Case Series of Jamestown Canyon Virus Infections with Neurologic Outcomes, Canada, 2011-2016.

Jamestown Canyon virus (JCV) is a mosquitoborne orthobunyavirus in the California serogroup that circulates throughout Canada and the United States. Most JCV exposures result in asymptomatic infection or a mild febrile illness, but JCV can also cause neurologic diseases, such as meningitis and encephalitis. We describe a case series of confirmed JCV-mediated neuroinvasive disease among persons from the provinces of British Columbia, Alberta, Quebec, and Nova Scotia, Canada, during 2011-2016. We highlight the case definitions, epidemiology, unique features and clinical manifestations, disease seasonality, and outcomes for those cases. Two of the patients (from Quebec and Nova Scotia) might have acquired JCV infections during travel to the northeastern region of the United States. This case series collectively demonstrates JCV's wide distribution and indicates the need for increased awareness of JCV as the underlying cause of meningitis/meningoencephalitis during mosquito season.

Raisonnement clinique : Avortement septique à Neisseria meningitidis.

Le choc septique post-avortement est une cause mondiale importante de mortalité maternelle, mais on l'observe rarement dans les pays développés. Nous décrivons ici un cas d'avortement septique associé à un nouvel agent pathogène : Neisseria meningitidis. Une femme multipare de 30 ans s'est trouvée en choc septique après un avortement spontané incomplet. Elle a reçu un traitement empirique par antibiotiques et vasopresseurs, a subi une dilatation-aspiration d'urgence et a été admise à l'unité de soins intensifs. L'hémoculture et l'analyse de tissus endométriaux se sont révélées positives à la bactérie N. meningitidis. L'antibiothérapie a été ajustée en fonction de la culture et la patiente s'est rétablie. Il importe de reconnaître le choc septique, d'administrer l'antibiothérapie et de neutraliser la source d'infection dans les plus brefs délais. Ici, nous décrivons un cas d'avortement septique associé à un agent pathogène inhabituel. Nous soulignons aussi l'importance d'utiliser une antibiothérapie empirique à large spectre suivie d'une antibiothérapie spécifique aux résultats de culture pour obtenir la meilleure couverture possible.

Clinical Conundrum: Neisseria meningitidis Septic Abortion.

Septic shock after abortion is an important cause of global maternal mortality but is rarely encountered in developed countries. We describe a case of septic abortion with a novel associated pathogen: Neisseria meningitidis. A 30-year-old multiparous woman presented in septic shock after an incomplete spontaneous abortion. She received empiric antibiotics and vasopressors, underwent an urgent dilatation and curettage, and was admitted to the intensive care unit. Her blood cultures and endometrial tissue were positive for N. meningitidis. Antibiotics were adjusted based on culture, and the patient recovered. Septic shock requires prompt identification, antibiotic administration, and source control. Here, we identify an uncommon pathogen associated with septic abortion and highlight the importance of broad empiric and subsequent culture-guided antibiotic choice to ensure coverage.

Cystic neutrophilic granulomatous mastitis - a review of 12 consecutive cases.

AIMS: Cystic neutrophilic granulomatous mastitis (CNGM) is an uncommon but increasingly recognised cause of mastitis, often associated with Corynebacterium ssp. infection. We studied the histopathological and clinical features of CNGM in a Canadian setting, and the work-up required to identify pathogenic microorganisms. METHODS AND RESULTS: A retrospective search for breast specimens with abscess, acute, chronic and/or granulomatous inflammation from 1998 to 2018 was performed. Haematoxylin and eosin slides were reviewed for typical histological features of CNGM. Histochemically stained slides for microorganisms were also reviewed. Repeat Gram stains were performed if initially negative. Electronic medical records were abstracted for microbiology results and relevant clinical data. Twelve cases were identified. All were female, aged 25-57 years, mainly Caucasian, with one Venezuelan and two of Chinese ethnicity. Most were parous (10 of 12); five of 12 had an endocrinopathy. Bacteria were identified in one or more specimens from eight of 12 patients; additional Gram stains revealed organisms in four of 12 cases. Of four bacterial cultures, one grew Corynebacterium kroppenstedtii. 16S polymerase chain reaction for three samples was negative. Two patients had multiple breast biopsies, showing early palisaded granulomas followed by classic features of CNGM. The patients had various management approaches, including surgery and antimicrobials. CONCLUSIONS: CNGM may present as palisaded granulomatous inflammation, without the expected 'cystic' pattern, suggesting that there is an evolution of histomorphology with this infection. Most patients with CNGM are parous, and there may be an association with endocrinopathies. Application of multiple Gram stains increases the yield of microorganism identification. Recognition of CNGM in breast biopsies and collaborative communications are essential to direct appropriate therapy.

