SARS‐CoV‐2 R.1 lineage variants that prevailed in Tokyo in March 2021

Nagano, Katsutoshi; Tani‐Sassa, Chihiro; Iwasaki, Yumi; Takatsuki, Yuna; Yuasa, Sonoka; Takahashi, Yuta; Nakajima, Jun; Sonobe, Kazunari; Ichimura, Naoya; Nukui, Yoko; Takeuchi, Hiroaki; Tanimoto, Kousuke; Tanaka, Yukië; Kimura, Akinori; Tohda, Shuji

doi:10.1002/jmv.27240

Cited by 12 publications

(5 citation statements)

References 9 publications

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“…The R.1 variant replaced the previous variants in March, as previously reported. 2 The Alpha variant represented the majority of infections in April and May. The first Delta variant case in our hospital was identified in mid‐May and the Delta variant was predominant in July and August.…”

Section: Resultsmentioning

confidence: 79%

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Viral loads and profile of the patients infected with SARS‐CoV‐2 Delta, Alpha, or R.1 variants in Tokyo

Tani‐Sassa

Iwasaki

Ichimura

et al. 2021

Journal of Medical Virology

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The rapid spread of the Delta variant of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) became a serious concern worldwide in summer 2021. We examined the copy number and variant types of all SARS‐CoV‐2‐positive patients who visited our hospital from February to August 2021 using polymerase chain reaction (PCR) tests. Whole genome sequencing was performed for some samples. The R.1 variant (B.1.1.316) was responsible for most infections in March, replacing the previous variant (B.1.1.214); the Alpha (B.1.1.7) variant caused most infections in April and May; and the Delta variant (B.1.617.2) was the most prevalent in July and August. There was no significant difference in the copy numbers among the previous variant cases (n = 29, median 3.0 × 104 copies/µl), R.1 variant cases (n = 28, 2.1 × 105 copies/µl), Alpha variant cases (n = 125, 4.1 × 105 copies/µl), and Delta variant cases (n = 106, 2.4 × 105 copies/µl). Patients with Delta variant infection were significantly younger than those infected with R.1 and the previous variants, possibly because many elderly individuals in Tokyo were vaccinated between May and August. There was no significant difference in mortality among the four groups. Our results suggest that the increased infectivity of Delta variant may be caused by factors other than the higher viral loads. Clarifying these factors is important to control the spread of Delta variant infection.

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Section: Resultsmentioning

confidence: 79%

“…We previously reported that the R.1 variant (the sublineage of B.1.1.316) rapidly replaced the previously existing strain, B.1.1.214 (originating from the European lineage), in Tokyo in March 2021. 2 After that, the Alpha variant (B.1.1.7) and the Delta variant prevailed.…”

Section: Introductionmentioning

confidence: 99%

Viral loads and profile of the patients infected with SARS‐CoV‐2 Delta, Alpha, or R.1 variants in Tokyo

Tani‐Sassa

Iwasaki

Ichimura

et al. 2021

Journal of Medical Virology

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“…Research has demonstrated that the scRNAseq technique is capable of identifying complex and rare cell populations, uncovering regulatory connections between genes, and tracking the progression of numerous cell lineages. [39][40][41] Recent advancements in spatial approaches have enabled the combination of spatial position of transcriptomic data proof with cellular barcodes, resulting in enhanced throughput to identify the origin of transcripts from hundreds of thousands of cells. The high-throughput and low-depth paradigm is a widely employed approach in experiments utilizing the genomics chromium platform.…”

Section: Single-cell Transcriptomics Studymentioning

confidence: 99%

“…Research has demonstrated that SARS-CoV-2 has the ability to utilize all ACE2 proteins as cell entrance receptors, with the exception of mouse ACE2. 41 During virus entry, the SARS-CoV-2 virus interacts with cells via its highly changeable spike (S) protein, which is composed of the S1 and S2 subunits. The S1 subunit's receptor binding domain (RBD) directly mediates virus attachment and entry, while the S2 subunit's fusion peptide (FP) promotes membrane fusion.…”

