key: cord-0889038-qkipdkbu
authors: Sexton, Mary Elizabeth; Waggoner, Jesse J; Carmola, Ludy R; Nguyen, Phuong-Vi; Wang, Ethan; Khosravi, Dara; Taz, Azmain; Arthur, Robert; Patel, Mit; Edara, Venkata-Viswanadh; Foster, Stephanie L; Moore, Kathryn M; Gagne, Matthew; Roberts-Torres, Jesmine; Henry, Amy R; Godbole, Sucheta; Douek, Daniel C; Rouphael, Nadine; Suthar, Mehul S; Piantadosi, Anne
title: Rapid detection and characterization of SARS-CoV-2 omicron variant in a returning traveler
date: 2022-01-17
journal: Clin Infect Dis
DOI: 10.1093/cid/ciac032
sha: 9cb45ddfc346a0c720ba3e97d3a6ca1e2519b93e
doc_id: 889038
cord_uid: qkipdkbu

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.

M a n u s c r i p t 2 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.

Key Words: SARS-CoV-2, omicron, multiplex PCR, genomic surveillance, vaccine M a n u s c r i p t 3 The SARS-CoV-2 omicron variant was identified in November 2021 and classified as a Variant of Concern (VOC) by the World Health Organization on November 26, 2021 [1] .

The omicron variant has been rapidly detected throughout the world, has demonstrated a concerning rise in frequency in some locations, and contains an unusually large number of mutations in the spike gene [2] , some of which have been associated with increased transmissibility and partial immune evasion in other SARS-CoV-2 lineages. Critical work is ongoing to understand the epidemiological, clinical, virological, and immunological implications of this variant.

We identified a previously-healthy woman in her 30s who presented with upper respiratory symptoms following a trip to South Africa and was diagnosed with COVID-19 upon return to Fulton County, Georgia, USA in November 2021, four days after identification of omicron as a VOC. She was fully-vaccinated with the Pfizer-BioNTech BNT162b2 mRNA vaccine as of February 2021 and had received a booster of the same vaccine in early October 2021. She had a negative PCR test prior to departing the United States and wore a medical-grade procedure mask and glasses on all flights. She stayed in a hotel in Cape Town for six days and attended an indoor, unmasked event with nine family members and friends, four of whom subsequently also tested positive for SARS-CoV-2. She had a negative PCR test 48 hours prior to return travel while asymptomatic, but then developed mild congestion on her last day in Cape Town, followed by a sore throat during travel home the next day. After arrival in Georgia, she also began experiencing nausea, fatigue, cough, and myalgias. She therefore had nasopharyngeal PCR testing performed at a community testing site on day 3 after symptom onset, which was positive. This sample was unable to be located during a contact tracing investigation. She never developed fevers, shortness of breath, or chest discomfort, and did not require medical attention. All symptoms had resolved by day 9, with the exception of ongoing myalgias and significant fatigue.

The patient was enrolled in a research study for emerging pathogens (Emory Institutional Review Board STUDY00022371). A mid-turbinate nasal swab was obtained on day 4 after symptom onset. Nucleic acids were extracted from 400µL of swab sample and A c c e p t e d M a n u s c r i p t 4 tested by rRT-PCR for the SARS-CoV-2 N2 target as previously described [3] , yielding a Ct value of 22.2. The sample was also tested for specific single nucleotide polymorphisms (SNPs) in the spike receptor binding motif using the previously described multiplex rRT-PCR Spike SNP assay [4, 5] . Briefly, the Spike SNP assay uses a single primer pair to amplify a 348bp region and tiled hydrolysis probes to differentiate mutations that are associated with VOC and variants of interest (VOI).

Within 24 hours after sample collection, Spike SNP results from this sample detected a variant sequence at amino acid position 417 and the mutation conferring N501Y ( Figure   1A ). It did not detect the mutations conferring L452R/L452Q, E484K, or F490S. This pattern of SNPs is consistent with the sequence expected for the omicron variant and different from results observed with prior VOCs/VOIs ( Figure 1A ) [6] [7] [8] . Interestingly, the T478K mutation was not detected in this sample, though 90% of omicron sequences bear this mutation.

SARS-CoV-2 sequencing libraries were generated using the SuperScript TM IV First Strand Synthesis kit (Thermo Fisher) followed by the Swift Amplicon SARS-CoV-2

Research Panel (Swift Biosciences) [9] . Sequencing was performed with paired-end 150bp reads on an Illumina MiSeq, and a total of 1,034,420 reads were generated for this sample.

The consensus SARS-CoV-2 genome was assembled using the viralrecon analysis pipeline [10] (github.com/nf-core/viralrecon) with reference sequence MN908947.3.

Within 72 hours after sample collection, the SARS-CoV-2 lineage from this sample's sequence was classified as B.1.1.529, and the variant as omicron, using cov-lineages.org [11] . The sequence of the spike protein confirmed results from the multiplex spike SNP PCR assay (Figure 1A) , and additionally detected both T478K and the adjacent mutation S477N.

The negative result for T478K by the Spike SNP assay is most likely because the mutation conferring S477N is located within the probe for T478K, preventing its binding. Overall, the spike sequence from this sample contained all mutations originally described for the omicron Table 1 ). The patient's post-infection serum was able to neutralize autologous virus with a FRNT 50 GMT of 687, substantially higher than neutralization of this virus by sera from the other seven individuals (Figure 1B) .

In all cases, neutralization of WA1 was 2.5-10 fold higher than the omicron variant. Overall, our work illustrates the strengths of a flexible, multimodal approach in the detection and characterization of emerging SARS-CoV-2 variants, which will inform ongoing and future public health surveillance. In addition to their clinical and public health benefits, surveillance efforts also serve as a critical foundation for studies characterizing the capacity of the SARS-CoV-2 omicron variant to escape natural immunity to prior strains and acquired immunity to vaccines, including boosters. A c c e p t e d M a n u s c r i p t 12 Figure 1 

Classification of Omicron (B.1.1.529): SARS-CoV-2 Variant of Concern

Triplex Real-Time RT-PCR for Severe Acute Respiratory Syndrome Coronavirus 2

SARS-CoV-2 variants in Paraguay: Detection and surveillance with a readily modifiable, multiplex real-time RT-PCR. medRxiv

Single-Amplicon Multiplex Real-Time Reverse Transcription-PCR with Tiled Probes To Detect SARS-CoV-2 spike Mutations Associated with Variants of Concern

Detection of a SARS-CoV-2 variant of concern in South Africa

Antibody-Mediated Neutralization of Authentic SARS-CoV-2 B.1.617 Variants Harboring L452R and T478K/E484Q

Sensitive Recovery of Complete SARS-CoV-2 Genomes from Clinical Samples by Use of Swift Biosciences' SARS-CoV-2 Multiplex Amplicon Sequencing Panel

nf-core/viralrecon: nf-core/viralrecon v2.2 -Tin Turtle

Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch

SARS-CoV-2 variants of concern and variants under investigation in England: technical briefing 33

We are very grateful to the patient for participating in this study and granting permission for this information to be presented in the case report. We would like to thank staff of the Emory Vaccine Center Hope Clinic for assistance with sample processing.