Norovirus (NoV) and sapovirus (SaV) are major viral pathogens causing acute gastroenteritis (AGE) in both children and adults in developed countries and are also responsible for large-scale outbreaks. However, in Quebec, Canada, there are limited and updated data with respect to the genotypes circulating and implicated in outbreaks, particularly for SaV. This study aimed to investigate the genetic diversity and genotype predominance of NoVs and SaVs associated with AGE outbreaks in Quebec, Canada. Confirmed NoV and SaV outbreaks from long-term care facilities and hospital settings between September 2011 and April 2016 were investigated (n = 252). NoVs and SaVs were genetically diverse: 21 RdRp-capsid combinations were identified, of which 10 are recombinants. NoV GII.4 New Orleans[P4 NewOrleans] was the predominant genotype from 2011 to 2013, and GII.4 Sydney[P31] was the predominant genotype from 2013 to 2015. In 2015-2016, no single genotype predominated; instead, GII.17[P17], GII.4 Sydney[P16], GII.4 Sydney[P31], and SaV GI.2 strains were co-circulating at similar frequencies. Notably, emerging global genotypes including GII.17[P17], GII.4 Sydney[P16], GII.2[P16], and GII.4 San Francisco[P31] were detected for the first time in Quebec. These findings may contribute to an enhanced understanding of NoV and SaV infection and spread, and to the development of candidate vaccines.

BackgroundA comprehensive description of the combined effect of SARS-CoV-2 and respiratory viruses other than SARS-CoV-2 (ORVs) on acute respiratory infection (ARI) hospitalizations is lacking. ObjectiveThis study aimed to compare the viral etiology of ARI hospitalizations before the pandemic (8 prepandemic influenza seasons, 2012-13 to 2019-20) and during 3 pandemic years (periods of increased SARS-CoV-2 and ORV circulation in 2020-21, 2021-22, and 2022-23) from an active hospital-based surveillance network in Quebec, Canada. MethodsWe compared the detection of ORVs and SARS-CoV-2 during 3 pandemic years to that in 8 prepandemic influenza seasons among patients hospitalized with ARI who were tested systematically by the same multiplex polymerase chain reaction (PCR) assay during periods of intense respiratory virus (RV) circulation. The proportions of infections between prepandemic and pandemic years were compared by using appropriate statistical tests. ResultsDuring prepandemic influenza seasons, overall RV detection was 92.7% (1384/1493) (respiratory syncytial virus [RSV]: 721/1493, 48.3%; coinfections: 456/1493, 30.5%) in children (<18 years) and 62.8% (2723/4339) (influenza: 1742/4339, 40.1%; coinfections: 264/4339, 6.1%) in adults. Overall RV detection in children was lower during pandemic years but increased from 58.6% (17/29) in 2020-21 (all ORVs; coinfections: 7/29, 24.1%) to 90.3% (308/341) in 2021-22 (ORVs: 278/341, 82%; SARS-CoV-2: 30/341, 8.8%; coinfections: 110/341, 32.3%) and 88.9% (361/406) in 2022-23 (ORVs: 339/406, 84%; SARS-CoV-2: 22/406, 5.4%; coinfections: 128/406, 31.5%). In adults, overall RV detection was also lower during pandemic years but increased from 43.7% (333/762) in 2020-21 (ORVs: 26/762, 3.4%; SARS-CoV-2: 307/762, 40.3%; coinfections: 7/762, 0.9%) to 57.8% (731/1265) in 2021-22 (ORVs: 179/1265, 14.2%; SARS-CoV-2: 552/1265, 43.6%; coinfections: 42/1265, 3.3%) and 50.1% (746/1488) in 2022-23 (ORVs: 409/1488, 27.5%; SARS-CoV-2: 337/1488, 22.6%; coinfections: 36/1488, 2.4%). No influenza or RSV was detected in 2020-21; however, their detection increased in the 2 subsequent years but did not reach prepandemic levels. Compared to the prepandemic period, the peaks of RSV hospitalization shifted in 2021-22 (16 weeks earlier) and 2022-23 (15 weeks earlier). Moreover, the peaks of influenza hospitalization shifted in 2021-22 (17 weeks later) and 2022-23 (4 weeks earlier). Age distribution was different compared to the prepandemic period, especially during the first pandemic year. ConclusionsSignificant shifts in viral etiology, seasonality, and age distribution of ARI hospitalizations occurred during the 3 pandemic years. Changes in age distribution observed in our study may reflect modifications in the landscape of circulating RVs and their contribution to ARI hospitalizations. During the pandemic period, SARS-CoV-2 had a low contribution to pediatric ARI hospitalizations, while it was the main contributor to adult ARI hospitalizations during the first 2 seasons and dropped below ORVs during the third pandemic season. Evolving RVs epidemiology underscores the need for increased scrutiny of ARI hospitalization etiology to inform tailored public health recommendations.

