image:Status of COVID-19 during the Tokyo 2020 Olympic and Paralympic Games view more
Credit: The Instutite of Medical Science, The University of Tokyo
In the middle of the COVID-19 pandemic, the Tokyo 2020 Olympic and Paralympic Games were held in the summer of 2021. Participants from over 200 countries or regions gathered in Japan. Scientifically understanding how the new coronavirus transmitted through such mass gatherings can be utilized for future events in similar situations.Just before the games, the Alpha variant (B.1.1.7) was being replaced with the more contagious Delta substrain AY.29, which harbors two additional characteristic mutations compared with its parent AY.4. It emerged in Japan and became dominant in Tokyo. Through genome analysis, we identified 118 AY.29 samples in 20 countries, and among these, at least 55 independent strains. While there are strains unrelated to the events such as a strain transmitted to the USA from Okinawa, there remains the possibility that 41 strains were associated with the Olympic and Paralympic participants. This study was published on August 3rd, 2022 in Frontiers in Microbiology.The research was organized by IMSUT (Prof. Seiya Imoto, Human Genome Center) and IBM Research (Takahiko Koyama, Research Staff Member, TJ Watson Research Center and Michiharu Kudo, Senior Technical Staff Member, IBM Research - Tokyo) groups. The article was published in Frontiers in Microbiology at 5:00 AM BST on August 3rd 2022.
Background /ChallengeThe new coronavirus has been rapidly evolving by accumulating mutations during the pandemic. Emergence of new variants have been dramatically affecting our lives. Nevertheless, mutations can be utilized to trace transmission routes. IMSUT and IBM developed the SARS-CoV-2 Variant Browser, which provides surveillance and tracing tools to researchers and public health officials*3,*4.In the summer of 2021, the Tokyo 2020 Olympic and Paralympic Games were finally held after a year of postponement. Participants from over 200 countries or regions visited Japan. Scientifically understanding how the new coronavirus propagated through a series of international mass gathering events can be utilized for future events not limited to COVID-19. In this study, we have analyzed the SARS-CoV-2 strains transmitted overseas during the time of the Olympic and Paralympic Games.
ResultJust before the games, the Alpha variant (B.1.1.7) was being replaced with the more contagious Delta variant AY.29, which harbors two additional characteristic mutations 5239C > T (NSP3 Y840Y) and 5514T > C (NSP3 V932A), compared with its parent AY.4. It emerged in Japan and became dominant in Tokyo (Figure1A, B). During the events, a total of 863 positive cases were reported (Figure 1C). Out of 863 positive cases, 174 cases occurred in Olympic visitors from abroad, and 80 cases occurred in Paralympic visitors from abroad.
By analyzing over 6 million genomes from the international genome database in GISAID and NCBI, we uncovered 118 samples of the Delta substrain AY.29 in 20 countries such as the USA, the UK, Canada, Germany, South Korea, Hong Kong, Thailand, and the Philippines (Figure2). At least 55 independent strains were propagated to overseas from Japan. Out of the exported 55 strains, 41 of them were collected after August 1st and with their ancestral strains collected in Greater Tokyo While there are strains unrelated to the events such as a strain transmitted to the USA from Okinawa via US military stationed in Okinawa, the possibility remains that 41 strains are associated with the returning Olympic and Paralympic participants.
The identified AY.29 samples appear to be the tip of the iceberg. In particular, it is difficult to grasp the whole picture in the countries and areas with low rates of genome surveillance. Among the 20 countries, most European and North American countries had vaccination rates over 50%, and sufficient genomic surveillance was conducted; transmissions seem contained. However, propagation to unvaccinated regions might have caused damage we cannot assess. Since samples in those unvaccinated countries are also undersampled with a longer lead time for data sharing, it will take longer to grasp the whole picture.Regarding the novel exogenous strains introduced into the Japanese population by the participants from abroad, we identified 61 novel exogenous strains in 900 unusual samples that dont have prefectural information. As we expect more international mass gathering events, it becomes more important to share the data and disclose information regarding SARS-CoV-2 in a timely manner. IMSUT will keep providing the information to researchers and public health officials.IMSUT has been conducting research in SARS-CoV-2 genomes to find new treatment methods and preventive measures by leveraging expertise obtained through genome and data science research to date. In the Tokyo 2020 Olympic and Paralympic Games, IMSUT played a role in analyzing SARS-CoV-2 genomes obtained in wastewater samples in the Tokyo 2020 Olympic and Paralympic village*5,*6. To accelerate socio-economic recovery from the COVID-19 pandemic, IMSUT will make efforts to contribute to proposing concrete measures.
