Hugues Charest

Institut National de Santé Publique du Québec (INSPQ), Quebec City, Quebec, Canada

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Publications (39)184.77 Total impact

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    ABSTRACT: Background and objectives: We assessed monovalent rotavirus (RV1) vaccine effectiveness (VE) in a high-income setting with RV1 predominant use, and examined the burden of pediatric rotavirus gastroenteritis following the implementation of an RV1-only vaccination program. Methods: We conducted active rotavirus gastroenteritis surveillance among children 8 weeks to <3 years of age at three hospitals. Participant information and vaccination histories were collected via parent/guardian interview and medical records. Stool specimens were tested for rotavirus; positive specimens were genotyped. The effect of increasing RV1 coverage on rotavirus prevalence was examined as a weekly time series via binomial regression with a log link function, using either categorical season or mean 2-dose rotavirus seasonal vaccine coverage as the exposure variable. As compared with RV1 vaccine formulation, rotavirus genotypes were classified as homotypic, partly-heterotypic, or heterotypic; prevalence of each was compared by season. A test-negative case-control design was used to examine RV1 VE against hospitalization or emergency visits. Results: We enrolled 866 participants in active surveillance; of these, 384 (44.3%) were eligible for VE analyses. After adjustment for season, we detected a 70.1% (95% CI: 21.9%, 88.6%) relative decrease in rotavirus prevalence in the 2013-14 season compared with 2012-13 season. On average, a 1% increase in ≥2-dose rotavirus coverage among children 1 year of age was associated with a 3.8% (95% CI: 1.8%, 5.8%) relative decrease in rotavirus prevalence. Rotavirus homotypic strain prevalence decreased, with 77% (95% CI: 68%, 89%) versus 8% (95% CI: 0%, 36%) prevalence during the 2011-12 and 2013-14 seasons, respectively. Adjusted 2-dose RV1 VE was 91.2% (95% CI: 61.6%, 98.0%). Conclusions: RV1 vaccine was highly effective to prevent rotavirus hospitalizations and emergency visits among children <3 years of age in a high-income setting with its predominant use. Our estimates were similar to high-income settings with concurrent RV1 and pentavalent vaccine use.
    Full-text · Article · Nov 2015 · Vaccine
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    ABSTRACT: Background: The 2014/15 influenza season in Canada was characterized by an early epidemic due to vaccine-mismatched influenza A(H3N2) viruses, disproportionately affecting elderly individuals ≥65-years-old. We assessed vaccine effectiveness (VE) against A(H3N2) hospitalization among elderly individuals during the peak weeks of the 2014/15 epidemic in Quebec, Canada. Methods: Nasal specimens and clinical/epidemiological data were collected within 7 days of illness onset from elderly patients admitted with respiratory symptoms to one of four participating hospitals between November 30, 2014 and January 13, 2015. Cases tested RT-PCR positive for influenza A(H3N2) and controls tested negative for any influenza. VE was assessed by test-negative case-control design. Results: There were 314 participants including 186 cases (62% vaccinated) and 128 controls (59% vaccinated) included in primary VE analysis. Median age was 81.5 years, two-thirds were admitted from the community and 91% had underlying comorbidity. Crude VE against A(H3N2) hospitalization was -17% (95%CI: -86% to 26%), decreasing to -23% (95%CI: -99 to 23%) with adjustment for age and comorbidity, and to -39% (95%CI: -142 to 20%) with additional adjustment for specimen collection interval, calendar time, type of residence and hospital. In sensitivity analyses, VE estimates were improved toward the null with restriction to participants admitted from the community (-2%; 95%CI: -105 to 49%) or with specimen collection ≤4 days since illness onset (- 8%; 95%CI: -104 to 43%) but further from the null with restriction to participants with comorbidity (-51%; 95%CI: -169 to 15%). Conclusion: The 2014/15 mismatched influenza vaccine provided elderly patients with no cross-protection against hospitalization with the A(H3N2) epidemic strain, reinforcing the need for adjunct protective measures among high-risk individuals and improved vaccine options.
