Your browser doesn't support javascript.
loading
Show: 20 | 50 | 100
Results 1 - 20 de 92
Filter
1.
Sci Rep ; 13(1): 17478, 2023 10 14.
Article in English | MEDLINE | ID: mdl-37838804

ABSTRACT

Omicron has become the dominant SARS-CoV-2 variant globally since December 2021, with distinct waves being associated with separate Omicron sublineages. Rapid detection of BA.1, BA.2, BA.4, and BA.5 was accomplished in the province of Alberta, Canada, through the design and implementation of real-time reverse transcriptase PCR assays targeting S:N501Y, S:ins214EPE, S:H69/V70, ORF7b:L11F, and M:D3N. Using the combination of results for each of these markers, samples could be designated as belonging to sublineages within BA.1, BA.2, BA.4, or BA.5. The analytical sensitivity of these markers ranged from 132 to 2229 copies/mL and in-laboratory accuracy was 98.9-100%. A 97.3% agreement using 12,592 specimens was demonstrated for the assays compared to genome sequencing. The use of these assays, combined with genome sequencing, facilitated the surveillance of SARS-CoV-2 lineages throughout a BA.5-dominated period.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , RNA-Directed DNA Polymerase , Reverse Transcriptase Polymerase Chain Reaction , Alberta , COVID-19 Testing
2.
ACS Meas Sci Au ; 3(4): 258-268, 2023 Aug 16.
Article in English | MEDLINE | ID: mdl-37600458

ABSTRACT

The targeted screening and sequencing approaches for COVID-19 surveillance need to be adjusted to fit the evolving surveillance objectives which necessarily change over time. We present the development of variant screening assays that can be applied to new targets in a timely manner and enable multiplexing of targets for efficient implementation in the laboratory. By targeting the HV69/70 deletion for Alpha, K417N for Beta, K417T for Gamma, and HV69/70 deletion plus K417N for sub-variants BA.1, BA.3, BA.4, and BA.5 of Omicron, we achieved simultaneous detection and differentiation of Alpha, Beta, Gamma, and Omicron in a single assay. Targeting both T478K and P681R mutations enabled specific detection of the Delta variant. The multiplex assays used in combination, targeting K417N and T478K, specifically detected the Omicron sub-variant BA.2. The limits of detection for the five variants of concern were 4-16 copies of the viral RNA per reaction. Both assays achieved 100% clinical sensitivity and 100% specificity. Analyses of 377 clinical samples and 24 wastewater samples revealed the Delta variant in 100 clinical samples (nasopharyngeal and throat swab) collected in November 2021. Omicron BA.1 was detected in 79 nasopharyngeal swab samples collected in January 2022. Alpha, Beta, and Gamma variants were detected in 24 wastewater samples collected in May-June 2021 from two major cities of Alberta (Canada), and the results were consistent with the clinical cases of multiple variants reported in the community.

3.
CMAJ ; 195(31): E1030-E1037, 2023 08 14.
Article in English | MEDLINE | ID: mdl-37580072

ABSTRACT

BACKGROUND: During the first year of the COVID-19 pandemic, the proportion of reported cases of COVID-19 among Canadians was under 6%. Although high vaccine coverage was achieved in Canada by fall 2021, the Omicron variant caused unprecedented numbers of infections, overwhelming testing capacity and making it difficult to quantify the trajectory of population immunity. METHODS: Using a time-series approach and data from more than 900 000 samples collected by 7 research studies collaborating with the COVID-19 Immunity Task Force (CITF), we estimated trends in SARS-CoV-2 seroprevalence owing to infection and vaccination for the Canadian population over 3 intervals: prevaccination (March to November 2020), vaccine roll-out (December 2020 to November 2021), and the arrival of the Omicron variant (December 2021 to March 2023). We also estimated seroprevalence by geographical region and age. RESULTS: By November 2021, 9.0% (95% credible interval [CrI] 7.3%-11%) of people in Canada had humoral immunity to SARS-CoV-2 from an infection. Seroprevalence increased rapidly after the arrival of the Omicron variant - by Mar. 15, 2023, 76% (95% CrI 74%-79%) of the population had detectable antibodies from infections. The rapid rise in infection-induced antibodies occurred across Canada and was most pronounced in younger age groups and in the Western provinces: Manitoba, Saskatchewan, Alberta and British Columbia. INTERPRETATION: Data up to March 2023 indicate that most people in Canada had acquired antibodies against SARS-CoV-2 through natural infection and vaccination. However, given variations in population seropositivity by age and geography, the potential for waning antibody levels, and new variants that may escape immunity, public health policy and clinical decisions should be tailored to local patterns of population immunity.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , COVID-19/epidemiology , Pandemics , Seroepidemiologic Studies , Alberta , Antibodies, Viral
4.
Emerg Microbes Infect ; 12(2): 2233638, 2023 Dec.
Article in English | MEDLINE | ID: mdl-37409382

