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1.
Front Immunol ; 12: 722027, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-34489971

RESUMEN

Approximately half of the SARS-CoV-2 infections occur without apparent symptoms, raising questions regarding long-term humoral immunity in asymptomatic individuals. Plasma levels of immunoglobulin G (IgG) and M (IgM) against the viral spike or nucleoprotein were determined for 25,091 individuals enrolled in a surveillance program in Wuhan, China. We compared 405 asymptomatic individuals who mounted a detectable antibody response with 459 symptomatic COVID-19 patients. The well-defined duration of the SARS-CoV-2 endemic in Wuhan allowed a side-by-side comparison of antibody responses following symptomatic and asymptomatic infections without subsequent antigen re-exposure. IgM responses rapidly declined in both groups. However, both the prevalence and durability of IgG responses and neutralizing capacities correlated positively with symptoms. Regardless of sex, age, and body weight, asymptomatic individuals lost their SARS-CoV-2-specific IgG antibodies more often and rapidly than symptomatic patients did. These findings have important implications for immunity and favour immunization programs including individuals after asymptomatic infections.


Asunto(s)
Anticuerpos Antivirales/sangre , Infecciones Asintomáticas/epidemiología , COVID-19/inmunología , Inmunidad Humoral , SARS-CoV-2/inmunología , Adulto , Anticuerpos Neutralizantes/inmunología , Formación de Anticuerpos , COVID-19/epidemiología , China , Monitoreo Epidemiológico , Femenino , Humanos , Inmunoglobulina G/inmunología , Inmunoglobulina M/inmunología , Masculino , Persona de Mediana Edad , Estudios Retrospectivos , SARS-CoV-2/patogenicidad , Adulto Joven
4.
Lancet Diabetes Endocrinol ; 9(9): 622-637, 2021 09.
Artículo en Inglés | MEDLINE | ID: mdl-34339631

RESUMEN

Childhood, adolescent, and young adult cancer survivors are at increased risk of reduced bone mineral density. Clinical practice surveillance guidelines are important for timely diagnosis and treatment of these survivors, which could improve bone mineral density parameters and prevent fragility fractures. Discordances across current late effects guidelines necessitated international harmonisation of recommendations for bone mineral density surveillance. The International Late Effects of Childhood Cancer Guideline Harmonization Group therefore established a panel of 36 experts from ten countries, representing a range of relevant medical specialties. The evidence of risk factors for very low and low bone mineral density and fractures, surveillance modality, timing of bone mineral density surveillance, and treatment of very low and low bone mineral density were evaluated and critically appraised, and harmonised recommendations for childhood, adolescent, and young adult cancer survivors were formulated. We graded the recommendations based on the quality of evidence and balance between potential benefits and harms. Bone mineral density surveillance is recommended for survivors treated with cranial or craniospinal radiotherapy and is reasonable for survivors treated with total body irradiation. Due to insufficient evidence, no recommendation can be formulated for or against bone mineral density surveillance for survivors treated with corticosteroids. This surveillance decision should be made by the survivor and health-care provider together, after careful consideration of the potential harms and benefits and additional risk factors. We recommend to carry out bone mineral density surveillance using dual-energy x-ray absorptiometry at entry into long-term follow-up, and if normal (Z-score > -1), repeat when the survivor is aged 25 years. Between these measurements and thereafter, surveillance should be done as clinically indicated. These recommendations facilitate evidence-based care for childhood, adolescent, and young adult cancer survivors internationally.


