tetano
Editor, Senior Moderator
Immun Inflamm Dis
. 2022 Jun;10(6):e634.
doi: 10.1002/iid3.634.
Precision health diagnostic and surveillance network uses S gene target failure (SGTF) combined with sequencing technologies to track emerging SARS-CoV-2 variants
Rafael Guerrero-Preston[SUP] 1 [/SUP], Vanessa Rivera-Amill[SUP] 2 [/SUP], Karem Caraballo[SUP] 1 [/SUP], Sebastian Rodríguez-Torres[SUP] 3 [/SUP], Ana Purcell-Wiltz[SUP] 1 4 [/SUP], Andrea A García[SUP] 2 [/SUP], Raphael S Torres[SUP] 2 [/SUP], Fernando T Zamuner[SUP] 5 [/SUP], Claudio Zanettini[SUP] 6 [/SUP], Matthew J MacKay[SUP] 7 [/SUP], Rachel Baits[SUP] 7 [/SUP], Daisy Salgado[SUP] 7 [/SUP], Gaurav Khullar[SUP] 7 [/SUP], Jessica Metti[SUP] 7 [/SUP], Timothy Baker[SUP] 7 [/SUP], Joel Dudley[SUP] 7 [/SUP], Keilyn Vale[SUP] 1 [/SUP], Gabriela Pérez[SUP] 8 [/SUP], Lorena De Jesús[SUP] 1 [/SUP], Yaima Miranda[SUP] 1 [/SUP], Denise Ortiz[SUP] 1 [/SUP], Amanda García-Negrón[SUP] 1 [/SUP], Liliana Viera[SUP] 9 [/SUP], Alberto Ortiz[SUP] 10 [/SUP], Jorge A Canabal[SUP] 10 [/SUP], Josefina Romaguera[SUP] 11 [/SUP], Ivonne Jiménez-Velázquez[SUP] 10 [/SUP], Luigi Marchionni[SUP] 5 [/SUP], José F Rodríguez-Orengo[SUP] 12 [/SUP], Adriana Baez[SUP] 13 [/SUP], Christopher E Mason[SUP] 7 [/SUP], David Sidransky[SUP] 5 [/SUP]
Affiliations
Abstract
Introduction: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic revealed a worldwide lack of effective molecular surveillance networks at local, state, and national levels, which are essential to identify, monitor, and limit viral community spread. SARS-CoV-2 variants of concern (VOCs) such as Alpha and Omicron, which show increased transmissibility and immune evasion, rapidly became dominant VOCs worldwide. Our objective was to develop an evidenced-based genomic surveillance algorithm, combining reverse transcription polymerase chain reaction (RT-PCR) and sequencing technologies to quickly identify highly contagious VOCs, before cases accumulate exponentially.
Methods: Deidentified data were obtained from 508,969 patients tested for coronavirus disease 2019 (COVID-19) with the TaqPath COVID-19 RT-PCR Combo Kit (ThermoFisher) in four CLIA-certified clinical laboratories in Puerto Rico (n = 86,639) and in three CLIA-certified clinical laboratories in the United States (n = 422,330).
Results: TaqPath data revealed a frequency of S Gene Target Failure (SGTF) > 47% for the last week of March 2021 in both, Puerto Rico and US laboratories. The monthly frequency of SGTF in Puerto Rico steadily increased exponentially from 4% in November 2020 to 47% in March 2021. The weekly SGTF rate in US samples was high (>8%) from late December to early January and then also increased exponentially through April (48%). The exponential increase in SGFT prevalence in Puerto Rico was concurrent with a sharp increase in VOCs among all SARS-CoV-2 sequences from Puerto Rico uploaded to Global Influenza Surveillance and Response System (GISAID) (n = 461). Alpha variant frequency increased from <1% in the last week of January 2021 to 51.5% of viral sequences from Puerto Rico collected in the last week of March 2021.
Conclusions: According to the proposed evidence-based algorithm, approximately 50% of all SGTF patients should be managed with VOCs self-quarantine and contact tracing protocols, while WGS confirms their lineage in genomic surveillance laboratories. Our results suggest this workflow is useful for tracking VOCs with SGTF.
Keywords: SARS-CoV-2; algorithms; genomics; population surveillance; precision medicine; public health.
