Sahadeo Nikita S D, Nicholls Soren, Moreira Filipe R R, O'Toole Áine, Ramkissoon Vernie, Whittaker Charles, Hill Verity, McCrone John T, Mohammed Nicholas, Ramjag Anushka, Brown Jordan Arianne, Hill Sarah C, Singh Risha, Nathaniel-Girdharrie Sue-Min, Hinds Avery, Ramkissoon Nuala, Parag Kris V, Nandram Naresh, Parasram Roshan, Khan-Mohammed Zobida, Edghill Lisa, Indar Lisa, Andrewin Aisha, Sealey-Thomas Rhonda, McMillan Pearl, Oyinloye Ayoola, George Kenneth, Potter Irad, Lee John, Johnson David, Charles Shawn, Singh Narine, Bisesor-McKenzie Jacquiline, Laws Hazel, Belmar-George Sharon, Keizer-Beache Simone, Greenaway-Duberry Sharra, Ashwood Nadia, Foster Jerome E, Georges Karla, Naidu Rahul, Ivey Marsha, Giddings Stanley, Haraksingh Rajini, Ramsubhag Adesh, Jayaraman Jayaraj, Chinnadurai Chinnaraja, Oura Christopher, Pybus Oliver G, St John Joy, Gonzalez-Escobar Gabriel, Faria Nuno R, Carrington Christine V F
Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago.
MRC Centre for Global Infectious Disease Analysis, Department for Infectious Disease Epidemiology, Imperial College London, London, United Kingdom.
PLOS Glob Public Health. 2023 Feb 22;3(2):e0001455. doi: 10.1371/journal.pgph.0001455. eCollection 2023.
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.
新冠疫情凸显了全球基因组监测对于监测严重急性呼吸综合征冠状病毒2（SARS-CoV-2）变体的出现和传播以及为公共卫生决策提供信息的重要性。直到2020年12月，大多数加勒比国家的病毒基因组监测能力都很有限。为克服这一限制，实施了“新冠：病原体控制与追踪的传染病分子流行病学（COVID-19 IMPACT）”项目，以在特立尼达和多巴哥（T&T）的西印度群岛大学（UWI）建立快速的SARS-CoV-2全基因组纳米孔测序，并为T&T和其他加勒比公共卫生机构成员国（CMS）提供所需的SARS-CoV-2测序服务。使用牛津纳米孔技术公司的MinION测序平台、ARTIC网络测序方案和生物信息学流程，在2020年12月5日至2021年12月31日期间，对从17个CMS收到的总共3610份SARS-CoV-2阳性RNA样本进行了现场测序。确定了91个Pango谱系，包括5个关注变体（VOC）的谱系。基因分析显示，至少有260次从其他全球区域传入CMS。对于17个CMS中的每一个，COVID-19 IMPACT实验室测序的报告新冠病例百分比从0.02%到3.80%不等（中位数=1.12%）。我们的研究提交给全球共享流感数据倡议组织（GISAID）的序列占截至2021年12月31日数据库中17个CMS所有SARS-CoV-2序列的73.3%。在项目过程中增加人员配备、改进流程和基础设施有助于减少向原始机构报告以及向GISAID上传序列的周转时间。我们在加勒比地区的基因组监测网络所获得的见解直接影响了CMS国家的非药物对策。然而，相关监测和临床数据的可用性有限，使得难以将观察到的SARS-CoV-2多样性和进化情况置于具体背景中，这凸显了开发用于收集和整合基因组测序数据及样本相关元数据的基础设施的必要性。