Publication
Takahiko Koyama*, Reitaro Tokumasu, Kotoe Katayama, Ayumu Saito, Michiharu Kudo and Seiya Imoto "Cross-border transmissions of the Delta substrain AY.29 during Tokyo Olympic and Paralympic Games" Frontiers in Microbiology Aug. 2022*Corresponding AuthorDOI: 10.3389/fmicb.2022.883849URL: https://www.frontiersin.org/articles/10.3389/fmicb.2022.883849
Research contact:Human Genome Center, The Institute of Medical Science, The University of TokyoSeiya Imoto, Director/ProfessorURL: https://www.ims.u-tokyo.ac.jp/imsut/en/lab/hgclink/page_00073.htmlMedia Contact:International Affairs Office, The Institute of Medical Science, The University of TokyoURLhttps://www.ims.u-tokyo.ac.jp/imsut/en/index.htmlReference:(*1) GISAID : https://www.gisaid.org/(*2) NCBIhttps://www.ncbi.nlm.nih.gov/sars-cov-2/(*3) Koyama T., Platt D., Parida L. Variant analysis of SARS-CoV-2 genomes. Bull World Health Organ. 2020;98:495-504.(*4) IBM and the Institute of Medical Science, the University of Tokyo develop a system for rapid analysis and visualization of viral genome mutations to reduce the risk of COVID-19 infection spreading in Japan: https://www.ims.u-tokyo.ac.jp/imsut/jp/about/press/page_00095.html(*5) Tracking SARS-CoV-2 during Tokyo 2020 via wastewater~Wastewater-based epidemiological tracking of COVID-19 in the Tokyo 2020 Olympic and Paralympic village showed that SARS-CoV-2 was present in areas without diagnosed individuals~: https://www.ims.u-tokyo.ac.jp/imsut/jp/about/press/page_00151.html(*6) Kitajima M., Murakami M., Iwamoto R., Katayama H., Imoto S. COVID-19 wastewater surveillance implemented in the Tokyo 2020 Olympic and Paralympic Village Journal of Travel Medicine Volume 29, Issue 3, April 2022.
Frontiers in Microbiology
Survey
Not applicable
Cross-border transmissions of the Delta substrain AY.29 during Tokyo Olympic and Paralympic Games
3-Aug-2022
Disclaimer: AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert system.
Read the rest here:
Cross-border transmissions of the Delta substrain AY.29 from Japan to the world during the Tokyo Olympic and Paralympic Games - EurekAlert
- The complete plastome sequences of invasive weed Parthenium hysterophorus: genome organization, evolutionary ... - Nature.com - February 18th, 2024 [February 18th, 2024]
- Multi-omic profiling reveals associations between the gut microbiome, host genome and transcriptome in patients with ... - Journal of Translational... - February 18th, 2024 [February 18th, 2024]
- Polymerase Chain Reaction (PCR) - National Human Genome Research Institute - February 18th, 2024 [February 18th, 2024]
- Genomic Time Machine Reveals Secrets of Human DNA - SciTechDaily - February 18th, 2024 [February 18th, 2024]
- 1 Million Unannotated Exons Discovered in the Human Genome - Technology Networks - February 18th, 2024 [February 18th, 2024]
- Hope for the night parrot: bird's full genome has been sequenced - Cosmos - February 18th, 2024 [February 18th, 2024]
- RevIT AAV Enhancer: Rev-up AAV genome production in upstream manufacturing - BioProcess Insider - February 18th, 2024 [February 18th, 2024]
- Multi-omics resources for the Australian southern stuttering frog (Mixophyes australis) reveal assorted antimicrobial ... - Nature.com - February 18th, 2024 [February 18th, 2024]
- Large-scale gene expression alterations introduced by structural variation drive morphotype diversification in Brassica ... - Nature.com - February 18th, 2024 [February 18th, 2024]
- Near-gapless and haplotype-resolved apple genomes provide insights into the genetic basis of rootstock-induced ... - Nature.com - February 18th, 2024 [February 18th, 2024]
- Secrets of Night Parrot unlocked after first genome sequenced - CSIRO - February 18th, 2024 [February 18th, 2024]
- CRISPR gene editing tool gets a revolutionary high-tech upgrade - Earth.com - February 18th, 2024 [February 18th, 2024]
- Ancient retroviruses played a key role in the evolution of vertebrate brains - EurekAlert - February 18th, 2024 [February 18th, 2024]
- Natural selection and genetic diversity maintenance in a parasitic wasp during continuous biological control application - Nature.com - February 18th, 2024 [February 18th, 2024]
- Hopes elusive parrots genome will provide answers - news.com.au - February 18th, 2024 [February 18th, 2024]
- MicroRNA is the master regulator of the genome researchers are learning how to treat disease by harnessing the ... - The Conversation - November 30th, 2023 [November 30th, 2023]