High Seroprevalence of Jamestown Canyon Virus among Deer and Humans, Nova Scotia, Canada.

Using residual serum samples from Nova Scotia, Canada, we found that 87.8% of tested deer and an estimated 20.6% of the human population were infected with Jamestown Canyon virus. Human seropositivity reached 48.2% in 1 region. This virus may be an underrecognized cause of disease in Nova Scotia.

Risk acceptance of human T-lymphotropic virus infection in solid organ transplantation-A survey of Atlantic Canadian ambulatory patients.

BACKGROUND: Human T-lymphotropic virus (HTLV) has an estimated prevalence of 12 per 100 000 in the general Canadian population (with higher rates in distinct groups) and is most commonly transmitted by breast feeding, sexual intercourse, sharing injection tools, and blood transfusions. A minority of those infected will develop severe disease. Health Canada mandates that people who are positive for HTLV are not suitable to be solid organ donors. Given the apparent low-disease burden of HTLV in Canada, we explored HTLV risk tolerance among patients, in the context of organ transplantations. METHODS: Using telephone, and in-person questionnaires, we assessed willingness of patients to accept the risk of HTLV infection in hypothetical scenarios in which they required an organ transplant for survival. RESULTS: Seventy-four outpatients attending various medical clinics participated in the survey. In a standard gamble scenario, 37.5% of respondents would have accepted a solid organ transplant regardless of HTLV risk, as compared to 27.3% and 24.6% accepting organ transplantation if there was a risk of human immunodeficiency virus (HIV) or of human virus Y (HVY; a fictitious virus describing HTLV in terms of neurological outcomes), respectively. Similarly, the median longevity traded to ensure a virus-free organ was 4-5 years regarding all viruses, except for HVY, for which the median time exchanged to ensure a virus-free organ was 10 (out of a possible 20) years. CONCLUSIONS: These data suggest that patients, though willing to accept some risk of viral infection, would not be willing to forgo HTLV screening of solid organs.

Taqman PACMAN: a simple molecular approach for positive rapid antigen test confirmation during periods of low prevalence.

Antigen-based rapid diagnostic tests (Ag-RDTs) were widely deployed to enhance SARS-CoV-2 testing capacity during the COVID-19 pandemic. Consistent with national guidance for low prevalence settings, positive Ag-RDTs were confirmed using nucleic acid amplification tests (NAATs) to avoid false positive results. However, increasing demands for positive Ag-RDT confirmation competed with other testing priorities in clinical laboratories. This work hypothesized that real-time RT-PCR without nucleic acid extraction (NAE) would be sufficiently sensitive to support positive Ag-RDT confirmation. Ag-RDT and NAAT results from community-based asymptomatic testing sites prior to the omicron variant wave were compared to calculate the weekly false positive rate (FPR) and false detection rate (FDR). Real-time RT-PCR was compared with and without NAE using 752 specimens previously tested positive for SARS-CoV-2 using commercial NAATs and 344 specimens from Ag-RDT-positive individuals. The impact of SARS-CoV-2 prevalence on laboratory resources required to sustain Ag-RDT confirmation was modeled for the RT-PCR with and without NAE. Overall, FPR was low [0.07% (222/330,763)] in asymptomatic testing sites, but FDR was high [30.7% (222/724)]. When RT-PCR was compared with and without NAE, 100% concordance was obtained with NAAT-positive specimens, including those from Ag-RDT-positive individuals. NAE-free RT-PCR significantly reduced time to results, human resources, and overall costs. A 30.7% FDR reaffirms the need for NAAT-based confirmation of positive Ag-RDT results during low SARS-CoV-2 prevalence. NAE-free RT-PCR was shown to be a simple and cost-sparing NAAT-based solution for positive Ag-RDT confirmation, and its implementation supported data-driven broader Ag-RDT deployment into communities, workplaces, and households. IMPORTANCE: Rapid antigen testing for SARS-CoV-2 was widely deployed during the COVID-19 pandemic. In settings of low prevalence, national guidance recommends that positive antigen test results be confirmed with molecular testing. Given the high testing burden on clinical laboratories during the COVID-19 pandemic, the high volume of positive antigen tests submitted for confirmatory testing posed challenges for laboratory workflow. This study demonstrated that a simple PCR method without prior nucleic acid purification is an accurate and cost-effective solution for positive rapid antigen test confirmation. Implementing this method allowed molecular confirmatory testing for positive antigen tests to be sustained as antigen testing was expanded into large populations such as workplaces, schools, and households.

