The Canadian VirusSeq Data Portal & Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology.

The COVID-19 pandemic led to a large global effort to sequence SARS-CoV-2 genomes from patient samples to track viral evolution and inform public health response. Millions of SARS-CoV-2 genome sequences have been deposited in global public repositories. The Canadian COVID-19 Genomics Network (CanCOGeN - VirusSeq), a consortium tasked with coordinating expanded sequencing of SARS-CoV-2 genomes across Canada early in the pandemic, created the Canadian VirusSeq Data Portal, with associated data pipelines and procedures, to support these efforts. The goal of VirusSeq was to allow open access to Canadian SARS-CoV-2 genomic sequences and enhanced, standardized contextual data that were unavailable in other repositories and that meet FAIR standards (Findable, Accessible, Interoperable and Reusable). In addition, the Portal data submission pipeline contains data quality checking procedures and appropriate acknowledgement of data generators that encourages collaboration. From inception to execution, the portal was developed with a conscientious focus on strong data governance principles and practices. Extensive efforts ensured a commitment to Canadian privacy laws, data security standards, and organizational processes. This Portal has been coupled with other resources like Viral AI and was further leveraged by the Coronavirus Variants Rapid Response Network (CoVaRR-Net) to produce a suite of continually updated analytical tools and notebooks. Here we highlight this Portal, including its contextual data not available elsewhere, and the 'Duotang', a web platform that presents key genomic epidemiology and modeling analyses on circulating and emerging SARS-CoV-2 variants in Canada. Duotang presents dynamic changes in variant composition of SARS-CoV-2 in Canada and by province, estimates variant growth, and displays complementary interactive visualizations, with a text overview of the current situation. The VirusSeq Data Portal and Duotang resources, alongside additional analyses and resources computed from the Portal (COVID-MVP, CoVizu), are all open-source and freely available. Together, they provide an updated picture of SARS-CoV-2 evolution to spur scientific discussions, inform public discourse, and support communication with and within public health authorities. They also serve as a framework for other jurisdictions interested in open, collaborative sequence data sharing and analyses.

The association between phylogenetic lineage and the subclinical phenotype of pulmonary tuberculosis: A retrospective 2-cohort study.

BACKGROUND: Subclinical pulmonary tuberculosis (PTB) is an asymptomatic disease state between established TB infection and symptomatic (clinical) TB disease. It is present in 20-25% of PTB patients in high-income countries. Mycobacterium tuberculosis complex (MTBC) genetic heterogeneity, and differential host immunological responses, have been implicated in its pathogenesis. METHODS: To determine the association between MTBC lineage and PTB disease phenotype, we used two retrospective cohorts of PTB patients in Canada and two independent lineage attribution methods (DNA fingerprinting and genome sequencing). The first cohort, Cohort 1, consisted of consecutively diagnosed PTB patients between 2014 and 2020. The second, Cohort 2, consisted of newly-arrived foreign-born PTB patients who either were or were not referred for post-landing medical surveillance between 2004 and 2017. Univariable and multivariable logistic regression models were sequentially fitted to both cohorts, adjusting for age, sex, disease type, drug resistance and HIV. Evolution of radiographic features was correlated to lineage in Cohort 2. FINDINGS: Cohort 1 and 2 included 874 (209 subclinical) and 111 (44 subclinical) patients, respectively. In both cohorts, subclinical patients were more likely than clinical patients to have relapse/retreatment disease, be smear-negative, have longer times-to-culture positivity and to harbor an ancestral MTBC lineage (Indo-Oceanic or Mycobacterium africanum). Relapse/retreatment disease and ancestral MTBC lineage were independent predictors of subclinical disease (ORs and 95% CIs in Cohort 1, 1.85 [1.07,3.28], p < 0.029 and 2.30 [1.66,3.18], p < 0.001, respectively, and Cohort 2, 5.74 [1.37-24.06], p < 0.017 and 3.21 (1.29,7.97], p < 0.012, respectively). The geographic distribution of Indo-Oceanic strains causing subclinical disease was uneven. Non-progressive lung disease was more common in patients infected with ancestral than modern lineages in Cohort 2, 56.0% vs 25.4%, p < 0.005. INTERPRETATION: MTBC lineage is a strong predictor of PTB disease phenotype. The genetic drivers of this association, and the relative contribution of other explanatory variables, are unknown.

