A discernable increase in the severe acute respiratory syndrome coronavirus 2 R.1 lineage carrying an E484K spike protein mutation in Japan

Sekizuka, Tsuyoshi; Itokawa, Kentaro; Hashino, Masanori; Okubo, Ken; Ohnishi, Asami; Goto, Keiko; Tsukagoshi, Hiroyuki; Ehara, Hayato; Nomoto, Ryohei; Ohnishi, Makoto; Kuroda, Makoto

doi:10.1016/j.meegid.2021.105013

Cited by 10 publications

(5 citation statements)

References 9 publications

(13 reference statements)

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“…To determine the phylogenetic background of E484K mutants, we conducted whole-genome sequencing on 112/401 E484K-positive but N501Y-negative mutants. Unlike with Japan, where R.1 has caused considerable community transmission ( 18 ), we detected only 10 R.1 variants, collected in February and March 2021, including 9 with the S255F mutation and belonging to the outbreak clusters from 6 different hospitals. Of the 112 E484K variants, 92% were of B.1.526 and related genetic backgrounds, consistent with the regional epidemiology in the Northeast during this time period ( 12 ).…”

Section: Resultsmentioning

confidence: 90%

Genomic Epidemiology and Serology Associated with a SARS-CoV-2 R.1 Variant Outbreak in New Jersey

Mathema

Chen

Wang

et al. 2022

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Section: Resultsmentioning

confidence: 90%

Genomic Epidemiology and Serology Associated with a SARS-CoV-2 R.1 Variant Outbreak in New Jersey

Mathema

Chen

Wang

et al. 2022

mBio

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“…The mutation was observed even in other lineages, which were isolated from different countries such as Japan (R.1 lineage), Germany, USA (B.1.1.345 lineage), Brazil, etc. (191)(192)(193)(194). Researchers reported that mutation helps in the immune escape event.…”

Section: E484kmentioning

confidence: 99%

A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations

et al. 2022

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The infective SARS-CoV-2 is more prone to immune escape. Presently, the significant variants of SARS-CoV-2 are emerging in due course of time with substantial mutations, having the immune escape property. Simultaneously, the vaccination drive against this virus is in progress worldwide. However, vaccine evasion has been noted by some of the newly emerging variants. Our review provides an overview of the emerging variants’ immune escape and vaccine escape ability. We have illustrated a broad view related to viral evolution, variants, and immune escape ability. Subsequently, different immune escape approaches of SARS-CoV-2 have been discussed. Different innate immune escape strategies adopted by the SARS-CoV-2 has been discussed like, IFN-I production dysregulation, cytokines related immune escape, immune escape associated with dendritic cell function and macrophages, natural killer cells and neutrophils related immune escape, PRRs associated immune evasion, and NLRP3 inflammasome associated immune evasion. Simultaneously we have discussed the significant mutations related to emerging variants and immune escape, such as mutations in the RBD region (N439K, L452R, E484K, N501Y, K444R) and other parts (D614G, P681R) of the S-glycoprotein. Mutations in other locations such as NSP1, NSP3, NSP6, ORF3, and ORF8 have also been discussed. Finally, we have illustrated the emerging variants’ partial vaccine (BioNTech/Pfizer mRNA/Oxford-AstraZeneca/BBIBP-CorV/ZF2001/Moderna mRNA/Johnson & Johnson vaccine) escape ability. This review will help gain in-depth knowledge related to immune escape, antibody escape, and partial vaccine escape ability of the virus and assist in controlling the current pandemic and prepare for the next.

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“…R.1 lineage containing only the E484K variant was first detected in Japan in November 2020 and partially prevalent in the third wave from October 2020 to February 2021 [ 17 ]. The E484K variant was reported as an escape variant from a monoclonal antibody that neutralizes SARS-CoV-2 [ 18 ].…”

Section: Discussionmentioning

confidence: 99%

A case of reinfection with a different variant of SARS-CoV-2: case report

et al. 2023

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Background Coronavirus disease 2019 (COVID-19) was previously thought to have a low reinfection rate, but there are concerns that the reinfection rate will increase with the emergence and spread of mutant variants. This report describes the case of a 36-year-old, non-immunosuppressed man who was infected twice by two different variants of COVID-19 within a relatively short period. Case presentation A 36-year-old Japanese man with no comorbidities was infected with the E484K variant (R.1 lineage) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Symptoms were mild and improved with symptomatic treatment alone. About four months later he presented to another outpatient department with high fever and headache. We diagnosed him as infected with the Alpha variant (B.1.1.7) of SARS-CoV-2 based on SARS-CoV-2 real-time reverse transcription polymerase chain reaction testing (RT-PCR). The patient was hospitalized with high fever. The patient received treatment in the form of anti-inflammatory therapy with corticosteroid and antibacterial chemotherapy. The patient improved without developing severe disease. Conclusion Concerns have been raised that the reinfection rate of COVID-19 will increase with the emergence of mutant variants. Particularly in mild cases, adequate amounts of neutralizing antibodies may not be produced, and reinfection may thus occur. Continued attention to sufficient infection control is thus essential.

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A discernable increase in the severe acute respiratory syndrome coronavirus 2 R.1 lineage carrying an E484K spike protein mutation in Japan

Cited by 10 publications

References 9 publications

Genomic Epidemiology and Serology Associated with a SARS-CoV-2 R.1 Variant Outbreak in New Jersey

Genomic Epidemiology and Serology Associated with a SARS-CoV-2 R.1 Variant Outbreak in New Jersey

A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations

A case of reinfection with a different variant of SARS-CoV-2: case report

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