Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan.

PLoS Pathogens
Yosuke Hirotsu, M. Omata

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%...Continue Reading

References

May 24, 2018·Bioinformatics·James HadfieldRichard A Neher
Apr 18, 2020·Infection Control and Hospital Epidemiology : the Official Journal of the Society of Hospital Epidemiologists of America·Yosuke HirotsuMasao Omata
Jul 17, 2020·Nature Microbiology·Andrew RambautOliver G Pybus
Oct 28, 2020·Nature·Jessica A PlantePei-Yong Shi
Dec 11, 2020·The New England Journal of Medicine·Fernando P PolackUNKNOWN C4591001 Clinical Trial Group
Dec 31, 2020·The New England Journal of Medicine·Lindsey R BadenUNKNOWN COVE Study Group
Feb 7, 2021·BMJ : British Medical Journal·Jacqui Wise
Feb 11, 2021·Emerging Infectious Diseases·Takahisa FujinoNorio Ohmagari
Feb 11, 2021·Nature·Zijun WangMichel C Nussenzweig
Feb 20, 2021·Emerging Infectious Diseases·Carolina K V NonakaBruno Solano de Freitas Souza
Feb 25, 2021·The New England Journal of Medicine·Noa DaganRan D Balicer
Mar 4, 2021·Nature Medicine·Constantinos Kurt WibmerPenny L Moore
Mar 5, 2021·Science·Nicholas G DaviesW John Edmunds
Mar 18, 2021·The New England Journal of Medicine·Kai WuDarin K Edwards

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Citations

Jun 4, 2021·International Journal of Infectious Diseases : IJID : Official Publication of the International Society for Infectious Diseases·Yosuke HirotsuMasao Omata
Aug 15, 2021·Virology Journal·Jalen SinghKaren Mossman
Nov 4, 2021·Cellular and Molecular Life Sciences : CMLS·Deepali GuptaPunit Kaur

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