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Volume 27, Number 4—April 2021
Research Letter

Novel SARS-CoV-2 Variant Identified in Travelers from Brazil to Japan

Takahisa Fujino, Hidetoshi Nomoto, Satoshi KutsunaComments to Author , Mugen Ujiie, Tetsuya Suzuki, Rubuna Sato, Tsuguto Fujimoto, Makoto Kuroda, Takaji Wakita, and Norio Ohmagari
Author affiliations: National Center for Global Health and Medicine, Tokyo, Japan (T. Fujino, H. Nomoto, S. Kutsuna, M. Ujiie, T. Suzuki, R. Sato, N. Ohmagari); Tohoku University, Miyagi, Japan (H. Nomoto, T. Suzuki, N. Ohmagari); National Institute of Infectious Diseases, Tokyo (T. Fujimoto, M. Kuroda, T. Wakita)

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Abstract

Multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with higher transmission potential have been emerging globally, including SARS-CoV-2 variants from the United Kingdom and South Africa. We report 4 travelers from Brazil to Japan in January 2021 infected with a novel SARS-CoV-2 variant with an additional set of mutations.

Coronavirus disease (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (1), has wreaked havoc worldwide. SARS-CoV-2 causes severe respiratory failure, often rapidly in susceptible patients. Moreover, new variants with estimated higher transmission rates have begun circulating globally, such as Variant of Concern 202012/01 (VOC-202012/01) from the United Kingdom and variant 501Y.V2 from South Africa (2). The virulence, reinfection potential, antibody response to, and efficacy of vaccines against these strains, are still unknown, posing a risk for future pandemics. We detected a previously unreported SARS-CoV-2 variant strain in a family arriving in Japan from Brazil.

On January 2, 2021, a healthy man in his 40s arrived at Haneda Airport, Tokyo, Japan, from Amazonas state in Brazil via Istanbul, Turkey. At the airport quarantine station, he and the 3 family members traveling with him tested positive for SARS-CoV-2 by quantitative real-time reverse transcription PCR. All 4 were asymptomatic and were accommodated in a government-designated quarantine facility to wait out the required 14-day quarantine.

On day 2 of their visit, a fever of 37.6°C developed in the man; on day 4, the man had a cough. On day 6, his oxygen saturation (SpO2) dropped to 93% on ambient air, and he was transferred to the National Center for Global Health and Medicine, a tertiary care hospital in Tokyo, for respiratory failure. The remaining 3 family members remained asymptomatic and continued to stay at the government-designated accommodation.

At admission, the patient had a cough and mild malaise. Physical examination was almost normal except for late inspiratory crackles in the bilateral lower lung fields. The patient’s body temperature was 37.4°C; blood pressure was 113/69 mm Hg and pulse rate 108 beats/min. The patient had a regular respiratory rate of 18 breaths/min and an SpO2 of 93% on ambient air. Laboratory tests showed a high C-reactive protein level of 10.47 mg/dL (reference range 0.00–0.14 mg/dL), but complete blood counts, renal function, liver function, and coagulation tests all were within reference ranges. Chest radiography and computed tomography showed ground-glass opacities in the lower lobes of both lungs.

We started the patient on treatment with 200 mg remdesivir, a subcutaneous injection of unfractionated heparin, and 6 mg oral dexamethasone on day 1 of admission. On day 2 of admission, the patient’s fever subsided, and his general condition improved marginally. On day 3, oxygen therapy was not needed, blood tests showed a decrease in C-reactive protein levels, and no adverse side effects of treatment were observed. He continued treatment with 100 mg/d remdesivir and unfractionated heparin until day 5 of admission and dexamethasone until day 7, during which time we observed no flare-up of symptoms.

We subjected the SARS-CoV-2 detected in the case-patient and in his family to whole-genome sequencing. Phylogenetic analysis suggested a novel variant (GISAID [https://www.gisaid.org] reference no. EPI_ISL_792681) belonging to pangolin lineage P.1 with 12 nonsynonymous mutations including K417T, E484K, and N501Y in the receptor-binding domain of the spike protein (N.R. Faria et al., unpub data, https://virological.org/t/genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-manaus-preliminary-findings/586). In addition, the variant strain we detected in the travelers had the N501Y mutation in the receptor-binding site of the spike protein, as noted in VOC-202012/01 and 501Y.V2, and the E484K mutation, similar to that noted in the 501Y strain.

