A longitudinal seroepidemiology study to evaluate antibody response to SARS-CoV-2 virus infection and vaccination in children in Calgary, Canada from July 2020 to April 2022: Alberta COVID-19 Childhood Cohort (AB3C) Study.

BACKGROUND: Measurement of SARS-CoV-2 antibody seropositivity is important to accurately understand exposure to infection and/or vaccination in specific populations. This study aimed to estimate the serologic response to SARS-CoV-2 virus infection and vaccination in children in Calgary, Alberta over a two-year period. METHODS: Children with or without prior SARS-CoV-2 infections, were enrolled in Calgary, Canada in 2020. Venous blood was sampled 4 times from July 2020 to April 2022 for SARS-CoV-2 nucleocapsid and spike antibodies. Demographic and clinical information was obtained including SARS-CoV-2 testing results and vaccination records. RESULTS: 1035 children were enrolled and 88.9% completed all 4 visits; median age 9 years (IQR: 5,13); 519 (50.1%) female; and 815 (78.7%) Caucasian. Before enrolment, 118 (11.4%) had confirmed or probable SARS-CoV-2. By April 2022, 39.5% of previously uninfected participants had a SARS-CoV-2 infection. Nucleocapsid antibody seropositivity declined to 16.4% of all infected children after more than 200 days post diagnosis. Spike antibodies remained elevated in 93.6% of unvaccinated infected children after more than 200 days post diagnosis. By April 2022, 408 (95.6%) children 12 years and older had received 2 or more vaccine doses, and 241 (61.6%) 5 to 11 year-old children had received 2 vaccine doses. At that time, all 685 vaccinated children had spike antibodies, compared with 94/176 (53.4%) of unvaccinated children. CONCLUSIONS: In our population, after the first peak of Omicron variant infections and introduction of COVID-19 vaccines for children, all vaccinated children, but just over one-half of unvaccinated children, had SARS-CoV-2 spike antibodies indicating infection and/or vaccination, highlighting the benefit of vaccination. It is not yet known whether a high proportion of seropositivity at the present time predicts sustained population-level protection against future SARS-CoV-2 transmission, infection or severe COVID-19 outcomes in children.

Clinical evaluation of nasopharyngeal, midturbinate nasal and oropharyngeal swabs for the detection of SARS-CoV-2.

In the setting of supply chain shortages of nasopharyngeal (NP) swabs, we sought to compare the ability of nasopharyngeal, midturbinate nasal, and oropharyngeal swabs (NPS, MTS, and OPS) to detect SARS-CoV-2. Community and hospitalized participants post-COVID-19 diagnosis were swabbed and tested for SARS-CoV-2 by PCR. Thirty-six participants had all 3 swabs collected. Using detection at any site as the standard, the percent positive agreements were 90% (95% CI 74.4-96.5), 80% (70.3-94.7) and 87% (62.7-90.5) for NPS, MTS, and OPS, respectively. Subsequently, 43 participants had OPS and NPS collected. Thirty-nine were positive with a percent positive agreement of 82.1% (95% CI 67.3-91.0) for OPS and 87.2% (73.3-94.4) for NPS. Combining all 79 patients tested, 67 were positive at either site with a positive agreement was 86.5% (76.4-92.7) for OPS and 91.1% (81.8-95.8) for NPS. OPS are an acceptable alternative to NPS for the detection of SARS-CoV-2 infections.

Detection and quantification of infectious severe acute respiratory coronavirus-2 in diverse clinical and environmental samples.

To explore the potential modes of Severe Acute Respiratory Coronavirus-2 (SARS-CoV-2) transmission, we collected 535 diverse clinical and environmental samples from 75 infected hospitalized and community patients. Infectious SARS-CoV-2 with quantitative burdens varying from 5 plaque-forming units/mL (PFU/mL) up to 1.0 × 106 PFU/mL was detected in 151/459 (33%) of the specimens assayed and up to 1.3 × 106 PFU/mL on fomites with confirmation by plaque morphology, PCR, immunohistochemistry, and/or sequencing. Infectious virus in clinical and associated environmental samples 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. SARS-CoV-2 isolated from patient respiratory tract samples caused illness in a hamster model with a minimum infectious dose of ≤ 14 PFU. Together, our findings offer compelling evidence that large respiratory droplet and contact (direct and indirect i.e., fomites) are important modes of SARS-CoV-2 transmission.