    Preview · Article · Jul 2015 · PLoS ONE
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    ABSTRACT: Here, we present the draft genome sequences of two toxigenic Corynebacterium ulcerans strains isolated from two different patients: one from a blood sample and the other from a scar exudate following surgery. Although these two strains harbor the diphtheria toxin gene tox, no full prophage sequences were found in the flanking regions. Copyright © 2015 Domingo et al.
    Full-text · Article · Jun 2015 · Genome Announcements
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    ABSTRACT: Background: Canada's Sentinel Physician Surveillance Network links genetic, antigenic, and vaccine effectiveness (VE) measures in an integrated platform of influenza monitoring, described here for the 2013-2014 influenza season of resurgent A(H1N1)pdm09 and late-season type B activity. Methods: VE was estimated as [1 - odds ratio] × 100% and compared vaccination status between individuals who tested positive (cases) and those who tested negative (controls) for influenza virus. Vaccine-virus relatedness was assessed by genomic sequence analysis and hemagglutination inhibition assays. Results: Analyses included 1037 controls (of whom 33% were vaccinated) and 663 cases (of whom 14% were vaccinated). A total of 415 cases tested positive for A(H1N1)pdm09 virus, 15 tested positive for A(H3N2) virus, 191 tested positive for B/Yamagata-lineage virus, 6 tested positive for B/Victoria-lineage virus, and 36 tested positive for viruses of unknown subtype or lineage. A(H1N1)pdm09 viruses belonged to clade 6B, distinguished by a K163Q substitution, but remained antigenically similar to the A/California/07/2009-like vaccine strain, with an adjusted VE of 71% (95% confidence interval [CI], 58%-80%). Most B/Yamagata-lineage viruses (83%) clustered phylogenetically with the prior (ie, 2012-2013) season's B/Wisconsin/01/2010-like clade 3 vaccine strain, while only 17% clustered with the current (ie, 2013-2014) season's B/Massachusetts/02/2012-like clade 2 vaccine strain. The adjusted VE for B/Yamagata-lineage virus was 73% (95% CI, 57%-84%), with a lower VE obtained after partial calendar-time adjustment for clade-mismatched B/Wisconsin/01/2010-like virus (VE, 63%; 95% CI, 41%-77%), compared with that for clade-matched B/Massachusetts/02/2012-like virus (VE, 88%; 95% CI, 48%-97%). No A(H3N2) viruses clustered with the A/Texas/50/2012-like clade 3C.1 vaccine strain, and more than half were antigenically mismatched, but sparse data did not support VE estimation. Conclusions: VE corresponded with antigenically conserved A(H1N1)pdm09 and lineage-matched B/Yamagata viruses with clade-level variation. Surveillance linking genotypic, phenotypic, and epidemiologic measures of vaccine-virus relatedness and effectiveness could better inform predictions of vaccine performance and reformulation.
    No preview · Article · Mar 2015 · The Journal of Infectious Diseases

  • No preview · Article · Jan 2015 · Eurosurveillance: bulletin europeen sur les maladies transmissibles = European communicable disease bulletin
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    ABSTRACT: Background HIV drug resistance represents a major threat for effective treatment. We assessed the trends in the frequency of drug resistance mutations and the monitored viral load (VL) in treatment-naïve (TN) and treatment-experienced (TE) individuals infected with HIV-1 in Québec, Canada, between 2001 and 2011. Methods and Findings Resistance data were obtained from 4,105 and 5,086 genotypic tests performed on TN and TE patients, respectively. Concomitantly, 274,161 VL tests were carried out in the Province. Changes over time in drug resistance frequency and in different categories of VL were assessed using univariate logistic regression. Multiple logistic regression was used to evaluate associations between the rates of certain mutations and antiretroviral prescriptions. From 2001 to 2011, the proportion of undetectable VL test results continually increased, from 42.1% to 75.9%, while a significant decrease in the frequency of resistance mutations associated with protease inhibitors [PI (from 54% to 16%)], nucleoside [NRTI (from 78% to 37%) and non-nucleoside reverse transcriptase inhibitors [NNRTI (from 44% to 31%)] was observed in TE patients. In TN individuals, the overall frequency of transmitted drug resistance was 13.1%. A multiple logistic regression analysis indicated that the introduction of co-formulated emtricitabine/tenofovir or emtricitabine/tenofovir/efavirenz was positively associated with the decrease of the frequency of the M184I/V mutations observed overtime (p = 0.0004). Conclusions We observed a significant decrease in the frequency of drug resistance mutations in TE patients, concomitant with a decrease in the proportion of patients with detectable viremia. These findings may be related to both the increased potencies and adherence to therapy associated with newer antiretroviral regimens. Nevertheless, our data demonstrate that broad use of antiretrovirals does not increase the level of circulating drug resistant variants.
