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Kawamura H, Arimura S, Saida R, Murata N, Shigemi A, Kodama Y, Nakamura M, Obama Y, Fukuyama R, Hamada Y, Shinkawa N, Sunagawa T, Kamiya H, Nishi J. Enhanced measures, including PCR-based screening and syndromic surveillance for nosocomial outbreaks of the COVID-19 Omicron variant, using descriptive epidemiology and whole-genome sequencing in a Japanese tertiary care hospital. J Infect Chemother 2024; 30:104-110. [PMID: 37717606 DOI: 10.1016/j.jiac.2023.09.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/21/2023] [Accepted: 09/13/2023] [Indexed: 09/19/2023]
Abstract
INTRODUCTION In this study, we aimed to analyze the effectiveness of enhanced preventive measures against nosocomial COVID-19 Omicron outbreaks based on those encountered. METHODS We introduced PCR-based screening and syndromic surveillance, in addition to standard and transmission-based precautions, during a COVID-19 outbreak in three wards of Kagoshima University Hospital, a Japanese tertiary care hospital, in February 2022, amid the Omicron variant endemic. Furthermore, we analyzed the descriptive epidemiology and whole-genome sequencing (WGS) of positive SARS-CoV-2 PCR samples from this outbreak. RESULTS PCR-based screening tests were conducted following the identification of three cases through syndromic surveillance. As a result, 30 individuals tested positive for SARS-CoV-2, including 13 inpatients, five attendant family members, and 12 healthcare workers across the three wards. Notably, no new infections were observed within eight days following the implementation of preventive measures. Among the SARS-CoV-2 genomes analyzed (n = 16; 53.3%), all strains were identified as belonged to BA.1.1 variant. Detailed analysis of descriptive and molecular epidemiology, incorporating single-nucleotide polymorphism analysis of WGS and clarification of transmission links, considering two potential entry routes to the hospital. CONCLUSIONS Introduction of additional preventive measures, including PCR-based screening and syndromic surveillance, in addition to WGS and descriptive epidemiology, is useful for the early intervention of nosocomial outbreaks and for revealing the transmission route of the COVID-19 Omicron variant.
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Affiliation(s)
- Hideki Kawamura
- Department of Infection Control and Prevention, Kagoshima University Hospital, 8-35-1 Sakuragaoka, Kagoshima, 890-8520, Japan.
| | - Shoko Arimura
- Department of Infection Control and Prevention, Kagoshima University Hospital, 8-35-1 Sakuragaoka, Kagoshima, 890-8520, Japan
| | - Ryuichi Saida
- Department of Infection Control and Prevention, Kagoshima University Hospital, 8-35-1 Sakuragaoka, Kagoshima, 890-8520, Japan
| | - Nao Murata
- Department of Infection Control and Prevention, Kagoshima University Hospital, 8-35-1 Sakuragaoka, Kagoshima, 890-8520, Japan
| | - Akari Shigemi
- Department of Infection Control and Prevention, Kagoshima University Hospital, 8-35-1 Sakuragaoka, Kagoshima, 890-8520, Japan
| | - Yuichi Kodama
- Department of Infection Control and Prevention, Kagoshima University Hospital, 8-35-1 Sakuragaoka, Kagoshima, 890-8520, Japan
| | - Masatoshi Nakamura
- Clinical Laboratory, Kagoshima University Hospital, 8-35-1 Sakuragaoka, Kagoshima, 890-8520, Japan
| | - Yuki Obama
- Clinical Laboratory, Kagoshima University Hospital, 8-35-1 Sakuragaoka, Kagoshima, 890-8520, Japan
| | - Ryuko Fukuyama
- Clinical Laboratory, Kagoshima University Hospital, 8-35-1 Sakuragaoka, Kagoshima, 890-8520, Japan
| | - Yuka Hamada
- Kagoshima Prefectural Institute for Environmental Research and Public Health, 11-40 Kinko-cho, Kagoshima, 892-0835, Japan
| | - Naomi Shinkawa
- Kagoshima Prefectural Institute for Environmental Research and Public Health, 11-40 Kinko-cho, Kagoshima, 892-0835, Japan
| | - Tomimasa Sunagawa
- Center for Field Epidemiology Intelligence, Research, and Professional Development, National Institute of Infectious Diseases, Toyama 1-23-1, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Hajime Kamiya
- Center for Surveillance, Immunization and Epidemiologic Research, National Institute of Infectious Diseases, Toyama 1-23-1, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Junichiro Nishi
- Department of Infection Control and Prevention, Kagoshima University Hospital, 8-35-1 Sakuragaoka, Kagoshima, 890-8520, Japan
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Nakagawa S, Katayama T, Jin L, Wu J, Kryukov K, Oyachi R, Takeuchi JS, Fujisawa T, Asano S, Komatsu M, Onami JI, Abe T, Arita M. SARS-CoV-2 HaploGraph: visualization of SARS-CoV-2 haplotype spread in Japan. Genes Genet Syst 2023; 98:221-237. [PMID: 37839865 DOI: 10.1266/ggs.23-00085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2023] Open
Abstract
Since the early phase of the coronavirus disease 2019 (COVID-19) pandemic, a number of research institutes have been sequencing and sharing high-quality severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes to trace the route of infection in Japan. To provide insight into the spread of COVID-19, we developed a web platform named SARS-CoV-2 HaploGraph to visualize the emergence timing and geographical transmission of SARS-CoV-2 haplotypes. Using data from the GISAID EpiCoV database as of June 4, 2022, we created a haplotype naming system by determining the ancestral haplotype for each epidemic wave and showed prefecture- or region-specific haplotypes in each of four waves in Japan. The SARS-CoV-2 HaploGraph allows for interactive tracking of virus evolution and of geographical prevalence of haplotypes, and aids in developing effective public health control strategies during the global pandemic. The code and the data used for this study are publicly available at: https://github.com/ktym/covid19/.
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Affiliation(s)
- So Nakagawa
- Bioinformation and DDBJ Center, National Institute of Genetics
- Department of Molecular Life Science, Tokai University School of Medicine
- Micro/Nano Technology Center, Tokai University
- Institute of Medical Sciences, Tokai University
| | | | | | - Jiaqi Wu
- Department of Molecular Life Science, Tokai University School of Medicine
| | - Kirill Kryukov
- Bioinformation and DDBJ Center, National Institute of Genetics
- Department of Informatics, National Institute of Genetics
| | - Rise Oyachi
- Department of Molecular Life Science, Tokai University School of Medicine
| | - Junko S Takeuchi
- Center for Clinical Sciences, National Center for Global Health and Medicine
| | | | - Satomi Asano
- Department of Informatics, National Institute of Genetics
| | - Momoka Komatsu
- Smart Information Systems, Faculty of Engineering, Niigata University
| | - Jun-Ichi Onami
- Research Center for Open Science and Data Platform, National Institute of Informatics
| | - Takashi Abe
- Bioinformation and DDBJ Center, National Institute of Genetics
- Smart Information Systems, Faculty of Engineering, Niigata University
| | - Masanori Arita
- Bioinformation and DDBJ Center, National Institute of Genetics
- Department of Informatics, National Institute of Genetics
- RIKEN Center for Sustainable Resource Science
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Kuribayashi ST, Kasamatsu A, Ikenoue C, Fukusumi M, Kamiya H, Shimada T, Tanaka T, Murakami K, McLellan RT, Sekizuka T, Kuroda M, Sunagawa T. SARS-CoV-2 Infection in Wrestlers after International Tournaments, April 2021. Emerg Infect Dis 2023; 29:2393-2395. [PMID: 37787491 PMCID: PMC10617332 DOI: 10.3201/eid2911.230278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023] Open
Abstract
Epidemiologic and genomic investigation of SARS-CoV-2 infections in members of Japan's national wrestling team after participation in international tournaments in 2021 revealed multiple lineages of SARS-CoV-2 not reported in Japan. The attack rate among wrestlers was high. Results suggest possible transmission during matches. We recommend early case detection and response practices.
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Hirata Y, Katano H, Iida S, Mine S, Nagasawa S, Makino Y, Motomura A, Ozono S, Sato Y, Sekizuka T, Kuroda M, Yamaguchi R, Inokuchi G, Torimitsu S, Akitomi S, Yajima D, Saitoh H, Suzuki T, Iwase H. Genomic analysis of SARS-CoV-2 in forensic autopsy cases of COVID-19. J Med Virol 2023; 95:e28990. [PMID: 37537838 DOI: 10.1002/jmv.28990] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/25/2023] [Accepted: 07/14/2023] [Indexed: 08/05/2023]
Abstract
Numerous genomic analyses of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been conducted, highlighting its variations and lineage transitions. Despite the importance of forensic autopsy in investigating deaths due to coronavirus disease 2019 (COVID-19), including out-of-hospital deaths, viral genomic analysis has rarely been reported due in part to postmortem changes. In this study, various specimens were collected from 18 forensic autopsy cases with SARS-CoV-2 infection. Reverse-transcription quantitative polymerase chain reaction revealed the distribution of the virus in the body, primarily in the respiratory organs. Next-generation sequencing determined the complete genome sequences in 15 of the 18 cases, although some cases showed severe postmortem changes or degradation of tissue RNA. Intrahost genomic diversity of the virus was identified in one case of death due to COVID-19. The accumulation of single-nucleotide variations in the lung of the case suggested the intrahost evolution of SARS-CoV-2. Lung of the case showed diffuse alveolar damage histologically and positivity for SARS-CoV-2 by immunohistochemical analysis and in situ hybridization, indicating virus-associated pneumonia. This study provides insights into the feasibility of genomic analysis of SARS-CoV-2 in forensic autopsy cases and the potential for uncovering important information in COVID-19 deaths, including out-of-hospital deaths.
