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1.
Microbiol Spectr ; : e0525622, 2023 Jun 08.
Article in English | MEDLINE | ID: covidwho-20238742

ABSTRACT

The 50% plaque reduction neutralization assay (PRNT50) has been previously used to assess the neutralization capacity of donor plasma against wild-type and variant of concern (VOC) severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Emerging data suggest that plasma with an anti-SARS-CoV-2 level of ≥2 × 104 binding antibody units/mL (BAU/mL) protects against SARS-CoV-2 Omicron BA.1 infection. Specimens were collected using a cross-sectional random sampling approach. For PRNT50 studies, 63 previously analyzed specimens by PRNT50 versus SARS-CoV-2 wild-type, Alpha, Beta, Gamma, and Delta were analyzed by PRNT50 versus Omicron BA.1. The 63 specimens plus 4,390 specimens (randomly sampled regardless of serological evidence of infection) were also tested using the Abbott SARS-CoV-2 IgG II Quant assay (anti-spike [S]; Abbott, Chicago, IL, USA; Abbott Quant assay). In the vaccinated group, the percentages of specimens with any measurable PRNT50 versus wild-type or VOC were wild type (21/25 [84%]), Alpha (19/25 [76%]), Beta (18/25 [72%]), Gamma (13/25 [52%]), Delta (19/25 [76%]), and Omicron BA.1 (9/25 [36%]). In the unvaccinated group, the percentages of specimens with any measurable PRNT50 versus wild type or VOC were wild-type SARS-CoV-2 (16/39 [41%]), Alpha (16/39 [41%]), Beta (10/39 [26%]), Gamma (9/39 [23%]), Delta (16/39 [41%]), and Omicron BA.1 (0/39) (Fisher's exact tests, vaccinated versus unvaccinated for each variant, P < 0.05). None of the 4,453 specimens tested by the Abbott Quant assay had a binding capacity of ≥2 × 104 BAU/mL. Vaccinated donors were more likely than unvaccinated donors to neutralize Omicron when assessed by a PRNT50 assay. IMPORTANCE SARS-CoV-2 Omicron emergence occurred in Canada during the period from November 2021 to January 2022. This study assessed the ability of donor plasma collected earlier (January to March 2021) to generate any neutralizing capacity against Omicron BA.1 SARS-CoV-2. Vaccinated individuals, regardless of infection status, were more likely to neutralize Omicron BA.1 than unvaccinated individuals. This study then used a semiquantitative binding antibody assay to screen a larger number of specimens (4,453) for individual specimens that might have high-titer neutralizing capacity against Omicron BA.1. None of the 4,453 specimens tested by the semiquantitative SARS-CoV-2 assay had a binding capacity suggestive of a high-titer neutralizing capacity against Omicron BA.1. These data do not imply that Canadians lacked immunity to Omicron BA.1 during the study period. Immunity to SARS-CoV-2 is complex, and there is still no wide consensus on correlation of protection to SARS-CoV-2.

2.
PLoS One ; 18(3): e0283715, 2023.
Article in English | MEDLINE | ID: covidwho-2281518

ABSTRACT

BACKGROUND: Vaccines against SARS-CoV-2 have been shown to reduce risk of infection as well as severe disease among those with breakthrough infection in adults. The latter effect is particularly important as immune evasion by Omicron variants appears to have made vaccines less effective at preventing infection. Therefore, we aimed to quantify the protection conferred by mRNA vaccination against hospitalization due to SARS-CoV-2 in adolescent and pediatric populations. METHODS: We retrospectively created a cohort of reported SARS-CoV-2 case records from Ontario's Public Health Case and Contact Management Solution among those aged 4 to 17 linked to vaccination records from the COVaxON database on January 19, 2022. We used multivariable logistic regression to estimate the association between vaccination and hospitalization among SARS-CoV-2 cases prior to and during the emergence of Omicron. RESULTS: We included 62 hospitalized and 27,674 non-hospitalized SARS-CoV-2 cases, with disease onset from May 28, 2021 to December 4, 2021 (Pre-Omicron) and from December 23, 2021 to January 9, 2022 (Omicron). Among adolescents, two mRNA vaccine doses were associated with an 85% (aOR = 0.15; 95% CI: [0.04, 0.53]; p<0.01) lower likelihood of hospitalization among SARS-CoV-2 cases caused by Omicron. Among children, one mRNA vaccine dose was associated with a 79% (aOR = 0.21; 95% CI: [0.03, 0.77]; p<0.05) lower likelihood of hospitalization among SARS-CoV-2 cases caused by Omicron. The calculation of E-values, which quantifies how strong an unmeasured confounder would need to be to nullify our findings, suggest that these effects are unlikely to be explained by unmeasured confounding. CONCLUSIONS: Despite immune evasion by SARS-CoV-2 variants, vaccination continues to be associated with a lower likelihood of hospitalization among adolescent and pediatric Omicron (B.1.1.529) SARS-CoV-2 cases, even when the vaccines do not prevent infection. Continued efforts are needed to increase vaccine uptake among adolescent and pediatric populations.


