ArticlePLoS pathogens2021
Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan.
Article in PLoS pathogens, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Unraveling the Mystery: COVID-19 and Diabetic Complications - A Journey from Pathophysiology to Treatment.Current diabetes reviews · 2026Review
- Clinical and molecular biomarkers predicting response to PARP inhibitors in ovarian cancer.Journal of gynecologic oncology · 2024Article
- Lung tropism in hospitalized patients following infection with SARS-CoV-2 variants from D614G to Omicron BA.2.Communications medicine · 2023Article
- Host Cell Entry and Neutralization Sensitivity of SARS-CoV-2 Lineages B.1.620 and R.1.Viruses · 2022Article
- Classification of Omicron BA.1, BA.1.1, and BA.2 sublineages by TaqMan assay consistent with whole genome analysis data.International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases · 2022Article
- SARS-CoV-2 Omicron sublineage BA.2 replaces BA.1.1: Genomic surveillance in Japan from September 2021 to March 2022.The Journal of infection · 2022Article
- SARS-CoV-2 Amino Acid Mutations Detection in Greek Patients Infected in the First Wave of the Pandemic.Microorganisms · 2022Article
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- Design of SARS-CoV-2 Variant-Specific PCR Assays Considering Regional and Temporal Characteristics.Applied and environmental microbiology · 2022Article
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- Direct comparison of Xpert Xpress, FilmArray Respiratory Panel, Lumipulse antigen test, and RT-qPCR in 165 nasopharyngeal swabs.BMC infectious diseases · 2022Article
- Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study.Computers in biology and medicine · 2022Article
- Limited spread of a rare spike E484K-harboring SARS-CoV-2 in Marseille, France.Archives of virology · 2022Article
- Molecular epidemiological features of SARS-CoV-2 in Japan, 2020-1.Virus evolution · 2022Article
- Article
- Estimating the strength of selection for new SARS-CoV-2 variants.Nature communications · 2021Article
- Structural and functional insights into the spike protein mutations of emerging SARS-CoV-2 variants.Cellular and molecular life sciences : CMLS · 2021Review
- Emergence of SARS-CoV-2 Variant B.1.575.2, Containing the E484K Mutation in the Spike Protein, in Pamplona, Spain, May to June 2021.Journal of clinical microbiology · 2021Article
- SARS-CoV-2 new variants: Characteristic features and impact on the efficacy of different vaccines.Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie · 2021Review
- SARS-CoV-2 B.1.1.7 lineage rapidly spreads and replaces R.1 lineage in Japan: Serial and stationary observation in a community.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2021Observational
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Abstract
We aimed to investigate novel emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages in Japan that harbor variants in the spike protein receptor-binding domain (RBD). The total nucleic acid contents of samples from 159 patients with coronavirus disease 2019 (COVID-19) were subjected to whole genome sequencing. The SARS-CoV-2 genome sequences from these patients were examined for variants in spike protein RBD. In January 2021, three family members (one aged in their 40s and two aged under 10 years old) were found to be infected with SARS-CoV-2 harboring W152L/E484K/G769V mutations. These three patients were living in Japan and had no history of traveling abroad. After identifying these cases, we developed a TaqMan assay to screen for the above hallmark mutations and identified an additional 14 patients with the same mutations. The associated virus strain was classified into the GR clade (Global Initiative on Sharing Avian Influenza Data [GISAID]), 20B clade (Nextstrain), and R.1 lineage (Phylogenetic Assignment of Named Global Outbreak [PANGO] Lineages). As of April 22, 2021, R.1 lineage SARS-CoV-2 has been identified in 2,388 SARS-CoV-2 entries in the GISAID database, many of which were from Japan (38.2%; 913/2,388) and the United States (47.1%; 1,125/2,388). Compared with that in the United States, the percentage of SARS-CoV-2 isolates belonging to the R.1 lineage in Japan increased more rapidly over the period from October 24, 2020 to April 18, 2021. R.1 lineage SARS-CoV-2 has potential escape mutations in the spike protein RBD (E484K) and N-terminal domain (W152L); therefore, it will be necessary to continue to monitor the R.1 lineage as it spreads around the world.
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