IDEAS home Printed from https://ideas.repec.org/a/gam/jijerp/v20y2023i8p5503-d1122876.html
   My bibliography  Save this article

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
    as

    Download full text from publisher

    File URL: https://www.mdpi.com/1660-4601/20/8/5503/pdf
    Download Restriction: no
    File URL: https://www.mdpi.com/1660-4601/20/8/5503/
    Download Restriction: no
    ---><---

    References listed on IDEAS

    as
    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. "Author Correction: A new coronavirus associated with human respiratory disease in China," Nature, Nature, vol. 580(7803), pages 7-7, April.
    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. "A new coronavirus associated with human respiratory disease in China," Nature, Nature, vol. 579(7798), pages 265-269, March.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Irizar, Patricia & Kapadia, Dharmi & Amele, Sarah & Bécares, Laia & Divall, Pip & Katikireddi, Srinivasa Vittal & Kibuchi, Eliud & Kneale, Dylan & McCabe, Ronan & Nazroo, James & Nellums, Laura B. & T, 2023. "Pathways to ethnic inequalities in COVID-19 health outcomes in the United Kingdom: A systematic map," Social Science & Medicine, Elsevier, vol. 329(C).
    2. Mubango Hazel & Muzariri Calvin, 2022. "Employee Engagement and Competitive Advantage during Covid 19 Pandemic in Small to Medium Enterprises, Catering Industry, Harare," International Journal of Research and Innovation in Social Science, International Journal of Research and Innovation in Social Science (IJRISS), vol. 6(4), pages 288-292, April.
    3. Giulia Orilisi & Marco Mascitti & Lucrezia Togni & Riccardo Monterubbianesi & Vincenzo Tosco & Flavia Vitiello & Andrea Santarelli & Angelo Putignano & Giovanna Orsini, 2021. "Oral Manifestations of COVID-19 in Hospitalized Patients: A Systematic Review," IJERPH, MDPI, vol. 18(23), pages 1-19, November.
    4. David Gomez-Zepeda & Danielle Arnold-Schild & Julian Beyrle & Arthur Declercq & Ralf Gabriels & Elena Kumm & Annica Preikschat & Mateusz Krzysztof Łącki & Aurélie Hirschler & Jeewan Babu Rijal & Chris, 2024. "Thunder-DDA-PASEF enables high-coverage immunopeptidomics and is boosted by MS2Rescore with MS2PIP timsTOF fragmentation prediction model," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    5. Francesco Gangi & Eugenio D'Angelo & Lucia Michela Daniele & Nicola Varrone, 2021. "Assessing the impact of socially responsible human resources management on company environmental performance and cost of debt," Corporate Social Responsibility and Environmental Management, John Wiley & Sons, vol. 28(5), pages 1511-1527, September.
    6. Miquel Oliu-Barton & Bary S. R. Pradelski & Nicolas Woloszko & Lionel Guetta-Jeanrenaud & Philippe Aghion & Patrick Artus & Arnaud Fontanet & Philippe Martin & Guntram B. Wolff, 2022. "The effect of COVID certificates on vaccine uptake, health outcomes, and the economy," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    7. Sneha Gautam & Cyril Samuel & Alok Sagar Gautam & Sanjeev Kumar, 2021. "Strong link between coronavirus count and bad air: a case study of India," Environment, Development and Sustainability: A Multidisciplinary Approach to the Theory and Practice of Sustainable Development, Springer, vol. 23(11), pages 16632-16645, November.
    8. Hengrui Liu & Sho Iketani & Arie Zask & Nisha Khanizeman & Eva Bednarova & Farhad Forouhar & Brandon Fowler & Seo Jung Hong & Hiroshi Mohri & Manoj S. Nair & Yaoxing Huang & Nicholas E. S. Tay & Sumin, 2022. "Development of optimized drug-like small molecule inhibitors of the SARS-CoV-2 3CL protease for treatment of COVID-19," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    9. Michael Messer, 2022. "Bivariate change point detection: Joint detection of changes in expectation and variance," Scandinavian Journal of Statistics, Danish Society for Theoretical Statistics;Finnish Statistical Society;Norwegian Statistical Association;Swedish Statistical Association, vol. 49(2), pages 886-916, June.
