Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K

Laiton‐Donato, Katherine; Usme-Ciro, José A.; Franco-Muñoz, Carlos; Álvarez-Díaz, Diego A.; Ruiz-Moreno, Héctor Alejandro; Reales-González, Jhonnatan; Prada, Diego Andrés; Corchuelo, Sheryll; Herrera-Sepúlveda, María T.; Naizaque, Julian; Santamaría, Gerardo del Cerro; Wiesner, Magdalena; Walteros, Diana Marcela; Martinez, Martha; Mercado-Reyes, Marcela

doi:10.3389/fmed.2021.697605

Cited by 6 publications

(3 citation statements)

References 27 publications

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“…While this was consistent with the report by Uriu et al, who reported lower neutralization titers against Mu relative to a parental D614G variant and Gamma [23], the magnitude of the difference was more noticeable in the present study. By contrast, Messali et al reported a slightly lower neutralization titer in the sera from BNT162b2-vaccinated volunteers against Mu relative to a B.1 isolate [26]. Although the differences observed between these studies may be due to the use of different platforms for the screening of neutralizing antibodies (i.e., pseudovirus or isolates), all these evidenced the resistance of the Mu variant to antibodies elicited by the BNT162b2 vaccine.…”

Section: Discussionmentioning

confidence: 84%

Low Neutralizing Antibody Titers against the Mu Variant of SARS-CoV-2 in 31 BNT162b2 Vaccinated Individuals in Colombia

Álvarez-Díaz

Muñoz²,

Tavera-Rodríguez

et al. 2022

Vaccines

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Global surveillance programs for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are showing the emergence of variants with mutations in the spike protein. Genomic and laboratory surveillance are important to determine if these variants may be more infectious or less susceptible to antiviral treatments and vaccine-induced antibodies. Three of the most predominant SARS-CoV-2 variants in Colombia during the epidemiological peaks of 2021 were isolated: Mu, a variant of interest; Gamma, a variant of concern; B.1.111, which lacks genetic markers associated with greater virulence. Microneutralization assays were performed by incubating 120 mean tissue culture infectious doses (TCID50) of each SARS-CoV-2 isolate with five two-fold serial dilutions of sera from 31 BNT162b2-vaccinated volunteers. The mean neutralization titer (MN50) was calculated by the Reed–Muench method. At the end of August, Mu represented 49% of coronavirus disease 2019 (COVID-19) cases in Colombia, followed by 25% of Gamma. In contrast, B.1.111 became almost undetectable. The evaluation of neutralizing antibodies suggests that patients vaccinated with BNT162b2 generate neutralizing antibody titers against the Mu variant at significantly lower concentrations relative to B.1.111 and Gamma. This study shows the importance of continuing surveillance programs of emerging variants, as well as the need to evaluate the neutralizing antibody response induced by other vaccines.

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Section: Discussionmentioning

confidence: 84%

Low Neutralizing Antibody Titers against the Mu Variant of SARS-CoV-2 in 31 BNT162b2 Vaccinated Individuals in Colombia

Álvarez-Díaz

Muñoz²,

Tavera-Rodríguez

et al. 2022

Vaccines

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“…Recently, new evidence from Colombian National Institute of Health, has shown that the mutation E484K is becoming associated with this lineage. In our study we found the E484K mutation in a single sample taken in December 2020 from a case with the B.1 lineage, parental lineage of B.1.111 ( Laiton-Donato et al, 2021 ).…”

Section: Discussionmentioning

confidence: 48%

“…All of our samples contain the Spike glycoprotein mutation D614G. This nucleotide substitution ( Laiton-Donato et al, 2021 ) rapidly turned into a worldwide prevalent mutation. Nevertheless, despite its high speed of transmission, recent evidence demonstrated that this amino acidic change on its own, is not associated with a particular phenotype ( Grubaugh et al, 2020 ; Isabel et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

Mutation profile of SARS-CoV-2 genome in a sample from the first year of the pandemic in Colombia

Bermúdez¹,

Chaparro-Solano

Pinzón-Rondón

et al. 2022

Infection, Genetics and Evolution

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The severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) is the etiopathogenic agent of COVID-19, a condition that has led to a formally recognized pandemic by March 2020 (World Health Organization –WHO). The SARS-CoV-2 genome is constituted of 29,903 base pairs, that code for four structural proteins (N, M, S, and E) and more than 20 non-structural proteins. Mutations in any of these regions, especially in those that encode for the structural proteins, have allowed the identification of diverse lineages around the world, some of them named as Variants of Concern (VOC) and Variants of Interest (VOI), according to the WHO and CDC. In this study, by using Next Generation Sequencing (NGS) technology, we sequenced the SARS-CoV-2 genome of 422 samples from Colombian residents, all of them collected between April 2020 and January 2021. We obtained genetic information from 386 samples, leading us to the identification of 14 new lineages circulating in Colombia, 13 of which were identified for the first time in South America. GH was the predominant GISAID clade in our sample. Most mutations were either missense (53.6%) or synonymous mutations (37.4%), and most genetic changes were located in the ORF1ab gene (63.9%), followed by the S gene (12.9%). In the latter, we identified mutations E484K, L18F, and D614G. Recent evidence suggests that these mutations concede important particularities to the virus, compromising host immunity, the diagnostic test performance, and the effectiveness of some vaccines. Some important lineages containing these mutations are the Alpha, Beta, and Gamma (WHO Label). Further genomic surveillance is important for the understanding of emerging genomic variants and their correlation with disease severity.

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Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2

Laiton‐Donato

Franco-Muñoz

Álvarez-Díaz

et al. 2021

Infection, Genetics and Evolution

116

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SARS-CoV-2 genetic diversity has the potential to impact the virus transmissibility and the escape from natural infection- or vaccine-elicited neutralizing antibodies. Here, we report the emergence of the B.1.621 lineage, considered a variant of interest (VOI) with the accumulation of several substitutions affecting the Spike protein, including the amino acid changes I95I, Y144T, Y145S and the insertion 146 N in the N-terminal domain, R346K, E484K and N501Y in the Receptor Binding Domain and P681H in the S1/S2 cleavage site of the Spike protein. The rapid increase in frequency and fixation in a relatively short time in some cities that were near the theoretical herd immunity suggests an epidemiologic impact. Further studies will be required to assess the biological and epidemiologic roles of the substitution pattern found in the B.1.621 lineage.

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Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K

Cited by 6 publications

References 27 publications

Low Neutralizing Antibody Titers against the Mu Variant of SARS-CoV-2 in 31 BNT162b2 Vaccinated Individuals in Colombia

Low Neutralizing Antibody Titers against the Mu Variant of SARS-CoV-2 in 31 BNT162b2 Vaccinated Individuals in Colombia

Mutation profile of SARS-CoV-2 genome in a sample from the first year of the pandemic in Colombia

Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2

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