Evolution and Epidemic Spread of SARS-CoV-2 in Colombia: A Year into the Pandemic

Predictors of mortality in hospitalised patients with COVID-19: a 1-year case-control study

BACKGROUND

A paucity of predictive models assessing risk factors for COVID-19 mortality that extend beyond age and gender in Latino population is evident in the current academic literature.

OBJECTIVES

To determine the associated factors with mortality, in addition to age and sex during the first year of the pandemic.

DESIGN

A case-control study with retrospective revision of clinical and paraclinical variables by systematic revision of clinical records was conducted. Multiple imputations by chained equation were implemented to account for missing variables. Classification and regression trees (CART) were estimated to evaluate the interaction of associated factors on admission and their role in predicting mortality during hospitalisation. No intervention was performed.

SETTING

High-complexity centre above 2640 m above sea level (masl) in Colombia.

PARTICIPANTS

A population sample of 564 patients admitted to the hospital with confirmed COVID-19 by PCR. Deceased patients (n=282) and a control group (n=282), matched by age, sex and month of admission, were included.

MAIN OUTCOME MEASURE

Mortality during hospitalisation.

MAIN RESULTS

After the imputation of datasets, CART analysis estimated 11 clinical profiles based on respiratory distress, haemoglobin, lactate dehydrogenase, partial pressure of oxygen to inspired partial pressure of oxygen ratio, chronic kidney disease, ferritin, creatinine and leucocytes on admission. The accuracy model for prediction was 80.4% (95% CI 71.8% to 87.3%), with an area under the curve of 78.8% (95% CI 69.63% to 87.93%).

CONCLUSIONS

This study discloses new interactions between clinical and paraclinical features beyond age and sex influencing mortality in COVID-19 patients. Furthermore, the predictive model could offer new clues for the personalised management of this condition in clinical settings.

Humoral immune response to SARS-CoV-2 and endemic coronaviruses in urban and indigenous children in Colombia

BACKGROUND

Although anti-SARS-CoV-2 humoral immune responses and epidemiology have been extensively studied, data gaps remain for certain populations such as indigenous people or children especially in low- and middle-income countries. To address this gap, we evaluated SARS-CoV-2 seroprevalence and humoral immunity towards the parental B.1 strain, local SARS-CoV-2 variants, and endemic coronaviruses in children from Colombia from March to April 2021.

METHODS

We performed a cross-sectional seroprevalence study with 80 children from Bogotá and expanded our analysis by comparing results with an independent observational study of 82 children from the Wiwa community living in the north-eastern Colombian territories. Antibody IgG titers towards SARS-CoV-2 and the endemic coronaviruses as well as ACE2 binding inhibition as a proxy for neutralization towards several SARS-CoV-2 variants were analyzed using two multiplex-based immunoassays.

RESULTS

While we find seroprevalence estimates of 21.3% in children from Bogotá, seroprevalence is higher with 34.1% in Wiwa children. We observe a robust induction of antibodies towards the surface-exposed spike protein, its S1-, S2- and receptor-binding-subdomains in all SARS-CoV-2 seropositive children. Only nucleocapsid-specific IgG is significantly lower in the indigenous participants. ACE2 binding inhibition is low for all SARS-CoV-2 variants examined. We observe a dominance of NL63 S1 IgG levels in urban and indigenous children which suggests an early exposure to this respiratory virus independent of living conditions and geographic location. SARS-CoV-2 seropositivity does not correlate with antibody levels towards any of the four endemic coronaviruses indicating the absence of cross-protective immunity.

CONCLUSIONS

Overall, antibody titers, but in particular ACE2 binding inhibition are low within Colombian samples, requiring further investigation to determine any potential clinical significance.

Seroprevalence, infection, and personal protective equipment use among Colombian healthcare workers during the COVID-19 pandemic

Introduction

Healthcare workers (HCWs) are at the forefront of the COVID-19 response and frequently come into close contact with patients and their virus-contaminated body fluids. Recent studies have identified differential risks of infection and the use of personal protective equipment (PPE) among HCWs. However, available data might be interpreted with caution because of differences in the national health systems, local implementation issues, and adherence limitations to guidelines. A comprehensive description of infection, exposure at work, and biosafety habits during the COVID-19 pandemic has not been conducted among the HCW groups in Latin American populations.

