Validation of reduced S-gene target performance and failure for rapid surveillance of SARS-CoV-2 variants.

SARS-CoV-2, the virus that causes COVID-19, has many variants capable of rapid transmission causing serious illness. Timely surveillance of new variants is essential for an effective public health response. Ensuring availability and access to diagnostic and molecular testing is key to this type of surveillance. This study utilized reverse transcription polymerase chain reaction (RT-PCR) and whole genome sequencing results from COVID-19-positive patient samples obtained through a collaboration between Aegis Sciences Corporation and Walgreens Pharmacy that has conducted more than 8.5 million COVID-19 tests at ~5,200 locations across the United States and Puerto Rico. Viral evolution of SARS-CoV-2 can lead to mutations in the S-gene that cause reduced or failed S-gene amplification in diagnostic PCR tests. These anomalies, labeled reduced S-gene target performance (rSGTP) and S-gene target failure (SGTF), are characteristic of variants carrying the del69-70 mutation, such as Alpha and Omicron (B.1.1.529, BA.1, and BA.1.1) lineages. This observation has been validated by whole genome sequencing and can provide presumptive lineage data following completion of diagnostic PCR testing in 24-48 hours from collection. Active surveillance of trends in PCR and sequencing results is key to the identification of changes in viral transmission and emerging variants. This study shows that rSGTP and SGTF can be utilized for near real-time tracking and surveillance of SARS-CoV-2 variants, and is superior to the use of SGTF alone due to the significant proportion of Alpha and Omicron (B.1.1.529, BA.1, and BA.1.1) lineages known to carry the del69-70 mutation and observed to have S-gene amplification. Adopting new tools and techniques to both diagnose acute infections and expedite identification of emerging variants is critical to supporting public health.

Urinary stone risk factors in the siblings of patients with calcium renal stones.

PURPOSE: We determined which, if any, urinary stone risk factors accurately discriminate stone forming and nonstone forming siblings of patients with calcium renal stones. MATERIALS AND METHODS: A total of 252 siblings of stone formers provided 2, 24-hour urine samples, which were sent overnight and analyzed at a central laboratory. Standard stone risk factors were measured and the supersaturation of calcium oxalate, calcium phosphate and uric acid was calculated. RESULTS: Discriminant functions were derived for each gender by multivariate analysis. In stone forming sisters higher urinary calcium and pH discriminated with a success rate of 70%. In stone forming brothers higher urinary calcium, lower urinary potassium and older age discriminated with a success rate of 79%. CONCLUSIONS: Select urinary measurements as well as age classify siblings into those with and without stones with fair accuracy. Calcium excretion and urinary pH in females, and calcium excretion, urinary potassium and age in males are feasible identifiers of stone forming siblings. To determine whether these measurements can be used to predict new stone onset may require years of observation of our current cohort.