ABSTRACT

Wastewater-based surveillance is a valuable approach for monitoring COVID-19 at community level. Monitoring SARS-CoV-2 variants of concern (VOC) in wastewater has become increasingly relevant when clinical testing capacity and case-based surveillance are limited. In this study, we ascertained the turnover of six VOC in Alberta wastewater from May 2020 to May 2022. Wastewater samples from nine wastewater treatment plants across Alberta were analysed using VOC-specific RT-qPCR assays. The performance of the RT-qPCR assays in identifying VOC in wastewater was evaluated against next generation sequencing. The relative abundance of each VOC in wastewater was compared to positivity rate in COVID-19 testing. VOC-specific RT-qPCR assays performed comparatively well against next generation sequencing; concordance rates ranged from 89% to 98% for detection of Alpha, Beta, Gamma, Omicron BA.1 and Omicron BA.2, with a slightly lower rate of 85% for Delta (p < 0.01). Elevated relative abundance of Alpha, Delta, Omicron BA.1 and BA.2 were each associated with increased COVID-19 positivity rate. Alpha, Delta and Omicron BA.2 reached 90% relative abundance in wastewater within 80, 111 and 62 days after their initial detection, respectively. Omicron BA.1 increased more rapidly, reaching a 90% relative abundance in wastewater after 35 days. Our results from VOC surveillance in wastewater correspond with clinical observations that Omicron is the VOC with highest disease burden over the shortest period in Alberta to date. The findings suggest that changes in relative abundance of a VOC in wastewater can be used as a supplementary indicator to track and perhaps predict COVID-19 burden in a population.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , COVID-19/epidemiology , Wastewater , Wastewater-Based Epidemiological Monitoring , COVID-19 Testing
5.
Am J Gastroenterol ; 118(9): 1693-1697, 2023 09 01.
Article in English | MEDLINE | ID: mdl-37216598

ABSTRACT

INTRODUCTION: We determined adverse events after 4 doses of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) vaccine in those with inflammatory bowel disease (IBD), associations between antibodies and injection site reactions (ISR), and risk of IBD flare. METHODS: Individuals with IBD were interviewed for adverse events to SARS-CoV-2 vaccine. Multivariable linear regression assessed the association between antibody titers and ISR. RESULTS: Severe adverse events occurred in 0.03%. ISR were significantly associated with antibody levels after the fourth dose (geometric mean ratio = 2.56; 95% confidence interval 1.18-5.57). No cases of IBD flare occurred. DISCUSSION: SARS-CoV-2 vaccines are safe for those with IBD. ISR after the fourth dose may indicate increased antibodies.


Subject(s)
COVID-19 Vaccines , COVID-19 , Inflammatory Bowel Diseases , Humans , Antibodies, Viral , COVID-19/epidemiology , COVID-19/prevention & control , COVID-19 Vaccines/adverse effects , Injection Site Reaction , SARS-CoV-2 , Vaccination
6.
Article in English | MEDLINE | ID: mdl-37008576

ABSTRACT

Background: A multi-country outbreak of monkeypox virus (MPXV) infections was identified by the World Health Organization in May 2022. The western Canadian province of Alberta identified its first case of MPXV in a returning traveller on June 2, 2022. We undertook a retrospective testing exercise to evaluate whether MPXV may have been circulating in the province earlier. Methods: Skin (genital and non-genital) and mucosal lesion swabs submitted for herpes simplex virus (HSV)/varicella zoster virus (VZV)/syphilis testing from male patients attending sexually-transmitted infection clinics across the province of Alberta from January 28 to May 30, 2022 were retrieved from storage. The population tested was selected based on the epidemiology of the current 2022 multi-country MPXV outbreak. Samples underwent viral nucleic acid extraction and testing for the presence of Orthopoxvirus DNA using a commercial real-time polymerase chain reaction (PCR) kit. Results: A total of 392 samples (representing 341 unique individuals of median age 31 years) were retrieved. Of them, 349 (89.0%) samples were submitted for HSV/VZV/syphilis testing, 13 (3.3%) for HSV/VZV only, and 30 (7.7%) for syphilis PCR only. None of the 392 samples tested were found to be positive for Orthopoxvirus DNA. Conclusions: The results of this study indicate that circulation of MPXV in a higher-risk population in Alberta, prior to the first case, was less likely. We recommend that other provinces/territories review their local epidemiology, context and resources prior to conducting similar studies.