Preventing Respiratory Viral Illness Invisibly (PRiVII): protocol for a pragmatic cluster randomized trial evaluating far-UVC light devices in long-term care facilities to reduce infections.

BACKGROUND: Respiratory viral illness (RVI)-e.g., influenza, COVID-19-is a serious threat in long-term care (LTC) facilities. Standard infection control measures are suboptimal in LTC facilities because of residents' cognitive impairments, care needs, and susceptibility to loneliness and mental illness. Further, LTC residents living with high degrees of frailty who contract RVIs often develop the so-called atypical symptoms (e.g., delirium, worse mobility) instead of typical cough and fever, delaying infection diagnosis and treatment. Although far-UVC (222 nm) light devices have shown potent antiviral activity in vitro, clinical efficacy remains unproven. METHODS: Following a study to assay acceptability at each site, this multicenter, double-blinded, cluster-randomized, placebo-controlled trial aims to assess whether far-UVC light devices impact the incidence of RVIs in LTC facilities. Neighborhoods within LTC facilities are randomized to receive far-UVC light devices (222 nm) or identical placebo light devices that emit only visible spectrum light (400-700 nm) in common areas. All residents are monitored for RVIs using both a standard screening protocol and a novel screening protocol that target atypical symptoms. The 3-year incidence of RVIs will be compared using intention-to-treat analysis. A cost-consequence analysis will follow. DISCUSSION: This trial aims to inform decisions about whether to implement far-UVC light in LTC facilities for RVI prevention. The trial design features align with this pragmatic intent. Appropriate additional ethical protections have been implemented to mitigate participant vulnerabilities that arise from conducting this study. Knowledge dissemination will be supported through media engagement, peer-reviewed presentations, and publications. TRIAL REGISTRATION: ClinicalTrials.gov NCT05084898. October 20, 2021.

Real-world evaluation of the Lucira Check-It COVID-19 loop-mediated amplification (LAMP) test.

IMPORTANCE: In hospitals during the COVID-19 pandemic, laboratory testing was important to reduce SARS-CoV-2 transmissions, while facilitating patient flow in the emergency department and pre-operative settings, and allowing for the safe return to work of exposed healthcare workers. Delayed test results from laboratory nucleic acid amplification tests (NAATs) posed a barrier to maximizing efficient patient flow and minimizing staffing shortages. This quality improvement project sought to evaluate the analytical and clinical performance of the Lucira Check-It COVID-19 Test, a point-of-care test that used NAAT technology, in the perioperative setting, emergency department, and community testing sites. We found the Lucira Check-It to have comparable performance to laboratory NAATs. It can be employed with little training for specimen collection, processing, and interpretation, and at a cost justifiable from the resources saved from avoiding sample transport and laboratory testing.

Neglected SARS-CoV-2 variants and potential concerns for molecular diagnostics: a framework for nucleic acid amplification test target site quality assurance.

IMPORTANCE: Molecular tests like polymerase chain reaction were widely used during the COVID-19 pandemic but as the pandemic evolved, so did SARS-CoV-2. This virus acquired mutations, prompting concerns that mutations could compromise molecular test results and be falsely negative. While some manufacturers may have in-house programs for monitoring mutations that could impact their assay performance, it is important to promptly report mutations in circulating viral strains that could adversely impact a diagnostic test result. However, commercial test target sites are proprietary, making independent monitoring difficult. In this study, SARS-CoV-2 test target sites were sequenced to monitor and assess mutations impact, and 29 novel mutations impacting SARS-CoV-2 detection were identified. This framework for molecular test target site quality assurance could be adapted to any molecular test, ensuring accurate diagnostic test results and disease diagnoses.

Hunting for mpox (monkeypox) mimickers: Use of the Biofire meningitis/encephalitis panel on lesion swabs to support alternative viral diagnoses.

