tetano
Editor, Senior Moderator
J Med Virol
. 2022 Apr 13.
doi: 10.1002/jmv.27770. Online ahead of print.
A pyrosequencing protocol for rapid identification of SARS-CoV-2 variants
Richard A Allen[SUP] 1 [/SUP], Christopher L Williams[SUP] 2 [/SUP], Yvonne Penrod[SUP] 1 [/SUP], Cindy McCloskey[SUP] 1 [/SUP], Kristin Carpenter-Azevedo[SUP] 3 [/SUP], Richard C Huard[SUP] 3 [/SUP], Ewa King[SUP] 3 [/SUP], S Terence Dunn[SUP] 2 [/SUP]
Affiliations
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 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. This article is protected by copyright. All rights reserved.
Keywords: Coronaviridae; Coronavirus; Pyrosequencing; SARS-CoV-2; Severe Acute Respiratory Syndrome; Spike Protein; Variant; monoclonal antibody treatment.
. 2022 Apr 13.
doi: 10.1002/jmv.27770. Online ahead of print.
A pyrosequencing protocol for rapid identification of SARS-CoV-2 variants
Richard A Allen[SUP] 1 [/SUP], Christopher L Williams[SUP] 2 [/SUP], Yvonne Penrod[SUP] 1 [/SUP], Cindy McCloskey[SUP] 1 [/SUP], Kristin Carpenter-Azevedo[SUP] 3 [/SUP], Richard C Huard[SUP] 3 [/SUP], Ewa King[SUP] 3 [/SUP], S Terence Dunn[SUP] 2 [/SUP]
Affiliations
- PMID: 35416308
- DOI: 10.1002/jmv.27770
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 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. This article is protected by copyright. All rights reserved.
Keywords: Coronaviridae; Coronavirus; Pyrosequencing; SARS-CoV-2; Severe Acute Respiratory Syndrome; Spike Protein; Variant; monoclonal antibody treatment.