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1
Huamán Saavedra, Juan Jorge. "SARS-COV-2 variants." Revista Médica de Trujillo 16, no. 1 (March 16, 2021): 1–2. http://dx.doi.org/10.17268/rmt.2020.v16i01.01.
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Scarpa, Fabio, Francesco Branda, Nicola Petrosillo, and Massimo Ciccozzi. "On the SARS-CoV-2 Variants." Infectious Disease Reports 16, no. 2 (March 26, 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 the Omicron variant have garnered significant attention due to their heightened transmissibility and immune evasion capabilities. In particular, the Omicron variant has presented a myriad of subvariants, raising concerns about its potential impact on public health. Despite the emergence of numerous variants, the vast majority have exhibited limited expansion capabilities and have not posed significant threats akin to early pandemic strains. Continued genomic surveillance is imperative to identify emerging variants of concern promptly. While genetic adaptation is intrinsic to viral evolution, effective public health responses must be grounded in empirical evidence to navigate the evolving landscape of the pandemic with resilience and precision.
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Liang, Hong-Yu, Yuyan Wu, Vicky Yau, Huan-Xin Yin, Scott Lowe, Rachel Bentley, Mubashir Ayaz Ahmed, Wenjing Zhao, and Chenyu Sun. "SARS-CoV-2 Variants, Current Vaccines and Therapeutic Implications for COVID-19." Vaccines 10, no. 9 (September 16, 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 essential. However, current treatment options are limited for COVID-19 caused by the SARS-CoV-2 variants. In this review, we describe current distribution, variation, biology, and clinical features of COVID-19 caused by SARS-CoV-2 variants (including Alpha (B.1.1.7 Lineage) variant, Beta (B.1.351 Lineage) variant, Gamma (P.1 Lineage) variant, Delta (B.1.617.2 Lineage) variant, and Omicron (B.1.1.529 Lineage) variant and others. In addition, we review currently employed vaccines in clinical or preclinical phases as well as potential targeted therapies in an attempt to provide better preventive and treatment strategies for COVID-19 caused by different SARS-CoV-2 variants.
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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 (May 3, 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 diagnostic screening RT-PCR-based method. A total of 144 SARS-CoV-2 positive samples were prospectively tested for known SARS-CoV2 variants using ViroQ® SC2 Variant rRT-PCR. Furthermore, the technique was validated using 25 SARS-CoV-2 negative nasal samples. Out of 144 SARS-CoV-2 positive samples, 118 (81.9%) were B.1.617.2 (Delta), 5 (3.5%) were Epsilon B.1.427/B.1.429, 1(0.7%) was Eta B.1.525, 2(1.4%) were SARS-CoV-2 Wild type, while 18 (12.5%) were undefined variant, and the delta strain was the most prevalent SARS-CoV-2 strain. Our study showed that variant-specific RT-PCR could be a useful tool for the rapid screening of SARS-CoV-2 variants.
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Caputo, Emilia, and Luigi Mandrich. "SARS-CoV-2: Searching for the Missing Variants." Viruses 14, no. 11 (October 26, 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 year, whereas the five omicron variants were isolated in three months, and after a successive four months period, the BA.2.75 variant was isolated. So, what is the temporal and phylogenetic correlation among all these variants? The analysis of common mutations among delta and the omicron variants revealed: i) a phylogenetic correlation among these variants; ii) the existence of BA.1 and BA.2 omicron variants a few months before being isolated; iii) at least three possible intermediate variants during the evolution of omicron; iv) the evolution of the BA.2.12.1, BA.4 and BA.5 variants from omicron BA.2; v) the centaurus variant evolution from omicron BA.2.12.1.
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Lauring, Adam S., and Preeti N. Malani. "Variants of SARS-CoV-2." JAMA 326, no. 9 (September 7, 2021): 880. http://dx.doi.org/10.1001/jama.2021.14181.
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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 and Delta plus variant themselves and did not compare the delta variant or delta plus variant with the original strain. It is hard to give a direct or apparent reason why the delta variant is more infectious and difficult to cure than the original strain. Therefore, this paper further compared the 3-D structures of homologous trimeric spike glycoproteins (S-proteins) and the receptor-binding domain between the SARS-COV-2 original strain and the SARS-COV-2 delta variant. By observing and analyzing the models of the above proteins in the PyMOL Molecular Graphics System, the reasons for the increase of infectivity of the delta variant can be interpreted in a direct way. This article also focuses on the data of the Indian cases from the JHU database to deeply analyze the relationship between the structure and transmission ability of the SARS-CoV-2 delta variant. Last but not least, the reproductive ability of SARS-CoV-2 can be reflected by the number of NAG (2-acetamido-2-deoxy-beta-D-glucopyranose). Through data analysis and protein structure research, we can better understand the characteristics of the binding of SARS-CoV-2 to the human receptor, thus providing a theoretical basis for accurately predicting virus variation. Through the comparative study of virus structure and infectiousness, this paper will provide a scientific basis for the relevant departments to improve epidemic prevention and improve the public's vigilance against virus variants.
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Lu, Yonghua, Tianfu Zhao, Ming Lu, Yaopeng Zhang, Xiang Yao, Guoyi Wu, Fangyin Dai, Fengxiu Zhang, and Guangxian Zhang. "The Analyses of High Infectivity Mechanism of SARS-CoV-2 and Its Variants." COVID 1, no. 4 (November 24, 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 infectivity. In particular, the S1 positive charge increased greatly in the Delta variant. The S1 positive charge increased, and due to the large negative charge of angiotensin-converting enzyme-2 (ACE2), this resulted in a large increase in Coulomb’s force between S1 and ACE2. This finding agrees with the expectation that the positive charges in the spike protein result in more negative charges on SARS-CoV-2 antibodies than that of SARS-CoV. Thus, the infectivity of a novel SARS-CoV-2 variant may be evaluated preliminarily by calculating the charge distribution.
