The Evolutionary Landscape of SARS-CoV-2 Variant B.1.1.519 and Its Clinical Impact in Mexico City

Abstract

The SARS-CoV-2 pandemic is one of the most concerning health problems around the globe. We reported the emergence of SARS-CoV-2 variant B.1.1.519 in Mexico City. We reported the effective reproduction number (Rt) of B.1.1.519 and presented evidence of its geographical origin based on phylogenetic analysis. We also studied its evolution via haplotype analysis and identified the most recurrent haplotypes. Finally, we studied the clinical impact of B.1.1.519. The B.1.1.519 variant was predominant between November 2020 and May 2021, reaching 90% of all cases sequenced in February 2021. It is characterized by three amino acid changes in the spike protein: T478K, P681H, and T732A. Its Rt varies between 0.5 and 2.9. Its geographical origin remain to be investigated. Patients infected with variant B.1.1.519 showed a highly significant adjusted odds ratio (aOR) increase of 1.85 over non-B.1.1.519 patients for developing a severe/critical outcome (p = 0.000296, 1.33–2.6 95% CI) and a 2.35-fold increase for hospitalization (p = 0.005, 1.32–4.34 95% CI). The continuous monitoring of this and other variants will be required to control the ongoing pandemic as it evolves.

Early Genomic, Epidemiological, and Clinical Description of the SARS-CoV-2 Omicron Variant in Mexico City

“…Never before had a VOC displaced other variants so quickly in Mexico City. In 2021, variant B.1.1.519 was totally displaced by Alpha, Gamma, and Delta in four months [ 6 ], while the Omicron variant displaced Delta in only one month. There was a correlation between the growth of the epidemic curve and the proportion of Omicron variants ( Figure 2 C).…”

“…Mexico City has been heavily affected by the COVID-19 pandemic. Two intense epidemic waves occurred in spring 2020 and winter 2020/2021, during which the heaviest toll of hospitalizations and deaths was observed [ 5 , 6 ]. A vaccination campaign began, starting with frontline health care workers and continuing for the rest of the population in descending age order, and was completed in the fall of 2021.…”

Early genomic, epidemiological, and clinical description of the SARS-CoV-2 Omicron variant in Mexico City

“…Never before had a variant of concern (VOC) displaced other variants so quickly in Mexico City, in 2021 variant B.1.1.519 was totally displaced by Alfa, Gamma and Delta in four months [5], while the Omicron variant displaced Delta in only one month. There was a correlation between the growth of the epidemic curve and the proportion of Omicron (Figure 2C).…”

“…Mexico City has been heavily affected by the COVID-19 pandemic. Two intense epidemic waves occurred in spring 2020 and winter 2020/2021, during which the heaviest toll of hospitalizations and deaths was observed [4,5]. A vaccination campaign began, starting with frontline healthcare workers and continuing in descending age order, and was completed in fall 2021 (http://vacunacovid.gob.mx/wordpress/calendario-vacunacion/).…”

Special Issue “Viral Infections in Developing Countries”

“…Additionally, research findings revealed unique amino acid substitutions by characterizing the mutational patterns and the effect on the corresponding proteins. Cedro-Tanda et al [7] reported the emergence and spread of the new B.1.1.519 variant in Mexico City in the beginning of 2021, and described its evolution, transmissibility, and association with relevant clinical traits. The authors observed that variant B.1.1.519 was significantly associated with severe disease, hospitalization, and death.…”