Genomic epidemiology of SARS-CoV-2 variants during the first two years of the pandemic in Colombia.

BACKGROUND: The emergence of highly transmissible SARS-CoV-2 variants has led to surges in cases and the need for global genomic surveillance. While some variants rapidly spread worldwide, other variants only persist nationally. There is a need for more fine-scale analysis to understand transmission dynamics at a country scale. For instance, the Mu variant of interest, also known as lineage B.1.621, was first detected in Colombia and was responsible for a large local wave but only a few sporadic cases elsewhere. METHODS: To better understand the epidemiology of SARS-Cov-2 variants in Colombia, we used 14,049 complete SARS-CoV-2 genomes from the 32 states of Colombia. We performed Bayesian phylodynamic analyses to estimate the time of variants' introduction, their respective effective reproductive number, and effective population size, and the impact of disease control measures. RESULTS: Here, we detect a total of 188 SARS-CoV-2 Pango lineages circulating in Colombia since the pandemic's start. We show that the effective reproduction number oscillated drastically throughout the first two years of the pandemic, with Mu showing the highest transmissibility (Re and growth rate estimation). CONCLUSIONS: Our results reinforce that genomic surveillance programs are essential for countries to make evidence-driven interventions toward the emergence and circulation of novel SARS-CoV-2 variants.

Colombia reported its first COVID-19 case on 6th March 2020. By April 2022, the country had reported over 6 million infections and over 135,000 deaths. Here, we aim to understand how SARS-CoV-2, the virus that causes COVID-19, spread through Colombia over this time and how the predominant version of the virus (variant) changed over time. We found that there were multiple introductions of different variants from other countries into Colombia during the first two years of the pandemic. The Gamma variant was dominant earlier in 2021 but was replaced by the Delta variant. The Mu variant had the highest potential to be transmitted. Our findings provide valuable insights into the pandemic in Colombia and highlight the importance of continued surveillance of the virus to guide the public health response.

Burden of COVID-19 in Córdoba, A Department of Colombia: Results of Disability-Adjusted Life-Years: Carga de COVID-19 en Córdoba, un Departamento de Colombia: Resultados de los Años de Vida Ajustados por Discapacidad.

OBJECTIVES: This study aimed to estimate the burden of acute COVID-19 in Córdoba, one of the most affected departments (states) in Colombia, through the estimation of disability-adjusted life-years (DALYs). METHODS: DALYs were estimated based on the number of cases of severe acute respiratory syndrome coronavirus 2 infection cases reported by official Colombian sources. A transition probability matrix among severity states was calculated using data obtained from a retrospective cohort that included 1736 COVID-19 confirmed subjects living in Córdoba. RESULTS: Córdoba had 120.23 deaths per 100 000 habitants during the study period (March 2020 to April 2021). Estimated total DALYs were 49 243 (2692 DALYs per 100 000 inhabitants), mostly attributed to fatal cases (99.7%). On average, 25 years of life were lost because of death by this infection. A relevant proportion of years of life lost because of COVID-19 (46.6%) was attributable to people < 60 years old and was greater in men. People ≥ 60 years old showed greater risk of progression to critical state than people between the age of 35 and 60 years (hazard ratio 2.5; 95% confidence interval 2.5-12.5) and younger than 35 years (9.1; 95% confidence interval 4.0-20.6). CONCLUSION: In Córdoba, premature mortality because of COVID-19 was substantially represented by people < 60 years old and was greater in males. Our data may be representative of Latin American populations with great infection spread during the first year of the pandemic and contribute to novel methodological aspects and parameter estimations that may be useful to measure COVID-19 burden in other countries of the region.

Immunogenicity and safety of a RBD vaccine against SARS-CoV-2 in a murine model.

INTRODUCTION: Although more than half of the world's population is already vaccinated, the appearance of new variants of concern puts public health at risk due to the generation of new immunogens against the virus as a crucial and relevant strategy in the control of these new variants. METHODS: A preclinical study used a potential vaccine candidate (RBD, SARS-CoV-2). Four groups of BALB/c mice were used, a control group, an adjuvant group, a group inoculated with one dose of RBD subunit protein, and the fourth group inoculated with two doses of RBD subunit protein. RESULTS: No inflammatory or cellular changes were shown in the mice's anatomopathological evaluation. Higher kinetics and 75% seroconversion were obtained in the mice inoculated with two doses of RBD (P < 0.0001). CONCLUSIONS: The application of two doses of the RBD vaccine candidate in BALB/c mice proved safe and immunogenic against SARS-CoV-2.

Human-to-dog transmission of SARS-CoV-2, Colombia.

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of the current COVID-19 pandemic, has evolved to have a wide range of hosts, including non-human primates, wild and domestic animals. The ACE2 protein has a high level of conservation and is the common receptor invertebrate species for a viral infection to occur; this receptor could give rise to anthroponotic events. This article describes the first event of symptomatic transmission in Latin America from a human to a dog by the B.1.625 lineage of SARS-CoV-2. We found 21 shared mutations in the complete genomes of viral sequences from owners and dogs. Further phylogenetic and molecular analysis showed that 100% co-localization of the clade helps to understand human-animal transmission. Prediction of the Spike protein structure of the sequenced virus and docking analyzes showed that the E484K mutation in the receptor-binding domain (RBD) could contribute to the viral affinity of dACE2. Therefore, close contact between SARS-CoV-2-infected humans and pets should be avoided to prevent the emergence of novel mutations of public health importance from anthroponotic events.

