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.

SARS-CoV-2 subgenomic RNA (sgRNA) may indicate actively replicating virus, but sgRNA abundance has not been systematically compared between SARS-CoV-2 variants. sgRNA was quantified in 169 clinical samples by rRT-PCR, demonstrating similar relative abundance among known variants. Thus, sgRNA detection can identify individuals with active viral replication regardless of variant.

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Widespread use of over-the-counter rapid diagnostic tests for SARS-CoV-2 has led to a decrease in availability of clinical samples for viral genomic surveillance. As an alternative sample source, we evaluated RNA isolated from BinaxNOW swabs stored at ambient temperature for SARS-CoV-2 rRT-PCR and full viral genome sequencing. 81 of 103 samples (78.6%) yielded detectable RNA, and 46 of 57 samples (80.7 %) yielded complete genome sequences. Our results illustrate that SARS-CoV-2 RNA extracted from used Binax test swabs provides an important opportunity for improving SARS-CoV-2 genomic surveillance, evaluating transmission clusters, and monitoring within-patient evolution.

Background Professional soccer athletes are at risk of acquiring SARS-CoV-2 when traveling or through domestic community transmission. The U.S. Major League Soccer (MLS) league uses protocol-based SARS-CoV-2 testing for identification of individuals with COVID-19. Methods Per MLS protocol, fully vaccinated players underwent SARS-CoV-2 RT-PCR testing weekly; unvaccinated players were tested every other day. Demographic and epidemiologic data (e.g., travel history) were collected from individuals who tested positive, and contact tracing was performed. Whole genome sequencing (WGS) was performed on positive specimens, and phylogenetic analyses were used to identify potential transmission patterns. Results In the fall of 2021, all 30 players from one MLS team underwent SARS-CoV-2 testing per protocol; 27 (90%) were vaccinated. One player who recently traveled to Africa tested positive for SARS-CoV-2; within the following two weeks, 10 additional players and 1 staff member without recent international travel history tested positive. WGS yielded full genome sequences for 10 samples, including one from the traveler. The traveler’s sample was Delta sublineage AY.36 and was closely related to a sequence from Africa. Nine samples yielded other Delta sublineages including AY.4 (n = 7), AY.39 (n = 1), and B.1.617.2 (n = 1). The seven AY.4 sequences clustered together; five were identical, suggesting a common source of infection. Transmission from a family member visiting from England to an MLS player was identified as the potential index case. The other two AY.4 sequences differed from this group by 1-3 nucleotides, as did a partial genome sequence from an additional team member. Conclusions WGS is a useful tool for understanding SARS-CoV-2 transmission dynamics in professional sports teams.