Asunto(s)
Densidad Ósea , Supervivientes de Cáncer/estadística & datos numéricos , Monitoreo Epidemiológico , Adolescente , Adulto , Enfermedades Óseas Metabólicas/complicaciones , Niño , Humanos , Factores de Riesgo , Adulto Joven
5.
Science ; 373(6557): 926-931, 2021 08 20.
Artículo en Inglés | MEDLINE | ID: mdl-34413238

RESUMEN

The relationship between community prevalence of Plasmodium falciparum and the burden of severe, life-threatening disease remains poorly defined. To examine the three most common severe malaria phenotypes from catchment populations across East Africa, we assembled a dataset of 6506 hospital admissions for malaria in children aged 3 months to 9 years from 2006 to 2020. Admissions were paired with data from community parasite infection surveys. A Bayesian procedure was used to calibrate uncertainties in exposure (parasite prevalence) and outcomes (severe malaria phenotypes). Each 25% increase in prevalence conferred a doubling of severe malaria admission rates. Severe malaria remains a burden predominantly among young children (3 to 59 months) across a wide range of community prevalence typical of East Africa. This study offers a quantitative framework for linking malaria parasite prevalence and severe disease outcomes in children.


Asunto(s)
Malaria Falciparum/epidemiología , Plasmodium falciparum , África Oriental/epidemiología , Factores de Edad , Teorema de Bayes , Niño , Preescolar , Monitoreo Epidemiológico , Hospitalización , Humanos , Incidencia , Lactante , Malaria Cerebral/epidemiología , Malaria Falciparum/prevención & control , Malaria Falciparum/transmisión , Modelos Estadísticos , Prevalencia , Factores de Riesgo , Índice de Severidad de la Enfermedad
6.
Bioanalysis ; 13(15): 1177-1182, 2021 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-34355577

RESUMEN

Robust surveillance testing is a key strategic plan to prevent COVID-19 outbreaks and slow the spread of the SARS-CoV-2 pandemic; however, limited resources, facilities and time often impair the implementation of a widespread surveillance effort. To mitigate these resource limitations, we employed a strategy of pooling samples, reducing reagent cost and processing time. Through utilizing academic faculty and labs, successful pooled surveillance testing was conducted throughout Fall 2020 semester to detect positive SARS-CoV-2 infections in a population of 4400 students. During the semester, over 25,000 individual COVID status evaluations were made by pooling eight individual samples into one quantitative reverse transcription polymerase chain reaction. This pooled surveillance strategy was highly effective at detecting infection and significantly reduced financial burden and cost by $3.6 million.


Asunto(s)
Prueba de COVID-19/métodos , COVID-19/epidemiología , Brotes de Enfermedades/prevención & control , Laboratorios/normas , Tamizaje Masivo/métodos , Monitoreo Epidemiológico , Humanos , Pandemias , SARS-CoV-2
7.
Viruses ; 13(8)2021 08 19.
Artículo en Inglés | MEDLINE | ID: mdl-34452513

RESUMEN

The recent emergence of SARS-CoV-2 in humans from a yet unidentified animal reservoir and the capacity of the virus to naturally infect pets, farmed animals and potentially wild animals has highlighted the need for serological surveillance tools. In this study, the luciferase immunoprecipitation systems (LIPS), employing the spike (S) and nucleocapsid proteins (N) of SARS-CoV-2, was used to examine the suitability of the assay for antibody detection in different animal species. Sera from SARS-CoV-2 naturally-infected mink (n = 77), SARS-CoV-2 experimentally-infected ferrets, fruit bats and hamsters and a rabbit vaccinated with a purified spike protein were examined for antibodies using the SARS-CoV-2 N and/or S proteins. From comparison with the known neutralization status of the serum samples, statistical analyses including calculation of the Spearman rank-order-correlation coefficient and Cohen's kappa agreement were used to interpret the antibody results and diagnostic performance. The LIPS immunoassay robustly detected the presence of viral antibodies in naturally infected SARS-CoV-2 mink, experimentally infected ferrets, fruit bats and hamsters as well as in an immunized rabbit. For the SARS-CoV-2-LIPS-S assay, there was a good level of discrimination between the positive and negative samples for each of the five species tested with 100% agreement with the virus neutralization results. In contrast, the SARS-CoV-2-LIPS-N assay did not consistently differentiate between SARS-CoV-2 positive and negative sera. This study demonstrates the suitability of the SARS-CoV-2-LIPS-S assay for the sero-surveillance of SARS-CoV-2 infection in a range of animal species.


