In:
PLOS Global Public Health, Public Library of Science (PLoS), Vol. 3, No. 2 ( 2023-2-22), p. e0001455-
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 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.
Type of Medium:
Online Resource
ISSN:
2767-3375
DOI:
10.1371/journal.pgph.0001455
DOI:
10.1371/journal.pgph.0001455.g001
DOI:
10.1371/journal.pgph.0001455.g002
DOI:
10.1371/journal.pgph.0001455.g003
DOI:
10.1371/journal.pgph.0001455.g004
DOI:
10.1371/journal.pgph.0001455.g005
DOI:
10.1371/journal.pgph.0001455.g006
DOI:
10.1371/journal.pgph.0001455.t001
DOI:
10.1371/journal.pgph.0001455.t002
DOI:
10.1371/journal.pgph.0001455.s001
DOI:
10.1371/journal.pgph.0001455.s002
DOI:
10.1371/journal.pgph.0001455.s003
DOI:
10.1371/journal.pgph.0001455.s004
DOI:
10.1371/journal.pgph.0001455.s005
DOI:
10.1371/journal.pgph.0001455.s006
DOI:
10.1371/journal.pgph.0001455.s007
DOI:
10.1371/journal.pgph.0001455.s008
DOI:
10.1371/journal.pgph.0001455.s009
Language:
English
Publisher:
Public Library of Science (PLoS)
Publication Date:
2023
detail.hit.zdb_id:
3101394-6
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