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Mishra, Mitali, Aleena Zahra, Lokendra V. Chauhan, Riddhi Thakkar, James Ng, Shreyas Joshi, Eric D. Spitzer, Luis A. Marcos, W. Ian Lipkin, and Nischay Mishra. "A Short Series of Case Reports of COVID-19 in Immunocompromised Patients." Viruses 14, no. 5 (April 29, 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 variants, and the identification of immunoreactive epitopes using a high-throughput coronavirus peptide array. The viral genome analysis revealed two SARS-CoV-2 variants (20A from a deceased patient and an Alpha variant from a recovered patient) with an eight amino-acid (aa) deletion within the N-terminal domain (NTD) of the surface glycoprotein. A higher NAb titer was present against the prototypic USA/WA1/2020 strain in vaccinated immunocompromised patients. NAb titer was absent against the Omicron variant and the cultured virus of the 20A variant with eight aa deletions in non-vaccinated patients. Our data suggest that fatal SARS-CoV-2 infections may occur in immunocompromised individuals even with high titers of NAb post-vaccination. Moreover, persistent SARS-CoV-2 infection may lead to the emergence of newer variants with additional mutations favoring the survival and fitness of the pathogen that include deletions in NAb binding sites in the SARS-CoV-2 surface glycoprotein.
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De Pace, Vanessa, Bianca Bruzzone, Andrea Orsi, Valentina Ricucci, Alexander Domnich, Giulia Guarona, Nadia Randazzo, et al. "Comparative Analysis of Five Multiplex RT-PCR Assays in the Screening of SARS-CoV-2 Variants." Microorganisms 10, no. 2 (January 27, 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 prepared and mapped to the reference genome. Then, specimens were screened for the detection of L452R, W152C, K417T, K417N, E484Q, E484K and N501Y mutations using the SARS-CoV-2 Variants II Assay Allplex, UltraGene Assay SARS-CoV-2 452R & 484K & 484Q Mutations V1, COVID-19 Ultra Variant Catcher, SARS-CoV-2 Extended ELITe MGB and Simplexa SARS-CoV-2 Variants Direct. The overall accuracy of these assays ranged from 96.9% to 100%. Specificity and sensitivity were 100% and 96–100%, respectively. We highly recommend the use of these assays as second-level tests in the routine workflow of SARS-CoV-2 laboratory diagnostics, as they are accurate, user friendly, low cost, may identify specific mutations in about 2–3 h and, therefore, optimize the surveillance of SARS-CoV-2 variants.
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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 (October 9, 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 in the future. This review provides an overview of the mechanism of SARS-CoV-2 infection and the current progress on anti-SARS-CoV-2 drugs.
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Tulimilli, SubbaRao V., Siva Dallavalasa, Chaithanya G. Basavaraju, Vinay Kumar Rao, Prashanth Chikkahonnaiah, SubbaRao V. Madhunapantula, and Ravindra P. Veeranna. "Variants of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and Vaccine effectiveness." Vaccines 10, no. 10 (October 19, 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.1.621), and Zeta (P.2); the second category; “Variants of Concern” consists of Omicron (B.1.1.529). The third and fourth categories include “Variants of Interest (VOI)”, and “Variants of High Consequence (VOHC)”, respectively, and contain no variants classified currently under these categories. The surge in VBM and VOC poses a significant threat to public health globally as they exhibit altered virulence, transmissibility, diagnostic or therapeutic escape, and the ability to evade the host immune response. Studies have shown that certain mutations increase the infectivity and pathogenicity of the virus as demonstrated in the case of SARS-CoV-2, the Omicron variant. It is reported that the Omicron variant has >60 mutations with at least 30 mutations in the Spike protein (“S” protein) and 15 mutations in the receptor-binding domain (RBD), resulting in rapid attachment to target cells and immune evasion. The spread of VBM and VOCs has affected the actual protective efficacy of the first-generation vaccines (ChAdOx1, Ad26.COV2.S, NVX-CoV2373, BNT162b2). Currently, the data on the effectiveness of existing vaccines against newer variants of SARS-CoV-2 are very scanty; hence additional studies are immediately warranted. To this end, recent studies have initiated investigations to elucidate the structural features of crucial proteins of SARS-CoV-2 variants and their involvement in pathogenesis. In addition, intense research is in progress to develop better preventive and therapeutic strategies to halt the spread of COVID-19 caused by variants. This review summarizes the structure and life cycle of SARS-CoV-2, provides background information on several variants of SARS-CoV-2 and mutations associated with these variants, and reviews recent studies on the safety and efficacy of major vaccines/vaccine candidates approved against SARS-CoV-2, and its variants.
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Rabaan, Ali A., Abbas Al Mutair, Khalid Hajissa, Amal H. Alfaraj, Jumana M. Al-Jishi, Mashael Alhajri, Sara Alwarthan, et al. "A Comprehensive Review on the Current Vaccines and Their Efficacies to Combat SARS-CoV-2 Variants." Vaccines 10, no. 10 (October 2, 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 variants of interest (VOIs) in the human population. These results advocate the designing and development of a panvaccine with the potential to neutralize all the possible emerging variants of SARS-CoV-2. In this context, recent discoveries suggest the design of SARS-CoV-2 panvaccines using nanotechnology, siRNA, antibodies or CRISPR-Cas platforms. Thereof, the present comprehensive review summarizes the current vaccine design approaches against SARS-CoV-2 infection, the role of genetic mutations in the emergence of new viral variants, the efficacy of existing vaccines in limiting the infection of emerging SARS-CoV-2 variants, and efforts or challenges in designing SARS panvaccines.
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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 (October 8, 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 in the Allplex SARS-CoV-2 Assay is related to delta/alpha variants. We analyzed the RdRp/S gene amplification curve using 94 samples confirmed as SARS-CoV-2 infection by the Allplex SARS-CoV-2 Assay from January to August, 2021. These positive samples identified variant types using the Novaplex SARS-CoV-2 Variants I and IV Assays. Overall, 17 samples showing a double curve and 11 samples showing a low amplification pattern were associated with alpha-/delta-type strains with variants in the P681 region. The double or low curve shown in the RdRp gene amplification curve had 100% sensitivity and 100% specificity for diagnosing delta/alpha variants. During the SARS-CoV-2 virus diagnostic RT-PCR test using the Allplex SARS-CoV-2 Assay, we could consider the presence of delta/alpha variants in the samples with double or low amplification curve of the RdRp/S gene channel. This PCR amplification curve abnormality enables rapid and cost-effective variant type prediction during SARS-CoV-2 diagnostic testing in clinical laboratories.
