A genome epidemiological study of SARS-CoV-2 introduction into Japan

Sekizuka, Tsuyoshi; Itokawa, Kentaro; Hashino, Masanori; Kawano-Sugaya, Tetsuro; Tanaka, Rina; Yatsu, Koji; Ohnishi, Asami; Goto, Keiko; Tsukagoshi, Hiroyuki; Ehara, Hayato; Sadamasu, Kenji; Taira, Masakatsu; Shibata, Shuzo; Nomoto, Ryohei; Hiroi, Satoshi; Toho, Miho; Shimada, Tomoe; Matsui, Takeshi; Sunagawa, Tomimasa; Kamiya, Hajime; Yahata, Yuichiro; Yamagishi, Takashi; Suzuki, Motoi; Wakita, Takaji; Kuroda, Makoto

doi:10.1101/2020.07.01.20143958

Cited by 12 publications

(15 citation statements)

References 15 publications

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“…High-quality genome sequences were obtained from 49 of the 89 patients who were enrolled in the clinical trial at hospital sites located across Japan. A previous genome surveillance study suggested that two introductions of SARS-CoV-2 to Japan occurred, the first one between January and February from China and the second one since March from Europe and North America [1]. The clades identified in our trial mirrored this trend.…”

Section: Sars-cov-2 Clade Representationsupporting

confidence: 77%

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Virological and genomic analysis of SARS-CoV-2 from a favipiravir clinical trial cohort

Suzuki

Imai

Sakurai

et al. 2021

Journal of Infection and Chemotherapy

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Introduction Several clinical studies have reported the efficacy of favipiravir in reducing viral load and shortening the duration of symptoms. However, the viability of SARS-CoV-2 in the context of favipiravir therapy and potential for resistance development is unclear. Methods We sequenced SARS-CoV-2 in nasopharyngeal specimens collected from patients who participated in a randomized clinical trial of favipiravir at hospitals across Japan between March and May 2020. Paired genomes were sequenced from those who remained RT-PCR-positive 5-8 days into favipiravir therapy. Daily nasopharyngeal specimens from 69 patients who were RT-PCR-positive at randomization were examined for a cytopathic effect (CPE). Results Some strains early in the trial belonged to clade 19B, whereas the majority belonged to clade 20B. The median time from the disease onset to negative CPE was 9 days. CPE strongly correlated with the time from disease onset, viral load, age and male sex. Among 23 patients for whom paired genomes were available, all except one had identical genomes. Two mutations were observed in one patient who received favipiravir, neither in the RdRp gene. Conclusions The SARS-CoV-2 genome distribution in this clinical trial conducted in Japan reflected the early influx of strains from China followed by replacement by strains from Europe. CPE was significantly associated with age, male sex and viral loads, but not with favipiravir therapy. There was no evidence of resistance development during favipiravir therapy.

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Section: Sars-cov-2 Clade Representationsupporting

confidence: 77%

“…Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, has claimed nearly three million lives worldwide. Japan has been affected since the relatively early stage of the pandemic, with initial influx of strains from China during the lunar new year followed by strains from Europe over the spring of 2020 [1].…”

Section: Introductionmentioning

confidence: 99%

Virological and genomic analysis of SARS-CoV-2 from a favipiravir clinical trial cohort

Suzuki

Imai

Sakurai

et al. 2021

Journal of Infection and Chemotherapy

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“…It is quite intriguing that D614G_KR is dominant despite the fact that comparable numbers of D614G and D614G_Q57H strains were introduced into Japan. For unknown reasons, strains other than D614G_KR are short lived in Japan( 19 ).…”