BACKGROUND: Mpox (formerly monkeypox) is an emerging zoonotic disease of public health concern that presents as a rash mimicking other common viral exanthems. Unlike traditional testing algorithms relying on several assays, the BioFire FilmArray meningitis/encephalitis (ME) panel simultaneously detects common viruses causing rashes; however, Biofire ME is only licensed for testing on cerebral spinal fluid. OBJECTIVES: This study evaluated use of the Biofire ME panel for detection and discrimination of herpes simplex virus types 1 and 2 (HSV-1 and HSV-2), varicella zoster virus (VZV), human herpesviruses type 6 (HHV-6), enteroviruses (EVs), and human paraechoviruses (HPeVs) from a dermal or mucocutaneous swabs collected in universal transport media (UTM). STUDY DESIGN: Results of the BioFire ME panel were compared against methods used during clinical testing. Ten-fold serial dilutions in UTM of cultured viruses were used to compare analytical sensitivity, and analytical specificity was assessed using panels of microorganisms in UTM. Clinical sensitivity and specificity were assessed using 20 positive specimens each for HHV-1, HHV-2, HHV-6, VZV, EVs, and HPeV, as well as 35 known negative specimens that included 15 mpox-positive specimens. RESULTS: Biofire ME was as sensitive as comparator methods, and correctly discriminated all HSV-1, HSV-2, VZV, HHV-6, EVs, and HPeVs from mpox and mpox-mimickers. Cross-reaction between EV and rhinoviruses A, B, and C were noted in the specificity panel. CONCLUSIONS: Swabs in UTM collected for mpox testing are suitable for use on the Biofire ME panel, allowing more streamlined diagnostic testing for viral exanthems in patients under investigation for mpox infection.

A vignette-based survey to assess clinical decision making regarding antibiotic use and hospitalization of patients with probable aseptic meningitis.

BACKGROUND: The many etiologies of meningitis influence disease severity - most viral causes are self-limiting, while bacterial etiologies require antibiotics and hospitalization. Aided by laboratory findings, the physician judges whether to admit and empirically treat the patient (presuming a bacterial cause), or to treat supportively as if it were viral. OBJECTIVE: To determine factors that lead infectious disease specialists to admit and treat in cases of suspected meningitis. METHODS: A clinical vignette describing a typical case of viral meningitis in the emergency department was presented to clinicians. They were asked to indicate on a Likert scale the likelihood of administering empirical antibiotics and admitting the patient from the vignette and for eight subsequent scenarios (with varied case features). The process was repeated in the context of an inpatient following initial observation and/or treatment. RESULTS: Participants were unlikely to admit or to administer antibiotics in the baseline scenario, but a low Glasgow Coma Score or a high cerebrospinal fluid (CSF) white blood cell count with a high neutrophil percentage led to empirical treatment and admission. These factors were less influential after a negative bacterial CSF culture. These same clinical variables led to maintaining treatment and hospitalization of the inpatient. CONCLUSIONS: Most participants chose not to admit or treat the patient in the baseline vignette. Confusion and CSF white blood cell count (and neutrophil predominance) were the main influences in determining treatment and hospitalization. A large range of response scores was likely due to differing regional practices or to different levels of experience.

HISTORIQUE: Les nombreuses étiologies de la méningite influent sur la gravité de la maladie. La plupart des causes virales sont spontanément résolutives, tandis que les étiologies bactériennes exigent la prise d'antibiotiques et une hospitalisation. À l'aide des résultats de laboratoire, le médecin évalue s'il doit hospitaliser le patient et le traiter de manière empirique (présumant une cause bactérienne) ou lui donner un traitement de soutien comme si la maladie était d'origine virale. OBJECTIF: Déterminer les facteurs qui incitent les infectiologues à hospitaliser et traiter des cas de méningite présumée. MÉTHODOLOGIE: Les cliniciens se sont fait présenter une saynète clinique décrivant un cas classique de méningite virale observé au département d'urgence. Les chercheurs ont invité les cliniciens à indiquer sur une échelle de Likert la probabilité d'administrer des antibiotiques empiriques et d'hospitaliser le patient d'après la saynète et huit autres scénarios (aux diverses caractéristiques). Les cliniciens ont repris le processus chez un patient hospitalisé après une observation initiale ou un traitement. RÉSULTATS: Les participants étaient peu susceptibles d'hospitaliser ou d'administrer des antibiotiques dans le scénario de base, mais un faible indice de coma de Glasgow ou une numération élevée des globules blancs dans le liquide céphalorachidien (LCR) associée à un fort pourcentage de neutrophiles donnait lieu à un traitement et une hospitalisation empiriques. Ces facteurs avaient moins d'influence après une culture bactérienne négative dans le LCR. Ces mêmes variables cliniques suscitaient le maintien du traitement et le prolongement de l'hospitalisation du patient hospitalisé. CONCLUSIONS: La plupart de participants choisissaient de ne pas hospitaliser ou traiter le patient observé dans la saynète de base. La confusion et la numération des globules blancs dans le LCR (et la prédominance en neutrophiles) étaient les principales influences pour déterminer le traitement et l'hospitalisation. La vaste plage d'indices de réponse était probablement attribuable à des pratiques régionales divergentes ou à divers niveaux d'expérience.