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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 (April 30, 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 pandemic. The WHO and its international sequencing networks continuously monitor SARS-CoV-2 mutations and inform countries about any changes that may be needed to respond to the variant, and prevent its spread where feasible. Multiple variants of the virus have emerged and become dominant in many countries since January 2021, with the Alpha, Beta, Gamma, Delta and Omicron variants being the most prominent to date. The paper was aimed to review the SARS-CoV-2 variants of concern (VOC).
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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 (April 11, 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-dependent RNA polymerase, and ORF8. Among 25,629 amino acid substitutions at 8484 polymorphic sites across the coding region of the SARS-CoV-2 genome, the D614G (93.88%) variant in spike and the P323L (93.74%) variant in RNA-dependent RNA polymerase were the dominant variants on six continents. As of January 2021, the genomic sequences of SARS-CoV-2 could be divided into at least 12 different clades. Distributions of SARS-CoV-2 clades were featured with temporal and geographical dynamics on six continents. Overall, this large-scale analysis provides a detailed mapping of SARS-CoV-2 variants in different geographic areas at different time points, highlighting the importance of evaluating highly prevalent variants in the development of SARS-CoV-2 antiviral drugs and vaccines.
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Tangwangvivat, Ratanaporn, Supaporn Wacharapluesadee, Papassorn Pinyopornpanish, Sininat Petcharat, Suthida Muangnoicharoen Hearn, Nattakarn Thippamom, Chadaporn Phiancharoen, et al. "SARS-CoV-2 Variants Detection Strategies in Wastewater Samples Collected in the Bangkok Metropolitan Region." Viruses 15, no. 4 (March 29, 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 to distinguish four SARS-CoV-2 variants, including Alpha, Beta, Delta, and Omicron. Multiple variants of Alpha–Delta and Delta–Omicron were detected in the wastewater samples in July 2021 and January 2022, respectively. These wastewater variant results mirrored the country data from clinical specimens deposited in GISAID. Our results demonstrated that wastewater surveillance using multiple signature mutation sites for SARS-CoV-2 variant detection is an appropriate strategy to monitor the presence of SARS-CoV-2 variants in the community at a low cost and with rapid turn-around time. However, it is essential to note that sequencing surveillance of wastewater samples should be considered complementary to whole genome sequencing of clinical samples to detect novel variants.
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Umunnakwe, Chijioke N., Zinhle N. Makatini, Mathapelo Maphanga, Anele Mdunyelwa, Khamusi M. Mlambo, Puseletso Manyaka, Monique Nijhuis, Annemarie Wensing, and Hugo A. Tempelman. "Evaluation of a commercial SARS-CoV-2 multiplex PCR genotyping assay for variant identification in resource-scarce settings." PLOS ONE 17, no. 6 (June 24, 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-time multiplex PCR genotyping assays offer an economical and fast solution for screening circulating and emerging variants while simultaneously complementing existing WGS approaches. In this study we evaluated the AllplexTM SARS-CoV-2 Variants II multiplex real-time PCR genotyping assay, Seegene (South Korea), and implemented it in retrospectively characterizing circulating SARS-CoV-2 variants in a rural South African setting between April and October 2021, prior to the emergence of the Omicron variant in South Africa. The AllplexTM SARS-CoV-2 Variants II real-time PCR assay demonstrated perfect concordance with whole-genome sequencing in detecting Beta and Delta variants and exhibited high specificity, sensitivity and reproducibility. Implementation of the assay in characterization of SARS-CoV-2 variants between April and October 2021 in a rural South African setting revealed a rapid shift from the Beta to the Delta variant between April and June. All specimens successfully genotyped in April were Beta variants and the Delta variant was not detected until May. By June, 78% of samples genotyped were Delta variants and in July >95% of all genotyped samples were Delta variants. The Delta variant continued to predominate through to the end of our analysis in October 2021. Taken together, a commercial SARS-CoV-2 variant genotyping assay detected the rapid rate at which the Delta variant displaced the Beta variant in Limpopo, an under-monitored province in South Africa. Such assays provide a quick and cost-effective method of monitoring circulating variants and should be used to complement genomic sequencing for COVID-19 surveillance especially in resource-scarce settings.
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Ramasamy, Santhamani, Abhinay Gontu, Sabarinath Neerukonda, Diana Ruggiero, Becky Morrow, Sheweta Gupta, Saranya Amirthalingam, et al. "SARS-CoV-2 Prevalence and Variant Surveillance among Cats in Pittsburgh, Pennsylvania, USA." Viruses 15, no. 7 (June 30, 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 viral RNA, 35 cats (12.86%) tested SARS-CoV-2-antibody-positive. Further, we compared a cat-specific experimental lateral flow assay (eLFA) and species-agnostic surrogate virus neutralization assay (sVNT) for SARS-CoV-2 antibody detection in cats (n = 71). The eLFA demonstrated 100% specificity compared to sVNT. The eLFA also showed 100% sensitivity for sera with >90% inhibition and 63.63% sensitivity for sera with 40–89% inhibition in sVNT. Using a variant-specific pseudovirus neutralization assay (pVNT) and antigen cartography, we found the presence of antibodies to pre-Omicron and Omicron SARS-CoV-2 variants. Hence, this approach proves valuable in identifying cat exposure to different SARS-CoV-2 variants. Our results highlight the continued exposure of cats to SARS-CoV-2 and warrant coordinated surveillance efforts.