Section: Discussionmentioning

confidence: 99%

Introductions and evolutions of SARS-CoV-2 strains in Japan

Tokumasu

Weeraratne

Snowdon

et al. 2021

Preprint

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COVID-19 caused by SARS-CoV-2 was first identified in Japan on January 15th, 2020, soon after the pandemic originated in Wuhan, China. Subsequently, Japan experienced three distinct waves of the outbreak in the span of a year and has been attributed to new exogenous strains and evolving existing strains. Japan engaged very early on in tracking different COVID-19 sub-strains and have sequenced approximately 5% of all confirmed cases. While Japan has enforced stringent airport surveillance on cross-border travelers and returnees, some carriers appear to have advanced through the quarantine stations undetected. In this study, 17112 genomes sampled in Japan were analyzed to understand the strains, heterogeneity and temporal evolution of different SARS-CoV-2 strains. We identified 11 discrete strains with a substantial number of cases with most strains possessing the spike (S) D614G and nucleocapsid (N) 203_204delinsKR mutations. Besides these variants, ORF1ab P3371S, A4815V, S1361P, and N P151L were also detected in nearly half the samples constituting the most common strain in Japan. 115 distinct strains have been introduced into Japan and 12 of them were introduced after strict quarantine policy was implemented. In particular, the B.1.1.7 strain, that emerged in the United Kingdom (UK) in September 2020, has been circulating in Japan since late 2020 after eluding cross-border quarantine stations. Similarly, the B.1.351 strain dubbed the South African variant, P.1 Brazilian strain and R.1 strain with the spike E484K mutation have been detected in Japan. At least four exogenous B.1.1.7 sub-strains have been independently introduced in Japan as of late January 2021, and these strains carry mutations that give selective advantage including N501Y, H69_V70del, and E484K that confer increased transmissibility, reduced efficacy to vaccines and possible increased virulence. It is imperative that the quarantine policy be revised, cross-border surveillance reinforced, and new public health measures implemented to mitigate further transmission of this deadly disease and to identify strains that may engender resistance to vaccines.

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“…On January 6, 2021, the NIID detected a new emerging strain (P.1 lineage) of SARS-CoV-2 at airport quarantine in four travelers who arrived from Brazil on 2 nd January 2021 [30-32] (Table 1). Subsequently, almost of P.1 lineage discovered in Manaus in Brazil and gradually spread worldwide [10, 11].…”

Section: Discussionmentioning

confidence: 99%

Discovery of SARS-CoV-2 strain of P.1 lineage harboring K417T/ E484K / N501Y by whole genome sequencing in the city, Japan

Hirotsu

Omata

2021

Preprint

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On the February 2020, the very first case was an American female from Diamond Princess cruise ship. Since, we have confirmed 136 patients infected with coronavirus disease 2019 (COVID-19) until February 2021. Here, we conducted the whole genome sequencing analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on samples from 70 of 136 patients (51.5%). These patients were infected in Diamond Princess cruise ship (n=1), Africa (n=2), Japan (n=66) and Brazil (n=1). The viral genome sequence of a patient on the Diamond Princess cruise ship in February 2020 was similar to that of original strain found in Wuhan, China (19A clade). Four patients, including two returnees from Africa and two lived in Japan, confirmed at the end of March 2020 had sequences similar to those of lineage with D614G mutation, which was endemic in Europe (20A [n=3] and 20B [n=1] clade). The 64 Japanese patients confirmed from September 2020 to January 2021 had sequences similar to those of the currently prevalent lineage (20B [n=58] and 20C clade [n=6]). Subsequent analysis revealed three mutations (K417T/ E484K / N501Y) in the receptor binding domain of the spike protein in a man in his 40s. The sequence was identical to the P.1 lineage (also known as 20J/501Y.V3) reported in Brazil. This is the first report of SARS-CoV-2 P.1 lineage identified in the city, Japan.

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A genome epidemiological study of SARS-CoV-2 introduction into Japan

Cited by 12 publications

References 15 publications

Virological and genomic analysis of SARS-CoV-2 from a favipiravir clinical trial cohort

Virological and genomic analysis of SARS-CoV-2 from a favipiravir clinical trial cohort

Introductions and evolutions of SARS-CoV-2 strains in Japan

Discovery of SARS-CoV-2 strain of P.1 lineage harboring K417T/ E484K / N501Y by whole genome sequencing in the city, Japan

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