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BACKGROUNDPoint of Care SARS-CoV-2 devices, such as the Abbott ID NOW have great potential, to help combat the COVID-19 pandemic. Starting in December, 2020, the ID NOW was implemented throughout the province of Alberta, Canada (population 4.4 million) in various settings. We aimed to assess the ID NOW performance during the BA.1 Omicron wave and compare it to previous waves. METHODSThe ID NOW was assessed in two distinct locations among symptomatic individuals: acute care (emergency room, urgent care, and hospitalized patients) and community assessment centres (AC) during the period January 5 - 18, 2022. Starting January 5, Omicron represented >95% of variants detected in our population. For every individual tested, two swabs were collected: one for ID NOW testing and the other for either reverse-transcriptase polymerase chain reaction (RT-PCR) confirmation of negative ID NOW results or for variant testing of positive ID NOW results. RESULTSA total of 3,041 paired samples were analyzed (1,139 RT-PCR positive). 1,873 samples were from 42 COVID-19 AC and 1,168 from 69 rural hospitals. ID NOW sensitivity for symptomatic individuals presenting to community AC and patients in hospital was 96.0% [95% confidence interval (CI) 94.5-97.3%, n=830 RT-PCR positive], and 91.6% (95% CI 87.9-94.4%, n=309 RT-PCR positive), respectively. SARS-CoV 2 positivity rate was very high for both populations (44.3% at AC, 26.5% in hospital). CONCLUSIONSSensitivity of ID NOW SARS-CoV-2, compared to RT-PCR, is very high during the BA.1 Omicron wave, and is significantly higher when compared to previous SARS-CoV-2 variant waves.
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Few studies have assessed for infectious SARS-CoV-2 in multiple types of clinical and environmental samples. In almost 500 samples from 75 hospitalized and community cases, we detected infectious virus with quantitative burdens varying from 5.0 plaque-forming units/mL (PFU/mL) up to 1.0x106 PFU/mL in clinical specimens and up to 1.3x106 PFU/mL on fomites including facial tissues, nasal prongs, call bells/cell phones, dentures, and sputum deposits with confirmation by plaque morphology, PCR, immunohistochemistry, and sequencing. Expectorated sputum samples had the highest percentage of positive samples and virus titers (71%, 2.9x102 to 5.2x105 PFU/mL), followed by saliva (58%, 10 to 4.6x104 PFU/mL), and cough samples without sputum (19%, 5 to 1.9x103 PFU/mL). We also detected infectious SARS-CoV-2 from patients hands (28%, 60 to 2.3x102 PFU/mL) but no infectious virus was found in continuous speech samples despite finding high levels of infectious virus in the associated nasopharynx, throat, or saliva specimens. We demonstrated infectious virus stability in clinical samples, including those dried for prolonged periods of time. Infectious virus correlated with time since symptom onset with no detection after 7-8 days in immunocompetent hosts and with N-gene based Ct values [≤] 25 significantly predictive of yielding plaques in culture. One PFU was associated with [~]105 copies of N gene RNA across a diversity of samples and times from symptom onset. Clinical salivary isolates caused illness in a hamster model with a minimum infectious dose of [≤]14 PFU/mL. Our findings of high quantitative burdens of infectious virus, stability even with drying, and a very low minimal infectious dose suggest multiple modes of transmission are exploited by SARS-CoV-2, including direct contact, large respiratory droplet, and fomite transmission and in the context of a high binding avidity to human cellular receptors, offer an explanation of the high contagiousness of this virus. Research in ContextO_ST_ABSEvidence before this studyC_ST_ABSWe searched the literature for articles that reported on the presence of infectious SARS-CoV-2 in patients samples from clinical and environmental sources. We found several key primary studies and systematic reviews providing valuable background on the carriage of infectious virus and the correlation with cycle threshold (Ct) and/or RNA copies/mL on PCR testing. Clinical correlations with respect to underlying clinical conditions and details on the onset of illness were not commonly reported with respect to the timing of obtaining