Genomic survey maps differences in the molecular complement of vesicle formation machinery between Giardia intestinalis assemblages.

Giardia intestinalis is a globally important microbial pathogen with considerable public health, agricultural, and economic burden. Genome sequencing and comparative analyses have elucidated G. intestinalis to be a taxonomically diverse species consisting of at least eight different sub-types (assemblages A-H) that can infect a great variety of animal hosts, including humans. The best studied of these are assemblages A and B which have a broad host range and have zoonotic transmissibility towards humans where clinical Giardiasis can range from asymptomatic to diarrheal disease. Epidemiological surveys as well as previous molecular investigations have pointed towards critical genomic level differences within numerous molecular pathways and families of parasite virulence factors within assemblage A and B isolates. In this study, we explored the necessary machinery for the formation of vesicles and cargo transport in 89 Canadian isolates of assemblage A and B G. intestinalis. Considerable variability within the molecular complement of the endolysosomal ESCRT protein machinery, adaptor coat protein complexes, and ARF regulatory system have previously been reported. Here, we confirm inter-assemblage, but find no intra-assemblage variation within the trafficking systems examined. This variation includes losses of subunits belonging to the ESCRTIII as well as novel lineage specific duplications in components of the COPII machinery, ARF1, and ARFGEF families (BIG and CYTH). Since differences in disease manifestation between assemblages A and B have been controversially reported, our findings may well have clinical implications and even taxonomic, as the membrane trafficking system underpin parasite survival, pathogenesis, and propagation.

Genomic analysis of Streptococcus pneumoniae serogroup 20 isolates in Alberta, Canada from 1993-2019.

In the province of Alberta, Canada, invasive disease caused by Streptococcus pneumoniae serogroup 20 (serotypes 20A/20B) has been increasing in incidence. Here, we characterize provincial invasive serogroup 20 isolates collected from 1993 to 2019 alongside invasive and non-invasive serogroup 20 isolates from the Global Pneumococcal Sequencing (GPS) Project collected from 1998 to 2015. Trends in clinical metadata and geographic location were evaluated, and serogroup 20 isolate genomes were subjected to molecular sequence typing, virulence and antimicrobial resistance factor mining, phylogenetic analysis and pangenome calculation. Two hundred and seventy-four serogroup 20 isolates from Alberta were sequenced, and analysed along with 95 GPS Project genomes. The majority of invasive Alberta serogroup 20 isolates were identified after 2007 in primarily middle-aged adults and typed predominantly as ST235, a sequence type that was rare among GPS Project isolates. Most Alberta isolates carried a full-length whaF capsular gene, suggestive of serotype 20B. All Alberta and GPS Project genomes carried molecular resistance determinants implicated in fluoroquinolone and macrolide resistance, with a few Alberta isolates exhibiting phenotypic resistance to azithromycin, clindamycin, erythromycin, tetracycline and trimethoprim-sulfamethoxazole, as well as non-susceptibility to tigecycline. All isolates carried multiple virulence factors including those involved in adherence, immune modulation and nutrient uptake, as well as exotoxins and exoenzymes. Phylogenetically, Alberta serogroup 20 isolates clustered with predominantly invasive GPS Project isolates from the USA, Israel, Brazil and Nepal. Overall, this study highlights the increasing incidence of invasive S. pneumoniae serogroup 20 disease in Alberta, Canada, and provides insights into the genetic and clinical characteristics of these isolates within a global context.

Tracking SARS-CoV-2 Omicron lineages using real-time reverse transcriptase PCR assays and prospective comparison with genome sequencing.