Subject(s)
COVID-19 , Vaccine Efficacy , Adolescent , Adult , Child , Humans , COVID-19/epidemiology , COVID-19/prevention & control , COVID-19 Vaccines , Hospitalization , mRNA Vaccines , Ontario/epidemiology , Retrospective Studies , SARS-CoV-2/genetics
3.
Clin Infect Dis ; 2022 Jul 06.
Article in English | MEDLINE | ID: covidwho-2233586

ABSTRACT

BACKGROUND: Pregnancy represents a physiological state associated with increased vulnerability to severe outcomes from infectious diseases, both for the pregnant person and developing infant. The SARS-CoV-2 pandemic may have important health consequences for pregnant individuals, who may also be more reluctant than non-pregnant people to accept vaccination. METHODS: We sought to estimate the degree to which increased severity of SARS-CoV-2 outcomes can be attributed to pregnancy using a population-based SARS-CoV-2 case file from Ontario, Canada. Due to varying propensity to receive vaccination, and changes in dominant circulating viral strains over time, a time-matched cohort study was performed to evaluate the relative risk of severe illness in pregnant women with SARS-CoV-2 compared to other SARS-CoV-2 infected women of childbearing age (10 to 49 years old). Risk of severe SARS-CoV-2 outcomes was evaluated in pregnant women and time-matched non-pregnant controls using multivariable conditional logistic regression. RESULTS: Compared to the rest of the population, non-pregnant women of childbearing age had an elevated risk of infection (standardized morbidity ratio (SMR) 1.28), while risk of infection was reduced among pregnant women (SMR 0.43). After adjustment for confounding pregnant women had a markedly elevated risk of hospitalization (adjusted OR 4.96, 95% CI 3.86 to 6.37) and ICU admission (adjusted OR 6.58, 95% CI 3.29 to 13.18). The relative increase in hospitalization risk associated with pregnancy was greater in women without comorbidities than in those with comorbidities (P for heterogeneity 0.004). CONCLUSIONS: Given the safety of SARS-CoV-2 vaccines in pregnancy, risk-benefit calculus strongly favours SARS-CoV-2 vaccination in pregnant women.

4.
Clin Infect Dis ; 2022 May 25.
Article in English | MEDLINE | ID: covidwho-2230536

ABSTRACT

BACKGROUND: The rapid development of safe and effective vaccines against the SARS-CoV-2 virus has been a singular scientific achievement. Confounding due to health seeking behaviours, circulating variants, and differential testing by vaccination status may bias analyses towards an apparent increase in infection severity following vaccination. METHODS: We used data from Ontario, Canada's Case and Contact Management database, merged to a provincial vaccination dataset (COVaxON) to create a time-matched cohort of individuals who were hospitalized with SARS-CoV-2 infection. Vaccinated individuals were matched to up to five unvaccinated individuals based on test date. Risk of ICU admission and death were evaluated using conditional logistic regression. Unmatched exploratory analyses were performed to identify sources of heterogeneity in vaccine effects. RESULTS: In 20,064 individuals (3,353 vaccinated and 16,711 unvaccinated) hospitalized with infection due to SARS-CoV-2 between January 1st, 2021 and January 5th, 2022, vaccination with 1, 2, or 3 doses significantly reduced the risk of ICU admission and death. An inverse dose-response relationship was observed between vaccine doses received and both outcomes (adjusted odds ratio (aOR) per additional dose for ICU admission: 0.66, 95% CI 0.62 to 0.71; aOR for death: 0.78, 95% CI 0.72 to 0.84). Reduction in risk was greater for ICU admission than for death (P for heterogeneity <0.05). INTERPRETATION: We identified decreased virulence of SARS-CoV-2 infections in vaccinated individuals, even when vaccines failed to prevent infection sufficiently severe to cause hospitalization. Even with diminished efficacy of vaccines against infection with novel VOCs, vaccines remain an important tool for reduction of ICU admission and mortality.