Effectiveness of the CoronaVac® vaccine in a region of the Colombian Amazon, was herd immunity achieved?

INTRODUCTION: Currently, more than 4.5 billion doses of SARS-CoV-2 vaccines have been applied worldwide. However, some developing countries are still a long way from achieving herd immunity through vaccination. In some territories, such as the Colombian Amazon, mass immunization strategies have been implemented with the CoronaVac® vaccine. Due to its proximity to Brazil, where one of the variants of interest of SARS-CoV-2 circulates. OBJECTIVE: To determine the effectiveness of the CoronaVac® vaccine in a population of the Colombian Amazon. METHODS: Between February 24, 2021, and August 10, 2021, a descriptive observational study was carried out in which a population of individuals over 18 years of age immunized with two doses of the CoronaVac® vaccine was evaluated. The study site was in the municipality of Mitú, Vaupés, in southeastern Colombia, a region located in the Amazon bordering Brazil. RESULTS: 99% of the urban population of the Mitú municipality were vaccinated with CoronaVac®. To date, 5.7% of vaccinated individuals have become ill, and only 0.1% of these require hospitalization. One death was attributable to COVID-19 has been reported among vaccinated individuals, and the vaccine has shown 94.3% effectiveness against mild disease and 99.9% against severe infection. CONCLUSIONS: The herd immunity achieved through mass vaccination in this population has made it possible to reduce the rate of complicated cases and mortality from COVID-19 in this region of the Colombian Amazon. HIGHLIGHTS: CoronaVac® has shown 94.3% effectiveness against mild disease and 99.9% against severe infection in this indigenous population. CoronaVac® reduces the mortality rate from 2.2% in 2020 to 0.22% in 2021. The herd immunity was achieved through mass vaccination in this region of the Colombian Amazon.

SARS-CoV-2 in eight municipalities of the Colombian tropics: high immunity, clinical and sociodemographic outcomes.

BACKGROUND: Serological evaluation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an alternative that allows us to determine the prevalence and dynamics of this infection in populations. The goal of this study was to determine the clinical and sociodemographic dynamics of SARS-CoV-2 infection in a region of the Colombian Caribbean. METHODS: Between July and November 2020, a cross-sectional observational study was carried out in Córdoba, located in northeast Colombia in the Caribbean area. Eight municipalities with the largest populations were chosen and 2564 blood samples were taken. A commercial enzyme-linked immunosorbent assay was used with the recombinant protein antigen N of SARS-CoV-2. The people included in the study were asked for sociodemographic and clinical data, which were analysed by statistical methods. RESULTS: A seroprevalence of 40.8% was obtained for SARS-CoV-2 in the Córdoba region. In the bivariate analysis, no differences were observed in seropositivity against SARS-CoV-2 for gender or age range (p>0.05). Higher seropositivity was found in low socio-economic status and symptomatic patients (p<0.0001). A total of 30.7% of the asymptomatic patients were seropositive for SARS-CoV-2, which could be linked to the spread of this infection. In the multivariate analysis, seroconversion was related to poverty and clinical manifestations such as anosmia and ageusia (p<0.05). CONCLUSIONS: The high seropositivity in Córdoba is due to widespread SARS-CoV-2 in this population. The relationship between seropositivity and socio-economic status suggests a higher exposure risk to the virus caused by informal economic activities in low-income groups. Clinical manifestations such as anosmia and ageusia could be clinical predictors of infection by the new emergent coronavirus.

High Prevalence of SARS-CoV-2 in an Indigenous Community of the Colombian Amazon Region.

Introduction. COVID-19 is a pathology caused by the SARS-CoV-2 virus. The World Health Organization (WHO) has reported more than 225 million cases and 4.5 million deaths worldwide. Objective: To describe the seropositivity, spatial distribution, and clinical and sociodemographic variables of SARS-CoV-2 in a community of the Colombian Amazon region. Methods. In December 2020, a cross-sectional observational study was carried out in a population located in the Colombian Amazon in the municipality of Mitú. Sociodemographic and clinical data were taken. Besides, 589 blood samples were taken, and an antibody detection was carried out with an ELISA and a recombinant protein N antigen of SARS-CoV-2. Results. A seropositivity of 57.6% was observed. The highest proportion of the infection is located in inter-municipal transport zones. The bivariate analysis did not show differences in the SARS-CoV-2 infection rate concerning the variables sex, age range, and the presence of comorbidities (p > 0.05). The bivariate and multivariate analysis showed that being symptomatic and presenting neurological manifestations of the upper respiratory tract are clinical variables associated with SARS-CoV-2 infection (p < 0.05). One of the causes of this virus's high spread in this community could be that 53.3% of the people were asymptomatic. Conclusions. Our data showed a high burden and transmission of SARS-CoV-2 in the indigenous community. This could be linked to cultural behaviors and the high infection rate in asymptomatic patients.

Using serological studies to assess COVID-19 infection fatality rate in developing countries: A case study from one Colombian department.

This study describe the infection fatality rate (IFR) by COVID-19 by age groups in one department of Colombia. It used results from a serological survey to stablish a closer estimation of the true proportion of infected people. It found an overall IFR of 0.24% quite lower than the overall CFR (5.6%). We conclude that CFR severely overestimate the lethality of COVID-19 in developing areas.