Viral dynamics of the SARS-CoV-2 Omicron Variant in Paediatric Patients; A prospective cohort study.

BACKGROUND: There are limited data on the viral dynamics of SARS-CoV-2 in children. Understanding viral load changes over the course of illness and duration of viral shedding may provide insight into transmission dynamics to inform public health and infection control decisions. METHODS: We conducted a prospective cohort study of children 18 years and younger with PCR confirmed SARS-CoV-2 between February 1, 2022 and March 14, 2022. SARS-CoV-2 testing occurred on daily samples for 10 days; a subset of participants completed daily rapid antigen testing (RAT). Viral RNA trajectories were described in relation to symptom onset and resolution. The associations between both time since symptom onset/resolution and non-infectious viral load were evaluated using a Cox proportional hazards model. FINDINGS: Among 101 children aged 2 to 17 years, the median time to study-defined non-infectious viral load was 5 days post symptom onset, with 75% meeting this threshold by 7 days, and 90% by 10 days. On the day of and day after symptom resolution, 43 of 87 (49%) and 52 (60%) had met the non-infectious thresholds, respectively. Of the 50 participants completing RAT, positivity at symptom onset and on the day after symptom onset was 67% (16/24) and 75% (14/20). On the first day where the non-infectious threshold was met, 61% (n = 27/44) of participant RAT results were positive. INTERPRETATION: Children often met the study-defined non-infectiousness threshold on the day after symptom resolution. RAT tests were often negative early in the course of illness and should not be relied on to exclude infection. CLINICAL TRIALS REGISTRATION: NCT05240183.

Utility of SARS-CoV-2 Genomic Sequencing for Understanding Transmission and School Outbreaks.

OBJECTIVE: An understanding of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) transmission in schools is important. It is often difficult, using epidemiological information alone, to determine whether cases associated with schools represent multiple introductions from the community or transmission within the school. We describe the use of whole genome sequencing (WGS) in multiple schools to investigate outbreaks of SARS-CoV-2 in the pre-Omicron period. STUDY DESIGN: School outbreaks were identified for sequencing by local public health units based on multiple cases without known epidemiological links. Cases of SARS-CoV-2 from students and staff from 4 school outbreaks in Ontario underwent WGS and phylogenetic analysis. The epidemiological clinical cohort data and genomic cluster data are described to help further characterize these outbreaks. RESULTS: A total of 132 positive SARS-CoV-2 cases among students and staff from 4 school outbreaks were identified with 65 (49%) of cases able to be sequenced with high-quality genomic data. The 4 school outbreaks consisted of 53, 37, 21 and 21 positive cases; within each outbreak there were between 8 and 28 different clinical cohorts identified. Among the sequenced cases, between 3 and 7 genetic clusters, defined as different strains, were identified in each outbreak. We found genetically different viruses within several clinical cohorts. CONCLUSIONS: WGS, together with public health investigation, is a useful tool to investigate SARS-CoV-2 transmission within schools. Its early use has the potential to better understand when transmission may have occurred, can aid in evaluating how well mitigation interventions are working and has the potential to reduce unnecessary school closures when multiple genetic clusters are identified.

The viral hepatitis B care cascade: A population-based comparison of immigrant groups.

