Identification of B.1.346 Lineage of SARS-CoV-2 in Japan: Genomic Evidence of Re-entry of Clade 20C

Abstract

SARS-CoV-2 whole-genome sequencing of samples from COVID-19 patients is useful for informing infection control. Datasets of these genomes assembled from multiple hospitals can give critical clues to regional or national trends in infection. Herein, we report a lineage summary based on data collected from hospitals located in the Tokyo metropolitan area. We performed SARS-CoV-2 whole-genome sequencing of specimens from 198 patients with COVID-19 at 13 collaborating hospitals located in the Kanto region. Phylogenetic analysis and fingerprinting of the nucleotide substitutions were performed to differentiate and classify the viral lineages. More than 90% of the identified strains belonged to Clade 20B, which has been prevalent in European countries since March 2020. Only two lineages (B.1.1.284 and B.1.1.214) were found to be predominant in Japan. However, one sample from a COVID-19 patient admitted to a hospital in the Kanto region in November 2020 belonged to the B.1.346 lineage of Clade 20C, which has been prevalent in the western United States since November 2020. The patient had no history of overseas travel or any known contact with anyone who had travelled abroad. Consequently,

Early SARS-CoV-2 dynamics and immune responses in unvaccinated participants of an intensely sampled longitudinal surveillance study

“…A number of SARS-CoV-2 strains emerged in Southern California in late 2020, spanning the November 2020-March 2021 COVID-19 surge, driven largely by mutations in the spike protein 26 and described by Zhang et al 27 . The dominant clades were: 20 A (lineage B.1.234 26 ), 20B (lineage B.1.1.220/B.1.1.222 26 ), 20 C (lineage B.1.346 28 ), and 20 G (lineage B.1.2 26 ). Clade CAL.20 C, later assigned the lineage B.1.427/B.1.429 29 , also was gaining prominence over this period 27 .…”

Multiple introductions of SARS-CoV-2 B.1.1.214 lineages from mainland Japan preceded the third wave of the COVID-19 epidemic in Hokkaido

“…Our previous work and other work on the genome sequence of SARS-CoV-2 obtained from Japan showed that most, if not all, of the lineages observed between June and November 2020 were the B.1.1.284 or B.1.1.214 lineages, both of which have been observed almost exclusively in Japan [ 11 , 16 ]. Further analysis of the metadata of B.1.1.284 and B.1.214 from Hokkaido alone and all Japan showed that the B.1.1.284 lineage was the most prevalent lineage during the late summer of 2020 and the B.1.1.214 lineage became more prevalent after October 2020 ( Fig.…”

“…Phylodynamic analysis [ 9 ], including subsampling, alignment, phylogenetic inference, temporal dating of ancestral nodes, and discrete trait geographic reconstruction, as well as inference of the most likely transmission events, was performed using the Nextstrain pipeline suite [ 10 ], as previously described [ 11 ]. Briefly, we aligned sequences, subsampled sequences (see below), added sequences from the rest of the world for phylogenetic context based on genomic proximity, reconstructed the phylogeny using IQ-Tree version 2.1.2 [ 12 ].…”