Clinical presentation of patients with aseptic meningitis, factors influencing treatment and hospitalization, and consequences of enterovirus cerebrospinal fluid polymerase chain reaction testing.

INTRODUCTION: Clinical and laboratory features of enteroviral meningitis may overlap with those of bacterial meningitis. In the present retrospective review, we compared features of enteroviral (EV)-positive and -negative patients to determine those that were most influential in admission, discharge and in anti-infective administration. METHODS: Data were analyzed from the records of 117 pediatric and adult patients who underwent cerebrospinal fluid (CSF) EV testing over a three-year period. RESULTS: The oldest EV-positive patient was 34 years of age and the occurrence of the disease was highly seasonal. EV-positive patients were more likely to report fever, rash, photophobia, short onset and exposure to an ill contact. A positive polymerase chain reaction (PCR) result was associated with relatively short hospitalization. Seizure and neurological symptoms were more strongly associated with a negative PCR test result. CSF characteristics did not discriminate well between patients with positive and negative PCR tests. Patients with imperfect Glasgow Coma Scores or with neurological symptoms were more likely to be admitted to hospital than those without. Fever and recent onset predicted determinants of anti-infective use. CONCLUSION: The present retrospective study confirms previous reports regarding seasonality and the young age of positive patients. Factors that indicate nonenteroviral etiology were appropriately also those that influenced hospitalization. Patients with EV meningitis were likely to be treated with empirical anti-infectives, and a substantial proportion continued to take antibiotics for more than 24 h after receiving the positive EV PCR test result. INTRODUCTION: Clinical and laboratory features of enteroviral meningitis may overlap with those of bacterial meningitis. In the present retrospective review, we compared features of enteroviral (EV)-positive and -negative patients to determine those that were most influential in admission, discharge and in anti-infective administration. METHODS: Data were analyzed from the records of 117 pediatric and adult patients who underwent cerebrospinal fluid (CSF) EV testing over a three-year period. RESULTS: The oldest EV-positive patient was 34 years of age and the occurrence of the disease was highly seasonal. EV-positive patients were more likely to report fever, rash, photophobia, short onset and exposure to an ill contact. A positive polymerase chain reaction (PCR) result was associated with relatively short hospitalization. Seizure and neurological symptoms were more strongly associated with a negative PCR test result. CSF characteristics did not discriminate well between patients with positive and negative PCR tests. Patients with imperfect Glasgow Coma Scores or with neurological symptoms were more likely to be admitted to hospital than those without. Fever and recent onset predicted determinants of anti-infective use. CONCLUSION: The present retrospective study confirms previous reports regarding seasonality and the young age of positive patients. Factors that indicate nonenteroviral etiology were appropriately also those that influenced hospitalization. Patients with EV meningitis were likely to be treated with empirical anti-infectives, and a substantial proportion continued to take antibiotics for more than 24 h after receiving the positive EV PCR test result.

HISTORIQUE: Les caractéristiques cliniques et de laboratoire de la méningite entérovirale peuvent chevaucher celles de la méningite bactérienne. Dans la présente analyse rétrospective, les chercheurs ont comparé les caractéristiques des patients positifs et négatifs à l'entérovirus (EV) pour déterminer celles qui avaient le plus d'influence sur l'admission, le congé et l'administration d'anti-infectieux. MÉTHODOLOGIE: Les chercheurs ont analysé les données tirées des dossiers de 117 patients pédiatriques et adultes qui avaient subi un test du liquide céphalorachidien (LCR) positif à l'EV sur une période de trois ans. RÉSULTATS: La patiente positive à l'EV la plus âgée avait 34 ans. L'occurrence de la maladie était hautement saisonnière. Les patients positifs à l'EV étaient plus susceptibles de déclarer de la fièvre, des éruptions, de la photophobie, une apparition rapide et une exposition à un contact malade. Les résultats positifs de la réaction en chaîne de la polymérase (PCR) s'associaient à une hospitalisation relativement courte. Les conclusions et les symptômes neurologiques étaient liés plus fortement aux résultats d'un test de PCR négatif. Les caractéristiques du LCR distinguaient mal les patients ayant des tests de PCR positifs de ceux ayant des résultats négatifs. Les patients dont l'indice de coma de Glasgow était imparfait ou qui avaient des symptômes neurologiques étaient plus susceptibles d'être hospitalisés que les autres. La fièvre et une apparition récente étaient prédictives de l'utilisation d'anti-infectieux. CONCLUSION: La présente étude rétrospective confirme les rapports antérieurs au sujet du caractère saisonnier et du jeune âge des patients positifs. Comme de juste, les facteurs indicateurs d'une étiologie non entérovirale étaient aussi ceux qui influaient sur l'hospitalisation. Les patients ayant une méningite EV étaient susceptibles d'être traités à l'aide d'anti-infectieux empiriques, et une forte proportion d'entre eux continuaient de prendre des antibiotiques pendant plus de 24 heures après avoir reçu le résultat du test PCR positif à EV.