Omicron has become the dominant SARS-CoV-2 variant globally since December 2021, with distinct waves being associated with separate Omicron sublineages. Rapid detection of BA.1, BA.2, BA.4, and BA.5 was accomplished in the province of Alberta, Canada, through the design and implementation of real-time reverse transcriptase PCR assays targeting S:N501Y, S:ins214EPE, S:H69/V70, ORF7b:L11F, and M:D3N. Using the combination of results for each of these markers, samples could be designated as belonging to sublineages within BA.1, BA.2, BA.4, or BA.5. The analytical sensitivity of these markers ranged from 132 to 2229 copies/mL and in-laboratory accuracy was 98.9-100%. A 97.3% agreement using 12,592 specimens was demonstrated for the assays compared to genome sequencing. The use of these assays, combined with genome sequencing, facilitated the surveillance of SARS-CoV-2 lineages throughout a BA.5-dominated period.

Genomic characterization of emerging invasive Streptococcus agalactiae serotype VIII in Alberta, Canada.

Invasive Group B Streptococcus (GBS) can infect pregnant women, neonates, and older adults. Invasive GBS serotype VIII is infrequent in Alberta; however, cases have increased in recent years. Here, genomic analysis was used to characterize fourteen adult invasive serotype VIII isolates from 2009 to 2021. Trends in descriptive clinical data and antimicrobial susceptibility results were evaluated for invasive serotype VIII isolates from Alberta. Isolate genomes were sequenced and subjected to molecular sequence typing, virulence and antimicrobial resistance gene identification, phylogenetic analysis, and pangenome determination. Multilocus sequencing typing identified eight ST42 (Clonal Complex; CC19), four ST1 (CC1), and two ST2 (CC1) profiles. Isolates were susceptible to penicillin, erythromycin, chloramphenicol, and clindamycin, apart from one isolate that displayed erythromycin and inducible clindamycin resistance. All isolates carried genes for peptide antibiotic resistance, three isolates for tetracycline resistance, and one for macrolide, lincosamide, and streptogramin resistance. All genomes carried targets currently being considered for protein-based vaccines (e.g., pili and/or Alpha family proteins). Overall, invasive GBS serotype VIII is emerging in Alberta, primarily due to ST42. Characterization and continued surveillance of serotype VIII will be important for outbreak prevention, informing vaccine development, and contributing to our understanding of the global epidemiology of this rare serotype.

Patient and ward related risk factors in a multi-ward nosocomial outbreak of COVID-19: Outbreak investigation and matched case-control study.

BACKGROUND: Risk factors for nosocomial COVID-19 outbreaks continue to evolve. The aim of this study was to investigate a multi-ward nosocomial outbreak of COVID-19 between 1st September and 15th November 2020, occurring in a setting without vaccination for any healthcare workers or patients. METHODS: Outbreak report and retrospective, matched case-control study using incidence density sampling in three cardiac wards in an 1100-bed tertiary teaching hospital in Calgary, Alberta, Canada. Patients were confirmed/probable COVID-19 cases and contemporaneous control patients without COVID-19. COVID-19 outbreak definitions were based on Public Health guidelines. Clinical and environmental specimens were tested by RT-PCR and as applicable quantitative viral cultures and whole genome sequencing were conducted. Controls were inpatients on the cardiac wards during the study period confirmed to be without COVID-19, matched to outbreak cases by time of symptom onset dates, age within ± 15 years and were admitted in hospital for at least 2 days. Demographics, Braden Score, baseline medications, laboratory measures, co-morbidities, and hospitalization characteristics were collected on cases and controls. Univariate and multivariate conditional logistical regression was used to identify independent risk factors for nosocomial COVID-19. RESULTS: The outbreak involved 42 healthcare workers and 39 patients. The strongest independent risk factor for nosocomial COVID-19 (IRR 3.21, 95% CI 1.47-7.02) was exposure in a multi-bedded room. Of 45 strains successfully sequenced, 44 (97.8%) were B.1.128 and differed from the most common circulating community lineages. SARS-CoV-2 positive cultures were detected in 56.7% (34/60) of clinical and environmental specimens. The multidisciplinary outbreak team observed eleven contributing events to transmission during the outbreak. CONCLUSIONS: Transmission routes of SARS-CoV-2 in hospital outbreaks are complex; however multi-bedded rooms play a significant role in the transmission of SARS-CoV-2.