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Affiliation(s)
- Yuichiro Hirata
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Legal Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Harutaka Katano
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Shun Iida
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Sohtaro Mine
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Sayaka Nagasawa
- Department of Legal Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yohsuke Makino
- Department of Legal Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Forensic Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Ayumi Motomura
- Department of Legal Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Forensic Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Legal Medicine, International University of Health and Welfare, Chiba, Japan
| | - Seiya Ozono
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yuko Sato
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Rutsuko Yamaguchi
- Department of Legal Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Forensic Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Go Inokuchi
- Department of Legal Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Forensic Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Suguru Torimitsu
- Department of Legal Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Forensic Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shinji Akitomi
- Department of Forensic Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Japan Medical Association Research Institute, Tokyo, Japan
| | - Daisuke Yajima
- Department of Legal Medicine, International University of Health and Welfare, Chiba, Japan
| | - Hisako Saitoh
- Department of Legal Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Forensic Dentistry, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hirotaro Iwase
- Department of Legal Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Forensic Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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5
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Imamura T, Watanabe A, Serizawa Y, Nakashita M, Saito M, Okada M, Ogawa A, Tabei Y, Soumura Y, Nadaoka Y, Nakatsubo N, Chiba T, Sadamasu K, Yoshimura K, Noda Y, Iwashita Y, Ishimaru Y, Seki N, Otani K, Imamura T, Griffith MM, DeToy K, Suzuki M, Yoshida M, Tanaka A, Yauchi M, Shimada T, Oshitani H. Transmission of COVID-19 in Nightlife, Household, and Health Care Settings in Tokyo, Japan, in 2020. JAMA Netw Open 2023; 6:e230589. [PMID: 36826818 PMCID: PMC9958531 DOI: 10.1001/jamanetworkopen.2023.0589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
IMPORTANCE There have been few studies on the heterogeneous interconnection of COVID-19 outbreaks occurring in different social settings using robust, surveillance epidemiological data. OBJECTIVES To describe the characteristics of COVID-19 transmission within different social settings and to evaluate settings associated with onward transmission to other settings. DESIGN, SETTING, AND PARTICIPANTS This is a case series study of laboratory-confirmed COVID-19 cases in Tokyo between January 23 and December 5, 2020, when vaccination was not yet implemented. Using epidemiological investigation data collected by public health centers, epidemiological links were identified and classified into 7 transmission settings: imported, nightlife, dining, workplace, household, health care, and other. MAIN OUTCOMES AND MEASURES The number of cases per setting and the likelihood of generating onward transmissions were compared between different transmission settings. RESULTS Of the 44 054 confirmed COVID-19 cases in this study, 25 241 (57.3%) were among male patients, and the median (IQR) age of patients was 36 (26-52) years. Transmission settings were identified in 13 122 cases, including 6768 household, 2733 health care, and 1174 nightlife cases. More than 6600 transmission settings were detected, and nightlife (72 of 380 [18.9%]; P < .001) and health care (119 [36.2%]; P < .001) settings were more likely to involve 5 or more cases than dining, workplace, household, and other settings. Nightlife cases appeared in the earlier phase of the epidemic, while household and health care cases appeared later. After adjustment for transmission setting, sex, age group, presence of symptoms, and wave, household and health care cases were less likely to generate onward transmission compared with nightlife cases (household: adjusted odds ratio, 0.03; 95% CI, 0.02-0.05; health care: adjusted odds ratio, 0.57; 95% CI, 0.41-0.79). Household settings were associated with intergenerational transmission, while nonhousehold settings mainly comprised transmission between the same age group. Among 30 932 cases without identified transmission settings, cases with a history of visiting nightlife establishments were more likely to generate onward transmission to nonhousehold settings (adjusted odds ratio, 5.30 [95% CI, 4.64-6.05]; P < .001) than those without such history. CONCLUSIONS AND RELEVANCE In this case series study, COVID-19 cases identified in nightlife settings were associated with a higher likelihood of spreading COVID-19 than household and health care cases. Surveillance and interventions targeting nightlife settings should be prioritized to disrupt COVID-19 transmission, especially in the early stage of an epidemic.
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Affiliation(s)
- Takeaki Imamura
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | | | | | | | - Mayuko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Mayu Okada
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Asamoe Ogawa
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Yukiko Tabei
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | | | - Yoko Nadaoka
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Naoki Nakatsubo
- Public Health and Disease Prevention Division, Suginami City Public Health Center, Tokyo, Japan
| | - Takashi Chiba
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Kenji Sadamasu
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | | | - Yoshihiro Noda
- Department of Plastic, Reconstructive and Aesthetic Surgery, Nippon Medical School, Tokyo, Japan
| | | | - Yuji Ishimaru
- Bureau of Social Welfare and Public Health, Tokyo Metropolitan Government, Tokyo, Japan
| | - Naomi Seki
- Ota City Public Health Center, Tokyo, Japan
| | - Kanako Otani
- National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Matthew Myers Griffith
- National Centre for Epidemiology and Population Health, the Australian National University, Canberra, Australia
| | - Kelly DeToy
- Division of Global Disease Epidemiology and Control, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Motoi Suzuki
- National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Atsuko Tanaka
- Bureau of Social Welfare and Public Health, Tokyo Metropolitan Government, Tokyo, Japan
| | | | - Tomoe Shimada
- National Institute of Infectious Diseases, Tokyo, Japan
| | - Hitoshi Oshitani
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
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6
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A Case of a Malignant Lymphoma Patient Persistently Infected with SARS-CoV-2 for More than 6 Months. Medicina (B Aires) 2023; 59:medicina59010108. [PMID: 36676732 PMCID: PMC9864643 DOI: 10.3390/medicina59010108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 12/25/2022] [Accepted: 12/28/2022] [Indexed: 01/06/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is an emerging infectious disease caused by severe acute respiratory syndrome 2 (SARS-CoV-2). There are many unknowns regarding the handling of long-term SARS-CoV-2 infections in immunocompromised patients. Here, we describe the lethal disease course in a SARS-CoV-2-infected patient during Bruton's tyrosine kinase inhibitor therapy. We performed whole-genome analysis using samples obtained during the course of the disease in a 63-year-old woman who was diagnosed with intraocular malignant lymphoma of the right eye in 2012. She had received treatment since the diagnosis. An autologous transplant was performed in 2020, but she experienced a worsening of the primary disease 26 days before she was diagnosed with a positive SARS-CoV-2 RT-PCR. Tirabrutinib was administered for the primary disease. A cluster of COVID-19 infections occurred in the hematological ward while the patient was hospitalized, and she became infected on day 0. During the course of the disease, she experienced repeated remission exacerbations of COVID-19 pneumonia and eventually died on day 204. SARS-CoV-2 whole-viral sequencing revealed that the patient shed the virus long-term. Viral infectivity studies confirmed infectious virus on day 189, suggesting that the patient might be still infectious. This case report describes the duration and viral genetic evaluation of a patient with malignant lymphoma who developed SARS-CoV-2 infection during Bruton's tyrosine kinase inhibitor therapy and in whom the infection persisted for over 6 months.
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Palyanova N, Sobolev I, Alekseev A, Glushenko A, Kazachkova E, Markhaev A, Kononova Y, Gulyaeva M, Adamenko L, Kurskaya O, Bi Y, Xin Y, Sharshov K, Shestopalov A. Genomic and Epidemiological Features of COVID-19in the Novosibirsk Region during the Beginning of the Pandemic. Viruses 2022; 14:v14092036. [PMID: 36146842 PMCID: PMC9501018 DOI: 10.3390/v14092036] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/07/2022] [Accepted: 09/09/2022] [Indexed: 11/16/2022] Open
Abstract
In this retrospective, single-center study, we conducted an analysis of 13,699 samples from different individuals obtained from the Federal Research Center of Fundamental and Translational Medicine, from 1 April to 30 May 2020 in Novosibirsk region (population 2.8 million people). We identified 6.49% positive for SARS-CoV-2 cases out of the total number of diagnostic tests, and 42% of them were from asymptomatic people. We also detected two asymptomatic people, who had no confirmed contact with patients with COVID-19. The highest percentage of positive samples was observed in the 80+ group (16.3%), while among the children and adults it did not exceed 8%. Among all the people tested, 2423 came from a total of 80 different destinations and only 27 of them were positive for SARS-CoV-2. Out of all the positive samples, 15 were taken for SARS-CoV-2 sequencing. According to the analysis of the genome sequences, the SARS-CoV-2 variants isolated in the Novosibirsk region at the beginning of the pandemic belonged to three phylogenetic lineages according to the Pangolin classification: B.1, B.1.1, and B.1.1.129. All Novosibirsk isolates contained the D614G substitution in the Spike protein, two isolates werecharacterized by an additional M153T mutation, and one isolate wascharacterized by the L5F mutation.