Prolonged SARS-CoV-2 infection following rituximab treatment: clinical course and response to therapeutic interventions correlated with quantitative viral cultures and cycle threshold values.

BACKGROUND: Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA is completed through reverse transcriptase-PCR (RT-PCR) from either oropharyngeal or nasopharyngeal swabs, critically important for diagnostics but also from an infection control lens. Recent studies have suggested that COVID-19 patients can demonstrate prolonged viral shedding with immunosuppression as a key risk factor. CASE PRESENTATION: We present a case of an immunocompromised patient with SARS-CoV-2 infection demonstrating prolonged infectious viral shedding for 189 days with virus cultivability and clinical relapse with an identical strain based on whole genome sequencing, requiring a multi-modal therapeutic approach. We correlated clinical parameters, PCR cycle thresholds and viral culture until eventual resolution. CONCLUSIONS: We successfully demonstrate resolution of viral shedding, administration of COVID-19 vaccination and maintenance of viral clearance. This case highlights implications in the immunosuppressed patient towards infection prevention and control that should consider those with prolonged viral shedding and may require ancillary testing to fully elucidate viral activity. Furthermore, this case raises several stimulating questions around complex COVID-19 patients around the role of steroids, effect of antiviral therapies in absence of B-cells, role for vaccination and the requirement of a multi-modal approach to eventually have successful clearance of the virus.

Development and validation of RT-PCR assays for testing for SARS-CoV-2.

Background: The recent emergence and rapid global spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) demonstrates the urgent need for laboratory-developed assays for clinical diagnosis and public health interventions in the absence of commercial assays. Methods: We outline the progression of reverse-transcriptase polymerase chain reaction (RT-PCR) assays that were developed and validated at the Alberta Precision Laboratories, Public Health Laboratory, Alberta, Canada, to respond to this pandemic. Initially, testing was performed using SARS-CoV-2-specific and pan-coronavirus gel-based assays that were soon superseded by real-time RT-PCR assays targeting the envelope and RNA-dependent RNA polymerase genes to accommodate the high anticipated volumes of samples. Throughput was further enhanced by multiplexing the different targets together with the co-detection of an internal extraction control. Results: These assays are comparable in sensitivity and specificity to the assays recommended by the World Health Organization and the US Centers for Disease Control and Prevention. Conclusions: The availability of real-time RT-PCR assays early in the pandemic was essential to provide valuable time to local health authorities to contain transmission and prepare for appropriate response strategies.

Historique: La récente émergence et la propagation mondiale rapide du coronavirus 2 du syndrome respiratoire aigu sévère (SARS-CoV-2) a démontré l'urgence de créer des dosages en laboratoire pour poser un diagnostic clinique et adopter des interventions sanitaires en l'absence de dosages commerciaux. Méthodologie: Les chercheurs exposent la progression des dosages d'amplification en chaîne par polymérase couplée à la transcriptase inverse (RT-PCR) mis au point et validés par les Alberta Precision Laboratories du Laboratoire de santé publique de l'Alberta, au Canada, pour répondre à cette pandémie. Les tests ont d'abord été effectués au moyen de dosages sur gel spécifiques au SARS-CoV-2 ou décelant tous les coronavirus, mais ont vite été remplacés par des dosages RT-PCR en temps réel ciblant l'enveloppe et les gènes d'ARN polymérase sous la dépendance d'ARN pour répondre au fort volume anticipé d'échantillons. Le criblage a également été renforcé par le multiplexage conjoint des différentes cibles et la codétection d'un contrôle d'extraction interne. Résultats: Ces dosages ont une sensibilité et une spécificité comparables à ceux recommandés par l'Organisation mondiale de la Santé et les Centers for Disease Control and Prevention des États-Unis. Conclusions: Il était essentiel de disposer de dosages RT-PCR au début de la pandémie pour que les autorités sanitaires locales puissent profiter de temps précieux pour contenir la transmission et préparer les stratégies de réponse appropriées.

