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SARS-CoV-2, responsible for the global COVID-19 pandemic, has undergone significant genetic changes, leading to various variants impacting transmissibility, severity, and vaccine efficacy. The methodology involved evaluating SARS-CoV-2 variants designated by WHO as Variants of Interest (VOIs) and Variants Under Monitoring (VUMs). Several noteworthy mutations including G446S, K417N, T478K, E484A, N501Y, and Y505H exhibit a strong pattern of convergent evolution across all these variants, particularly at antigenic sites within the spike protein. Conformational epitopes mapping and antigenicity shift analyses implicated epitope changes which were compared for therapeutic purposes. VUMs BA.2.86 and XBB.2.3 show significant antigenicity changes and epitope dynamics, correlating with high root mean square deviation values and epitope expansions or contractions. Nonsynonymous mutations are predominant in all variants, suggesting functional changes affecting transmissibility and immune evasion. VOIs XBB.1.5, BA.2.86, and CH.1.1 show high solvent-accessible surface area and radius of gyration, indicating structural expansion and increased epitope availability. In contrast, stable VOI EG.5.1 displays minimal structural changes and moderate epitope expansions. We evaluated two classes of antibodies for their effectiveness in neutralizing SARS-CoV-2 variants. Antibodies CC12.1 and P4A1 from Class I, alongside CV07-250, P5A-2G9, and MW05 from Class II, display strong binding across multiple variants, indicating broad neutralizing capabilities. Specifically, P4A1 shows the highest affinity for EG.5 and EG.5.1, while MW05 exhibits the strongest binding to XBB.1.5, CH.1.1, and XBB.2.3, highlighting their potent neutralization potential. This study aims to elucidate epitope variations in evolving SARS-CoV-2 strains, offering critical insights for developing targeted interventions against current challenges posed by the virus., Competing Interests: Declaration of competing interest The authors declare no conflict of interest., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Background: The COVID-19 pandemic had a major impact on indigenous populations. Understanding the viral dynamics within this population is essential to create targeted protection measures., Methods: A total of 204 SARS-CoV-2 positive samples collected between May 2020 and November 2021 from an indigenous area in Mato Grosso do Sul (MS), Midwestern Brazil, were screened. Samples were submitted to whole genome sequencing using the Nanopore sequencing platform. Clinical, demographic, and phylogenetic data were analyzed., Results: We found the co-circulation of six main SARS-CoV-2 lineages in the indigenous population, with the Zeta lineage being the most prevalent (27.66%), followed by B.1.1 (an ancestral strain) (20.21%), Gamma (14.36%) and Delta (13.83%). Other lineages represent 45.74% of the total. Our phylogenetic reconstruction indicates that multiple introduction events of different SARS-CoV-2 lineages occurred in the indigenous villages in MS. The estimated indigenous population mortality rate was 1.47%. Regarding the ethnicity of our cohort, 64.82% belong to the Guarani ethnicity, while 33.16% belong to the Terena ethnicity, with a slightly higher prevalence of males (53.43%) among females. Other ethnicities represent 2.01%. We also observed that almost all patients (89.55%) presented signs and symptoms related to COVID-19, being the most prevalent cough, fever, sore throat, and headache., Discussion: Our results revealed that multiple independent SARS-CoV-2 introduction events had occurred through time, probably due to indigenous mobility, since the villages studied here are close to urban areas in MS. The mortality rate was slightly below of the estimation for the state in the period studied, which we believe could be related to the small number of samples evaluated, the underreporting of cases and deaths among this population, and the inconsistency of secondary data available for this study., Conclusion: In this study, we showed the circulation of multiple SARS-CoV-2 variants in this population, which should be isolated and protected as they belong to the most fragile group due to their socioeconomic and cultural disparities. We reinforce the need for constant genomic surveillance to monitor and prevent the spread of new emerging viruses and to better understand the viral dynamics in these populations, making it possible to direct specific actions., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 de Oliveira, de Rezende, Navarini, Marchioro, Torres, Croda, Croda, Gonçalves, Xavier, de Castro, Lima, Iani, Adelino, Iani, Aburjaile, Ferraz Demarchi, Taira, Zardin, Fonseca, Giovanetti, Andrews, Alcantara and Simionatto.)