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Affiliation(s)
- Natalia Palyanova
- Laboratory of Molecular Epidemiology and Biodiversity of Viruses, Research Institute of Virology, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, Russia
- Correspondence:
| | - Ivan Sobolev
- Laboratory of Molecular Epidemiology and Biodiversity of Viruses, Research Institute of Virology, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, Russia
| | - Alexander Alekseev
- Laboratory of Molecular Epidemiology and Biodiversity of Viruses, Research Institute of Virology, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, Russia
| | - Alexandra Glushenko
- Laboratory of Molecular Epidemiology and Biodiversity of Viruses, Research Institute of Virology, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, Russia
| | - Evgeniya Kazachkova
- Laboratory of Molecular Epidemiology and Biodiversity of Viruses, Research Institute of Virology, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, Russia
| | - Alexander Markhaev
- Laboratory of Molecular Epidemiology and Biodiversity of Viruses, Research Institute of Virology, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, Russia
| | - Yulia Kononova
- Laboratory of Molecular Epidemiology and Biodiversity of Viruses, Research Institute of Virology, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, Russia
| | - Marina Gulyaeva
- Laboratory of Molecular Epidemiology and Biodiversity of Viruses, Research Institute of Virology, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, Russia
- Department of Natural Science, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Lubov Adamenko
- Laboratory of Molecular Epidemiology and Biodiversity of Viruses, Research Institute of Virology, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, Russia
| | - Olga Kurskaya
- Laboratory of Molecular Epidemiology and Biodiversity of Viruses, Research Institute of Virology, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, Russia
| | - Yuhai Bi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Institute of Microbiology, Center for Influenza Research and Early-Warning (CASCIRE), Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Yuhua Xin
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Kirill Sharshov
- Laboratory of Molecular Epidemiology and Biodiversity of Viruses, Research Institute of Virology, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, Russia
| | - Alexander Shestopalov
- Laboratory of Molecular Epidemiology and Biodiversity of Viruses, Research Institute of Virology, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, Russia
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8
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Attwood SW, Hill SC, Aanensen DM, Connor TR, Pybus OG. Phylogenetic and phylodynamic approaches to understanding and combating the early SARS-CoV-2 pandemic. Nat Rev Genet 2022; 23:547-562. [PMID: 35459859 PMCID: PMC9028907 DOI: 10.1038/s41576-022-00483-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2022] [Indexed: 01/05/2023]
Abstract
Determining the transmissibility, prevalence and patterns of movement of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is central to our understanding of the impact of the pandemic and to the design of effective control strategies. Phylogenies (evolutionary trees) have provided key insights into the international spread of SARS-CoV-2 and enabled investigation of individual outbreaks and transmission chains in specific settings. Phylodynamic approaches combine evolutionary, demographic and epidemiological concepts and have helped track virus genetic changes, identify emerging variants and inform public health strategy. Here, we review and synthesize studies that illustrate how phylogenetic and phylodynamic techniques were applied during the first year of the pandemic, and summarize their contributions to our understanding of SARS-CoV-2 transmission and control.
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Affiliation(s)
- Stephen W Attwood
- Department of Zoology, University of Oxford, Oxford, UK.
- Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK.
| | - Sarah C Hill
- Department of Pathobiology and Population Sciences, Royal Veterinary College, University of London, London, UK
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Thomas R Connor
- Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK
- School of Biosciences, Cardiff University, Cardiff, UK
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, UK.
- Department of Pathobiology and Population Sciences, Royal Veterinary College, University of London, London, UK.
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9
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Neutralizing-antibody response to SARS-CoV-2 for 12 months after the COVID-19 workplace outbreaks in Japan. PLoS One 2022; 17:e0273712. [PMID: 36040882 PMCID: PMC9426944 DOI: 10.1371/journal.pone.0273712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 08/11/2022] [Indexed: 11/19/2022] Open
Abstract
This study aimed to elucidate the 12-month durability of neutralizing antibodies (NAbs) against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in patients infected during the 2020 workplace outbreaks of coronavirus disease 2019 (COVID-19) in Japan. We followed 33 Japanese patients infected with SARS-CoV-2 in April 2020 for 12 months (12M). Patients were tested for NAbs and for antibodies against the SARS-CoV-2 nucleocapsid (anti-NC-Ab) and antibodies against the spike receptor-binding domain (anti-RBD-Ab). Tests were performed at 2M, 6M, and 12M after the primary infection (api) with commercially available test kits. In 90.9% (30/33) of patients, NAbs persisted for 12M api, though the median titers significantly declined from 78.7% (interquartile range [IQR]: 73.0–85.0%) at 2M, to 59.8% (IQR: 51.2–77.9) at 6M (P = 0.008), and to 56.2% (IQR: 39.6–74.4) at 12M (P<0.001). An exponential decay model showed that the NAb level reached undetectable concentrations at 35.5 months api (95% confidence interval: 26.5–48.0 months). Additionally, NAb titers were significantly related to anti-RBD-Ab titers (rho = 0.736, P<0.001), but not to anti-NC-Ab titers. In most patients convalescing from COVID-19, NAbs persisted for 12M api. This result suggested that patients need a booster vaccination within one year api, even though NAbs could be detected for over two years api. Anti-RBD-Ab titers could be used as a surrogate marker for predicting residual NAb levels.
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10
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Matsumura Y, Nagao M, Yamamoto M, Tsuchido Y, Noguchi T, Shinohara K, Yukawa S, Inoue H, Ikeda T. Transmissibility of SARS-CoV-2 B.1.1.214 and Alpha Variants during 4 COVID-19 Waves, Kyoto, Japan, January 2020-June 2021. Emerg Infect Dis 2022; 28. [PMID: 35710464 PMCID: PMC9328921 DOI: 10.3201/eid2808.220420] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Household transmission is a primary source of SARS-CoV-2 spread. We used COVID-19 epidemiologic investigation data and viral genome analysis data collected in the city of Kyoto, Japan, during January 2020–June 2021 to evaluate the effects of different settings and viral strains on SARS-CoV-2 transmission. Epidemiologic investigations of 5,061 COVID-19 cases found that the most common category for close contact was within households (35.3%); this category also had the highest reverse transcription PCR positivity. The prevalent viral lineage shifted from B.1.1.214 in the third wave to the Alpha variant in the fourth wave. The proportion of secondary cases associated with households also increased from the third to fourth waves (27% vs. 29%). Among 564 contacts from 206 households, Alpha variant was significantly associated with household transmission (odds ratio 1.52, 95% CI 1.06–2.18) compared with B.1.1.214. Public health interventions targeting household contacts and specific variants could help control SARS-CoV-2 transmission.
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11
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Goto K, Komatsu K, Sekizuka T, Ebisawa H, Ootake M, Honda M, Nagata N, Yoshida D, Yanaoka T, Kimura H, Kuroda M. Detection of SARS-CoV-2 Genome for over 100 Days after COVID-19 Onset. Jpn J Infect Dis 2022; 75:620-622. [PMID: 35908868 DOI: 10.7883/yoken.jjid.2021.841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019, is spreading globally. In general, the viral genome becomes undetectable within a couple of weeks after infection. Herein, we report a case of long-term detection of the SARS-CoV-2 genome from the same individual for 106 days. Whole genome sequencing was performed on specimens taken at the onset of the disease and at 2 months after onset, and the B.1.1.7 lineage was detected in both samples. Comparison of the full-length sequences revealed a single-base difference and no amino acid mutations. This is the first case in Japan where the virus was detected over a long time, and the full-length sequences were compared.
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Affiliation(s)
- Keiko Goto
- Department of Virology, Ibaraki Prefectural Institute of Public Health, Japan
| | - Kenichi Komatsu
- Department of Internal Medicine, Ibaraki Western Medical Center, Japan
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Japan
| | - Hiromi Ebisawa
- Department of Internal Medicine, Ibaraki Western Medical Center, Japan
| | | | | | - Noriko Nagata
- Department of Virology, Ibaraki Prefectural Institute of Public Health, Japan
| | - Daisuke Yoshida
- Department of Virology, Ibaraki Prefectural Institute of Public Health, Japan
| | - Toshikazu Yanaoka
- Department of Virology, Ibaraki Prefectural Institute of Public Health, Japan
| | - Hirokazu Kimura
- Department of Health Science, Gunma Paz University Graduate School, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Japan
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12
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Inaida S, Paul RE, Matsuno S. Viral transmissibility of SARS-CoV-2 accelerates in the winter, similarly to influenza epidemics. Am J Infect Control 2022; 50:1070-1076. [PMID: 35605752 PMCID: PMC9121648 DOI: 10.1016/j.ajic.2022.05.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/09/2022] [Accepted: 05/13/2022] [Indexed: 02/06/2023]
Abstract
The transmissibility of SARS-CoV-2 is anticipated to increase in the winter because of increased viral survival in cold damp air and thus would exacerbate viral spread in community. Analysis to capture the seasonal trend is needed to be prepared for future epidemics. We compared regression models for the 5-week case prior to each epidemic peak week for both the COVID-19 and influenza epidemics in winter and summer. The weekly case increase ratio was compared, using non-paired t tests between seasons. In order to test the robustness of seasonal transmission patterns, the normalized weekly case numbers of COVID-19 and influenza case rates of all seasons were assessed in a combined quadratic regression analysis. In winter, the weekly case increase ratio accelerated before epidemic peaks, similarly, for both COVID-19 and influenza. The quadratic regression models of weekly cases were observed to be convex curves in the winter and concave curves in the spring/summer for both COVID-19 and influenza. A significant increase of case increase ratio (3.19 [95%CI:0.01-6.37, P = .049]) of the COVID-19 and influenza epidemics was observed in winter as compared to spring/summer before the epidemic peak. The epidemic of COVID-19 was found to mirror that of influenza, suggesting a strong underlying seasonal transmissibility. Influenza epidemics can potentially be a useful reference for the COVID-19 epidemics.
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13
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Kinoshita R, Jung SM, Kobayashi T, Akhmetzhanov AR, Nishiura H. Epidemiology of coronavirus disease 2019 (COVID-19) in Japan during the first and second waves. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2022; 19:6088-6101. [PMID: 35603392 DOI: 10.3934/mbe.2022284] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Following the emergence and worldwide spread of coronavirus disease 2019 (COVID-19), each country has attempted to control the disease in different ways. The first patient with COVID-19 in Japan was diagnosed on 15 January 2020, and until 31 October 2020, the epidemic was characterized by two large waves. To prevent the first wave, the Japanese government imposed several control measures such as advising the public to avoid the 3Cs (closed spaces with poor ventilation, crowded places with many people nearby, and close-contact settings such as close-range conversations) and implementation of "cluster buster" strategies. After a major epidemic occurred in April 2020 (the first wave), Japan asked its citizens to limit their numbers of physical contacts and announced a non-legally binding state of emergency. Following a drop in the number of diagnosed cases, the state of emergency was gradually relaxed and then lifted in all prefectures of Japan by 25 May 2020. However, the development of another major epidemic (the second wave) could not be prevented because of continued chains of transmission, especially in urban locations. The present study aimed to descriptively examine propagation of the COVID-19 epidemic in Japan with respect to time, age, space, and interventions implemented during the first and second waves. Using publicly available data, we calculated the effective reproduction number and its associations with the timing of measures imposed to suppress transmission. Finally, we crudely calculated the proportions of severe and fatal COVID-19 cases during the first and second waves. Our analysis identified key characteristics of COVID-19, including density dependence and also the age dependence in the risk of severe outcomes. We also identified that the effective reproduction number during the state of emergency was maintained below the value of 1 during the first wave.