5.
Health Care Manag Sci ; 26(2): 301-312, 2023 Jun.
Article in English | MEDLINE | ID: covidwho-2209415

ABSTRACT

Low rates of vaccination, emergence of novel variants of SARS-CoV-2, and increasing transmission relating to seasonal changes and relaxation of mitigation measures leave many US communities at risk for surges of COVID-19 that might strain hospital capacity, as in previous waves. The trajectories of COVID-19 hospitalizations differ across communities depending on their age distributions, vaccination coverage, cumulative incidence, and adoption of risk mitigating behaviors. Yet, existing predictive models of COVID-19 hospitalizations are almost exclusively focused on national- and state-level predictions. This leaves local policymakers in urgent need of tools that can provide early warnings about the possibility that COVID-19 hospitalizations may rise to levels that exceed local capacity. In this work, we develop a framework to generate simple classification rules to predict whether COVID-19 hospitalization will exceed the local hospitalization capacity within a 4- or 8-week period if no additional mitigating strategies are implemented during this time. This framework uses a simulation model of SARS-CoV-2 transmission and COVID-19 hospitalizations in the US to train classification decision trees that are robust to changes in the data-generating process and future uncertainties. These generated classification rules use real-time data related to hospital occupancy and new hospitalizations associated with COVID-19, and when available, genomic surveillance of SARS-CoV-2. We show that these classification rules present reasonable accuracy, sensitivity, and specificity (all ≥ 80%) in predicting local surges in hospitalizations under numerous simulated scenarios, which capture substantial uncertainties over the future trajectories of COVID-19. Our proposed classification rules are simple, visual, and straightforward to use in practice by local decision makers without the need to perform numerical computations.


Subject(s)
COVID-19 , Humans , SARS-CoV-2 , Hospitalization , Hospitals , Age Distribution
6.
PLOS Digit Health ; 1(12): e0000164, 2022 Dec.
Article in English | MEDLINE | ID: covidwho-2196812

ABSTRACT

Cross-sector partnerships are vital for maintaining resilient health systems; however, few studies have sought to empirically assess the barriers and enablers of effective and responsible partnerships during public health emergencies. Through a qualitative, multiple case study, we analyzed 210 documents and conducted 26 interviews with stakeholders in three real-world partnerships between Canadian health organizations and private technology startups during the COVID-19 pandemic. The three partnerships involved: 1) deploying a virtual care platform to care for COVID-19 patients at one hospital, 2) deploying a secure messaging platform for physicians at another hospital, and 3) using data science to support a public health organization. Our results demonstrate that a public health emergency created time and resource pressures throughout a partnership. Given these constraints, early and sustained alignment on the core problem was critical for success. Moreover, governance processes designed for normal operations, such as procurement, were triaged and streamlined. Social learning, or the process of learning from observing others, offset some time and resource pressures. Social learning took many forms ranging from informal conversations between individuals at peer organisations (e.g., hospital chief information officers) to standing meetings at the local university's city-wide COVID-19 response table. We also found that startups' flexibility and understanding of the local context enabled them to play a highly valuable role in emergency response. However, pandemic fueled "hypergrowth" created risks for startups, such as introducing opportunities for deviation away from their core value proposition. Finally, we found each partnership navigated intense workloads, burnout, and personnel turnover through the pandemic. Strong partnerships required healthy, motivated teams. Visibility into and engagement in partnership governance, belief in partnership impact, and strong emotional intelligence in managers promoted team well-being. Taken together, these findings can help to bridge the theory-to-practice gap and guide effective cross-sector partnerships during public health emergencies.