Investigating the Sensitivity of Nasal or Throat Swabs: Combination of Both Swabs Increases the Sensitivity of SARS-CoV-2 Rapid Antigen Tests.

The COVID-19 pandemic has been hallmarked by several waves of variants of concern (VoCs), each with novel challenges. Currently, the highly transmissible Omicron VoC is predominant worldwide, and sore throat is common, among other cold-like symptoms. Anecdotes on social media have suggested that sampling one's throat can increase the sensitivity for Omicron detection by antigen-based rapid testing devices (Ag-RDTs). This work aimed to improve the local testing strategy and determine whether the sensitivity of Ag-RDTs designed for nasal sampling is altered with the use of self-administered throat swabs in self-perceived asymptomatic individuals. This investigation used a common Ag-RDT (i.e., Abbott Panbio COVID-19 Ag rapid test device) to compare three sampling sites: nasal swab, throat swab, and combined nasal/throat. All Ag-RDT results were confirmed with molecular testing from residual test buffer. Compared to reverse transcriptase PCR (RT-PCR), samples from nasal or throat swabs each detected 64.5% of SARS-CoV-2 cases; however, combining the contributions of each swab increased the positive percent agreement (PPA) with RT-PCR to 88.7%. This trend was also evident with the Rapid Response Ag-RDT (BTNX), which uses more flexible swabs than does the Panbio. When nasal swab collection was compared to paired sampling of the nose/throat using a single swab with the Panbio Ag-RDT, the PPAs were 68.4% and 81.6%, respectively. No false-positive results were observed with nasal, throat, or combined nasal/throat sampling. Self-administered throat and nasal/throat swabs both had >90% acceptability. These findings support the use of self-collected combined nasal/throat sampling for Ag-RDT-based SARS-CoV-2 detection in self-perceived asymptomatic individuals. IMPORTANCE This quality project demonstrates that combining the results of nasal and throat swabs or using a combined single swab of the throat and nares resulted in increased detection of SARS-CoV-2 using a rapid antigen test, in an asymptomatic population. Importantly, no false positives were detected, and over 90% of people were willing to perform the combination swab. These types of projects are instrumental in informing local practices to improve testing strategies. These data support the option of using a combined nasal/throat swab in our local setting to enhance the detection of Omicron.

Comparison between Nasal and Nasopharyngeal Swabs for SARS-CoV-2 Rapid Antigen Detection in an Asymptomatic Population, and Direct Confirmation by RT-PCR from the Residual Buffer.

Containment measures employed during the COVID-19 pandemic included prompt recognition of cases, isolation, and contact tracing. Bilateral nasal (NA) swabs applied to a commercial antigen-based rapid diagnostic test (Ag-RDT) offer a simpler and more comfortable alternative to nasopharyngeal (NP) collection; however, little is known about the sensitivity of this method in an asymptomatic population. Participants in community-based asymptomatic testing sites were screened for SARS-CoV-2 using an Ag-RDT with NP sampling. Positive individuals returned for confirmatory molecular testing and consented to repeating the Ag-RDT using a bilateral NA swab for comparison. Residual test buffer (RTB) from Ag-RDTs was subjected to real-time reverse transcription-PCR (RT-PCR). Of 123,617 asymptomatic individuals, 197 NP Ag-RDT-positive participants were included, with 175 confirmed positive by RT-PCR. Of these cases, 154 were identified from the NA swab collection with Ag-RDT, with a sensitivity of 88.0% compared to the NP swab collection. Stratifying results by RT-PCR cycle threshold demonstrated that sensitivity of the nasal collection method varied based on the cycle threshold (CT) value of the paired RT-PCR sample. RT-PCR testing on the RTB from the Ag-RDT using NP and NA swab collections resulted in 100.0% and 98.7% sensitivity, respectively. NA swabs provide an adequate alternative to NP swab collection for use with Ag-RDT, with the recognition that the test is most sensitive in specimens with high viral loads. With the high sensitivity of RT-PCR testing on RTB from Ag-RDT, a more streamlined approach to confirmatory testing is possible without recollection or use of paired collections strategies. IMPORTANCE Nasal swabbing for SARS-CoV-2 (COVID-19) comes with many benefits but is slightly less sensitive than traditional nasopharyngeal swabbing; however, confirmatory lab-based testing could be performed directly from the residual buffer from either sample type.

