[Show abstract][Hide abstract] ABSTRACT: Background. Canada's Sentinel Physician Surveillance Network (SPSN) links genetic, antigenic and vaccine effectiveness (VE) measures in an integrated platform of influenza monitoring, described here for the 2013-14 season of resurgent A(H1N1)pdm09 and late-season influenza B activity. Methods. VE was estimated as [1-OddsRatio]x100% comparing vaccination status between influenza test-positive cases and test-negative controls. Vaccine-virus relatedness was assessed by genomic sequence analysis and hemagglutination-inhibition assay. Results. Analyses included 1037 controls (33%vaccinated) and 663 cases (15%vaccinated): 415 A(H1N1)pdm09, 15 A(H3N2), 191 B/Yamagata-lineage, 6 B/Victoria-lineage, 36 unknown subtype/lineage. A(H1N1)pdm09 viruses belonged to clade-6B, distinguished by a K163Q substitution, but remained antigenically-similar to A/California/07/2009-like vaccine with adjusted-VE of 71%(95%CI=58-80%). Most (83%) B/Yamagata-lineage viruses clustered phylogenetically with the prior 2012-13 season's B/Wisconsin/01/2010-like clade-3 vaccine-strain while only 17% clustered with the current 2013-14 season's B/Massachusetts/02/2012-like clade-2 vaccine-strain. B/Yamagata-lineage adjusted-VE was 73%(95%CI=56-83%), lower with partial calendar-time adjustment for clade-mismatched B/Wisconsin/01/2010-like (VE=63%;95%CI=41-77%) versus clade-matched B/Massachusetts/02/2012-like (VE=88%;95%CI=48-97%) viruses. No 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. 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.
The Journal of Infectious Diseases 03/2015; DOI:10.1093/infdis/jiv177 · 5.78 Impact Factor
[Show abstract][Hide abstract] 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).
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.
PLoS ONE 10/2014; 9(10):e109420. DOI:10.1371/journal.pone.0109420 · 3.23 Impact Factor
[Show abstract][Hide abstract] 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.
[Show abstract][Hide abstract] 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.
PLoS ONE 08/2014; 9(8):e103852. DOI:10.1371/journal.pone.0103852 · 3.23 Impact Factor
[Show abstract][Hide abstract] 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.
PLoS ONE 03/2014; 9(3):e92153. DOI:10.1371/journal.pone.0092153 · 3.23 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Background. We estimate vaccine effectiveness (VE) against both influenza A/subtypes and B/lineages in Canada for the 2011-12 trivalent inactivated influenza vaccine (TIV) with components entirely unchanged from 2010-11 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-adjustedOddsRatio]X100 for RT-PCR-confirmed influenza in vaccinated versus non-vaccinated 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%CI:52-92%): circulating viruses were HI-characterized as vaccine-matched and bore just 2 amino-acid (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%): 71%(95%CI:40-86%) for lineage-matched B/Victoria and 27%(95%CI-21-56%) for lineage-mismatched B/Yamagata. For both influenza A and B types, VE was similar among recipients of either 2010-11 or 2011-12 TIV alone, higher when vaccinated both seasons.Conclusions. Phenotypic and genotypic characterization of circulating and vaccine viruses enhances understanding of TIV performance, shown in 2011-12 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.
The Journal of Infectious Diseases 01/2014; 210(1). DOI:10.1093/infdis/jiu048 · 5.78 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The recent emergence of influenza A (H7N9) emphasizes the need for its rapid detection. While commercial nucleic acid amplification tests (NAATs) are commonly used to detect seasonal influenza, this study demonstrates the analytical sensitivity of commercial assays is highly variable compared to CDC-based in-house NAATs for the detection of H7N9.
[Show abstract][Hide abstract] 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
[Show abstract][Hide abstract] 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
Eurosurveillance: bulletin europeen sur les maladies transmissibles = European communicable disease bulletin 01/2013; 18(5). · 4.66 Impact Factor
[Show abstract][Hide abstract] 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.
[Show abstract][Hide abstract] 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.
The Journal of Infectious Diseases 04/2012; 205(12):1858-68. DOI:10.1093/infdis/jis283 · 5.78 Impact Factor
[Show abstract][Hide abstract] 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 (χ(2) = 33.9, P < .001). Scalar expansion of large clusters over 11 months (interquartile range, 3.5-25.5 months) correlated with cluster membership size (r(2) = 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.
The Journal of Infectious Diseases 10/2011; 204(7):1115-9. DOI:10.1093/infdis/jir468 · 5.78 Impact Factor
[Show abstract][Hide abstract] 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.
Journal of Medical Virology 05/2011; 83(5):751-9. DOI:10.1002/jmv.22047 · 2.22 Impact Factor
[Show abstract][Hide abstract] 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.
