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Viruses
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SARS-CoV-2 and COVID-19 in Latin America
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SARS-CoV-2 and COVID-19 in Latin America

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "SARS-CoV-2 and COVID-19".

Deadline for manuscript submissions: closed (30 November 2021) | Viewed by 36828

Special Issue Editors

Dr. Eurico Arruda

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Guest Editor
Ribeirao Preto Medical School, University of São Paulo (FMRP- USP), Ribeirão Preto, São Paulo, Brazil
Interests: viral pathogenesis; host-pathogen interaction; rhinovirus, enterovirus; picornavirus
Prof. Dr. Helena Lage Ferreira

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Guest Editor
Department of Veterinary Medicine, ZMV-FZEA, University of Sao Paulo (USP), Av. Duque de Caxias Norte 225, Pirassununga 13635-900, SP, Brazil
Interests: avulavirus; newcastle disease virus; subgenotype; influenza A virus (H5N8); avian influenza; wild birds
Special Issues, Collections and Topics in MDPI journals
Dr. José Luiz Proença Módena

E-Mail Website
Guest Editor
Institute of Biology at the University of Campinas (IB- UNICAMP), Campinas, São Paulo, Brazil‎
Interests: coronavirus; emerging viruses; zika virus; SARS-CoV-2
Dr. William Marciel de Souza

E-Mail Website
Guest Editor
Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
Interests: virology; genomic and evolutionary studies of zoonotic; emerging and re-emergent viruses

Special Issue Information

Dear Colleagues,

The pandemic of coronavirus disease 19 (COVID-19), caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), is the most significant threat to human health that humanity has faced in over 100 years. The consequences for public health, economy, and social endeavors are already devastating. As of March 16th, 2021, more than 120 million cases have been confirmed worldwide, resulting in over 2.6 million deaths. Approximately one-third of global COVID-19 deaths have occurred in Latin America and the Caribbean, while vaccinated people in the region represent only about 7% of the world’s vaccines. The COVID-19 pandemic brought an extra heavy burden to Latin America, a region already stricken by severe income inequality, fragile health systems, and political instability, resulting in an unprecedented humanitarian crisis. Therefore, Latin America is one of the most critical yet neglected hotspots of COVID-19 globally.

For this Special Issue, we encourage colleagues to submit original manuscripts and reviews about epidemiology, surveillance, genomics, pathogenesis and basic virology studies of SARS-CoV-2 done in Latin America and the Caribbean. Reports on SARS-CoV-2 infections in animals are also welcome. Manuscripts describing national and regional SARS-COV-2 prevalence, development and evaluation of vaccines, new methods for prevention and treatment of COVID-19, as well as new diagnostic technologies created by Latin American scientists are also encouraged. We want this Special Issue of Viruses to portray the COVID-19 pandemic in Latin American and the Caribbean.

Thank you.

Dr. Eurico Arruda
Prof. Dr. Helena Lage Ferreira
Dr. José Luiz Proença Módena
Dr. William Marciel de Souza
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Viruses is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • SARS-CoV-2
  • COVID-19
  • Latin America
  • COVID-19 Vaccines
  • epidemiology
  • surveillance
  • genomics
  • pathogenesis

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Related Special Issue

Published Papers (9 papers)

