercial clinical kit. We ident

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Arakawa, Hiroshi. "Mutation signature of SARS-CoV-2 variants raises questions to their natural origins." June 1, 2022. https://doi.org/10.5281/zenodo.6601991.

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SARS-CoV-2 variants, such as Omicron, have acquired a number of mutations. These novel mutations have raised concerns regarding the continued efficacy of the antibodies generated in response to vaccination. In this study I show that the evolution of the SARS-CoV-2 variant Omicron, does not appear to follow a Darwinian trajectory. The mutations in the Omicron variant are heavily biased toward nonsynonymous substitutions rather than synonymous substitutions. Interestingly, mutations affecting the spike gene of the Omicron variant are almost exclusively nonsynonymous. Moreover, a nonsynonymous su

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Liang, Kang-Hao, Pao-Yin Chiang, Shih-Han Ko, et al. "Antibody cocktail effective against variants of SARS-CoV-2." Journal of Biomedical Science 28, no. 1 (2021). http://dx.doi.org/10.1186/s12929-021-00777-9.

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Abstract Background Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), an RNA virus with a high mutation rate. Importantly, several currently circulating SARS-CoV-2 variants are associated with loss of efficacy for both vaccines and neutralizing antibodies. Methods We analyzed the binding activity of six highly potent antibodies to the spike proteins of SARS-CoV-2 variants, assessed their neutralizing abilities with pseudovirus and authentic SARS-CoV-2 variants and evaluate efficacy of antibody cocktail in Delta SARS-CoV-2-infected ha

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Ogihara, Shinji, Kotaro Aoki, Mami Nagashima, Kenji Sadamasu, Yoshikazu Ishii, and Kazuhiro Tateda. "Performance evaluation of Novaplex SARS-CoV-2 variants assay kit series for SARS-CoV-2 detection using single nucleotide polymorphisms." Access Microbiology 4, no. 10 (2022). http://dx.doi.org/10.1099/acmi.0.000447.

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have received increasing attention globally because of their increased transmissibility and potential to escape immunity. Although whole-genome sequencing is the gold standard method for SARS-CoV-2 mutation detection and lineage determination, it is costly and time-consuming. However, SARS-CoV-2 variants can be identified based on select variant-specific single nucleotide polymorphisms (SNPs) in the spike protein-encoding gene (S). This study validated and compared the limit of detection (LOD) of L452R, N501Y, HV69/70 del an

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Huang, Baoying, and Wenjie Tan. "SARS-CoV-2 Variants." Infectious Diseases & Immunity Publish Ahead of Print (August 31, 2021). http://dx.doi.org/10.1097/id9.0000000000000019.

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S, Sugin Lal Jabaris. "Prevalence, Effectiveness of Vaccination and Genomics of Omicron-A New Variant of SARS-CoV-2." Pulmonary & Respiratory Medicine 1, no. 1 (2022). http://dx.doi.org/10.52803/22418isj.

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Omicron is a new variant of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and globally it created a challenging and hostile situation. it is highly contagious and has spread to more than 150 countries. Omicron variant has critical mutations in the spike protein than other Variants of Concern (VoC) -Alpha, Beta, Gamma, and Delta and Variants of Interest (VoI) – Mu, Lambda. According to the latest WHO report, the United Kingdom has reported the highest number of SARS-CoV-2 Omicron variant cases. Unlike the previous SARS-CoV-2 variants including Delta, the present variant, Omicron

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S, Sugin Lal Jabaris. "Prevalence, Effectiveness of Vaccination and Genomics of Omicron-A New Variant of SARS-CoV-2." Pulmonary & Respiratory Medicine 1, no. 1 (2022). http://dx.doi.org/10.52803/419psi22.

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Omicron is a new variant of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and globally it created a challenging and hostile situation. it is highly contagious and has spread to more than 150 countries. Omicron variant has critical mutations in the spike protein than other Variants of Concern (VoC) -Alpha, Beta, Gamma, and Delta and Variants of Interest (VoI) – Mu, Lambda. According to the latest WHO report, the United Kingdom has reported the highest number of SARS-CoV-2 Omicron variant cases. Unlike the previous SARS-CoV-2 variants including Delta, the present variant, Omicron

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