Rapid Detection and Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Omicron Variant in a Returning Traveler

Abstract

Our case report describes the rapid detection of the SARS-CoV-2 omicron variant using a combination of targeted spike SNP PCR and viral genome sequencing. This case occurred in a fully vaccinated and boosted returning traveler with mild symptoms who was identified through community surveillance rather than presentation for clinical care.

Global emerging Omicron variant of SARS-CoV-2: Impacts, challenges and strategies

“…In Malaysia, scientists have used Allplex Master Assay (SARS-CoV-2 specific) (having 98.7% sensitivity) along with Variants I assay (having 100% sensitivity) for detection of the S protein mutation of Omicron and other VOCs [140] . By the combined use of single nucleotide polymorphism (SNP) PCR (targeting the S protein region) and sequencing of the viral genome, Omicron variant can be quickly detected [141] . There is a report on sequencing of the whole genome in Italy for B.1.1.529 variant identification [142] .…”

Emergence of SARS-CoV-2 Omicron (B.1.1.529) variant, salient features, high global health concerns and strategies to counter it amid ongoing COVID-19 pandemic

“…During the SARS-CoV-2 genomic surveillance in the state of Georgia, a combination of Spike SNP PCR assay (taking only 2 h and 12 min run time) and genome sequencing and lineage classification (72 h) provided an on time diagnosis for Omicron. Additionally, the SNP analysis enabled the assay to distinguish between the other VOCs and Omicron and the assay may be further modified as per the requirements to detect new mutations if required ( Sexton et al, 2022 ). Omicron has been detected in an aircraft wastewater sample using the CDC N1, CDC N2, and del (69–70) RT-qPCR assays per guidance from the WHO and sequencing further confirmed the presence of Omicron belonging to BA.1 sub-lineage ( Ahmed et al, 2022 ).…”

Omicron variant: Current insights and future directions

“…An accurate diagnosis for Omicron was made during the SARS-CoV-2 genomic surveillance in the state of Georgia using a combination of the Spike SNP PCR test (2 hours and 12 minutes of run time) and genome sequencing and lineage classification (72 hours). The test was furthermore able to differentiate between the other VOCs and Omicron owing to the SNP analysis, and it may be further changed in accordance with the needs to identify new mutations if necessary ( Sexton et al, 2022 ). Following the WHO's instructions, Omicron was found in an airplane wastewater sample using the CDC N1, CDC N2, and del (69-70) RT-qPCR tests.…”