key: cord-0753874-b715jaak
authors: Nagano, Katsutoshi; Tani‐Sassa, Chihiro; Iwasaki, Yumi; Takatsuki, Yuna; Yuasa, Sonoka; Takahashi, Yuta; Nakajima, Jun; Sonobe, Kazunari; Ichimura, Naoya; Nukui, Yoko; Takeuchi, Hiroaki; Tanimoto, Kousuke; Tanaka, Yukie; Kimura, Akinori; Tohda, Shuji
title: SARS‐CoV‐2 R.1 lineage variants that prevailed in Tokyo in March 2021
date: 2021-08-05
journal: J Med Virol
DOI: 10.1002/jmv.27240
sha: c7216c5f31a9b7e3e7accfb5f5915f96408ba137
doc_id: 753874
cord_uid: b715jaak

The spread of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) variants, such as B.1.1.7 and B.1.351, has become a crucial issue worldwide. Therefore, we began testing all patients with COVID‐19 for the N501Y and E484K mutations by using polymerase chain reaction (PCR)‐based methods. Nasopharyngeal swab samples from 108 patients who visited our hospital between February and April 2021 were analyzed. The samples were analyzed using reverse transcription‐PCR with melting curve analysis to detect the N501Y and E484K mutations. A part of the samples was also subjected to whole‐genome sequencing (WGS). Clinical parameters such as mortality and admission to the intensive care unit were analyzed to examine the association between increased disease severity and the E484K mutation. The ratio of cases showing the 501N + 484K mutation rapidly increased from 8% in February to 46% in March. WGS revealed that the viruses with 501N + 484K mutation are R.1 lineage variants. Evidence of increased disease severity related to the R.1 variants was not found. We found that the R.1 lineage variants rapidly prevailed in Tokyo in March 2021, which suggests the increased transmissibility of R.1 variants, while they showed no increased severity.

Since the beginning of 2021, the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants such as B.1.1.7 known as UK type, B.1.351 (South Africa type), and P.1 (Brazil type) has become a crucial issue worldwide. [1] [2] [3] [4] We are also aware of this issue at our hospital, Tokyo Medical and Dental University Hospital, which mainly treats patients with severe coronavirus disease 2019 (COVID-19) from all over Tokyo. Therefore, we began testing all samples from outpatients and inpatients who tested polymerase chain reaction (PCR)-positive for SARS-CoV-2 for its associated mutations, N501Y and E484K, using PCR-based melting curve analysis. We found that the conventional strains ( The Melting curve analyses of the PCR products were performed according to the manufacturer's instructions, and the 501N, 501Y, 484E, and 484K types were determined by the melting temperature.

Using a part of the samples that showed 501N + 484E, 501N + 484K, and 501Y + 484E, whole-genome sequencing (WGS) was performed using a next-generation sequencer to specify the lineages.

To investigate whether the 501N + 484K variants are involved in the increased severity of the disease, we compared elements from the patients' clinical profiles, such as mortality and admission to the intensive care unit (ICU), between 501N + 484E and 501N + 484K patients who were discharged by April 30. 

The number of cases by the three variant types in each month is shown in Figure 1A . Samples for which the 501 or 484 type could not be determined were classified as untyped. In February, the 501N + 484E type accounted for 80% of cases and the 501N + 484K type for 8%. In March, the 501N + 484K type increased to 46% and the 501Y + 484E type appeared at the end of March. In April, along with the rapid increase of patients with COVID-19, the 501Y + 484E variant type increased and accounted for about half of all cases. The type of 501Y + 484K, which corresponds to the B.1.351 and P.1 variants, was not found during the three-month study period. The E484K mutation has been reported to cause immune escape. 7 The preventive effects of antibodies produced by vaccination can be diminished by E484K mutations. In fact, outbreaks of R.1 variants in a nursing facility that occurred after the residents and personnel were vaccinated were reported, although the infection rate of the vaccinated people was significantly lower than that of unvaccinated people. 8 As the vaccines are thought to be effective for the UK variants, 7 it is possible that R. 

Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England

CMMID COVID-19 Working Group, et al. Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7

Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma

Detection of SARS-CoV-2 lineage P.1 in patients from a region with exponentially increasing hospitalisation rate

PANGO lineages database

Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity

COVID-19 outbreak associated with a SARS-CoV-2 R.1 lineage variant in a skilled nursing facility after vaccination program-Kentucky

SARS-CoV-2 R.1 lineage variants that prevailed in Tokyo in

The authors declare that there are no conflict of interests.

Conceived and designed the study: Katsutoshi Nagano, Chihiro Tani 

The data and protocol of RT-PCR are available from the corresponding author upon request.

http://orcid.org/0000-0002-5689-9858Shuji Tohda http://orcid.org/0000-0002-2642-5459