Réjean Dion’s research while affiliated with Institut National de Santé Publique du Québec (INSPQ) and other places

Background The coronavirus disease (COVID-19) pandemic has affected residents in long-term care facilities (LTCF) significantly. Understanding transmission dynamics in this setting is crucial to control the spread of COVID-19 in this population. Using whole genome sequencing (WGS) of SARS-CoV-2, we aimed to delineate the points of introduction and transmission pathways in a large LTCF in Quebec, Canada. Methods Between 2020-10-28 and 2021-01-09, COVID-19 cases occurred in 102 residents and 111 HCW at a 387-bed LTCF; cases were distributed in 11 units on 6 floors. As part of outbreak analysis, SARS-CoV-2 isolates underwent WGS using the Oxford Nanopore Minion and the Artic V3 protocol. Lineage attribution and sequence types (ST, within 3 mutations) were assigned based on Pangolin classification and variant analysis. Epidemiologic data including date of positive PCR test, resident room number and HCW work location were collected. Self-reported high-risk exposures were collected by HCW questionnaire via phone interview after consent. Cases and their ST, geo-temporal relations and HCW-reported exposures were examined via network plots and geography-based epidemic curves to infer points of introduction and paths of transmission. Results Of 170 isolates available from 100/102 residents and 70/111 HCW, 130 (76.4%) were successfully sequenced. Phylogenetic analysis revealed 7 separate introductions to the LTCF. Grouping of ST by units was observed, with temporal appearance of ST supporting HCW introduction in 7/11 units. Proportion of phone interview completion was low at 35% (26/70). Few HCW recalled specific high-risk exposures. Recalled exposures supported by genetic linkage revealed potential between-unit introductions from HCW-to-HCW transmission at work and outside the workplace (e.g. carpooling). On one unit, a wandering resident was identified as a likely source of transmission to other residents (Figure 1). Network plot of cases clustered by geographic unit, colour-coded by sequence type. Circles represent residents; addition signs represent healthcare workers. Blue lines represent identified high-risk exposures. Node labels represent floor and unit identifiers; 2 units per floor. Conclusion We demonstrate the complex genomic epidemiology of a multi-unit LTCF outbreak, putting into evidence the importance of a multi-faceted approach to limit transmission. This analysis highlights the utility of using WGS to uncover unsuspected transmission routes, such as HCW contact outside work, which can prompt new infection control measures. Disclosures All Authors: No reported disclosures

Background Québec was the Canadian province most impacted by COVID-19, with 401,462 cases as of September 24th, 2021, and 11,347 deaths due mostly to a very severe first pandemic wave. In April 2020, we assembled the Coronavirus Sequencing in Québec (CoVSeQ) consortium to sequence SARS-CoV-2 genomes in Québec to track viral introduction events and transmission within the province. Methods Using genomic epidemiology, we investigated the arrival of SARS-CoV-2 to Québec. We report 2921 high-quality SARS-CoV-2 genomes in the context of > 12,000 publicly available genomes sampled globally over the first pandemic wave (up to June 1st, 2020). By combining phylogenetic and phylodynamic analyses with epidemiological data, we quantify the number of introduction events into Québec, identify their origins, and characterize the spatiotemporal spread of the virus. Results Conservatively, we estimated approximately 600 independent introduction events, the majority of which happened from spring break until 2 weeks after the Canadian border closed for non-essential travel. Subsequent mass repatriations did not generate large transmission lineages (> 50 sequenced cases), likely due to mandatory quarantine measures in place at the time. Consistent with common spring break and “snowbird” destinations, most of the introductions were inferred to have originated from Europe via the Americas. Once introduced into Québec, viral lineage sizes were overdispersed, with a few lineages giving rise to most infections. Consistent with founder effects, the earliest lineages to arrive tended to spread most successfully. Fewer than 100 viral introductions arrived during spring break, of which 7–12 led to the largest transmission lineages of the first wave (accounting for 52–75% of all sequenced infections). These successful transmission lineages dispersed widely across the province. Transmission lineage size was greatly reduced after March 11th, when a quarantine order for returning travellers was enacted. While this suggests the effectiveness of early public health measures, the biggest transmission lineages had already been ignited prior to this order. Conclusions Combined, our results reinforce how, in the absence of tight travel restrictions or quarantine measures, fewer than 100 viral introductions in a week can ensure the establishment of extended transmission chains.

