Cohort Profile of the Chilean COVID-19 Biorepository: a Multicentric initiative for multi-omics research on COVID-19 and LONG-COVID in a Latin American population
Authors: Signore Iskra A. , Donoso Gerardo , Bocchieri Pamela , Tobar-Calfucoy Eduardo A. , Yáñez Cristian E. , Carvajal-Silva Laura , Silva Andrea X. , Otth Carola , Claudio Cappelli L. , Jorquera Héctor Valenzuela , Zapata-Contreras Daniela , Espinosa-Parrilla Yolanda , Pacheco Paula Zúñiga , Fuentes-Guajardo Macarena , Monardes-Ramírez Virginia A. , Velasquez Pia Kochifas , Muñoz Christian A. , Dorador Cristina , García-Araya Jonathan , Campillay-Véliz Claudia P. , Echeverria Cesar , Santander Rodolfo Alejandro , Cerpa Leslie C. , Martínez Matías F. , Quiñones Luis Abel , Lamoza Galleguillos Eduardo Roberto , Hidalgo Juan Saez , Nova-Lamperti Estefanía , Sanhueza Sergio , Giacaman Annesi , Acosta-Jamett Gerardo , Verdugo Cristóbal , Plaza Anita , Verdugo Claudio , Selman Carolina , Verdugo Ricardo Alejandro , Colombo Alicia 
Published: December 2023

Purpose

Molecular mechanisms underlying COVID-19 susceptibility and severity are still poorly understood. The presence of genetic risk factors associated with ethnic background has been suggested, highlighting non-European ancestry as a risk factor for hospitalization in the United States. However, the representation of non-European populations in genomic case-control and cohort studies remains insufficient, and Latin American populations have been significantly understudied. Addressing this gap, we established The Chilean COVID-19 Biorepository, a multicentric endeavor comprising high-quality biological samples and associated data collected throughout Chile under stringent biobanking standards that ensure high quality, reproducibility, and interoperability.

Participants

The Chilean COVID-19 Biorepository was established by a network of nine nodes distributed in five macro-zones nationwide. The study enrolled adult participants living in Chile who had tested positive for SARS-CoV-2 infection and provided broad written informed consent. Blood samples were collected with EDTA and processed to store blood, plasma, buffy-coat, and DNA. Quality control measures, such as Standard Preanalytical Code (SPREC), incident reporting, DNA concentration, and absorbance ratio (260/280), were implemented to ensure the reliability and quality of the collected samples. Sociodemographic data, habits, clinical information, use of medications, and preexisting pathologies were registered. A weekly iterative workflow was implemented to ensure the quality and integrity of specimens and data.

Findings to date

Between October 2020 and February 2021, 2262 participants were recruited, pseudonymized, and categorized by disease severity into six categories, from asymptomatic to lethal. Notably, the Biorepository exhibited high compliance rates (>90%) across all quality control assessed items, reflecting high adherence to biobanking standards. A noteworthy feature of this cohort is the self-identification of 279 participants (12.3%) into thirteen different ethnic groups. Amerindian ancestry from genome-wide genetic data was 44.0%[SD15.5%] and increased to 61.2%[SD19.5%] when considering participants who identified as Native South Americans. As a data-contributor partner of the COVID-19 Host Genetics Initiative, the Chilean COVID-19 Biorepository has contributed to the publication of a second updated genome-wide association study, further enhancing our knowledge of the role of host genetics in susceptibility and severity to SARS-CoV-2.

Future plans

The Chilean COVID-19 Biorepository, under the leadership of Latin American researchers from a Latin American country, substantially adds to the integration of Latin American populations in the global collections landscape. Just as ocurred with the COVID-19 Host Genetics Initiative, we expect that this repository will attract global network collaborations for comparative studies on the effects of COVID-19 across diverse populations, including exploring potential genetic advantages or disadvantages in the context of SARS-CoV-2 infection. Researchers involved in establishing this biorepository are currently associated within a collaborative initiative known as COVID-19 Genomics Network (C19-GenoNet), aimed to accelerate the identification of genetic factors in both hosts and pathogens that influence the short and long-term outcomes of SARS-CoV-2 infection.

The broad informed consent utilized enables longitudinal cohort follow-up, thereby allowing for investigating the long-term consequences of SARS-CoV-2 infection, particularly concerning long-COVID. Thus, participants of this cohort were re-contacted to assess the development of long-COVID through a survey-based approach. The re-contact and recruitment procedures yielded a high response rate (82.11%), demonstrating strong participant engagement. In this case as well, this cohort has been leveraged by collaboration with the COVID-19 Host Genetics Initiative for the forthcoming publication of a genome-wide association study on long-COVID.

The concerted endeavors invested in this Chilean initiative have led to the establishment and consolidation of C19-GenoNet as both a research network and a biobanking network. A comprehensive catalog of the C19-GenoNet biobank network has been created and is accessible online athttps://redcovid.uchile.cl/.

STRENGHT AND LIMITATIONS OF THIS STUDY

This study is one of the largest cohorts of COVID-19 patients with associated Biobank reported so far in Latin America.

The study’s design and rigorous weekly monitoring ensured effective collection of high-quality simples and maximized the quality and completeness of data, with the ability to re-contact participants in case of problematic information.

There were no control or reliable information about the time between the infection and the sampling, which may hamper the comparison of some parameters among cases due to transcriptional dynamics after SARS-CoV-2 infection.

The study is based on a self-reported survey, which may represent a bias when analyzing specific clinical phenotypes.