9.
Microbiol Spectr ; 10(5): e0281122, 2022 Oct 26.
Article in English | MEDLINE | ID: covidwho-2038255

ABSTRACT

There is evidence that COVID-19 convalescent plasma may improve outcomes of patients with impaired immune systems; however, more clinical trials are required. Although we have previously used a 50% plaque reduction/neutralization titer (PRNT50) assay to qualify convalescent plasma for clinical trials and virus-like particle (VLP) assays to validate PRNT50 methodologies, these approaches are time-consuming and expensive. Here, we characterized the ability of the Abbott severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) IgG II Quant assay to identify high- and low-titer plasma for wild-type and variant (Alpha, Beta, Gamma, and Delta) SARS-CoV-2 characterized by both VLP assays and PRNT50. Plasma specimens previously tested in wild-type, Alpha, Beta, Gamma, and Delta VLP neutralization assays were selected based on availability. Selected specimens were evaluated by the Abbott SARS-CoV-2 IgG II Quant assay [Abbott anti-Spike (S); Abbott, Chicago, IL], and values in units per milliliter were converted to binding antibody units (BAU) per milliliter. Sixty-three specimens were available for analysis. Abbott SARS-CoV-2 IgG II Quant assay values in BAU per milliliter were significantly different between high- and low-titer specimens for wild-type (Mann-Whitney U = 42, P < 0.0001), Alpha (Mann-Whitney U = 38, P < 0.0001), Beta (Mann-Whitney U = 29, P < 0.0001), Gamma (Mann-Whitney U = 0, P < 0.0001), and Delta (Mann-Whitney U = 42, P < 0.0001). A conservative approach using the highest 95% confidence interval (CI) values from wild-type and variant of concern (VOC) SARS-CoV-2 experiments would identify a potential Abbott SARS-CoV-2 IgG II Quant assay cutoff of ≥7.1 × 103 BAU/mL. IMPORTANCE The United States Food and Drug Administration (FDA) issued an Emergency Use Authorization (EUA) for the use of COVID-19 convalescent plasma (CCP) to treat hospitalized patients with COVID-19 in August 2020. However, by 4 February 2021, the FDA had revised the convalescent plasma EUA. This revision limited the authorization for high-titer COVID-19 convalescent plasma and restricted patient groups to hospitalized patients with COVID-19 early in their disease course or hospitalized patients with impaired humoral immunity. Traditionally our group utilized 50% plaque reduction/neutralization titer (PRNT50) assays to qualify CCP in Canada. Since that time, the Abbott SARS-CoV-2 IgG II Quant assay (Abbott, Chicago IL) was developed for the qualitative and quantitative determination of IgG against the SARS-CoV-2. Here, we characterized the ability of the Abbott SARS-CoV-2 IgG II Quant assay to identify high- and low-titer plasma for wild-type and variant (Alpha, Beta, Gamma, and Delta) SARS-CoV-2.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , Antibodies, Viral , Immunoglobulin G , Antibodies, Neutralizing
10.
Prev Med Rep ; 30: 101993, 2022 Dec.
Article in English | MEDLINE | ID: covidwho-2031627

ABSTRACT

The long-term dynamics of COVID-19 disease incidence and public health measures may impact individuals' precautionary behaviours as well as support for measures. The objectives of this study were to assess longitudinal changes in precautionary behaviours and support for public health measures. Survey data were collected online from 1030 Canadians in each of 5 cycles in 2020: June 15-July 13; July 22-Aug 8; Sept 7-15; Oct 14-21; and Nov 12-17. Precautionary behaviour increased over the study period in the context of increasing disease incidence. When controlling for the stringency of public health measures and disease incidence, mixed effects logistic regression models showed these behaviours did not significantly change over time. Odds ratios for avoiding contact with family and friends ranged from 0.84 (95% CI 0.59-1.20) in September to 1.25 (95% CI 0.66-2.37) in November compared with July 2020. Odds ratios for attending an indoor gathering ranged from 0.86 (95% CI 0.62-1.20) in August to 1.71 (95% CI 0.95-3.09) in October compared with July 2020. Support for non-essential business closures increased over time with 2.33 (95% CI 1.14-4.75) times higher odds of support in November compared to July 2020. Support for school closures declined over time with lower odds of support in September (OR 0.66 [95% CI 0.45-0.96]), October (OR 0.48 [95% CI 0.26-0.87]), and November (OR 0.39 [95% CI 0.19-0.81]) compared with July 2020. In summary, respondents' behaviour mirrored government guidance between July and November 2020 and supported individual precautionary behaviour and limitations on non-essential businesses over school closures.