Introduction During the 2022 mpox outbreak, the province of Quebec, Canada, prioritized first doses for pre-exposure vaccination of people at high mpox risk, delaying second doses due to limited supply. We estimated single-dose mpox vaccine effectiveness (VE) adjusting for virus exposure risk based only on surrogate indicators available within administrative databases (eg, clinical record of sexually transmitted infections) or supplemented by self-reported risk factor information (eg, sexual contacts).Methods We conducted a test-negative case-control study between 19 June and 24 September 2022. Information from administrative databases was supplemented by questionnaire collection of self-reported risk factors specific to the 3-week period before testing. Two study populations were assessed: all within the administrative databases (All-Admin) and the subset completing the questionnaire (Sub-Quest). Logistic regression models adjusted for age, calendar-time and exposure-risk, the latter based on administrative indicators only (All-Admin and Sub-Quest) or with questionnaire supplementation (Sub-Quest).Results There were 532 All-Admin participants, of which 199 (37%) belonged to Sub-Quest. With exposure-risk adjustment based only on administrative indicators, single-dose VE estimates were similar among All-Admin and Sub-Quest populations at 35% (95% confidence interval [CI]:-2 to 59) and 30% (95% CI:-38 to 64), respectively. With adjustment supplemented by questionnaire information, the Sub-Quest VE estimate increased to 65% (95% CI:1-87), with overlapping confidence intervals.Conclusions Using only administrative data, we estimate one vaccine dose reduced the mpox risk by about one-third; whereas, additionally adjusting for self-reported risk factor information revealed greater vaccine benefit, with one dose instead estimated to reduce the mpox risk by about two-thirds. Inadequate exposure-risk adjustment may substantially under-estimate mpox VE.

Background There is a need to understand the duration of infectivity of primary and recurrent COVID-19 and identify predictors of loss of infectivity. Methods Prospective observational cohort study with serial viral culture, rapid antigen detection test (RADT) and RT-PCR on nasopharyngeal specimens of healthcare workers with COVID-19. The primary outcome was viral culture positivity as indicative of infectivity. Predictors of loss of infectivity were determined using multivariate regression model. The performance of the US CDC criteria (fever resolution, symptom improvement and negative RADT) to predict loss of infectivity was also investigated. Results 121 participants (91 female [79.3%]; average age, 40 years) were enrolled. Most (n=107, 88.4%) had received ≥3 SARS-CoV-2 vaccine doses, and 20 (16.5%) had COVID-19 previously. Viral culture positivity decreased from 71.9% (87/121) on day 5 of infection to 18.2% (22/121) on day 10. Participants with recurrent COVID-19 had a lower likelihood of infectivity than those with primary COVID-19 at each follow-up (day 5 OR, 0.14; p<0.001]; day 7 OR, 0.04; p=0.003]) and were all non-infective by day 10 (p=0.02). Independent predictors of infectivity included prior COVID-19 (adjusted OR [aOR] on day 5, 0.005; p=0.003), a RT-PCR Ct value <23 (aOR on day 5, 22.75; p<0.001), but not symptom improvement or RADT result. The CDC criteria would identify 36% (24/67) of all non-infectious individuals on Day 7. However, 17% (5/29) of those meeting all the criteria had a positive viral culture. Conclusions Infectivity of recurrent COVID-19 is shorter than primary infections. Loss of infectivity algorithms could be optimized.

