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1.
Euro Surveill ; 27(38)2022 09.
Artículo en Inglés | MEDLINE | ID: covidwho-2054865

RESUMEN

Influenza virus circulation virtually ceased in Canada during the COVID-19 pandemic, re-emerging with the relaxation of restrictions in spring 2022. Using a test-negative 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.


Asunto(s)
COVID-19 , Vacunas contra la Influenza , Gripe Humana , Canadá/epidemiología , Humanos , Subtipo H3N2 del Virus de la Influenza A , Gripe Humana/epidemiología , Gripe Humana/prevención & control , Pandemias/prevención & control , Eficacia de las Vacunas
2.
Microbiol Spectr ; 10(1): e0068121, 2022 02 23.
Artículo en Inglés | MEDLINE | ID: covidwho-1691411

RESUMEN

The N501Y amino acid mutation caused by a single point substitution A23063T in the spike gene of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is possessed by three variants of concern (VOCs), B.1.1.7, B.1.351, and P.1. A rapid screening tool using this mutation is important for surveillance during the coronavirus disease 2019 (COVID-19) pandemic. We developed and validated a single nucleotide polymorphism real-time reverse transcription PCR assay using allelic discrimination of the spike gene N501Y mutation to screen for potential variants of concern and differentiate them from SARS-CoV-2 lineages without the N501Y mutation. A total of 160 clinical specimens positive for SARS-CoV-2 were characterized as mutant (N501Y) or N501 wild type by Sanger sequencing and were subsequently tested with the N501Y single nucleotide polymorphism real-time reverse transcriptase PCR assay. Our assay, compared to Sanger sequencing for single nucleotide polymorphism detection, demonstrated positive percent agreement of 100% for all 57 specimens displaying the N501Y mutation, which were confirmed by Sanger sequencing to be typed as A23063T, including one specimen with mixed signal for wild type and mutant. Negative percent agreement was 100% in all 103 specimens typed as N501 wild type, with A23063 identified as wild type by Sanger sequencing. The identification of circulating SARS-CoV-2 lineages carrying an N501Y mutation is critical for surveillance purposes. Current identification methods rely primarily on Sanger sequencing or whole-genome sequencing, which are time consuming, labor intensive, and costly. The assay described herein is an efficient tool for high-volume specimen screening for SARS-CoV-2 VOCs and for selecting specimens for confirmatory Sanger or whole-genome sequencing. IMPORTANCE During the coronavirus disease 2019 (COVID-19) pandemic, several variants of concern (VOCs) have been detected, for example, B.1.1.7, B.1.351, P.1, and B.1.617.2. The VOCs pose a threat to public health efforts to control the spread of the virus. As such, surveillance and monitoring of these VOCs is of the utmost importance. Our real-time RT-PCR assay helps with surveillance by providing an easy method to quickly survey SARS-CoV-2 specimens for VOCs carrying the N501Y single nucleotide polymorphism (SNP). Samples that test positive for the N501Y mutation in the spike gene with our assay can be sequenced to identify the lineage. Thus, our assay helps to focus surveillance efforts and decrease turnaround times.


Asunto(s)
COVID-19/diagnóstico , Mutación Missense , Mutación Puntual , Reacción en Cadena en Tiempo Real de la Polimerasa/métodos , SARS-CoV-2/genética , Glicoproteína de la Espiga del Coronavirus/genética , Alelos , Sustitución de Aminoácidos , COVID-19/epidemiología , COVID-19/virología , Genes Virales , Humanos , Tamizaje Masivo , Ontario/epidemiología , Polimorfismo de Nucleótido Simple , Vigilancia de la Población , Prevalencia , Reproducibilidad de los Resultados , Sensibilidad y Especificidad
3.
Infect Control Hosp Epidemiol ; 43(9): 1179-1183, 2022 09.
Artículo en Inglés | MEDLINE | ID: covidwho-1586120

RESUMEN

OBJECTIVES: Performance characteristics of SARS-CoV-2 nucleic acid detection assays are understudied within contexts of low pre-test probability, including screening asymptomatic persons without epidemiological links to confirmed cases, or asymptomatic surveillance testing. SARS-CoV-2 detection without symptoms may represent presymptomatic or asymptomatic infection, resolved infection with persistent RNA shedding, or a false-positive test. This study assessed the positive predictive value of SARS-CoV-2 real-time reverse transcription polymerase chain reaction (rRT-PCR) assays by retesting positive specimens from 5 pre-test probability groups ranging from high to low with an alternate assay. METHODS: In total, 122 rRT-PCR positive specimens collected from unique patients between March and July 2020 were retested using a laboratory-developed nested RT-PCR assay targeting the RNA-dependent RNA polymerase (RdRp) gene followed by Sanger sequencing. RESULTS: Significantly fewer (15.6%) positive results in the lowest pre-test probability group (facilities with institution-wide screening having ≤3 positive asymptomatic cases) were reproduced with the nested RdRp gene RT-PCR assay than in each of the 4 groups with higher pre-test probability (individual group range, 50.0%-85.0%). CONCLUSIONS: Large-scale SARS-CoV-2 screening testing initiatives among low pre-test probability populations should be evaluated thoroughly prior to implementation given the risk of false-positive results and consequent potential for harm at the individual and population level.


Asunto(s)
COVID-19 , Ácidos Nucleicos , COVID-19/diagnóstico , Prueba de COVID-19 , Humanos , Valor Predictivo de las Pruebas , Probabilidad , ARN , ARN Polimerasa Dependiente del ARN , Reacción en Cadena en Tiempo Real de la Polimerasa , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa , Transcripción Reversa , SARS-CoV-2/genética
4.
Clin Infect Dis ; 71(16): 2285-2288, 2020 11 19.
Artículo en Inglés | MEDLINE | ID: covidwho-1153173

RESUMEN

Influenza vaccine effectiveness against influenza and noninfluenza respiratory viruses (NIRVs) was assessed by test-negative design using historic datasets of the community-based Canadian Sentinel Practitioner Surveillance Network, spanning 2010-2011 to 2016-2017. Vaccine significantly reduced the risk of influenza illness by >40% with no effect on coronaviruses or other NIRV risk.


Asunto(s)
Infecciones por Coronavirus/epidemiología , Vacunas contra la Influenza/inmunología , Gripe Humana/prevención & control , Infecciones del Sistema Respiratorio/virología , Adolescente , Adulto , Anciano , Canadá/epidemiología , Estudios de Casos y Controles , Niño , Preescolar , Infecciones por Coronavirus/etiología , Femenino , Humanos , Inmunogenicidad Vacunal , Lactante , Vacunas contra la Influenza/administración & dosificación , Gripe Humana/epidemiología , Masculino , Persona de Mediana Edad , Infecciones del Sistema Respiratorio/prevención & control , Estudios Retrospectivos , Factores de Riesgo , Estaciones del Año , Vigilancia de Guardia , Adulto Joven
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