COVID-19 outbreak among physicians at a Canadian curling bonspiel: a descriptive observational study.

BACKGROUND: Transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is known to occur among individuals who congregate in large groups, especially during indoor activities. Our objective was to provide a detailed clinical description of an outbreak of coronavirus disease 2019 (COVID-19) that occurred after a sporting and social event during the early days of the pandemic. METHODS: We conducted a descriptive study of a curling bonspiel in Edmonton held on Mar. 11-14, 2020. We used standardized interviews between Apr. 17 and May 5, 2020, to collect demographic data, travel history, symptoms (type, onset and duration), self-reported testing results for SARS-CoV-2 ribonucleic acid (RNA) using reverse transcription polymerase chain reaction (RT-PCR), and clinical outcomes. We also obtained results of convalescent SARS-CoV-2 immunoglobulin G serology. RESULTS: All 73 curlers (55 active health care workers) who participated in the bonspiel were interviewed for the study. Convalescent SARS-CoV-2 immunoglobulin G serology was completed in 62 (85%) participants. Of the 73 participants (55 [75%] male, median age 51 [range 26-79] yr, 58 [79%] physicians), 40 curlers (55%) tested positive for SARS-CoV-2 RNA by RT-PCR; an additional 16 participants developed symptoms but had negative swabs or were not tested (14 were probable cases), for a 74% attack rate (confirmed or probable cases). Anosmia with ageusia or dysgeusia occurred in 39 of 54 (72%) confirmed or probable cases. The clinical course was mild in most participants (1 emergency visit, no hospital admissions). Transmission likely occurred from multiple individuals with minor nonspecific symptoms during the event, possibly during shared meals. INTERPRETATION: The 74% attack rate (confirmed or probable cases) highlights the infectivity of SARS-CoV-2 during sporting and social events. This reinforces the need for public health measures (masking, physical distancing and limiting the size of social gatherings) during future waves of COVID-19 in Canada.

COVID-19 screening of asymptomatic patients admitted through emergency departments in Alberta: a prospective quality-improvement study.

BACKGROUND: The prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection among asymptomatic patients admitted to hospital has implications for personal protective equipment use, testing strategy and confidence in the safety of acute care services. Our aim was to estimate the positivity rate of reverse transcription polymerase chain reaction (RT-PCR) testing among people admitted to hospital without symptoms of coronavirus disease 2019 (COVID-19) in Alberta, Canada. METHODS: Between Apr. 9 and May 24, 2020, we screened for COVID-19 symptoms and tested for SARS-CoV-2 infection in all consecutive adult patients (≥ 18 yr) admitted via emergency department to 3 Alberta hospitals. We summarized the parameters of the epidemic curve and assessed the performance of symptom screening versus RT-PCR results on nasopharyngeal or oropharyngeal swab samples. RESULTS: The study period encompassed Alberta's initial epidemic curve, with peak active cases per 100 000 of 71.4 (0.07%) on Apr. 30, 2020, and 14.7 and 14.6 at the beginning (Apr. 9, 2020) and end (May 24, 2020), respectively. Testing for SARS-CoV-2 infection (64.9% throat and 35.1% nasopharyngeal swabs) was done on 3375 adults (mean age 51, standard deviation 21, yr; 51.5% men). None of the asymptomatic patients (n = 1814) tested positive, and 71 of those with symptoms tested positive (n = 1561; 4.5%, 95% confidence interval [CI] 3.6%-5.7%). Sensitivity of symptom screening (v. RT-PCR) was 100% (95% CI 95%-100%), and specificity was 55% (95% CI 53%-57%). Posttest probabilities for prevalence of SARS-CoV-2 infection ranging from 1.5 to 14 times the peak prevalence of active cases during the study did not change when we assumed lower sensitivity (92%). INTERPRETATION: In a region with low disease prevalence where protocolized symptom assessment was in place during the admission process, we did not identify people admitted to hospital without COVID-19 symptoms who were RT-PCR positive. There may not be additive benefit to universal testing of asymptomatic patients on hospital admission in a setting of low pretest probability and strong public health containment.