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Research

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19 pages, 1887 KiB  
Article
Comparative Analysis of Circulating Levels of SARS-CoV-2 Antibodies and Inflammatory Mediators in Healthcare Workers and COVID-19 Patients
by Luzia Maria de-Oliveira-Pinto, Victor Edgar Fiestas Solórzano, Maria de Lourdes Martins, Caroline Fernandes-Santos, Paula Hesselberg Damasco, Marilda Agudo Mendonça Teixeira de Siqueira, Helver Gonçalves Dias, Alex Pauvolid-Corrêa, Paulo Vieira Damasco and Elzinandes Leal de Azeredo
Viruses 2022, 14(3), 455; https://doi.org/10.3390/v14030455 - 23 Feb 2022
Cited by 6 | Viewed by 2163
Abstract
Advances in knowledge of the pathophysiology of COVID-19 have been acquired; however, the host factors that could explain the mild and severe forms of the disease are not fully understood. Thus, we proposed to evaluate anti-SARS-CoV-2 antibodies and the inflammatory response of different [...] Read more.
Advances in knowledge of the pathophysiology of COVID-19 have been acquired; however, the host factors that could explain the mild and severe forms of the disease are not fully understood. Thus, we proposed to evaluate anti-SARS-CoV-2 antibodies and the inflammatory response of different groups of individuals, including healthcare workers (HCW), sick and dead COVID-19 patients and also recovered patients to contribute to this knowledge gap. Our objective is to relate the clinical evolution of these individuals with the level of detection and functionality of specific antibodies and with the production of inflammatory mediators. As main findings, IgA and IgG anti-SARS-CoV-2 were detected in asymptomatic HCW. IFN-γ and TNF-α levels were higher in symptomatic HCWs than patients with COVID-19 and those who died. Patients who died had higher levels of IL-6, IL-10, and CCL2/MCP-1. We found an imbalance between antiviral and pro-inflammatory mediators in the groups, in which IFN-γ and TNF-α seem to be more associated with protection and IL-6 and CCL2/MCP-1 with pathology. Our work is pioneering the Brazilian population and corroborates data from people from other countries. Full article
(This article belongs to the Special Issue SARS-CoV-2 and COVID-19 in Latin America)
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10 pages, 633 KiB  
Article
High SARS-CoV-2 Prevalence among Healthcare Workers in Cochabamba, Bolivia
by Paola Mariela Saba Villarroel, María del Rosario Castro Soto, Verónica Undurraga, Heydi Sanz, Ana María Jaldín, Laetitia Ninove, Elif Nurtop, Laura Pezzi, Souand Mohamed Ali, Abdennour Amroun, Morgan Seston and Xavier de Lamballerie
Viruses 2022, 14(2), 232; https://doi.org/10.3390/v14020232 - 25 Jan 2022
Cited by 6 | Viewed by 3151
Abstract
Healthcare workers (HCWs) are at increased risk of SARS-CoV-2 infection. The aim of the study was to estimate the SARS-CoV-2 seroprevalence among HCWs in Cochabamba, Bolivia and to determine the potential risk factors. In January 2021, a cross-sectional SARS-CoV-2 seroprevalence study was conducted [...] Read more.
Healthcare workers (HCWs) are at increased risk of SARS-CoV-2 infection. The aim of the study was to estimate the SARS-CoV-2 seroprevalence among HCWs in Cochabamba, Bolivia and to determine the potential risk factors. In January 2021, a cross-sectional SARS-CoV-2 seroprevalence study was conducted in 783 volunteer clinical and non-clinical HCWs in tertiary care facilities. It was based on IgG detection using ELISA, chemiluminiscence, and seroneutralisation tests from dried blood spots. Analysis revealed a high seroprevalence (43.4%) of SARS-CoV-2 IgG antibodies. The combination of anosmia and ageusia (OR: 68.11; 95%-CI 24.83–186.80) was predictive of seropositivity. Belonging to the cleaning staff (OR: 1.94; 95%-CI 1.09–3.45), having more than two children in the same house (OR: 1.74; 95%-CI 1.12–2.71), and having been in contact with a close relative with COVID-19 (OR: 3.53; 95%-CI 2.24–5.58) were identified as risk factors for seropositivity in a multivariate analysis. A total of 47.5% of participants had received medication for COVID-19 treatment or prevention, and only ~50% of symptomatic subjects accessed PCR or antigenic testing. This study confirms a massive SARS-CoV-2 attack rate among HCWs in Cochabamba by the end of January 2021. The main risk factors identified are having a low-skilled job, living with children, and having been in contact with an infected relative in the household. Full article
(This article belongs to the Special Issue SARS-CoV-2 and COVID-19 in Latin America)
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20 pages, 7137 KiB  
Article