The DataHarmonizer: a tool for faster data harmonization, validation, aggregation and analysis of pathogen genomics contextual information.

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, they must be interpreted using contextual data (metadata). Contextual data include 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 their 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.

Evolving strategy for an evolving virus: Development of real-time PCR assays for detecting all SARS-CoV-2 variants of concern.

In order to detect the SARS-CoV-2 variants of concern (VOCs), five real-time reverse transcriptase PCR (rRT-PCR) assays were designed to target the critical discriminatory mutations responsible for the following amino acid changes in the spike protein: two Δ69-70 + N501Y + E gene triplexes (one optimized for Alpha [B.1.1.7] and one optimized for Omicron [B.1.1.529]), a K417N + 242-244 wild-type duplex, a K417T + E484K duplex, and a L452R + P681 + E484Q triplex. Depending on the assay, sensitivity was 98.97-100% for the detection of known VOC-positive samples, specificity was 97.2-100%, limit of detection was 2-116 copies/reaction, intra- and interassay variability was less than 5%, and no cross-reactivity with common respiratory pathogens was observed with any assay. A subset of rRT-PCR- positive VOC samples were further characterized by genome sequencing. A comparison of the lineage designation by the VOC rRT-PCR assays and genome sequencing for the detection of the Alpha, Beta, Gamma, Delta and Omicron variants showed clinical sensitivities of 99.97-100 %, clinical specificities of 99.6-100 %, positive predictive values of 99.8-100%, and negative predictive values of 99.98-100 %. We have implemented these rRT-PCR assays targeting discriminatory single nucleotide polymorphisms for ongoing VOC screening of SARS-CoV-2 positive samples for surveillance purposes. This has proven extremely useful in providing close to real-time molecular surveillance to monitor the emergence of Alpha, the replacement of Alpha by Delta, and the replacement of Delta by Omicron. While the design, validation and implementation of the variant specific PCR targets is an ever-evolving approach, we find the turn-around-time, high throughput and sensitivity to be a useful complementary approach for SARS-CoV-2 genome sequencing for surveillance purposes in the province of Alberta, Canada.

How much do smear-negative patients really contribute to tuberculosis transmissions? Re-examining an old question with new tools.

BACKGROUND: Sputum smear microscopy is a common surrogate for tuberculosis infectiousness. Previous estimates that smear-negative patients contribute 13-20% of transmissions and are, on average, 20 to 25% as infectious as smear-positive cases are understood to be high. Herein, we use an ideal real-world setting, a comprehensive dataset, and new high-resolution techniques to more accurately estimate the true transmission risk of smear-negative cases. METHODS: We treated all adult culture-positive pulmonary TB patients diagnosed in the province of Alberta, Canada from 2003 to 2016 as potential transmitters. The primary data sources were the Alberta TB Registry and the Provincial Laboratory for Public Health. We measured, as primary outcomes, the proportion of transmissions attributable to smear-negative sources and the relative transmission rate. First, we replicated previous studies by using molecular (DNA) fingerprint clustering. Then, using a prospectively collected registry of TB contacts, we defined transmission events as active TB amongst identified contacts who either had a 100% DNA fingerprint match to the source case or a clinical diagnosis. We supplemented our analysis with genome sequencing on temporally and geographically linked DNA fingerprint clusters of cases not identified as contacts. FINDINGS: There were 1176 cases, 563 smear-negative and 613 smear-positive, and 23,131 contacts. Replicating previous studies, the proportion of transmissions attributable to smear-negative source cases was 16% (95% CI, 12-19%) and the relative transmission rate was 0.19 (95% CI, 0.14-0.26). With our combined approach, the proportion of transmission was 8% (95% CI, 3-14%) and the relative transmission rate became 0.10 (95% CI, 0.05-0.19). INTERPRETATION: When we examined the same outcomes as in previous studies but refined transmission ascertainment with the addition of conventional epidemiology and genomics, we found that smear-negative cases were ∼50% less infectious than previously thought. FUNDING: Alberta Innovates Health Solutions.

