SARS-CoV-2 B.1.1.7 lineage rapidly spreads and replaces R.1 lineage in Japan: Serial and stationary observation in a community

https://doi.org/10.1016/j.meegid.2021.105088Get rights and content

Highlights

  • WGS of SARS-CoV-2 in 325 patients in a community of Japan from Feb 2020 to Jun 2021.

  • The transition of viral lineage was observed during four waves of infection spread.

  • B.1.1.214 rapidly declined after the emergence of the R.1 lineage with E484K.

  • R.1 temporally expanded, but declined rapidly after the influx of B.1.1.7 (Alpha).

  • B.1.617.2 (Delta) has just been detected and the VOC needs to be studied continuously.

Abstract

Background

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) circulates in the world and acquires mutations during evolution. To identify the new emergent variants, the surveillance of the variants of concern (VOC) and variants of interest (VOI) is ongoing. This study aimed to determine how the transition of viral lineage occurred by stationary genome analysis in Yamanashi, Japan.

Methods

We performed the whole genome sequencing using SARS-CoV-2 positive samples collected from February 2020 to the end of June 2021. Viral lineage was defined by the Phylogenetic Assignment of Named Global Outbreak (PANGO) lineages.

Results

We successfully obtained 325 viral genome sequences and the number of analyzed samples accounted for 15.4% of the total 2109 COVID-19 patients identified in our district. We identified 13 types of viral lineages including R.1, P.1, B.1.1.7 (Alpha) and B.1.617.2 (Delta). These virus lineages had distinct periods of expansion and decline. After the emerging of the R.1 lineage harboring E484K variant (designated VOI in Japan), the prevalent B.1.1.214 lineage were no longer identified. The R.1 lineages were temporarily prevalent afterwards, but the influx of B.1.1.7 lineage (designated VOC) led to a decline in R.1. Currently, B.1.1.7 has become dominant after mid-April 2021.

Conclusion

We clearly elucidated the transition and replacement of viral lineage by the community-based analysis. The virus completely replaced by more infectious lineages, therefore, it will be necessary to continue to monitor the VOC and VOI.

Keywords

SARS-CoV-2
Genome
B.1.1.7
VOC
VOI

Cited by (0)

View Abstract