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1.
Infect Control Hosp Epidemiol ; : 1-5, 2021 Aug 09.
Article in English | MEDLINE | ID: covidwho-1586120

ABSTRACT

OBJECTIVES: Performance characteristics of SARS-CoV-2 nucleic acid detection assays are understudied within contexts of low pre-test probability, including screening asymptomatic persons without epidemiological links to confirmed cases, or asymptomatic surveillance testing. SARS-CoV-2 detection without symptoms may represent presymptomatic or asymptomatic infection, resolved infection with persistent RNA shedding, or a false-positive test. This study assessed the positive predictive value of SARS-CoV-2 real-time reverse transcription polymerase chain reaction (rRT-PCR) assays by retesting positive specimens from 5 pre-test probability groups ranging from high to low with an alternate assay. METHODS: In total, 122 rRT-PCR positive specimens collected from unique patients between March and July 2020 were retested using a laboratory-developed nested RT-PCR assay targeting the RNA-dependent RNA polymerase (RdRp) gene followed by Sanger sequencing. RESULTS: Significantly fewer (15.6%) positive results in the lowest pre-test probability group (facilities with institution-wide screening having ≤3 positive asymptomatic cases) were reproduced with the nested RdRp gene RT-PCR assay than in each of the 4 groups with higher pre-test probability (individual group range, 50.0%-85.0%). CONCLUSIONS: Large-scale SARS-CoV-2 screening testing initiatives among low pre-test probability populations should be evaluated thoroughly prior to implementation given the risk of false-positive results and consequent potential for harm at the individual and population level.

2.
Ann Epidemiol ; 65: 84-92, 2022 01.
Article in English | MEDLINE | ID: covidwho-1525672

ABSTRACT

BACKGROUND: Inequities in the burden of COVID-19 were observed early in Canada and around the world, suggesting economically marginalized communities faced disproportionate risks. However, there has been limited systematic assessment of how heterogeneity in risks has evolved in large urban centers over time. PURPOSE: To address this gap, we quantified the magnitude of risk heterogeneity in Toronto, Ontario from January to November 2020 using a retrospective, population-based observational study using surveillance data. METHODS: We generated epidemic curves by social determinants of health (SDOH) and crude Lorenz curves by neighbourhoods to visualize inequities in the distribution of COVID-19 and estimated Gini coefficients. We examined the correlation between SDOH using Pearson-correlation coefficients. RESULTS: Gini coefficient of cumulative cases by population size was 0.41 (95% confidence interval [CI]:0.36-0.47) and estimated for: household income (0.20, 95%CI: 0.14-0.28); visible minority (0.21, 95%CI:0.16-0.28); recent immigration (0.12, 95%CI:0.09-0.16); suitable housing (0.21, 95%CI:0.14-0.30); multigenerational households (0.19, 95%CI:0.15-0.23); and essential workers (0.28, 95%CI:0.23-0.34). CONCLUSIONS: There was rapid epidemiologic transition from higher- to lower-income neighborhoods with Lorenz curve transitioning from below to above the line of equality across SDOH. Moving forward necessitates integrating programs and policies addressing socioeconomic inequities and structural racism into COVID-19 prevention and vaccination programs.


Subject(s)
COVID-19 , Geography , Humans , Ontario/epidemiology , Retrospective Studies , SARS-CoV-2 , Socioeconomic Factors
3.
CMAJ ; 193(28): E1098-E1106, 2021 07 19.
Article in French | MEDLINE | ID: covidwho-1435633

ABSTRACT

CONTEXTE: Le déploiement de mesures de gestion des éclosions de SRAS-CoV-2 dans les établissements de soins de longue durée en Ontario a permis d'en réduire la fréquence et la gravité. Nous décrivons ici les données épidémiologiques et de laboratoire d'une de ces premières éclosions en Ontario afin de déterminer les facteurs associés à son importance et les impacts des interventions progressives de lutte contre les infections appliquées pendant la durée de l'éclosion. MÉTHODES: Nous avons obtenu du bureau de santé la liste des cas et les données de l'éclosion afin de décrire les cas chez les résidents et le personnel, leur gravité et leur distribution dans le temps et à l'intérieur de l'établissement touché. Quand elles étaient disponibles, nous avons obtenu des données concernant les échantillons soumis au laboratoire de Santé publique Ontario et effectué un séquençage complet et une analyse phylogénétique des échantillons viraux de l'éclosion. RÉSULTATS: Sur les 65 résidents de l'établissement de soins de longue durée, 61 (94 %) ont contracté le SRAS-CoV-2, le taux de létalité étant de 45 % (28/61). Parmi les 67 employés initiaux, 34 (51 %) ont contracté le virus, et aucun n'est décédé. Lorsque l'éclosion a été déclarée, 12 employés, 2 visiteurs et 9 résidents présentaient des symptômes. Parmi les résidents, les cas se trouvaient dans 3 des 4 secteurs de l'établissement. L'analyse phylogénétique a montré une forte similitude des séquences; une seule autre souche de SRAS-CoV-2 génétiquement distincte a été identifiée chez un employé à la troisième semaine de l'éclosion. Après le déploiement de toutes les mesures de gestion de l'éclosion, aucun cas n'a été identifié parmi les 26 nouveaux employés appelés en renfort. INTERPRÉTATION: La propagation rapide et non détectée du virus dans un établissement de soins de longue durée a donné lieu à des taux élevés d'infection chez les résidents et le personnel. L'application progressive de mesures de gestion après le pic de l'éclosion a permis d'éviter la contamination du personnel appelé en renfort et fait désormais partie des politiques à long terme de prévention des éclosions en Ontario.