    Full-text · Article · Oct 2014 · PLoS ONE
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    ABSTRACT: During peak weeks of seasonal influenza epidemics, severe respiratory infections without laboratory confirmation are typically attributed to influenza. In this prospective study, specimens and demographic and clinical data were collected from adults admitted with respiratory symptoms to 4 hospitals during the 8-10 peak weeks of 2 influenza seasons. Specimens were systematically tested for influenza and 13 other respiratory viruses (ORVs) by using the Luminex RVP FAST assay. At least 1 respiratory virus was identified in 46% (21% influenza, 25% noninfluenza; 2% coinfection) of the 286 enrolled patients in 2011-2012 and in 62% (46% influenza, 16% noninfluenza; 3% coinfection) of the 396 enrolled patients in 2012-2013. Among patients aged ≥75 years, twice as many ORVs (32%) as influenza viruses (14%) were detected in 2011-2012. During both seasons, the most frequently detected ORVs were enteroviruses/rhinoviruses (7%), respiratory syncytial virus (6%), human metapneumovirus (5%), coronaviruses (4%), and parainfluenza viruses (2%). Disease severity was similar for influenza and ORVs during both seasons. Although ORV contribution relative to influenza varies by age and season, during the peak weeks of certain influenza seasons, ORVs may be a more frequent cause of elderly hospitalization than influenza.
    Preview · Article · Sep 2014 · Open Forum Infectious Diseases
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    ABSTRACT: During the summer of 2012, a major Legionella pneumophila serogroup 1 outbreak occurred in Quebec City, Canada, which caused 182 declared cases of Legionnaire's disease and included 13 fatalities. Legionella pneumophila serogroup 1 isolates from 23 patients as well as from 32 cooling towers located in the vicinity of the outbreak were recovered for analysis. In addition, 6 isolates from the 1996 Quebec City outbreak and 4 isolates from patients unrelated to both outbreaks were added to allow comparison. We characterized the isolates using pulsed-field gel electrophoresis, sequence-based typing, and whole genome sequencing. The comparison of patients-isolated strains to cooling tower isolates allowed the identification of the tower that was the source of the outbreak. Legionella pneumophila strain Quebec 2012 was identified as a ST-62 by sequence-based typing methodology. Two new Legionellaceae plasmids were found only in the epidemic strain. The LVH type IV secretion system was found in the 2012 outbreak isolates but not in the ones from the 1996 outbreak and only in half of the contemporary human isolates. The epidemic strains replicated more efficiently and were more cytotoxic to human macrophages than the environmental strains tested. At least four Icm/Dot effectors in the epidemic strains were absent in the environmental strains suggesting that some effectors could impact the intracellular replication in human macrophages. Sequence-based typing and pulsed-field gel electrophoresis combined with whole genome sequencing allowed the identification and the analysis of the causative strain including its likely environmental source.