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Affiliation(s)
- Ryo Kinoshita
- School of Public Health, Kyoto University, Kyoto, Japan
- National Institute of Infectious Diseases, Center of Surveillance Immunization and Epidemiologic Research, Tokyo, Japan
| | - Sung-Mok Jung
- School of Public Health, Kyoto University, Kyoto, Japan
- Graduate School of Medicine, Hokkaido University, Sapporo, Japan
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14
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Ode H, Nakata Y, Nagashima M, Hayashi M, Yamazaki T, Asakura H, Suzuki J, Kubota M, Matsuoka K, Matsuda M, Mori M, Sugimoto A, Imahashi M, Yokomaku Y, Sadamasu K, Iwatani Y. Molecular-Epidemiological Features of SARS-CoV-2 in Japan, 2020-2021. Virus Evol 2022; 8:veac034. [PMID: 35478716 PMCID: PMC9037363 DOI: 10.1093/ve/veac034] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/12/2022] [Accepted: 04/07/2022] [Indexed: 11/24/2022] Open
Abstract
There were five epidemic waves of coronavirus disease 2019 in Japan between 2020 and 2021. It remains unclear how the domestic waves arose and abated. To better understand this, we analyzed the pangenomic sequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and characterized the molecular epidemiological features of the five epidemic waves in Japan. In this study, we performed deep sequencing to determine the pangenomic SARS-CoV-2 sequences of 1,286 samples collected in two cities far from each other, Tokyo Metropolis and Nagoya. Then, the spatiotemporal genetic changes of the obtained sequences were compared with the sequences available in the Global Initiative on Sharing All Influenza Data (GISAID) database. A total of 873 genotypes carrying different sets of mutations were identified in the five epidemic waves. Phylogenetic analysis demonstrated that sharp displacements of lineages and genotypes occurred between consecutive waves over the 2 years. In addition, a wide variety of genotypes were observed in the early half of each wave, whereas a few genotypes were detected across Japan during an entire wave. Phylogenetically, putative descendant genotypes observed late in each wave displayed regional clustering and evolution in Japan. The genetic diversity of SARS-CoV-2 displayed uneven dynamics during each epidemic wave in Japan. Our findings provide an important molecular epidemiological basis to aid in controlling future SARS-CoV-2 epidemics.
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Affiliation(s)
- Hirotaka Ode
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya 460-0001, Japan
| | - Yoshihiro Nakata
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya 460-0001, Japan
- Division of Basic Medicine, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Mami Nagashima
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Tokyo169-0073, Japan
| | - Masaki Hayashi
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Tokyo169-0073, Japan
| | - Takako Yamazaki
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Tokyo169-0073, Japan
| | - Hiroyuki Asakura
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Tokyo169-0073, Japan
| | - Jun Suzuki
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Tokyo169-0073, Japan
| | - Mai Kubota
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya 460-0001, Japan
| | - Kazuhiro Matsuoka
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya 460-0001, Japan
| | - Masakazu Matsuda
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya 460-0001, Japan
| | - Mikiko Mori
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya 460-0001, Japan
- Division of Basic Medicine, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Atsuko Sugimoto
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya 460-0001, Japan
| | - Mayumi Imahashi
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya 460-0001, Japan
| | - Yoshiyuki Yokomaku
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya 460-0001, Japan
| | - Kenji Sadamasu
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Tokyo169-0073, Japan
| | - Yasumasa Iwatani
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya 460-0001, Japan
- Division of Basic Medicine, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
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15
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Sekizuka T, Itokawa K, Saito M, Shimatani M, Matsuyama S, Hasegawa H, Saito T, Kuroda M. Genome Recombination between Delta and Alpha Variants of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Jpn J Infect Dis 2022; 75:415-418. [DOI: 10.7883/yoken.jjid.2021.844] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Japan
| | - Kentaro Itokawa
- Pathogen Genomics Center, National Institute of Infectious Diseases, Japan
| | - Masumichi Saito
- Center for Emergency Preparedness and Response, National Institute of Infectious Diseases, Japan
| | - Michitsugu Shimatani
- Center for Research Planning and Coordination, National Institute of Infectious Diseases, Japan
| | - Shutoku Matsuyama
- Center for Influenza and Respiratory Virus Research, National Institute of Infectious Diseases, Japan
| | - Hideki Hasegawa
- Center for Influenza and Respiratory Virus Research, National Institute of Infectious Diseases, Japan
| | - Tomoya Saito
- Center for Emergency Preparedness and Response, National Institute of Infectious Diseases, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Japan
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16
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Hibiya K, Iwata H, Kinjo T, Shinzato A, Tateyama M, Ueda S, Fujita J. Incidence of common infectious diseases in Japan during the COVID-19 pandemic. PLoS One 2022; 17:e0261332. [PMID: 35020724 PMCID: PMC8754328 DOI: 10.1371/journal.pone.0261332] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 11/29/2021] [Indexed: 11/18/2022] Open
Abstract
Recent reports indicate that respiratory infectious diseases were suppressed during the novel coronavirus disease-2019 (COVID-19) pandemic. COVID-19 led to behavioral changes aimed to control droplet transmission or contact transmission. In this study, we examined the incidence of common infectious diseases in Japan during the COVID-19 pandemic. COVID-19 data were extracted from the national data based on the National Epidemiological Surveillance of Infectious Diseases (NESID). Common infectious diseases were selected from notifiable infectious diseases under the NESID. The epidemic activity of the diseases during 2015-2020 was evaluated based on the Infectious Disease Weekly Reports published by the National Institute of Infectious Diseases. Each disease was then categorized according to the route of transmission. Many Japanese people had adopted hygienic activities, such as wearing masks and hand washing, even before the COVID-19 pandemic. We examined the correlation between the time-series of disease counts of common infectious diseases and COVID-19 over time using cross-correlation analysis. The weekly number of cases of measles, rotavirus, and several infections transmitted by droplet spread, was negatively correlated with the weekly number of cases of COVID-19 for up to 20 weeks in the past. According to the difference-in-differences analysis, the activity of influenza and rubella was significantly lower starting from the second week in 2020 than that in 2015-2019. Only legionellosis was more frequent throughout the year than in 2015-2019. Lower activity was also observed in some contact transmitted, airborne-transmitted, and fecal-oral transmitted diseases. However, carbapenem-resistant Enterobacteriaceae, exanthema subitum, showed the same trend as that over the previous 5 years. In conclusion, our study shows that public health interventions for the COVID-19 pandemic may have effectively prevented the transmission of most droplet-transmitted diseases and those transmitted through other routes.
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Affiliation(s)
- Kenji Hibiya
- Department of Infectious, Respiratory and Digestive Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara-cho, Okinawa, Japan
- Department of Diagnostic Pathology, University of the Ryukyus Hospital, Nishihara-cho, Okinawa, Japan
- * E-mail:
| | - Hiroyoshi Iwata
- Clinical Pharmacology & Therapeutics, University of The Ryukyus School of Medicine, Nishihara-cho, Okinawa, Japan
| | - Takeshi Kinjo
- Department of Infectious, Respiratory and Digestive Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara-cho, Okinawa, Japan
| | - Akira Shinzato
- Department of Infectious, Respiratory and Digestive Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara-cho, Okinawa, Japan
| | - Masao Tateyama
- Department of Infectious, Respiratory and Digestive Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara-cho, Okinawa, Japan
| | - Shinichiro Ueda
- Clinical Pharmacology & Therapeutics, University of The Ryukyus School of Medicine, Nishihara-cho, Okinawa, Japan
| | - Jiro Fujita
- Department of Infectious, Respiratory and Digestive Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara-cho, Okinawa, Japan
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17
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Pro108Ser mutation of SARS-CoV-2 3CL pro reduces the enzyme activity and ameliorates the clinical severity of COVID-19. Sci Rep 2022; 12:1299. [PMID: 35079088 PMCID: PMC8789791 DOI: 10.1038/s41598-022-05424-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 01/12/2022] [Indexed: 11/13/2022] Open
Abstract
Recently, an international randomized controlled clinical trial showed that patients with SARS-CoV-2 infection treated orally with the 3-chymotrypsin-like protease (3CLpro) inhibitor PF-07321332 within three days of symptom onset showed an 89% lower risk of COVID-19-related hospital admission/ death from any cause as compared with the patients who received placebo. Lending support to this critically important result of the aforementioned trial, we demonstrated in our study that patients infected with a SARS-Cov-2 sub-lineage (B.1.1.284) carrying the Pro108Ser mutation in 3CLpro tended to have a comparatively milder clinical course (i.e., a smaller proportion of patients required oxygen supplementation during the clinical course) than patients infected with the same sub-lineage of virus not carrying the mutation. Characterization of the mutant 3CLpro revealed that the Kcat/Km of the 3CLpro enzyme containing Ser108 was 58% lower than that of Pro108 3CLpro. Hydrogen/deuterium-exchange mass spectrometry (HDX-MS) revealed that the reduced activity was associated with structural perturbation surrounding the substrate-binding region of the enzyme, which is positioned behind and distant from the 108th amino acid residue. Our findings of the attenuated clinical course of COVID-19 in patients infected with SARS-CoV-2 strains with reduced 3CLpro enzymatic activity greatly endorses the promising result of the aforementioned clinical trial of the 3CLpro inhibitor.