Genetic Analysis of SARS-CoV-2 Variants in Mexico during the First Year of the COVID-19 Pandemic
by Blanca Taboada, Selene Zárate, Pavel Iša, Celia Boukadida, Joel Armando Vazquez-Perez, José Esteban Muñoz-Medina, José Ernesto Ramírez-González, Andreu Comas-García, Concepción Grajales-Muñiz, Alma Rincón-Rubio, Margarita Matías-Florentino, Alejandro Sanchez-Flores, Edgar Mendieta-Condado, Jerome Verleyen, Gisela Barrera-Badillo, Lucía Hernández-Rivas, Fidencio Mejía-Nepomuceno, José Arturo Martínez-Orozco, Eduardo Becerril-Vargas, Susana López, Irma López-Martínez, Santiago Ávila-Ríos and Carlos F. Ariasadd Show full author list remove Hide full author list
Viruses 2021, 13(11), 2161; https://doi.org/10.3390/v13112161 - 26 Oct 2021
Cited by 29 | Viewed by 5192
Abstract
During the first year of the SARS-CoV-2 pandemic in Mexico, more than two million people were infected. In this study, we analyzed full genome sequences from 27 February 2020 to 28 February 2021 to characterize the geographical and temporal distribution of SARS-CoV-2 lineages [...] Read more.
During the first year of the SARS-CoV-2 pandemic in Mexico, more than two million people were infected. In this study, we analyzed full genome sequences from 27 February 2020 to 28 February 2021 to characterize the geographical and temporal distribution of SARS-CoV-2 lineages and identify the most common circulating lineages during this period. We defined six different geographical regions with particular dynamics of lineage circulation. The Northeast and Northwest regions were the ones that exhibited the highest lineage diversity, while the Central south and South/Southeast regions presented less diversity with predominance of a certain lineage. Additionally, by late February 2021, lineage B.1.1.519 represented more than 89% of all circulating lineages in the country. Full article
(This article belongs to the Special Issue SARS-CoV-2 and COVID-19 in Latin America)
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17 pages, 1733 KiB  
Article
Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay
by Natalia Rego, Cecilia Salazar, Mercedes Paz, Alicia Costábile, Alvaro Fajardo, Ignacio Ferrés, Paula Perbolianachis, Tamara Fernández-Calero, Veronica Noya, Matias R. Machado, Mariana Brandes, Rodrigo Arce, Mailen Arleo, Tania Possi, Natalia Reyes, María Noel Bentancor, Andrés Lizasoain, Viviana Bortagaray, Ana Moller, Odhille Chappos, Nicolas Nin, Javier Hurtado, Melissa Duquía, Maria Belén González, Luciana Griffero, Mauricio Méndez, Maria Pía Techera, Juan Zanetti, Emiliano Pereira, Bernardina Rivera, Matías Maidana, Martina Alonso, Pablo Smircich, Ighor Arantes, Daiana Mir, Cecilia Alonso, Julio Medina, Henry Albornoz, Rodney Colina, Gonzalo Bello, Pilar Moreno, Gonzalo Moratorio, Gregorio Iraola and Lucía Spangenbergadd Show full author list remove Hide full author list
Viruses 2021, 13(9), 1801; https://doi.org/10.3390/v13091801 - 10 Sep 2021
Cited by 7 | Viewed by 3416
Abstract
Uruguay controlled the viral dissemination during the first nine months of the SARS-CoV-2 pandemic. Unfortunately, towards the end of 2020, the number of daily new cases exponentially increased. Herein, we analyzed the country-wide genetic diversity of SARS-CoV-2 between November 2020 and April 2021. [...] Read more.
Uruguay controlled the viral dissemination during the first nine months of the SARS-CoV-2 pandemic. Unfortunately, towards the end of 2020, the number of daily new cases exponentially increased. Herein, we analyzed the country-wide genetic diversity of SARS-CoV-2 between November 2020 and April 2021. We identified that the most prevalent viral variant during the first epidemic wave in Uruguay (December 2020–February 2021) was a B.1.1.28 sublineage carrying Spike mutations Q675H + Q677H, now designated as P.6, followed by lineages P.2 and P.7. P.6 probably arose around November 2020, in Montevideo, Uruguay’s capital department, and rapidly spread to other departments, with evidence of further local transmission clusters; it also spread sporadically to the USA and Spain. The more efficient dissemination of lineage P.6 with respect to P.2 and P.7 and the presence of mutations (Q675H and Q677H) in the proximity of the key cleavage site at the S1/S2 boundary suggest that P.6 may be more transmissible than other lineages co-circulating in Uruguay. Although P.6 was replaced by the variant of concern (VOC) P.1 as the predominant lineage in Uruguay since April 2021, the monitoring of the concurrent emergence of Q675H + Q677H in VOCs should be of worldwide interest. Full article
(This article belongs to the Special Issue SARS-CoV-2 and COVID-19 in Latin America)
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Review