11.
CMAJ ; 194(24): E848, 2022 Jun 20.
Article in English | MEDLINE | ID: covidwho-1938456
12.
Microbiol Spectr ; 10(3): e0113422, 2022 06 29.
Article in English | MEDLINE | ID: covidwho-1874515

ABSTRACT

Our group has previously used laboratory and commercially developed assays to understand the IgG responses to SARS-CoV-2 antigens, including nucleocapsid (N), spike (S), and receptor binding domain (RBD), in Canadian blood donors. In this current study, we analyzed 17,428 available and previously characterized retention samples collected from April 2020 to March 2021. The analysis compared the characteristics of the Abbott SARS-CoV-2 IgG II Quant assay (Abbott anti-spike [S], Abbott, Chicago, IL) against four other IgG assays. The Abbott anti-S assay has a qualitative threshold of 50 AU/mL. The four comparator assays were the Abbott anti-nucleocapsid (N) assay and three commonly used Canadian in-house IgG enzyme-linked immunosorbent assays (ELISAs) recognizing distinct recombinant viral antigens, full-length spike glycoprotein, glycoprotein RBD, and nucleocapsid. The strongest qualitative relationship was between Sinai RBD and the Abbott anti-S assay (kappa, 0.707; standard error [SE] of kappa, 0.018; 95% confidence interval, 0.671 to 0.743). We then scored each previously characterized specimen as positive when two anti-SARS-COV-2 assays identified anti-SARS-CoV-2 IgG in the specimen. Using this composite reference standard approach, the sensitivity of the Abbott anti-S assay was 95.96% (95% confidence interval [CI], 93.27 to 97.63%). The specificity of the Abbott anti-S assay was 99.35% (95% CI, 99.21 to 99.46%). Our study provides context on the use of commonly used SARS-CoV-2 serologies in Canada and identifies how these assays qualitatively compare to newer commercial assays. Our next steps are to assess how well the Abbott anti-S assays quantitatively detect wild-type and SARS-CoV-2 variants of concern. IMPORTANCE We describe the qualitative test characteristics of the Abbott SARS-CoV-2 IgG II Quant assay against four other anti-SARS-CoV-2 IgG assays commonly used in Canada. Although there is no gold standard for identifying anti-SARS-CoV-2 seropositivity, aggregate standards can be used to assess seropositivity. In this study, we used a specimen bank of previously well-characterized specimens collected between April 2020 and March 2021. The Abbott anti-S assay showed the strongest qualitative relationship with a widely used laboratory-developed IgG assay for the SARS-CoV-2 receptor binding domain. Using the composite reference standard approach, we also showed that the Abbott anti-S assay was highly sensitive and specific. As new anti-SARS-CoV-2 assays are developed, it is important to compare their test characteristics against other assays that have been extensively used in prior research.


Subject(s)
COVID-19 , SARS-CoV-2 , Antibodies, Viral , Blood Donors , COVID-19/diagnosis , Canada , Enzyme-Linked Immunosorbent Assay , Humans , Immunoglobulin G , Sensitivity and Specificity
13.
Clin Infect Dis ; 75(1): e69-e75, 2022 08 24.
Article in English | MEDLINE | ID: covidwho-1816037

ABSTRACT

BACKGROUND: Novel variants of concern (VOCs) have been associated with both increased infectivity and virulence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The virulence of SARS-CoV-2 is closely linked to age. Whether relative increases in virulence of novel VOCs are similar across the age spectrum or are limited to some age groups is unknown. METHODS: We created a retrospective cohort of people in Ontario, Canada, who tested positive for SARS-CoV-2 and were screened for VOCs (n = 259 984) between 7 February 2021 and 31 October 2021. Cases were classified as N501Y-positive VOC, probable Delta VOC, or VOC undetected. We constructed age-specific logistic regression models to evaluate associations between N501Y-postive or Delta VOC infections and infection severity using hospitalization, intensive care unit (ICU) admission, and death as outcome variables. Models were adjusted for sex, comorbidity, vaccination status, and temporal trends. RESULTS: Infection with either N501Y-positive or Delta VOCs was associated with significant elevations in risk of hospitalization, ICU admission, and death across age groups compared with infections where a VOC was not detected. The Delta VOC increased hospitalization risk in children aged <10 years by a factor of 2.5 (adjusted odds ratio; 95% confidence interval, 1.3 to 5.0) compared with non-VOCs. There was a significant inverse relationship between age and relative increase in risk of death with the Delta VOC, with younger age groups showing a greater relative increase in risk of death than older individuals. CONCLUSIONS: SARS-CoV-2 VOCs appear to be associated with increased relative virulence of infection in all age groups, though low absolute numbers of outcomes in younger individuals make estimates in these groups imprecise.