ABSTRACT Background The primary objective of influenza immunization programs is to reduce the risk and burden of severe outcomes. To inform optimal program strategies, we monitored influenza hospitalizations over several seasons of varying subtype predominance, stratified by age, comorbidity and vaccination status. Methods We assembled data from an active hospital-based surveillance network involving systematic swabbing and PCR-confirmation of influenza virus infection by type/subtype during peak-weeks of seven influenza seasons (2012/13 to 2018/19) in Quebec, Canada. We estimated seasonal, population-based incidence of influenza-associated hospitalizations (interpreted as risk) by subtype, age, comorbidity and vaccine status, and derived the number-needed-to-vaccinate to prevent one hospitalization per stratum. Results The average seasonal incidence of influenza-associated hospitalization was 89/100,000 (95%CI: 86, 93), lower during A(H1N1) (49-82/100,000) than A(H3N2) seasons (73-143/100,000). Overall risk followed a J-shaped age pattern, highest among infants 0-5 months and adults ≥75 years. Hospitalization risks were highest for children <5 years during A(H1N1) but for adults ≥75 years during A(H3N2) subtype- predominant seasons. Age-adjusted hospitalization risks were 7-fold higher among individuals with versus without comorbidities (214 versus 30/100,000). The number-needed-to-vaccinate to prevent hospitalization was 82-fold lower for ≥75-years-olds with comorbidity (n=1,995), who comprised 39% of all hospitalizations, than for healthy 18-64-year-olds (n=163,488), who comprised just 6% of all hospitalizations. Conclusions In the context of broad-based influenza immunization programs (targeted or universal), severe outcome risks should be simultaneously examined by subtype, age, comorbidity, and vaccine status. Policymakers require such detail to prioritize further promotional efforts and expenditures toward the greatest and most efficient program impact. 40-word summary This hospital-based study involving systematic PCR testing over seven seasons revealed important differences in influenza hospitalization risk by subtype, age, comorbidity, and vaccination status. The findings highlight the need for data-driven decision-making to optimize vaccination strategies and minimize healthcare burden.

Background. Influenza immunization programs aim to reduce the risk and burden of severe outcomes. To inform optimal program strategies, we monitored influenza hospitalizations over 7 seasons, stratified by age, comorbidity, and vaccination status. Methods. We assembled data from 4 hospitals involved in an active surveillance network with systematic collection of nasal samples and polymerase chain reaction testing for influenza virus in all patients admitted through the emergency department with acute respiratory infection during the 2012-2013 to 2018-2019 influenza seasons in Quebec, Canada. We estimated seasonal, population-based incidence of influenza-associated hospitalizations by subtype predominance, age, comorbidity, and vaccine status, and derived the number needed to vaccinate to prevent 1 hospitalization per stratum. Results. The average seasonal incidence of influenza-associated hospitalization was 89/100 000 (95% confidence interval, 86-93), lower during A(H1N1) (49-82/100 000) than A(H3N2) seasons (73-143/100 000). Overall risk followed a J-shaped age pattern, highest among infants 0-5 months and adults >= 75 years old. Hospitalization risks were highest for children <5 years old during A(H1N1) but for highest adults aged >= 75 years during A(H3N2) seasons. Age-adjusted hospitalization risks were 7-fold higher among individuals with versus without comorbid conditions (214 vs 30/100 000, respectively). The number needed to vaccinate to prevent hospitalization was 82-fold lower for >= 75-years-olds with comorbid conditions (n = 1995), who comprised 39% of all hospitalizations, than for healthy 18-64-year-olds (n = 163 488), who comprised just 6% of all hospitalizations Conclusions. In the context of broad-based influenza immunization programs (targeted or universal), severe outcome risks should be simultaneously examined by subtype, age, comorbidity, and vaccine status. Policymakers require such detail to prioritize promotional efforts and expenditures toward the greatest and most efficient program impact.

The Canadian Sentinel Practitioner Surveillance Network reports mid-season 2023/24 influenza vaccine effectiveness (VE) of 63% (95% CI: 51–72) against influenza A(H1N1)pdm09, lower for clade 5a.2a.1 (56%; 95% CI: 33–71) than clade 5a.2a (67%; 95% CI: 48–80), and lowest against influenza A(H3N2) (40%; 95% CI: 5–61). The Omicron XBB.1.5 vaccine protected comparably well, with VE of 47% (95% CI: 21–65) against medically attended COVID-19, higher among people reporting a prior confirmed SARS-CoV-2 infection at 67% (95% CI: 28–85).