Asunto(s)
Anticuerpos Antivirales/sangre , COVID-19/veterinaria , Visón/inmunología , SARS-CoV-2/inmunología , Animales , COVID-19/diagnóstico , COVID-19/epidemiología , COVID-19/inmunología , Prueba Serológica para COVID-19 , Quirópteros/inmunología , Proteínas de la Nucleocápside de Coronavirus/inmunología , Monitoreo Epidemiológico , Hurones/inmunología , Inmunoprecipitación , Mesocricetus/inmunología , Fosfoproteínas/inmunología , Conejos/inmunología , Estudios Seroepidemiológicos , Glicoproteína de la Espiga del Coronavirus/inmunología
8.
Viruses ; 13(7)2021 07 14.
Artículo en Inglés | MEDLINE | ID: mdl-34372573

RESUMEN

West Nile (WNV) and Usutu (USUV) viruses are mosquito-borne flaviviruses. Thanks to their importance as zoonotic diseases, a regional plan for surveillance of Arboviruses was implemented in Emilia-Romagna in 2009. The province of Ferrara belongs to the Emilia-Romagna region, and it is an endemic territory for these viruses, with favorable ecological conditions for abundance of mosquitoes and wild birds. From 2015 to 2019, we collected 1842 dead-found birds at a wildlife rehabilitation center, which were analysed by three different PCRs for the detection of WNV and USUV genomes. August was characterized by the highest infection rate for both viruses. Columbiformes scored the highest USUV prevalence (8%), while Galliformes and Strigiformes reported the highest prevalence for WNV (13%). Among Passeriformes (the most populated Order), Turdus merula was the most abundant species and scored the highest prevalence for both viruses. To optimize passive surveillance plans, monitoring should be focused on the summer and towards the avian species more prone to infection by both viruses.


Asunto(s)
Aves/virología , Infecciones por Flavivirus/epidemiología , Fiebre del Nilo Occidental/epidemiología , Animales , Culicidae/virología , Monitoreo Epidemiológico/veterinaria , Flavivirus/genética , Flavivirus/patogenicidad , Infecciones por Flavivirus/veterinaria , Italia/epidemiología , Enfermedades Transmitidas por Vectores/epidemiología , Enfermedades Transmitidas por Vectores/veterinaria , Fiebre del Nilo Occidental/veterinaria , Virus del Nilo Occidental/genética , Virus del Nilo Occidental/patogenicidad
9.
Viruses ; 13(7)2021 07 14.
Artículo en Inglés | MEDLINE | ID: mdl-34372574

RESUMEN

The mosquito-borne flavivirus, Kedougou virus (KEDV), first isolated in Senegal in 1972, is genetically related to dengue, Zika (ZIKV) and Spondweni viruses (SPOV). Serological surveillance studies in Senegal and isolation of KEDV in the Central African Republic indicate occurrence of KEDV infections in humans, but to date, no disease has been reported. Here, we assembled the coding-complete genome of a 1958 isolate of KEDV from a pool of Aedes circumluteolus mosquitoes collected in Ndumu, KwaZulu-Natal, South Africa. The AR1071 Ndumu KEDV isolate bears 80.51% pairwise nucleotide identity and 93.34% amino acid identity with the prototype DakAar-D1470 strain and was co-isolated with SPOV through intracerebral inoculation of suckling mice and passage on VeroE6 cells. This historical isolate expands the known geographic and temporal range of this relatively unknown flavivirus, aiding future temporal phylogenetic calibration and diagnostic assay refinement.


