Brenno Vinícius Martins Henrique, Helder Andrey Rocha Gomes, Marina da Costa Ribeiro, Bruna Cândido Guido, Ricardo Camargo, Lucas Luiz Vieira, Mariana Matos Roll, Jordan Barros da Silva, Glaura Regina de Castro E Caldo Lima, Fabiano José Queiroz Costa, Agenor de Castro Moreira Dos Santos Júnior
Targeted ORF8-N Sanger sequencing was a useful temporary contingency during NGS reagent shortages but offered lower phylogenetic resolution than WGS.
BACKGROUND: Global shortages of next-generation sequencing (NGS) reagents threatened SARS-CoV-2 genomic surveillance in low- and middle-income countries during the COVID-19 pandemic.
METHODS: During the 2021 NGS reagent shortages, we implemented targeted ORF8-N Sanger sequencing for SARS-CoV-2 variant surveillance in Brazilian public health laboratories.
RESULTS: In silico analysis of whole-genome sequencing (WGS)-derived SARS-CoV-2 genomes from the Federal District, Brazil, showed that the ORF8-N target discriminated the major 2021 lineages (Gamma and Delta) and enabled analysis of ˃300 samples despite constrained NGS access.
CONCLUSIONS: Targeted ORF8-N Sanger sequencing was a useful temporary contingency during NGS reagent shortages but offered lower phylogenetic resolution than WGS.