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18
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Ishikawa F, Udaka Y, Oyamada H, Ishino K, Tokimatsu I, Sagara H, Kiuchi Y. Genetic epidemiology using whole genome sequencing and haplotype networks revealed the linkage of SARS-CoV-2 infection in nosocomial outbreak. Infect Prev Pract 2021; 3:100190. [PMID: 34841243 PMCID: PMC8611819 DOI: 10.1016/j.infpip.2021.100190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 11/17/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND A characteristic feature of SARS-CoV-2 is its ability to transmit from pre- or asymptomatic patients, complicating the tracing of infection pathways and causing outbreaks. Despite several reports that whole genome sequencing (WGS) and haplotype networks are useful for epidemiologic analysis, little is known about their use in nosocomial infections. AIM We aimed to demonstrate the advantages of genetic epidemiology in identifying the link in nosocomial infection by comparing single nucleotide variations (SNVs) of isolates from patients associated with an outbreak in Showa University Hospital. METHODS We used specimens from 32 patients in whom COVID-19 had been diagnosed using clinical reverse transcription-polymerase chain reaction tests. RNA of SARS-CoV-2 from specimens was reverse-transcribed and analysed using WGS. SNVs were extracted and used for lineage determination, phylogenetic tree analysis, and median-joining analysis. FINDINGS The lineage of SARS-CoV-2 that was associated with outbreak in Showa University Hospital was B.1.1.214, which was consistent with that found in the Kanto metropolitan area during the same period. Consistent with canonical epidemiological observations, haplotype network analysis was successful for the classification of patients. Additionally, phylogenetic tree analysis revealed three independent introductions of the virus into the hospital during the outbreak. Further, median-joining analysis indicated that four patients were directly infected by any of the others in the same cluster. CONCLUSION Genetic epidemiology with WGS and haplotype networks is useful for tracing transmission and optimizing prevention strategies in nosocomial outbreaks.
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Key Words
- COVID-19, coronavirus disease 2019
- Epidemiological analysis
- GISAID, Global Initiative on Sharing All Influenza Data
- Haplotype networks
- KMA, Kanto metropolitan area
- NJ, neighbour-joining
- Phylogenetic tree analysis
- RT-PCR, reverse transcription-polymerase chain reaction
- SARS-CoV-2, severe acute respiratory syndrome coronavirus 2
- SNVs, single nucleotide variations
- SUH, Showa University Hospital
- Severe acute respiratory syndrome coronavirus 2
- VOC, variant of concern
- WGS, whole genome sequencing
- Whole genome sequencing
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Affiliation(s)
- Fumihiro Ishikawa
- PCR Centre for COVID-19, Showa University Hospital, Tokyo, Japan
- Centre for Biotechnology, Showa University, Tokyo, Japan
| | - Yuko Udaka
- PCR Centre for COVID-19, Showa University Hospital, Tokyo, Japan
- Department of Pharmacology, Showa University School of Medicine, Tokyo, Japan
| | - Hideto Oyamada
- PCR Centre for COVID-19, Showa University Hospital, Tokyo, Japan
- Department of Pharmacology, Showa University School of Medicine, Tokyo, Japan
| | - Keiko Ishino
- PCR Centre for COVID-19, Showa University Hospital, Tokyo, Japan
- Division of Infection Control Sciences, Department of Clinical Pharmacy, Showa University School of Pharmacy, Tokyo, Japan
| | - Issei Tokimatsu
- Division of Infectious Diseases, Department of Internal Medicine, Showa University School of Medicine, Tokyo, Japan
| | - Hironori Sagara
- Division of Respiratory Medicine and Allergology, Department of Internal Medicine, Showa University School of Medicine, Tokyo, Japan
| | - Yuji Kiuchi
- PCR Centre for COVID-19, Showa University Hospital, Tokyo, Japan
- Department of Pharmacology, Showa University School of Medicine, Tokyo, Japan
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19
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Lin C, da Silva E, Sahukhan A, Palou T, Buadromo E, Hoang T, Howden BP. Towards Equitable Access to Public Health Pathogen Genomics in the Western Pacific. THE LANCET REGIONAL HEALTH. WESTERN PACIFIC 2021; 18:100321. [PMID: 34841379 PMCID: PMC8610764 DOI: 10.1016/j.lanwpc.2021.100321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/13/2021] [Accepted: 10/21/2021] [Indexed: 10/26/2022]
Abstract
The COVID-19 pandemic has increased interest and understanding of the utility of pathogen genomics across the Western Pacific region. Access to genomic data enhances surveillance and response to COVID-19, and will also support surveillance of other infectious diseases and antimicrobial resistant pathogens. Models of access can be determined based on intended purpose, use and sustainability. Achieving equitable access to genomics across the Western Pacific will contribute to the development of a regional public health genomics network to respond to major disease threats in the future.
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Affiliation(s)
- Chantel Lin
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne, Victoria 3000, Australia
| | | | | | - Theresa Palou
- National Coordinating Centre, Ministry of Health, Islander Dr, Port Moresby, Papua New Guinea
| | - Eka Buadromo
- The Pacific Community (SPC), Suva, Fiji, 95 Promenade Roger Laroque, BP D5, 98848 Noumea, New Caledonia
| | - Tuyet Hoang
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne, Victoria 3000, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne, Victoria 3000, Australia
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20
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Shimura T, Abe K, Takenouchi T, Yamada M, Suzuki H, Suematsu M, Nakakubo S, Kamada K, Konno S, Teshima T, Kosaki K. Multiple introductions of SARS-CoV-2 B.1.1.214 lineages from mainland Japan preceded the third wave of the COVID-19 epidemic in Hokkaido. Travel Med Infect Dis 2021; 44:102210. [PMID: 34822976 PMCID: PMC8606351 DOI: 10.1016/j.tmaid.2021.102210] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 11/12/2021] [Accepted: 11/15/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND The third wave of the COVID-19 epidemic in the island of Hokkaido, the second largest island in Japan, began abruptly in October 2020. METHODS We conducted a phylodynamic analysis of the SARS-CoV-2 genome sequences obtained from tertiary medical centers in the Greater Tokyo Area and Sapporo, the largest city in the island of Hokkaido, and genome sequences published by GISAID, an international SARS-CoV-2 genome database. We also analyzed the statistics on the person-nights of travelers in the island of Hokkaido from the Greater Tokyo Area in 2019 versus 2020. RESULTS At least eight sub-lineages belonging to the B.1.1.214 lineage were introduced to the island of Hokkaido from the island of Honshu, the mainland of Japan from late July to November 2020, during the governmental travel promotion program. Five of the eight sub-lineages originated from the Greater Tokyo Area. Comparison of the monthly ratios of the person-nights of travelers in the island of Hokkaido from the Greater Tokyo Area in 2019 and 2020 revealed that the highest value occurred in October 2020. CONCLUSION We contend that the Japanese governmental travel promotion program contributed to the introduction of the B.1.1.214 sub-lineages from the main island of Honshu to the island of Hokkaido, and drove the third wave in Hokkaido, even if we are unable to establish the causality.
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Affiliation(s)
- Takako Shimura
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Kodai Abe
- Department of Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Toshiki Takenouchi
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Mamiko Yamada
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Hisato Suzuki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Makoto Suematsu
- Department of Biochemistry, Keio University School of Medicine, Tokyo, Japan
| | - Sho Nakakubo
- Department of Respiratory Medicine, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Keisuke Kamada
- Department of Respiratory Medicine, Hokkaido University Faculty of Medicine, Sapporo, Japan; Department of Mycobacterium Reference and Research, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Satoshi Konno
- Department of Respiratory Medicine, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Takanori Teshima
- Department of Hematology, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan.
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21
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Highly Neutralizing COVID-19 Convalescent Plasmas Potently Block SARS-CoV-2 Replication and Pneumonia in Syrian Hamsters. J Virol 2021; 96:e0155121. [PMID: 34818068 PMCID: PMC8865546 DOI: 10.1128/jvi.01551-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Despite various attempts to treat severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected patients with COVID-19 convalescent plasmas, neither appropriate approach nor clinical utility has been established. We examined the efficacy of administration of highly neutralizing COVID-19 convalescent plasma (hn-plasmas) and such plasma-derived IgG administration using the Syrian hamster COVID-19 model. Two hn-plasmas, which were in the best 1% of 340 neutralizing activity-determined convalescent plasmas, were intraperitoneally administered to SARS-CoV-2-infected hamsters, resulting in a significant reduction of viral titers in lungs by up to 32-fold compared to the viral titers in hamsters receiving control nonneutralizing plasma, while with two moderately neutralizing plasmas (mn-plasmas) administered, viral titer reduction was by up to 6-fold. IgG fractions purified from the two hn-plasmas also reduced viral titers in lungs more than those from the two mn-plasmas. The severity of lung lesions seen in hamsters receiving hn-plasmas was minimal to moderate as assessed using microcomputerized tomography, which histological examination confirmed. Western blotting revealed that all four COVID-19 convalescent plasmas variably contained antibodies against SARS-CoV-2 components, including the receptor-binding domain and S1 domain. The present data strongly suggest that administering potent neutralizing activity-confirmed COVID-19 convalescent plasmas would be efficacious in treating patients with COVID-19. IMPORTANCE Convalescent plasmas obtained from patients who recovered from a specific infection have been used as agents to treat other patients infected with the very pathogen. To treat using convalescent plasmas, despite that more than 10 randomized controlled clinical trials have been conducted and more than 100 studies are currently ongoing, the effects of convalescent plasma against COVID-19 remained uncertain. On the other hand, certain COVID-19 vaccines have been shown to reduce the clinical COVID-19 onset by 94 to 95%, for which the elicited SARS-CoV-2-neutralizing antibodies are apparently directly responsible. Here, we demonstrate that highly neutralizing effect-confirmed convalescent plasmas significantly reduce the viral titers in the lung of SARS-CoV-2-infected Syrian hamsters and block the development of virally induced lung lesions. The present data provide a proof of concept that the presence of highly neutralizing antibody in COVID-19 convalescent plasmas is directly responsible for the reduction of viral replication and support the use of highly neutralizing antibody-containing plasmas in COVID-19 therapy with convalescent plasmas.