BACKGROUND AND AIMS: The global burden of viral hepatitis B is substantial, and monitoring infections across the care cascade is important for elimination efforts. There is little information on care disparities by immigration status, and we aimed to quantify disease burden among immigrant subgroups. APPROACH AND RESULTS: In this population-based, retrospective cohort study, we used linked laboratory and health administrative records to describe the HBV care cascade in five distinct stages: (1) lifetime prevalence; (2) diagnosis; (3) engagement with care; (4) treatment initiation; and (5) treatment continuation. Infections were identified based on at least one reactive antigen or nucleic acid test, and lifetime prevalence was estimated as the sum of diagnosed and estimated undiagnosed cases. Care cascades were compared between long-term residents and immigrant groups, including subgroups born in hepatitis B endemic countries. Stratified analyses and multivariable Poisson regression were used to identify drivers for cascade progression. Between January 1997 and December 2014, 2,014,470 persons were included, 50,475 with infections, of whom 30,118 were engaged with care, 11,450 initiated treatment, and 6554 continued treatment >1 year. Lifetime prevalence was estimated as 163,309 (1.34%) overall, 115,722 (3.42%) among all immigrants, and 50,876 (9.37%) among those from highly endemic countries. Compared to long-term residents, immigrants were more likely to be diagnosed (adjusted rate ratio [aRR], 4.55; 95% CI, 4.46, 4.63), engaged with care (aRR, 1.07; 95% CI, 1.04, 1.09), and initiate treatment (aRR, 1.09; 95% CI, 1.03, 1.16). CONCLUSIONS: In conclusion, immigrants fared well compared to long-term residents along the care cascade, having higher rates of diagnosis and slightly better measures in subsequent cascade stages, although intensified screening efforts and better strategies to facilitate linkage to care are still needed.

Impact of coronavirus disease 2019 (COVID-19) pre-test probability on positive predictive value of high cycle threshold severe acute respiratory coronavirus virus 2 (SARS-CoV-2) real-time reverse transcription polymerase chain reaction (RT-PCR) test results.

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.

Provincial implementation supports for socio-demographic data collection during COVID-19 in Ontario's public health system.

SETTING: The Ontario government implemented a regulatory change to mandate the collection of socio-demographic (SD) data for individuals who tested positive for COVID-19. This change was informed by evidence of COVID-19's disproportionate impact on marginalized communities and calls for broader collection of SD data. Given the scarcity of similar efforts, there is a significant knowledge gap around implementing standardized SD data collection in public health settings. INTERVENTION: Public Health Ontario provided collaborative support for the implementation of SD data collection, grounded in health equity principles, evidence, and best practices. We supported the addition of SD fields in Ontario's COVID-19 data collection systems, issued data entry guidance, hosted webinars for training and learning exchange, and published a resource to support the data collection process. The current focus is on building sustainability and quality improvement through continued engagement of public health units. OUTCOMES: By November 28, 2020, almost 80% of COVID-19 cases had information recorded for at least one SD question (individual questions, range 46.8-67.0%). We hosted three webinars for the field, and the data collection resource was viewed almost 650 times. Practitioners continue to express needs for support on applying equity principles to data analysis and interpretation, and community engagement on data collection and use. IMPLICATIONS: Sharing knowledge on responsive implementation supports in collaboration with the field and using current evidence and guidance will strengthen public health practice for SD data collection. Laying this groundwork will also improve the likelihood of success and sustainability of these equity-focused efforts.

RéSUMé: LIEU: Le gouvernement de l'Ontario a appliqué une modification réglementaire exigeant la collecte de données sociodémographiques (SD) sur les personnes testées positives pour la COVID-19. Cette modification découle des preuves de l'impact disproportionné de la COVID-19 dans les populations marginalisées et appelle à une collecte élargie des données SD. Comme les démarches similaires sont rares, il y a de grandes lacunes au sujet de la mise en œuvre de la collecte de données SD standardisées dans les milieux de la santé publique. INTERVENTION: Santé publique Ontario a collaboré à la mise en œuvre d'une collecte de données SD ancrée dans les principes, les données probantes et les pratiques exemplaires de l'équité en santé. Nous avons appuyé l'ajout de champs SD dans les systèmes ontariens de collecte de données sur la COVID-19, fourni des orientations sur la saisie des données, organisé des webinaires de formation et d'échange de connaissances et publié un document à l'appui du processus de collecte de données. La priorité est actuellement accordée au renforcement de la durabilité et à l'amélioration de la qualité grâce à la participation continue des bureaux de santé publique. RéSULTATS: Au 28 novembre 2020, pour près de 80 % des cas de COVID-19, il existait des informations sur au moins une question SD (questions individuelles, intervalle de 46,8 à 67,0 %). Nous avions organisé trois webinaires pour le personnel de terrain, et notre document sur la collecte de données avait été consulté près de 650 fois. Les praticiens continuent à nous demander de l'aide pour appliquer les principes d'équité à l'analyse et à l'interprétation des données et pour faire participer les communautés à la collecte et à l'utilisation des données. CONSéQUENCES: Le partage des connaissances sur les supports de mise en œuvre adaptés, en collaboration avec le terrain et en faisant appel aux connaissances et aux orientations actuelles, renforcera la collecte de données SD dans la pratique en santé publique. En posant ces bases, nous améliorons aussi les chances de réussite et la durabilité de ces démarches axées sur l'équité.

