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Using numbers of SARS-CoV-2 variants detected in Japan as at 13 June 2021, relative instantaneous reproduction numbers (R) of the R.1, Alpha, and Delta variants with respect to other strains circulating in Japan were estimated at 1.25, 1.44, and 1.95. Depending on the assumed serial interval distributions, R varies from 1.20–1.32 for R.1, 1.34–1.58 for Alpha, and 1.70–2.30 for Delta. The frequency of Delta is expected to take over Alpha in Japan before 23 July 2021.


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  1. World Health Organization (WHO). SARS-CoV-2 Variants of Concern and Variants of Interest. Geneva: WHO; 2021. Available from: https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/
  2. Rambaut A, Holmes EC, O’Toole Á, Hill V, McCrone JT, Ruis C, et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol. 2020;5(11):1403-7.  https://doi.org/10.1038/s41564-020-0770-5  PMID: 32669681 
  3. Tokyo Metropolitan Government. Updates on COVID-19 in Tokyo. Tokyo: Tokyo Metropolitan Government; 2021. Available from: https://stopcovid19.metro.tokyo.lg.jp/en
  4. Shu Y, McCauley J. GISAID: Global initiative on sharing all influenza data - from vision to reality. Euro Surveill. 2017;22(13):30494.  https://doi.org/10.2807/1560-7917.ES.2017.22.13.30494  PMID: 28382917 
  5. Fraser C. Estimating individual and household reproduction numbers in an emerging epidemic. PLoS One. 2007;2(8):e758.  https://doi.org/10.1371/journal.pone.0000758  PMID: 17712406 
  6. Tokyo Metropolitan Government. Disaster Prevention Information. Tokyo: Tokyo Metropolitan Government; 2021. Available from: https://www.bousai.metro.tokyo.lg.jp/taisaku/saigai/1013388/1014026.html
  7. Pawitan Y. In All Likelihood: Statistical Modelling and Inference Using Likelihood. Croydon: Oxford University Press; 2013.
  8. Johnson SG. The NLopt nonlinear-optimization package. 2020. Available from: http://github.com/stevengj/nlopt
  9. Rowan T. Functional Stability Analysis of Numerical Algorithms. Ph.D. Thesis. Austin: University of Texas, Austin; 1990.
  10. Campbell F, Archer B, Laurenson-Schafer H, Jinnai Y, Konings F, Batra N, et al. Increased transmissibility and global spread of SARS-CoV-2 variants of concern as at June 2021. Euro Surveill. 2021;26(24):2100509.  https://doi.org/10.2807/1560-7917.ES.2021.26.24.2100509  PMID: 34142653 
  11. Nishiura H, Linton NM, Akhmetzhanov AR. Serial interval of novel coronavirus (COVID-19) infections. Int J Infect Dis. 2020;93:284-6.  https://doi.org/10.1016/j.ijid.2020.02.060  PMID: 32145466 
  12. Piantham, C., Linton, N. M., Nishiura, H., & Ito, K. Estimating the elevated transmissibility of the B.1.1.7 strain over previously circulating strains in England using GISAID sequence frequencies. medRxiv. 2021. doi: https://doi.org/10.1101/2021.03.17.21253775 
  13. Ministry of Health. Labour and Welfare. Reports from Advisory Board Members for COVID-19. Tokyo: Ministry of Health, Labour and Welfare; 2021. Available from: https://www.mhlw.go.jp/stf/seisakunitsuite/bunya/0000121431_00256.html
  14. Volz, E., Mishra, S., Chand, M., Barrett, J. C., Johnson, R., Geidelberg, L., et al. Transmission of SARS-CoV-2 Lineage B.1.1.7 in England: Insights from linking epidemiological and genetic data. medRxiv, 2020.2012.2030.20249034. doi: https://doi.org/10.1101/2020.12.30.20249034 
  15. Nakajo K, Nishiura H. Assessing Interventions against Coronavirus Disease 2019 (COVID-19) in Osaka, Japan: A Modeling Study. J Clin Med. 2021;10(6):1256.  https://doi.org/10.3390/jcm10061256  PMID: 33803634 
  16. Government CIOs' portal, Japan. COVID-19 Vaccination in Japan. 2021. Available from: https://cio.go.jp/en/index.php

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