Background: COVID-19 is diagnosed via detection of SARS-CoV-2 RNA using real time reverse-transcriptase polymerase chain reaction (rtRT-PCR). Performance of many SARS-CoV-2 rtRT-PCR assays is not entirely known due to the lack of a gold standard. We sought to evaluate the false negative rate (FNR) and sensitivity of our laboratory-developed SARS-CoV-2 rtRT-PCR targeting the envelope (E) and RNA-dependent RNA-polymerase (RdRp) genes. Methods: SARS-CoV-2 rtRT-PCR results at the Public Health Laboratory (Alberta, Canada) from January 21 to April 18, 2020 were reviewed to identify patients with an initial negative rtRT-PCR followed by a positive result on repeat testing within 14 days (defined as discordant results). Negative samples from these discordant specimens were re-tested using three alternate rtRT-PCR assays (targeting the E gene and N1/N2 regions of the nucleocapsid genes) to assess for false negative (FN) results. Results: During the time period specified, 95,919 patients (100,001 samples) were tested for SARS-CoV-2. Of these, 49 patients were found to have discordant results including 49 positive and 52 negative swabs. Repeat testing of 52 negative swabs found five FNs (from five separate patients). Assuming 100% specificity of the diagnostic assay, the FNR and sensitivity in this group of patients with discordant testing was 9.3% (95% CI 1.5–17.0%) and 90.7% (95% CI 82.6–98.9%) respectively. Conclusions: Studies to understand the FNR of routinely used assays are important to confirm adequate clinical performance. In this study, most FN results were due to low amounts of SARS-CoV-2 virus concentrations in patients with multiple specimens collected during different stages of infection. Post-test clinical evaluation of each patient is advised to ensure that rtRT-PCR results are not the only factor in excluding COVID-19.

To determine the incidence of influenza and noninfluenza respiratory viruses (NIRVs) pre-/post-implementation of public health measures aimed to decrease coronavirus disease 2019 (COVID-19) transmission using population-based surveillance data. We hypothesized that such measures could reduce the burden of respiratory viruses (RVs) transmitting via the same routes. An interrupted time-series analysis of RV surveillance data in Alberta, Canada, from May 2017 to July 2020 was conducted. The burden of influenza and NIRVs before and after intervention initiation at week 11 was compared. The analysis was adjusted for seasonality, overdispersion, and autocorrelation. During the study period, an average of 708 and 4056 weekly respiratory multiplex molecular panels were conducted pre-/post-intervention, respectively. We found significant reductions in test positivity rates in the postintervention period for influenza (-94.3%; 95% CI, -93.8 to 97.4%; P<.001) and all NIRVs (-76.5%; 95% CI, -77.3 to -75.8%; P<.001) in the crude model, and -86.2% (95% CI, -91.5 to -77.4%: P<.001) and -75% (95% CI, -79.7 to -69.3%; P<.001), respectively, in the adjusted models. Subanalyses for individual viruses showed significant decreases in respiratory syncytial virus, human metapneumovirus, enterovirus/rhinovirus, and parainfluenza. For non–severe acute respiratory coronavirus 2 human coronaviruses, the decline was not statistically significant after adjustment (-22.3%; 95% CI, -49.3 to +19%, P=.246). The implementation of COVID-19 public health measures likely resulted in reduced transmission of common RVs. Although drastic lockdowns are unlikely to be required given widespread COVID-19 vaccination, targeted implementation of such measures can lower RV disease burden. Studies to evaluate relative contributions of individual interventions are warranted.

Using SARS-CoV-2 serology testing, we assessed the proportion of people in Alberta, Canada (population 4.4 million) positive for COVID-19 antibodies, indicating previous infection, during the first two waves of the COVID-19 pandemic (prior to vaccination programs). Linking these results with sociodemographic population data provides valuable information as to which groups of the population are more likely to have been infected with the SARS-CoV-2 virus to help facilitate public health decision-making and interventions.

