Implementation of a COVID-19 Genomic Surveillance Regional Network for Latin America and Caribbean region.

Rodrigo Fasce,Enrique Perez,Alexander Augusto Martinez Caballero,Barbara Parra,Sylvain Aldighieri,Andrea Vicari,Baochuan Lin,Marilda Siqueira,Fernando Couto Motta,Jorge Fernandez,Lucas Freitas,Juliana Almeida Leite,Andrés Castillo,Leticia Franco,Paola Resende,Lionel Gresh,Jairo Mendez-Rico,Jean-Marc Gabastou

doi:10.1371/journal.pone.0252526

Abstract

The timely release of SARS-CoV-2 first genomic sequences allowed the identification of the etiologic agent and development of diagnostic protocols. Genomic sequencing was a crucial step in generating data for driving laboratory response and detections of SARS-CoV-2 since the start of the COVID-19 pandemic. Because of all the progression and achievements that timely release of genetic sequence data represents in the public health response, the Pan American Health Organization (PAHO) in collaboration with countries’ public health laboratories, started implementation of a network for strengthening the Latin America and Caribbean (LAC) region on timely generation of SARS-CoV-2 genomic data. Here we describe the implementation of the COVID-19 Genomic Surveillance Regional Network in the Americas region during the beginning of the pandemic. The establishment of this network has strengthened laboratory response capacity at the country level, as well as facilitated timely release of SARS-CoV-2 genomic information to be used to complement the multiple response strategies for COVID-19 pandemic mitigation. As genomic epidemiology is useful for guiding public health decisions on outbreak and response, we also analysed the first SARS-CoV-2 genomic sequence data from countries of the Latin America and Caribbean Region.

Highlights

For some countries that rely on external sequencing for generating genomic sequence data (GSD), almost 100% of the data are being generated through the network (Table 1)
The COVID-19 Genomic Surveillance Regional Network is the first large-scale genomic sequencing network implemented in the Latin America and Caribbean (LAC) Region to generate data as part of the actions and public health response to a pandemic
This network formalizes the work already being carried out by participating laboratories performing in house sequencing of SARS-CoV-2, providing a space for discussion and information sharing on genomic sequencing

Summary

Introduction

Public release of this novel coronavirus genomic data allowed the development of the first molecular diagnostic protocol released and published by the Charite –Universitatsmedizin Berlin Institute of Virology, Germany on the WHO webpage in less than 15 days after the cluster notification to WHO [4, 5]. The timely release of the first genomic sequences allowed the development of diagnostic protocols, and the identification of the etiologic agent causing this outbreak. This novel coronavirus showed to be different from the severe acute respiratory syndrome coronavirus, and was eventually named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the International Committee on Taxonomy of Viruses (ICTV) [6]. Genomic sequencing was a crucial step for generating data for driving laboratory response and laboratory case detections of SARS-CoV-2 since the first notifications of the novel coronavirus outbreak, COVID-19 pandemic [7, 8]

Methods

Results

Conclusion