    Full-text · Article · Aug 2014 · PLoS ONE
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    ABSTRACT: Influenza vaccine effectiveness (VE) is generally interpreted in the context of vaccine match/mismatch to circulating strains with evolutionary drift in the latter invoked to explain reduced protection. During the 2012-13 season, however, detailed genotypic and phenotypic characterization shows that low VE was instead related to mutations in the egg-adapted H3N2 vaccine strain rather than antigenic drift in circulating viruses. Component-specific VE against medically-attended, PCR-confirmed influenza was estimated in Canada by test-negative case-control design. Influenza A viruses were characterized genotypically by amino acid (AA) sequencing of established haemagglutinin (HA) antigenic sites and phenotypically through haemagglutination inhibition (HI) assay. H3N2 viruses were characterized in relation to the WHO-recommended, cell-passaged vaccine prototype (A/Victoria/361/2011) as well as the egg-adapted strain as per actually used in vaccine production. Among the total of 1501 participants, influenza virus was detected in 652 (43%). Nearly two-thirds of viruses typed/subtyped were A(H3N2) (394/626; 63%); the remainder were A(H1N1)pdm09 (79/626; 13%), B/Yamagata (98/626; 16%) or B/Victoria (54/626; 9%). Suboptimal VE of 50% (95%CI: 33-63%) overall was driven by predominant H3N2 activity for which VE was 41% (95%CI: 17-59%). All H3N2 field isolates were HI-characterized as well-matched to the WHO-recommended A/Victoria/361/2011 prototype whereas all but one were antigenically distinct from the egg-adapted strain as per actually used in vaccine production. The egg-adapted strain was itself antigenically distinct from the WHO-recommended prototype, and bore three AA mutations at antigenic sites B [H156Q, G186V] and D [S219Y]. Conversely, circulating viruses were identical to the WHO-recommended prototype at these positions with other genetic variation that did not affect antigenicity. VE was 59% (95%CI:16-80%) against A(H1N1)pdm09, 67% (95%CI: 30-85%) against B/Yamagata (vaccine-lineage) and 75% (95%CI: 29-91%) against B/Victoria (non-vaccine-lineage) viruses. These findings underscore the need to monitor vaccine viruses as well as circulating strains to explain vaccine performance. Evolutionary drift in circulating viruses cannot be regulated, but influential mutations introduced as part of egg-based vaccine production may be amenable to improvements.
    Full-text · Article · Mar 2014 · PLoS ONE
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    ABSTRACT: The 2013/14 influenza season to date in Canada has been characterised by predominant (90%) A(H1N1) pdm09 activity. Vaccine effectiveness (VE) was assessed in January 2014 by Canada's sentinel surveillance network using a test-negative case-control design. Interim adjusted-VE against medically-attended laboratory-confirmed influenza A(H1N1) pdm09 infection was 74% (95% CI: 58-83). Relative to vaccine, A(H1N1) pdm09 viruses were antigenically similar and genetically well conserved, with most showing just three mutations across the 50 amino acids comprising antigenic sites of the haemagglutinin protein.
    No preview · Article · Feb 2014 · Eurosurveillance: bulletin europeen sur les maladies transmissibles = European communicable disease bulletin
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    ABSTRACT: The 2013/14 influenza season to date in Canada has been characterised by predominant (90%) A(H1N1)pdm09 activity. Vaccine effectiveness (VE) was assessed in January 2014 by Canada's sentinel surveillance network using a test-negative case-control design. Interim adjusted-VE against medically-attended laboratory-confirmed influenza A(H1N1)pdm09 infection was 74% (95% CI: 58-83). Relative to vaccine, A(H1N1)pdm09 viruses were antigenically similar and genetically well conserved, with most showing just three mutations across the 50 amino acids comprising antigenic sites of the haemagglutinin protein.
    Full-text · Article · Feb 2014 · Eurosurveillance: bulletin europeen sur les maladies transmissibles = European communicable disease bulletin
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    ABSTRACT: Background: We estimate vaccine effectiveness (VE) against both influenza A/subtypes and B/lineages in Canada for the 2011-2012 trivalent inactivated influenza vaccine (TIV) with components entirely unchanged from the 2010-2011 TIV and in the context of phenotypic and genotypic characterization of circulating viruses. Methods: In a test-negative case-control study VE was estimated as [1-(adjusted)OddsRatio] × 100 for RT-PCR-confirmed influenza in vaccinated vs nonvaccinated participants. Viruses were characterized by hemagglutination inhibition (HI) and sequencing of antigenic sites of the hemagglutinin (HA) gene. Results: There were 1507 participants. VE against A(H1N1)pdm09 was 80% (95% confidence interval [CI], 52%-92%): circulating viruses were HI-characterized as vaccine-matched and bore just 2 aminoacid (AA) differences from vaccine. VE against A/H3N2 was 51% (95% CI, 10%-73%): circulating viruses were HI-characterized as vaccine-related but bore ≥11AA differences from vaccine. VE against influenza B was 51% (95% CI, 26%-67%) in total: 71% (95% CI, 40%-86%) for lineage-matched B/Victoria and 27% (95% CI, -21% to 56%) for lineage-mismatched B/Yamagata. For both influenza A and B types, VE was similar among recipients of either 2010-2011 or 2011-2012 TIV alone, higher when vaccinated both seasons. Conclusions: Phenotypic and genotypic characterization of circulating and vaccine viruses enhances understanding of TIV performance, shown in 2011-2012 to be substantial against well-conserved A(H1N1)pdm09 and lineage-matched influenza B, suboptimal against genetic-variants of A/H3N2, and further reduced against lineage-mismatched influenza B. With unchanged vaccine components, protection may extend beyond a single season.