Combined oropharyngeal/nares and nasopharyngeal swab sampling remain effective for molecular detection of SARS-CoV-2 Omicron variant.

The world has experienced several waves of SARS-CoV-2 variants of concern (VoCs) throughout the COVID-19 pandemic since the first cases in December 2019. The Omicron VoC has increased transmission, compared to its predecessors, and can present with sore throat and other cold-like symptoms. Given the predominance of throat symptoms, and previous work demonstrating better sensitivity using antigen-based rapid detection tests when a throat swab is included in the standard nasal sampling, this quality improvement project sought to ensure ongoing suitability of both combined oropharyngeal/nares (OPN) and nasopharyngeal (NP) swab sampling used throughout the pandemic. Consenting participants meeting Public Health testing criteria (mostly symptomatic or a close contact of a known case) were enrolled, and paired NP and OPN swabs were subjected to nucleic acid amplification testing (NAAT). Comparing paired specimens from 392 participants sensitivity of NP swabs was 89.1 % (95 % CI, 78.8-94.9), and that of OPN was 98.4 % (95 % CI: 90.9->99.9) (P-value 0.052). This project demonstrated that both NP and combined OPN swabs detected the Omicron variant with similar sensitivity by NAAT, supporting the continued use of either swab collection for SARS-CoV-2 molecular detection.

Avoiding False-Positive SARS-CoV-2 Rapid Antigen Test Results with Point-of-Care Molecular Testing on Residual Test Buffer.

Antigen-based rapid diagnostic tests (Ag-RDTs) have been widely used for the detection of SARS-CoV-2 during the coronavirus disease 2019 (COVID-19) pandemic. In settings of low disease prevalence, such as asymptomatic community testing, national guidelines recommend confirmation of positive Ag-RDT results with a nucleic acid amplification test (NAAT). This often requires patients to be recalled for repeat specimen recollection and subsequent testing in reference laboratories. This project assessed the use of a point-of-care molecular NAAT for SARS-CoV-2 detection (i.e., ID NOW), which was performed on-site at a volunteer-led asymptomatic community testing site on the residual test buffer (RTB) from positive Ag-RDTs. The ID NOW NAAT assay was performed on RTB from two Ag-RDTs: the Abbott Panbio and BTNX Rapid Response assays. Results of ID NOW were compared to real-time RT-PCR at a reference laboratory. Along with investigations into the clinical performance of ID NOW on RTB, analytical specificity was assessed with a panel of various respiratory organisms. Of the Ag-RDTs results evaluated, all 354 Ag-RDTs results characterized as true positives by RT-PCR were accurately identified with ID NOW testing of RTB. No SARS-CoV-2 detections by ID NOW were observed from 10 specimens characterized as false-positive Ag-RDTs, or from contrived specimens with various respiratory organisms. The use of on-site molecular testing on RTB provides a suitable option for rapid confirmatory testing of positive Ag-RDTs, thereby obviating the need for specimen recollection for molecular testing at local reference laboratories. IMPORTANCE During the COVID-19 pandemic, rapid antigen tests have been widely used for the detection of SARS-CoV-2. These simple devices allow rapid test results. However, false-positive results may occur. As such, individuals with positive rapid tests often must return to testing centers to have a second swab collected, which is then transported to a specialized laboratory for confirmation using molecular tests. As an alternative to requiring a repeat visit and a prolonged turn-around time for result confirmation, this project evaluated whether the leftover material from rapid antigen tests could be confirmed directly on a portable point-of-care molecular instrument. Using this approach, molecular confirmation of positive antigen tests could be performed in less than 15 min, and the results were equivalent to laboratory-based confirmation. This procedure eliminates the need for individuals to return to testing centers following a positive rapid antigen test and ensures accurate antigen test results through on-site confirmation.

Factors contributing to a coronavirus disease 2019 (COVID-19) outbreak on a mixed medical-surgical unit in a Canadian acute-care hospital.

