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Genomic Surveillance of SARS-CoV-2 Variants in the Dominican Republic and Emergence of a Local Lineage

Author

Listed:
  • Robert Paulino-Ramírez

    (Instituto de Medicina Tropical y Salud Global, Universidad Iberoamericana, Research Hub, Santo Domingo 22333, Dominican Republic)

  • Pablo López

    (RCMI Center for Research Resources, Ponce Research Institute, Ponce, PR 00716-2348, USA)

  • Sayira Mueses

    (Instituto de Medicina Tropical y Salud Global, Universidad Iberoamericana, Research Hub, Santo Domingo 22333, Dominican Republic)

  • Paula Cuevas

    (Instituto de Medicina Tropical y Salud Global, Universidad Iberoamericana, Research Hub, Santo Domingo 22333, Dominican Republic)

  • Maridania Jabier

    (Instituto de Medicina Tropical y Salud Global, Universidad Iberoamericana, Research Hub, Santo Domingo 22333, Dominican Republic
    Servicio Nacional de Salud (SNS), Ministry of Health, Santo Domingo 10201, Dominican Republic)

  • Vanessa Rivera-Amill

    (RCMI Center for Research Resources, Ponce Research Institute, Ponce, PR 00716-2348, USA
    Basic Sciences Department, School of Medicine, Ponce Health Sciences University, Ponce, PR 00716-2348, USA)

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.

Suggested Citation

  • Robert Paulino-Ramírez & Pablo López & Sayira Mueses & Paula Cuevas & Maridania Jabier & Vanessa Rivera-Amill, 2023. "Genomic Surveillance of SARS-CoV-2 Variants in the Dominican Republic and Emergence of a Local Lineage," IJERPH, MDPI, vol. 20(8), pages 1-14, April.
    • Handle: RePEc:gam:jijerp:v:20:y:2023:i:8:p:5503-:d:1122876
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    References listed on IDEAS

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    1. Fan Wu & Su Zhao & Bin Yu & Yan-Mei Chen & Wen Wang & Zhi-Gang Song & Yi Hu & Zhao-Wu Tao & Jun-Hua Tian & Yuan-Yuan Pei & Ming-Li Yuan & Yu-Ling Zhang & Fa-Hui Dai & Yi Liu & Qi-Min Wang & Jiao-Jiao , 2020. "A new coronavirus associated with human respiratory disease in China," Nature, Nature, vol. 579(7798), pages 265-269, March.
    2. Fan Wu & Su Zhao & Bin Yu & Yan-Mei Chen & Wen Wang & Zhi-Gang Song & Yi Hu & Zhao-Wu Tao & Jun-Hua Tian & Yuan-Yuan Pei & Ming-Li Yuan & Yu-Ling Zhang & Fa-Hui Dai & Yi Liu & Qi-Min Wang & Jiao-Jiao , 2020. "Author Correction: A new coronavirus associated with human respiratory disease in China," Nature, Nature, vol. 580(7803), pages 7-7, April.
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