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22
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Wagatsuma K, Sato R, Yamazaki S, Iwaya M, Takahashi Y, Nojima A, Oseki M, Abe T, Phyu WW, Tamura T, Sekizuka T, Kuroda M, Matsumoto HH, Saito R. Genomic Epidemiology Reveals Multiple Introductions of Severe Acute Respiratory Syndrome Coronavirus 2 in Niigata City, Japan, Between February and May 2020. Front Microbiol 2021; 12:749149. [PMID: 34777297 PMCID: PMC8581661 DOI: 10.3389/fmicb.2021.749149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/04/2021] [Indexed: 01/19/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) has caused a serious disease burden and poses a tremendous public health challenge worldwide. Here, we report a comprehensive epidemiological and genomic analysis of SARS-CoV-2 from 63 patients in Niigata City, a medium-sized Japanese city, during the early phase of the pandemic, between February and May 2020. Among the 63 patients, 32 (51%) were female, with a mean (±standard deviation) age of 47.9 ± 22.3 years. Fever (65%, 41/63), malaise (51%, 32/63), and cough (35%, 22/63) were the most common clinical symptoms. The median Ct value after the onset of symptoms lowered within 9 days at 20.9 cycles (interquartile range, 17–26 cycles), but after 10 days, the median Ct value exceeded 30 cycles (p < 0.001). Of the 63 cases, 27 were distributed in the first epidemic wave and 33 in the second, and between the two waves, three cases from abroad were identified. The first wave was epidemiologically characterized by a single cluster related to indoor sports activity spread in closed settings, which included mixing indoors with families, relatives, and colleagues. The second wave showed more epidemiologically diversified events, with most index cases not related to each other. Almost all secondary cases were infected by droplets or aerosols from closed indoor settings, but at least two cases in the first wave were suspected to be contact infections. Results of the genomic analysis identified two possible clusters in Niigata City, the first of which was attributed to clade S (19B by Nexstrain clade) with a monophyletic group derived from the Wuhan prototype strain but that of the second wave was polyphyletic suggesting multiple introductions, and the clade was changed to GR (20B), which mainly spread in Europe in early 2020. These findings depict characteristics of SARS-CoV-2 transmission in the early stages in local community settings during February to May 2020 in Japan, and this integrated approach of epidemiological and genomic analysis may provide valuable information for public health policy decision-making for successful containment of chains of infection.
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Affiliation(s)
- Keita Wagatsuma
- Division of International Health (Public Health), Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Ryosuke Sato
- Niigata City Public Health and Sanitation Center, Niigata, Japan
| | - Satoru Yamazaki
- Niigata City Public Health and Sanitation Center, Niigata, Japan
| | - Masako Iwaya
- Niigata City Public Health and Sanitation Center, Niigata, Japan
| | | | - Akiko Nojima
- Niigata City Public Health and Sanitation Center, Niigata, Japan
| | - Mitsuru Oseki
- Division of Health Science, Niigata City Institute of Public Health and Environment, Niigata, Japan
| | - Takashi Abe
- Division of Bioinformatics, Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Wint Wint Phyu
- Division of International Health (Public Health), Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Tsutomu Tamura
- Virology Section, Niigata Prefectural Institute of Public Health and Environmental Science, Niigata, Japan
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Haruki H Matsumoto
- Division of Health and Welfare, Niigata Prefectural Government Office, Niigata, Japan
| | - Reiko Saito
- Division of International Health (Public Health), Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
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23
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Oulas A, Richter J, Zanti M, Tomazou M, Michailidou K, Christodoulou K, Christodoulou C, Spyrou GM. In depth analysis of Cyprus-specific mutations of SARS-CoV-2 strains using computational approaches. BMC Genom Data 2021; 22:48. [PMID: 34773976 PMCID: PMC8590444 DOI: 10.1186/s12863-021-01007-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/26/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND This study aims to characterize SARS-CoV-2 mutations which are primarily prevalent in the Cypriot population. Moreover, using computational approaches, we assess whether these mutations are associated with changes in viral virulence. METHODS We utilize genetic data from 144 sequences of SARS-CoV-2 strains from the Cypriot population obtained between March 2020 and January 2021, as well as all data available from GISAID. We combine this with countries' regional information, such as deaths and cases per million, as well as COVID-19-related public health austerity measure response times. Initial indications of selective advantage of Cyprus-specific mutations are obtained by mutation tracking analysis. This entails calculating specific mutation frequencies within the Cypriot population and comparing these with their prevalence world-wide throughout the course of the pandemic. We further make use of linear regression models to extrapolate additional information that may be missed through standard statistical analysis. RESULTS We report a single mutation found in the ORF1ab gene (nucleotide position 18,440) that appears to be significantly enriched within the Cypriot population. The amino acid change is denoted as S6059F, which maps to the SARS-CoV-2 NSP14 protein. We further analyse this mutation using regression models to investigate possible associations with increased deaths and cases per million. Moreover, protein structure prediction tools show that the mutation infers a conformational change to the protein that significantly alters its structure when compared to the reference protein. CONCLUSIONS Investigating Cyprus-specific mutations for SARS-CoV-2 can lead to a better understanding of viral pathogenicity. Researching these mutations can generate potential links between viral-specific mutations and the unique genomics of the Cypriot population. This can not only lead to important findings from which to battle the pandemic on a national level, but also provide insights into viral virulence worldwide.
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Affiliation(s)
- Anastasis Oulas
- Bioinformatics Department, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.
- The Cyprus School of Molecular Medicine, Nicosia, Cyprus.
| | - Jan Richter
- Molecular Virology Department, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Maria Zanti
- Bioinformatics Department, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, Nicosia, Cyprus
- Biostatistics Unit, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Marios Tomazou
- Bioinformatics Department, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, Nicosia, Cyprus
- Neurogenetics Department, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Kyriaki Michailidou
- The Cyprus School of Molecular Medicine, Nicosia, Cyprus
- Biostatistics Unit, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Kyproula Christodoulou
- The Cyprus School of Molecular Medicine, Nicosia, Cyprus
- Neurogenetics Department, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Christina Christodoulou
- The Cyprus School of Molecular Medicine, Nicosia, Cyprus
- Molecular Virology Department, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - George M Spyrou
- Bioinformatics Department, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, Nicosia, Cyprus
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24
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Hishiki T, Usui K, An T, Suzuki R, Sakuragi JI, Tanaka Y, Matsuki Y, Kawai J, Kogo Y, Hayashizaki Y, Takasaki T. Isolation of SARS-CoV-2 from COVID-19 patients and an asymptomatic individual. Jpn J Infect Dis 2021; 75:277-280. [PMID: 34719530 DOI: 10.7883/yoken.jjid.2021.292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, China, in December 2019. Despite the recent introduction of vaccines against SARS-CoV-2, more effective vaccines and antiviral drugs must be developed. Here, we isolated five SARS-CoV-2 strains from four patients with coronavirus disease (COVID-19) and an asymptomatic individual using pharyngeal swabs, nasopharyngeal swabs, and sputum samples. Cytopathic effects in inoculated Vero cells were observed between days 3 and 7. SARS-CoV-2 infection was confirmed by quantitative reverse-transcription polymerase chain reaction (RT-qPCR) and next-generation sequencing. Phylogenetic analyses of the whole genome sequences showed that the virus isolates from the clinical samples were belonged to the Wuhan and European lineages. These findings and isolated viruses may contribute to the development of diagnostic tools, vaccines, and antiviral drugs for COVID-19.
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Affiliation(s)
- Takayuki Hishiki
- Department of Microbiology, Kanagawa Prefectural Institute of Public Health, Japan
| | - Kengo Usui
- RIKEN Center for Integrative Medical Science, Japan
| | - Tadaichi An
- RIKEN Center for Integrative Medical Science, Japan
| | - Rieko Suzuki
- Department of Microbiology, Kanagawa Prefectural Institute of Public Health, Japan
| | - Jun-Ichi Sakuragi
- Department of Microbiology, Kanagawa Prefectural Institute of Public Health, Japan
| | - Yuki Tanaka
- RIKEN Center for Integrative Medical Science, Japan
| | - Yu Matsuki
- RIKEN Center for Integrative Medical Science, Japan
| | - Jun Kawai
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Japan
| | - Yasushi Kogo
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Japan
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25
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Imamura T, Ko YK, Furuse Y, Imamura T, Jindai K, Miyahara R, Sando E, Yasuda I, Tsuchiya N, Saito M, Suzuki M, Oshitani H. Epidemiological factors associated with COVID-19 clusters in medical and social welfare facilities. Jpn J Infect Dis 2021; 75:281-287. [PMID: 34719529 DOI: 10.7883/yoken.jjid.2021.288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Characteristics of COVID-19 clusters in medical and social welfare facilities, and factors associated with cluster size are still not fully understood. We reviewed COVID-19 cases identified from January 15 to April 30 of 2020 in Japan, and analyzed factors associated with cluster size in medical and social welfare facilities. In the study, COVID-19 clusters were identified in 56 medical and 34 social welfare facilities. Numbers of cases in those facilities reached their peaks after the peak of general population. Duration of occurrence of new cases in clusters showed a positive correlation with the number of cases in both types of facilities (rho = 0.44, p < 0.001; and rho = 0.69, p < 0.001, respectively). However, number of days between the first case in the prefecture and the onset of clusters showed a negative correlation with the number of cases only in clusters in social welfare facilities (rho = -0.4, p = 0.004). Our results suggested that COVID-19 cases in those facilities were prevalent in the latter phase of the community transmissions, although the underlying mechanisms for such trend could be different between medical and social welfare facilities.