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24 pages, 485 KiB  
Review
The Role of Serology Testing in the Context of Immunization Policies for COVID-19 in Latin American Countries
by Carlos E. dos Santos Ferreira, Hector Gómez-Dantés, Nancy C. Junqueira Bellei, Eduardo López, Katya A. Nogales Crespo, Miguel O’Ryan and Julieta Villegas
Viruses 2021, 13(12), 2391; https://doi.org/10.3390/v13122391 - 29 Nov 2021
Cited by 10 | Viewed by 3806
Abstract
This review aims to explore the role and value of serology testing in the context of COVID-19 immunization policies in Latin American countries and the barriers and challenges to the adequate use and uptake of this tool. It builds on a review of [...] Read more.
This review aims to explore the role and value of serology testing in the context of COVID-19 immunization policies in Latin American countries and the barriers and challenges to the adequate use and uptake of this tool. It builds on a review of the academic literature, evidence, and existing policies, and includes a multistage process of discussion and feedback by a group of five experts. Regional and country-level evidence and resources from five focus countries—Argentina, Brazil, Chile, Colombia, and Mexico—were collected and analyzed. This review contains an overview of (1) the impact of the SARS-CoV-2 pandemic, the variants of concern and current testing strategies, (2) the introduction of COVID-19 vaccination, (3) the potential use of serology testing to support immunization initiatives, (4) the current frameworks for the use of serology testing in the region, and (5) the barriers and challenges to implementing serology testing in the context of COVID-19 immunization policies, including a discussion on the potential actions required to address these barriers and facilitate the uptake of this strategy in the region. Stakeholders can use elements of this document to guide timely decision-making, raise awareness, and inspire further studies. Full article
(This article belongs to the Special Issue SARS-CoV-2 and COVID-19 in Latin America)

