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

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.

Fig 1. Locations of current laboratories part of the COVID-19 Genomic Surveillance Regional Network in the Americas region.

CENETROP—Centro Nacional de Enfermedades Tropicales (Bolivia); DLSP–Departamento Laboratorio de Salud Pública (Uruguay); FIOCRUZ–Fundação Oswaldo Cruz (Brazil); IAL–Instituto Adolfo Lutz (Brazil); ICGES -Instituto Conmemorativo Gorgas de Estudios de la Salud (Panama); IEC–Instituto Evandro Chagas (Brazil); INCIENSA—Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (Costa Rica); InDRE—Instituto de Diagnóstico y Referencia Epidemiológicos (Mexico); INHRR—Instituto Nacional de Higiene Rafael Rangel (Venezuela); INS–Instituto Nacional de Salud (Colombia); INS–Instituto Nacional de Salud (Peru); INSPI–Instituto Nacional de Investigación en Salud Pública (Ecuador); ISPCH–Instituto de Salud Pública (Chile); LCSP–Laboratorio Central de Salud Pública (Paraguay); LNS–Laboratorio Nacional de Salud (Guatemala); LNSP–Laboratoire National de Santé Publique (Haiti); LNV—Laboratorio Nacional de Virología (Honduras); MALBRAN—Administración Nacional de Laboratorios e Institutos de Salud “Dr. Carlos G. Malbrán” (Argentina); PHL–Best dos Santos Public Health Laboratory (Barbados); RL-MoH–Reference Laboratory of the Ministry of Health (Bahamas); UWI–University of West Indies (Jamaica). Red–In house sequencing; Blue–External sequencing; Yellow–Reference Sequencing Laboratories.

Fig 2

(A) Genetic groups and (B) E484K, N501Y and K417N spike mutations identified among SARS-CoV-2 circulating in Latin America and the Caribbean regions, epidemiologic weeks 1/2020-3/2021.

Fig 3. Maximum-likelihood phylogeny of the SARS-COV-2 circulating in Latin America and the Caribbean regions.

Countries sequences marked by colored circles.