Background. There is a need to understand the duration of infectivity of primary and recurrent coronavirus disease 2019 (COVID-19) and identify predictors of loss of infectivity. Methods. Prospective observational cohort study with serial viral culture, rapid antigen detection test (RADT) and reverse transcription polymerase chain reaction (RT-PCR) on nasopharyngeal specimens of healthcare workers with COVID-19. The primary outcome was viral culture positivity as indicative of infectivity. Predictors of loss of infectivity were determined using multivariate regression model. The performance of the US Centers for Disease Control and Prevention (CDC) criteria (fever resolution, symptom improvement, and negative RADT) to predict loss of infectivity was also investigated. Results. In total, 121 participants (91 female [79.3%]; average age, 40 years) were enrolled. Most (n = 107, 88.4%) had received >= 3 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine doses, and 20 (16.5%) had COVID-19 previously. Viral culture positivity decreased from 71.9% (87/121) on day 5 of infection to 18.2% (22/121) on day 10. Participants with recurrent COVID-19 had a lower likelihood of infectivity than those with primary COVID-19 at each follow-up (day 5 odds ratio [OR], 0.14; P < .001]; day 7 OR, 0.04; P = .003]) and were all non-infective by day 10 (P = .02). Independent predictors of infectivity included prior COVID-19 (adjusted OR [aOR] on day 5, 0.005; P = .003), an RT-PCR cycle threshold [Ct] value <23 (aOR on day 5, 22.75; P < .001) but not symptom improvement or RADT result. The CDC criteria would identify 36% (24/67) of all non-infectious individuals on day 7. However, 17% (5/29) of those meeting all the criteria had a positive viral culture. Conclusions. Infectivity of recurrent COVID-19 is shorter than primary infections. Loss of infectivity algorithms could be optimized. [GRAPHICS] .

The Canadian Sentinel Practitioner Surveillance Network estimated vaccine effectiveness (VE) during the unusually early 2022/23 influenza A(H3N2) epidemic. Like vaccine, circulating viruses were clade 3C.2a1b.2a.2, but with genetic diversity affecting haemagglutinin positions 135 and 156, and reassortment such that H156 viruses acquired neuraminidase from clade 3C.2a1b.1a. Vaccine provided substantial protection with A(H3N2) VE of 54% (95% CI: 38 to 66) overall. VE was similar against H156 and vaccine-like S156 viruses, but with potential variation based on diversity at position 135.

BACKGROUND:Monkeypox, a viral zoonotic disease, is causing a global outbreak outside of endemic areas.OBJECTIVE:To characterize the outbreak of monkeypox in Montréal, the first large outbreak in North America.DESIGN:Epidemiologic and laboratory surveillance data and a phylogenomic analysis were used to describe and place the outbreak in a global context.SETTING:Montréal, Canada.PATIENTS:Probable or confirmed cases of monkeypox.MEASUREMENTS:Epidemiologic, clinical, and demographic data were aggregated. Whole-genome sequencing and phylogenetic analysis were performed for a set of outbreak sequences. The public health response and its evolution are described.RESULTS:Up to 18 October 2022, a total of 402 cases of monkeypox were reported mostly among men who have sex with men (MSM), most of which were suspected to be acquired through sexual contact. All monkeypox genomes nested within the B.1 lineage. Montréal Public Health worked closely with the affected communities to control the outbreak, becoming the first jurisdiction to offer 1 dose of the Modified Vaccinia Ankara-Bavarian Nordic vaccine as preexposure prophylaxis (PrEP) to those at risk in early June 2022. Two peaks of cases were seen in early June and July (43 and 44 cases per week, respectively) followed by a decline toward near resolution of the outbreak in October. Reasons for the biphasic peak are not fully elucidated but may represent the tempo of vaccination and/or several factors related to transmission dynamics and case ascertainment.LIMITATIONS:Clinical data are self-reported. Limited divergence among sequences limited genomic epidemiologic conclusions.CONCLUSION:A large outbreak of monkeypox occurred in Montréal, primarily among MSM. Successful control of the outbreak rested on early and sustained engagement with the affected communities and rapid offer of PrEP vaccination to at-risk persons.PRIMARY FUNDING SOURCE:None.

