key: cord-0900987-m855r7gg
authors: Hirotsu, Yosuke; Omata, Masao
title: Discovery of a SARS-CoV-2 variant 1 from the P.1 lineage harboring K417T/E484K/N501Y mutations in Kofu, Japan
date: 2021-03-23
journal: J Infect
DOI: 10.1016/j.jinf.2021.03.013
sha: 999dd8442f6a9b795e16583cbe8e67d7a9e10be2
doc_id: 900987
cord_uid: m855r7gg

nan

In this Journal, Tang and colleagues recently commented on the introduction of the South African SARS-CoV-2 variant 501Y.V2 into the United Kingdom [1] . Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants are not always related to increased threat to human health because the virus acquires genomic diversity during the course of its life cycle [2] . However, some of these mutations have been shown to be associated with attenuation of the neutralizing activity of antibodies [3] . During the ongoing evolution of SARS-CoV-2, newly emerging lineages are likely to be circulating in the human population and genomic surveillance will be important for evaluating the emergence, spread, vaccine efficacy, and transmissibility of these lineages.

Currently, an emergent D614G mutation in the spike glycoprotein of SARS-CoV-2 is prevalent globally [4] . More recently, new emerging lineages with spike protein mutations have been discovered in the United Kingdom (B.1.1.7 lineage, 20I/501Y.V1, also named VOC 202012/01) [5] , South Africa (B.1.351 lineage, 20H/501Y.V2) [6] , and Brazil (P.1 lineage, 20J/501Y.V3) [7, 8] . All of these lineages have a N501Y mutation in the receptor binding domain (RBD), which directly binds to the angiotensin converting enzyme 2 (ACE2) receptor of the host cell, contributing to increased transmissibility. Both B.1.351 and P.1 lineages also have additional K417N/T and E484K mutations. K417N/T, E484K, and N501Y confer reduced neutralizing activity of convalescent and mRNA vaccine-elicited serum [3] .

To determine the genomic characteristics of the SARS-CoV-2 variant identified in the Kofu, Japan, we started whole genome sequencing analysis using the Ion Torrent Table 1 ), suggesting global prevalence.

In summary, we have confirmed the emergence of five clades over time.

Consecutive analysis identified SARS-CoV-2 variant 20J/501Y.V3 (P.1 lineage) in a patient and detected mutations that are identical to those of the original P.1 variant discovered in Brazil [7] . This is the first report of 20J/501Y.V3 (P.1 lineage) in Kofu, Japan. 

None. 

Introduction of the South African SARS-CoV-2 variant 501Y.V2 into the UK

No evidence for increased transmissibility from recurrent mutations in SARS-CoV-2

mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants

Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus

European Centre for Disease Prevention and Control: Rapid increase of a SARS-CoV-2 variant with multiple spike protein mutations observed in the United Kingdom

Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa

Genomic characterisation of an emergent SARS-CoV-2 lineage in Manaus: preliminary findings

Gonçalves et al: Phylogenetic relationship of SARS-CoV-2 sequences from Amazonas with emerging Brazilian variants harboring mutations E484K and N501Y in the Spike protein

Pooling RT-qPCR testing for SARS-CoV-2 in 1000 individuals of healthy and infection-suspected patients

Nasopharyngeal Swabs from 1,033 Patients using the LUMIPULSE SARS-CoV-2

Antigen Test: Comparison with RT-qPCR

We thank the researchers who deposited the SARS-CoV-2 sequencing data in the GISAID.We also thank Masato Kondo, Ryota Tanaka, and Kazuo Sakai (Thermo Fisher Scientific) for technical help, all of the medical and ancillary hospital staff.