Section: Genomic Mutation Analysismentioning

confidence: 99%

Application of Omics and Bioinformatics Technologies in Response to COVID-19 Pandemic

Aga,

Woldesemayat

2024

Mol Cell Biomed Sci

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The medical biotechnology community has undertaken significant endeavors to gain a comprehensive understanding of SARS-CoV-2’s biology and pathogenesis mechanisms. Omics approaches and technologies have been widely employed in the fight against SARS-CoV-2. Since the onset of the virus outbreak, researchers have demonstrated how recent omics and bioinformatics technological advancements have contributed to the diagnosis, vaccine development, treatment, and control of disease transmission. Studies conducted since the outbreak have been collected and summarized, with a focus on bioinformatics approaches and their contribution to controlling this pandemic. Developments and advanced omics technology in connection to the COVID-19 pandemic have been analyzed. The multi-omics technology, which offers various strategies in identifying potential diagnostics, therapeutics, studies of variants of concern, and drug repurposing approaches, has been assessed. Pandemic response has seen the application of multi-omics and pan-genomics approaches, including genomics, metabolomics, transcriptomics, proteomics, epigenomics, clustered regularly interspaced short palindromic repeats (CRISPR) technology, host-pathogen interactions, artificial intelligence, and machine learning in various research areas. Additionally, bioinformatics and mathematical modeling have played a significant role in disease control. The use of smart technologies to control virus transmission and predict patients’ health conditions and treatment outcomes has also been crucial. Transcriptome analysis has emerged as a major application, contributing to the generation of new knowledge on viral sequences and intracellular signaling pathways that regulate viral infection and pathogenesis mechanisms. The sequencing of the virus has paved the way for the use of omics technologies and an integrative technique in combating the pandemic. In general, the advancement of omics technology during this pandemic has been fascinating and has contributed a significant role to the science of health biotechnology in general and omics and bioinformatics in particular.Keywords: bioinformatics, coronavirus, COVID-19, omics, SARS COV-2

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“… 31 R.1 variants is a lineage first detected in USA and Europe, which rapidly prevailed in Tokyo in March, 2021. 60 And B.1.525 (also called Eta variant), which charactered by the carrying of signature mutations of VOCs, is first identified in Nigeria and poses incredible risk on unvaccinated population in Africa. Also, the possible resistance to vaccine‐induced immunity will facilitate its worldwide spreading.…”

Section: Genomics Analysis Of Sars‐cov‐2mentioning

confidence: 99%

Application of omics technology to combat the COVID‐19 pandemic

Yang

Yan²,

Zhong³

2021

MedComm

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As of August 27, 2021, the ongoing pandemic of coronavirus disease 2019 (COVID‐19), caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), has spread to over 220 countries, areas, and territories. Thus far, 214,468,601 confirmed cases, including 4,470,969 deaths, have been reported to the World Health Organization. To combat the COVID‐19 pandemic, multiomics‐based strategies, including genomics, transcriptomics, proteomics, and metabolomics, have been used to study the diagnosis methods, pathogenesis, prognosis, and potential drug targets of COVID‐19. In order to help researchers and clinicians to keep up with the knowledge of COVID‐19, we summarized the most recent progresses reported in omics‐based research papers. This review discusses omics‐based approaches for studying COVID‐19, summarizing newly emerged SARS‐CoV‐2 variants as well as potential diagnostic methods, risk factors, and pathological features of COVID‐19. This review can help researchers and clinicians gain insight into COVID‐19 features, providing direction for future drug development and guidance for clinical treatment, so that patients can receive appropriate treatment as soon as possible to reduce the risk of disease progression.

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SARS‐CoV‐2 R.1 lineage variants that prevailed in Tokyo in March 2021

Cited by 12 publications

References 9 publications

Viral loads and profile of the patients infected with SARS‐CoV‐2 Delta, Alpha, or R.1 variants in Tokyo

Viral loads and profile of the patients infected with SARS‐CoV‐2 Delta, Alpha, or R.1 variants in Tokyo

Application of Omics and Bioinformatics Technologies in Response to COVID-19 Pandemic

Application of omics technology to combat the COVID‐19 pandemic

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