Subject(s)
COVID-19 , SARS-CoV-2 , Age Factors , COVID-19/epidemiology , Child , Humans , Ontario/epidemiology , Retrospective Studies , Virulence
14.
CMAJ ; 194(16): E573-E580, 2022 04 25.
Article in English | MEDLINE | ID: covidwho-1808587

ABSTRACT

BACKGROUND: The speed of vaccine development has been a singular achievement during the COVID-19 pandemic, although uptake has not been universal. Vaccine opponents often frame their opposition in terms of the rights of the unvaccinated. We sought to explore the impact of mixing of vaccinated and unvaccinated populations on risk of SARS-CoV-2 infection among vaccinated people. METHODS: We constructed a simple susceptible-infectious-recovered compartmental model of a respiratory infectious disease with 2 connected subpopulations: people who were vaccinated and those who were unvaccinated. We simulated a spectrum of patterns of mixing between vaccinated and unvaccinated groups that ranged from random mixing to complete like-with-like mixing (complete assortativity), in which people have contact exclusively with others with the same vaccination status. We evaluated the dynamics of an epidemic within each subgroup and in the population as a whole. RESULTS: We found that the risk of infection was markedly higher among unvaccinated people than among vaccinated people under all mixing assumptions. The contact-adjusted contribution of unvaccinated people to infection risk was disproportionate, with unvaccinated people contributing to infections among those who were vaccinated at a rate higher than would have been expected based on contact numbers alone. We found that as like-with-like mixing increased, attack rates among vaccinated people decreased from 15% to 10% (and increased from 62% to 79% among unvaccinated people), but the contact-adjusted contribution to risk among vaccinated people derived from contact with unvaccinated people increased. INTERPRETATION: Although risk associated with avoiding vaccination during a virulent pandemic accrues chiefly to people who are unvaccinated, their choices affect risk of viral infection among those who are vaccinated in a manner that is disproportionate to the portion of unvaccinated people in the population.


Subject(s)
COVID-19 , Communicable Diseases , COVID-19/epidemiology , COVID-19/prevention & control , Humans , Pandemics/prevention & control , SARS-CoV-2 , Vaccination
15.
Can Commun Dis Rep ; 46(8): 198-204, 2020 Jun 04.
Article in English | MEDLINE | ID: covidwho-1791648

ABSTRACT

BACKGROUND: Severe acute respiratory syndrome virus 2 (SARS-CoV-2), likely a bat-origin coronavirus, spilled over from wildlife to humans in China in late 2019, manifesting as a respiratory disease. Coronavirus disease 2019 (COVID-19) spread initially within China and then globally, resulting in a pandemic. OBJECTIVE: This article describes predictive modelling of COVID-19 in general, and efforts within the Public Health Agency of Canada to model the effects of non-pharmaceutical interventions (NPIs) on transmission of SARS-CoV-2 in the Canadian population to support public health decisions. METHODS: The broad objectives of two modelling approaches, 1) an agent-based model and 2) a deterministic compartmental model, are described and a synopsis of studies is illustrated using a model developed in Analytica 5.3 software. RESULTS: Without intervention, more than 70% of the Canadian population may become infected. Non-pharmaceutical interventions, applied with an intensity insufficient to cause the epidemic to die out, reduce the attack rate to 50% or less, and the epidemic is longer with a lower peak. If NPIs are lifted early, the epidemic may rebound, resulting in high percentages (more than 70%) of the population affected. If NPIs are applied with intensity high enough to cause the epidemic to die out, the attack rate can be reduced to between 1% and 25% of the population. CONCLUSION: Applying NPIs with intensity high enough to cause the epidemic to die out would seem to be the preferred choice. Lifting disruptive NPIs such as shut-downs must be accompanied by enhancements to other NPIs to prevent new introductions and to identify and control any new transmission chains.

