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Precision health diagnostic and surveillance network uses S gene target failure (SGTF) combined with sequencing technologies to track emerging SARS-CoV-2 variants.
Guerrero-Preston, Rafael; Rivera-Amill, Vanessa; Caraballo, Karem; Rodríguez-Torres, Sebastian; Purcell-Wiltz, Ana; García, Andrea A; Torres, Raphael S; Zamuner, Fernando T; Zanettini, Claudio; MacKay, Matthew J; Baits, Rachel; Salgado, Daisy; Khullar, Gaurav; Metti, Jessica; Baker, Timothy; Dudley, Joel; Vale, Keilyn; Pérez, Gabriela; De Jesús, Lorena; Miranda, Yaima; Ortiz, Denise; García-Negrón, Amanda; Viera, Liliana; Ortiz, Alberto; Canabal, Jorge A; Romaguera, Josefina; Jiménez-Velázquez, Ivonne; Marchionni, Luigi; Rodríguez-Orengo, José F; Baez, Adriana; Mason, Christopher E; Sidransky, David.
  • Guerrero-Preston R; LifeGene-Biomarks, Inc, San Juan, Puerto Rico.
  • Rivera-Amill V; Center for Research Resources, Ponce Health Sciences University-Ponce Research Institute, Ponce, Puerto Rico.
  • Caraballo K; LifeGene-Biomarks, Inc, San Juan, Puerto Rico.
  • Rodríguez-Torres S; University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.
  • Purcell-Wiltz A; LifeGene-Biomarks, Inc, San Juan, Puerto Rico.
  • García AA; Biology Department, University of Puerto Rico, Río, Piedras, Puerto Rico.
  • Torres RS; Center for Research Resources, Ponce Health Sciences University-Ponce Research Institute, Ponce, Puerto Rico.
  • Zamuner FT; Center for Research Resources, Ponce Health Sciences University-Ponce Research Institute, Ponce, Puerto Rico.
  • Zanettini C; Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
  • MacKay MJ; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, Cornell University, New York, New York, USA.
  • Baits R; Tempus Labs, Inc, Chicago, Illinois, USA.
  • Salgado D; Tempus Labs, Inc, Chicago, Illinois, USA.
  • Khullar G; Tempus Labs, Inc, Chicago, Illinois, USA.
  • Metti J; Tempus Labs, Inc, Chicago, Illinois, USA.
  • Baker T; Tempus Labs, Inc, Chicago, Illinois, USA.
  • Dudley J; Tempus Labs, Inc, Chicago, Illinois, USA.
  • Vale K; Tempus Labs, Inc, Chicago, Illinois, USA.
  • Pérez G; LifeGene-Biomarks, Inc, San Juan, Puerto Rico.
  • De Jesús L; Neurology Medicine Department, Palmetto General Hospital, Miami, Florida, USA.
  • Miranda Y; LifeGene-Biomarks, Inc, San Juan, Puerto Rico.
  • Ortiz D; LifeGene-Biomarks, Inc, San Juan, Puerto Rico.
  • García-Negrón A; LifeGene-Biomarks, Inc, San Juan, Puerto Rico.
  • Viera L; LifeGene-Biomarks, Inc, San Juan, Puerto Rico.
  • Ortiz A; Department of Surgery, University of Puerto Rico School of Medicine, San Juan, Puerto Rico.
  • Canabal JA; Internal Medicine Department, University of Puerto Rico School of Medicine, San, Juan, Puerto Rico.
  • Romaguera J; Internal Medicine Department, University of Puerto Rico School of Medicine, San, Juan, Puerto Rico.
  • Jiménez-Velázquez I; Obstetrics and Gynecology Department, University of Puerto Rico School of Medicine, San Juan, Puerto Rico.
  • Marchionni L; Internal Medicine Department, University of Puerto Rico School of Medicine, San, Juan, Puerto Rico.
  • Rodríguez-Orengo JF; Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
  • Baez A; Biochemistry Department, University of Puerto Rico School of Medicine, San Juan, Puerto Rico.
  • Mason CE; Otolaryngology Department, University of Puerto Rico School of Medicine, San Juan, Puerto Rico.
  • Sidransky D; Tempus Labs, Inc, Chicago, Illinois, USA.
Immun Inflamm Dis ; 10(6): e634, 2022 06.
Article in English | MEDLINE | ID: covidwho-1850065
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.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Diagnostic study / Observational study / Prognostic study Topics: Long Covid / Variants Limits: Humans Country/Region as subject: North America Language: English Journal: Immun Inflamm Dis Year: 2022 Document Type: Article Affiliation country: Iid3.634

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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Diagnostic study / Observational study / Prognostic study Topics: Long Covid / Variants Limits: Humans Country/Region as subject: North America Language: English Journal: Immun Inflamm Dis Year: 2022 Document Type: Article Affiliation country: Iid3.634