The severe acute respiratory syndrome coronavirus (SARS-CoV)-2 responsible for the global COVID-19 pandemic has caused almost 760 million confirmed cases and 7 million deaths worldwide, as of end-February 2023. Since the beginning of the first COVID-19 case, several virus variants have emerged: Alpha (B1.1.7), Beta (B135.1), Gamma (P.1), Delta (B.1.617.2) and then Omicron (B.1.1.529) and its sublineages. All variants have diversified in transmissibility, virulence, and pathogenicity. All the newly emerging SARS-CoV-2 variants appear to contain some similar mutations associated with greater "evasiveness" of the virus to immune defences. From early 2022 onward, several Omicron subvariants named BA.1, BA.2, BA.3, BA.4, and BA.5, with comparable mutation forms, have followed. After the wave of contagions caused by Omicron BA.5, a new Indian variant named Centaurus BA.2.75 and its new subvariant BA.2.75.2, a second-generation evolution of the Omicron variant BA.2, have recently been identified. From early evidence, it appears that this new variant has higher affinity for the cell entry receptor ACE-2, making it potentially able to spread very fast. According to the latest studies, the BA.2.75.2 variant may be able to evade more antibodies in the bloodstream generated by vaccination or previous infection, and it may be more resistant to antiviral and monoclonal antibody drug treatments. In this manuscript, the authors highlight and describe the latest evidences and critical issues have emerged on the new SARS-CoV-2 variants., (© 2023. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with increased transmissibility, virulence and immune escape abilities have heavily altered the COVID-19 pandemic's course. Deciphering local and global transmission patterns of those variants is thus key in building a profound understanding of the virus' spread around the globe. In the present study, we investigate SARS-CoV-2 variant epidemiology in Côte d'Ivoire, Western sub-Saharan Africa. We therefore generated 234 full SARS-CoV-2 genomes stemming from Central and Northern Côte d'Ivoire. Covering the first and second pandemic wave the country had been facing, we identified 20 viral lineages and showed that in Côte d'Ivoire the second pandemic wave in 2021 was driven by the spread of the Alpha (B.1.1.7) and Eta (B.1.525) variant. Our analyses are consistent with a limited number of international introductions of Alpha and Eta into Côte d'Ivoire, and those introduction events mostly stemmed from within the West African subregion. This suggests that subregional travel to Côte d'Ivoire had more impact on local pandemic waves than direct intercontinental travel., (© 2023. The Author(s).)

The epidemiological surveillance of SARS-CoV-2 by means of whole-genome sequencing has revealed the emergence and co-existence of multiple viral lineages or subtypes throughout the world. Moreover, it has been shown that several subtypes of this virus display particular phenotypes, such as increased transmissibility or reduced susceptibility to neutralizing antibodies, leading to the denomination of Variants of Interest (VOI) or Variants of Concern (VOC). Thus, subtyping of SARS-CoV-2 is a crucial step for the surveillance of this pathogen. Here, we present Covidex, an open-source, alignment-free machine learning subtyping tool. It is a shiny web app that allows an ultra-fast and accurate classification of SARS-CoV-2 genome sequences into the three most used nomenclature systems (GISAID, Nextstrain, Pango lineages). It also categorizes input sequences as VOI or VOC, according to current definitions. The program is cross-platform compatible and it is available via Source-Forge https://sourceforge.net/projects/covidex or via the web application http://covidex.unlu.edu.ar., (Copyright © 2022 The Authors. Published by Elsevier B.V. All rights reserved.)

Background: COVID-19 has posed unforeseen circumstances and throttled major economies worldwide. India has witnessed two waves affecting around 31 million people representing 16% of the cases globally. To date, the epidemic waves have not been comprehensively investigated to understand pandemic progress in India., Objective: Here, we aim for pan Indian cross-sectional evolutionary analysis since inception of SARS-CoV-2., Methods: High quality genomes, along with their collection date till 26th July 2021, were downloaded. Whole genome-based phylogeny was obtained. Further, the mutational analysis was performed using SARS-CoV-2 first reported from Wuhan (NC&#95;045512.2) as reference., Results: Based on reported cases and mutation rates, we could divide the Indian epidemic into seven phases. The average mutation rate for the pre-first wave was <11, which elevated to 17 in the first wave and doubled in the second wave (∼34). In accordance with mutation rate, VOCs and VOIs started appearing in the first wave (1.5%), which dominated the second (∼96%) and post-second wave (100%). Nation-wide mutational analysis depicted >0.5 million mutation events with four major mutations in >19,300 genomes, including two mutations in coding (spike (D614G), and NSP 12b (P314L) of rdrp), one silent mutation (NSP3 F106F) and one extragenic mutation (5' UTR 241)., Conclusion: Whole genome-based phylogeny could demarcate post-first wave isolates from previous ones by point of diversification leading to incidences of VOCs and VOIs in India. Such analysis is crucial in the timely management of pandemic., (Copyright © 2021. Published by Elsevier B.V.)