specimens for culture. Few studies carefully assessed the presence of infectious virus in cough samples, sputum, nasal secretions, hands, and common high touch surfaces. A few published works were found on factors which may be associated with shedding of infectious virus. Added value of this studyWe assessed the presence of infectious virus shedding in almost 500 specimens from 75 patients with COVID-19 in both the hospital and community setting. High titers of infectious virus were detected in multiple clinical and environmental samples. The longest duration of recovery of infectious virus in a fomite sample was from a dried facial tissue found at a patients bedside table, used at least 9 hours earlier. Cough specimens revealed infectious virus in 28% of specimens with infectious virus titers as high as 5.2x105 PFU/mL. Hand samples contained infectious virus with titers ranging from 55 to 2.3x102 PFU/mL. Infectious viral loads correlated with N-gene based Ct values and showed that Ct values [≤] 25 were predictive of yielding plaques in culture. These experiments also showed that infectious virus is most often recovered during a 7 to 8-day period following illness onset in immunocompetent persons, and during that time the ratio of RNA/PFU in these clinical specimens varies relatively little, with a ratio [~]160,000:1. Infectious virus may be recovered for weeks to several months in immunosuppressed persons. We also showed that virus recovered from saliva specimens, representing a commonly encountered fomite sample, caused infection in the Syrian hamster model, hence demonstrating the infectiousness of the virus sourced from this type of specimen. A challenge dose as low as 14 PFU/mL yielded infection in this model. Implications of all the available evidenceWe have shown that SARS-CoV-2 is relatively easy to culture when obtained early in the course of illness and there are high levels of cultivatable SARS-CoV-2 in multiple types of clinical specimens and common fomites, including high-touch surfaces and demonstrated their infectiousness in a mammalian host. Our results demonstrate the presence of high quantitative burdens of SARS-CoV-2 in sputum, saliva, and droplets from coughing, which would lend support to large respiratory droplet transmission, hands which would support direct contact transmission, and fomites which would promote indirect contact transmission. We were unable to detect any infectious virus in continuous speech samples which suggests that brief conversations, without coughing or sneezing, pose little risk of transmitting SARS-CoV-2. Our findings provide an explanation for the high contagiousness of this virus and support current public health measures and infection prevention and control guidelines including physical distancing, hand hygiene, masking, and cleaning and disinfection.
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OBJECTIVESFrequent screening of SARS-CoV-2 among asymptomatic populations using antigen-based point of care tests (APOCT) is occurring globally with limited clinical performance data. The positive predictive value (PPV) of two APOCT used in the asymptomatic screening of SARS-CoV-2 among healthcare workers (HCW) at continuing care (CC) sites across Alberta, Canada was evaluated. METHODSBetween February 22 and May 2, 2021, CC sites implemented SARS-CoV-2 voluntary screening of their asymptomatic HCW. Onsite testing with Abbott Panbio or BD Veritor occurred on a weekly or twice weekly basis. Positive APOCT were confirmed with a real-time reverse-transcriptase polymerase chain reaction (rRT-PCR) reference method. RESULTSA total of 71,847 APOCT (17,689 Veritor and 54,158 Panbio) were performed among 369 CC sites. Eighty-seven (0.12%) APOCT were positive, of which 39 (0.05%) confirmed as true positives using rRT-PCR. Use of the Veritor and Panbio resulted in a 76.6% and 30.0% false positive detection, respectively (p<0.001). This corresponded to a 23.4% and 70.0% PPV for the Veritor and Panbio, respectively. CONCLUSIONSFrequent screening of SARS-CoV-2 among asymptomatic HCW in CC, using APOCT, resulted in a very low detection rate and a high detection of false positives. Careful assessment between the risks vs benefits of APOCT programs in this population needs to be thoroughly considered before implementation.
