Abstract
Using numbers of SARS-CoV-2 variants detected in Japan as at 13 June 2021, relative instantaneous reproduction numbers (RRI) 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, RRI 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.
Highlights
Multiple SARS-CoV-2 variants are circulating in Japan and because of the high transmissibility of the VOC, the replacement of locally circulating strains by Alpha and Delta VOC poses a serious public health threat in Japan
Using the numbers of SARS-CoV-2 variants found in the GISAID database [4] and those detected by PCR in Tokyo, we estimate the relative instantaneous reproduction numbers (RRI ) of the R.1 variant and the Alpha and Delta VOC with respect to other strains circulating in Japan before the introduction of the Alpha and Delta VOC and R.1
If the lineage Ai emerges with an initial frequency of qAi at calendar time ti, the likelihood function of parameters s 1, ..., sn and q 1(t 1), ..., qn for observing NAi (d 1), ..., NA 1(dk ), ..., NAn (d 1), ..., NAn sequences of lineages A 1, ..., An, at calendar times d 1, ..., dk is given by the following formula: Relative instantaneous reproduction number Dec 01 Dec 11 Dec 21 Dec 31 Jan 10 Jan 20 Jan 30 Feb 09 Feb 19 Mar 01 Mar 11 Mar 21 Mar 31 Apr 10 Apr 20 Apr 30 May 10 May 20 May 30 Jun 09 Jun 19 Jun 29 Jul 09
Summary
Predicted dominance of variant Delta of SARS-CoV-2 before Tokyo Olympic Games, Japan, July 2021. Using numbers of SARS-CoV-2 variants detected in Japan as at 13 June 2021, relative instantaneous reproduction numbers (RRI) 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. Multiple SARS-CoV-2 variants are circulating in Japan and because of the high transmissibility of the VOC, the replacement of locally circulating strains by Alpha and Delta VOC poses a serious public health threat in Japan. Using the numbers of SARS-CoV-2 variants found in the GISAID database [4] and those detected by PCR in Tokyo, we estimate the relative instantaneous reproduction numbers (RRI ) of the R.1 variant and the Alpha and Delta VOC with respect to other strains circulating in Japan before the introduction of the Alpha and Delta VOC and R.1. The instantaneous reproduction numbers of lineage a and A 1, ..., An at calendar time t are represented as follows:
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