Historique: En mai 2022, l'Organisation mondiale de la Santé a déclaré une flambée multinationale d'infection par le virus de la variole simienne (MPXV). Le 2 juin 2022, la province de l'Alberta, dans l'Ouest canadien, a recensé son premier cas de MPXV chez un voyageur de retour de l'étranger. Les chercheurs ont entrepris un exercice de dépistage rétrospectif pour évaluer la possibilité que le MPXV ait circulé auparavant dans la province. Méthodologie: Les chercheurs ont extrait de l'entreposage les écouvillons des lésions cutanées (génitales et non génitales) et muqueuses soumis en vue de dépister le virus herpès simplex (VHS), le virus varicelle-zona (VZV) et le virus de la syphilis des patients de sexe masculin qui avaient fréquenté les cliniques d'infections transmises sexuellement de la province de l'Alberta entre le 28 janvier et le 30 mai 2022. Ils ont sélectionné la population soumise au dépistage en fonction de l'épidémiologie de la flambée multinationale de MPXV en 2022. Les écouvillons ont été soumis à l'extraction et au test des acides nucléiques viraux pour dépister la présence d'ADN de l'Orthopoxvirus au moyen d'un test commercial d'amplification en chaîne par polymérase (PCR). RÉsultats: Les chercheurs ont extrait un total de 392 échantillons (représentant 341 personnes uniques d'un âge médian de 31 ans). De ce nombre, 349 (89,0 %) avaient été soumis au test PCR du VHS, du VZV et de la syphilis, 13 (3,3 %), du VHS et du VZV seulement et 30 (7,7 %), de la syphilis seulement. Aucun des 392 échantillons n'a donné de résultat positif à l'ADN de l'Orthopoxvirus. Conclusions: D'après les résultats de la présente étude, il est peu probable que le MPXV ait circulé dans la population plus vulnérable de l'Alberta avant la détection du premier cas. Les chercheurs recommandent que les autres provinces et territoires examinent leur épidémiologie locale, le contexte et les ressources avant de procéder à des études de ce type.

7.
PLoS One ; 18(4): e0284046, 2023.
Article in English | MEDLINE | ID: mdl-37023007

ABSTRACT

BACKGROUND: Measurement of SARS-CoV-2 antibody seropositivity is important to accurately understand exposure to infection and/or vaccination in specific populations. This study aimed to estimate the serologic response to SARS-CoV-2 virus infection and vaccination in children in Calgary, Alberta over a two-year period. METHODS: Children with or without prior SARS-CoV-2 infections, were enrolled in Calgary, Canada in 2020. Venous blood was sampled 4 times from July 2020 to April 2022 for SARS-CoV-2 nucleocapsid and spike antibodies. Demographic and clinical information was obtained including SARS-CoV-2 testing results and vaccination records. RESULTS: 1035 children were enrolled and 88.9% completed all 4 visits; median age 9 years (IQR: 5,13); 519 (50.1%) female; and 815 (78.7%) Caucasian. Before enrolment, 118 (11.4%) had confirmed or probable SARS-CoV-2. By April 2022, 39.5% of previously uninfected participants had a SARS-CoV-2 infection. Nucleocapsid antibody seropositivity declined to 16.4% of all infected children after more than 200 days post diagnosis. Spike antibodies remained elevated in 93.6% of unvaccinated infected children after more than 200 days post diagnosis. By April 2022, 408 (95.6%) children 12 years and older had received 2 or more vaccine doses, and 241 (61.6%) 5 to 11 year-old children had received 2 vaccine doses. At that time, all 685 vaccinated children had spike antibodies, compared with 94/176 (53.4%) of unvaccinated children. CONCLUSIONS: In our population, after the first peak of Omicron variant infections and introduction of COVID-19 vaccines for children, all vaccinated children, but just over one-half of unvaccinated children, had SARS-CoV-2 spike antibodies indicating infection and/or vaccination, highlighting the benefit of vaccination. It is not yet known whether a high proportion of seropositivity at the present time predicts sustained population-level protection against future SARS-CoV-2 transmission, infection or severe COVID-19 outcomes in children.