16.
CMAJ Open ; 10(1): E190-E195, 2022.
Article in English | MEDLINE | ID: covidwho-1737356

ABSTRACT

BACKGROUND: As the largest city in Canada, Toronto has played an important role in the dynamics of SARS-CoV-2 transmission in Ontario, and the burden of disease across Toronto neighbourhoods has shown considerable heterogeneity. The purpose of this study was to investigate the spatial variation of sporadic SARS-CoV-2 cases in Toronto neighbourhoods by detecting clusters of increased risk and investigating effects of neighbourhood-level risk factors on rates. METHODS: Data on sporadic SARS-CoV-2 cases, at the neighbourhood level, for Jan. 25 to Nov. 26, 2020, were obtained from the City of Toronto COVID-19 dashboard. We used a flexibly shaped spatial scan to detect clusters of increased risk of sporadic COVID-19. We then used a generalized linear geostatistical model to investigate whether average household size, population density, dependency ratio and prevalence of low-income households were associated with sporadic SARS-CoV-2 rates. RESULTS: We identified 3 clusters of elevated risk of SARS-CoV-2 infection, with standardized morbidity ratios ranging from 1.59 to 2.43. The generalized linear geostatistical model found that average household size (relative risk [RR] 2.17, 95% confidence interval [CI] 1.80-2.61) and percentage of low-income households (RR 1.03, 95% CI 1.02-1.04) were significant predictors of sporadic SARS-CoV-2 cases at the neighbourhood level. INTERPRETATION: During the study period, 3 clusters of increased risk of sporadic SARS-CoV-2 infection were identified, and average household size and percentage of low-income households were found to be associated with sporadic SARS-CoV-2 rates at the neighbourhood level. The findings of this study can be used to target resources and create policy to address inequities that are shown through heterogeneity of SARS-CoV-2 cases at the neighbourhood level in Toronto, Ontario.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/epidemiology , Humans , Ontario/epidemiology , Pandemics , SARS-CoV-2/genetics , Spatial Analysis
17.
Microbiol Spectr ; 10(1): e0256321, 2022 02 23.
Article in English | MEDLINE | ID: covidwho-1700249

ABSTRACT

We have previously used composite reference standards and latent class analysis (LCA) to evaluate the performance of laboratory assays in the presence of tarnished gold standards. Here, we apply these techniques to repeated, cross-sectional study of Canadian blood donors, whose sera underwent parallel testing with four separate SARS-CoV-2 antibody assays. We designed a repeated cross-sectional design with random cross-sectional sampling of all available retention samples (n = 1500/month) for a 12 -month period from April 2020 until March 2021. Each sample was evaluated for SARS-CoV-2 IgG antibodies using four assays an Abbott Architect assay targeting the nucleocapsid antigen (Abbott-NP, Abbott, Chicago IL) and three in-house IgG ELISAs recognizing distinct recombinant viral antigens: full-length spike glycoprotein (Spike), spike glycoprotein receptor binding domain (RBD) and nucleocapsid (NP). We used two analytic approaches to estimate SAR-CoV-2 seroprevalence: a composite reference standard and LCA. Using LCA to estimate true seropositivity status based on the results of the four antibody tests, we estimated that seroprevalence increased from 0.8% (95% CI: 0.5-1.4%) in April 2020 to 6.3% (95% CI: 5.1-7.6%) in March 2021. Our study provides further support for the use of LCA in upcoming public health crises, epidemics, and pandemics when a gold standard assay may not be available or identifiable. IMPORTANCE Here, we describe an approach to estimating seroprevalence in a low prevalence setting when multiple assays are available and yet no known gold standard exists. Because serological studies identify cases through both diagnostic testing and surveillance, and otherwise silent, unrecognized infections, serological data can be used to estimate the true infection fatality ratio of a disease. However, seroprevalence studies rely on assays with imperfect sensitivity and specificity. Seroreversion (loss of antibody response) also occurs over time, and with the advent of vaccination, distinction of antibody response resulting from vaccination as opposed to antibody response due to infection has posed an additional challenge. Our approach indicates that seroprevalence on Canadian blood donors by the end of March 2021was less than 10%. Our study supports the use of latent class analysis in upcoming public health crises, epidemics, and pandemics when a gold standard assay may not be available or identifiable.


Subject(s)
Antibodies, Viral/blood , Blood Donors/statistics & numerical data , COVID-19/blood , SARS-CoV-2/immunology , Adult , Aged , COVID-19/epidemiology , COVID-19/virology , Canada/epidemiology , Coronavirus Nucleocapsid Proteins/analysis , Coronavirus Nucleocapsid Proteins/immunology , Cross-Sectional Studies , Enzyme-Linked Immunosorbent Assay , Female , Humans , Male , Middle Aged , SARS-CoV-2/genetics , Seroepidemiologic Studies , Spike Glycoprotein, Coronavirus/analysis , Spike Glycoprotein, Coronavirus/immunology , Young Adult
19.
BMC Public Health ; 21(1): 2040, 2021 11 08.
Article in English | MEDLINE | ID: covidwho-1505694

