Abstract
Next-generation sequencing (NGS) is the primary method used to monitor the distribution and emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants around the world; however, it is costly and time-consuming to perform and is not widely available in low-resourced geographical regions. Pyrosequencing has the potential to augment surveillance efforts by providing information on specific targeted mutations for rapid identification of circulating and emerging variants. The current study describes the development of a reverse transcription (RT)-PCR-pyrosequencing assay targeting >65 spike protein gene (S) mutations of SARS-CoV-2, which permits differentiation of commonly reported variants currently circulating in the United States with a high degree of confidence. Variants typed using the assay included B.1.1.7 (Alpha), B.1.1.529 (Omicron), B.1.351 (Beta), B.1.375, B.1.427/429 (Epsilon), B.1.525 (Eta), B.1.526.1 (Iota), B.1.617.1 (Kappa), B.1.617.2 (Delta), B.1.621 (Mu), P1 (Gamma), and B.1.1 variants, all of which were confirmed by the NGS data. An electronic typing tool was developed to aid in the identification of variants based on mutations detected by pyrosequencing. The assay could provide an important typing tool for rapid identification of candidate patients for monoclonal antibody therapies and a method to supplement SARS-CoV-2 surveillance efforts by identification of circulating variants and novel emerging lineages.
Keywords: Coronaviridae; SARS-CoV-2; coronavirus; monoclonal antibody treatment; pyrosequencing; severe acute respiratory syndrome; spike protein; variant.
【저자키워드】 SARS-CoV-2, coronavirus, Spike protein, Severe acute respiratory syndrome, Coronaviridae, Variant., monoclonal antibody treatment, pyrosequencing, 【초록키워드】 coronavirus, therapy, Mutation, B.1.351, monoclonal antibody, Sequencing, NGS, variant, Delta, B.1.617.2, severe acute respiratory syndrome Coronavirus, omicron, variants, Spike protein, Severe acute respiratory syndrome, Surveillance, B.1.1.7, Epsilon, B.1.617.1, Next-generation sequencing, Patient, Gamma, Alpha, Beta, reverse transcription, B.1.1.529, United States, respiratory, differentiation, distribution, information, Coronaviridae, lineages, B.1.621, monoclonal antibody treatment, pyrosequencing, Eta, Iota, SARS-CoV-2 surveillance, (Beta), (Alpha), monoclonal antibody therapies, confidence, acute respiratory syndrome, acute respiratory syndrome coronavirus, acute respiratory syndrome coronavirus 2, B.1.1, effort, circulating, B.1.525, geographical regions, MONITOR, circulating variants, reported, the United State, costly, time-consuming, circulating variant, 【제목키워드】 protocol, SARS-CoV-2 variant,