Subject(s)
COVID-19 , SARS-CoV-2 , Child , Female , Humans , Child, Preschool , Male , Alberta/epidemiology , COVID-19/epidemiology , COVID-19/prevention & control , COVID-19 Vaccines , Antibody Formation , COVID-19 Testing , Seroepidemiologic Studies , Vaccination , Antibodies, Viral
8.
J Med Microbiol ; 72(2)2023 Feb.
Article in English | MEDLINE | ID: mdl-36848403

ABSTRACT

Introduction. Starting in December, 2020, the ID NOW was implemented throughout the province of Alberta, Canada (population 4.4 million) in various settings.Gap statement. ID NOW's test performance with SARS-CoV-2 Omicron variant BA.1 is unknown.Aim. To assess the ID NOW performance among symptomatic individuals during the BA.1 Omicron wave and compare it to previous SARS-CoV-2 variant waves.Methodology. The ID NOW was assessed in two locations among symptomatic individuals: rural hospitals and community assessment centres (AC) during the period 5-18 January 2022. Starting 5 January, Omicron represented >95 % of variants detected in our population. For every individual tested, two swabs were collected: one for ID NOW testing and the other for either reverse-transcriptase polymerase chain reaction (RT-PCR) confirmation of negative ID NOW results or for variant testing of positive ID NOW results.Results. A total of 3041 paired samples were analysed (1139 RT-PCR positive). From this, 1873 samples were from 42 COVID-19 AC and 1168 from 69 rural hospitals. ID NOW sensitivity for symptomatic individuals presenting to community AC and rural hospitals was 96.0 % [95 % confidence interval (CI) 94.5-97.3 %, n=830 RT-PCR positive], and 91.6 % (95 % CI 87.9-94.4 %, n=309 RT-PCR positive), respectively. SARS-CoV-2 positivity rate was very high for both populations (44.3 % at AC, 26.5 % in hospital).Conclusions. Sensitivity of ID NOW SARS-CoV-2, compared to RT-PCR, is very high during the BA.1 Omicron wave, and is significantly higher when compared to previous SARS-CoV-2 variant waves.


Subject(s)
COVID-19 , Humans , COVID-19/diagnosis , COVID-19/epidemiology , SARS-CoV-2/genetics , Canada , Hospitals
9.
J Environ Sci (China) ; 125: 843-850, 2023 Mar.
Article in English | MEDLINE | ID: mdl-36375966

ABSTRACT

With a unique and large size of testing results of 1,842 samples collected from 12 wastewater treatment plants (WWTP) for 14 months through from low to high prevalence of COVID-19, the sensitivity of RT-qPCR detection of SARS-CoV-2 RNA in wastewater that correspond to the communities was computed by using Probit analysis. This study determined the number of new COVID-19 cases per 100,000 population required to detect SARS-CoV-2 RNA in wastewater at defined probabilities and provided an evidence-based framework of wastewater-based epidemiology surveillance (WBE). Input data were positive and negative test results of SARS-CoV-2 RNA in wastewater samples and the corresponding new COVID-19 case rates per 100,000 population served by each WWTP. The analyses determined that RT-qPCR-based SARS-CoV-2 RNA detection threshold at 50%, 80% and 99% probability required a median of 8 (range: 4-19), 18 (9-43), and 38 (17-97) of new COVID-19 cases /100,000, respectively. Namely, the positive detection rate at 50%, 80% and 99% probability were 0.01%, 0.02%, and 0.04% averagely for new cases in the population. This study improves understanding of the performance of WBE SARS-CoV-2 RNA detection using the large datasets and prolonged study period. Estimated COVID-19 burden at a community level that would result in a positive detection of SARS-CoV-2 in wastewater is critical to support WBE application as a supplementary warning/monitoring system for COVID-19 prevention and control.


Subject(s)
COVID-19 , Humans , COVID-19/epidemiology , SARS-CoV-2/genetics , Wastewater/analysis , RNA, Viral/genetics , RNA, Viral/analysis , Alberta/epidemiology
10.
Clin Microbiol Infect ; 29(2): 247-252, 2023 Feb.
Article in English | MEDLINE | ID: mdl-36096431