Asunto(s)
Infecciones por Flavivirus/epidemiología , Flavivirus/genética , Aedes/virología , Animales , Monitoreo Epidemiológico , Flavivirus/metabolismo , Flavivirus/patogenicidad , Infecciones por Flavivirus/genética , Historia del Siglo XX , Humanos , Mosquitos Vectores/virología , Filogenia , Sudáfrica/epidemiología , Enfermedades Transmitidas por Vectores/historia
11.
Artículo en Inglés | MEDLINE | ID: mdl-34315360

RESUMEN

Abstract: Nationwide surveillance of Creutzfeldt-Jakob disease and other human prion diseases is performed by the Australian National Creutzfeldt-Jakob Disease Registry (ANCJDR). National surveillance encompasses the period since 1 January 1970, with prospective surveillance occurring from 1 October 1993. Over this prospective surveillance period, considerable developments have occurred in pre-mortem diagnostics; in the delineation of new disease subtypes; and in a heightened awareness of prion diseases in healthcare settings. Surveillance practices of the ANCJDR have evolved and adapted accordingly. This report summarises the activities of the ANCJDR during 2020. Since the ANCJDR began offering diagnostic cerebrospinal fluid (CSF) 14-3-3 protein testing in Australia in September 1997, the annual number of referrals has steadily increased. In 2020, 510 domestic CSF specimens were referred for 14-3-3 protein testing and 85 persons with suspected human prion disease were formally added to the national register. As of 31 December 2020, just over half (44 cases) of the 85 suspect case notifications remain classified as 'incomplete'; 27 cases were excluded through either detailed clinical follow-up (9 cases) or neuropathological examination (18 cases); 18 cases were classified as 'definite' and eleven as 'probable' prion disease. For 2020, sixty percent of all suspected human-prion-disease-related deaths in Australia underwent neuropathological examination. No cases of variant or iatrogenic CJD were identified. The SARS-CoV-2 pandemic did not affect prion disease surveillance outcomes in Australia.


Asunto(s)
Proteínas 14-3-3/líquido cefalorraquídeo , COVID-19/epidemiología , Síndrome de Creutzfeldt-Jakob/epidemiología , Vigilancia de la Población , Enfermedades por Prión/epidemiología , Adulto , Anciano , Anciano de 80 o más Años , Australia/epidemiología , Síndrome de Creutzfeldt-Jakob/líquido cefalorraquídeo , Síndrome de Creutzfeldt-Jakob/patología , Notificación de Enfermedades , Monitoreo Epidemiológico , Femenino , Humanos , Masculino , Persona de Mediana Edad , Neuropatología , Enfermedades por Prión/líquido cefalorraquídeo , Estudios Prospectivos , Sistema de Registros
12.
Epidemiol Infect ; 149: e164, 2021 06 28.
Artículo en Inglés | MEDLINE | ID: mdl-34196266

RESUMEN

An outbreak surveillance system for Salmonella integrating whole genome sequencing (WGS) and epidemiological data was developed in South East and London in 2016-17 to assess local WGS clusters for triage and investigation. Cases genetically linked within a 5 single-nucleotide polymorphism (SNP) single linkage cluster were assessed using a set of locally agreed thresholds based on time, person and place, for reporting to local health protection teams (HPTs). Between September 2016 and September 2017, 230 unique 5-SNP clusters (442 weekly reports) of non-typhoidal Salmonella 5-SNP WGS clusters were identified, of which 208 unique 5-SNP clusters (316 weekly reports) were not reported to the HPTs. In the remaining 22 unique clusters (126 weekly clusters) reported to HPTs, nine were known active outbreak investigations, seven were below locally agreed thresholds and six exceeded local thresholds. A common source or vehicle was identified in four of six clusters that exceeded locally agreed thresholds. This work demonstrates that a threshold-based surveillance system, taking into account time, place and genetic relatedness, is feasible and effective in directing the use of local public health resources for risk assessment and investigation of non-typhoidal Salmonella clusters.