Abstract Background Factors associated with loss of infectivity in healthcare workers (HCWs) with COVID-19 are poorly understood. Understanding predictive factors could help optimize return-to-work criteria and minimize absenteeism. Methods Prospective observational cohort study of HCWs with COVID-19 conducted between Feb 20 2022 and March 6 2023 in 20 institutions in Montreal, Canada, with clinical/laboratory follow-up on Day 5, 7 and 10 of infection. Infectivity was determined by viral culture (Vero E6 cells) on nasopharyngeal swabs. Predictors of loss of infectivity were investigated by univariate and multivariate logistic regression. Results Overall, 121 participants (79.3% female, mean age 40 years) were recruited. Most (n=107, 88.4%) had received ≥3 vaccines and 20 (16.5%) had a history of prior COVID-19. The proportion of HCWs with a positive viral culture decreased from 71.9% on day 5 of infection to 18.2% on day 10. The proportion of HCWs with a positive RT-PCR decreased from 93.3% (112/120) on day 5 (median Ct value, 23.4 [IQR, 20.6-27.9]) to 61.2% (74/120) on day 10 (median Ct value, 32.5 [IQR, 28.5 to undetectable]). Rapid antigen detection test (RADT) positivity decreased from 81.5% on day 5 to 34.2% on day 10. Participants with recurrent COVID-19 had lower likelihood of infectivity at each visit (OR on day 5, 0.14; 95% CI 0.05-0.40; p< 0.001; OR on day 7, 0.04; 95% CI, 0.01-0.33; p=0.003) and none were infective on day 10 (p=0.02). At each visit, recurrent cases had higher median RT-PCR Ct values than primary infections (p< 0.03) and were more likely to have a negative RADT result (p< 0.01). By multivariate analysis, ongoing infectivity was associated with a RT-PCR Ct value < 23 (adjusted OR [aOR] on day 5, 22.75; p< 0.001; aOR on Day 7, 182.30; p< 0.001; and aOR on Day 10; 24.71; p=0.02). A history of previous COVID-19 was associated with a lower probability of infectivity on Day 5 (aOR, 0.005; p=0.003). By contrast, symptom improvement (including fever) and RADT result were not independent predictors of loss of infectivity. Conclusion A lower RT-PCR Ct value is associated with ongoing infectivity, whereas COVID-19 reinfection is a predictor of loss of infectivity. These findings could help optimize return-to-work algorithms. Disclosures All Authors: No reported disclosures

We performed viral culture of nasopharyngeal specimens in individuals aged 79 and older, infected with severe acute respiratory coronavirus virus 2 (SARS-CoV-2), 10 days after symptom onset. A positive viral culture was obtained in 10 (45%) of 22 participants, including 4 (33%) of 12 individuals with improving symptoms. The results of this small study suggest that infectivity may be prolonged among older individuals.

Abstract Introduction/Background The 2022 Monkeypox virus outbreak shed attention on an illness that is rare in non-endemic countries. Children are at risk of severe disease based on case series from previous outbreaks. Tecovirimat may be considered as a therapy in young children. Its efficacy and safety profile, however, have never been formally studied. This case report presents the first laboratory-confirmed case of monkeypox virus infection in a Canadian infant and its management. Case Description A 2-month-old infant presented to an emergency department with a vesiculopustular skin rash. A week before, parents noticed an eruptive cluster of 3 fluid-filled vesicles on the infant’s forehead. In the next days, vesiculopustular lesions appeared on his body. One spike of temperature was reported with no other sign of illness. On physical examination, a dozen umbilicated well-circumscribed vesico-pustules were observed with minimal skin inflammation. They ranged from 2 to 5 mm in size and were scattered over the face, trunk and limbs including palms and soles. In addition, 3 confluent crusted umbilicated lesions were present on the forehead. Discussion Differential diagnosis included varicella zoster virus, herpes simplex virus, and enteroviral infections. Empiric intravenous acyclovir was initiated pending specimen analysis. Bacterial culture and viral PCRs were negative on CSF and skin specimens. Due to transmission of monkeypox in the local adult population, orthopoxvirus was tested by PCR. The result was positive on a skin specimen and was later confirmed by the National Microbiology Laboratory of Canada. Because of the patient’s age and ongoing new lesions, tecovirimat was initiated. After 24 hours, new lesions stopped appearing and regression and crusting of active lesions were noted. Treatment was continued for 14 days without adverse events. Although parents denied similar symptoms, an epidemiological link was postulated, given work exposure in a setting with high risk of transmission in one of them. This case adds insight on the clinical features, the course of disease and management in infants. This 2-month-old infant did not develop any complication from the illness and was among the youngest patients with monkeypox to be treated with tecovirimat. Conclusion As monkeypox infection remains rare in children and may convey a higher risk for severe disease, a high degree of suspicion is warranted for clinicians caring for children. Monkeypox should be included in the differential diagnosis of an unexplained vesiculopustular rash. Finally, tecovirimat as a treatment for monkeypox infection in children was shown here to be safe and effective, even when started late in the evolution.