A public health response to a newly diagnosed case of hepatitis C associated with lapse in Infection Prevention and Control practices in a dental setting in Ontario, Canada.

BACKGROUND: Haliburton, Kawartha, Pine Ridge District Health Unit (HKPRDHU) investigated an exposure in an Ontario operatory dental facility related to a newly diagnosed hepatitis C virus (HCV) infection caused by a virus with an uncommon hepatitis C genotype. Lapses in Infection Prevention and Control (IPAC) and a second epidemiologically-linked case (with the same uncommon hepatitis C genotype) were identified, prompting a broader public health response and outbreak investigation. OBJECTIVES: a) To describe the investigation of a newly diagnosed case of hepatitis C; b) to describe the broader public health response, and c) to address a paucity in the literature related to the risk of disease transmission in dental settings due to IPAC lapses. METHODS: A collaborative approach with two dental practices, public health partners and regulatory bodies was used. An IPAC inspection was completed to determine and mitigate the risk of blood borne infection transmission within the facilities. Appropriate protocols were followed for the IPAC investigation and public health response. RESULTS: The investigation identified a risk of potential HCV transmission between two cases linked to the same dental facility. There were no other epi-linked cases of HCV identified. Challenges included a lack of adherence to IPAC standards in one of the dental settings and awareness in the dental community regarding HCV transmission, coordination with regulatory bodies and public health experts and low uptake of laboratory testing by patients. CONCLUSION: Despite the unique challenges associated with the investigation, HKPRDHU conducted a successful IPAC lapse investigation and public health response. Public health units need to maintain collaborative approaches with regulated health professionals, their regulatory bodies and public health experts.

Viral hepatitis C cascade of care: A population-level comparison of immigrant and long-term residents.

BACKGROUND & AIMS: Viral hepatitis C represents a major global burden, particularly among immigrant-receiving countries such as Canada, where knowledge of disparities in hepatitis C virus among immigrant groups for micro-elimination efforts is lacking. We quantify the hepatitis C cascades of care among immigrants and long-term residents prior to the introduction of direct-acting antiviral medications. METHODS: Using laboratory and health administrative records, we described the hepatitis C virus cascades of care in terms of diagnosis, engagement with care, treatment initiation, and clearance in Ontario, Canada (1997-2014). We stratified the cascade by immigrant and long-term resident groups and identify drivers at each stage using multivariable Poisson regression. RESULTS: We included 940 245 individuals in the study with an estimated hepatitis C prevalence of 167 923 (1.4%) overall, 23 759 (0.7%) among all immigrants, and 6019 (1.1%) among immigrants from hepatitis C endemic countries. Overall there were 104 616 individuals with reactive antibody results, 73 861 tested for viral RNA, 52 388 with viral RNA detected, 50 805 genotyped, 13 159 on treatment and 3919 with evidence of viral clearance. Compared to long-term residents, immigrants showed increased nucleic-acid testing (aRR: 1.09 [95%CI: 1.08, 1.10]), treatment initiation (aRR: 1.46 [95%CI: 1.38, 1.54]), and higher clearance rates (aRR: 1.07 [95%CI: 1.03, 1.11]). CONCLUSIONS: Hepatitis C virus is more prevalent among long-term residents compared to immigrants overall, however, immigrants from endemic countries are an important subgroup to consider for future screening and linkage to care initiatives. These findings are prior to the introduction of newer medications and provide a population-based benchmark for follow-up studies and evaluation of treatment programs and surveillance activities.