    Full-text · Article · Jan 2014 · The Journal of Infectious Diseases
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    ABSTRACT: The recent emergence of influenza A virus (H7N9) emphasizes the need for its rapid detection. While commercial nucleic acid amplification tests (NAATs) are commonly used to detect seasonal influenza virus, this study demonstrated that the analytical sensitivity of commercial assays is highly variable compared to that of CDC-based in-house NAATs for the detection of H7N9.
    Full-text · Article · Aug 2013 · Journal of clinical microbiology
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    ABSTRACT: Background: In 2012, a major L. pneumophila serogroup 1 (LP1) outbreak occurred in Quebec city, Canada, causing 181 reported cases including 13 fatalities. LP is a ubiquitous Gram-negative bacteria within freshwater and manmade aquatic environments such as cooling tower systems and spas. Infection in human occurs though inhalation of droplets carrying the infectious bacteria. Strains genotyping of LP is essential for the identification of an outbreak source. Pulsed-field gel electrophoresis (PFGE) is the reference method for laboratory investigations. Objective: To evaluate whether other typing methods could improved the molecular epidemiology of this outbreak, we compared profiles obtained with PFGE to Sequence-based typing (SBT) and to whole genome sequencing (WGS). Methods: LP1 strains recovered from patients were analyzed using PFGE and SBT. Water samples from cooling towers located near outbreak cases were cultured according to AFNOR guidelines. and analyzed by both molecular methods. WGS was performed on MiSeq (Illumina) with Nextera XT kit for generating libraries from all patient strains, a subset of the environmental strains and some strains from a previous outbreak that occurred in the same area. Sequence assembly was performed using Ray assembler. Results: 23 LP1 strains obtained from human cases were characterized. Among these, 22 strains displayed a unique PFGE pattern. 131 cooling tower samples from 70 buildings were cultured. We obtained 146 LP1 strains from 33 samples. Among environmental strains, 6 different PFGE patterns were identified. Only one environmental strain harbored the same PFGE pattern as patients and the cooling tower was determined to be the source of the outbreak. SBT was performed on 53 strains (23 human strains and 30 from environment) with a minimum of one strain typed for each PFGE pattern. This method was less discriminatory than PFGE since the same SBT type harbored more than one PFGE pattern type. Comparison of SBT types showed that all strains had already been described in North America and Europe. Phylogenetic analysis of sequences obtained with WGS showed the clustering of patient strains with the matching strain from the cooling tower, in perfect agreement with PFGE and SBT results. It also revealed that this cluster was unrelated to strains from the previous outbreak. Conclusion: PFGE has proven its utility for outbreak investigation. However, SBT is useful for strain comparison to international databases. WGS confirmed the finding of the two typing
    No preview · Conference Paper · Apr 2013
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    ABSTRACT: The 2012/13 influenza season in Canada has been characterised to date by early and moderately severe activity, dominated (90%) by the A(H3N2) subtype. Vaccine effectiveness (VE) was assessed in January 2013 by Canada’s sentinel surveillance network using a test-negative case–control design. Interim adjusted- VE against medically attended laboratory-confirmed influenza A(H3N2) infection was 45% (95% CI: 13–66). Influenza A(H3N2) viruses in Canada are similar to the vaccine, based on haemagglutination inhibition; however, antigenic site mutations are described in the haemagglutinin gene.