Using genomic epidemiology, we investigated the arrival of SARS-CoV-2 to Québec, the Canadian province most impacted by COVID-19, with >280,000 positive cases and >10,000 deaths in a population of 8.5 million as of March 1st, 2021. We report 2,921 high-quality SARS-CoV-2 genomes in the context of >12,000 publicly available genomes sampled globally over the first pandemic wave (up to June 1st, 2020). By combining phylogenetic and phylodynamic analyses with epidemiological data, we quantify the number of introduction events into Québec, identify their origins, and characterize the spatio-temporal spread of the virus. Conservatively, we estimated at least 500 independent introduction events, the majority of which happened from spring break until two weeks after the Canadian border closed for non-essential travel. Subsequent mass repatriations did not generate large transmission lineages (>50 cases), likely due to mandatory quarantine measures in place at the time. Consistent with common spring break and 'snowbird' destinations, most of the introductions were inferred to have originated from Europe via the Americas. Fewer than 100 viral introductions arrived during spring break, of which 5-10 led to the largest transmission lineages of the first wave (accounting for 36-58% of all sequenced infections). These successful viral transmission lineages dispersed widely across the province, consistent with founder effects and superspreading dynamics. Transmission lineage size was greatly reduced after March 11th, when a quarantine order for returning travelers was enacted. While this suggests the effectiveness of early public health measures, the biggest transmission lineages had already been ignited prior to this order. Combined, our results reinforce how, in the absence of tight travel restrictions or quarantine measures, fewer than 100 viral introductions in a week can ensure the establishment of extended transmission chains.

The aim of this study was to describe the epidemiology of human cryptosporidiosis in Québec from 2016 to 2017 and to identify possible exposures associated with the disease, and the dominant Cryptosporidium species in circulation. A descriptive analysis was performed on data collected from the provincial notifiable infectious diseases registry and the epidemiological investigation. Fecal sample were sent to the Laboratoire de santé publique du Québec for molecular characterization. In Québec, from January 1, 2016 to December 31, 2017, a total of 201 confirmed cases of cryptosporidiosis were notified. A peak in the number of reported cases was observed at the end of the summer. The regional public health department with the highest adjusted incidence rate for sex and age group for both years was that of Nunavik, in the north of Québec. A higher average annual incidence rate was observed for females between the ages of 20 to 34 years compared to males. Overall, for both males and females the distribution appeared to be bimodal with a first peak in children younger than five years old and a second peak in adults from 20 to 30 years of age. Molecular characterization showed that 23% (11/47) of cases were infected with C. hominis while 74% (35/47) were infected with C. parvum. Meanwhile, subtyping results identified by gp60 sequencing, show that all C. parvum subtypes belonged to the IIa family, whereas the subtypes for C. hominis belonged to the Ia, Ib, and Id families. Finally, the epidemiological investigation showed that diarrhea was the most common reported symptom with 99% (72/73) of investigated cases having experienced it. This first brief epidemiological portrait of cryptosporidiosis in Québec has allowed for the description, both at the provincial and regional level, of the populations that could be particularly vulnerable to the disease.

We conducted a recent investigation in Quebec, Canada, concerning Canadian deer hunters who went to the United States to hunt deer and returned with symptoms of fever, severe headache, myalgia, and articular pain of undetermined etiology. Further investigation identified that a group of 10 hunters from Quebec attended a hunting retreat in Illinois (USA) during November 22-December 4, 2018. Six of the 10 hunters had similar symptoms and illness onset dates. Serologic tests indicated a recent toxoplasmosis infection for all symptomatic hunters, and the risk factor identified was consumption of undercooked deer meat. Among asymptomatic hunters, 2 were already immune to toxoplasmosis, 1 was not immune, and the immune status of 1 remains unknown. Outbreaks of acute toxoplasmosis infection are rare in North America, but physicians should be aware that such outbreaks could become more common.