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Medel-Martinez, Ana, Cristina Paules, María Peran, Pilar Calvo, Sara Ruiz-Martinez, María Ormazabal Cundin, Alberto Cebollada-Solanas, et al. "Placental Infection Associated with SARS-CoV-2 Wildtype Variant and Variants of Concern." Viruses 15, no. 9 (September 13, 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 by RT-PCR, and the viral variant was determined by whole genome sequencing. A total of 104 placentas were examined, among which 54 cases belonged to the Pre-VOC group and 50 cases belonged to the VOC group. Sixteen positive placental RT-PCR tests for SARS-CoV-2 were reported. The NGS analysis confirmed the SARS-CoV-2 lineage in placenta tissue. All samples corresponded to the Pre-VOC group, whereas no placental presence of SARS-CoV-2 was detected in the VOC group (16, 29.6% vs. 0, 0.0% p = 0.000). Preterm birth (9, 16.7% vs. 2, 4%; p = 0.036) and hypertensive disorders of pregnancy (14, 25.9% vs. 3, 6%; p = 0.003) were more frequent in the Pre-VOC group than in the VOC group. Finally, the VOC group was composed of 23 unvaccinated and 27 vaccinated pregnant women; no differences were observed in the sub-analysis focused on vaccination status. In summary, SARS-CoV-2-positive placentas were observed only in pregnancies infected by SARS-CoV-2 wildtype. Thus, placental SARS-CoV-2 presence could be influenced by SARS-CoV-2 variants, infection timing, or vaccination status. According to our data, the current risk of SARS-CoV-2 placental infection after maternal COVID disease during pregnancy should be updated.
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Avgeris, Margaritis, Panagiotis G. Adamopoulos, Aikaterini Galani, Marieta Xagorari, Dimitrios Gourgiotis, Ioannis P. Trougakos, Nikolaos Voulgaris, Meletios-Athanasios Dimopoulos, Nikolaos S. Thomaidis, and Andreas Scorilas. "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 (August 7, 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 reverse transcription and nested PCR-based amplification of targeted regions. Three-dimensional (3D) structure models were generated to examine the predicted structural modification caused by genomic variants. WBE of SARS-CoV-2 revealed to be assay dependent, and significantly improved sensitivity achieved by assay combination (94%) vs. single-assay screening (30%–60%). Targeted DNA-seq allowed the quantification of SARS-CoV-2 mutations/variants in wastewater, which agreed with COVID-19 patients’ sequencing data. A mutational analysis indicated the prevalence of D614G (S) and P323L (RdRP) variants, as well as of the Β.1.1.7/alpha variant of concern, in agreement with the frequency of Β.1.1.7/alpha variant in clinical samples of the same period of the third pandemic wave at the national level. Our assays provide an innovative cost-effective platform for real-time monitoring and early-identification of SARS-CoV-2 variants at community/population levels.
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Aboagye, Frank T., Lawrence Annison, Henry Kwadwo Hackman, Maame E. Acquah, Yvonne Ashong, Isaac Owusu-Frimpong, Bill C. Egyam, Sharon Annison, George Osei-Adjei, and Samuel Antwi-Baffour. "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 December 2022. Nasopharyngeal samples were collected from 268 consenting participants. Samples were subjected to nucleic acid extraction and followed by real-time polymerase chain reaction for the detection and quantification of SARS-CoV-2 RNA. SARS-CoV-2 positive samples were subsequently subjected to variant identification using rapid PCR. Findings. The prevalence of SARS-CoV-2 within the Accra Metropolis was 30.2%. The majority of the SARS-CoV-2 infection was diagnosed in females, participants aged 41–50 years, and symptomatic participants. Participants aged ≤10 years and females recorded the highest viral load while participants aged 41–50 years recorded the highest number of infections. The SARS-CoV-2 variants detected were Alpha (64.2%), Delta (22.2%), and Omicron (13.6%). Predictors of SARS-CoV-2 infection identified were chills, cough, headache, body weakness, sore throat, and dyspnoea in order of decreasing association with SARS-CoV-2 infection. There was a strong association between symptom status, gender, age, and SARS-CoV-2 infection. Conclusion. There was a high prevalence of SARS-CoV-2 within the Accra Metropolis postlockdown within the sampling period. The Alpha variant of SARS-CoV-2 is the predominant circulating variant, and persons presenting with symptoms are most likely to be diagnosed with COVID-19. Children aged ≤10 years serve as a reservoir for infection transmission.
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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 (March 31, 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 resulting in the rapid emergence of new variants with higher fitness and survival value. The recently emerged VOC, the omicron variant (B.1.1.529), was first reported from South African samples, and it has a large number of mutations some of which are concerning as per the preliminary evidence. Owing to the dynamism of mutations in the SARS-CoV-2 genome, we may expect many unexpected events as far as the emergence of variants, virulence, and transmissibility is concerned. However, as an evolutionary trade-off strategy, the virulence of SARS-CoV-2 might get reduced with an increase in the transmissibility to attain a wider host range. The intermingling of vaccinated and unvaccinated individuals provides the virus opportunity to amplify by infecting the unvaccinated individuals and causing breakthrough infections. Moreover, the prevalence of different variants of SARS-CoV-2 has been different in different geographic zones as far as the cases and causalities are concerned. Sustained viral surveillance and monitoring with region-wise variant-specific preventive strategies are required to prevent and contain the outbreak of emerging variants of SARS-CoV-2.