. 2022 Jun;10(6):e634.
doi: 10.1002/iid3.634.
Precision health diagnostic and surveillance network uses S gene target failure (SGTF) combined with sequencing technologies to track emerging SARS-CoV-2 variants
Rafael Guerrero-Preston[SUP] 1 [/SUP], Vanessa Rivera-Amill[SUP] 2 [/SUP], Karem Caraballo[SUP] 1 [/SUP], Sebastian Rodríguez-Torres[SUP] 3 [/SUP], Ana Purcell-Wiltz[SUP] 1 4 [/SUP], Andrea A García[SUP] 2 [/SUP], Raphael S Torres[SUP] 2 [/SUP], Fernando T Zamuner[SUP] 5 [/SUP], Claudio Zanettini[SUP] 6 [/SUP], Matthew J MacKay[SUP] 7 [/SUP], Rachel Baits[SUP] 7 [/SUP], Daisy Salgado[SUP] 7 [/SUP], Gaurav Khullar[SUP] 7 [/SUP], Jessica Metti[SUP] 7 [/SUP], Timothy Baker[SUP] 7 [/SUP], Joel Dudley[SUP] 7 [/SUP], Keilyn Vale[SUP] 1 [/SUP], Gabriela Pérez[SUP] 8 [/SUP], Lorena De Jesús[SUP] 1 [/SUP], Yaima Miranda[SUP] 1 [/SUP], Denise Ortiz[SUP] 1 [/SUP], Amanda García-Negrón[SUP] 1 [/SUP], Liliana Viera[SUP] 9 [/SUP], Alberto Ortiz[SUP] 10 [/SUP], Jorge A Canabal[SUP] 10 [/SUP], Josefina Romaguera[SUP] 11 [/SUP], Ivonne Jiménez-Velázquez[SUP] 10 [/SUP], Luigi Marchionni[SUP] 5 [/SUP], José F Rodríguez-Orengo[SUP] 12 [/SUP], Adriana Baez[SUP] 13 [/SUP], Christopher E Mason[SUP] 7 [/SUP], David Sidransky[SUP] 5 [/SUP]
Affiliations
- PMID: 35634961
- DOI: 10.1002/iid3.634
Abstract
Introduction: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic revealed a worldwide lack of effective molecular surveillance networks at local, state, and national levels, which are essential to identify, monitor, and limit viral community spread. SARS-CoV-2 variants of concern (VOCs) such as Alpha and Omicron, which show increased transmissibility and immune evasion, rapidly became dominant VOCs worldwide. Our objective was to develop an evidenced-based genomic surveillance algorithm, combining reverse transcription polymerase chain reaction (RT-PCR) and sequencing technologies to quickly identify highly contagious VOCs, before cases accumulate exponentially.
Methods: Deidentified data were obtained from 508,969 patients tested for coronavirus disease 2019 (COVID-19) with the TaqPath COVID-19 RT-PCR Combo Kit (ThermoFisher) in four CLIA-certified clinical laboratories in Puerto Rico (n = 86,639) and in three CLIA-certified clinical laboratories in the United States (n = 422,330).
Results: TaqPath data revealed a frequency of S Gene Target Failure (SGTF) > 47% for the last week of March 2021 in both, Puerto Rico and US laboratories. The monthly frequency of SGTF in Puerto Rico steadily increased exponentially from 4% in November 2020 to 47% in March 2021. The weekly SGTF rate in US samples was high (>8%) from late December to early January and then also increased exponentially through April (48%). The exponential increase in SGFT prevalence in Puerto Rico was concurrent with a sharp increase in VOCs among all SARS-CoV-2 sequences from Puerto Rico uploaded to Global Influenza Surveillance and Response System (GISAID) (n = 461). Alpha variant frequency increased from <1% in the last week of January 2021 to 51.5% of viral sequences from Puerto Rico collected in the last week of March 2021.
Conclusions: According to the proposed evidence-based algorithm, approximately 50% of all SGTF patients should be managed with VOCs self-quarantine and contact tracing protocols, while WGS confirms their lineage in genomic surveillance laboratories. Our results suggest this workflow is useful for tracking VOCs with SGTF.
Keywords: SARS-CoV-2; algorithms; genomics; population surveillance; precision medicine; public health.