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Sahadeo NSD, Nicholls S, Moreira FRR, O'Toole Á, Ramkissoon V, Whittaker C, Hill V, McCrone JT, Mohammed N, Ramjag A, Jordan AB, Hill SC, Singh R, Nathaniel-Girdharrie SM, Hinds A, Ramkissoon N, Parag KV, Nandram N, Parasram R, Khan-Mohammed Z, Edghill L, Indar L, Andrewin A, Sealey-Thomas R, McMillan P, Oyinloye A, George K, Potter I, Lee J, Johnson D, Charles S, Singh N, Bisesor-McKenzie J, Laws H, Belmar-George S, Keizer-Beache S, Greenaway-Duberry S, Ashwood N, Foster JE, Georges K, Naidu R, Ivey M, Giddings S, Haraksingh R, Ramsubhag A, Jayaraman J, Chinnadurai C, Oura C, Pybus OG, St John J, Gonzalez-Escobar G, Faria NR, Carrington CVF. Correction: Implementation of Genomic Surveillance of SARS-CoV-2 in the Caribbean: Lessons learned for sustainability in resource-limited settings. PLOS Glob Public Health 2023; 3:e0002393. [PMID: 37695757 PMCID: PMC10495005 DOI: 10.1371/journal.pgph.0002393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
[This corrects the article DOI: 10.1371/journal.pgph.0001455.].
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Sahadeo NSD, Nicholls S, Moreira FRR, O’Toole Á, Ramkissoon V, Whittaker C, Hill V, McCrone JT, Mohammed N, Ramjag A, Brown Jordan A, Hill SC, Singh R, Nathaniel-Girdharrie SM, Hinds A, Ramkissoon N, Parag KV, Nandram N, Parasram R, Khan-Mohammed Z, Edghill L, Indar L, Andrewin A, Sealey-Thomas R, McMillan P, Oyinloye A, George K, Potter I, Lee J, Johnson D, Charles S, Singh N, Bisesor-McKenzie J, Laws H, Belmar-George S, Keizer-Beache S, Greenaway-Duberry S, Ashwood N, Foster JE, Georges K, Naidu R, Ivey M, Giddings S, Haraksingh R, Ramsubhag A, Jayaraman J, Chinnadurai C, Oura C, Pybus OG, St. John J, Gonzalez-Escobar G, Faria NR, Carrington CVF. Implementation of genomic surveillance of SARS-CoV-2 in the Caribbean: Lessons learned for sustainability in resource-limited settings. PLOS Glob Public Health 2023; 3:e0001455. [PMID: 36963002 PMCID: PMC10022082 DOI: 10.1371/journal.pgph.0001455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 01/26/2023] [Indexed: 02/24/2023]
Abstract
The COVID-19 pandemic highlighted the importance of global genomic surveillance to monitor the emergence and spread of SARS-CoV-2 variants and inform public health decision-making. Until December 2020 there was minimal capacity for viral genomic surveillance in most Caribbean countries. To overcome this constraint, the COVID-19: Infectious disease Molecular epidemiology for PAthogen Control & Tracking (COVID-19 IMPACT) project was implemented to establish rapid SARS-CoV-2 whole genome nanopore sequencing at The University of the West Indies (UWI) in Trinidad and Tobago (T&T) and provide needed SARS-CoV-2 sequencing services for T&T and other Caribbean Public Health Agency Member States (CMS). Using the Oxford Nanopore Technologies MinION sequencing platform and ARTIC network sequencing protocols and bioinformatics pipeline, a total of 3610 SARS-CoV-2 positive RNA samples, received from 17 CMS, were sequenced in-situ during the period December 5th 2020 to December 31st 2021. Ninety-one Pango lineages, including those of five variants of concern (VOC), were identified. Genetic analysis revealed at least 260 introductions to the CMS from other global regions. For each of the 17 CMS, the percentage of reported COVID-19 cases sequenced by the COVID-19 IMPACT laboratory ranged from 0·02% to 3·80% (median = 1·12%). Sequences submitted to GISAID by our study represented 73·3% of all SARS-CoV-2 sequences from the 17 CMS available on the database up to December 31st 2021. Increased staffing, process and infrastructural improvement over the course of the project helped reduce turnaround times for reporting to originating institutions and sequence uploads to GISAID. Insights from our genomic surveillance network in the Caribbean region directly influenced non-pharmaceutical countermeasures in the CMS countries. However, limited availability of associated surveillance and clinical data made it challenging to contextualise the observed SARS-CoV-2 diversity and evolution, highlighting the need for development of infrastructure for collecting and integrating genomic sequencing data and sample-associated metadata.