During 2016-2017 and 2017-2018 influenza A(H3N2) epidemics, updated clade 3C.2a vaccine bore egg-adaptation mutations and circulating 3C.2a viruses showed substantial genetic diversity. Vaccine effectiveness by phylogenetic subcluster and prior vaccination history reveal informative heterogeneity underpinning subtype-specific findings. Background The influenza A(H3N2) vaccine was updated from clade 3C.3a in 2015-2016 to 3C.2a for 2016-2017 and 2017-2018. Circulating 3C.2a viruses showed considerable hemagglutinin glycoprotein diversification and the egg-adapted vaccine also bore mutations. Methods Vaccine effectiveness (VE) in 2016-2017 and 2017-2018 was assessed by test-negative design, explored by A(H3N2) phylogenetic subcluster and prior season's vaccination history. Results In 2016-2017, A(H3N2) VE was 36% (95% confidence interval [CI], 18%-50%), comparable with (43%; 95% CI, 24%-58%) or without (33%; 95% CI, -21% to 62%) prior season's vaccination. In 2017-2018, VE was 14% (95% CI, -8% to 31%), lower with (9%; 95% CI, -18% to 30%) versus without (45%; 95% CI, -7% to 71%) prior season's vaccination. In 2016-2017, VE against predominant clade 3C.2a1 viruses was 33% (95% CI, 11%-50%): 18% (95% CI, -40% to 52%) for 3C.2a1a defined by a pivotal T135K loss of glycosylation; 60% (95% CI, 19%-81%) for 3C.2a1b (without T135K); and 31% (95% CI, 2%-51%) for other 3C.2a1 variants (with/without T135K). VE against 3C.2a2 viruses was 45% (95% CI, 2%-70%) in 2016-2017 but 15% (95% CI, -7% to 33%) in 2017-2018 when 3C.2a2 predominated. VE against 3C.2a1b in 2017-2018 was 37% (95% CI, -57% to 75%), lower at 12% (95% CI, -129% to 67%) for a new 3C.2a1b subcluster (n = 28) also bearing T135K. Conclusions Exploring VE by phylogenetic subcluster and prior vaccination history reveals informative heterogeneity. Pivotal mutations affecting glycosylation sites, and repeat vaccination using unchanged antigen, may reduce VE.

Different serological assays were rapidly generated to study humoral responses against the SARS-CoV-2 Spike glycoprotein. Due to the intrinsic difficulty of working with SARS-CoV-2 authentic virus, most serological assays use recombinant forms of the Spike glycoprotein or its receptor binding domain (RBD). Cell-based assays expressing different forms of the Spike, as well as pseudoviral assays, are also widely used. To evaluate whether these assays recapitulate findings generated when the Spike is expressed in its physiological context (at the surface of the infected primary cells), we developed an intracellular staining against the SARS-CoV-2 nucleocapsid (N) to distinguish infected from uninfected cells. Human airway epithelial cells (pAECs) were infected with authentic SARS-CoV-2 D614G or Alpha variants. We observed robust cell-surface expression of the SARS-CoV-2 Spike at the surface of the infected pAECs using the conformational-independent anti-S2 CV3-25 antibody. The infected cells were also readily recognized by plasma from convalescent and vaccinated individuals and correlated with several serological assays. This suggests that the antigenicity of the Spike present at the surface of the infected primary cells is maintained in serological assays involving expression of the native full-length Spike.

Influenza virus circulation virtually ceased in Canada during the COVID-19 pandemic, re- emerging with the relaxation of restrictions in spring 2022. Using a testnegative design, the Canadian Sentinel Practitioner Surveillance Network reports 2021/22 vaccine effectiveness of 36% ( 95% CI: -38 to 71) against late-season illness due to influenza A(H3N2) clade 3C.2a1b.2a.2 viruses, considered antigenically distinct from the 3C.2a1b.2a.1 vaccine strain. Findings reinforce the World Health Organization's decision to update the 2022/23 northern hemisphere vaccine to a more representative A(H3N2) clade 3C.2a1b. 2a. 2 strain.