ABSTRACT

OBJECTIVE: Diagnostic evaluation of the ID NOW coronavirus disease 2019 (COVID-19) assay in various real-world settings among symptomatic and asymptomatic individuals. METHODS: Depending on the setting, the ID NOW testing was performed using oropharyngeal swabs (OPSs) taken from patients with symptoms suggestive of COVID-19, asymptomatic close contacts, or asymptomatic individuals as part of outbreak point prevalence screening. From January to April 2021, a select number of sites switched from using OPS to combined oropharyngeal and nasal swab (O + NS) for ID NOW testing. For every individual tested, two swabs were collected by a health care worker: one swab (OPS or O + NS) for ID NOW testing and a separate swab (OPS or nasopharyngeal swab) for RT-PCR. RESULTS: A total of 129 112 paired samples were analysed (16 061 RT-PCR positive). Of these, 81 697 samples were from 42 COVID-19 community collection sites, 16 924 samples were from 69 rural hospitals, 1927 samples were from nine emergency shelters and addiction treatment facilities, 23 802 samples were from six mobile units that responded to 356 community outbreaks, and 4762 O + NS swabs were collected from three community collection sites and one emergency shelter. The ID NOW assay sensitivity was the highest among symptomatic individuals presenting to community collection sites (92.5%; 95% CI, 92.0-93.0%) and the lowest for asymptomatic individuals associated with community outbreaks (73.9%; 95% CI, 69.8-77.7%). Specificity was >99% in all populations tested. DISCUSSION: The sensitivity of ID NOW severe acute respiratory syndrome coronavirus 2 testing is the highest when used in symptomatic community populations not seeking medical care. Sensitivity and positive predictive value drop by approximately 10% when tested on asymptomatic populations. Using combined oropharyngeal and nasal swabs did not improve the performance of ID NOW assay.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , COVID-19/diagnosis , COVID-19/epidemiology , COVID-19 Testing , Clinical Laboratory Techniques , Prospective Studies , Specimen Handling , Sensitivity and Specificity , Nasopharynx
11.
Infect Control Hosp Epidemiol ; 44(5): 805-808, 2023 05.
Article in English | MEDLINE | ID: mdl-34866560

ABSTRACT

To assess the burden of respiratory virus coinfections with severe acute respiratory coronavirus virus 2 (SARS-CoV-2), this study reviewed 4,818 specimens positive for SARS-CoV-2 and tested using respiratory virus multiplex testing. Coinfections with SARS-CoV-2 were uncommon (2.8%), with enterovirus or rhinovirus as the most prevalent target (88.1%). Respiratory virus coinfection with SARS-CoV-2 remains low 1 year into the coronavirus disease 2019 (COVID-19) pandemic.


Subject(s)
COVID-19 , Coinfection , Enterovirus Infections , Humans , SARS-CoV-2 , Coinfection/epidemiology , Alberta , Pandemics
13.
ACS ES T Water ; 2(11): 2243-2254, 2022 Nov 11.
Article in English | MEDLINE | ID: mdl-36380772

ABSTRACT

The correlations between SARS-CoV-2 RNA levels in wastewater from 12 wastewater treatment plants and new COVID-19 cases in the corresponding sewersheds of 10 communities were studied over 17 months. The analysis from the longest continuous surveillance reported to date revealed that SARS-CoV-2 RNA levels correlated well with temporal changes of COVID-19 cases in each community. The strongest correlation was found during the third wave (r = 0.97) based on the population-weighted SARS-CoV-2 RNA levels in wastewater. Different correlations were observed (r from 0.51 to 0.86) in various sizes of communities. The population in the sewershed had no observed effects on the strength of the correlation. Fluctuation of SARS-CoV-2 RNA levels in wastewater mirrored increases and decreases of COVID-19 cases in the corresponding community. Since the viral shedding to sewers from all infected individuals is included, wastewater-based surveillance provides an unbiased and no-discriminate estimation of the prevalence of COVID-19 compared with clinical testing that was subject to testing-seeking behaviors and policy changes. Wastewater-based surveillance on SARS-CoV-2 represents a temporal trend of COVID-19 disease burden and is an effective and supplementary monitoring when the number of COVID-19 cases reaches detectable thresholds of SARS-CoV-2 RNA in wastewater of treatment facilities serving various sizes of populations.