    Full-text · Article · Feb 2013 · Eurosurveillance: bulletin europeen sur les maladies transmissibles = European communicable disease bulletin
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    ABSTRACT: During the 2010-2011 winter, a large number of outbreaks due to influenza A/H3N2 at long-term care facilities, including higher-than-expected attack rates among vaccinated staff, were reported in some regions of Canada. Interim analysis from the community-based sentinel surveillance system showed circulating H3N2 variants and suboptimal vaccine effectiveness (VE), assessed here for the entire season's data set. Nasal/nasopharyngeal swabs and epidemiologic details were collected from patients presenting to sentinel sites within 7 days of onset of influenza-like illness. Cases tested positive for influenza by real-time reverse-transcription polymerase chain reaction; controls tested negative. Odds ratios for medically attended, laboratory-confirmed influenza in vaccinated vs nonvaccinated participants were used to derive adjusted VE. Viruses were characterized by hemagglutination inhibition (HI), and the hemagglutinin genes of a subset were sequenced to explore vaccine relatedness. Final 2010-2011 VE analysis included 1718 participants (half aged 20-49 years), 93 with A(H1N1)pdm09, 408 with A/H3N2, and 199 with influenza B. Among adults aged 20-49 years, adjusted VE was 65% (95% confidence interval [CI], 8%-87%) for A(H1N1)pdm09 and 66% (95% CI, 10%-87%) for influenza B. Vaccine effectiveness was substantially lower for A/H3N2, at 39% (95% CI, 0%-63%). Phylogenetic analysis identified 2 circulating H3N2 variant clades, A/HongKong/2121/2010 (87%) and A/Victoria/208/2009 (11%), bearing multiple amino acid substitutions at antigenic sites (12 and 8, respectively) compared with the H3N2 vaccine component used in Canada (A/Victoria/210/2009[NYMC X-187]). However, HI characterized all H3N2 isolates as well matched to the vaccine. Public health observations of increased facility H3N2 outbreaks were consistent with the sentinel network's detection of genetic variants and suboptimal VE but not with conventional HI characterization. We highlight the utility of a multicomponent sentinel surveillance platform that incorporates genotypic, phenotypic, and epidemiologic indicators into the assessment of influenza virus, new variant circulation, vaccine relatedness, and VE.
    Full-text · Article · Apr 2012 · Clinical Infectious Diseases
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    ABSTRACT: To estimate influenza vaccine effectiveness (VE) for the 2007-2008 season and assess the sentinel surveillance system in Canada for monitoring virus evolution and impact on VE. Nasal/nasopharyngeal swabs and epidemiologic details were collected from patients presenting to a sentinel physician within 7 days of influenza-like illness onset. Cases tested positive for influenza A/B virus by real-time polymerase chain reaction; controls tested negative. Hemagglutination inhibition (HI) and gene sequencing explored virus relatedness to vaccine. VE was calculated as 1 minus the odds ratio for influenza in vaccinated versus nonvaccinated participants, with adjustment for confounders. Of 1425 participants, 21% were vaccinated. Influenza virus was detected in 689 (48%), of which isolates from 663 were typed/subtyped: 189 (29%) were A/H1, 210 (32%) were A/H3, and 264 (40%) were B. Of A/H1N1 isolates, 6% showed minor HI antigenic mismatch to vaccine, with greater variation based on genetic identity. All A/H3N2 isolates showed moderate antigenic mismatch, and 98% of influenza B virus isolates showed major lineage-level mismatch to vaccine. Adjusted VE for A/H1N1, A/H3N2, and B components was 69% (95% confidence interval [CI], 44%-83%), 57% (95% CI, 32%-73%), and 55% (95% CI, 32%-70%), respectively, with an overall VE of 60% (95% CI, 45%-71%). Detailed antigenic and genotypic analysis of influenza viruses was consistent with epidemiologic estimates of VE showing cross-protection. A routine sentinel surveillance system that combines detailed virus and VE monitoring annually, as modeled in Canada, may guide improved vaccine selection and protection.
