A Sanger sequencing-based method for a rapid and economic generation of SARS-CoV-2 epidemiological data: A proof of concept study to assess the prevalence of the A23403G SNP (D614G) mutation in Quito, Ecuador.

Abstract

The Single Nucleotide Polymorphism (SNP) A23403G associated with the D to G change in position 614 of the SARS-CoV-2 spike protein has recently become dominant. The most utilized and robust approach is the study of whole genome sequences, generally available at public databases. However, this technology is not suited for massive testing as it requires expensive reagents, equipment, and infrastructure. Consequently, developing rapid and accessible protocols will be fundamental for producing epidemiological data linked to this SNP, especially in countries with limited resources. This report has evaluated an easy cost-effective approach, based on sanger sequencing, for detection of the A23403G (D614G) mutation. This strategy was tested in SARS-CoV-2 positive samples collected in Quito during March and October of 2020. In March, a total of 264 out of 1319 samples yielded positive results (20%), while 777 out of 5032 (15%) did so in October. From these cases, almost all samples were associated with the G23403 (G614) variant (>98%). This technique proved to be reliable, reproducible, and might be expandable to study other mutations without major protocol amendments. The application of this method allowed the production of epidemiological data regarding the A23403G (D614G) mutation in Quito, where no previous reports were available. This approach will be crucial for producing relevant information for public health management, especially during the ongoing pandemic.