Other

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11 pages, 2389 KiB  
Brief Report
Prevalence of SARS-CoV-2 Variants of Concern and Variants of Interest in COVID-19 Breakthrough Infections in a Hospital in Monterrey, Mexico
by Kame A. Galán-Huerta, Samantha Flores-Treviño, Daniel Salas-Treviño, Paola Bocanegra-Ibarias, Ana M. Rivas-Estilla, Eduardo Pérez-Alba, Sonia A. Lozano-Sepúlveda, Daniel Arellanos-Soto and Adrián Camacho-Ortiz
Viruses 2022, 14(1), 154; https://doi.org/10.3390/v14010154 - 14 Jan 2022
Cited by 8 | Viewed by 3184
Abstract
SARS-CoV-2 variants of concern (VOCs) or of interest (VOIs) causing vaccine breakthrough infections pose an increased risk to worldwide public health. An observational case-control study was performed of SARS-CoV-2 vaccine breakthrough infections in hospitalized or ambulatory patients in Monterrey, Mexico, from April through [...] Read more.
SARS-CoV-2 variants of concern (VOCs) or of interest (VOIs) causing vaccine breakthrough infections pose an increased risk to worldwide public health. An observational case-control study was performed of SARS-CoV-2 vaccine breakthrough infections in hospitalized or ambulatory patients in Monterrey, Mexico, from April through August 2021. Vaccination breakthrough was defined as a SARS-CoV-2 infection that occurred any time after 7 days of inoculation with partial (e.g., first dose of two-dose vaccines) or complete immunization (e.g., second dose of two-dose vaccines or single-dose vaccine, accordingly). Case group patients (n = 53) had partial or complete vaccination schemes with CanSino (45%), Sinovac (19%), Pfizer/BioNTech (15%), and AstraZeneca/Oxford (15%). CanSino was administered most frequently in ambulatory patients (p < 0.01). The control group (n = 19) received no COVID-19 vaccines. Among SARS-CoV-2 variants detected by whole-genome sequencing, VOC Delta B.1.617.2 predominated in vaccinated ambulatory patients (p < 0.01) and AY.4 in hospitalized patients (p = 0.04); VOI Mu B.1.621 was detected in four (7.55%) vaccinated patients. SARS-CoV-2 breakthrough infections in our hospital occurred mostly in patients vaccinated with CanSino due to the higher prevalence of CanSino vaccine administration in our population. These patients developed mild COVID-19 symptoms not requiring hospitalization. The significance of this study lies on the detection of SARS-CoV-2 variants compromising the efficacy of local immunization therapies in Monterrey, Mexico. Full article
(This article belongs to the Special Issue SARS-CoV-2 and COVID-19 in Latin America)
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8 pages, 1222 KiB  
Brief Report
Presence of SARS-CoV-2 RNA on Surfaces of Public Places and a Transportation System Located in a Densely Populated Urban Area in South America
by Juan José Guadalupe, María I. Rojas, Gabriela Pozo, Maria P. Erazo-Garcia, Pamela Vega-Polo, Martín Terán-Velástegui, Forest Rohwer and María de Lourdes Torres
Viruses 2022, 14(1), 19; https://doi.org/10.3390/v14010019 - 23 Dec 2021
Cited by 9 | Viewed by 3846
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly transmissible RNA virus that causes COVID-19. Being aware of the presence of the virus on different types of surfaces and in different environments, and having a protocol for its detection, is important to [...] Read more.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly transmissible RNA virus that causes COVID-19. Being aware of the presence of the virus on different types of surfaces and in different environments, and having a protocol for its detection, is important to understand the dynamics of the virus and its shedding patterns. In Ecuador, the detection of viral RNA in urban environmental samples has not been a priority. The present study analyzed samples from two densely populated neighborhoods and one public transportation system in Quito, Ecuador. Viral RNA presence was assessed using RT-LAMP. Twenty-eight out of 300 surfaces tested positive for SARS-CoV-2 RNA (9.33%). Frequently touched surfaces, especially in indoor spaces and on public transportation, were most likely to be positive for viral RNA. Positivity rate association for the two neighborhoods and for the surface type was not found. This study found viral RNA presence on urban surfaces; this information provides an insight into viral dissemination dynamics. Monitoring environmental SARS-CoV-2 could support the public health prevention strategies in Quito, Ecuador. Full article
(This article belongs to the Special Issue SARS-CoV-2 and COVID-19 in Latin America)
