A tool for the cheap and rapid screening of SARS-CoV-2 variants of concern (VoCs) by Sanger sequencing

• DOI: 10.1128/spectrum.05064-22
• Publication Date: 2023-09-07T13:01:25Z
• Authors: Germán Burgos; Andrés Ambuludí; ; Diana Morales-Jadán; Miguel Angel Garc...; Claire Muslin; Vinicio Armijos-J...; Mateo Carvajal; Erika Muñoz; Rommel Guevara; Belén Prado; Sully Marquez; Josefina Coloma; Michelle Grunauer; Gabriel Trueba; Verónica Barragán; Patricio Rojas-Silva; Paúl Cárdenas
• Keywords: Sanger sequencing

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging virus that, since March 2020, has been responsible for a global and ongoing pandemic. Its rapid spread over the past nearly 3 years caused novel variants to arise. To monitor circulation emergence of SARS-CoV-2 variants, surveillance systems based on nucleotide mutations are required. In this regard, we searched in spike, ORF8, nucleocapsid genes detect variable sites among variants. We describe polymorphic genetic regions that enable us differentiate between Alpha, Beta, Gamma, Delta, Omicron concern (VoCs). found 21 relevant mutations, 13 which unique lineages BA.1/BA.1.1, BA.2, BA.3, BA.4, BA.5. This profile enables discrimination VoCs using only four reverse transcription PCR fragments Sanger sequencing, offering cheaper faster alternative whole-genome sequencing surveillance. IMPORTANCE Our work describes new (Sanger sequencing-based) screening methodology SARS-CoV-2, performing amplifications few target diagnostic Using developed work, were able discriminate following VoCs: (BA.1/BA.1.1, BA.5). becomes important, especially low-income countries where current methodologies like next-generation have prohibitive costs. Furthermore, detection would allow sanitary authorities take measures limit therefore reduce probability dispersion. With methodological approach, previously unreported several found.