Background: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) circulates in the world and acquires mutations during evolution. To identify the new emergent variants, the surveillance of the variants of concern (VOC) and variants of interest (VOI) is ongoing. This study aimed to determine how the transition of viral lineage occurred by stationary genome analysis in Yamanashi, Japan., Methods: We performed the whole genome sequencing using SARS-CoV-2 positive samples collected from February 2020 to the end of June 2021. Viral lineage was defined by the Phylogenetic Assignment of Named Global Outbreak (PANGO) lineages., Results: We successfully obtained 325 viral genome sequences and the number of analyzed samples accounted for 15.4% of the total 2109 COVID-19 patients identified in our district. We identified 13 types of viral lineages including R.1, P.1, B.1.1.7 (Alpha) and B.1.617.2 (Delta). These virus lineages had distinct periods of expansion and decline. After the emerging of the R.1 lineage harboring E484K variant (designated VOI in Japan), the prevalent B.1.1.214 lineage were no longer identified. The R.1 lineages were temporarily prevalent afterwards, but the influx of B.1.1.7 lineage (designated VOC) led to a decline in R.1. Currently, B.1.1.7 has become dominant after mid-April 2021., Conclusion: We clearly elucidated the transition and replacement of viral lineage by the community-based analysis. The virus completely replaced by more infectious lineages, therefore, it will be necessary to continue to monitor the VOC and VOI., (Copyright © 2021 Elsevier B.V. All rights reserved.)

Vaccines represent one of the most impactful public health advances in human history, playing a fundamental role in reducing the transmission and, in some cases, eliminating infectious diseases. Since the sudden appearance of the SARS-CoV-2 virus and the onset of the global health emergency, several vaccines have been designed and licensed to address the COVID-19 pandemic in 185 countries around the world. It is therefore important to be aware of the different types of vaccines available and the facts regarding their efficacy and safety. The World Health Organization (WHO) reported as of November 8, 2022, 12,885,748,541 doses of COVID-19 vaccines administered worldwide, while, in Mexico, the secretary of health reported as of December 23, 2022, 227,341,091 doses of COVID-19 vaccines. As more vaccines are approved, it is important to track data on vaccination efforts in Mexico and discuss the need to incorporate effective preparedness and response mechanisms that include innovative vaccine production platforms in our country. The objective of this manuscript is to present to the reader the current vaccines approved against COVID-19, the variants of interest and concern identified by WHO, and to discuss the implications regarding the emergence of the new variants on the efficacy and safety of licensed vaccines.

On 5 May 2023, WHO declared the end of coronavirus disease 2019 (COVID-19) as a public health emergency of international concern. However, the risk of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants causing rapid and high surges in cases and deaths remained. In Malaysia, five COVID-19 waves during the pandemic phase were well characterized, but similar studies focusing on the endemic phase were lacking. Hence, we retrieved 14,965 SARS-CoV-2 genomic sequences from the GISAID EpiCoV database for clade, lineage, and phylogenetic analysis in order to provide an insight into the population dynamics of SARS-CoV-2 that circulated in Malaysia from June 2022 to April 2023. The dominance of the Omicron variants was observed, and two new waves of infections driven by BA.5.2 and XBB.1, respectively, were detected. Data as of April 2023 also pointed to a possible eighth wave driven by XBB.1.9. Although new variants associated with higher transmissibility were behind the multiple surges, these subsequent waves had lower intensities as compared to the fourth and fifth waves. The on-going circulation and evolution of SARS-CoV-2 mean that COVID-19 still poses a serious threat, necessitating active genomic surveillance for early warning of potential new variants of concern. [ABSTRACT FROM AUTHOR]