Background: Molecular phylogenetics are generally used to confirm hepatitis C virus (HCV) transmission events. In addition, the Laboratoire de santé publique du Québec (LSPQ) has been using molecular phylogenetics for surveillance of HCV genotyping since November 2001. Objectives: To describe the emergence of a specific lineage of HCV genotype 4d (G4d) and its characteristics using molecular phylogenetics as a surveillance tool for identifying HCV strain clustering. Methods: The LSPQ prospectively applied Sanger sequencing and phylogenetic analysis to determine the HCV genotype on samples collected from November 2001 to December 2017. When a major G4d cluster was identified, demographic information, HIV-infection status and syphilis test results were analyzed. Results: Phylogenetic analyses performed on approximately 22,000 cases identified 122 G4d cases. One major G4d cluster composed of 37 cases was singled out. Two cases were identified in 2010, 10 from 2011–2014 and 25 from 2015–2017. Cases in the cluster were concentrated in two urban health regions. Compared to the other G4d cases, cluster cases were all male (p<0.001) and more likely to be HIV-positive (adjusted risk ratio: 4.4; 95% confidence interval: 2.5–7.9). A positive syphilis test result was observed for 27 (73%) of the cluster cases. The sequences in this cluster and of four outlier cases were located on the same monophyletic lineage as G4d sequences reported in HIV-positive men who have sex with men (MSM) in Europe. Conclusion: Molecular phylogenetics enabled the identification and surveillance of ongoing transmission of a specific HCV G4d lineage in HIV-positive and HIV-negative men in Quebec and its cross-continental spread. This information can orient intervention strategies to avoid transmission of HCV in MSM.

Background: Molecular phylogenetics are generally used to confirm hepatitis C virus (HCV) transmission events. In addition, the Laboratoire de santé publique du Québec (LSPQ) has been using molecular phylogenetics for surveillance of HCV genotyping since November 2001. Objectives: To describe the emergence of a specific lineage of HCV genotype 4d (G4d) and its characteristics using molecular phylogenetics as a surveillance tool for identifying HCV strain clustering. Methods: The LSPQ prospectively applied Sanger sequencing and phylogenetic analysis to determine the HCV genotype on samples collected from November 2001 to December 2017. When a major G4d cluster was identified, demographic information, HIV-infection status and syphilis test results were analyzed. Results: Phylogenetic analyses performed on approximately 22,000 cases identified 122 G4d cases. One major G4d cluster composed of 37 cases was singled out. Two cases were identified in 2010, 10 from 2011-2014 and 25 from 2015-2017. Cases in the cluster were concentrated in two urban health regions. Compared to the other G4d cases, cluster cases were all male (p<0.001) and more likely to be HIV-positive (adjusted risk ratio: 4.4; 95% confidence interval: 2.5-7.9). A positive syphilis test result was observed for 27 (73%) of the cluster cases. The sequences in this cluster and of four outlier cases were located on the same monophyletic lineage as G4d sequences reported in HIV-positive men who have sex with men (MSM) in Europe. Conclusion: Molecular phylogenetics enabled the identification and surveillance of ongoing transmission of a specific HCV G4d lineage in HIV-positive and HIV-negative men in Quebec and its cross-continental spread. This information can orient intervention strategies to avoid transmission of HCV in MSM.

Background: A small village in Nunavik, Quebec experienced a tuberculosis (TB) outbreak in 2012-2013 and then a resurgence in 2015-2016. Cases were still occurring, despite the fact that contact tracing had already been conducted on one quarter of the population. A decision was taken to conduct large-scale screening of the population for TB. Objective: To describe the results of a population-based TB screening intervention designed to identify individuals with latent TB infection (LTBI) or active TB requiring treatment. Methodology: The history of TB infection (either active TB or LTBI, defined as a positive tuberculin skin test result of at least five mm induration) and treatment (considered adequate if at least 80% of prescribed doses were taken) were determined. Those who were two years of age and older and had not been included in contact tracing after June 1, 2015 were included for TB screening (n=1,026 eligible individuals). Screening included a nurse assessment, tuberculin skin test (TST) for those with previous negative TST or of unknown status and chest X-ray for the others. Results: Of the eligible individuals in the affected village, 1,004 (98%) participated in the screening. Of these, 30% had a history of previous TB infection. A TST screening was administered to 71% of the participants, 10% of whom had positive results. Assessments were performed on 425 participants and 385 underwent a chest X-ray. Fifty-two cases of previously diagnosed active TB and three cases of new active TB were documented. In addition, there were 247 individuals with LTBI who had been previously identified (191 were found to have had adequate LTBI treatment, 56 were found to have had inadequate LTBI treatment) and 69 were identified with de novo LTBI. In addition, 633 participants were found to have no TB infection. There were 125 participants who were referred for LTBI treatment. Follow-up information was available for 120 and 85 (71%) of these completed the treatment. Conclusion: Within this northern village, which had persistent TB transmission despite classic control measures, population-based screening had a high degree of coverage and was an effective way to detect additional cases of individuals with active TB and those with LTBI.