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Unselt, Desiree, Katherine Knudsen, Christopher Rounds, Janet Doolittle-Hall, Fernando Torres, Jennifer Sims, and Jennifer Mason. "Abstract 437: Characterization of SARS-CoV-2 using the Ion AmpliSeq SARS-CoV-2 research panel." Cancer Research 82, no. 12_Supplement (June 15, 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, this assay allows for accurate characterization of the dominant SARS-CoV-2 variant. This assay’s performance was analytically validated for the detection of mutations (substitutions, insertions, and deletions) in RNA derived from nasopharyngeal (NP) swabs. Method: The Ion AmpliSeq SARS-CoV-2 Research panel consists of two primer pair pools generating 237 amplicons specific to the SARS-CoV-2 virus. Reverse transcription of the RNA was performed using the SuperScript VILO cDNA Synthesis kit. Library preparation was then completed using the Ion AmpliSeq Library Kit Plus kit. The final library was quantified, normalized, pooled, and sequenced. Raw sequencing data was aligned to the AmpliSeq SARS-CoV-2 Research panel, using the MN908947.3 reference genome. Variants were called using the Torrent Variant Caller and annotated using the COVID19AnnotateSnpEff plugin. The reference-guided iterative assembler IRMA was used to produce a single consensus sequence consisting of the reference genome sequence modified to include sequence variations supported by the reads. The Pangolin COVID-19 lineage assigner software tool was used to assign SARS-CoV-2 lineage. Analytical validation was completed using controls (Twist Biosciences, BEI Resources, ATCC) and RNA derived from NP swabs. Accuracy and specificity were examined by evaluating the correctness of calling true negative variants compared to false positive and all other variant calls, respectively. Precision and limit of detection (LoD) were examined by evaluating the concordance of variants across replicate samples. Limit of Blank (LoB) was calculated as the 95th percentile of reads per amplicon in the negative samples. Results: Accuracy of base calling, specificity, and precision were 100% for SNVs, insertions, and deletions above 25% allele frequency. LoD was determined to be 576 viral copies/mL. LoB was determined to be 202 reads per amplicon. Pangolin lineage assignment was 100% for all samples. Conclusions: This panel accurately characterizes SARS-CoV-2 variants, allowing for accurate consensus sequence generation, mutation annotation, and lineage assignment. Citation Format: Desiree Unselt, Katherine Knudsen, Christopher Rounds, Janet Doolittle-Hall, Fernando Torres, Jennifer Sims, Jennifer Mason. Characterization of SARS-CoV-2 using the Ion AmpliSeq SARS-CoV-2 research panel [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 437.
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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 (August 16, 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 substitutions (S mutations), dominate the mutations found in other RNA viruses. The N mutation bias in the SARS-CoV2 proto-variants was found in the spike gene as well as several other genes. The analysis of the ratio of N to S mutations in general RNA viruses revealed that the probability that an RNA virus spontaneously evolves a proto-variant is between 1.5 × 10−9 and 2.7 × 10−26 under natural conditions. These results suggest that SARS-CoV-2 variants did not emerge via a canonical route.
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Naji, Hassan. "Notable Variants of SARS-CoV-2." European Journal of Medical and Health Sciences 3, no. 2 (March 20, 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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Shy, Cherng-Gueih, Jian-He Lu, Hui-Chen Lin, Min-Nan Hung, Hsiu-Chun Chang, Meng-Lun Lu, How-Ran Chao, Yao-Shen Chen, and Pi-Sheng Wang. "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 (January 27, 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 2021. Seventeen patients were infected by Delta-SARS-CoV-2 and 1 person died during the Pingtung outbreak. The Public Health Bureau of Pingtung County Government stopped the Delta-SARS-CoV-2 outbreak within 1 month through measures such as epidemic investigation, rapid gene sequencing, rapidly expanding isolation, expanded screening of the Delta-SARS-CoV-2 antigen for people who lived in regional villages, and indirect intervention, including rapid vaccination, short lockdown period, and travel restrictions. Indirect environmental factors, such as low levels of air pollution, tropic weather in the summer season, and rural areas might have accelerated the ability to control the Delta-SARS-CoV-2 spread. This successful experience might be recommended as a successful formula for the unvaccinated or insufficiently vaccinated regions.
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Zhao, Gan, Zhiyu Zhang, Yuan Ding, Jiawang Hou, Ying Liu, Mengying Zhang, Cheng Sui, 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 (February 22, 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, vaccine pipelines, and delivery, are keys to developing a next-generation COVID-19 vaccine. In this study, we designed several DNA constructs based on codon-optimized spike coding regions of several SARS-CoV-2 variants and analyzed their cross-reactive antibodies, including neutralizing antibodies, and cellular immune responses against several VOCs in C57BL/6 mice. The results revealed that different SARS-CoV-2 VOCs induced different cross-reactivity; pBeta, a DNA vaccine encoding the spike protein of the Beta variant, elicited broader cross-reactive neutralizing antibodies against other variants including the Omicron variants BA.1 and BA.4/5. This result demonstrates that the spike antigen from the Beta variant potentially serves as one of the antigens for multivalent vaccine design and development against variants of SARS-CoV-2.
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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 (August 24, 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 importance. In this study we introduce a Mass Spectrometry (MS)-based methodology for the diagnosis of SARS-CoV-2 in propagated in cell-culture. This methodology enables the universal identification of SARS-CoV-2, as well as variant-specific discrimination. The universal identification of SARS-CoV-2 is based on conserved markers shared by all variants, while the identification of specific variants relies on variant-specific markers. Determining a specific set of peptides for a given variant consists of a multistep procedure, starting with an in-silico search for variant-specific tryptic peptides, followed by a tryptic digest of a cell-cultured SARS-CoV-2 variant, and identification of these markers by HR-LC-MS/MS analysis. As a proof of concept, this approach was demonstrated for four representative VOCs compared to the wild-type Wuhan reference strain. For each variant, at least two unique markers, derived mainly from the spike (S) and nucleocapsid (N) viral proteins, were identified. This methodology is specific, rapid, easy to perform and inexpensive. Therefore, it can be applied as a diagnostic tool for pathogenic variants.
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Burki, Talha. "Understanding variants of SARS-CoV-2." Lancet 397, no. 10273 (February 2021): 462. http://dx.doi.org/10.1016/s0140-6736(21)00298-1.
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Choi, Jun Yong, and Davey M. Smith. "SARS-CoV-2 Variants of Concern." Yonsei Medical Journal 62, no. 11 (2021): 961. http://dx.doi.org/10.3349/ymj.2021.62.11.961.
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Vinson, Valda. "Defenses against SARS-CoV-2 variants." Science 373, no. 6556 (August 12, 2021): 754.2–754. http://dx.doi.org/10.1126/science.373.6556.754-b.
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Krause, Philip R., Thomas R. Fleming, Ira M. Longini, Richard Peto, Sylvie Briand, David L. Heymann, Valerie Beral, et al. "SARS-CoV-2 Variants and Vaccines." New England Journal of Medicine 385, no. 2 (July 8, 2021): 179–86. http://dx.doi.org/10.1056/nejmsr2105280.
