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

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Abstract

Three COVID-19 waves in Japan have been characterized by the presence of distinct PANGO lineages (B.1.1. 162, B.1.1.284, and B.1.1.214). Recently, in addition to the B.1.1.7 lineage, which shows 25% abundance, an R.1 lineage carrying the E484K mutation in the spike protein was found to show up to 40% predominance. E484K could be a pivotal amino acid substitution with the potential to mediate immune escape; thus, more attention should be paid to such potential variants of concern to avoid the emergence of mutants of concern. Such comprehensive real-time genome surveillance has become essential for the containment of COVID-19 clusters.

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Nextstrain: real-time tracking of pathogen evolution

James Hadfield, Colin Megill, Sidney Bell … (2018)

Abstract Summary Understanding the spread and evolution of pathogens is important for effective public health measures and surveillance. Nextstrain consists of a database of viral genomes, a bioinformatics pipeline for phylodynamics analysis, and an interactive visualization platform. Together these present a real-time view into the evolution and spread of a range of viral pathogens of high public health importance. The visualization integrates sequence data with other data types such as geographic information, serology, or host species. Nextstrain compiles our current understanding into a single accessible location, open to health professionals, epidemiologists, virologists and the public alike. Availability and implementation All code (predominantly JavaScript and Python) is freely available from github.com/nextstrain and the web-application is available at nextstrain.org.

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A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology

Andrew Rambaut, Edward C. Holmes, Aine O’Toole … (2020)

The ongoing pandemic spread of a novel human coronavirus, SARS-COV-2, associated with severe pneumonia disease (COVID-19), has resulted in the generation of tens of thousands of virus genome sequences. The rate of genome generation is unprecedented, yet there is currently no coherent nor accepted scheme for naming the expanding phylogenetic diversity of SARS-CoV-2. We present a rational and dynamic virus nomenclature that uses a phylogenetic framework to identify those lineages that contribute most to active spread. Our system is made tractable by constraining the number and depth of hierarchical lineage labels and by flagging and de-labelling virus lineages that become unobserved and hence are likely inactive. By focusing on active virus lineages and those spreading to new locations this nomenclature will assist in tracking and understanding the patterns and determinants of the global spread of SARS-CoV-2.

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SARS-CoV-2 variant B.1.1.7 is susceptible to neutralizing antibodies elicited by ancestral Spike vaccines

Xiaoying Shen, Haili Tang, Charlene B. McDanal … (2021)

All current vaccines for COVID-19 utilize ancestral SARS-CoV-2 Spike with the goal of generating protective neutralizing antibodies. The recent emergence and rapid spread of several SARS-CoV-2 variants carrying multiple Spike mutations raise concerns about possible immune escape. One variant, first identified in the United Kingdom (B.1.1.7, also called 501Y.V1 or 20I), contains eight Spike mutations with potential to impact antibody therapy, vaccine efficacy and risk of reinfection. Here we show that B.1.1.7 remains sensitive to neutralization, albeit at moderately reduced levels (∼2-fold), by serum samples from convalescent individuals and recipients of an mRNA vaccine (mRNA-1273, (Moderna) and a protein nanoparticle vaccine (NVX-CoV2373, Novavax). A subset of monoclonal antibodies to the receptor binding domain (RBD) of Spike are less effective against the variant while others are largely unaffected. These findings indicate that variant B.1.1.7 is unlikely to be a major concern for current vaccines or for an increased risk of reinfection.

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Author and article information

Journal

Journal ID (nlm-ta): Infect Genet Evol

Journal ID (iso-abbrev): Infect Genet Evol

Title: Infection, Genetics and Evolution

Publisher: The Authors. Published by Elsevier B.V.

ISSN (Print): 1567-1348

ISSN (Electronic): 1567-7257

Publication date PMC-release: 2 August 2021

Publication date (Print): October 2021

Publication date (Electronic): 2 August 2021

Volume: 94

Page: 105013

Affiliations

[a ]Pathogen Genomics Center, National Institute of Infectious Diseases, Shinjyuku, Tokyo, Japan

[b ]Hokkaido Institute of Public Health, Hokkaido, Japan

[c ]Sapporo City Institute of Public Health, Hokkaido, Japan

[d ]Ibaraki Prefectural Institute of Public Health, Ibaraki, Japan

[e ]Gunma Prefectural Institute of Public Health and Environmental Sciences, Gunma, Japan

[f ]Saitama Prefectural Institute of Public Health, Yoshimi, Saitama, Japan

[g ]Kobe Institute of Health, Kobe, Hyogo, Japan

[h ]National Institute of Infectious Diseases, Shinjyuku, Tokyo, Japan

Author notes

[* ]Corresponding author at: Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan.

Article

Publisher Item ID: S1567-1348(21)00311-7 Publisher ID: 105013

DOI: 10.1016/j.meegid.2021.105013

PMC ID: 8327703

PubMed ID: 34352360

SO-VID: 044456c1-314c-4f99-9093-3b90419c8a3c

License:

Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.

History

Date received : 11 April 2021

Date revision received : 14 July 2021

Date accepted : 20 July 2021

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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

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Novel Coronavirus Disease COVID-19

Most cited references 8

Nextstrain: real-time tracking of pathogen evolution

A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology

SARS-CoV-2 variant B.1.1.7 is susceptible to neutralizing antibodies elicited by ancestral Spike vaccines

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Cited by 8

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