Aspectos técnicos e operacionais de um modelo de serviço de vigilância genômica para COVID-19 no estado do Ceará

Abstract

The variants of concern (VOCs) of SARS-CoV-2 are the result of the evolutionary process of the virus since its emergence and constitute a threat to public health worldwide. The precise identification of these variants has become essential for targeting measures to contain the COVID-19 pandemic, including in the state of Ceará. This identification is mainly done through sequencing the complete genome of the virus, a costly and laborious method that requires several steps of sample preparation and processing. Faster, more cost-effective methods have been developed for the objective determination of VOCs predominant in the state and of greater epidemiological relevance due to their greater capacity for transmission, dissemination, and vaccine escape. Chronologically, the first VOC identified in the state of Ceará was the Gamma variant, which originally emerged in late 2020 in the state of Amazonas and quickly spread to other Brazilian states and abroad, becoming the main responsible for the second pandemic wave in Ceará. The second most expressive VOC that was introduced in the State was the Delta variant, which despite having appeared in late 2020 in India, the first records were registered in Brazil from April 2021, becoming the predominant variant, including in the State, during the second half of 2021. In this context, the installation of a Genomic Surveillance Service in Ceará working together with a referenced laboratory for the diagnosis of COVID-19 of the state health network (Centro de Hematologia e Hemoterapia do Ceará/Hemoce) it constituted a public health need, both for priority screening of cases under investigation, for monitoring the viral population and its evolutionary process, and finally for timely reporting to health surveillance agencies. The present work proposes a service model for Genomic Surveillance in the state of Ceará, conceived by a multicentric network of laboratories participating in Fiocruz, through the design of workflows, standardization, andoptimization of the proposed model, through the evaluation of the scope of the service to cover most municipalities in the state and comparative analysis of data with other surveillance services in Brazil. In a second moment, the main problems and complications associated with the proposed model were gathered and potential analytical solutions were presented, through testing and re-testing with control, agreement of results with molecular assays of rtPCR by indirect method of inference and the optimization of genomic sequencing procedures and data quality control. Finally, the impact and relevance of constituting a reference service in genomic surveillance for the state is reported.