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Ozverel, Cenk Serhan, Pinar Tulay, Mahmut Cerkez Ergoren, Emrah Guler, Buket Baddal, Kaya Suer, and Tamer Sanlidag. "SARS-CoV-2 Alpha Variant Infection of a Patient Immunized by Inactive Sinovac (CoronaVac) Vaccine." EuroBiotech Journal 6, no. 1 (January 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. However, there is no report showing the efficacy of these vaccines on these variants. This case study describes a thirty-eight-year-old male reported to be infected with SARS-CoV-2 alpha variant following two doses of inactive CoronaVac administration with a protective level of SARS-CoV-2 specific antibodies. The variant analysis of the virus reported to be positive for N501Y mutation.This is the first case in the literature demonstrating that inactive SARS-CoV-2 vaccine might have a lower efficacy on alpha variant.
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Asirwatham, Alison, Michelle Hillman, Lyba Khan, Lisa M. Sangermano, Katherine Leung, and Heidi K. Leftwich. "SARS-CoV-2 Variants in Pregnancy [ID 2683546]." Obstetrics & Gynecology 143, no. 5S (May 2024): 5S—6S. http://dx.doi.org/10.1097/01.aog.0001012916.05693.cc.
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INTRODUCTION: We examined the effect of infection with each of the most common SARS-CoV-2 variants during pregnancy on the development of preeclampsia. METHODS: This was an IRB-approved retrospective cohort study of patients at our academic hospital from January 1, 2019 to December 30, 2022. Primary outcomes were rates of preeclampsia among those with and without SARS-CoV-2 infection during pregnancy, specifically comparing the periods when the most common SARS-CoV-2 variants (Alpha, March 15 to June 21, 2021; Delta, June 21 to December 20, 2021; and Omicron, December 20, 2021 to December 30, 2022) were the most frequently diagnosed variant. The secondary outcome was characteristics of placental pathology. RESULTS: Six thousand three hundred fifty-eight charts were reviewed, 6,182 met inclusion criteria, and 657 tested positive for SARS-CoV-2 during pregnancy. There were 109 cases prior to the identification of the Alpha variant, 14 Alpha, 72 Delta, and 462 Omicron cases. All variants were associated with an increase in preeclampsia (P=.006). In adjusted models, the pre-Alpha infection was associated with a 2.12-fold increase in preeclampsia (P=.003), and Omicron infection was associated with 2.11-fold increase in severe preeclampsia (P=.01). Infections with Omicron and Delta were associated with an increase in placental intervillous thrombi (30.8% and 16.5% versus 12.5% in no infection; P=.014). Intervillous thrombi was seen 3.25 times more after Delta infection in adjusted models (P=.001). CONCLUSION: Adjusted models showed an increase in preeclampsia rates with pre-Alpha and severe preeclampsia with Omicron variant infections. Delta infection was associated with an increase in thrombotic vasculopathy within the placenta. These findings suggest differing levels of concern by viral variant and may help direct counseling should additional variants emerge.
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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 (June 1, 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 mRNA vaccines were stable at various temperatures for different time periods. Unlike SARS2-S (RBD-del) mRNA, SARS2-S (SARS-RBD) mRNA elicited effective T-cell responses and potent antibodies specific to both SARS-CoV-2 S and SARS-CoV RBD proteins. It induced strong neutralizing antibodies against pseudotyped SARS-CoV-2 and SARS-CoV infections and protected immunized mice from the challenge of the SARS-CoV-2 Omicron variant and SARS-CoV by significantly reducing the viral titers in the lungs after Omicron challenge and by completely preventing SARS-CoV-induced weight loss and death. SARS2-S (SARS-RBD)-immunized serum antibodies protected naïve mice from the SARS-CoV challenge, with its protective efficacy positively correlating with the neutralizing antibody titers. These findings indicate that this mRNA vaccine has the potential for development as an effective vaccine against current and future SARS-CoV-2 variants and SARS-CoV.
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Dao, Thi Loi, Van Thuan Hoang, Philippe Colson, Jean Christophe Lagier, Matthieu Million, Didier Raoult, Anthony Levasseur, and Philippe Gautret. "SARS-CoV-2 Infectivity and Severity of COVID-19 According to SARS-CoV-2 Variants: Current Evidence." Journal of Clinical Medicine 10, no. 12 (June 15, 2021): 2635. http://dx.doi.org/10.3390/jcm10122635.
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Background: We conducted this review to summarize the relation between viral mutation and infectivity of SARS-CoV-2 and also the severity of COVID-19 in vivo and in vitro. Method: Articles were identified through a literature search until 31 May 2021, in PubMed, Web of Science and Google Scholar. Results: Sixty-three studies were included. To date, most studies showed that the viral mutations, especially the D614G variant, correlate with a higher infectivity than the wild-type virus. However, the evidence of the association between viral mutation and severity of the disease is scant. A SARS-CoV-2 variant with a 382-nucleotide deletion was associated with less severe infection in patients. The 11,083G > U mutation was significantly associated with asymptomatic patients. By contrast, ORF1ab 4715L and S protein 614G variants were significantly more frequent in patients from countries where high fatality rates were also reported. The current evidence showed that variants of concern have led to increased infectivity and deteriorating epidemiological situations. However, the relation between this variant and severity of COVID-19 infection was contradictory. Conclusion: The COVID-19 pandemic continues to spread worldwide. It is necessary to anticipate large clinical cohorts to evaluate the virulence and transmissibility of SARS-CoV-2 mutants.
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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 (April 22, 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, which has mutated to evade acquired immunity, SARS-CoV-2 appeared to mutate to target individuals who have not been previously infected. The Omicron variant, which emerged in late 2021, demonstrates significant mutations that set it apart from previous variants. The rapid mutation rate of SARS-CoV-2 has now reached a level comparable to 30 years of influenza variation. The most recent variant, JN.1, exhibits a discernible trajectory of change distinct from previous Omicron variants.
