Epidemiological Interactions of Influenza and SARS-CoV-2 within a University Population During Omicron B.1.1.529 Outbreak (preprint)

The COVID-19 Pandemic has prompted innovation and research to further understand not only SARS-CoV-2, but other respiratory viruses as well. Since the start of the pandemic there has been a lack in influenza collection and surveillance. In October 2021 the Life Sciences Testing Center at Northeastern University implemented the TaqPath COVID-19, Flu A, Flu B combo kit to test for multiple respiratory diseases among the Universitys population. During this time the SARS-CoV-2 variant of concern, Omicron B.1.1.529, became the dominant strain in the greater Boston area. During this time an inverse correlation in the detection of positive SARS-CoV-2 and Influenza A was observed. More data is needed to determine if this observed inverse correlation on positivity rate is linked to public health measures or biological mechanism within the immune system.

Performance of the TaqMan COVID-19 Pooling Kit for detection of SARS-CoV-2 in Asymptomatic and Symptomatic populations at an Institution of Higher Education (preprint)

Clinical evidence for asymptomatic cases of coronavirus disease (COVID-19) has reinforced the significance of effective surveillance testing programs. Quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) assays are considered the gold standard for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA. However, the labor and resource requirements can be prohibitive with respect to large testing volumes associated with the pandemic. Pooled testing algorithms may serve to increase testing capacity with more efficient resource utilization. Due to the lack of carefully curated cohorts, there is limited evidence for the applicability of RT-PCR pooling in asymptomatic COVID-19 cases. In this study, we compared the analytical sensitivity of the TaqMan SARS-CoV-2 Pooling Assay to detect one positive sample in a pool of five anterior nare swabs in symptomatic and asymptomatic cohorts at an institute of higher education. Positive pools were deconvoluted and each individual sample was retested using the TaqPath COVID-19 Combo Kit. Both assays target the open reading frame (ORF) 1ab, nucleocapsid (N), and spike (S) gene of the strain that originated in Wuhan, Hubei, China. Qualitative results demonstrated absolute agreement between pooled and deconvoluted samples in both cohorts. Independent t-test performed on Ct shifts confirmed an insignificant difference between cohorts with p-values of 0.306 (Orf1ab), 0.147 (N), and 0.052 (S). All negative pools were correctly reported as negative. Thus, pooled PCR testing up to five samples is a valid method for surveillance testing of students and staff in a university setting, especially when the prevalence is expected to be low.

Two Stage Hierarchical Group Testing Strategy to Increase SARS-CoV-2 Testing Capacity at an Institution of Higher Education: A Retrospective Analysis (preprint)

Population testing for severe acute respiratory syndrome 2 (SAR-CoV-2) is necessary owing to the possibility of viral transmission from asymptomatic cases, yet scarcity of reagents and equipment has added to the cost-prohibitive implementation of screening campaigns at institutions of higher education. The high analytical sensitivities of leading nucleic acid amplification diagnostic methods allow for group testing to increase testing capacity. A feasibility study was performed using an optimized testing configuration model for pooling three, five, and ten samples. Following the standard RNA extraction and purification workflow for quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) method using Thermo Fisher TaqPath™ COVID-19 multiplex primers and probes for the ORF1ab, N, and S genes, matrix and dilution effects were assessed using pooled negative samples as the diluent. Probit analysis produced a limit of detection of 16075 (ORF1ab), 1308 (N), and 1180182 (S) genomic copy equivalents per milliliter. Trials comparing neat to 1:5 dilution for 34 weak-to-strongly positive samples demonstrated average threshold cycle (CT) shifts of 2.31±1.16 (ORF1ab), 2.23±1.12 (N), and 2.79±1.40 (S). Notwithstanding observed S gene dropouts, the false negative rate was unaffected. As the ratio of asymptomatic positive to symptomatic positive SARS-CoV-2 infected individuals was approximately 4:1 and the average prevalence was 0.16% since we started testing in August 2020, pooled testing was identified as a viable, cost-effective option for monitoring the Northeastern University community.