- "Ground-Breaking" Release of World's Largest Whole Genome Resource - Inside Precision Medicine - November 30th, 2023 [November 30th, 2023]
- Pangenome analysis reveals genomic variations associated with domestication traits in broomcorn millet - Nature.com - November 30th, 2023 [November 30th, 2023]
- Global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome ... - Nature.com - November 30th, 2023 [November 30th, 2023]
- Genome characteristics of atypical porcine pestivirus from abortion cases in Shandong Province, China - Virology Journal - Virology Journal - November 30th, 2023 [November 30th, 2023]
- Correcting modification-mediated errors in nanopore sequencing by nucleotide demodification and reference-based ... - Nature.com - November 30th, 2023 [November 30th, 2023]
- CRISPR-Based "Genome Shredding" Technique Shows Promise in Treating Glioblastoma - Inside Precision Medicine - November 30th, 2023 [November 30th, 2023]
- Genome wide analysis revealed conserved domains involved in the effector discrimination of bacterial type VI secretion ... - Nature.com - November 30th, 2023 [November 30th, 2023]
- TRISH to investigate the effects of spaceflight on the human genome, central nervous system - Odessa American - November 30th, 2023 [November 30th, 2023]
- The venom preceded the stinger: Genomic studies shed light on the origins of bee venom - EurekAlert - November 30th, 2023 [November 30th, 2023]
- Integrating genomic and multiomic data for Angelica sinensis provides insights into the evolution and biosynthesis of ... - Nature.com - November 30th, 2023 [November 30th, 2023]
- Genetic diversity and ancestry of the Khmuic-speaking ethnic groups ... - Nature.com - September 21st, 2023 [September 21st, 2023]
- Researchers to Apply Genome Analysis to Childhood Cancers; Goal ... - The Japan News - September 21st, 2023 [September 21st, 2023]
- How Bats' Genomes May Help Them Avoid Cancer and Survive ... - Technology Networks - September 21st, 2023 [September 21st, 2023]
- Longitudinal genomic surveillance of carriage and transmission of ... - Nature.com - September 21st, 2023 [September 21st, 2023]
- Whole genomes from bacteria collected at diagnostic units around ... - Nature.com - September 21st, 2023 [September 21st, 2023]
- Genome-wide identification of lncRNA & mRNA for T2DM | PGPM - Dove Medical Press - September 21st, 2023 [September 21st, 2023]
- Tasmanian tiger RNA is first to be recovered from an extinct animal - Nature.com - September 21st, 2023 [September 21st, 2023]
- Loneliness and depression: bidirectional mendelian randomization ... - Nature.com - September 21st, 2023 [September 21st, 2023]
- Rome Therapeutics adds $72 million to Series B round to harness ... - OutSourcing-Pharma.com - September 21st, 2023 [September 21st, 2023]
- Mystery of 'living fossil' tree frozen in time for 66 million years finally ... - Livescience.com - September 21st, 2023 [September 21st, 2023]
- Why the human genome could be healthcares holy grail - Yahoo Finance - May 4th, 2023 [May 4th, 2023]
- Scientists Compare Genomes of 240 Mammals to Understand Human DNA - The New York Times - May 4th, 2023 [May 4th, 2023]
- Genomes From 240 Mammalian Species Help Explain 100 Years Of Evolution And Human Disease - ABP Live - May 4th, 2023 [May 4th, 2023]
- 'Deletions' from the human genome may be what made us human - Yale News - May 4th, 2023 [May 4th, 2023]
- GeneDx Adds Buccal Swab as Non-Invasive Whole Genome ... - GlobeNewswire - May 4th, 2023 [May 4th, 2023]
- Whole-genome sequencing used to track down genes behind familial glioma - Medical Xpress - May 4th, 2023 [May 4th, 2023]
- Wiggly proteins guard the genome: Dynamic network in the pores of ... - Science Daily - May 4th, 2023 [May 4th, 2023]
- Genome-Wide Splicing Quantitative Expression Locus Analysis ... - Cancer Discovery - May 4th, 2023 [May 4th, 2023]
- Digital Genome Market is expand at a CAGR of 8.6% to reach USD ... - Digital Journal - May 4th, 2023 [May 4th, 2023]
- High School Students Learn the Basics of Base Editing to Cure GFP ... - University of California San Diego - May 4th, 2023 [May 4th, 2023]
- Genomic researchers gain access to CSIRO's AI-powered data ... - Microsoft - May 4th, 2023 [May 4th, 2023]
- Archaic hominin traits through the splicing lens - Nature.com - May 4th, 2023 [May 4th, 2023]
- Critical bug in genome sequencing device scores '10' on CVSS ratings - SC Media - May 4th, 2023 [May 4th, 2023]