Characterization of Swine Influenza A(H1N2) Variant, Alberta, Canada, 2020.

Influenza strains circulating among swine populations can cause outbreaks in humans. In October 2020, we detected a variant influenza A subtype H1N2 of swine origin in a person in Alberta, Canada. We initiated a public health, veterinary, and laboratory investigation to identify the source of the infection and determine whether it had spread. We identified the probable source as a local pig farm where a household contact of the index patient worked. Phylogenetic analysis revealed that the isolate closely resembled strains found at that farm in 2017. Retrospective and prospective surveillance using molecular testing did not identify any secondary cases among 1,532 persons tested in the surrounding area. Quick collaboration between human and veterinary public health practitioners in this case enabled a rapid response to a potential outbreak.

SARS-COV-2 recombinant Receptor-Binding-Domain (RBD) induces neutralizing antibodies against variant strains of SARS-CoV-2 and SARS-CoV-1.

SARS-CoV-2 is the etiological agent of COVID19. There are currently several licensed vaccines approved for human use and most of them target the spike protein in the virion envelope to induce protective immunity. Recently, variants that spread more quickly have emerged. There is evidence that some of these variants are less sensitive to neutralization in vitro, but it is not clear whether they can evade vaccine induced protection. In this study, we tested SARS-CoV-2 spike RBD as a vaccine antigen and explored the effect of formulation with Alum/MPLA or AddaS03 adjuvants. Our results show that RBD induces high titers of neutralizing antibodies and activates strong cellular immune responses. There is also significant cross-neutralization of variants B.1.1.7 and B.1.351 and to a lesser extent, SARS-CoV-1. These results indicate that recombinant RBD can be a viable candidate as a stand-alone vaccine or as a booster shot to diversify our strategy for COVID19 protection.

Precision Response to the Rise of the SARS-CoV-2 B.1.1.7 Variant of Concern by Combining Novel PCR Assays and Genome Sequencing for Rapid Variant Detection and Surveillance.

SARS-CoV-2 variants of concern (VOCs) have emerged as a global threat to the COVID-19 pandemic response. We implemented a combined approach to quickly detect known VOCs while continuously monitoring for evolving mutations of the virus. To rapidly detect VOCs, two real-time reverse transcriptase PCR assays were designed and implemented, targeting the spike gene H69/V70 deletion and the N501Y mutation. The H69/V70 deletion and N501Y mutation assays demonstrated accuracies of 98.3% (95% CI 93.8 to 99.8) and 100% (95% CI 96.8 to 100), limits of detection of 1,089 and 294 copies/ml, and percent coefficients of variation of 0.08 to 1.16% and 0 to 2.72% for the two gene targets, respectively. No cross-reactivity with common respiratory pathogens was observed with either assay. Implementation of these tests allowed the swift escalation in testing for VOCs from 2.2% to ∼100% of all SARS-CoV-2-positive samples over 12 January to 9 February 2021, and resulted in the detection of a rapid rise of B.1.1.7 cases within the province of Alberta, Canada. A prospective comparison of the VOC assays to genome sequencing for the detection of B.1.1.7, combined detection of P.1 and B.1.351, and wild-type (i.e., non-VOC) lineages showed sensitivities of 98.2 to 100%, specificities of 98.9 to 100%, positive predictive values of 76.9% to 100%, and negative predictive values of 96 to 100%. Variant screening results inform sampling strategies for regular surveillance by genome sequencing, thus allowing rapid identification of known VOCs while continuously monitoring the evolution of SARS-CoV-2 in the province. IMPORTANCE Different strains, or variants, of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, the virus that causes COVID-19) have emerged that have higher levels of transmission, less susceptibility to our immune response, and possibly cause more severe disease than previous strains of the virus. Rapid detection of these variants of concern is important to help contain them and prevent them from spreading widely within the population. This study describes two newly developed tests that are able to identify and differentiate the variants of concern from regular strains of SARS-CoV-2. These tests are faster and simpler than the main, gold standard method of identifying variants of concern (genome sequencing). These tests also demonstrated a high correlation with genome sequencing and allowed for the rapid and accurate detection of the rise of B.1.1.7 (one of the variants of concern) in the province of Alberta, Canada.