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10 pages, 2229 KiB  
Case Report
Case Study of Two Post Vaccination SARS-CoV-2 Infections with P1 Variants in CoronaVac Vaccinees in Brazil
by Cassia F. Estofolete, Cecilia A. Banho, Guilherme R. F. Campos, Beatriz de C. Marques, Livia Sacchetto, Leila S. Ullmann, Fabio S. Possebon, Luana F. Machado, Juliana D. Syrio, João P. Araújo Junior, Cintia Bittar, Paula Rahal, Suzana M. A. Lobo, Helena Lage Ferreira, Nikos Vasilakis and Mauricio L. Nogueira
Viruses 2021, 13(7), 1237; https://doi.org/10.3390/v13071237 - 26 Jun 2021
Cited by 22 | Viewed by 5314
Abstract
The rapid development of efficacious and safe vaccines against coronavirus disease 2019 (COVID-19) has been instrumental in mitigating the transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Moreover, the emergence of SARS-CoV-2 variants raised concerns on the efficacy of these vaccines. Herein, [...] Read more.
The rapid development of efficacious and safe vaccines against coronavirus disease 2019 (COVID-19) has been instrumental in mitigating the transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Moreover, the emergence of SARS-CoV-2 variants raised concerns on the efficacy of these vaccines. Herein, we report two cases of breakthrough infections with the P1 variant in patients vaccinated with CoronaVac, which is one of the two vaccines authorized for emergency use in the Brazilian immunization program. Our observations suggest that the vaccine reduced the severity of the disease and highlight the potential risk of illness following vaccination and subsequent infection with the P1 variant as well as for continued efforts to prevent and diagnose infection in vaccinated persons. Full article
(This article belongs to the Special Issue SARS-CoV-2 and COVID-19 in Latin America)
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11 pages, 1723 KiB  
Brief Report
Seroprevalence of Anti-SARS-CoV-2 Antibodies in Blood Donors from Nuevo Leon State, Mexico, during 2020: A Retrospective Cross-Sectional Evaluation
by Natalia Martinez-Acuña, Diana Minerva Avalos-Nolazco, Diana Raquel Rodriguez-Rodriguez, Cynthia Gabriela Martinez-Liu, Kame Alberto Galan-Huerta, Gerardo Raymundo Padilla-Rivas, Javier Ramos-Jimenez, Sergio Ayala-de-la-Cruz, Eduardo Cienfuegos-Pecina, Erik Alejandro Diaz-Chuc, Rogelio Cazares-Tamez, Amador Flores-Arechiga, Fernando Perez-Chavez, Daniel Arellanos-Soto, Sonia Amelia Lozano-Sepulveda, Elvira Garza-Gonzalez, Consuelo Treviño-Garza, Roberto Montes-de-Oca-Luna, Aurora Beatriz Lee-Gonzalez, Manuel Enrique de-la-O-Cavazos and Ana Maria Rivas-Estillaadd Show full author list remove Hide full author list
Viruses 2021, 13(7), 1225; https://doi.org/10.3390/v13071225 - 24 Jun 2021
Cited by 7 | Viewed by 3865
Abstract
The progression and distribution of the SARS-CoV-2 pandemic are continuously changing over time and can be traced by blood donors’ serological survey. Here, we investigated the seroprevalence of anti-SARS-CoV-2 antibodies in blood donors in Nuevo Leon, Mexico during 2020 as a strategy for [...] Read more.
The progression and distribution of the SARS-CoV-2 pandemic are continuously changing over time and can be traced by blood donors’ serological survey. Here, we investigated the seroprevalence of anti-SARS-CoV-2 antibodies in blood donors in Nuevo Leon, Mexico during 2020 as a strategy for the rapid evaluation of the spread of SARS-CoV-2 and asymptomatic case detection. We collected residual plasma samples from blood donors who attended two regional donation centers from January to December of 2020 to identify changes in anti-SARS-CoV-2 IgG prevalence. Plasma samples were analyzed on the Abbott Architect instrument using the commercial Abbott SARS-CoV-2 IgG chemiluminescent assay. We found a total of 99 reactive samples from 2068 analyzed plasma samples, resulting in a raw prevalence of 4.87%. Donors aged 18–49 years were more likely to be seropositive compared to those aged >50 years (p < 0.001). Weekly seroprevalence increased from 1.8% during the early pandemic stage to 27.59% by the end of the year. Prevalence was 1.46-fold higher in females compared to males. Case geographical mapping showed that Monterrey city recorded the majority of SARS-CoV-2 cases. These results show that there is a growing trend of seroprevalence over time associated with asymptomatic infection that is unnoticed under the current epidemiological surveillance protocols. Full article
(This article belongs to the Special Issue SARS-CoV-2 and COVID-19 in Latin America)
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