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Affiliation(s)
- Tadatsugu Imamura
- Japan International Cooperation Agency, Japan.,Center for Postgraduate Education and Training, National Center for Child Health and Development, Japan
| | - Yura K Ko
- Department of Virology, Tohoku University Graduate School of Medicine, Japan.,Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Japan
| | - Yuki Furuse
- Institute for Frontier Life and Medical Sciences, Kyoto University, Japan
| | - Takeaki Imamura
- Department of Virology, Tohoku University Graduate School of Medicine, Japan
| | - Kazuaki Jindai
- Department of Healthcare Epidemiology, Kyoto University, Japan
| | - Reiko Miyahara
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Japan.,Medical Genome Science Project, National Center for Global Health and Medicine, Japan
| | - Eiichiro Sando
- Department of General Internal Medicine & Clinical Infectious Diseases, Fukushima Medical University, Japan
| | - Ikkoh Yasuda
- Department of General Internal Medicine & Clinical Infectious Diseases, Fukushima Medical University, Japan
| | - Naho Tsuchiya
- Yamato-Clinic, Japan.,Tohoku Medical Megabank Organization, Tohoku University, Japan
| | | | - Mayuko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, Japan
| | - Motoi Suzuki
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Japan
| | - Hitoshi Oshitani
- Department of Virology, Tohoku University Graduate School of Medicine, Japan
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26
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Toyokawa T, Shimada T, Hayamizu T, Sekizuka T, Zukeyama Y, Yasuda M, Nakamura Y, Okano S, Kudaka J, Kakita T, Kuroda M, Nakasone T. Transmission of SARS-CoV-2 during a 2-h domestic flight to Okinawa, Japan, March 2020. Influenza Other Respir Viruses 2021; 16:63-71. [PMID: 34605181 PMCID: PMC8652895 DOI: 10.1111/irv.12913] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/08/2021] [Accepted: 09/11/2021] [Indexed: 01/02/2023] Open
Abstract
Background Coronavirus disease (COVID‐19), caused by severe acute respiratory syndrome coronavirus (SARS‐CoV‐2), has rapidly spread globally. Potentially infected individuals travel on commercial aircraft. Thus, this study aimed to investigate and test the association between the use of face masks, physical distance, and COVID‐19 among passengers and flight attendants exposed to a COVID‐19 passenger in a domestic flight. Methods This observational study investigated passengers and flight attendants exposed to COVID‐19 on March 23, 2020, on board a flight to Naha City, Japan. Secondary attack rates were calculated. Whole‐genome sequencing of SARS‐CoV‐2 was used to identify the infectious linkage between confirmed cases in this clustering. The association between confirmed COVID‐19 and proximity of passengers' seats to the index case and/or the use of face masks was estimated using logistic regression. Results Fourteen confirmed and six probable cases were identified among passengers and flight attendants. The secondary attack rate was 9.7%. Twelve of 14 SARS‐CoV‐2 genome sequences in confirmed cases were identical to that of the index case or showed only one nucleotide mutation. Risk factors for infection included not using a face mask (adjusted odds ratio [aOR]: 7.29, 95% confidence interval [95% CI]: 1.86‐28.6), partial face mask use (aOR: 3.0, 95% CI: 0.83‐10.8), and being seated within two rows from the index patient (aOR: 7.47, 95% CI: 2.06‐27.2). Conclusion SARS‐CoV‐2 was transmitted on the airplane. Nonuse of face masks was identified as an independent risk factor for contracting COVID‐19 on the airplane.
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Affiliation(s)
- Takao Toyokawa
- COVID-19 Response Team, Naha City Public Health Center, Naha-shi, Okinawa, Japan
| | - Tomoe Shimada
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases (NIID), Shinjuku-ku, Tokyo, Japan
| | - Takahiro Hayamizu
- COVID-19 Response Team, Naha City Public Health Center, Naha-shi, Okinawa, Japan
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases (NIID), Shinjuku-ku, Tokyo, Japan
| | - Yuji Zukeyama
- COVID-19 Response Team, Naha City Public Health Center, Naha-shi, Okinawa, Japan
| | - Miyako Yasuda
- COVID-19 Response Team, Naha City Public Health Center, Naha-shi, Okinawa, Japan
| | - Yuko Nakamura
- COVID-19 Response Team, Naha City Public Health Center, Naha-shi, Okinawa, Japan
| | - Sho Okano
- Regional Health Division, Department of Public Health and Medical Care, Okinawa Prefectural Government, Naha-shi, Okinawa, Japan
| | - Jun Kudaka
- Regional Health Division, Department of Public Health and Medical Care, Okinawa Prefectural Government, Naha-shi, Okinawa, Japan
| | - Tetsuya Kakita
- Okinawa Prefectural Institute of Health and Environment, Uruma-shi, Okinawa, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases (NIID), Shinjuku-ku, Tokyo, Japan
| | - Tadashi Nakasone
- COVID-19 Response Team, Naha City Public Health Center, Naha-shi, Okinawa, Japan
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27
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Sekizuka T, Itokawa K, Hashino M, Okubo K, Ohnishi A, Goto K, Tsukagoshi H, Ehara H, Nomoto R, Ohnishi M, Kuroda M. A discernable increase in the severe acute respiratory syndrome coronavirus 2 R.1 lineage carrying an E484K spike protein mutation in Japan. INFECTION GENETICS AND EVOLUTION 2021; 94:105013. [PMID: 34352360 PMCID: PMC8327703 DOI: 10.1016/j.meegid.2021.105013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 07/14/2021] [Accepted: 07/20/2021] [Indexed: 01/22/2023]
Abstract
Three COVID-19 waves in Japan have been characterized by the presence of distinct PANGO lineages (B.1.1. 162, B.1.1.284, and B.1.1.214). Recently, in addition to the B.1.1.7 lineage, which shows 25% abundance, an R.1 lineage carrying the E484K mutation in the spike protein was found to show up to 40% predominance. E484K could be a pivotal amino acid substitution with the potential to mediate immune escape; thus, more attention should be paid to such potential variants of concern to avoid the emergence of mutants of concern. Such comprehensive real-time genome surveillance has become essential for the containment of COVID-19 clusters.
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Affiliation(s)
- Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Shinjyuku, Tokyo, Japan
| | - Kentaro Itokawa
- Pathogen Genomics Center, National Institute of Infectious Diseases, Shinjyuku, Tokyo, Japan
| | - Masanori Hashino
- Pathogen Genomics Center, National Institute of Infectious Diseases, Shinjyuku, Tokyo, Japan
| | | | - Asami Ohnishi
- Sapporo City Institute of Public Health, Hokkaido, Japan
| | - Keiko Goto
- Ibaraki Prefectural Institute of Public Health, Ibaraki, Japan
| | - Hiroyuki Tsukagoshi
- Gunma Prefectural Institute of Public Health and Environmental Sciences, Gunma, Japan
| | - Hayato Ehara
- Saitama Prefectural Institute of Public Health, Yoshimi, Saitama, Japan
| | | | - Makoto Ohnishi
- National Institute of Infectious Diseases, Shinjyuku, Tokyo, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Shinjyuku, Tokyo, Japan.
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28
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Arima Y, Kanou K, Arashiro T, K Ko Y, Otani K, Tsuchihashi Y, Takahashi T, Miyahara R, Sunagawa T, Suzuki M. Epidemiology of Coronavirus Disease 2019 in Japan: Descriptive Findings and Lessons Learned through Surveillance during the First Three Waves. JMA J 2021; 4:198-206. [PMID: 34414313 PMCID: PMC8355718 DOI: 10.31662/jmaj.2021-0043] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 11/09/2022] Open
Abstract
Introduction Coronavirus disease 2019 (COVID-19) has caused unprecedented global morbidity and mortality. Japan has faced three epidemic "waves" of COVID-19 from early 2020 through early 2021. Here we narratively review the three waves in Japan, describe the key epidemiologic features of COVID-19, and discuss lessons learned. Methods We assessed publicly available surveillance data, routine surveillance reports, and other relevant sources-multiple indicators were monitored to improve interpretation of surveillance data. Weekly trends for each wave were described based on the number of case notifications; number of tests performed; proportion of those tests that were positive for the novel coronavirus; the prevalent number of COVID-19 hospitalizations (total hospitalizations and those categorized as severe); and number of COVID-19 deaths. For each indicator and wave, we recorded the first calendar week to show an increase over two consecutive previous weeks, along with the peak week. Results The spring wave was characterized by detection of cases imported from China, followed by notifications of sporadic cases without travel history, clusters, and mild/asymptomatic cases. The summer wave saw a large increase in notifications and a younger age distribution, but in the context of increased testing with lower test positivity. The winter wave brought considerable morbidity and mortality, surpassing the cumulative case counts and fatalities from the earlier waves, with high peak values. Overall, relative to the first wave, the burden of severe outcomes was lower in the second and higher in the third wave, but varied by prefecture. In all three waves, severe outcomes peaked after notification counts and test positivity peaked; severe outcomes were also consistently skewed toward the elderly. Conclusions Important lessons were learned from each wave and across waves-some aspects remained constant, while others changed over time. In order to rapidly detect an increase in incidence, continuous, timely, and sensitive surveillance-using multiple information sources with careful interpretations-will be key in COVID-19 control.