Phenotypic changes in group B streptococci grown in the presence of the polyols, erythritol, sorbitol and mannitol.

BACKGROUND: Group B streptococci (GBS) are important neonatal bacterial pathogens that can cause severe invasive disease in the newborn. It is thought that in many cases of invasive neonatal GBS disease, the bacteria ascend the vagina into the uterus and infect the amniotic fluid surrounding the fetus. Important constituents of this environment include the polyols or sugar alcohols of which erythritol, sorbitol and mannitol are examples. The aim of our study was to investigate the effect of polyols on GBS grown in media containing these sugar alcohols. RESULTS: GBS incubated in varying concentrations of polyols (erythritol, sorbitol or mannitol) did not display any significant enhancement or inhibition of bacterial growth. However, growth of GBS in the presence of erythritol significantly increased the surface expression of GBS-PGK (a plasminogen binding protein) 1.25 to 1.5-fold depending on the erythritol concentration and significantly enhanced the survival in human blood 3X to 18X depending on the concentration of polyol used. Interestingly, GBS grown in 1% erythritol significantly increased invasion by the bacteria of HeLa cells (epithelial cell line) (150% vs 100%) however, at higher concentrations (2% or 4% of polyol) the number of CFUs was significantly reduced (55-75% vs 100%) suggesting higher concentrations of polyols may inhibit invasion. Erythritol also increased GBS hemolytic activity as well as enhancing biofilm formation 1.4X to 3.3X depending on the concentration of polyol used. CONCLUSIONS: GBS grown in the presence of polyols alters the bacteria's phenotype resulting in changes associated with GBS virulence. This effect was greatest for the polyol erythritol.

Histoplasmosis acquired in Alberta, Canada: an epidemiological and genomic study.

BACKGROUND: The classic geographical range of histoplasmosis in North America primarily includes the states and provinces adjacent to the Ohio, Mississippi, and St Lawrence riverways. Although Alberta, Canada is not typically considered a region of risk for histoplasmosis, cases with suspected local acquisition have been reported. We aimed to investigate the epidemiology and geographical distribution of cases of histoplasmosis in Alberta to assess evidence for local acquisition of infections, using genomic analysis for corroboration. METHODS: We did an epidemiological and genomic investigation, in which laboratory-confirmed cases of histoplasmosis were reviewed in Alberta from 2011, when the disease became reportable, until 2018. We used data attained from Alberta Health. Travel and exposure histories and clinical features were reviewed. Definite local acquisition was defined as a case without previous travel outside Alberta or associated with a common-source outbreak within the province, whereas probable local acquisition was a sporadic case with travel outside Alberta but compelling local exposures. Genomes of selected case isolates were analysed, including those from cases suspected to have been locally acquired and imported. FINDINGS: Between Jan 1, 2011, and June 30, 2018, 45 cases of histoplasmosis were identified. Participants had a median age of 53 years (range 17-77) and 32 [71%] were male. Among 34 patients with documented travel histories, ten (29%) had never left the province. 11 cases were of definite local acquisition, including eight cases from three common-source outbreaks and three sporadic cases in patients who had never travelled outside Alberta. The common-source outbreaks all involved exposure to bats or their droppings in chimneys or attics of private dwellings or churches. Four patients had travelled outside Alberta but compelling evidence was seen for local exposure to bat guano. Genome sequencing showed that isolates from cases of definite and probable local acquisition clustered together and were genetically distinct from isolates from suspected imported cases and other published isolates. INTERPRETATION: Using epidemiological and genomic analyses, we established that cases of histoplasmosis have been acquired in Alberta, thus expanding the geographical range of Histoplasma spp much further northwest than was previously appreciated. Histoplasmosis should be considered in patients with compatible symptoms outside areas of classic geographical risk. FUNDING: None.