A Public Health Laboratory Response to the Pandemic.

An outbreak of coronavirus disease 2019 (COVID-19) caused by a novel coronavirus (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) began in Wuhan, Hubei, China, in December 2019 and spread rapidly worldwide. The response by the Alberta Precision Laboratories, Public Health Laboratory (ProvLab), AB, Canada, included the development and implementation of nucleic acid detection-based assays and dynamic changes in testing protocols for the identification of cases as the epidemic curve increased exponentially. This rapid response was essential to slow down and contain transmission and provide valuable time to the local health authorities to prepare appropriate response strategies. As of May 24, 2020, 236,077 specimens were tested, with 6,475 (2.74%) positives detected in the province of Alberta, Canada. Several commercial assays are now available; however, the response from commercial vendors to develop and market validated tests is a time-consuming process. In addition, the massive global demand made it difficult to secure a reliable commercial supply of testing kits and reagents. A public health laboratory serves a unique and important role in the delivery of health care. One of its functions is to anticipate and prepare for novel emerging pathogens with a plan for pandemic preparedness. Here, we outline the response that involved the development and deployment of testing methodologies that evolved as SARS-CoV-2 spread worldwide, the challenges encountered, and mitigation strategies. We also provide insight into the organizational structure of how a public health response is coordinated in Alberta, Canada, and its benefits.

Evaluation of Six Commercial Mid- to High-Volume Antibody and Six Point-of-Care Lateral Flow Assays for Detection of SARS-CoV-2 Antibodies.

Coronavirus disease (COVID) serological tests are essential to determine the overall seroprevalence of a population and to facilitate exposure estimates within that population. We performed a head-to-head assessment of enzyme immunoassays (EIAs) and point-of-care lateral flow assays (POCTs) to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies. Demographics, symptoms, comorbidities, treatment, and mortality of patients whose sera were used were also reviewed. Six EIAs (Abbott, Affinity, Bio-Rad, DiaSorin, Euroimmun, and Roche) and six POCTs (BTNX, Biolidics, Deep Blue, Genrui, Getein BioTech, and Innovita) were evaluated for the detection of SARS-CoV-2 antibodies in known COVID-19-infected individuals. Sensitivity of EIAs ranged from 50 to 100%, with only four assays having overall sensitivities of >95% after 21 days after symptom onset. Notably, cross-reactivity with other respiratory viruses (parainfluenza virus [PIV-4] [n = 5], human metapneumovirus [hMPV] [n = 3], rhinovirus/enterovirus [n = 1], CoV-229E [n = 2], CoV-NL63 [n = 2], and CoV-OC43 [n = 2]) was observed; however, overall specificity of EIAs was good (92 to 100%; all but one assay had specificity above 95%). POCTs were 0 to 100% sensitive >21 days after onset, with specificity ranging from 96 to 100%. However, many POCTs had faint banding and were often difficult to interpret. Serology assays can detect SARS-CoV-2 antibodies as early as 10 days after symptom onset. Serology assays vary in their sensitivity based on the marker (IgA/IgM versus IgG versus total) and by manufacturer; however, overall only 4 EIAs and 4 POCTs had sensitivities of >95% >21 days after symptom onset. Cross-reactivity with other seasonal coronaviruses is of concern. Serology assays should not be used for the diagnosis of acute infection but rather in carefully designed serosurveys to facilitate understanding of seroprevalence in a population and to identify previous exposure to SARS-CoV-2.

Hemorrhagic encephalopathy associated with COVID-19.

The mechanisms for neurological complications of COVID-19, the disease caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), are not yet well understood. We present a critically ill man with a COVID-19-associated hemorrhagic encephalopathy. SARS-CoV-2 RNA was not detected in cerebrospinal fluid (CSF) or blood. CSF analyses suggested dysregulation of pro-inflammatory cytokine pathways, particularly tumor necrosis factor-α and interleukin-6, consistent with a cytokine release syndrome. The patient gradually recovered with supportive care and neurological rehabilitation. Awareness of this clinical entity may facilitate the identification of patients with a potentially remediable cause of encephalopathy in COVID-19.