Objective: To identify preventable factors that contribute to the cross transmission of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) to patients in healthcare facilities. Design: A case-control study was conducted among inpatients on a coronavirus disease 2019 (COVID-19) outbreak unit. Setting: This study was conducted in a medical-surgical unit of a tertiary-care hospital in Nova Scotia in May 2021. Patients: Patients hospitalized on the unit for at least 12 hours and healthcare workers (HCW) working on the unit within 2 weeks of outbreak declaration were included. Methods: Risk factors for SARS-CoV-2 infection were analyzed using simple and multiple logistic regression. Whole-genome sequencing (WGS) was performed to identify SARS-CoV-2 strain relatedness. Network analysis was used to describe patient accommodation. Results: SARS-CoV-2 infections were identified in 21 patients (29.6%) and 11 HCWs (6.6%). WGS data revealed 4 distinct clades of related sequences. Several factors likely contributed to the outbreak, including failure to identify SARS-CoV-2, a largely incomplete or unvaccinated population, and patient wandering behaviors. The most significant risk factor for SARS-CoV-2 infection was room sharing with an infectious patient, which was the only factor that remained statistically significant following multivariate analysis (odds ratio [OR], 9.2l; 95% confidence interval [CI], 2.04-41.67; P = .004). Conclusions: This outbreak likely resulted from admission of 2 patients with COVID-19, with subsequent transmissions to 17 patients and 11 staff. WGS and bioinformatics analyses were critical to identifying previously unrecognized nosocomial transmissions of SARS-CoV-2. This study supports strategies to reduce nosocomial transmissions of SARS-CoV-2, such as single-patient rooms, promotion of COVID-19 vaccination, and infection prevention and control measures including management of wandering behaviors.

Host associations between fungal root endophytes and boreal trees.

Fungal root endophytes colonize root tissue concomitantly with mycorrhizal fungi, but their identities and host preferences are largely unknown. We cultured fungal endophytes from surface-sterilized Cenococcum geophilum ectomycorrhizae of Betula papyrifera, Abies balsamea, and Picea glauca from two boreal sites in eastern Canada. Isolates were initially grouped on the basis of cultural morphology and then identified by internal transcribed spacer ribosomal DNA sequencing or by PCR restriction fragment length polymorphism. Phylogenetic analysis of the sequence data revealed 31 distinct phylotypes among the isolates, comprising mainly members of the ascomycete families Helotiaceae, Dermateaceae, Myxotrichaceae, and Hyaloscyphaceae, although other fungi were also isolated. Multivariate analyses indicate a clear separation among the endophyte communities colonizing each host tree species. Some phylotypes were evenly distributed across the roots of all three host species, some were found preferentially on particular hosts, and others were isolated from single hosts only. The results indicate that fungal root endophytes of boreal trees are not randomly distributed, but instead form relatively distinct assemblages on different host tree species.

Reliable detection of SARS-CoV-2 with patient-collected swabs and saline gargles: A three-headed comparison on multiple molecular platforms.

With increasing demands for SARS-CoV-2 testing, as well as the shortages for testing supplies, collection devices, and trained healthcare workers (HCWs) to collect specimens, self-collection is an attractive prospect to reduce the need for HCWs and expenditure of personal protective equipment. Apart from the traditional nasopharyngeal swab used for SARS-CoV-2 detection, alternative specimens have been validated such as a combined swabs of the oropharynx and anterior nares (OP/N), or throat samples using saline gargles. Both the alternative specimen types are amenable to self-collection. Objectives. This study aimed to compare the sensitivity of HCW-collected (OP/N) swabs, self-collected OP/N swabs, and self-collected saline gargles. Among 38 individuals previously testing positive for SARS-CoV-2 (or their close contacts), two self-collected specimen types (OP/N and saline gargles) were compared to HCW-collected OP/N swabs. SARS-CoV-2 testing was performed on three molecular assays: a laboratory-developed test (LDT), and two commercial assays on automated platforms: Cobas 6800 (Roche Diagnostics) and Panther (Hologic). The sensitivity of self-collected OP/N swabs was equivalent to healthcare worker (HCW)-collected OP/N swabs at 100.0 % [92.6%-100.0%] for all three molecular tests. The sensitivity of saline gargles was not significantly different than HCW-collected OP/N swabs, but varied slightly between instruments at 93.8 % [85.9%-93.8%] for the LDT, 96.8 % [88.6%-96.8%] for the Cobas assay, and 96.7 % [89.2%-96.9%] for the Panther assay. Overall, self-collection using OP/N swabs or saline gargles are reasonable alternatives to HCW-based collections for SARS-CoV-2 detection, and could facilitate broader surveillance strategies.