Access to rapid and accurate detection of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) RNA is essential for controlling the current global pandemic of Coronavirus Disease 2019 (COVID-19). In this study, the use of oral rinses and posterior oropharyngeal saliva as an alternative to swab collection methods from symptomatic and asymptomatic healthcare workers for the detection of SARS-CoV-2 RNA by RT-PCR was evaluated. For saliva samples, the overall agreement with oropharyngeal swabs (OPS) was 93% (Ƙ=0.84) with a sensitivity of 96.7% (95%CI:83.3-99.8%). The agreement between saliva and nasopharyngeal swabs was 97.7% (Ƙ=0.93) with a sensitivity of 94.1% (95% CI:73.0-99.7%). Oral rinses were compared with NPS only, with an overall agreement of 85.7% (Ƙ=0.65), and a sensitivity of 63% (95% CI:46.6-77.8%). The agreement between a laboratory-developed test based on the CDC RT-PCR and two commercial assays, the Xpert Xpress SARS-CoV-2 and the Cobas SARS-CoV-2 was also evaluated. The overall agreement was higher than 90%. Finally, SARS-CoV-2 RNA in saliva samples was shown to be stable, with no changes in viral loads over 24 hours at both room temperature and 4ºC. While the dilution of SARS-CoV-2 in oral rinses precluded its acceptability as a sample type, posterior oropharyngeal saliva was an acceptable alternative sample type for SARS-CoV-2 RNA detection.

The Alpha (B.1.1.7) and Omicron (B.1.1.529, BA.1, BA.4 and BA.5) variants of concern (VOC) share several mutations in their spike gene, including mutations resulting in the deletion of two amino acids at position 69 and 70 (del 69–70) in the Spike protein. Del 69–70 causes failure to detect the S gene target on a widely used, commercial test, the TaqPath SARS-CoV-2 RT-PCR (Thermo Fisher). The S gene target failure (SGTF) signature has been used to preliminarily infer the presence of Alpha and Omicron VOC. We evaluated the accuracy of the SGTF signature in identifying these two variants through analysis of all positive SARS-CoV-2 samples tested on the TaqPath RT-PCR and sequenced by next generation sequencing between December 2020 to July 2022. 2324 samples were successfully sequenced including 914 SGTF positive samples. The sensitivity and specificity of the SGTF signature was 99.6% (95% CI 96.1–99.9%) and 98.6% (95% CI 99.2–99.8%) for the Alpha variant and 99.6% (95% CI 98.9–99.9%) and 99.8% (95% CI 99.4–99.9%) for the Omicron variant. At the peak of their corresponding wave, the positive predictive value of the SGTF was 98% for Alpha and 100% for Omicron. The accuracy of the SGTF signature was high, making this genomic signature a rapid and accurate proxy for identification of these variants in real-world laboratory settings.

Background There is limited information on the risk of hospital-acquired COVID-19 among high-risk hospitalized patients after exposure to an infected patient or healthcare worker (HCW) in a non-outbreak setting. Methods This study was conducted at a tertiary care cancer center in New York City from March 10, 2020, until February 28, 2021. In early April 2020, the study institution implemented universal SARS-CoV-2 testing at admission and retesting every three days through the hospital stay. Contact tracing records were reviewed for all exposures to SARS-CoV-2 positive patients and HCWs. Results From March 10, 2020, to February 28, 2021, 11,348 unique patients who were SARS-CoV-2 PCR negative at the time of admission underwent 31,662 post-admission tests during their hospitalization, and 112 tested positive (0.98%). Among these, 49 patients housed in semi-private rooms during admission resulted in 74 close contacts and 14 secondary infections within 14 days, for an overall attack rate of 18.9%. Among those exposed to a roommate undergoing an aerosol-generating procedure (AGP), the attack rate was 35.7%. WGS corroborated transmission in 6/8 evaluated pairs. In addition, three transmission events occurred in 214 patients with significant exposure to 105 COVID-19 positive healthcare workers (1.4%). Conclusion The overall risk of hospital-acquired COVID-19 is low for hospitalized cancer patients, even during periods of high community prevalence. However, shared occupancy with an unrecognized case is associated with a high secondary attack rate in exposed roommates.

This study examined 266 individuals from various populations including African American, East Asian, South Asian, European, and mixed populations to evaluate the ForenSeq™ Signature Prep Kit Primer Mix B. Focus was placed on phenotypic and biogeographical ancestry predictions by Illumina's Universal Analysis Software (UAS). These outcomes were compared to those obtained through web‐tools developed at the Erasmus Medical Center (EMC) and available from the Forensic Resource/Reference on Genetics‐knowledge base (FROG‐kb), as well as to eye color predictions by the 8‐plex system. Due to drop‐outs, predictions for eye and hair color by UAS failed for various samples in each run. By including reads below thresholds, predictions could be obtained for all samples through the web‐tools. Eye and hair color predictions for African Americans, East Asians, and South Asians showed no errors. Difficulties however, were noted in intermediate (neither blue nor brown) eye color predictions. These were mitigated by the 8‐plex system through exclusion of one eye color (e.g. “not brown”). Additionally, notable discrepancies were observed in hair color predictions, where some black/dark‐brown haired individuals were predicted to have blond hair. Overall, ancestry predictions were more accurate by FROG‐kb compared to UAS, which did not predict South Asian ancestry, particularly Indian individuals.

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Multi locus sequence typing (MLST) is a low resolution but rapid genotyping method for Clostridioides difficile. Whole-genome sequencing (WGS) has emerged as the new gold standard for C. difficile typing but cost and lack of standardization still limits broad utilization. this study, we evaluated the potential to combine the portability of MLST with the increased resolution of WGS for a cost-saving approach to routine C. difficile typing. C. difficile strains from two New York City hospitals (Hospital A and Hospital B) were selected. WGS single nucleotide polymorphism (wgSNP) were performed using established methods. Sequence types (ST) were determined using PubMLST while wgSNP analysis was performed using the Bionumerics software. An additional analysis of a subset of data (Hospital A) was made comparing the Bionumerics software to the CosmosID pipeline. Cost and turn-around time to results were compared for the algorithmic approach of MLST followed by wgSNP versus direct wgSNP. Among the 202 C. difficile isolates typed, 91% (n=185/203) clustered within the representative ST, showing a high agreement between MLST and wgSNP. While clustering was similar between the Bionumerics and CosmosID pipelines, large differences in the overall number of SNPs was noted. Two-step algorithm for routine typing results in significantly lower cost than routine use of WGS. Our results suggest that using MLST as a first step in routine typing of C. difficile followed by WGS for MLST concordant strains is a less technically demanding, cost-saving approach for performing C. difficile typing than WGS alone without loss of discriminatory power.

Mutations in the genome of SARS-CoV-2 can affect the performance of molecular diagnostic assays. In some cases, such as S-gene target failure, the impact can serve as a unique indicator of a particular SARS-CoV-2 variant and provide a method for rapid detection.

In this retrospective study of 105 SARS COV-2 infected cancer patients with longitudinal nasopharyngeal sampling, the duration of viral shedding and time to attain cycle threshold >30 was longer in patients with hematologic malignancy than those with solid tumors. These findings have important public health implications.