Background: SARS-CoV-2 infection can present with a broad clinical differential that includes many other respiratory viruses; therefore, accurate tests are crucial to distinguish true COVID-19 cases from pathogens that do not require urgent public health interventions. Co-circulation of other respiratory viruses is largely unknown during the COVID-19 pandemic but would inform strategies to rapidly and accurately test patients with respiratory symptoms. Methods: This study retrospectively examined 298,415 respiratory specimens collected from symptomatic patients for SARS-CoV-2 testing in the three months since COVID-19 was initially documented in the province of Alberta, Canada (March-May, 2020). By focusing on 52,285 specimens that were also tested with the Luminex Respiratory Pathogen Panel for 17 other pathogens, this study examines the prevalence of 18 potentially co-circulating pathogens and their relative rates in prior years versus since COVID-19 emerged, including four endemic coronaviruses. Results: SARS-CoV-2 was identified in 2.2% of all specimens. Parallel broad multiplex testing detected additional pathogens in only 3.4% of these SARS-CoV-2-positive specimens: significantly less than in SARS-CoV-2-negative specimens (p < 0.0001), suggesting very low rates of SARS-CoV-2 co-infection. Furthermore, the overall co-infection rate was significantly lower among specimens with SARS-CoV-2 detected (p < 0.0001). Finally, less than 0.005% of all specimens tested positive for both SARS-CoV-2 and any of the four endemic coronaviruses tested, strongly suggesting neither co-infection nor cross-reactivity between these coronaviruses. Conclusions: Broad respiratory pathogen testing rarely detected additional pathogens in SARS-CoV-2-positive specimens. While helpful to understand co-circulation of respiratory viruses causing similar symptoms as COVID-19, ultimately these broad tests were resource-intensive and inflexible in a time when clinical laboratories face unprecedented demand for respiratory virus testing, with further increases expected during influenza season. A transition from broad, multiplex tests toward streamlined diagnostic algorithms targeting respiratory pathogens of public health concern could simultaneously reduce the overall burden on clinical laboratories while prioritizing testing of pathogens of public health importance. This is particularly valuable with ongoing strains on testing resources, exacerbated during influenza seasons.

: COVID-19 seroprevalence studies use serum/plasma samples to detect SARS-CoV-2 IgG. Data supporting alternate specimen types and freeze-thaw antibody stability is lacking. The stability of IgG and other immunoglobulins in multiple blood sample types stored in differing conditions and multiple freeze-thaw cycles (FTCs) was evaluated. : Serum, plasma, and heparinized-plasma samples were collected from COVID-19 recovered individuals. Samples underwent testing for SARS-CoV-2 antibodies upon collection, after each of 10–12 FTCs, and storage at -70°C, -20°C, 4°C, and room-temperature for 10–12 days using four high-throughput commercial assays, two rapid-test cassettes, a manual ELISA, and a surrogate neutralization assay. : All three specimen types were collected from 34 COVID-19 recovered seropositive individuals (≥21 days post-symptoms). Using the Architect and Liaison assays, a positive qualitative SARS-CoV-2 IgG result was detected daily up to 12 FTCs and up to 10 days of storage at different temperatures. An additional 25 plasma samples consistently demonstrated detection of SARS-CoV-2 antibodies daily after 12 FTCs and storage at -20°C using two rapid test cassette assays (SD Biosensor and Hangzhou All Test), manual (Beijing Wantai) and surrogate neutralization (GenScript) ELISAs, and two high-throughput assays (Roche Elecsys nucleocapsid and spike). IgM antibodies were less frequently detected by one of the rapid test cassette assays. : Serum, plasma, and heparinized-plasma constitute reliable samples for SARS-CoV-2 antibody detection. In particular, the IgG response was stable and reliably detected after multiple FTCs and storage at common laboratory conditions. IgM detection was variable due to the labile nature of this antibody class.

Frequent screening of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) among asymptomatic populations using antigen-based point-of-care tests (APOCTs) is occurring globally with limited clinical performance data. The positive predictive value (PPV) of two APOCTs used in the asymptomatic screening of SARS-CoV-2 among health care workers (HCWs) at continuing care (CC) sites across AB, Canada, was evaluated. Between 22 February and 2 May 2021, CC sites implemented SARS-CoV-2 voluntary screening of their asymptomatic HCWs. On-site testing with Abbott Panbio or BD Veritor occurred on a weekly or twice-weekly basis.