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Pathogen genomics is a critical tool for public health surveillance, infection control, outbreak investigations, as well as research. In order to make use of pathogen genomics data, it must be interpreted using contextual data (metadata). Contextual data includes sample metadata, laboratory methods, patient demographics, clinical outcomes, and epidemiological information. However, the variability in how contextual information is captured by different authorities and how it is encoded in different databases poses challenges for data interpretation, integration, and its use/re-use. The DataHarmonizer is a template-driven spreadsheet application for harmonizing, validating, and transforming genomics contextual data into submission-ready formats for public or private repositories. The tool’s web browser-based JavaScript environment enables validation and its offline functionality and local installation increases data security. The DataHarmonizer was developed to address the data sharing needs that arose during the COVID-19 pandemic, and was used by members of the Canadian COVID Genomics Network (CanCOGeN) to harmonize SARS-CoV-2 contextual data for national surveillance and for public repository submission.In order to support coordination of international surveillance efforts, we have partnered with the Public Health Alliance for Genomic Epidemiology to also provide a template conforming to its SARS-CoV-2 contextual data specification for use worldwide. Templates are also being developed for One Health and foodborne pathogens. Overall, the DataHarmonizer tool improves the effectiveness and fidelity of contextual data capture as well as its subsequent usability. Harmonization of contextual information across authorities, platforms and systems globally improves interoperability and reusability of data for concerted public health and research initiatives to fight the current pandemic and future public health emergencies. While initially developed for the COVID-19 pandemic, its expansion to other data management applications and pathogens is already underway.
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COVID-19RESUMEN
Background: We report characteristics and outcomes of adults admitted to Canadian Immunization Research Network (CIRN) Serious Outcomes Surveillance (SOS) Network hospitals with COVID-19 in 2020. Methods: Adult patients with laboratory-confirmed COVID-19 admitted to eleven sites in Ontario, Quebec, Alberta and Nova Scotia up to December 31, 2020 were enrolled in this prospective observational cohort study. Age, sex, demographics, housing, exposure characteristics, Clinical Frailty Scale, comorbidities, and outcomes including length of stay, intensive care unit (ICU) admission, mechanical ventilation, and survival were conducted. Descriptive analyses and multivariable logistic regressions were conducted. Findings: Among 2011 patients, mean age was 71·0 (range 19-105) years. 45·7% were women and 74·0% were white. 21·5% were admitted from Assisted Living facilities, 8·2% from long term care, and 2·1% from homeless shelters. The full spectrum of frailty was represented in both younger and older age groups. The majority (61·7% of adults <65 and 91·2% of those >=65) had at least one underlying comorbidity and 27·2% had obesity. Mortality was 14·3% among those not admitted to ICU, and 24·6% for those admitted to ICU. Older age and higher frailty were associated with reduced ICU admission but increased mortality. Obesity was independently associated with ICU admission but not with death. Associations between underlying comorbidities and adverse outcomes were attenuated but persisted when adjusting for frailty.Interpretation: Frailty and age were independent predictors of lower ICU use and higher mortality; when accounting for frailty, obesity was not an independent predictor of mortality, and associations of comorbidities with mortality were weakened.Funding Statement: Funding was provided by the Public Health Agency of Canada and the Canadian Institutes of Health Research.Declaration of Interests: MKA reports grant funding from the Public Health Association of Canada, CIHR, Canadian Frailty Network, Sanofi Pasteur and GSK group of companies, and payments from Pfizer, Sanofi Pasteur and Seqirus outside the submitted work. AM reports payments from GSK, Seqirus and Sanofi Pasteur, outside the submitted work. JEM reports payments from RestorBio, Sanofi, GSK, Merck and Medicago outside of the submitted work. TFH reports grants from Pfizer and GSK. ML reports payments from Sanofi, Medicago, Sequirus, and Pfizer outside the submitted work. SAM reports grants and payments from Pfizer, GSK, Merck, Novartis and Sanofi, outside the submitted work. JG, JJL, GB, LV, ME, DM-C, AA, KW, ST, SS, AMc and KK report no conflicts of interest.Ethics Approval Statement: The protocol for active COVID-19 surveillance has been approved by each local site’s Research Ethics Board.
