Dataset Information

Global spread of a Japan-originated Delta lineage of SARS-CoV-2 after the Tokyo Olympics is most likely unrelated to the Olympics.

ABSTRACT: Participants of the 2021 Summer Olympics in Tokyo were required to adhere to strict health protocols, and there were no major local outbreaks within the separation bubbles. However, based on viral genomic data, we report that the Japan-specific Delta variants did spread out globally during or after the Olympics.

SUBMITTER: Shimura T

PROVIDER: S-EPMC8903406 | biostudies-literature | 2022 Feb

REPOSITORIES: biostudies-literature

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Global spread of a Japan-originated Delta lineage of SARS-CoV-2 after the Tokyo Olympics is most likely unrelated to the Olympics.

Shimura Takako T Kosaki Kenjiro K

Journal of travel medicine 20220208

Participants of the 2021 Summer Olympics in Tokyo were required to adhere to strict health protocols, and there were no major local outbreaks within the separation bubbles. However, based on viral genomic data, we report that the Japan-specific Delta variants did spread out globally during or after the Olympics. ...[more]

PMID: 35137177

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Project description:There has been a decreasing trend in new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cases and fatalities worldwide. The virus has been evolving, indicating the potential emergence of new variants and uncertainties. These challenges necessitate continued efforts in disease control and mitigation strategies. We investigated a small cluster of SARS-CoV-2 Omicron variant infections containing a common set of genomic mutations, which provided a valuable model for investigating the transmission mechanism of genetic alterations. We conducted a study at a medical center in Japan during the Omicron surge (sub-lineage BA.5), sequencing the entire SARS-CoV-2 genomes from infected individuals and evaluating the phylogenetic tree and haplotype network among the variants. We compared the mutations present in each strain within the BA.5 strain, TKYnat2317, which was first identified in Tokyo, Japan. From June 29th to July 4th 2022, nine healthcare workers (HCWs) tested positive for SARS-CoV-2 by real-time PCR. During the same period, five patients also tested positive by real-time PCR. Whole genome sequencing revealed that the infected patients belonged to either the isolated BA.2 or BA.5 sub-lineage, while the healthcare worker infections were classified as BF.5. The phylogenetic tree and haplotype network clearly showed the specificity and similarity of the HCW cluster. We identified 12 common mutations in the cluster, including I110V in nonstructural protein 4 (nsp4), A1020S in the Spike protein, and H47Y in ORF7a, compared to the BA.5 reference. Additionally, one case had the extra nucleotide-deletion mutation I27* in ORF10, and low frequencies of genetic alterations were also found in certain instances. The results of genome sequencing showed that the nine HCWs shared a set of genetic mutations, indicating transmission within the cluster. Minor mutations observed in five HCW individuals suggested the emergence of new virus variants. Five amino acid substitutions occurred in nsp3, which could potentially affect virus replication or immune escape. Intra-host evolution also generated additional mutations. The cluster exhibited a mild disease course, with individuals in this case, recovering without requiring any medical treatments. Further investigation is needed to understand the relationship between the genetic evolution of the virus and the symptoms.

Project description:PurposeRanking of nations by medal tally is a popular feature of the Olympics, but such ranking is a poor measure of sporting prowess or engagement until the tallies are adjusted for major factors beyond the control of individual nations. Here we estimate and adjust for effects of total population, economy expressed as gross domestic product per capita, absolute latitude and Muslim population proportion on total medal counts in female, male, mixed and all events at the Pyeongchang winter and Tokyo summer Olympics and Paralympics.MethodsThe statistical model was multiple linear over-dispersed Poisson regression. Population and economy were log-transformed; their linear effects were expressed in percent per percent units and evaluated in magnitude as the factor effects of two between-nation standard deviations (SD). The linear effect of absolute latitude was expressed and evaluated as the factor effect of 30° (approximately 2 SD). The linear effect of Muslim proportion was expressed as the factor effect of 100% vs. 0% Muslim. Nations were ranked on the basis of actual vs. predicted all-events medal counts.ResultsAt the Pyeongchang Olympics, effects of population and economy were 0.7-0.8 %/% and 1.1-1.7 %/% (welldefined extremely large increases for 2 SD), factor effects of 30° of latitude were 11-17 (welldefined extremely large increases), and factor effects of 100% Muslim population were 0.08-0.69 (extremely large to moderate reductions, albeit indecisive). Effects at the Tokyo Olympics were similar in magnitude, including those of latitude, which were surprisingly still positive although diminished (large to very large increases). Effects at the Pyeongchang and Tokyo Paralympics were generally similar to those at the Olympics, but the effects of economy were diminished (large to very large increases). After adjustment of medal tallies for these effects, nations that reached the top-10 medalists in both winter games were Austria, Belarus, Kazakhstan, Slovakia and Ukraine, but only Azerbaijan reached the top-10 in both summer games.ConclusionAdjusting medal counts for demographic and geographic factors provides a comparison of nations' sporting prowess or engagement that is more in keeping with the Olympic ideal of fair play and more useful for nations' Olympic-funding decisions.

Dataset Information

Global spread of a Japan-originated Delta lineage of SARS-CoV-2 after the Tokyo Olympics is most likely unrelated to the Olympics.

Publications

Global spread of a Japan-originated Delta lineage of SARS-CoV-2 after the Tokyo Olympics is most likely unrelated to the Olympics.

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