[Show abstract][Hide abstract] ABSTRACT: To assess the effectiveness of the pandemic influenza A/H1N1 vaccine used in Canada during autumn 2009.
Test negative incident case-control study based on sentinel physician surveillance system.
Community based clinics contributing to sentinel networks in British Columbia, Alberta, Ontario, and Quebec, Canada.
552 patients who presented to a sentinel site within seven days of onset of influenza-like illness during the primary analysis period between 8 November and 5 December 2009; participants were mostly (>80%) children and adults under 50 years old.
Monovalent AS03 adjuvanted pandemic influenza A/H1N1 vaccine as the predominant formulation (>95%) distributed in Canada.
Vaccine effectiveness calculated as 1-(odds ratio for influenza in vaccinated (received pandemic H1N1 vaccine at least two weeks before onset of influenza-like illness) versus unvaccinated participants), with adjustment for age, comorbidity, province, timeliness of specimen collection, and week of illness onset. Sensitivity analyses explored the influence of varying analysis periods between 1 November and 31 December, receipt of trivalent seasonal influenza vaccine, and restriction to participants without comorbidity.
During the primary analysis period, pandemic H1N1 was detected by reverse transcription polymerase chain reaction in 209/552 (38%) participants; rates were highest in children and young adults (40%) and lowest in people aged 65 or over (9%). Among the 209 cases, 35 (17%) reported comorbidity compared with 80/343 (23%) controls. Two (1%) cases had received pandemic H1N1 vaccine at least two weeks before the onset of illness, compared with 58/343 (17%) controls, all single dose. Adjusted vaccine effectiveness overall was 93% (95% confidence interval 69% to 98%). High estimates of vaccine protection-generally at least 90%-were maintained across most sensitivity analyses.
Although limited by a small number of vaccine failures, this study suggests that the monovalent AS03 adjuvanted vaccine used in Canada during autumn 2009 was highly effective in preventing medically attended, laboratory confirmed pandemic H1N1 illness, with reference in particular to a single dose in children and young adults.
[Show abstract][Hide abstract] ABSTRACT: To describe and compare the characteristics of children hospitalized with novel influenza A (H1N1) during two successive waves.
This was a medical chart review of all children hospitalized in a French Canadian pediatric hospital in Montreal in the spring and fall of 2009 with a positive real-time polymerase chain reaction for novel influenza A (H1N1) and flu-like symptoms.
We included 202 children with a median age of 4.9 (range 0.1-18) years. Demographic and clinical features of the children in the two waves were similar. One or more underlying medical conditions were found in 59% of the children. Clinical findings at admission were: fever (98%), cough (88%), congestion/rhinorrhea (58%), gastrointestinal symptoms (47%), oxygen saturation below 95% (33%), sore throat (20%), and neurological symptoms (9%). Admission to the intensive care unit was required for 22 (11%) children, and 14 patients needed respiratory support. During the second wave, the median duration of stay was shorter (3 vs. 4 days, p=0.003) and oseltamivir was used more often (84% vs. 40%, p<0.001).
Children hospitalized during the two successive waves of H1N1 were mainly school-aged and suffered from moderate disease. Although clinical features and severity of disease were similar, oseltamivir was prescribed more frequently and the length of hospital stay was shorter in the second wave.
International journal of infectious diseases: IJID: official publication of the International Society for Infectious Diseases 02/2011; 15(2):e122-30. DOI:10.1016/j.ijid.2010.08.006 · 2.33 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Noroviruses (NoVs) are the leading cause of infectious gastroenteritis worldwide. Real-time reverse transcription PCR (real-time RT-PCR) is the preferred method of NoV detection for the majority of testing laboratories. Although the accepted target region for molecular detection assays is the conserved ORF1/ORF2 junction, multiple variations have been published with differences in primers, probes, reagents, multiplexing, etc.
We assessed the detection limit for GII.4 NoV real-time RT-PCR assays as well as the ability to detect the non-GII.4 NoV genotypes in each participating laboratory.
A panel of 25 RNA samples was circulated to 18 testing laboratories for comparison of their real-time RT-PCR procedures for NoV detection.
Multiple protocols with slight differences in reagents or conditions successfully detected 10 genome equivalents or fewer of NoV per reaction. Multiplex procedures were significantly associated (p=0.04) with false negative results, particularly for a GI.2 strain. Sensitive detection was associated with false positive results (p=0.03).
Overall, the data indicate that comparable results are produced under slightly different assay conditions.
Journal of clinical virology: the official publication of the Pan American Society for Clinical Virology 11/2010; 50(2):109-13. DOI:10.1016/j.jcv.2010.10.008 · 3.47 Impact Factor