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COVID-19 , Enfermedad de Niemann-Pick Tipo C , Obesidad , Distrofia MiotónicaRESUMEN
Background: As of March 2021, three SARS-CoV-2 variants of concern (VOC) have been identified (B.1.1.7, B.1.351 and P.1) and been detected in over 111 countries. Despite their widespread circulation, little is known about their transmission characteristics. There is a need to understand current evidence on VOCs before practice and policy decisions can be made. This study aimed to map the evidence related to the transmission characteristics of three VOCs. Methods: A rapid scoping review approach was used. Seven databases were searched on February 21, 2021 for terms related to VOCs, transmission, public health and health systems. A grey literature search was conducted on February 26, 2021. Title/abstracts were screened independently by one reviewer, while full texts were screened in duplicate. Data were extracted using a standardized form which was co-developed with infectious disease experts. A second data extractor verified the results. Studies were included if they reported on at least one of the VOCs and transmissibility. Animal studies and modeling studies were excluded. The final report was reviewed by content experts. Results: Of the 1796 articles and 67 grey literature sources retrieved, 16 papers and 7 grey sources were included. Included studies used a wide range of designs and methods. The majority (n=20) reported on B.1.1.7. Risk of transmission, reported in 15 studies, was 45-71% higher for B.1.1.7 compared to non-VOCs, while R0 was 75-78% higher and the reported Rt ranged from 1.1-2.8. There was insufficient evidence on the transmission risk of B.1.35.1 and P.1. Twelve studies discussed the mechanism of transmission of VOCs. Evidence suggests an increase in viral load among VOCs based on cycle threshold values, and possible immune evasion due to increased ACE2 binding capacity of VOCs. However, findings should be interpreted with caution due to the variability in study designs and methods. Conclusion: VOCs appear to be more transmissible than non-VOCs, however the mechanism of transmission is unclear. With majority of studies focusing on the B.1.1.7 VOC, more research is needed to build upon these preliminary findings. It is recommended that decision-makers continue to monitor VOCs and emerging evidence on this topic to inform public health policy.
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Enfermedades TransmisiblesRESUMEN
Background The SARS-CoV-2 (Severe Acute Respiratory Syndrome coronavirus 2) has led to more than 114 million COVID-19 cases and >2.5 million deaths worldwide. Epidemiological analysis has revealed that the risk of developing severe COVID-19 increases with age. Despite a disproportionate number of older individuals and long-term care facilities being affected by SARS-CoV-2 and COVID-19, very little is understood about the immune responses and development of humoral immunity in the extremely old person after SARS-CoV-2 infection. Here we investigated the development of humoral immunity in centenarians following a SARS-CoV-2 outbreak in a long-term care facility. Methods Extreme aged individuals and centenarians who were residents in a long-term care facility and infected with or exposed to SARS-CoV-2 were investigated for the development of antibodies to SARS-CoV-2. Blood samples were collected from positive and bystander individuals 30 and 60 days after original diagnosis of SARS-CoV-2 infection. Plasma was used to quantify IgG, IgA, and IgM isotypes and subsequent subclasses of antibodies specific for SARS-CoV-2 spike protein. The function of anti-spike was then assessed by virus neutralization assays against the native SARS-CoV-2 virus. Findings Fifteen long-term care residents were investigated for SARS-CoV-2 infection. All individuals had a Clinical Frailty scale score ≥5 and were of extreme older age or were centenarians. Six women with a median age of 98.8 years tested positive for SARS-CoV-2. Anti-spike IgG antibody titers were the highest titers observed in our cohort with all IgG positive individuals having virus neutralization ability. Additionally, 5 out of the 6 positive participants had a robust IgA anti-SARS-CoV-2 response. In all 5, antibodies were detected after 60 days from initial diagnosis. Interpretation Extreme older frail individuals and centenarians were able to elicit robust IgG and IgA antibodies directed toward SARS-CoV-2 spike protein. The antibodies were able to neutralize the virus. Humoral responses were still detectable after 60 days from initial diagnosis. Together, these data suggest that recovered participants who are of extreme old age would be protected if re-exposed to the same SARS-CoV-2 viral variant. Considering the threat of SARS-CoV-2 and COVID-19 to older age groups and long-term care facilities, the humoral responses to SARS-CoV-2 in older age groups is of public health importance and has implications to vaccine responses. Funding Canadian Institutes of Health Research (CIHR), NIH/NIAID, Genome Atlantic. VIDO receives operational funding from the Canada Foundation for Innovation through the Major Science Initiatives Fund and by Government of Saskatchewan through Innovation Saskatchewan.