Like most of the RNA viruses, SARS-CoV-2 continuously mutates. Although many mutations have an insignificant impact on the virus properties, mutations in the surface protein, especially those in the receptor-binding domain, may lead to immune or vaccine escape variants, or altered binding activities to both the cell receptor and the drugs targeting such a protein. The current study intended to assess the ability of different variants of interest (VOIs) and variants of concern (VOCs) of SARS-CoV-2 for their affinities of binding to different repurposed drugs. Seven FDA approved drugs, namely, camostat, nafamostat mesylate, fenofibrate, umifenovir, nelfinavir, cefoperazone and ceftazidime, were selected based on their reported in vitro and clinical activities against SARA-CoV-2. The S1 protein subunit from eleven different variants, including the latest highly contiguous omicron variant, were used as targets for the docking study. The docking results revealed that all tested drugs possess moderate to high binding energies to the receptor-binding domain (RBD) of the S1 protein for all different variants. Cefoperazone was found to possess the highest binding energy to the RBD of the S1 protein of all the eleven variants. Ceftazidime was the second-best drug in terms of binding affinity towards the S1 RBD of the investigated variants. On the other hand, fenofibrate showed the least binding affinity towards the RBD of the S1 protein of all eleven variants. The binding affinities of anti-spike drugs varied among different variants. Most of the interacting amino acid residues of the receptor fall within the RBD (438–506).

Rationale: SARS-CoV-2 has been identified as a highly infective and contagious viral infection. The SARS-CoV-2 pandemic has been spread worldwide and affected more than 210 countries. Globally, the fast spread of novel SARS-CoV-2 variants has been mostly attributed to international travel. Patient concerns: We are reporting the genomic evidence of SARS-CoV-2 Eta VOI among two international travelers. Both travelers were males from Nigeria aged 24 and 34 years and both were asymptomatic. Diagnosis: The nasopharyngeal swab samples were in both travelers positive by real-time RT-PCR followed by COVIDSeq-NGS. Interventions: Paracetamol 3 times daily for 5 days. Outcomes: Patient recovered completely within 10 days and discharged after 14 days of quarantine duration. Lessons: This report highlights genomic variation of SARS-CoV-2 among the travelers. For managing the present health crisis, molecular identification of viral variants present in different geographical locations will be very helpful.

Rationale: SARS-CoV-2 has been identified as a highly infective and contagious viral infection. The SARS-CoV-2 pandemic has been spread worldwide and affected more than 210 countries. Globally, the fast spread of novel SARS-CoV-2 variants has been mostly attributed to international travel. Patient concerns: We are reporting the genomic evidence of SARSCoV-2 Eta VOI among two international travelers. Both travelers were males from Nigeria aged 24 and 34 years and both were asymptomatic. Diagnosis: The nasopharyngeal swab samples were in both travelers positive by real-time RT-PCR followed by COVIDSeq-NGS. Interventions: Paracetamol 3 times daily for 5 days. Outcomes: Patient recovered completely within 10 days and discharged after 14 days of quarantine duration. Lessons: This report highlights genomic variation of SARSCoV-2 among the travelers. For managing the present health crisis, molecular identification of viral variants present in different geographical locations will be very helpful. [ABSTRACT FROM AUTHOR]

Over the two years that we have been experiencing the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) pandemic, our challenges have been the race to develop vaccines and the difficulties in fighting against new variants due to the rapid ability of the virus to evolve. In this sense, different organizations have identified and classified the different variants that have been emerging, distinguishing between variants of concern (VOC), variants of interest (VOI), or variants under monitoring (VUM). The following review aims to describe the latest updates focusing on VOC and already de-escalated variants, as well as to describe the impact these have had on the global situation. Understanding the intrinsic properties of SARS-CoV-2 and its interaction with the immune system and vaccination is essential to make out the underlying mechanisms that have led to the appearance of these variants, helping to determine the next steps for better public management of this pandemic. [ABSTRACT FROM AUTHOR]

In addition to the rapid, global spread of SARS-CoV-2, new and comparatively more contagious variants are of considerable concern. These emerging mutations have become a threat to the global public health, creating COVID-19 surges in different countries. However, information on these emerging variants is limited and scattered. In this review, we discuss new variants that have emerged worldwide and identify several variants of concern, such as B.1.1.7, B.1.351, P.1, B.1.617.2 and B.1.1.529, and their basic characteristics. Other significant variants such as C.37, B.1.621, B.1.525, B.1.526, AZ.5, C.1.2, and B.1.617.1 are also discussed. This review highlights the clinical characteristics of these variants, including transmissibility, pathogenicity, susceptible population, and re-infectivity. It provides the latest information on the recent variants of SARS-CoV-2. The summary of this information will help researchers formulate reasonable strategies to curb the ongoing COVID-19 pandemic. [ABSTRACT FROM AUTHOR]