- Novel Genomic Approach Ensures Better Diagnosis of Hereditary ... - Technology Networks - May 4th, 2023 [May 4th, 2023]
- Intellia Therapeutics: Leading the Way in Revolutionary Genome ... - Best Stocks - May 4th, 2023 [May 4th, 2023]
- Visual tracking of viral infection dynamics reveals the synergistic ... - Nature.com - May 4th, 2023 [May 4th, 2023]
- Genome | Genome LLC | United States - March 31st, 2023 [March 31st, 2023]
- Belarus: EU and WHO deliver equipment for research of genomes of infectious disease agents - EIN News - February 24th, 2023 [February 24th, 2023]
- Gene vs. genome: Definition, function, and impact - January 30th, 2023 [January 30th, 2023]
- Big cog in the wheel: As Covid worries reappear, Insacogs genome sequencing ability must be aided by govts - Times of India - December 25th, 2022 [December 25th, 2022]
- CapitalGainsReport Sector Spotlight: Healthcare Penny Stocks On The Move (ARDX, WHSI, BNGO) - Marketscreener.com - November 25th, 2022 [November 25th, 2022]
- Genome Insight and Kun-hee Lee Child Cancer & Rare Disease Project Team of SNUH (Seoul National University Hospital) Made an Agreement About a... - November 23rd, 2022 [November 23rd, 2022]
- Genome-wide association study reveals distinct genetic associations related to leaf hair density in two lineages of wheat-wild relative Aegilops... - October 19th, 2022 [October 19th, 2022]
- The Global Genomics Market to Exhibit Growth at a CAGR of 16.90% During the Forecast Period (20222027) | DelveInsight - Yahoo Finance - October 19th, 2022 [October 19th, 2022]
- Illumina and GenoScreen Partner to Expand Access to Genomic Testing for Multidrug-Resistant Tuberculosis - PR Newswire - October 19th, 2022 [October 19th, 2022]
- Superresolution Method Poised to Better Gene Function Understanding - Photonics.com - October 19th, 2022 [October 19th, 2022]
- Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians - Nature.com - October 15th, 2022 [October 15th, 2022]
- How a New Battery Data Genome Project Will Use Vast Amounts of Information to Build Better EVs - InsideClimate News - October 15th, 2022 [October 15th, 2022]
- Scientists Reconstruct the Genome of the 180-Million-Year-Old Common Ancestor of All Mammals - SciTechDaily - October 15th, 2022 [October 15th, 2022]
- Combining OSMAC, metabolomic and genomic methods for the production and annotation of halogenated azaphilones and ilicicolins in termite symbiotic... - October 15th, 2022 [October 15th, 2022]
- Concerted expansion and contraction of immune receptor gene repertoires in plant genomes - Nature.com - October 15th, 2022 [October 15th, 2022]
- Uncovering the Full Variant Continuum with Pioneering Solutions from Bionano - Inside Precision Medicine - October 15th, 2022 [October 15th, 2022]
- Metagenomic analysis of viromes in tissues of wild Qinghai vole from the eastern Tibetan Plateau | Scientific Reports - Nature.com - October 15th, 2022 [October 15th, 2022]
- Research Assistant in Molecular and Genome Editing Therapeutics job with KINGS COLLEGE LONDON | 311876 - Times Higher Education - October 15th, 2022 [October 15th, 2022]
- Lessons learnt from COVID-19 shed light on future pandemic preparedness - The Peter Doherty Institute for Infection and Immunity - October 15th, 2022 [October 15th, 2022]
- From Neanderthal genome to Nobel prize: meet geneticist Svante Pbo - Nature.com - October 8th, 2022 [October 8th, 2022]
- Revealing the genome organization of the earliest common ancestor of all mammals - Tech Explorist - October 8th, 2022 [October 8th, 2022]
- Mitochondrial DNA Is Working Its Way Into the Human Genome - Technology Networks - October 8th, 2022 [October 8th, 2022]
- Animated Map: Where to Find Water on Mars - Visual Capitalist - October 8th, 2022 [October 8th, 2022]
- Reconstruction of The First Mammal's Genome Suggests It Had 38 Chromosomes - ScienceAlert - October 6th, 2022 [October 6th, 2022]
- Genomic Science Breakthroughs Are Happening Faster Than Ever Thanks to HPC - CIO - October 6th, 2022 [October 6th, 2022]
- Genome Of Ancient Humans Is The Winning Field Of 2022's Nobel Prize in Medicine - IFLScience - October 6th, 2022 [October 6th, 2022]
- ASU professor to study new genome editing tools with NIH Innovator Award - ASU News Now - October 6th, 2022 [October 6th, 2022]
- New R&D norms to fast-track research on genome-edited crops - The Financial Express - October 6th, 2022 [October 6th, 2022]