Genomic epidemiology of SARS-CoV-2 transmission lineages in Ecuador

Gutierrez, Bernardo; Márquez, Sully; Prado-Vivar, Belén; Becerra-Wong, Mónica; Guadalupe, Juan José; Cândido, Darlan da Silva; Fernández‐Cadena, Juan Carlos; Morey-León, Gabriel; Armas-Gonzalez, Rubén; Andrade-Molina, Derly; Bruno, Alfredo; Mora, Doménica de; Olmedo, Maritza; Portugal, Denisse; González, Manuel; Orlando, Alberto; Drexler, Jan Felix; Moreira-Soto, Andrés; Sander, Anna-Lena; Kühne, Arne; Patiño, Leandro; Carrazco-Montalvo, Andrés; Mestanza, Orson; Zurita, Jeannete; Sevillano, Gabriela; Plessis, Louis du; McCrone, John; Coloma, Joséfina; Trueba, Gabriel; Barragán, Verónica; Rojas-Silva, Patricio; Grunauer, Michelle; Kraemer, Moritz U. G.; Faria, Nuno Rodrigues; Escalera-Zamudio, Marina; Pybus, Oliver G.; Cárdenas, Paúl

doi:10.1093/ve/veab051

Cited by 18 publications

(13 citation statements)

References 63 publications

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“…Of note, antibody responses in naturally infected persons supported past infection with strains bearing similarities to early SARS-CoV-2 isolates and the Gamma variant (Figure 2, panel D). Antibody reactivity in naturally infected persons was thus in concordance with the circulation of SARS-CoV-2 variants in South America during the time of sampling in late 2020 (12), supporting the robustness of our data.…”

Section: Effectiveness Of Naturallysupporting

confidence: 83%

Effectiveness of Naturally Acquired and Vaccine-Induced Immune Responses to SARS-CoV-2 Mu Variant

Oliveira-Filho¹,

Rincón-Orozco²,

Jones-Cifuentes³

et al. 2022

Emerg. Infect. Dis.

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D iverse SARS-CoV-2 variants have arisen during the pandemic. As of May 4, 2022, there had been 2 recognized variants of concern (VOC), Delta and Omicron, in addition to earlier emerging VOCs Alpha, Beta, and Gamma and strains previously categorized as variants of interest (VOI). Many VOIs have been understudied in terms of pathogenesis, transmissibility, and potential for immune escape. Delta and Omicron illustrate how variants emerging in tropical settings can spread globally.Mu was first reported as a VOI in early January 2021 in northern Colombia. While outcompeting other locally circulating variants, Mu spread to additional countries, such as Ecuador, United States, Mexico, and Spain; as of early 2022, it was still circulating at low levels in Colombia (1). Mu caused 70% of all COVID-19 cases in Colombia during May-July 2021 (Figure 1), a period which also accounted for the highest number of deaths in Colombia during the pandemic, suggesting substantial

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Section: Effectiveness Of Naturallysupporting

confidence: 83%

Effectiveness of Naturally Acquired and Vaccine-Induced Immune Responses to SARS-CoV-2 Mu Variant

Oliveira-Filho¹,

Rincón-Orozco²,

Jones-Cifuentes³

et al. 2022

Emerg. Infect. Dis.

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“…Estimating time trees for large alignments can be computationally intractable. Thus, we follow a computation strategy similar to du Plessis et al 59 and Gutierrez et al 60 that involves (1) estimating an evolutionary rate using a subsample of the genome dataset of interest and (2) using a simpler computational approach to estimate time trees for the complete genome dataset. For step (1), we randomly selected a maximum of 20 sequences per state (except for Paraíba and Rondônia, which had only 15 and nine sequences available, respectively, during the study period).…”

Section: Methodsmentioning

confidence: 99%

Spatial and temporal fluctuations in COVID-19 fatality rates in Brazilian hospitals

Whittaker

Hawryluk

Souza

et al. 2022

Nat Med

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The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Gamma variant of concern has spread rapidly across Brazil since late 2020, causing substantial infection and death waves. Here we used individual-level patient records after hospitalization with suspected or confirmed coronavirus disease 2019 (COVID-19) between 20 January 2020 and 26 July 2021 to document temporary, sweeping shocks in hospital fatality rates that followed the spread of Gamma across 14 state capitals, during which typically more than half of hospitalized patients aged 70 years and older died. We show that such extensive shocks in COVID-19 in-hospital fatality rates also existed before the detection of Gamma. Using a Bayesian fatality rate model, we found that the geographic and temporal fluctuations in Brazil’s COVID-19 in-hospital fatality rates were primarily associated with geographic inequities and shortages in healthcare capacity. We estimate that approximately half of the COVID-19 deaths in hospitals in the 14 cities could have been avoided without pre-pandemic geographic inequities and without pandemic healthcare pressure. Our results suggest that investments in healthcare resources, healthcare optimization and pandemic preparedness are critical to minimize population-wide mortality and morbidity caused by highly transmissible and deadly pathogens such as SARS-CoV-2, especially in low- and middle-income countries.

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“…For both data sets, the previous analysis revealed that most MG data clustered within a large Brazilian clade, which comprehended thousands of genome sequences. As traditional Bayesian phylogenetic methods struggle to deal with data sets with these dimensions ( Gutierrez et al. 2021 ), we were prompted to estimate dated phylogenies using a recently developed method from the BEASTv.1.10.5 (pre-release Thorney v0.1.1) package ( Suchard et al.…”

Section: Methodsmentioning

confidence: 99%

Tracking the turnover of SARS-CoV-2 VOCs Gamma to Delta in a Brazilian state (Minas Gerais) with a high-vaccination status

et al. 2022

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The emergence and global dissemination of SARS-CoV-2 variants of concern (VOC) have been described as the main factor driving the COVID-19 pandemic. In Brazil, the Gamma variant dominated the epidemiological scenario during the first period of 2021. Many Brazilian regions detected the Delta variant after its first description and documented its spread. To monitor the introduction and spread of VOC Delta, we performed genotyping-PCR and genome sequencing in ten regional sentinel units from June to October 2021 in the State of Minas Gerais (MG). We documented the introduction and spread of Delta, comprising 70% of the cases eight weeks later. Comparing the viral loads of the Gamma and Delta dominance periods, we provide additional evidence that the latter is more transmissible. The spread and dominance of Delta did not culminate in the increase in cases and deaths, suggesting that the vaccination may have restrained the epidemic growth. Analysis of 224 novel Delta genomes revealed that Rio de Janeiro state was the primary source for disseminating this variant in the state of MG. We present the establishment of Delta, providing evidence of its enhanced transmissibility and showing that this variant shift did not aggravate the epidemiological scenario in a high immunity setting.

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Genomic epidemiology of SARS-CoV-2 transmission lineages in Ecuador

Cited by 18 publications

References 63 publications

Effectiveness of Naturally Acquired and Vaccine-Induced Immune Responses to SARS-CoV-2 Mu Variant

Effectiveness of Naturally Acquired and Vaccine-Induced Immune Responses to SARS-CoV-2 Mu Variant

Spatial and temporal fluctuations in COVID-19 fatality rates in Brazilian hospitals

Tracking the turnover of SARS-CoV-2 VOCs Gamma to Delta in a Brazilian state (Minas Gerais) with a high-vaccination status

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