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Affiliation(s)
- Nikita S. D. Sahadeo
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Soren Nicholls
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Filipe R. R. Moreira
- MRC Centre for Global Infectious Disease Analysis, Department for Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Áine O’Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Vernie Ramkissoon
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, Department for Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Verity Hill
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - John T. McCrone
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Nicholas Mohammed
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Anushka Ramjag
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Arianne Brown Jordan
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Sarah C. Hill
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, London, United Kingdom
| | - Risha Singh
- Caribbean Public Health Agency (CARPHA), Headquartered in Port of Spain, Republic of Trinidad and Tobago
| | | | - Avery Hinds
- Ministry of Health, Port of Spain, Republic of Trinidad and Tobago
| | - Nuala Ramkissoon
- Ministry of Health, Port of Spain, Republic of Trinidad and Tobago
| | - Kris V. Parag
- MRC Centre for Global Infectious Disease Analysis, Department for Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Naresh Nandram
- Ministry of Health, Port of Spain, Republic of Trinidad and Tobago
| | - Roshan Parasram
- Ministry of Health, Port of Spain, Republic of Trinidad and Tobago
| | | | - Lisa Edghill
- Caribbean Public Health Agency (CARPHA), Headquartered in Port of Spain, Republic of Trinidad and Tobago
| | - Lisa Indar
- Caribbean Public Health Agency (CARPHA), Headquartered in Port of Spain, Republic of Trinidad and Tobago
| | | | | | | | | | | | - Irad Potter
- Ministry of Health and Social Development, Road Town, Tortola, British Virgin Islands
| | - John Lee
- Ministry of Health and Wellness, George Town, Grand Cayman, Cayman Islands
| | - David Johnson
- Ministry of Health, Wellness and New Health Investment, Roseau, Dominica
| | | | | | | | - Hazel Laws
- Ministry of Health, Basseterre, Saint Kitts and Nevis
| | | | - Simone Keizer-Beache
- Ministry of Health, Wellness and the Environment, Kingstown, Saint Vincent and the Grenadines
| | | | - Nadia Ashwood
- Ministry of Health, Agriculture, Sports and Human Services, Grand Turk, Turks and Caicos Islands
| | - Jerome E. Foster
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Karla Georges
- School of Veterinary Medicine, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Rahul Naidu
- School of Dentistry, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Marsha Ivey
- Department of Clinical Medical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Stanley Giddings
- Department of Clinical Medical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Rajini Haraksingh
- Department of Life Sciences, Faculty of Sciences of Technology, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Adesh Ramsubhag
- Department of Life Sciences, Faculty of Sciences of Technology, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Jayaraj Jayaraman
- Department of Life Sciences, Faculty of Sciences of Technology, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Chinnaraja Chinnadurai
- Department of Life Sciences, Faculty of Sciences of Technology, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Christopher Oura
- School of Veterinary Medicine, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Oliver G. Pybus
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, London, United Kingdom
| | - Joy St. John
- Caribbean Public Health Agency (CARPHA), Headquartered in Port of Spain, Republic of Trinidad and Tobago
| | - Gabriel Gonzalez-Escobar
- Caribbean Public Health Agency (CARPHA), Headquartered in Port of Spain, Republic of Trinidad and Tobago
| | - Nuno R. Faria
- MRC Centre for Global Infectious Disease Analysis, Department for Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
- Departamento de Moléstias Infecciosas e Parasitárias e Instituto de Medicina Tropical da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Christine V. F. Carrington
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
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