    Full-text · Article · Apr 2012 · The Journal of Infectious Diseases
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    ABSTRACT: Phylodynamic analysis and epidemiologic data identified 3 patterns of spread of primary human immunodeficiency virus type 1 infection (PHI) among men who have sex with men (2001–2009): 420 unique PHIs, 102 small clusters (2–4 PHIs per cluster, n = 280), and 46 large clusters (5–31 PHIs per cluster, n = 450). Large clusters disproportionately increased from 25.2% of PHIs in 2005 to 39.1% in 2009 (χ2 = 33.9, P < .001). Scalar expansion of large clusters over 11 months (interquartile range, 3.5–25.5 months) correlated with cluster membership size (r2 = 0.174, F = 4.424, P = .047). PHI cohort data revealed variations in social networks and risk behaviors among the 3 groups, suggesting the need for tailored prevention measures.
    Full-text · Article · Oct 2011 · The Journal of Infectious Diseases
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    ABSTRACT: We used genotypic and phylogenetic analysis to determine integrase diversity among subtypes, and studied natural polymorphisms and mutations implicated in resistance to integrase inhibitors (INI) in treatment-naïve persons (n = 220) and -experienced individuals (n = 24). Phylogenetics revealed 7 and 10% inter-subtype diversity in the integrase and reverse transcriptase (RT)/protease regions, respectively. Integrase sequencing identified a novel A/B recombinant in which all viruses in a male-sex-male (MSM) transmission cluster (n = 12) appeared to possess subtype B in integrase and subtype A in the remainder of the pol region. Natural variations and signature polymorphisms were observed at codon positions 140, 148, 151, 157, and 160 among HIV subtypes. These variations predicted higher genetic barriers to G140S and G140C in subtypes C, CRF02_AG, and A/CRF01_AE, as well as higher genetic barriers toward acquisition of V151I in subtypes CRF02_AG and A/CRF01_AE. The E157Q and E160Q mutational motif was observed in 35% of INI-naïve patients harboring subtype C infections, indicating intra-subtype variations. Thirteen patients failed raltegravir (RAL)-containing regimens within 8 ± 1 months, in association with the major Q148K/R/H and G140A/S (n = 8/24) or N155H (n = 5/24) mutational pathways. Of note, the remaining patients on RAL regimens for 14 ± 3 months harbored no or only minor integrase mutations/polymorphisms (T66I, T97A, H114P, S119P, A124S, G163R, I203M, R263K). These results demonstrate the importance of understanding subtype variability in the development of resistance to INIs.
    Full-text · Article · May 2011 · Journal of Medical Virology
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    ABSTRACT: The recent pandemic of the 2009 pandemic influenza A (H1N1) infrequently caused severe disease. We describe 2 cases of 2009 H1N1 influenza with rapid progression resulting in respiratory failure and need for prolonged intensive care support. Real-time polymerase chain reaction amplification for influenza A (using a Centers for Disease Control and Prevention protocol) and the 2009 H1N1 influenza (using an in-house protocol) was performed on serial respiratory and serum specimens from both patients collected over 3 weeks. Both patients repeatedly demonstrated 2009 H1N1 influenza in respiratory specimens. Evidence of influenza A viremia was also detected in both cases, although it was confirmed as 2009 H1N1 influenza in only one. The presence of viremia in cases of severe 2009 H1N1 influenza has potential prognostic and therapeutic implications. Detection of viremia may be useful as a predictive marker for severe disease. Antiviral agents with low serum levels may be ineffective if administered to patients with influenza viremia.
    Full-text · Article · Mar 2011 · Diagnostic microbiology and infectious disease

Publication Stats

1k Citations
184.77 Total Impact Points

Institutions

  • 2005-2015
    • Institut National de Santé Publique du Québec (INSPQ)
      • Laboratoire de Santé Publique du Québec
      Quebec City, Quebec, Canada
  • 2014
    • Université du Québec à Montréal
      Montréal, Quebec, Canada
  • 2013-2014
    • Université de Montréal
      • Department of Pathology and Microbiology
      Montréal, Quebec, Canada
  • 2008-2012
    • Health Canada
      Ottawa, Ontario, Canada
  • 2009
    • University of British Columbia - Vancouver
      Vancouver, British Columbia, Canada