Dataset Information

Analysis of 329,942 SARS-CoV-2 records retrieved from GISAID database.

ABSTRACT:

Background

The SARS-CoV-2 virus caused a worldwide pandemic - although none of its predecessors from the coronavirus family ever achieved such a scale. The key to understanding the global success of SARS-CoV-2 is hidden in its genome.

Materials and methods

We retrieved data for 329,942 SARS-CoV-2 records uploaded to the GISAID database from the beginning of the pandemic until the January 8, 2021. A Python variant detection script was developed to process the data using pairwise2 from the BioPython library. Sequence alignments were performed for every gene separately (except ORF1ab, which was not studied). Genomes less than 26,000 nucleotides long were excluded from the research. Clustering was performed using HDBScan.

Results

Here, we addressed the genetic variability of SARS-CoV-2 using 329,942 samples. The analysis yielded 155 SNPs and deletions in more than 0.3% of the sequences. Clustering results suggested that a proportion of people (2.46%) was infected with a distinct subtype of the B.1.1.7 variant, which contained four to six additional mutations (G28881A, G28882A, G28883С, A23403G, A28095T, G25437T). Two clusters were formed by mutations in the samples uploaded predominantly by Denmark and Australia (1.48% and 2.51%, respectively). A correlation coefficient matrix detected 160 pairs of mutations (correlation coefficient greater than 0.7). We also addressed the completeness of the GISAID database, patient gender, and age. Finally, we found ORF6 and E to be the most conserved genes (96.15% and 94.66% of the sequences totally match the reference, respectively). Our results indicate multiple areas for further research in both SARS-CoV-2 studies and health science.

SUBMITTER: Zelenova M

PROVIDER: S-EPMC8547852 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Similar Datasets

Project description:PurposeTo assess the risk of vaccine-associated uveitis (VAU) following SARS-CoV-2 vaccination and evaluate uveitis onset interval and clinical presentations in the patients.DesignA retrospective study from December 11, 2020, to May 9, 2022, using the Centers for Disease Control and Prevention (CDC) Vaccine Adverse Events Reporting System (VAERS).ParticipantsPatients diagnosed with VAU following administration of BNT162b2 (Pfizer-BioNTech), mRNA-1273 (Moderna), and Ad26.COV2.S (Janssen) vaccine, worldwide.MethodsA descriptive analysis of the demographics, clinical history and presentation was performed. We evaluated the correlation between the three vaccines and continuous and categorical variables. A post-hoc analysis was performed between uveitis onset-interval after vaccination, and age, dose, and vaccine type. Finally, a 30-day risk analysis for VAU onset post-vaccination was performed.Main outcome measuresThe estimated global crude reporting rate, observed to expected ratio of VAU in the United States, associated ocular and systemic presentations, and onset duration.ResultsA total of 1094 cases of VAU were reported from 40 countries with an estimated crude reporting rate (per million doses) of 0.57, 0.44, and 0.35 for BNT162b2, mRNA-1273, and Ad26.COV2.S, respectively. The observed to expected ratio of VAU for the cases reports from the United States was comparable for BNT162b2 (0.023), mRNA-1273 (0.025), and Ad26.COV2.S (0.027). Most cases of VAU were reported in patients who received BNT162b2 (n=853, 77.97%). The mean age of patients with VAU was 46.24±16.93 years, and 68.65% (n=751) were women. Most cases were reported after the first dose (n=452, 41.32%) and within the first week (n=591, 54.02%) of the vaccination. The onset interval for VAU was significantly longer in patients who received mRNA-1273 (21.22± 42.74 days) compared to BNT162b2 (11.42 ± 23.16 days) and rAd26.COV2.S (12.69 ± 16.02 days) vaccines (p<0.0001). The post-hoc analysis revealed a significantly shorter interval of onset for the BNT162b2 compared to the mRNA 1273 vaccine (p<0.0001) and the first dose compared to the second dose (p=0.0021). The 30-day risk analysis showed a significant difference between the three vaccines (p<0.0001).ConclusionsThe low crude reporting rate and observed-expected ratio suggests a low safety concern for VAU. This study provides insights into possible temporal association between reported VAU events and SARS-CoV-2 vaccines, however further investigations are required to delineate the associated immunological mechanisms.