Retrospective testing of respiratory specimens for COVID-19 to assess for earlier SARS-CoV-2 infections in Alberta, Canada.

Background: The first case of coronavirus disease 2019 (COVID-19) in Alberta, Canada, was confirmed on March 5, 2020. Because the virus testing criteria had changed significantly over this time period, we wanted to ascertain whether previous cases of COVID-19 had been missed in the province. Methods: Our aim was to retrospectively evaluate specimens submitted for respiratory virus testing from December 1, 2019, through March 7, 2020, for undetected severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections before the first confirmed case. Results: Testing of 23,517 samples (representing 23,394 patients) identified 1 patient positive for SARS-CoV-2. This specimen was collected on February 24, 2020, from a patient with symptoms consistent with COVID-19 who had recently returned from the western United States. Phylogenetic analysis confirmed this viral isolate belonged to lineage B.1. The epidemiology of this case is consistent with those of other early cases before sustained community transmission, which included a travel history outside of Canada. Conclusion: This exercise provides support that local public health pandemic planning was satisfactory and timely.

Historique: Le premier cas de maladie à coronavirus 2019 (COVID-19) en Alberta, au Canada, a été confirmé le 15 mars 2020. Puisque les critères de dépistage ont beaucoup évolué pendant cette période, les chercheurs voulaient vérifier si des cas antérieurs de COVID-19 avaient été omis dans la province. Méthodologie: Les chercheurs ont procédé à l'évaluation rétrospective d'échantillons soumis en vue du dépistage d'un virus respiratoire entre le 1er décembre 2019 et le 7 mars 2020, afin de retracer les infections par le coronavirus 2 du syndrome respiratoire aigu sévère (SARS-CoV-2) non décelées avant le premier cas confirmé. Résultats: Le dépistage de 23 517 échantillons (représentant 23 394 patients) a fait ressortir un patient positif au SARS-CoV-2. Le prélèvement avait été effectué le 24 février 2020 chez un patient éprouvant des symptômes correspondant à la COVID-19 revenu récemment de l'ouest des États-Unis. L'analyse phylogénétique a confirmé que l'isolat viral appartenait à la lignée B.1. L'épidémiologie de ce cas est compatible avec celle des autres premiers cas précédant une transmission communautaire soutenue, qui incluait un voyage à l'extérieur du Canada. Conclusion: Cet exercice appuie la pertinence et la rapidité de la planification sanitaire locale de la pandémie.

Interim estimates of 2019/20 vaccine effectiveness during early-season co-circulation of influenza A and B viruses, Canada, February 2020.

Interim results from Canada's Sentinel Practitioner Surveillance Network show that during a season characterised by early co-circulation of influenza A and B viruses, the 2019/20 influenza vaccine has provided substantial protection against medically-attended influenza illness. Adjusted VE overall was 58% (95% confidence interval (CI): 47 to 66): 44% (95% CI: 26 to 58) for A(H1N1)pdm09, 62% (95% CI: 37 to 77) for A(H3N2) and 69% (95% CI: 57 to 77) for influenza B viruses, predominantly B/Victoria lineage.

Mycobacterium chimaera Encephalitis Following Cardiac Surgery: A New Syndrome.

