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Title: Genomic surveillance of SARS-CoV-2 variants in the Dominican Republic and emergence of a local lineage
Autores: Paulino-Ramírez, Robert
López, P.
Mueses Jiménez, Sayira P.
Cuevas Martínez, Paula
Jabier Frías, Maridania
Rivera-Amill, V.
Researchers (UNIBE): Paulino-Ramírez, Robert 
Mueses Jiménez, Sayira P. 
Cuevas Martínez, Paula 
Jabier Frías, Maridania 
Affiliations: Instituto de Medicina Tropical y Salud Global (IMTSAG) 
Instituto de Medicina Tropical y Salud Global (IMTSAG) 
Instituto de Medicina Tropical y Salud Global (IMTSAG) 
Instituto de Medicina Tropical y Salud Global (IMTSAG) 
Research area: Ciencias de la Salud
Keywords: SARS-CoV-2; Mutations; Variants of concern
Issue Date: 2023
Publisher: Frontiers Media S.A.
Source: International Journal of Environmental Research and Public Health, 20(8), 5503; 2023
Journal: International Journal of Environmental Research and Public Health 
Volume: 20
Issue: 8
Start page: 5503
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.
DOI: ijerph20085503
Appears in Collections:Publicaciones del IMTSAG-UNIBE
Publicaciones indexadas en Scopus / Web of Science

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