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Targeted ORF8-N Sanger Sequencing as a SARS-CoV-2 Surveillance Contingency During Supply Shortages
Brenno Vinícius Martins Henrique1,2, Helder Andrey Rocha Gomes3, Marina da Costa Ribeiro2
1Laboratório Central de Saúde Pública do Distrito Federal, Brasília, DF, Brasil.
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.
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