We report the cases of 3 patients with fatal, disseminated Mycobacterium chimaera infections following cardiac surgeries. Progressive neurocognitive decline and death were explained by active granulomatous encephalitis, with widespread involvement of other organs. This syndrome is clinically elusive and, thus, may have caused deaths in prior reported series.

Genomic Epidemiology of Major Extraintestinal Pathogenic Escherichia coli Lineages Causing Urinary Tract Infections in Young Women Across Canada.

BACKGROUND: A few extraintestinal pathogenic Escherichia coli (ExPEC) multilocus sequence types (STs) cause the majority of community-acquired urinary tract infections (UTIs). We examine the genomic epidemiology of major ExPEC lineages, specifically factors associated with intestinal acquisition. METHODS: A total of 385 women with UTI caused by E. coli across Canada were asked about their diet, travel, and other exposures. Genome sequencing was used to determine both ST and genomic similarity. Logistic regression was used to identify factors associated with the acquisition of and infection with major ExPEC STs relative to minor ExPEC STs. RESULTS: ST131, ST69, ST73, ST127, and ST95 were responsible for 54% of all UTIs. Seven UTI clusters were identified, but genomes from the ST95, ST127, and ST420 clusters exhibited as few as 3 single nucleotide variations across the entire genome, suggesting recent acquisition. Furthermore, we identified a cluster of UTIs caused by 6 genetically-related ST1193 isolates carrying mutations in gyrA and parC. The acquisition of and infection with ST69, ST95, ST127, and ST131 were all associated with increased travel. The consumption of high-risk foods such as raw meat or vegetables, undercooked eggs, and seafood was associated with acquisition of and infection with ST69, ST127, and ST131, respectively. CONCLUSIONS: Reservoirs may aid in the dissemination of pandemic ExPEC lineages in the community. Identifying ExPEC reservoirs may help prevent future emergence and dissemination of high-risk lineages within the community setting.

Paradoxical clade- and age-specific vaccine effectiveness during the 2018/19 influenza A(H3N2) epidemic in Canada: potential imprint-regulated effect of vaccine (I-REV).

IntroductionThe Canadian Sentinel Practitioner Surveillance Network reports vaccine effectiveness (VE) for the 2018/19 influenza A(H3N2) epidemic.AimTo explain a paradoxical signal of increased clade 3C.3a risk among 35-54-year-old vaccinees, we hypothesise childhood immunological imprinting and a cohort effect following the 1968 influenza A(H3N2) pandemic.MethodsWe assessed VE by test-negative design for influenza A(H3N2) overall and for co-circulating clades 3C.2a1b and 3C.3a. VE variation by age in 2018/19 was compared with amino acid variation in the haemagglutinin glycoprotein by year since 1968.ResultsInfluenza A(H3N2) VE was 17% (95% CI: -13 to 39) overall: 27% (95% CI: -7 to 50) for 3C.2a1b and -32% (95% CI: -119 to 21) for 3C.3a. Among 20-64-year-olds, VE was -7% (95% CI: -56 to 26): 6% (95% CI: -49 to 41) for 3C.2a1b and -96% (95% CI: -277 to -2) for 3C.3a. Clade 3C.3a VE showed a pronounced negative dip among 35-54-year-olds in whom the odds of medically attended illness were > 4-fold increased for vaccinated vs unvaccinated participants (p < 0.005). This age group was primed in childhood to influenza A(H3N2) viruses that for two decades following the 1968 pandemic bore a serine at haemagglutinin position 159, in common with contemporary 3C.3a viruses but mismatched to 3C.2a vaccine strains instead bearing tyrosine.DiscussionImprinting by the first childhood influenza infection is known to confer long-lasting immunity focused toward priming epitopes. Our findings suggest vaccine mismatch may negatively interact with imprinted immunity. The immunological mechanisms for imprint-regulated effect of vaccine (I-REV) warrant investigation.