Objective

To describe SARS-CoV-2 seroprevalence, infections, and extent of PPE use during the COVID-19 pandemic among HCWs at three different times, including dental practitioners (DP), nursing assistants (NA), physicians (P), and respiratory therapists (RT), from Bogotá, Colombia. Methods: After IRB approval, this cross-sectional study included 307 HCWs. Participants provided nasopharyngeal swabs and blood samples to detect viral RNA (RT-qPCR) and IgM/IgG anti-SARS-CoV-2 (ELFA-ELISA) at baseline (BL) and two follow-ups. Infection prevalence was defined as the number of positive-tested participants (RT-qPCR and/or IgM). Data on clinical status and biosafety habits were collected each time.

Results

Differential infection prevalence was found among HCWs through the study timeline (BL: RT-qPCR = 2.6%, IgM = 1.6%; follow-up 1 (45 days after BL): RT-qPCR = 4.5%, IgM = 3.9%; follow-up 2 (60 days after BL): RT-qPCR = 3.58%, IgM = 1.3%. Dental practitioners showed a higher infection frequency in BL and follow-up 1. IgG-positive tested HCWs percentage progressively increased from BL to follow-ups among the whole sample while index values decreased. Limitations in N95 availability and a high perception of occupational risk were reported.

Conclusion

A low prevalence of active SARS-CoV-2 infections among HCWs groups was found. Over time, there was an increase in participants showing IgG antibodies, although the levels of these antibodies in the blood decreased. Additionally, HCWs reported limitations in the availability of PPE as well as a variation in their safety practices.

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.

Estudio de los desenlaces perioperatorios de la apendicitis aguda durante la pandemia por COVID-19: un estudio observacional analítico de cohorte

Introducción. La condición de pandemia por COVID-19 impactó a la sociedad y los sistemas de salud a nivel mundial. Las adaptaciones institucionales procuraron mantener la calidad de la atención a pesar de un contexto organizacional desfavorable. La apendicitis aguda requirió ser manejada en un nuevo escenario institucional. El objetivo de este estudio fue evaluar la efectividad del tratamiento quirúrgico de la apendicitis durante la pandemia. Métodos. Estudio observacional analítico, retrospectivo, en el que se incluyeron pacientes sometidos a apendicectomía, antes y durante la pandemia por COVID-19. Se evaluaron las complicaciones, infección del sitio operatorio, reingresos y estancia hospitalaria. Adicionalmente, se analizaron los desenlaces en los 3 picos epidemiológicos de la pandemia. Se efectuaron estadísticas descriptivas y analíticas entre los grupos a comparar. Resultados. Se incluyeron 1521 pacientes con apendicitis, 48,3 % operados antes y 51,7 % durante la pandemia. No hubo diferencias entre los grupos en complicaciones (p=0,352), infección del sitio operatorio (p=0,191), reingreso en los primeros 30 días (p=0,605) y estancia hospitalaria (p=0,514). El manejo de la apendicitis durante el tercer pico fue similar a las prácticas habituales. El tiempo de evolución fue mayor durante la pandemia (p=0,04) y los pacientes fueron llevados a cirugía más pronto que previo a la pandemia (p<0,001). > <0,001). Conclusiones. No se evidenció un incremento de complicaciones quirúrgicas, reingresos, estancia hospitalaria ni infección del sitio operatorio en los pacientes operados durante la pandemia. Hubo un efecto favorable para los pacientes como consecuencia de la adaptación institucional en la pandemia por COVID-19.

SARS-CoV-2 in a tropical area of Colombia, a remarkable conversion of presymptomatic to symptomatic people impacts public health

Background

The ability of SARS-CoV-2 to remain in asymptomatic individuals facilitates its dissemination and makes its control difficult. Objective. To establish a cohort of asymptomatic individuals, change to the symptomatic status, and determine the most frequent clinical manifestations. 

Methods

Between April 9 and August 9, 2020, molecular diagnosis of SARS-CoV-2 infection was confirmed in 154 asymptomatic people in contact with subjects diagnosed with COVID-19. Nasopharyngeal swabs were performed on these people in different hospitals in Córdoba, the Caribbean area of Colombia. The genes E, RdRp, and N were amplified with RT-qPCR. Based on the molecular results and the Cq values, the patients were subsequently followed up through telephone calls to verify their health conditions.

Results

Overall, of 154 asymptomatic individuals, 103 (66.9%) remained asymptomatic, and 51 (33.1%) changed to symptomatic. The most frequent clinical manifestations in young people were anosmia and arthralgia. Adults showed cough, ageusia, and odynophagia; in the elderly were epigastralgia, dyspnea, and headache. Mortality was 8%.