14.
J Assoc Med Microbiol Infect Dis Can ; 7(3): 186-195, 2022 Sep.
Article in English | MEDLINE | ID: mdl-36337598

ABSTRACT

BACKGROUND: Serological assays designed to detect SARS-CoV-2 antibodies are being used in serological surveys and other specialized applications. As a result, and to ensure that the outcomes of serological testing meet high quality standards, evaluations are required to assess the performance of these assays and the proficiency of laboratories performing them. METHODS: A panel of 60 plasma/serum samples from blood donors who had reverse transcriptase-polymerase chain reaction (RT-PCR) confirmed SARS-CoV-2 infections and 21 SARS-CoV-2 negative samples were secured and distributed to interested laboratories within Canada (n = 30) and the United States (n = 1). Participating laboratories were asked to provide details on the diagnostic assays used, the platforms the assays were performed on, and the results obtained for each panel sample. Laboratories were blinded with respect to the expected outcomes. RESULTS: The performance of the different assays evaluated was excellent, with the high-throughput platforms of Roche, Ortho, and Siemens demonstrating 100% sensitivity. Most other high-throughput platforms had sensitivities of >93%, with the exception of the IgG assay using the Abbott ARCHITECT which had an average sensitivity of only 87%. The majority of the high-throughput platforms also demonstrated very good specificities (>97%). CONCLUSION: This proficiency study demonstrates that most of the SARS-CoV-2 serological assays utilized by provincial public health or hospital laboratories in Canada have acceptable sensitivity and excellent specificity.


HISTORIQUE: Les dosages sérologiques conçus pour dépister les anticorps anti-SRAS-CoV-2 sont utilisés dans les études sérologiques et d'autres applications spécialisées. Par conséquent, et pour s'assurer que leurs résultats respectent des normes de qualité, il faut procéder à des évaluations de leur performance et de la compétence des laboratoires à les effectuer. MÉTHODOLOGIE: Les chercheurs ont obtenu une batterie de 60 prélèvements de plasma et de sérum chez des donneurs dont l'amplification en chaîne par polymérase après transcription inverse (RT-PCR) avait confirmé des infections par le SRAS-CoV-2 et de 21 prélèvements dont les résultats étaient négatifs au SRAS-CoV-2 et les ont distribués aux laboratoires intéressés du Canada (n = 30) et des États-Unis (n = 1). Ils ont invité les laboratoires participants à fournir de l'information détaillée sur les dosages diagnostiques utilisés, les plateformes sur lesquelles les dosages étaient exécutés et les résultats obtenus pour chaque échantillon. Les chercheurs ont demandé aux laboratoires participants de fournir de l'information détaillée sur les dosages diagnostiques utilisés, les plateformes sur lesquelles les dosages ont été effectués, et les résultats obtenus à l'égard de chaque échantillon. Les laboratoires ont mené les études à l'insu des résultats escomptés. RÉSULTATS: Les divers dosages avaient une excellente exécution, les plateformes à haut débit de Roche, d'Ortho et de Siemens démontrant une sensibilité de 100 %. La plupart des autres plateformes à haut débit avaient des sensibilités de plus de 93 %, à l'exception des dosages des IgG faisant appel à l'analyseur ARCHITECT d'Abbott, dont la sensibilité moyenne était de seulement 87 %. La majorité des plateformes à haut débit avaient également une très bonne spécificité (plus de 97 %). CONCLUSION: La présente étude de compétence démontre que la plupart des dosages sérologiques du SRAS-CoV-2 évalués dans des laboratoires sanitaires provinciaux ou les laboratoires hospitaliers du Canada possèdent une sensibilité acceptable et une excellente spécificité.

16.
J Clin Virol ; 156: 105292, 2022 11.
Article in English | MEDLINE | ID: mdl-36108404

ABSTRACT

The accurate measurement of serological response to SARS-CoV-2 vaccination is needed to correlate responses with effective protective immunity. The World Health Organization (WHO) has created an international standard to allow harmonization of immune response assessment to an arbitrary unit across different commercial assays; however, the accuracy of reporting of SARS-CoV-2 spike antibody titers in international standard units (BAU or IU/mL) from commercial assays is not well studied. Here, we report the performance comparison of four quantitative commercial assays testing for SARS-CoV-2 spike immunoglobins using the WHO's international standard. Sera, EDTA-plasma and heparinized plasma collected from individuals who are vaccine naïve or received BNT162b2 (Pfizer/BioNTech), mRNA-1273 (Moderna) or ChAdOx1-S (Oxford-AstraZeneca) were tested using Abbott Architect AdviseDx SARS-CoV-2 IgG II, DiaSorin LIAISON SARS-CoV-2 TrimericS IgG, Roche Elecsys Anti-SARS-CoV-2 S and GenScript cPass SARS-CoV-2 surrogate virus neutralization assays. The sensitivities ranged from 90% to 100%, and specificities from 88% to 100%. These four assays had excellent agreement (0.79-0.93) and correlation (0.87-0.97); however, Passing-Bablok regression analysis indicated that data generated by these assays were not comparable. Our data suggests that natural SARS-CoV-2 infection elicited a greater antibody response compared to vaccines, evident by a significantly higher neutralizing antibody titer in unvaccinated individuals who seroconverted.