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Alexiev, Ivailo, Ivan Ivanov, Marta Giovanetti, Eleonora Cella, Ivan Stoikov, Deyan Donchev, Lyubomira Grigorova, 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 (August 9, 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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Xing, Lixiao, Xinfeng Xu, Wei Xu, Zezhong Liu, Xin Shen, Jie Zhou, Ling Xu, et al. "A Five-Helix-Based SARS-CoV-2 Fusion Inhibitor Targeting Heptad Repeat 2 Domain against SARS-CoV-2 and Its Variants of Concern." Viruses 14, no. 3 (March 13, 2022): 597. http://dx.doi.org/10.3390/v14030597.
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The prolonged duration of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic has resulted in the continuous emergence of variants of concern (VOC, e.g., Omicron) and variants of interest (VOI, e.g., Lambda). These variants have challenged the protective efficacy of current COVID-19 vaccines, thus calling for the development of novel therapeutics against SARS-CoV-2 and its VOCs. Here, we constructed a novel fusion inhibitor-based recombinant protein, denoted as 5-Helix, consisting of three heptad repeat 1 (HR1) and two heptad repeat 2 (HR2) fragments. The 5-Helix interacted with the HR2 domain of the viral S2 subunit, the most conserved region in spike (S) protein, to block homologous six-helix bundle (6-HB) formation between viral HR1 and HR2 domains and, hence, viral S-mediated cell–cell fusion. The 5-Helix potently inhibited infection by pseudotyped SARS-CoV-2 and its VOCs, including Delta and Omicron variants. The 5-Helix also inhibited infection by authentic SARS-CoV-2 wild-type (nCoV-SH01) strain and its Delta variant. Collectively, our findings suggest that 5-Helix can be further developed as either a therapeutic or prophylactic to treat and prevent infection by SARS-CoV-2 and its variants.
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Van Dusen, John, Haley LeBlanc, Nicholas Nastasi, Jenny Panescu, Austin Shamblin, Jacob W. Smith, Michael G. Sovic, et al. "Identification of SARS-CoV-2 variants in indoor dust." PLOS ONE 19, no. 2 (February 9, 2024): e0297172. http://dx.doi.org/10.1371/journal.pone.0297172.
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Environmental surveillance of pathogens underlying infectious disease is critical to ensure public health. Recent efforts to track SARS-CoV-2 have utilized wastewater sampling to infer community trends in viral abundance and variant composition. Indoor dust has also been used for building-level inferences, though to date no sequencing data providing variant-scale resolution have been reported from dust samples, and strategies to monitor circulating variants in dust are needed to help inform public health decisions. In this study, we demonstrate that SARS-CoV-2 lineages can be detected and sequenced from indoor bulk dust samples. We collected 93 vacuum bags from April 2021 to March 2022 from buildings on The Ohio State University’s (OSU) Columbus campus, and the dust was used to develop and apply an amplicon-based whole-genome sequencing protocol to identify the variants present and estimate their relative abundances. Three variants of concern were detected in the dust: Alpha, Delta, and Omicron. Alpha was found in our earliest sample in April 2021 with an estimated frequency of 100%. Delta was the primary variant present from October of 2021 to January 2022, with an average estimated frequency of 91% (±1.3%). Omicron became the primary variant in January 2022 and was the dominant strain in circulation through March with an estimated frequency of 87% (±3.2%). The detection of these variants on OSU’s campus correlates with the circulation of these variants in the surrounding population (Delta p<0.0001 and Omicron p = 0.02). Overall, these results support the hypothesis that dust can be used to track COVID-19 variants in buildings.
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Cocherie, Théophile, Karen Zafilaza, Valentin Leducq, Stéphane Marot, Vincent Calvez, Anne-Geneviève Marcelin, and Eve Todesco. "Epidemiology and Characteristics of SARS-CoV-2 Variants of Concern: The Impacts of the Spike Mutations." Microorganisms 11, no. 1 (December 22, 2022): 30. http://dx.doi.org/10.3390/microorganisms11010030.
Full textAbstract:
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 substitution. These variants were replaced by the Delta variant in summer 2021, carrying unique mutations like the L452R substitution and associated with higher virulence. It was in turn quickly replaced by the Omicron variant at the end of 2021, which has predominated since then, characterized by its large number of mutations. The successive appearance of variants of concern showed a dynamic evolution of SARS-CoV-2 through the selection and accumulation of mutations. This has not only allowed progressive improvement of the transmissibility of SARS-CoV-2, but has also participated in a better immune escape of the virus. This review brings together acquired knowledge about SARS-CoV-2 variants of concern and the impacts of the Spike mutations.
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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 (June 17, 2022): 221–26. http://dx.doi.org/10.4314/ajcem.v23i3.1.
Full textAbstract:
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 SARS-CoV-2 variants. To review the evolution of these variants, we searched different online database sources using keywords such as “source of SARS-CoV-2”, “SARS-CoV-2 origin”, “evolution of SARS-CoV-2”, “SARS-CoV-2 variants”, “variants of concern”, “variants of interest”, and “variants of high consequence”. This was to enable us give a good report about the various variants of SARS-CoV-2 that have emerged so far, and the public health challenges posed by them.
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Boshah, Hattan, Faris Samkari, Alexander U. Valle-Pérez, Sarah M. Alsawaf, Ali H. Aldoukhi, Panayiotis Bilalis, Salwa A. Alshehri, Hepi H. Susapto, and Charlotte A. E. Hauser. "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.
Full textAbstract:
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 synthesized two ACE2-derived peptides, P1 and P25, to target and potentially inhibit SARS-CoV-2 cell entry. These peptides were evaluated in vitro using pseudoviruses that contained the SARS-CoV-2 original spike protein, the Delta-mutated spike protein, or the Omicron spike protein. An in silico investigation was also done for these peptides to evaluate the interaction of the synthesized peptides and the SARS-CoV-2 variants. The P25 peptide showed a promising inhibition potency against the tested pseudoviruses and an even higher inhibition against the Omicron variant. The IC50 of the Omicron variant was 60.8 μM, while the IC50s of the SARS-CoV-2 original strain and the Delta variant were 455.2 μM and 546.4 μM, respectively. The in silico experiments also showed that the amino acid composition design and structure of P25 boosted the interaction with the spike protein. These findings suggest that ACE2-derived peptides, such as P25, have the potential to inhibit SARS-CoV-2 cell entry in vitro. However, further in vivo studies are needed to confirm their therapeutic efficacy against emerging variants.
