First sequenced cases of Omicron BA.2 sublineage in Ecuador

• Published in: Virus research 2023-09, Vol.334, p.199169-199169, Article 199169
• Main Authors: Andrade-Molina, D.A., Morey-León, G.A., Muñoz-Mawyin, K.E., Cruz-Fatuly, F.F., Fernández-Cadena, J.C., Cárdenas, P.
• Format: Article
• Language: English
• Subjects: BA.2; Ecuador; Omicron; SARS-CoV-2
• ISSN: 0168-1702; 1872-7492
• DOI: 10.1016/j.virusres.2023.199169

•First BA.2 sequenced variant registered in Ecuador, in 5 persons who had been vaccinated and not vaccinated.•Firsts sequenced cases of BA.2 were determined by routine genomic surveillance of SARS-CoV-2 by RT-PCR genotyping analysis and confirmation was conducted using whole genome sequencing.•The first sequenced case of BA.2 is an international introduction, and four other cases suggest a scenario of local spread. The largest wave of infection with SARS-CoV-2 virus in Ecuador was observed in mid-December 2021 and early January 2022, driven by B.1.1.529/BA (Omicron) variant. During the second half of March, an increase in the number of daily cases was observed and coincided with the emergence of the BA.2 variant, which we describe in the present study. The first sequenced five cases of SARS-CoV-2 21L/BA.2 in Ecuador were identified using variant specific genotyping by qPCR and confirmed by whole genome sequencing (WGS). The first sequenced Ecuadorian BA.2 isolate was obtained from a person with international travel history who became symptomatic 3 days after travelling, whereas in the other cases no travel history was recorded.