Open AccessPrecision health diagnostic and surveillance network uses S gene target failure (SGTF) combined with sequencing technologies to track emerging SARS‐CoV‐2 variants
Author(s) -
GuerreroPreston Rafael,
RiveraAmill Vanessa,
Caraballo Karem,
RodríguezTorres Sebastian,
PurcellWiltz 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,
GarcíaNegrón Amanda,
Viera Liliana,
Ortiz Alberto,
Canabal Jorge A.,
Romaguera Josefina,
JiménezVelázquez Ivonne,
Marchionni Luigi,
RodríguezOrengo José F.,
Baez Adriana,
Mason Christopher E.,
Sidransky David
Publication year - 2022
Publication title -
immunity, inflammation and disease
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.918
H-Index - 18
ISSN - 2050-4527
DOI - 10.1002/iid3.634
Subject(s) - track (disk drive) , covid-19 , computational biology , computer science , genetics , biology , medicine , infectious disease (medical specialty) , pathology , disease , operating system
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.