Conclusions

A proportion of 33% of presymptomatic individuals was found, of which four of them died. This high rate could indicate a silent transmission, contributing significantly to the epidemic associated with SARS-CoV-2.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-022-07575-0.

Safety and efficacy of convalescent plasma for severe COVID-19: a randomized, single blinded, parallel, controlled clinical study

Background

Convalescent plasma (CP) has been widely used to treat COVID-19 and is under study. However, the variability in the current clinical trials has averted its wide use in the current pandemic. We aimed to evaluate the safety and efficacy of CP in severe coronavirus disease 2019 (COVID-19) in the early stages of the disease.

Methods

A randomized controlled clinical study was conducted on 101 patients admitted to the hospital with confirmed severe COVID-19. Most participants had less than 14 days from symptoms onset and less than seven days from hospitalization. Fifty patients were assigned to receive CP plus standard therapy (ST), and 51 were assigned to receive ST alone. Participants in the CP arm received two doses of 250 mL each, transfused 24 h apart. All transfused plasma was obtained from "super donors" that fulfilled the following criteria: titers of anti-SARS-CoV-2 S1 IgG ≥ 1:3200 and IgA ≥ 1:800 antibodies. The effect of transfused anti-IFN antibodies and the SARS-CoV-2 variants at the entry of the study on the overall CP efficacy was evaluated. The primary outcomes were the reduction in viral load and the increase in IgG and IgA antibodies at 28 days of follow-up. The per-protocol analysis included 91 patients.

Results

An early but transient increase in IgG anti-S1-SARS-CoV-2 antibody levels at day 4 post-transfusion was observed (Estimated difference [ED], − 1.36; 95% CI, − 2.33 to − 0.39; P = 0.04). However, CP was not associated with viral load reduction in any of the points evaluated. Analysis of secondary outcomes revealed that those patients in the CP arm disclosed a shorter time to discharge (ED adjusted for mortality, 3.1 days; 95% CI, 0.20 to 5.94; P = 0.0361) or a reduction of 2 points on the WHO scale when compared with the ST group (HR adjusted for mortality, 1.6; 95% CI, 1.03 to 2.5; P = 0.0376). There were no benefits from CP on the rates of intensive care unit admission (HR, 0.82; 95% CI, 0.35 to 1.9; P = 0.6399), mechanical ventilation (HR, 0.66; 95% CI, 0.25 to 1.7; P = 0.4039), or mortality (HR, 3.2; 95% CI, 0.64 to 16; P = 0.1584). Anti-IFN antibodies and SARS-CoV-2 variants did not influence these results.

Conclusion

CP was not associated with viral load reduction, despite the early increase in IgG anti-SARS-CoV-2 antibodies. However, CP is safe and could be a therapeutic option to reduce the hospital length of stay.

Trial registration NCT04332835

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-022-07560-7.

Epidemiological Dynamics of SARS-CoV-2 Variants During Social Protests in Cali, Colombia

Background

The third wave of the global health crisis attributed to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus reached Colombia in March 2021. Over the following 6 months, it was interpolated by manifestations of popular disapproval to the actual political regime—with multiple protests sprouting throughout the country. Large social gatherings seeded novel coronavirus disease 2019 (COVID-19) variants in big cities and propagated their facile spread, leading to increased rates of hospitalizations and deaths.

Methods

In this article, we evaluate the effective reproduction number (Rt) dynamics of SARS-CoV-2 in Cali, Colombia, between 4 April 2021 and 31 July 2021 based on the analysis of 228 genomes.

Results

Our results showed clear contrast in Rt values between the period of frequent protests (Rt &gt; 1), and the preceding and following months (Rt &lt; 1). Genomic analyses revealed 16 circulating SARS-CoV-2 lineages during the initial period—including variants of concern (VOCs) (Alpha, Gamma, and Delta) and variants of interest (VOIs) (Lambda and Mu). Furthermore, we noticed the Mu variant dominating the COVID-19 distribution schema as the months progressed. We identified four principal clusters through phylogenomic analyses—each one of potentially independent introduction to the city. Two of these were associated with the Mu variant, one associated with the Gamma variant, and one with the Lambda variant.

Conclusion

Our results chronicle the impact of large group assemblies on the epidemiology of COVID-19 during this intersection of political turmoil and sanitary crisis in Cali, Colombia. We emphasize upon the effects of limited biosecurity strategies (which had characterized this time period), on the spread of highly virulent strains throughout Cali and greater Colombia.