    10. José M. Núñez-Sánchez & Jesús Molina-Gómez & Pere Mercadé-Melé & Santiago Almadana-Abón, 2024. "Boosting Competitiveness Through the Alignment of Corporate Social Responsibility, Strategic Management and Compensation Systems in Technology Companies: A Case Study," Sustainability, MDPI, vol. 16(21), pages 1-15, October.
    11. Alessandro Germani & Livia Buratta & Elisa Delvecchio & Claudia Mazzeschi, 2020. "Emerging Adults and COVID-19: The Role of Individualism-Collectivism on Perceived Risks and Psychological Maladjustment," IJERPH, MDPI, vol. 17(10), pages 1-15, May.
    12. Ioannis Kontoyiannis & Lambros Mertzanis & Athina Panotopoulou & Ioannis Papageorgiou & Maria Skoularidou, 2022. "Bayesian context trees: Modelling and exact inference for discrete time series," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 84(4), pages 1287-1323, September.
    13. Gabriela Dias Noske & Yun Song & Rafaela Sachetto Fernandes & Rod Chalk & Haitem Elmassoudi & Lizbé Koekemoer & C. David Owen & Tarick J. El-Baba & Carol V. Robinson & Glaucius Oliva & Andre Schutzer , 2023. "An in-solution snapshot of SARS-COV-2 main protease maturation process and inhibition," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    14. Eugene Song & Jae-Eun Lee & Seola Kwon, 2021. "Effect of Public Empathy with Infection-Control Guidelines on Infection-Prevention Attitudes and Behaviors: Based on the Case of COVID-19," IJERPH, MDPI, vol. 18(24), pages 1-18, December.
    15. Kow-Tong Chen, 2022. "Emerging Infectious Diseases and One Health: Implication for Public Health," IJERPH, MDPI, vol. 19(15), pages 1-4, July.
    16. Sui Zhang & Minghao Wang & Zhao Yang & Baolei Zhang, 2021. "A Novel Predictor for Micro-Scale COVID-19 Risk Modeling: An Empirical Study from a Spatiotemporal Perspective," IJERPH, MDPI, vol. 18(24), pages 1-16, December.
    17. Shujuan Li & Lingli Zhu & Lidan Zhang & Guoyan Zhang & Hongyan Ren & Liang Lu, 2023. "Urbanization-Related Environmental Factors and Hemorrhagic Fever with Renal Syndrome: A Review Based on Studies Taken in China," IJERPH, MDPI, vol. 20(4), pages 1-20, February.
    18. Umit Cirakli & Ibrahim Dogan & Mehmet Gozlu, 2022. "The Relationship Between COVID-19 Cases and COVID-19 Testing: a Panel Data Analysis on OECD Countries," Journal of the Knowledge Economy, Springer;Portland International Center for Management of Engineering and Technology (PICMET), vol. 13(3), pages 1737-1750, September.
    19. Neeltje van Doremalen & Jonathan E. Schulz & Danielle R. Adney & Taylor A. Saturday & Robert J. Fischer & Claude Kwe Yinda & Nazia Thakur & Joseph Newman & Marta Ulaszewska & Sandra Belij-Rammerstorfe, 2022. "ChAdOx1 nCoV-19 (AZD1222) or nCoV-19-Beta (AZD2816) protect Syrian hamsters against Beta Delta and Omicron variants," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    20. Jaeyong Lee & Calem Kenward & Liam J. Worrall & Marija Vuckovic & Francesco Gentile & Anh-Tien Ton & Myles Ng & Artem Cherkasov & Natalie C. J. Strynadka & Mark Paetzel, 2022. "X-ray crystallographic characterization of the SARS-CoV-2 main protease polyprotein cleavage sites essential for viral processing and maturation," Nature Communications, Nature, vol. 13(1), pages 1-13, December.

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:gam:jijerp:v:20:y:2023:i:8:p:5503-:d:1122876. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: MDPI Indexing Manager (email available below). General contact details of provider: https://www.mdpi.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.