Human noroviruses are among the main causes of acute gastroenteritis worldwide. Frozen raspberries have been linked to several norovirus food-related outbreaks. However, the extraction of norovirus RNA from frozen raspberries remains challenging. Recovery yields are low and PCR inhibitors limit the sensitivity of the detection methodologies. In 2017, 724 people from various regions of the Province of Quebec, Canada, were infected by noroviruses and the outbreak investigation pointed to frozen raspberries as a putative source. A new magnetic silica bead approach was used for the extraction of viruses from different outbreak samples. The RNA extracts were tested by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and five samples were confirmed positive for norovirus by RT-qPCR amplicon sequencing. A multiplex long-range two-step RT-PCR approach was developed to amplify norovirus ORF2 and ORF3 capsid genes from the positive frozen raspberry RNA extracts and other sequencing strategies were also explored. These capsid genes were sequenced by Next-Generation Sequencing. Phylogenetic analyses confirmed the presence of multiple genotypes (GI.3, GI.6, and GII.17) and intra-genotype variants in some of the frozen raspberry samples. Variants of genotype GI.3 and GI.6 had 100% homology with sequences from patient samples. Similar strains were also reported in previous outbreaks. Confirmation approaches based on sequencing the norovirus capsid genes using Next-Generation Sequencing can be applied at trace level contaminations and could be useful to assess risk and assist in source tracking.

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The objective of this study was to validate the use of spring water gargle (SWG) as an alternative to oral and nasopharyngeal swab (ONPS) for SARS‐CoV‐2 detection with a laboratory‐developed test. Healthcare workers and adults from the general population, presenting to one of two COVID‐19 screening clinics in Montréal and Québec City, were prospectively recruited to provide a gargle sample in addition to the standard ONPS. The paired specimens were analyzed using thermal lysis followed by a laboratory‐developed nucleic acid amplification test (LD‐NAAT) to detect SARS‐CoV‐2, and comparative performance analysis was performed. An individual was considered infected if a positive result was obtained on either sample. A total of 1297 adult participants were recruited. Invalid results (n = 18) were excluded from the analysis. SARS‐CoV‐2 was detected in 144/1279 (11.3%) participants: 126 from both samples, 15 only from ONPS, and 3 only from SWG. Overall, the sensitivity was 97.9% (95% CI: 93.7–99.3) for ONPS and 89.6% (95% CI: 83.4–93.6; p = 0.005) for SWG. The mean ONPS cycle threshold (Ct) value was significantly lower for the concordant paired samples as compared to discordant ones (22.9 vs. 32.1; p < 0.001). In conclusion, using an LD‐NAAT with thermal lysis, SWG is a less sensitive sampling method than the ONPS. However, the higher acceptability of SWG might enable a higher rate of detection from a population‐based perspective. Nonetheless, in patients with a high clinical suspicion of COVID‐19, a repeated analysis with ONPS should be considered. The sensitivity of SWG using NAAT preceded by chemical extraction should be evaluated.

The seasonal nature of outbreaks of respiratory viral infections with increased transmission during low temperatures has been well established. Accordingly, temperature has been suggested to play a role on the viability and transmissibility of SARS-CoV-2, the virus responsible for the COVID-19 pandemic. The receptor-binding domain (RBD) of the Spike glycoprotein is known to bind to its host receptor angiotensin-converting enzyme 2 (ACE2) to initiate viral fusion. Using biochemical, biophysical, and functional assays to dissect the effect of temperature on the receptor-Spike interaction, we observed a significant and stepwise increase in RBD-ACE2 affinity at low temperatures, resulting in slower dissociation kinetics. This translated into enhanced interaction of the full Spike glycoprotein with the ACE2 receptor and higher viral attachment at low temperatures. Interestingly, the RBD N501Y mutation, present in emerging variants of concern (VOCs) that are fueling the pandemic worldwide (including the B.1.1.7 (α) lineage), bypassed this requirement. This data suggests that the acquisition of N501Y reflects an adaptation to warmer climates, a hypothesis that remains to be tested.