The Omicron variant of concern: The genomics, diagnostics, and clinical characteristics in children

Setiabudi, Djatnika; Sribudiani, Yunia; Hermawan, Kartika; Andriyoko, Basti; Nataprawira, Heda Melinda

doi:10.3389/fped.2022.898463

Cited by 26 publications

(30 citation statements)

References 55 publications

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“…Like other RNA viruses, SARS-CoV-2 continuously mutates, resulting in the emergence of SARS-CoV-2 variants, which may have different pathological effects [ 74 ]. The variants B.1.617.2 (Delta), B.1.466.2, B.1.470, B.1.1.7 (Alfa), B.1.351 (Beta), P.1 (Gamma), P.2 (Zeta), and B.1.1.529 (Omicron) are among the most notable SARS-CoV-2 variants due to their potential to enhance biological threats [ 75 , 76 , 77 , 78 ]. Four mutations (N501Y, 69-70del (69/70 deletion), K417N, and E484K) in the spike protein may be linked to the potential biological effects of some of these variants.…”

Section: Detection and Quantification Of Sars-cov-2mentioning

confidence: 99%

Real-Time Polymerase Chain Reaction: Current Techniques, Applications, and Role in COVID-19 Diagnosis

Artika

Dewi

Nainggolan

et al. 2022

Genes

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Successful detection of the first SARS-CoV-2 cases using the real-time polymerase chain reaction (real-time PCR) method reflects the power and usefulness of this technique. Real-time PCR is a variation of the PCR assay to allow monitoring of the PCR progress in actual time. PCR itself is a molecular process used to enzymatically synthesize copies in multiple amounts of a selected DNA region for various purposes. Real-time PCR is currently one of the most powerful molecular approaches and is widely used in biological sciences and medicine because it is quantitative, accurate, sensitive, and rapid. Current applications of real-time PCR include gene expression analysis, mutation detection, detection and quantification of pathogens, detection of genetically modified organisms, detection of allergens, monitoring of microbial degradation, species identification, and determination of parasite fitness. The technique has been used as a gold standard for COVID-19 diagnosis. Modifications of the standard real-time PCR methods have also been developed for particular applications. This review aims to provide an overview of the current applications of the real-time PCR technique, including its role in detecting emerging viruses such as SARS-CoV-2.

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Section: Detection and Quantification Of Sars-cov-2mentioning

confidence: 99%

Real-Time Polymerase Chain Reaction: Current Techniques, Applications, and Role in COVID-19 Diagnosis

Artika

Dewi

Nainggolan

et al. 2022

Genes

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“…All the Omicron subvariants share eleven common mutations in the RBD of the spike protein, which is responsible for enhanced transmission, evasion, antibody neutralization, and RNA expression ( 76 ). Omicron variant can evade neutralizing antibody (NA) and weaken existing COVID-19 vaccine protection, but vaccine boosters can boost immunity ( 77 ) and improve the efficacy by 12-35 fold ( 78 ). However, most of the neutralizing monoclonal antibodies which are approved by the FDA for the treatment of SARS‐CoV‐2 variants, are ineffective against the Omicron variant except for Sotrovimab, and recent studies revealed that the Omicron BA.2 is also resistant to Sotrovimab ( 79 ).…”

Section: Discussionmentioning

confidence: 99%

Uncovering the information immunology journals transmitted for COVID-19: A bibliometric and visualization analysis

et al. 2022

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BackgroundSince the global epidemic of the coronavirus disease 2019 (COVID-19), a large number of immunological studies related to COVID-19 have been published in various immunology journals. However, the results from these studies were discrete, and no study summarized the important immunological information about COVID-19 released by these immunology journals. This study aimed to comprehensively summarize the knowledge structure and research hotspots of COVID-19 published in major immunology journals through bibliometrics.MethodsPublications on COVID-19 in major immunology journals were obtained from the Web of Science Core Collection. CiteSpace, VOSviewer, and R-bibliometrix were comprehensively used for bibliometric and visual analysis.Results1,331 and 5,000 publications of 10 journals with high impact factors and 10 journals with the most papers were included, respectively. The USA, China, England, and Italy made the most significant contributions to these papers. University College London, National Institute of Allergy and Infectious Diseases, Harvard Medical School, University California San Diego, and University of Pennsylvania played a central role in international cooperation in the immunology research field of COVID-19. Yuen Kwok Yung was the most important author in terms of the number of publications and citations, and the H-index. CLINICAL INFECTIOUS DISEASES and FRONTIERS IN IMMUNOLOGY were the most essential immunology journals. These immunology journals mostly focused on the following topics: “Delta/Omicron variants”, “cytokine storm”, “neutralization/neutralizing antibody”, “T cell”, “BNT162b2”, “mRNA vaccine”, “vaccine effectiveness/safety”, and “long COVID”.ConclusionThis study systematically uncovered a holistic picture of the current research on COVID-19 published in major immunology journals from the perspective of bibliometrics, which will provide a reference for future research in this field.

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“…It was found that BA.3 has 34 mutations, including R216, which is a unique mutation. Further, compared to BA.1, BA.3 showed a higher capability to transmit among people [12]. Our literature review will thoroughly explain the current state of Omicron emergence, particularly by comparing different omicron subvariants, including BA.2, BA.1, and BA.3.…”

Section: N Introductionmentioning

confidence: 99%

The emergence of SARS-CoV-2 Omicron subvariants: current situation and future trends

et al. 2022

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The SARS-CoV-2 Omicron variant (B.1.1.529) has been the most recent variant of concern (VOC) established by the World Health Organization (WHO). Because of its greater infectivity and immune evasion, this variant quickly became the dominant type of circulating SARS-CoV-2 worldwide. Our literature review thoroughly explains the current state of Omicron emergence, particularly by comparing different omicron subvariants, including BA.2, BA.1, and BA.3. Such elaboration would be based on structural variations, mutations, clinical manifestation, transmissibility, pathogenicity, and vaccination effectiveness. The most notable difference between the three subvariants is the insufficiency of deletion (Δ69-70) in the spike protein, which results in a lower detection rate of the spike (S) gene target known as (S) gene target failure (SGTF). Furthermore, BA.2 had a stronger affinity to the human Angiotensin-converting Enzyme (hACE2) receptor than other Omicron sub-lineages. Regarding the number of mutations, BA.1.1 has the most (40), followed by BA.1, BA.3, and BA.3 with 39, 34, and 31 mutations, respectively. In addition, BA.2 and BA.3 have greater transmissibility than other sub-lineages (BA.1 and BA.1.1). These characteristics are primarily responsible for Omicron's vast geographical spread and high contagiousness rates, particularly BA.2 sub-lineages.

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The Omicron variant of concern: The genomics, diagnostics, and clinical characteristics in children

Cited by 26 publications

References 55 publications

Real-Time Polymerase Chain Reaction: Current Techniques, Applications, and Role in COVID-19 Diagnosis

Real-Time Polymerase Chain Reaction: Current Techniques, Applications, and Role in COVID-19 Diagnosis

Uncovering the information immunology journals transmitted for COVID-19: A bibliometric and visualization analysis

The emergence of SARS-CoV-2 Omicron subvariants: current situation and future trends

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