Cross-Border Transmissions of the Delta Substrain AY.29 During Tokyo Olympic and Paralympic Games

Abstract

Tokyo Olympic and Paralympic Games, postponed for the COVID-19 pandemic, were finally held in the summer of 2021. Just before the games, the Alpha variant was being replaced with the more contagious Delta variant. AY.4 substrain AY.29, which harbors two additional characteristic mutations of 5239C > T (NSP3 Y840Y) and 5514T > C (NSP3 V932A), emerged in Japan and became dominant in Tokyo by the time of the Olympic Games. Variants of SARS-CoV-2 genomes were performed to extract AY.29 Delta substrain samples with 5239C > T and 5514T > C. Phylogenetic analysis was performed to illustrate how AY.29 strains evolved and were introduced into countries abroad. Simultaneously, ancestral searches were performed for the overseas AY.29 samples to identify their origins in Japan using the maximum variant approach. As of January 10, 2022, 118 samples were identified in 20 countries. Phylogenetic analysis and ancestral searches identified 55 distinct introductions into those countries. The United States had 50 samples with 10 distinct introductions, and the United Kingdom had 13 distinct strains introduced in 18 samples. Other countries or regions with multiple introductions were Canada, Germany, South Korea, Hong Kong, Thailand, and the Philippines. Among the 20 countries, most European and North American countries have vaccination rates over 50% and sufficient genomic surveillances are conducted; transmissions seem contained. However, propagation to unvaccinated regions might have caused unfathomable damages. 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. More rigorous departure screenings for the participants from the unvaccinated countries might have been necessary.

Keywords: AY-29; COVID-19; Olympic Games; Paralympic Games; SARS-CoV-2; cross-border transmission; delta variant.

FIGURE 1

(A) Histogram of strains by lineages in Tokyo. (B) Number of daily new COVID-19 positive cases in Japan. (C) Number of daily new COVID-19 positive cases among Olympic and Paralympic participants.

FIGURE 2

Variant Analysis of SARS-CoV-2 genomes sampled in Tokyo, Japan between July 1st and September 10, 2021. AY.29 Delta substrain is dominant in the period. Variants are colored depending on the type of mutations (missense, synonymous, non-coding, stop-gained, and frameshift). 3CLPro, 3C like protease; del, deletion; delins, deletion–insertion; E, envelope protein; ExoN, 3’-5’ exonuclease; M, membrane glycoprotein; N, nucleocapsid phosphoprotein; NA, not applicable; NSP, non-structural protein; OMT, O-methyltransferase; ORF, open reading frame; RdRp, RNA-dependent RNA polymerase; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; S, spike glycoprotein; UTR, untranslated region.

FIGURE 3

Phylogenetic analysis of AY.29 strains. All overseas samples were combined with randomly selected 1,000 AY.29 genomes in Japan. The exported strains of the two largest clusters in the AY.29 exported strains were labeled in green.