Implementation of genomic surveillance of SARS-CoV-2 in the Caribbean: Lessons learned for sustainability in resource-limited settings
Nikita Sahadeo, Soren Nicholls, Filipe Romero Rebello Moreira, Áine O’Toole, Vernie Ramkissoon, Charles Whittaker, Verity Hill, John T. McCrone, Nicholas Mohammed, Anushka Ramjag, Arianne Brown Jordan, Sarah C. Hill, Risha Singh, Sue-Min Nathaniel-Girdharrie, Avery Hinds, Nuala Ramkissoon, Kris V. Parag, Naresh Nandram, Roshan Parasram, Zobida Khan-Mohammed, Lisa Edghill, Lisa Indar, Aisha Andrewin, Rhonda Sealey-Thomas, Pearl McMillan, Ayoola Oyinloye, Kenneth George, Irad Potter, John Lee, D. Barrie Johnson, Shawn Charles, Narine Singh, Jacquiline Bisesor-McKenzie, Hazel Laws, Sharon Belmar-George, Simone Keizer-Beache, Sharra Greenaway-Duberry, Nadia Ashwood, J. E. Foster, Karla Georges, Rahul Naidu, Marsha Ivey, Stanley Giddings, Rajini Haraksingh, Adesh Ramsubhag, Jayaraj Jayaraman, C. Chinnaraja, Christopher Oura, Oliver G. Pybus, Joy St. John, Gabriel González-Escobar, Nuno R. Faria, Christine V. F. Carrington
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.