Genomic Surveillance of SARS-CoV-2 Variants in the Dominican Republic and Emergence of a Local Lineage
Open Access
- 13 April 2023
- journal article
- research article
- Published by MDPI AG in International Journal of Environmental Research and Public Health
- Vol. 20 (8), 5503
- https://doi.org/10.3390/ijerph20085503
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an RNA virus that evolves over time, leading to new variants. In the current study, we assessed the genomic epidemiology of SARS-CoV-2 in the Dominican Republic. A total of 1149 SARS-CoV-2 complete genome nucleotide sequences from samples collected between March 2020 and mid-February 2022 in the Dominican Republic were obtained from the Global Initiative on Sharing All Influenza Data (GISAID) database. Phylogenetic relationships and evolution rates were analyzed using the maximum likelihood method and the Bayesian Markov chain Monte Carlo (MCMC) approach. The genotyping details (lineages) were obtained using the Pangolin web application. In addition, the web tools Coronapp, and Genome Detective Viral Tools, among others, were used to monitor epidemiological characteristics. Our results show that the most frequent non-synonymous mutation over the study period was D614G. Of the 1149 samples, 870 (75.74%) were classified into 8 relevant variants according to Pangolin/Scorpio. The first Variants Being Monitored (VBM) were detected in December 2020. Meanwhile, in 2021, the variants of concern Delta and Omicron were identified. The mean mutation rate was estimated to be 1.5523 × 10−3 (95% HPD: 1.2358 × 10−3, 1.8635 × 10−3) nucleotide substitutions per site. We also report the emergence of an autochthonous SARS-CoV-2 lineage, B.1.575.2, that circulated from October 2021 to January 2022, in co-circulation with the variants of concern Delta and Omicron. The impact of B.1.575.2 in the Dominican Republic was minimal, but it then expanded rapidly in Spain. A better understanding of viral evolution and genomic surveillance data will help to inform strategies to mitigate the impact on public health.Funding Information
- Universidad Iberoamericana
- Research Vice-provost Office
- National Health Service (SNS) of the Dominican Republic’s Ministry of Health
- Research Centers in Minority Institutions (RCMI) Center for Research Resources
- National Institute on Minority Health and Health Disparities (MD007579)
This publication has 67 references indexed in Scilit:
- MAFFT online service: multiple sequence alignment, interactive sequence choice and visualizationBriefings in Bioinformatics, 2017
- GISAID: Global initiative on sharing all influenza data – from vision to realityEurosurveillance, 2017
- W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysisNucleic Acids Research, 2016
- Reconstructing the Timing and Dispersion Routes of HIV-1 Subtype B Epidemics in The Caribbean and Central America: A Phylogenetic StoryPLOS ONE, 2013
- Effect of Biodiversity Changes in Disease Risk: Exploring Disease Emergence in a Plant-Virus SystemPLoS Pathogens, 2012
- Recombination, Reservoirs, and the Modular Spike: Mechanisms of Coronavirus Cross-Species TransmissionJournal of Virology, 2010
- Jalview Version 2—a multiple sequence alignment editor and analysis workbenchBioinformatics, 2009
- Broadening of Neutralization Activity to Directly Block a Dominant Antibody-Driven SARS-Coronavirus Evolution PathwayPLoS Pathogens, 2008
- Bayesian Coalescent Inference of Past Population Dynamics from Molecular SequencesMolecular Biology and Evolution, 2005
- MODELTEST: testing the model of DNA substitution.Bioinformatics, 1998