Validating viral hepatitis B and C diagnosis codes: a retrospective analysis using Ontario's health administrative data.

OBJECTIVE: We aimed to determine the criterion validity of using diagnosis codes for hepatitis B virus (HBV) and hepatitis C virus (HCV) to identify infections. METHODS: Using linked laboratory and administrative data in Ontario, Canada, from January 2004 to December 2014, we validated HBV/HCV diagnosis codes against laboratory-confirmed infections. Performance measures (sensitivity, specificity, and positive predictive value) were estimated via cross-validated logistic regression and we explored variations by varying time windows from 1 to 5 years before (i.e., prognostic prediction) and after (i.e., diagnostic prediction) the date of laboratory confirmation. Subgroup analyses were performed among immigrants, males, baby boomers, and females to examine the robustness of these measures. RESULTS: A total of 1,599,023 individuals were tested for HBV and 840,924 for HCV, with a resulting 41,714 (2.7%) and 58,563 (7.0%) infections identified, respectively. HBV/HCV diagnosis codes ± 3 years of laboratory confirmation showed high specificity (99.9% HBV; 99.8% HCV), moderate positive predictive value (70.3% HBV; 85.8% HCV), and low sensitivity (12.8% HBV; 30.8% HCV). Varying the time window resulted in limited changes to performance measures. Diagnostic models consistently outperformed prognostic models. No major differences were observed among subgroups. CONCLUSION: HBV/HCV codes should not be the only source used for monitoring the population burden of these infections, due to low sensitivity and moderate positive predictive values. These results underscore the importance of ongoing laboratory and reportable disease surveillance systems for monitoring viral hepatitis in Ontario.

RéSUMé: OBJECTIF: Nous avons cherché à déterminer le critère de validité de l'utilisation des codes de diagnostic du virus de l'hépatite B (VHB) et du virus de l'hépatite C (VHC) pour identifier les infections. MéTHODES: En utilisant des données de laboratoire et administratives couplées en Ontario, au Canada, de janvier 2004 à décembre 2014, nous avons validé les codes de diagnostic du VHB/VHC contre les infections confirmées en laboratoire. Les mesures du rendement (sensibilité, spécificité et valeur prédictive positive) ont été estimées par régression logistique croisée et nous avons exploré les variations en variant les fenêtres temporelles de 1 à 5 ans avant (c.-à-d. prédiction pronostique) et après (c.-à-d. prédiction diagnostique) la date de confirmation en laboratoire. Des analyses de sous-groupes ont été effectuées auprès d'immigrants, d'hommes, de baby-boomers et de femmes pour examiner la robustesse de ces mesures. RéSULTATS: 1 599 023 individus ont été testés pour le VHB et 840 924 pour le VHC, dont 41 714 (2,7 %) et 58 563 (7,0 %) infections ont été identifiées, respectivement. Les codes de diagnostic VHB/VHC ± 3 ans de confirmation en laboratoire ont montré une spécificité élevée (99,9 % VHB; 99,8 % VHC), une valeur prédictive positive modérée (70,3 % VHB; 85,8 % VHC) et une faible sensibilité (12,8 % VHB; 30,8 % VHC). La variation de la fenêtre temporelle a entraîné des changements limités aux mesures du rendement. Les modèles diagnostiques ont constamment surpassé les modèles pronostiques. Aucune différence majeure n'a été observée entre les sous-groupes. CONCLUSION: Les codes VHB/VHC ne devraient pas être la seule source utilisée pour surveiller la charge de population de ces infections, en raison de la faible sensibilité et des valeurs prédictives positives modérées. Ces résultats soulignent l'importance des systèmes continus de surveillance des maladies à déclaration obligatoire en laboratoire pour surveiller l'hépatite virale en Ontario.