Subject(s)
COVID-19 , SARS-CoV-2 , Antibodies, Neutralizing , Antibodies, Viral , BNT162 Vaccine , COVID-19/diagnosis , COVID-19 Vaccines , Edetic Acid , Humans , Immunoglobulin G , Spike Glycoprotein, Coronavirus , World Health Organization
17.
Infect Dis (Lond) ; 54(9): 666-676, 2022 09.
Article in English | MEDLINE | ID: mdl-35642330

ABSTRACT

BACKGROUND: The COVID-19 pandemic has necessitated the need to rapidly make public health decisions. We systematically evaluated SARS-CoV-2 seropositivity to understand local COVID-19 epidemiology and support evidence-based public health decision making. METHODS: Residual blood samples were collected for SARS-CoV-2 receptor binding domain (RBD) IgG testing over a 1-5 day period monthly from 26 February 2021-9 July 2021 from six clinical laboratories across the province of Alberta, Canada. Monthly crude and adjusted (for age and gender) seropositivity were calculated. Results were linked to provincial administrative, laboratory, and vaccine databases. RESULTS: 60,632 individual blood samples were tested. Vaccination data were available for 98.8% of samples. Adjusted RBD IgG positivity rose from 11.9% (95% confidence interval [CI] 11.9-12.0%) in March 2021 to 70.2% (95% CI 70.2-70.3%) in July 2021 (p < .0001). Seropositivity rose from 9.4% (95% CI 9.3-9.4%) in March 2021 to 20.2% (95% CI 20.1-20.2%) in July 2021 in unvaccinated Albertans. Unvaccinated seropositive individuals were from geographic areas with significantly (p < .001) lower median household income, lower proportion of married/common-law relationships, larger average household size and higher proportions of visible minorities compared to seronegative unvaccinated individuals. In July 2021, the age groups with the lowest and highest seropositivity in unvaccinated Albertans were those ≥80 years (12.0%, 95% CI 5.3-18.6%) and 20-29 years (24.2%, 95% CI 19.6-28.8%), respectively. Of seropositive unvaccinated individuals, 50.2% (95% CI 45.9-54.5%) had no record of prior SARS-CoV-2 molecular testing. CONCLUSIONS: Longitudinal surveillance of SARS-CoV-2 seropositivity with data linkage is valuable for decision-making during the pandemic.


Subject(s)
COVID-19 , SARS-CoV-2 , Aged, 80 and over , Alberta/epidemiology , Antibodies, Viral , COVID-19/epidemiology , COVID-19/prevention & control , Humans , Immunoglobulin G , Pandemics , Vaccination
18.
J Virol Methods ; 307: 114553, 2022 09.
Article in English | MEDLINE | ID: mdl-35644262

ABSTRACT

In order to detect the SARS-CoV-2 variants of concern (VOCs), five real-time reverse transcriptase PCR (rRT-PCR) assays were designed to target the critical discriminatory mutations responsible for the following amino acid changes in the spike protein: two Δ69-70 + N501Y + E gene triplexes (one optimized for Alpha [B.1.1.7] and one optimized for Omicron [B.1.1.529]), a K417N + 242-244 wild-type duplex, a K417T + E484K duplex, and a L452R + P681 + E484Q triplex. Depending on the assay, sensitivity was 98.97-100% for the detection of known VOC-positive samples, specificity was 97.2-100%, limit of detection was 2-116 copies/reaction, intra- and interassay variability was less than 5%, and no cross-reactivity with common respiratory pathogens was observed with any assay. A subset of rRT-PCR- positive VOC samples were further characterized by genome sequencing. A comparison of the lineage designation by the VOC rRT-PCR assays and genome sequencing for the detection of the Alpha, Beta, Gamma, Delta and Omicron variants showed clinical sensitivities of 99.97-100 %, clinical specificities of 99.6-100 %, positive predictive values of 99.8-100%, and negative predictive values of 99.98-100 %. We have implemented these rRT-PCR assays targeting discriminatory single nucleotide polymorphisms for ongoing VOC screening of SARS-CoV-2 positive samples for surveillance purposes. This has proven extremely useful in providing close to real-time molecular surveillance to monitor the emergence of Alpha, the replacement of Alpha by Delta, and the replacement of Delta by Omicron. While the design, validation and implementation of the variant specific PCR targets is an ever-evolving approach, we find the turn-around-time, high throughput and sensitivity to be a useful complementary approach for SARS-CoV-2 genome sequencing for surveillance purposes in the province of Alberta, Canada.


