Implementation of genomic surveillance of Sars-CoV-2 in the Caribbean

Lessons learned for sustainability in resource-limited settings

Bibliographic Data

ID19591908
AuthorsNikita S D Sahadeo (0000-0003-3990-9601, University of the West Indies, corresponding author), Soren Nicholls (University of the West Indies, corresponding author), Filipe Romero Rebello Moreira (0000-0002-7162-5070, London Centre for Neglected Tropical Disease Research, corresponding author), Áine O’Toole (0000-0001-8083-474X, University of Edinburgh, corresponding author), Vernie Ramkissoon (University of the West Indies, corresponding author), Charles Whittaker (0000-0002-5003-2575, London Centre for Neglected Tropical Disease Research, corresponding author), Verity Hill (0000-0002-3509-8146, University of Edinburgh, corresponding author), J T McCrone (0000-0002-9846-8917, University of Edinburgh, corresponding author), Nicholas Mohammed (0000-0001-9565-2957, University of the West Indies, corresponding author), Anushka Ramjag (University of the West Indies, corresponding author), Arianne Brown Jordan (0000-0002-4146-3920, University of the West Indies, corresponding author), Sarah C Hill (0000-0002-2995-2596, Royal Veterinary College, corresponding author), Risha Singh (0000-0001-5560-0730, Caribbean Public Health Agency, corresponding author), Sue-Min Nathaniel-Girdharrie (Caribbean Public Health Agency, corresponding author), Avery Hinds (Ministry of Health, corresponding author), Nuala Ramkissoon (Ministry of Health, corresponding author), Kris V Parag (0000-0002-7806-3605, London Centre for Neglected Tropical Disease Research, corresponding author), Naresh Nandram (Ministry of Health, corresponding author), Roshan Parasram (0000-0003-4461-3805, Ministry of Health, corresponding author), Zobida Khan-Mohammed (Ministry of Health, corresponding author), Lisa Edghill (Caribbean Public Health Agency, corresponding author), Lisa Indar (Caribbean Public Health Agency, corresponding author), Aisha Andrewin (corresponding author), Rhonda Sealey-Thomas (American University of Antigua, corresponding author), Pearl McMillan (Ministry of Health, corresponding author), Ayoola Oyinloye (corresponding author), Kenneth George (Ministry of Health, corresponding author), Irad Potter (United States Virgin Islands Department of Health, corresponding author), John Lee (0000-0002-0914-2975, University College of the Cayman Islands, corresponding author), David Johnson (0000-0002-2323-6847), D Barrie Johnson (0000-0001-7348-4016, Dominica State College, corresponding author), Shawn Charles (corresponding author), Narine Singh (University of Guyana, corresponding author), Jacquiline Bisesor-McKenzie (Ministry of Health, corresponding author), Hazel Laws (corresponding author), Sharon Belmar-George (Ministry of Health and Wellness, corresponding author), Simone Keizer-Beache (corresponding author), Sharra Greenaway-Duberry (0009-0007-5179-5906, Ministry of Health and Social Services, corresponding author), Nadia Ashwood (corresponding author), J E Foster (0000-0001-5699-3791, University of the West Indies, corresponding author), Karla Georges (0000-0001-5910-1429, University of the West Indies, corresponding author), Rahul Naidu (0000-0001-9901-6712, University of the West Indies, corresponding author), Marsha Ivey (0000-0002-3205-1748, University of the West Indies, corresponding author), Stanley Giddings (0000-0003-3709-6686, University of the West Indies, corresponding author), Rajini Haraksingh (0000-0002-6644-8874, University of the West Indies, corresponding author), Adesh Ramsubhag (0000-0002-5863-0457, University of the West Indies, corresponding author), Jayaraj Jayaraman (0000-0002-4910-8712, University of the West Indies, corresponding author), Chinnaraja Chinnadurai, C Chinnaraja (0000-0002-4461-4720, University of the West Indies, corresponding author), Christopher Oura (0000-0001-9393-5347, University of the West Indies, corresponding author), Oliver G Pybus (0000-0002-8797-2667, Royal Veterinary College, corresponding author), Joy St John (Caribbean Public Health Agency, corresponding author), Gabriel Gonzalez-Escobar (0000-0001-9577-5754, Caribbean Public Health Agency, corresponding author), Nuno Rodrigues Faria (0000-0001-8839-2798, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, corresponding author), Christine V F Carrington (0000-0001-6533-9302, University of the West Indies, corresponding author)
EditorsMarguerite Massinga Loembe (0000-0002-7822-566X)
Year2023
Volume3
Issue2
Pagese0001455
Publication date2023-02-22
Peer ReviewedYes
Open AccessYes
TypeARTICLE
VenuePLOS Global Public Health (JOURNAL)
Journal identifiersISSN: 2767-3375 • E-ISSN: 2767-3375
PublisherPublic Library of Science (PLoS) (PUBLISHER)
DOI10.1371/journal.pgph.0001455
PMID36963002
OpenAlexW4321488413
LanguageEN
Citations received3
References cited28

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 5 th 2020 to December 31 st 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 31 st 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

Biology · Disease · DNA sequencing · Gene · Genome · Genomics · Geography · Minion · Nanopore sequencing · Pandemic · Public health · Whole genome sequencing · COVID-19 Clinical Research Studies · Medicine · SARS-CoV-2 and COVID-19 Research · SARS-CoV-2 detection and testing · Genetics · Virology