The Effect of Changes in Cervical Cancer Screening Guidelines on Chlamydia Testing.

PURPOSE: Many chlamydia infections are identified through screening, which is frequently offered to females concomitantly with cervical cancer screening. Recent cervical cancer screening guidelines recommend screening less frequently and starting later. We sought to evaluate the impact of the May 2012 Ontario, Canada, cervical cancer screening guideline change on Papanicolaou (Pap) and chlamydia trachomatis (chlamydia) testing and incidence. METHODS: We extracted population-based physician billing claims data to identify Pap and chlamydia tests and public health surveillance data to identify chlamydia cases. We used interrupted time series analysis of quarterly data spanning 2 years before and after the guideline change and fitted segmented linear regression or rational functions to the outcomes using autoregressive integrated moving average models. Outcomes were stratified by sex and age group. RESULTS: Two years after the guideline change, we observed reduced chlamydia testing in females, with the greatest relative reduction (25.5%) among those aged 15 to 19 years. We also observed decreases in reported chlamydia incidence for females aged 15 to 19 years and 20 to 24 years (relative reductions of 16.8% and 14.4%, respectively). Chlamydia incidence remained the same for males, despite increased chlamydia testing. CONCLUSIONS: Recent cervical cancer screening guideline changes in Ontario were associated with reduced chlamydia testing and reported new cases of chlamydia in females. Females aged 15 to 19 years, who are at high risk for chlamydia if sexually active, and who no longer warrant cervical cancer screening, were disproportionately affected. Females should be tested for chlamydia based on risk, regardless of need for Pap testing.

Health-related quality of life, comorbidities and mortality in pulmonary nontuberculous mycobacterial infections: A systematic review.

Nontuberculous mycobacterial (NTM) infections are increasing in disease frequency worldwide. This systematic review examines health-related quality of life (HRQOL), comorbidities and mortality associated with pulmonary NTM disease. We searched MEDLINE, EMBASE, CINAHL, Scopus Life Sciences, conference proceedings and Google (earliest date available to February 2015) for primary studies. Eligible studies compared populations with and without pulmonary NTM disease in high-income jurisdictions. We excluded studies on HIV/AIDS. All languages were accepted. Two reviewers followed MOOSE and PRISMA reporting guidelines and independently appraised quality using STROBE. All studies were summarized qualitatively regardless of quality. Of 3193 citations screened, we included 17 studies mostly from Taiwan (n = 5) and the USA (n = 4). Two studies assessed HRQOL; one assessed comorbidities, 11 assessed mortality, and three assessed multiple outcomes. Populations with pulmonary NTM reported significantly worse or similar HRQOL than the general population, depending on the instruments used. Some suggested greater prevalence of having bronchiectasis (n = 2) and greater risk of developing pulmonary tuberculosis (n = 1). Most (n = 7) suggested no difference in mortality, although only one was age-matched and gender-matched to the general population. Four suggested NTM populations had higher mortality-two of which compared with the general population and were deemed of high quality, while two compared with non-NTM patients from hospital. High clinical heterogeneity in study design may explain discordant results. Bias assessments and controlling for confounding were carried out poorly. No consistent trends were observed although there is suggestion of an increased health burden from respiratory diseases and increased mortality associated with pulmonary NTM disease.

Coverage from Ontario, Canada's school-based HPV vaccine program: the first three years.