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Venkatakrishnan, A. J., Praveen Anand, Patrick J. Lenehan, Rohit Suratekar, Bharathwaj Raghunathan, Michiel J. M. Niesen, and Venky Soundararajan. "On the Origins of Omicron’s Unique Spike Gene Insertion." Vaccines 10, no. 9 (September 9, 2022): 1509. http://dx.doi.org/10.3390/vaccines10091509.
Full textAbstract:
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 lineages constituting ~5.8 million SARS-CoV-2 genomes. Omicron’s Spike protein harbors 26 amino acid mutations (23 substitutions, 2 deletions, and 1 insertion) that are distinct compared to other variants of concern. While the substitution and deletion mutations appeared in previous SARS-CoV-2 lineages, the insertion mutation (ins214EPE) was not previously observed in any other SARS-CoV-2 lineage. Here, we consider and discuss various mechanisms through which the nucleotide sequence encoding for ins214EPE could have been acquired, including local duplication, polymerase slippage, and template switching. Although we are not able to definitively determine the mechanism, we highlight the plausibility of template switching. Analysis of the homology of the inserted nucleotide sequence and flanking regions suggests that this template-switching event could have involved the genomes of SARS-CoV-2 variants (e.g., the B.1.1 strain), other human coronaviruses that infect the same host cells as SARS-CoV-2 (e.g., HCoV-OC43 or HCoV-229E), or a human transcript expressed in a host cell that was infected by the Omicron precursor.
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MONETTI, M., B. POZZETTO, C. PLOTTON, and X. GOCKO. "LE VIRUS SARS-COV-2 ET SES VARIANTS." EXERCER 32, no. 171 (March 1, 2021): 118–27. http://dx.doi.org/10.56746/exercer.2021.171.118.
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En ce mois de février 2021, la pandémie de Covid-19 pose de nouvelles questions aux soignants et aux usagers de la santé. Les principales questions concernent les variants du Sars-CoV-2. Que sait-on du Sars-CoV-2 ? Qu’est-ce qu’un variant ? Ces variants sont-ils plus transmissibles et plus dangereux ? Les patients avec un antécédent de Covid-19 peuvent-ils se réinfecter ? Les trois vaccins actuellement disponibles en France (2 à ARNm et 1 à vecteur adénovirus non réplicatif) sont-ils efficaces sur ces variants ? Cette revue narrative de la littérature fournit des éléments de réponse à ces questions prégnantes en février 2021.
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Sammartino, Josè Camilla, Irene Cassaniti, Alessandro Ferrari, Federica Giardina, Guglielmo Ferrari, Federica Zavaglio, Stefania Paolucci, 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 (April 29, 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 measured. Results were compared with those obtained from unvaccinated COVID-19 recovered patients. Overall, a better SARS-CoV-2 NT Abs response was observed in recovered vaccinated subjects after three doses of the vaccine when compared to unvaccinated patients and vaccinated subjects with only two doses. Additionally, the lowest level of response was observed against the Omicron variant. In conclusion, third doses of BNT162b2 vaccine seems to elicit a sustained response against the large majority of variants.
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Liang, Kang-Hao, Pao-Yin Chiang, Shih-Han Ko, Yu-Chi Chou, Ruei-Min Lu, Hsiu-Ting Lin, Wan-Yu Chen, et al. "Antibody cocktail effective against variants of SARS-CoV-2." Journal of Biomedical Science 28, no. 1 (November 23, 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 hamster models as prophylactic and post-infection treatments. Results The tested RBD-chAbs, except RBD-chAb-25, maintained binding ability to spike proteins from SARS-CoV-2 variants. However, only RBD-chAb-45 and -51 retained neutralizing activities; RBD-chAb-1, -15, -25 and -28 exhibited diminished neutralization for all SARS-CoV-2 variants. Notably, several cocktails of our antibodies showed low IC50 values (3.35–27.06 ng/ml) against the SARS-CoV-2 variant pseudoviruses including United Kingdom variant B.1.1.7 (Alpha), South Africa variant B.1.351 (Beta), Brazil variant P1 (Gamma), California variant B.1.429 (Epsilon), New York variant B.1.526 (Iota), and India variants, B.1.617.1 (Kappa) and B.1.617.2 (Delta). RBD-chAb-45, and -51 showed PRNT50 values 4.93–37.54 ng/ml when used as single treatments or in combination with RBD-chAb-15 or -28, according to plaque assays with authentic Alpha, Gamma and Delta SARS-CoV-2 variants. Furthermore, the antibody cocktail of RBD-chAb-15 and -45 exhibited potent prophylactic and therapeutic effects in Delta SARS-CoV-2 variant-infected hamsters. Conclusions The cocktail of RBD-chAbs exhibited potent neutralizing activities against SARS-CoV-2 variants. These antibody cocktails are highly promising candidate tools for controlling new SARS-CoV-2 variants, including Delta.
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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 (October 27, 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 and E484K as variant-specific SNPs of the S gene and RdRP as a SARS-CoV-2-specific gene, using the Novaplex SARS-CoV-2 variants assay kit series. For three SARS-CoV-2 lineages (B.1.617.2, B.1.1.7 and R.1), one strain per lineage was used. Variant-specific SNPs of the S gene were analysed using the Novaplex SARS-CoV-2 variants I assay and Novaplex SARS-CoV-2 variants II assay kits. Validation confirmed the LODs of the variant kits. The LOD for each target variant-specific SNP and RdRP was five RNA copies per reaction. The Novaplex SARS-CoV-2 variants assay kit series performs well and the LOD for SARS-CoV-2 detection and variant-specific SNP detection are consistent. The kits are suitable for use as routine laboratory tests for SARS-CoV-2 and variant-specific SNP detection in a single step, saving time and labour.
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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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