ABSTRACT

BACKGROUND: A variety of public health measures have been implemented during the COVID-19 pandemic in Canada to reduce contact between individuals. The objective of this study was to provide empirical contact pattern data to evaluate the impact of public health measures, the degree to which social contacts rebounded to normal levels, as well as direct public health efforts toward age- and location-specific settings. METHODS: Four population-based cross-sectional surveys were administered to members of a paid panel representative of Canadian adults by age, gender, official language, and region of residence during May (Survey 1), July (Survey 2), September (Survey 3), and December (Survey 4) 2020. A total of 4981 (Survey 1), 2493 (Survey 2), 2495 (Survey 3), and 2491 (Survey 4) respondents provided information about the age and setting for each direct contact made in a 24-h period. Contact matrices were constructed and contacts for those under the age of 18 years imputed. The next generation matrix approach was used to estimate the reproduction number (Rt) for each survey. Respondents with children under 18 years estimated the number of contacts their children made in school and extracurricular settings. RESULTS: Estimated Rt values were 0.49 (95% CI: 0.29-0.69) for May, 0.48 (95% CI: 0.29-0.68) for July, 1.06 (95% CI: 0.63-1.52) for September, and 0.81 (0.47-1.17) for December. The highest proportion of reported contacts occurred within the home (51.3% in May), in 'other' locations (49.2% in July) and at work (66.3 and 65.4% in September and December). Respondents with children reported an average of 22.7 (95% CI: 21.1-24.3) (September) and 19.0 (95% CI 17.7-20.4) (December) contacts at school per day per child in attendance. CONCLUSION: The skewed distribution of reported contacts toward workplace settings in September and December combined with the number of reported school-related contacts suggest that these settings represent important opportunities for transmission emphasizing the need to support and ensure infection control procedures in both workplaces and schools.


Subject(s)
COVID-19 , Pandemics , Adolescent , Adult , Canada/epidemiology , Child , Cross-Sectional Studies , Humans , Public Health , SARS-CoV-2
20.
CMAJ ; 193(42): E1619-E1625, 2021 10 25.
Article in English | MEDLINE | ID: covidwho-1496561

ABSTRACT

BACKGROUND: Between February and June 2021, the initial wild-type strains of SARS-CoV-2 were supplanted in Ontario, Canada, by new variants of concern (VOCs), first those with the N501Y mutation (i.e., Alpha/B1.1.17, Beta/B.1.351 and Gamma/P.1 variants) and then the Delta/B.1.617 variant. The increased transmissibility of these VOCs has been documented, but knowledge about their virulence is limited. We used Ontario's COVID-19 case data to evaluate the virulence of these VOCs compared with non-VOC SARS-CoV-2 strains, as measured by risk of hospitalization, intensive care unit (ICU) admission and death. METHODS: We created a retrospective cohort of people in Ontario who tested positive for SARS-CoV-2 and were screened for VOCs, with dates of test report between Feb. 7 and June 27, 2021. We constructed mixed-effect logistic regression models with hospitalization, ICU admission and death as outcome variables. We adjusted models for age, sex, time, vaccination status, comorbidities and pregnancy status. We included health units as random intercepts. RESULTS: Our cohort included 212 326 people. Compared with non-VOC SARS-CoV-2 strains, the adjusted elevation in risk associated with N501Y-positive variants was 52% (95% confidence interval [CI] 42%-63%) for hospitalization, 89% (95% CI 67%-117%) for ICU admission and 51% (95% CI 30%-78%) for death. Increased risk with the Delta variant was more pronounced at 108% (95% CI 78%-140%) for hospitalization, 235% (95% CI 160%-331%) for ICU admission and 133% (95% CI 54%-231%) for death. INTERPRETATION: The increasing virulence of SARS-CoV-2 VOCs will lead to a considerably larger, and more deadly, pandemic than would have occurred in the absence of the emergence of VOCs.


Subject(s)
COVID-19/mortality , SARS-CoV-2/pathogenicity , Age Distribution , COVID-19/transmission , Comorbidity , Female , Hospitalization/statistics & numerical data , Humans , Intensive Care Units/statistics & numerical data , Male , Ontario/epidemiology , Pandemics , Pregnancy , Retrospective Studies , Risk Assessment , Vaccination Coverage/statistics & numerical data
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