BACKGROUND: In 2007, Ontario implemented a school-based human papillomavirus (HPV) vaccination program targeting grade 8 girls. Girls may complete the series in grade 9 (extended eligibility). Limitations in the existing provincial data sources for assessing HPV vaccine coverage in Ontario prompted the use of two surveys of Health Units (HUs) to calculate provincial vaccine coverage for the first three years of the vaccination program. METHODS: We surveyed Ontario's 36 HUs in March and November 2011 to obtain vaccine coverage information, including source of denominator data, and use of local information systems. The second survey was necessary in order to assess coverage including extended eligibility for the third year. HU-reported HPV vaccine coverage was compared to coverage estimates obtained from two provincial systems: the Immunization Records Information System (IRIS) and the HPV reimbursement database, a system used to remunerate HUs for HPV vaccine doses administered. RESULTS: 100% of HUs participated in the two surveys. The provincial coverage estimates using HU-reported data were: 51% (2007-2008), 58% (2008-2009), and 59% (2009-2010) with large variation by HU. Coverage increased significantly over time. The number of HUs that were able to report on doses given as part of extended eligibility also increased over time (47% in 2007-2008 to 89% in 2009-2010; p=0.0008). Comparisons across the three data sources (survey, IRIS and reimbursement database) revealed significantly different coverage estimates. Class or school lists were the most common source of denominator data used by HUs (27/36, 75%), however independent schools were not included by all. CONCLUSIONS: As not all HUs were able to report on HPV vaccine coverage including extended eligibility doses these findings likely underestimate the true coverage attained by Ontario's program. Although coverage is below the Canadian Immunization Committee benchmark of 80% within two years of program implementation, the upward trend in coverage is encouraging.

Online communication as a potential travel medicine research tool: analysis of messages posted on the TravelMed listserv.

BACKGROUND: Access to the Internet and electronic mail has created opportunities for online discussion that can facilitate medical education and clinical problem solving. Research into the use of these information technologies is increasing and the analysis of these tools can support and guide the activities of professional organizations, including educational endeavors. OBJECTIVE: The initial objective was to analyze patterns of information exchange on the International Society of Travel Medicine's (ISTM) travel health electronic mailing list related to a specific area of society interest. Secondary objectives included the analysis of listserv use in relation to subscriber demographics and rates of participation to support travel health educational activities. METHODS: This study examined the use of the ISTM TravelMed listserv over an 8-month period from January 1, 2006, to July 31, 2006. Descriptive data analysis included TravelMed user demographics, the type of posting, the topic and frequency of postings, and the source of information provided. RESULTS: During the study period, 911 (47%) of the eligible ISTM members subscribed to the TravelMed listserv. About 369 of these subscribers posted 1,710 individual messages. About 1,506 (88%) postings were educational; 207 (12%) postings were administrative. A total of 389 (26%) of the educational postings were primary queries and 1,120 (74%) were responses, with a mean string length of 2.9 responses per query (range: 1-51). Twenty participants contributed 40% of the educational postings. The topics with the most frequent postings were vaccines and vaccine-preventable diseases (473/31%) and malaria (258/17%). Postings focused on special populations, including pregnant women or immigrants, comprised a total of 14 postings (<1%). CONCLUSIONS: During the study period, a limited number of ISTM members (19%) authored postings on the listserv. Regular discussion centered on a limited number of recurring topics. The analysis provides several opportunities for the support of educational initiatives, clinical problem solving, and program evaluation.

Health and foreign policy: influences of migration and population mobility.

International interest in the relationship between globalization and health is growing, and this relationship is increasingly figuring in foreign policy discussions. Although many globalizing processes are known to affect health, migration stands out as an integral part of globalization, and links between migration and health are well documented. Numerous historical interconnections exist between population mobility and global public health, but since the 1990s new attention to emerging and re-emerging infectious diseases has promoted discussion of this topic. The containment of global disease threats is a major concern, and significant international efforts have received funding to fight infectious diseases such as malaria, tuberculosis and HIV/AIDS (human immunodeficiency virus/acquired immune deficiency syndrome). Migration and population mobility play a role in each of these public health challenges. The growing interest in population mobility's health-related influences is giving rise to new foreign policy initiatives to address the international determinants of health within the context of migration. As a result, meeting health challenges through international cooperation and collaboration has now become an important foreign policy component in many countries. However, although some national and regional projects address health and migration, an integrated and globally focused approach is lacking. As migration and population mobility are increasingly important determinants of health, these issues will require greater policy attention at the multilateral level.