Genome Recombination between the Delta and Alpha Variants of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)

Tsuyoshi Sekizuka; Kentaro Itokawa; Masumichi Saito; Michitsugu Shimatani; Shutoku Matsuyama; Hideki Hasegawa; Tomoya Saito; Makoto Kuroda

doi:10.7883/yoken.JJID.2021.844

Short Communications

Genome Recombination between the Delta and Alpha Variants of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)

Tsuyoshi Sekizuka, Kentaro Itokawa, Masumichi Saito, Michitsugu Shimatani, Shutoku Matsuyama, Hideki Hasegawa, Tomoya Saito, Makoto Kuroda

Author information

Tsuyoshi Sekizuka
Pathogen Genomics Center, National Institute of Infectious Diseases, Japan
Kentaro Itokawa
Pathogen Genomics Center, National Institute of Infectious Diseases, Japan
Masumichi Saito
Center for Emergency Preparedness and Response, National Institute of Infectious Diseases, Japan
Michitsugu Shimatani
Center for Research Planning and Coordination, National Institute of Infectious Diseases, Japan
Shutoku Matsuyama
Center for Influenza and Respiratory Virus Research, National Institute of Infectious Diseases, Murayama Branch, Japan
Hideki Hasegawa
Center for Influenza and Respiratory Virus Research, National Institute of Infectious Diseases, Murayama Branch, Japan
Tomoya Saito
Center for Emergency Preparedness and Response, National Institute of Infectious Diseases, Japan
Makoto Kuroda
Pathogen Genomics Center, National Institute of Infectious Diseases, Japan

Keywords: SARS-CoV-2, genome recombination, alpha variant, delta variant

JOURNAL FREE ACCESS

2022 Volume 75 Issue 4 Pages 415-418

DOI https://doi.org/10.7883/yoken.JJID.2021.844

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Abstract

Prominent genomic recombination has been observed between the Delta and Alpha variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), isolated from clinical specimens in Japan. Interestingly, the recombination variant detected in this study carries a spike protein identical to that in the domestic Delta variant, thereby suggesting that further risks would not be associated with infectivity and immune escape. The recombinant was classified as an XC lineage in the PANGOLIN database. It is necessary to intensively study such marked genetic variations and characterize emerging variants after careful verification of their lineage and clade assignment.

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