Asunto(s)
Brotes de Enfermedades , Genoma Bacteriano/genética , Infecciones por Salmonella/epidemiología , Salmonella/genética , Análisis por Conglomerados , ADN Bacteriano/genética , Notificación de Enfermedades , Inglaterra/epidemiología , Monitoreo Epidemiológico , Humanos , Polimorfismo de Nucleótido Simple , Salud Pública , Medición de Riesgo , Salmonella/clasificación , Salmonella/aislamiento & purificación , Infecciones por Salmonella/microbiología , Secuenciación Completa del Genoma
13.
Genome Biol ; 22(1): 196, 2021 07 01.
Artículo en Inglés | MEDLINE | ID: mdl-34210356

RESUMEN

In response to the ongoing SARS-CoV-2 pandemic in the UK, the COVID-19 Genomics UK (COG-UK) consortium was formed to rapidly sequence SARS-CoV-2 genomes as part of a national-scale genomic surveillance strategy. The network consists of universities, academic institutes, regional sequencing centres and the four UK Public Health Agencies. We describe the development and deployment of CLIMB-COVID, an encompassing digital infrastructure to address the challenge of collecting and integrating both genomic sequencing data and sample-associated metadata produced across the COG-UK network.


Asunto(s)
Nube Computacional , Genómica/organización & administración , SARS-CoV-2/genética , COVID-19/epidemiología , Monitoreo Epidemiológico , Genoma Viral , Humanos , Análisis de Secuencia de ADN , Reino Unido , Interfaz Usuario-Computador , Secuenciación Completa del Genoma
14.
Epidemiol Infect ; 149: e171, 2021 07 30.
Artículo en Inglés | MEDLINE | ID: mdl-34325754

RESUMEN

Monitoring the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) community-wide transmission with a suitable and effective sampling method would be of great support for public health response to the spreading due to asymptomatic subjects in the community.Here, we describe how using saliva samples for SARS-CoV-2 detection has allowed for a weekly surveillance of a small business company and the early detection of coronavirus disease 2019 cases.As on 23rd March, two cases were detected and investigated, and control measures were rapidly applied.


Asunto(s)
COVID-19/prevención & control , Brotes de Enfermedades/prevención & control , SARS-CoV-2/aislamiento & purificación , Saliva/virología , Adulto , Anciano , COVID-19/diagnóstico , COVID-19/epidemiología , Prueba de Ácido Nucleico para COVID-19 , Trazado de Contacto , Monitoreo Epidemiológico , Femenino , Humanos , Italia/epidemiología , Masculino , Persona de Mediana Edad , SARS-CoV-2/inmunología
16.
Viruses ; 13(6)2021 06 03.
Artículo en Inglés | MEDLINE | ID: mdl-34205134

RESUMEN

This observational study evaluated SARS-CoV-2 IgG seroprevalence and related clinical, demographic, and occupational factors among workers at the largest tertiary care University-Hospital of Northwestern Italy and the University of Turin after the first pandemic wave of March-April 2020. Overall, about 10,000 individuals were tested; seropositive subjects were retested after 5 months to evaluate antibodies waning. Among 8769 hospital workers, seroprevalence was 7.6%, without significant differences related to job profile; among 1185 University workers, 3.3%. Self-reporting of COVID-19 suspected symptoms was significantly associated with positivity (Odds Ratio (OR) 2.07, 95%CI: 1.76-2.44), although 27% of seropositive subjects reported no previous symptom. At multivariable analysis, contacts at work resulted in an increased risk of 69%, or 24% for working in a COVID ward; contacts in the household evidenced the highest risk, up to more than five-fold (OR 5.31, 95%CI: 4.12-6.85). Compared to never smokers, being active smokers was inversely associated with seroprevalence (OR 0.60, 95%CI: 0.48-0.76). After 5 months, 85% of previously positive subjects still tested positive. The frequency of SARS-COV-2 infection among Health Care Workers was comparable with that observed in surveys performed in Northern Italy and Europe after the first pandemic wave. This study confirms that infection frequently occurred as asymptomatic and underlines the importance of household exposure, seroprevalence (OR 0.60, 95%CI: 0.48-0.76).