Subject(s)
COVID-19 , Real-Time Polymerase Chain Reaction , SARS-CoV-2 , COVID-19/diagnosis , Humans , Mutation , RNA, Viral/genetics , Real-Time Polymerase Chain Reaction/methods , SARS-CoV-2/genetics , Sensitivity and Specificity
19.
J Appl Lab Med ; 7(4): 834-841, 2022 06 30.
Article in English | MEDLINE | ID: mdl-35258088

ABSTRACT

BACKGROUND: Point-of-care SARS-CoV-2 antigen tests have great potential to help combat the COVID-19 pandemic. In the performance of a rapid, antigen-based SARS-CoV-2 test (RAT), our study had 3 main objectives: to determine the accuracy of nasal swabs, the accuracy of using nasopharyngeal swabs for nasal collection (nasalNP), and the effectiveness of using residual extraction buffer for real-time reverse-transcriptase PCR (RT-PCR) confirmation of positive RAT (rPan). METHODS: Symptomatic adults recently diagnosed with COVID-19 in the community were recruited into the study. Nasal samples were collected using either a nasalNP or nasal swab and tested immediately with the RAT in the individual's home by a health care provider. 500 µL of universal transport media was added to the residual extraction buffer after testing and sent to the laboratory for SARS-CoV-2 testing using RT-PCR. Parallel throat swabs tested with RT-PCR were used as the reference comparators. RESULTS: One hundred and fifty-five individuals were included in the study (99 nasal swabs, 56 nasalNP). Sensitivities of nasal samples tested on the RAT using either nasal or nasalNP were 89.0% [95% confidence interval (CI) 80.7%-94.6%] and 90.2% (95% CI 78.6%-96.7%), respectively. rPan positivity agreement compared to throat RT-PCR was 96.2%. CONCLUSIONS: RAT reliably detect SARS-CoV-2 from symptomatic adults in the community presenting within 7 days of symptom onset using nasal swabs or nasalNP. High agreement with rPan can avoid the need for collecting a second swab for RT-PCR confirmation or testing of variants of concern from positive RAT in this population.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/diagnosis , COVID-19 Testing , Humans , Nasopharynx , Pandemics , Reverse Transcriptase Polymerase Chain Reaction , SARS-CoV-2/genetics
20.
J Virol Methods ; 301: 114468, 2022 03.
Article in English | MEDLINE | ID: mdl-35051444

ABSTRACT

The processing of swabs for respiratory virus detection involves vortexing while still in the viral transport medium (VTM). The effect of not vortexing swabs prior to analysis has not been studied extensively for SARS-CoV-2 detection, and presents an opportunity to improve pre-analytic laboratory workflow. We aimed to assess the impact of not vortexing nasopharyngeal/throat swabs submitted in VTM for SARS-CoV-2 testing. To assess the impact of not vortexing swabs, 277 swab samples were tested for SARS-CoV-2 RNA in paired vortexed and non-vortexed aliquots using eight routine nucleic acid amplification assays. We compared the qualitative (positive/negative) and semi-quantitative (cycle threshold, Ct) results. Following discordant analysis, all but one non-vortexed sample had the same qualitative result as the vortexed sample. 27.4 % of samples were SARS-CoV-2 positive. Comparison of Ct values revealed an apparent reduction in human cellular nucleic acid in the non-vortexed samples (mean Ct values of 24.0 and 26.5 for vortexed and non-vortexed samples, respectively, p < 0.0001) and increased Ct values for non-vortexed samples using a laboratory-developed SARS-CoV-2 assay (mean Ct values of 4.1 and 4.2 for vortexed and non-vortexed samples, respectively; p < 0.0001), but this was not observed for a more automated commercial SARS-CoV-2 assay (mean Ct values of 15.2 for both vortexed and non-vortexed samples, respectively; p = 0.68). While vortexing swabs appears to improve the recovery of cellular material, it does not have an appreciable impact on the qualitative sensitivity of SARS-CoV-2 nucleic acid tests, which may support omission of this step and simplification of front-end sample processing.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19 Testing , Humans , Nasopharynx , Pharynx , Pilot Projects , RNA, Viral/genetics , Specimen Handling/methods
SELECTION OF CITATIONS
SEARCH DETAIL
...