Dataset Information

Codon usage divergence in Delta variants (B.1.617.2) of SARS-CoV-2.

ABSTRACT: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spreads all over the world and brings great harm to humans in many countries. Many new SARS-CoV-2 variants appeared during its transmission. In the present study, the Delta variants (B.1.617.2) of SARS-CoV-2, which have appeared in many countries, were considered for analysis. In order to evaluate the evolutionary divergence of the Delta variants(B.1.617.2), the codon usage divergence in Delta variants (B.1.617.2) of SARS-CoV-2 was compared to that of the SARS-CoV-2 genomes emerged before June 2020. All Delta variants (B.1.617.2) and 350 early genomes of SARS-CoV-2 in the NCBI database were downloaded. Codon usage pattern including the basic composition, the GC ratio of the third position (GC3) and the first two positions (GC12) in codons, overall GC contents, the effective number of codons (ENC), the codon bias index (CBI), the relative synonymous codon usage (RSCU) values, etc., of all concerned important gene sequences were all calculated. Codon usage divergence of them was calculated via summing their standard deviations. The results suggested that base compositions in both Delta variants (B.1.617.2) of SARS-CoV-2 and the early SARS-CoV-2 genomes were similar to each other. However, the internal codon usage divergence for most genes in Delta variants (B.1.617.2) was significantly wider than that of SARS-CoV-2. The RSCU values were further used to explore the synonymous and non-synonymous mutations in the sequences of the Delta variants (B.1.617.2), and the results showed the synonymous mutations are more obvious than the non-synonymous in the concerned sequences. The related codon usage divergence analysis is helpful for further study on the adaptability and disease prognosis of the SARS-CoV-2 variants.

SUBMITTER: Li G

PROVIDER: S-EPMC8641433 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Similar Datasets

Project description:ImportanceThe Delta variant (B.1.617.2) is estimated to be more transmissible than previous strains of SARS-CoV-2, especially among children and adolescents. However, to our knowledge, there are no reports confirming this to date.ObjectiveTo gain a better understanding of the association of age with susceptibility to the Delta variant of SARS-CoV-2.Design, setting, and participantsThis decision analytic model used an age-structured compartmental model using the terms symptom onset (S), exposure (E), infectious (I), and quarantine (Q) (SEIQ) to estimate the age-specific force of infection, combining age-specific contact matrices and observed distribution of periods between each stage of infection (E to I [ie, latent period], I given S, and S to Q [ie, diagnostic delay]) developed in a previous contact tracing study. A bayesian inference method was used to estimate the age-specific force of infection (S to E) and, accordingly, age-specific susceptibility. The age-specific susceptibility during the third wave (ie, before Delta, from October 15 to December 22, 2020, when the COVID-19 vaccination campaign was not yet launched) and the fourth wave (ie, the Delta-driven wave, from June 27 to August 21, 2021) in Korea were compared. As vaccine uptake increased, individuals who were vaccinated were excluded from the susceptible population in accordance with vaccine effectiveness against the Delta variant. This nationwide epidemiologic study included individuals who were diagnosed with COVID-19 during the study period in Korea. Data were analyzed from September to November 2021.ExposuresAge group during the third wave (ie, before Delta) and fourth wave (ie, Delta-driven) of the COVID-19 pandemic in South Korea.Main outcomes and measuresAge-specific susceptibility during the third and fourth waves was estimated.ResultsAmong 106 866 confirmed COVID-19 infections (including 26 597 infections and 80 269 infections during the third and fourth waves of COVID-19 in Korea, respectively), a significant difference in age-specific susceptibility to the Delta vs pre-Delta variant was found in the younger age group. After adjustment for contact pattern and vaccination status, the increase in susceptibility to the Delta vs pre-Delta variant was estimated to be highest in the group aged 10 to 15 years, approximately doubling (1.92-fold increase [95% CI, 1.86-fold to 1.98-fold]), whereas in the group aged 50 years or more, susceptibility to the Delta vs pre-Delta variant remained stable at an approximately 1-fold change (eg, among individuals aged 50-55 years: 0.997-fold [95% CI, 0.989-fold to 1.001-fold).Conclusions and relevanceIn this study, the Delta variant of SARS-CoV-2 was estimated to propagate more easily among children and adolescents than pre-Delta strains, even after adjusting for contact pattern and vaccination status.

Dataset Information

Codon usage divergence in Delta variants (B.1.617.2) of SARS-CoV-2.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets