Precision Health Diagnostic and Surveillance Network uses S Gene Target Failure (SGTF) combined with sequencing technologies to identify emerging SARS-CoV-2 variants

Abstract

Several genomic epidemiology tools have been developed to track the public and population health impact of SARS-CoV-2 community spread worldwide. A SARS-CoV-2 Variant of Concern (VOC) B.1.1.7, known as 501Y.V1, which shows increased transmissibility, has rapidly become the dominant VOC in the United States (US). Our objective was to develop an evidenced-based genomic surveillance algorithm that combines RT-PCR and sequencing technologies to identify VOCs. Deidentified data were obtained from 508,969 patients tested for 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 US (n=422,330). 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 is concurrent with a sharp increase in VOCs among all SARS-CoV-2 sequences from Puerto Rico uploaded to GISAID (n=461). B.1.1.7 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. The exponential increase in SGTF and B.1.1.7 prevalence in Puerto Rico and US requires an urgent response. According to the proposed evidence-based algorithm, approximately 50% of all positive samples should be managed as potential B.1.1.7 carriers with VOC quarantine and contact tracing protocols while their lineage is confirmed by WGS in surveillance laboratories. Patients infected with VOCs should be effectively triaged for isolation, contact tracing and follow-up treatment purposes.

SARS-CoV-2 Variant Surveillance Using Tandem Targeted RT-PCR-based Genotyping Assays and Whole Genome Sequencing

“…3,11-15 While WGS has proven to be an invaluable tool for identification of new variants, the cost as well as turnaround times for sample processing and data analysis remain challenging for wide implementation. 4-6,8 This demonstrates that genotyping assays offer a fast, reliable, and cost-effective method for monitoring of known SARS-CoV-2 variants within a population.…”

“…A side-by-side cost analysis was performed by comparing the mutation panel genotyping approach for VOC surveillance to the WGS, with respect to cost of instrumentation, consumables, staff, computing capacity and data storage and other variables (Figure 1C). [4][5][6]8 The average cost per sample for the genotyping approach using a 12-assay mutation panel was calculated to be over 8 times lower than WGS, without factoring in the longer turn-around-time for obtaining the WGS results when compared to RT-PCR. 5,6,8…”

“…Our results showed that our mutation panels were able to accurately assign lineages to VOC as confirmed with WGS. Although genotyping assays can only assign samples to lineages that are already defined in the database, a key feature of genotyping assays is that they can be rapidly updated as new VOC exhibiting new combinations of mutations arise [4][5][6] , which can be powerful given the rapid emergence and spread of previous VOC. 3,[10][11][12]14 This study showed that when comparing surveillance technical costs, the 12-Assay Mutation panels afforded 98.88% VOC determination at >8 times cheaper than WGS testing per sample, and costs can be further reduced by targeting selected VOC.…”

“…Our results showed that our mutation panels were able to accurately assign lineages to VOC as confirmed with WGS. Although genotyping assays can only assign samples to lineages that are already defined in the database, a key feature of genotyping assays is that they can be rapidly updated as new VOC exhibiting new combinations of mutations arise 4-6 , which can be powerful given the rapid emergence and spread of previous VOC. 3,10-12,14…”

“…[1][2][3] Since September 2020 several variants of SARS-CoV-2 have emerged that have been labeled variants of concern (VOC) or variants under monitoring (VUM) based on their properties such as increased transmissibility, virulence, or impact on the performance of therapeutics, vaccines, or diagnostic tests. [1][2][3][4][5][6][7] Alpha (B.1.1.7), Beta (B.1.351) and Gamma (P.1) VOC circulated in the first half of 2021, before the emergence of Delta (B.1.617.2) VOC replaced Alpha as the dominant variant in July 2021. 3,5,6 Recently a new VOC, Omicron (B.1.1.529), has emerged and currently accounts for 99.5% of all SARS-CoV-2 cases in the United States.…”