We did not observe any remarkable difference in the clinical course of this case-patient compared with COVID-19 cases caused by other known SARS-CoV-2 strains. According to multiple modeling analyses, the new VOC-202012/01 variant could be more infectious than previous strains and might have <70% increased transmissibility (35). Moreover, PCR testing and genomic analysis for this strain suggested an increased viral load in VOC-202012/01 variant. Another strain, 501Y.V2 from South Africa, also has been suggested to have increased transmissibility (H. Tegally et al., unpub. data, https://doi.org/10.1101/2020.12.21.20248640). However, to date, no definitive evidence has shown that either VOC-202012/01 or 501Y.V2 are associated with a more severe COVID-19 cases.

The symptoms in this patient were relatively mild, although short-term oxygen administration was necessary. Onset of pneumonia a week after the onset of disease also followed the conventional clinical course. However, because the patient was young and had no underlying conditions, this case cannot be generalized.

In conclusion, we identified a novel variant strain of SARS-CoV-2 in 4 travelers from Brazil. Variant strains are appearing across the world now, and quarantine systems need to be strengthened. We hope to elucidate the infectivity, pathogenicity, and relationship of SARS-CoV-2 variants to vaccines while continuing to take conventional precautions against novel variant strains.

Dr. Fujino is a physician at the National Center for Global Health and Medicine in Shinjuku-ku, Tokyo, Japan. His main research interest is hematology.

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Acknowledgments

We thank Tsuyoshi Sekizuka, Kentaro Itokawa, Masanori Hashino, Nozomu Hanaoka, Nobuo Koizumi, and Tsuguto Fujimoto for assistance with PCR testing and whole-genome sequencing, and we thank the clinical staff at the National Center for Global Health and Medicine for their dedicated clinical practice and patient care.

This work was supported by the Health, Labor, and Welfare Policy Research Grants, Research on Emerging and Re-emerging Infectious Diseases and Immunization (grant no. 20HA1006).

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References

  1. World Health Organization. Coronavirus disease (COVID-19) situation reports. Weekly epidemiological update—19 January 2021 [cited 2021 Jan 21]. https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports
  2. World Health Organization. SARS-CoV-2 variant [cited 2021 Jan 21]. https://www.who.int/csr/don/31-december-2020-sars-cov2-variants/en/
  3. European Centre for Disease Prevention and Control. Rapid increase of a SARS-CoV-2 variant with multiple spike protein mutations observed in the United Kingdom; December 20, 2020 [cited 2021 Jan 21]. https://www.ecdc.europa.eu/sites/default/files/documents/SARS-CoV-2-variant-multiple-spikeprotein-mutations-United-Kingdom.pdf
  4. The New and Emerging Respiratory Virus Threats Advisory Group (NERVTAG). NERVTAG meeting on SARS-CoV-2 variant under investigation VUI-202012/01. 2020 Dec 18 [cited 2021 Jan 21]. https://app.box.com/s/3lkcbxepqixkg4mv640dpvvg978ixjtf/file/756963730457
  5. New and Emerging Respiratory Virus Threats Advisory Group. NERVTAG/SPI-M Extraordinary meeting on SARS-CoV-2 variant of concern 202012/01 (variant B.1.1.7). Note of meeting 2020 Dec 21 [cited 2021 Jan 21]. https://app.box.com/s/3lkcbxepqixkg4mv640dpvvg978ixjtf/file/756964987830

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Suggested citation for this article: Fujino T, Nomoto H, Kutsuna S, Ujiie M, Suzuki T, Sato R, et al. Novel SARS-CoV-2 variant identified in travelers from Brazil to Japan. Emerg Infect Dis. 2021 Apr [date cited]. https://doi.org/10.3201/eid2704.210138

DOI: 10.3201/eid2704.210138

Original Publication Date: February 10, 2021

Table of Contents – Volume 27, Number 4—April 2021

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Satoshi Kutsuna, Disease Control and Prevention Center, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan

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Page created: February 02, 2021
Page updated: February 10, 2021
Page reviewed: February 10, 2021
The conclusions, findings, and opinions expressed by authors contributing to this journal do not necessarily reflect the official position of the U.S. Department of Health and Human Services, the Public Health Service, the Centers for Disease Control and Prevention, or the authors' affiliated institutions. Use of trade names is for identification only and does not imply endorsement by any of the groups named above.
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