SARS-CoV-2 viral variants can rapidly be identified for clinical decision making and population surveillance using a high-throughput digital droplet PCR assay.

Epidemiologic surveillance of circulating SARS-CoV-2 variants is essential to assess impact on clinical outcomes and vaccine efficacy. Whole genome sequencing (WGS), the gold-standard to identify variants, requires significant infrastructure and expertise. We developed a digital droplet polymerase chain reaction (ddPCR) assay that can rapidly identify circulating variants of concern/interest (VOC/VOI) using variant-specific mutation combinations in the Spike gene. To validate the assay, 800 saliva samples known to be SARS-CoV-2 positive by RT-PCR were used. During the study (July 2020-March 2022) the assay was easily adaptable to identify not only existing circulating VAC/VOI, but all new variants as they evolved. The assay can discriminate nine variants (Alpha, Beta, Gamma, Delta, Eta, Epsilon, Lambda, Mu, and Omicron) and sub-lineages (Delta 417N, Omicron BA.1, BA.2). Sequence analyses confirmed variant type for 124/124 samples tested. This ddPCR assay is an inexpensive, sensitive, high-throughput assay that can easily be adapted as new variants are identified.

Surveillance of Severe Acute Respiratory Syndrome Coronavirus 2 and Variants Using Digital Droplet Polymerase Chain Reaction at a Large University and Healthcare System in California.

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with different infectivity, transmission potential, and morbidity change the characteristics of local epidemics and affect vaccine effectiveness. As part of the University of Southern California COVID-19 Pandemic Research Center's efforts to understand, control, and inform local community on coronavirus disease 2019 (COVID-19), we implemented a SARS-CoV-2 surveillance program among students, employees, and USC Keck Medical Center patients. We present the epidemiology and distribution of SARS-CoV-2 and its variants among the population. Methods: We used digital droplet reverse-transcriptase polymerase chain reaction (PCR) to analyze in real-time remnant SARS-CoV-2 PCR-positive saliva specimens stored at the USC Keck Medicine laboratory between September 2020 and April 2022. Samples were tested for the original strain (A20) and 9 SARS-CoV-2 variants: α(B.1.1.7, Q.1-Q.8), ß(B.1.351, B.1.351.2, B.1.351.3), γ(P.1, P.1.1, P.1.2), δ(B.1.617.2), δ+(or δ417N), ε(B.1.427 and B.1.429), η(B.1.525), λ(C.37) and ο(B.1.1.529, ΒΑ.1, BA.2). We reviewed deidentified health information from positive cases including demographics, history of COVID-19 (eg, symptoms, hospitalizations, and repeat infections), and COVID-19 vaccination status. Results: We reviewed 1169 cases and determined the variant type of 482 specimens: 77 specimens were original strain, 119 "Delta", 165 "Omicron". The original strain was detected during the third and fourth quarters of 2020. The Delta variant appeared during the second quarter of 2021, whereas Omicron appeared in the fourth quarter of 2021. Conclusions: Prospectively tracking SARS-CoV-2 variants in a university population and a hospital system, utilizing a low-cost, high-throughput PCR assay, was feasible. Local variant monitoring remains important to inform prevention and control efforts among university and clinical settings.

Adolescents may accurately self-collect pharyngeal and rectal clinical specimens for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae infection.

BACKGROUND: The COVID-19 pandemic illuminated the benefits of telemedicine. Self-collected specimens are a promising alternative to clinician-collected specimens when in-person testing is not feasible. In this study, we assessed the adequacy of self-collected pharyngeal and rectal specimens for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae among individuals undergoing chlamydia and gonorrhea screening. METHODS: We used data from a large cohort study that included male and female adolescents between the ages of 12-24 years. We considered self-collected specimens adequate for clinical use if the human synthase gene (a control target of the assay) was detected in the specimen. RESULTS: In total, 2,458 specimens were included in the analysis. The human synthase gene was detected in 99.2% (2,439/2,458) of all self-collected specimens, 99.5% (1,108/1,114) of the pharyngeal specimens, and 99.0% (1,331/1,344) of the rectal specimens. CONCLUSION: Self-collected pharyngeal and rectal specimens demonstrated a very high proportion of human gene presence, suggesting that self-collection was accurate. A limitation of this study is that the sample adequacy control detects the presence or absence of the human hydroxymethylbilane synthase gene, but it does not indicate the specific anatomic origin of the human hydroxymethylbilane synthase gene. Self-collected specimens may be an appropriate alternative to clinician-collected specimens.