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Affiliation(s)
- Yuzo Arima
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kazuhiko Kanou
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takeshi Arashiro
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yura K Ko
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kanako Otani
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yuuki Tsuchihashi
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takuri Takahashi
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Reiko Miyahara
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tomimasa Sunagawa
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Motoi Suzuki
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
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29
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Homma Y, Katsuta T, Oka H, Inoue K, Toyoshima C, Iwaki H, Yamashita Y, Shinomiya H. The incubation period of the SARS-CoV-2 B1.1.7 variant is shorter than that of other strains. J Infect 2021; 83:e15-e17. [PMID: 34146596 PMCID: PMC8225994 DOI: 10.1016/j.jinf.2021.06.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 06/13/2021] [Indexed: 11/24/2022]
Affiliation(s)
- Yoshito Homma
- Department of Infectious Disease, Ehime Prefectural Central Hospital, 83 Kasugamachi Matsuyama, Ehime 790-0024, Japan.
| | - Tomoya Katsuta
- Department of Respiratory Medicine, Ehime Prefectural Central Hospital, 83 Kasugamachi Matsuyama, Ehime 790-0024, Japan
| | - Hideaki Oka
- Division of Kidney Center, Matsuyama Red Cross Hospital, 1, Bunkyo-cho, Matsuyama, Ehime 790-8524, Japan
| | - Koji Inoue
- Department of Respiratory Medicine, Ehime Prefectural Central Hospital, 83 Kasugamachi Matsuyama, Ehime 790-0024, Japan
| | - Chitoshi Toyoshima
- Ehime Prefectural Institute of Public Health and Environmental Science, 8-234 Sanbancho, Matsuyama, Ehime 790-0003, Japan
| | - Hiromi Iwaki
- Ehime Prefectural Institute of Public Health and Environmental Science, 8-234 Sanbancho, Matsuyama, Ehime 790-0003, Japan
| | - Yasutaka Yamashita
- Ehime Prefectural Institute of Public Health and Environmental Science, 8-234 Sanbancho, Matsuyama, Ehime 790-0003, Japan
| | - Hiroto Shinomiya
- Ehime Prefectural Institute of Public Health and Environmental Science, 8-234 Sanbancho, Matsuyama, Ehime 790-0003, Japan
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30
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Suzuki M, Imai T, Sakurai A, Komoto S, Ide T, Lim CK, Shintani A, Doi Y, Murata T. Virological and genomic analysis of SARS-CoV-2 from a favipiravir clinical trial cohort. J Infect Chemother 2021; 27:1350-1356. [PMID: 34176716 PMCID: PMC8196299 DOI: 10.1016/j.jiac.2021.06.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/01/2021] [Accepted: 06/09/2021] [Indexed: 12/23/2022]
Abstract
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 the 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 19 B, whereas the majority belonged to clade 20 B. The median time from the disease onset to negative CPE was 9 days. CPE was 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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Affiliation(s)
- Masahiro Suzuki
- Department of Microbiology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Takumi Imai
- Department of Medical Statistics, Osaka City University Graduate School of Medicine, Osaka, Osaka, Japan
| | - Aki Sakurai
- Department of Infectious Diseases, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Satoshi Komoto
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Tomihiko Ide
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan; Center for Joint Research Facilities Support, Research Promotion and Support Headquarters, Fujita Health University, Toyoake, Aichi, Japan
| | - Chang Kweng Lim
- Department of Virology I, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | - Ayumi Shintani
- Department of Medical Statistics, Osaka City University Graduate School of Medicine, Osaka, Osaka, Japan
| | - Yohei Doi
- Department of Microbiology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan; Department of Infectious Diseases, Fujita Health University School of Medicine, Toyoake, Aichi, Japan; Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - Takayuki Murata
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
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31
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Identification of B.1.346 Lineage of SARS-CoV-2 in Japan: Genomic Evidence of Re-entry of Clade 20C. Keio J Med 2021; 70:44-50. [PMID: 33853975 DOI: 10.2302/kjm.2021-0005-oa] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
SARS-CoV-2 whole-genome sequencing of samples from COVID-19 patients is useful for informing infection control. Datasets of these genomes assembled from multiple hospitals can give critical clues to regional or national trends in infection. Herein, we report a lineage summary based on data collected from hospitals located in the Tokyo metropolitan area. We performed SARS-CoV-2 whole-genome sequencing of specimens from 198 patients with COVID-19 at 13 collaborating hospitals located in the Kanto region. Phylogenetic analysis and fingerprinting of the nucleotide substitutions were performed to differentiate and classify the viral lineages. More than 90% of the identified strains belonged to Clade 20B, which has been prevalent in European countries since March 2020. Only two lineages (B.1.1.284 and B.1.1.214) were found to be predominant in Japan. However, one sample from a COVID-19 patient admitted to a hospital in the Kanto region in November 2020 belonged to the B.1.346 lineage of Clade 20C, which has been prevalent in the western United States since November 2020. The patient had no history of overseas travel or any known contact with anyone who had travelled abroad. Consequently, the Clade 20C strain belonging to the B.1.346 lineage appeared likely to have been imported from the western United States to Japan across the strict quarantine barrier. B.1.1.284 and B.1.1.214 lineages were found to be predominant in the Kanto region, but a single case of the B.1.346 lineage of clade 20C, probably imported from the western United States, was also identified. These results illustrate that a decentralized network of hospitals offers significant advantages as a highly responsive system for monitoring regional molecular epidemiologic trends.
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32
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Shirato K, Tomita Y, Katoh H, Yamada S, Fukushi S, Matsuyama S, Takeda M. Performance evaluation of real-time RT-PCR assays for detection of severe acute respiratory syndrome coronavirus-2 developed by the National Institute of Infectious Diseases, Japan. Jpn J Infect Dis 2021; 74:465-472. [PMID: 33642428 DOI: 10.7883/yoken.jjid.2020.1079] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Soon after the December 2019 outbreak of coronavirus disease 2019 in Wuhan, China, a protocol for real-time RT-PCR assay detection of severe acute respiratory syndrome coronavirus (SARS-CoV-2) was established by the National Institute of Infectious Diseases (NIID) in Japan. The protocol used Charité's nucleocapsid (Sarbeco-N) and NIID's nucleocapsid (NIID-N2) assays. During the following months, SARS-CoV-2 spread causing a global pandemic, and a variety of SARS-CoV-2 sequences were registered to public databases, such as the Global Initiative on Sharing All Influenza Data (GISAID). In this study, we evaluated the newly developed S2 assay (NIID-S2) to replace the Sarbeco-N assay and the performance of NIID-N2 and NIID-S2 assays, referring mismatches in the primer/probe targeted region. We found the analytical sensitivity and specificity of the NIID-S2 set were comparable to the NIID-N2 assay, and the detection rate for clinical specimens was identical to that of the NIID-N2 assay. Furthermore, among available sequences (approximately 192,000), the NIID-N2 and NIID-S2 sets had 2.6% and 1.2% mismatched sequences, respectively, although most of these mismatches did not affect the amplification efficiency, with the exception of the 3' end of the NIID-N2 forward primer. These findings indicate that the previously developed NIID-N2 assay remains suitable for the detection SARS-CoV-2 with support of the newly developed NIID-S2 set.
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Affiliation(s)
- Kazuya Shirato
- Department of Virology III, National Institute of Infectious Disease, Japan
| | - Yuriko Tomita
- Department of Virology III, National Institute of Infectious Disease, Japan
| | - Hiroshi Katoh
- Department of Virology III, National Institute of Infectious Disease, Japan
| | - Souichi Yamada
- Departiment of Virology I, National Institute of Infectious Disease, Japan
| | - Shuetsu Fukushi
- Departiment of Virology I, National Institute of Infectious Disease, Japan
| | - Shutoku Matsuyama
- Department of Virology III, National Institute of Infectious Disease, Japan
| | - Makoto Takeda
- Department of Virology III, National Institute of Infectious Disease, Japan
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33
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Sekizuka T, Itokawa K, Yatsu K, Tanaka R, Hashino M, Kawano-Sugaya T, Ohnishi M, Wakita T, Kuroda M. COVID-19 genome surveillance at international airport quarantine stations in Japan. J Travel Med 2021; 28:5999912. [PMID: 33236052 PMCID: PMC7717395 DOI: 10.1093/jtm/taaa217] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/14/2020] [Accepted: 11/16/2020] [Indexed: 11/16/2022]
Abstract
A coronavirus disease (COVID-19) genome surveillance has been conducted at four international airports in Japan, revealing a potential imported COVID-19 risk from multiple countries. The quarantine surveillance based on genome sequencing can enhance sequencing efforts worldwide, as returning travelers may serve as excellent sentinels for the global pandemic.
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Affiliation(s)
- Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Kentaro Itokawa
- Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Koji Yatsu
- Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Rina Tanaka
- Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Masanori Hashino
- Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Tetsuro Kawano-Sugaya
- Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Makoto Ohnishi
- National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Takaji Wakita
- National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
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34
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Ohnishi A, Namekawa Y, Fukui T. Universality in COVID-19 spread in view of the Gompertz function. PROGRESS OF THEORETICAL AND EXPERIMENTAL PHYSICS 2020; 2020:ptaa148. [PMCID: PMC7665699 DOI: 10.1093/ptep/ptaa148] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 09/06/2020] [Accepted: 09/23/2020] [Indexed: 05/25/2023]
Abstract
We demonstrate that universal scaling behavior is observed in the current corona virus (SARS-CoV-2) spread, the COVID-19 pandemic, in various countries. We analyze the numbers of infected people who tested positive (cases) in selected eleven countries (Japan, USA, Russia, Brazil, China, Italy, Indonesia, Spain, South Korea, UK, and Sweden). By using the double exponential function called the Gompertz function, fG(x) = exp(–e–x), the number of cases is well described as N(t) = N0fG(γ(t – t0)), where N0, γ and t0 are the final number of cases, the damping rate of the infection probability and the peak time of the daily number of new cases, dN(t)/dt, respectively. The scaled data of cases in most of the analyzed countries are found to collapse onto a common scaling function fG(x) with x = γ(t – t0) being the scaling variable in the range of fG(x) ± 0.05. The recently proposed indicator so-called the K value, the increasing rate of cases in one week, is also found to show universal behavior. The mechanism for the Gompertz function to appear is discussed from the time dependence of the produced pion numbers in nucleus-nucleus collisions, which is also found to be described by the Gompertz function.
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Affiliation(s)
- Akira Ohnishi
- Yukawa Institute for Theoretical Physics, Kyoto University, Kyoto, Japan
| | - Yusuke Namekawa
- Yukawa Institute for Theoretical Physics, Kyoto University, Kyoto, Japan
| | - Tokuro Fukui
- Yukawa Institute for Theoretical Physics, Kyoto University, Kyoto, Japan
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35
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[SARS-CoV-2 genomics and its application to genome surveillance]. Uirusu 2020; 70:147-154. [PMID: 34544929 DOI: 10.2222/jsv.70.147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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