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

Mary Elizabeth Sexton; Jesse J Waggoner; Ludy R Carmola; Phuong Vi Nguyen; Ethan Wang; Dara Khosravi; Azmain Taz; Robert A Arthur; Mit Patel; Venkata Viswanadh Edara; Stephanie L Foster; Kathryn M Moore; Matthew Gagne; Jesmine Roberts-Torres; Amy R Henry; Sucheta Godbole; Daniel C Douek; Nadine Rouphael; Mehul S Suthar; Anne Piantadosi

doi:10.1093/cid/ciac032

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

Clin Infect Dis. 2022 Aug 24;75(1):e350-e353. doi: 10.1093/cid/ciac032.

Authors

Mary Elizabeth Sexton¹, Jesse J Waggoner¹, Ludy R Carmola², Phuong Vi Nguyen¹, Ethan Wang², Dara Khosravi², Azmain Taz², Robert A Arthur³, Mit Patel⁴, Venkata Viswanadh Edara^{4

5

6}, Stephanie L Foster^{4

5

6}, Kathryn M Moore^{4

5

6}, Matthew Gagne⁷, Jesmine Roberts-Torres⁷, Amy R Henry⁷, Sucheta Godbole⁷, Daniel C Douek⁷, Nadine Rouphael^{1

8}, Mehul S Suthar^{4

5

6

9}, Anne Piantadosi^{1

2}

Affiliations

¹ Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA.
² Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA.
³ Emory Integrated Computational Core, Emory Integrated Core Facilities, Emory University, Atlanta, Georgia, USA.
⁴ Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA.
⁵ Emory Vaccine Center, Emory University, Atlanta, Georgia, USA.
⁶ Yerkes National Primate Research Center, Atlanta, Georgia, USA.
⁷ Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA.
⁸ Hope Clinic of the Emory Vaccine Center, Emory University School of Medicine, Decatur, Georgia, USA.
⁹ Department of Microbiology and Immunology, Emory University, Atlanta, Georgia, USA.

Abstract

We describe rapid detection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant using targeted spike single-nucleotide polymorphism polymerase chain reaction 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 clinical care.

Keywords: Omicron; SARS-CoV-2; genomic surveillance; multiplex PCR; vaccine.

Publication types

Case Reports
Research Support, U.S. Gov't, P.H.S.
Research Support, N.I.H., Intramural
Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural

MeSH terms

COVID-19* / diagnosis
Genome, Viral
Humans
Polymerase Chain Reaction
SARS-CoV-2* / genetics

Supplementary concepts

SARS-CoV-2 variants

Abstract

Publication types

MeSH terms

Supplementary concepts

Grants and funding