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Identification of B.1.346 lineage of SARS-CoV-2 in Japan: Genomic evidence of re-entry of Clade 20C
Abe Kodai; Shimura Takako; Takenouchi Toshiki; Iwasaki Yuka; Ishizu Hirotsugu; Uwamino Yoshifumi; Uno Shunsuke; Gotoh Jun; Tachikawa Natsuo; Takeuchi Yuriko; Katayama Junpei; Nozaki Hiroyuki; Fujii Susumu; Seki Shikou; Nakamura Morio; Uda Kazuhiro; Misumi Takahiko; Ishihara Jun; Yamada Kenichiro; Kanai Toshio; Murai Shinji; Araki Kazuhiro; Ebihara Tamotsu; Shiomi Haruhiko; Hasegawa Naoki; Amagai Masayuki; Kitagawa Yuko; Suematsu Makoto; Kosaki Kenjiro.
Affiliation
  • Abe Kodai; Keio University, School of Medicine
  • Shimura Takako; Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
  • Takenouchi Toshiki; Department of Pediatrics, Keio University School of Medicine
  • Iwasaki Yuka; Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan
  • Ishizu Hirotsugu; Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan
  • Uwamino Yoshifumi; Department of Laboratory Medicine, Keio University School of Medicine, Tokyo, Japan
  • Uno Shunsuke; Division of Infection Diseases and Infection Control, Keio University Hospital, Tokyo, Japan: Department of Infectious Diseases, Keio University School of Medic
  • Gotoh Jun; Saiseikai Yokohamashi Tobu Hospital, Kanagawa, Japan
  • Tachikawa Natsuo; Yokohama Municipal Citizen Hospital
  • Takeuchi Yuriko; Hiratsuka City Hospital
  • Katayama Junpei; Hiratsuka City Hospital
  • Nozaki Hiroyuki; Kawasaki City Hospital
  • Fujii Susumu; Ogikubo Hospital
  • Seki Shikou; Tokyo medical center
  • Nakamura Morio; Tokyo Saiseikai Central Hospital
  • Uda Kazuhiro; Division of Infectious Diseases, Department of Pediatrics, Tokyo Metropolitan Childrens Medical Center, Tokyo, Japan
  • Misumi Takahiko; Saiseikai Yokohamashi Tobu Hospital, Kanagawa, Japan
  • Ishihara Jun; Yokohama Municipal Citizen Hospital
  • Yamada Kenichiro; Hiratsuka City Hospital
  • Kanai Toshio; Kawasaki City Hospital
  • Murai Shinji; Ogikubo Hospital
  • Araki Kazuhiro; Tokyo medical center
  • Ebihara Tamotsu; Tokyo Saiseikai Central Hospital
  • Shiomi Haruhiko; Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan
  • Hasegawa Naoki; Division of Infection Diseases and Infection Control, Keio University Hospital, Tokyo, Japan: Department of Infectious Diseases, Keio University School of Medic
  • Amagai Masayuki; Department of Dermatology, Keio University School of Medicine
  • Kitagawa Yuko; Department of Surgery, Keio University School of Medicine, Tokyo, Japan
  • Suematsu Makoto; Department of Biochemistry, Keio University School of Medicine, Tokyo, Japan
  • Kosaki Kenjiro; Center for Medical Genetics, Keio University
Preprint in English | medRxiv | ID: ppmedrxiv-21250798
Journal article
A scientific journal published article is available and is probably based on this preprint. It has been identified through a machine matching algorithm, human confirmation is still pending.
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ABSTRACT
ObjectivesWhole SARS-CoV-2 genome sequencing from COVID-19 patients is useful for infection control and regional trends evaluation. We report a lineage data collected from hospitals in the Kanto region of Japan. MethodsWe performed whole genome sequencing in specimens of 198 COVID-19 patients at 13 collaborating hospitals in the Kanto region. Phylogenetic analysis and fingerprinting of the nucleotide substitutions underwent to differentiate and classify the viral lineages. ResultsMore than 90% of the strains belonged to Clade 20B and two lineages (B.1.1.284 and B.1.1.214) have been detected predominantly in the Kanto region. However, one sample from a COVID-19 patient in November 2020, belonged to the B.1.346 lineage of Clade 20C, which has been prevalent in western United States. The patient had no history of overseas travel and no contact with anyone who had travelled abroad, suggesting that this strain appeared likely to have been imported from western United States, across the strict quarantine barrier. ConclusionB.1.1.284 and B.1.1.214 have been identified predominantly in the Kanto region and B.1.346 of clade 20C in one patient was probably imported from western United States. These results illustrate that a decentralized network of hospitals can be significantly advantageous for monitoring regional molecular epidemiologic trends. Highlights{middle dot} Whole SARS-CoV-2 genome sequencing is useful for infection control {middle dot} B.1.1.284 and B.1.1.214 have been identified predominantly in the Kanto region {middle dot} B.1.346 of Clade 20C was detected in one COVID-19 patient in November {middle dot} Molecular genomic data sharing provides benefits to public health against COVID-19
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Full text: Available Collection: Preprints Database: medRxiv Type of study: Experimental_studies / Prognostic study Language: English Year: 2021 Document type: Preprint
Full text: Available Collection: Preprints Database: medRxiv Type of study: Experimental_studies / Prognostic study Language: English Year: 2021 Document type: Preprint
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