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

Castañeda, Sergio; Patiño, Luz Helena; Muñoz, Marina; Ballesteros, Nathalia; Guerrero-Araya, Enzo; Paredes-Sabja, Daniel; Flórez, Carolina; Gómez, Sergio; Ramírez-Santana, Carolina; Salguero, Gustavo; Gallo, Juan Esteban; Paniz‐Mondolfi, Alberto; Ramírez, Juan David

doi:10.3390/vaccines9080837

Cited by 12 publications

(16 citation statements)

References 53 publications

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“…4 A). These findings were consistent with the lineage distribution profiles reported for Colombia in the analyzed timeline [ 19 ]. Interestingly, C2 (B.1.111) had a heterogeneous distribution in the regions of origin (Bogota and Medellin), which shows a loss of geographic delimitation of this lineage with a high global distribution.…”

Section: Discussionsupporting

confidence: 92%

“…Comparative genomics analyses were developed to evaluate the phylogenomic relationships for the 43 genomes obtained in this study in the context of 2,170 genomes from a representative selection of all SARS-CoV-2 lineages obtained from NextClade tool v 1.5.4 ( https://clades.nextstrain.org/ ). For this, the total dataset with 2,213 genomes was aligned and used to build a maximum likelihood (ML) in NextClade following the pipeline of analysis previously published [ 19 ].…”

Section: Methodsmentioning

confidence: 99%

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

et al. 2022

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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

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Section: Discussionsupporting

confidence: 92%

Section: Methodsmentioning

confidence: 99%

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

et al. 2022

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“…In Colombia, the first case of COVID-19 was reported on March 6, 2020. In 2021, 229 million cases of SARS-CoV-2 were reported, and by that date, 1491 lineages of SARS-CoV-2 were circulating [ 1 , 2 ]. The pandemic shows an epidemiological problem lies in the virus’s ability to remain in asymptomatic people.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2022

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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.

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“…A wide range of strategies has been implemented to mitigate these surges of cases. That includes restrictions on mobility (such as school and airport closures), advice on mask use and physical distancing in public places, and vaccination 4–7 . Nevertheless, the current number of cases shows that the transmission of the virus is far from being under control, and those mitigation strategies may be insufficient 8 .…”

Section: Background and Summarymentioning

confidence: 99%

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

Silva

Rivero

Douglas

et al. 2022

Preprint

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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. To provide a better understanding of the epidemiology of SARS-Cov-2 variants in Colombia, we used 14,049 complete SARS-CoV-2 genomes from the 32 states of Colombia, and 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. We detected a total of 188 SARS-CoV-2 Pango lineages circulating in Colombia since the start of the pandemic. We showed 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). Our results reinforce that genomic surveillance programs are essential for countries to make evidence-driven interventions towards the emergence and circulation of novel SARS-CoV-2 variants.

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

Cited by 12 publications

References 53 publications

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

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

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

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

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