Subject(s)
COVID-19/epidemiology , Long-Term Care/statistics & numerical data , Pandemics , SARS-CoV-2 , Adult , Aged , Aged, 80 and over , Female , Humans , Male , Middle Aged , Ontario/epidemiology , Retrospective Studies , Young Adult
4.
CMAJ ; 193(19): E681-E688, 2021 05 10.
Article in English | MEDLINE | ID: covidwho-1231266

ABSTRACT

BACKGROUND: The implementation of outbreak management measures has decreased the frequency and severity of SARS-CoV-2 outbreaks in Ontario long-term care homes. We describe the epidemiological and laboratory data from one of the first such outbreaks in Ontario to assess factors associated with its severity, and the impact of progressive interventions for infection control over the course of the outbreak. METHODS: We obtained line list and outbreak data from the public health unit to describe resident and staff cases, severity and distribution of cases over time and within the outbreak facility. Where available, we obtained data on laboratory specimens from the Public Health Ontario Laboratory and performed whole genome sequencing and phylogenetic analysis of viral specimens from the outbreak. RESULTS: Among 65 residents of the long-term care home, 61 (94%) contracted SARS-CoV-2, with a case fatality rate of 45% (28/61). Among 67 initial staff, 34 (51%) contracted the virus and none died. When the outbreak was declared, 12 staff, 2 visitors and 9 residents had symptoms. Resident cases were located in 3 of 4 areas of the home. Phylogenetic analysis showed tight clustering of cases, with only 1 additional strain of genetically distinct SARS-CoV-2 identified from a staff case in the third week of the outbreak. No cases were identified among 26 new staff brought into the home after full outbreak measures were implemented. INTERPRETATION: Rapid and undetected viral spread in a long-term care home led to high rates of infection among residents and staff. Progressive implementation of outbreak measures after the peak of cases prevented subsequent staff cases and are now part of long-term care outbreak policy in Ontario.


Subject(s)
COVID-19/epidemiology , Long-Term Care , Nursing Homes , COVID-19/mortality , COVID-19/prevention & control , COVID-19/virology , Humans , Infection Control , Ontario/epidemiology , Pandemics , Phylogeny , SARS-CoV-2/genetics
5.
J Clin Virol Plus ; 1(1): 100010, 2021 Jun.
Article in English | MEDLINE | ID: covidwho-1141968

ABSTRACT

Background: Travel-related dissemination of SARS-CoV-2 continues to contribute to the global pandemic. A novel SARS-CoV-2 lineage (B.1.177) reportedly arose in Spain in the summer of 2020, with subsequent spread across Europe linked to travel by infected individuals. Surveillance and monitoring through the use of whole genome sequencing (WGS) offers insights into the global and local movement of pathogens such as SARS-CoV-2 and can detect introductions of novel variants. Methods: We analysed the genomes of SARS-CoV-2 sequenced for surveillance purposes from specimens received by Public Health Ontario (Sept 6 - Oct 10, 2020), collected from individuals in eastern Ontario, which comprised the study sample. Taxonomic lineages were identified using pangolin (v2.08) and phylogenetic analysis incorporated publicly available genomes covering the same time period as the study sample. Epidemiological data collected from laboratory requisitions and standard reportable disease case investigation was integrated into the analysis. Results: Genomic surveillance identified a COVID-19 case with SARS-CoV-2 lineage B.1.177 from an individual in eastern Ontario in late September, 2020. The individual had recently returned from Europe. Genomic analysis with publicly available data indicate the most closely related genomes to this specimen were from Southern Europe. Genomic surveillance did not identify further cases with this lineage. Conclusions: Genomic surveillance allowed for early detection of a novel SARS-CoV-2 lineage in Ontario which was deemed to be travel related. This type of genomic-based surveillance is a key tool to measure the effectiveness of public health measures such as mandatory self-isolation for returned travellers, aimed at preventing onward transmission of newly introduced lineages of SARS-CoV-2.

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