Asunto(s)
Anticuerpos Antivirales/sangre , COVID-19/epidemiología , COVID-19/inmunología , Personal de Salud/estadística & datos numéricos , Inmunoglobulina G/sangre , Centros de Atención Terciaria/estadística & datos numéricos , Adulto , Anciano , Estudios Transversales , Monitoreo Epidemiológico , Femenino , Humanos , Italia/epidemiología , Masculino , Persona de Mediana Edad , Prevalencia , Estudios Prospectivos , Estudios Seroepidemiológicos , Encuestas y Cuestionarios
17.
Arch Virol ; 166(9): 2461-2468, 2021 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-34212242

RESUMEN

Bovine coronavirus (BCoV) can be spread by animal activity. Although cattle farming is widespread in Turkey, there are few studies of BCoV. The aim of this study was to evaluate the current situation regarding BCoV in Turkey. This is the first study reporting the full-length nucleotide sequences of BCoV spike (S) genes in Turkey. Samples were collected from 119 cattle with clinical signs of respiratory (n = 78) or digestive tract (n = 41) infection on different farms located across widely separated provinces in Turkey. The samples were screened for BCoV using RT-nested PCR targeting the N gene, which identified BCoV in 35 samples (9 faeces and 26 nasal discharge). RT-PCR analysis of the S gene produced partial/full-length S gene sequences from 11 samples (8 faeces and 3 nasal discharge samples). A phylogenetic tree of the S gene sequences was made to analyze the genetic relationships among BCoVs from Turkey and other countries. The results showed that the local strains present in faeces and nasal discharge samples had many different amino acid changes. Some of these changes were shown in previous studies to be critical for tropism. This study provides new data on BCoV in Turkey that will be valuable in designing effective vaccine approaches and control strategies.


Asunto(s)
Enfermedades de los Bovinos/epidemiología , Infecciones por Coronavirus/veterinaria , Coronavirus Bovino/genética , Diarrea/veterinaria , ARN Viral/genética , Infecciones del Sistema Respiratorio/veterinaria , Glicoproteína de la Espiga del Coronavirus/genética , Agricultura , Sustitución de Aminoácidos , Animales , Bovinos , Enfermedades de los Bovinos/virología , Infecciones por Coronavirus/epidemiología , Infecciones por Coronavirus/virología , Coronavirus Bovino/clasificación , Diarrea/epidemiología , Diarrea/virología , Monitoreo Epidemiológico/veterinaria , Evolución Molecular , Heces/virología , Humanos , Mutación , Cavidad Nasal/virología , Filogenia , Infecciones del Sistema Respiratorio/epidemiología , Infecciones del Sistema Respiratorio/virología , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa , Análisis de Secuencia de ADN , Turquia/epidemiología
18.
Arch Virol ; 166(9): 2541-2549, 2021 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-34258664

RESUMEN

The SARS-CoV-2 spike protein Q677P/H mutation and furin cleavage site (FCS) have been shown to affect cell tropism and virus transmissibility. Here, we analyzed the frequency of Q677P/H and FCS point mutations in 1,144,793 human and 1042 animal spike protein sequences and from those of the emergent variants B.1.1.7, B.1.351, P.1, B.1.429 + B.1.427, and B.1.525, which were deposited in the database of the GISAID Initiative. Different genetic polymorphisms, particularly P681H and A688V, were detected in the FCS, mainly in human isolates, and otherwise, only pangolin and bat sequences had these mutations. Multiple FCS amino acid deletions such as Δ680SPRRA684 and Δ685RSVA688 were only detected in eight and four human isolates, respectively. Surprisingly, deletion of the entire FCS motif as Δ680SPRRARSVA688 and Δ680SPRRARSVAS689 was detected only in three human isolates. On the other hand, analysis of FCS from emergent variants showed no deletions in the FCS except for spike P681del, which was detected in seven B.1.1.7 isolates from the USA. Spike Q677P was detected only once in variant, B.1.1.7, whereas Q677H was detected in all variants, i.e., B.1.1.7 (n = 1938), B.1.351 (n = 28), P.1 (n = 9), B.1.429 + B.1.427 (n = 132), and B.1.525 (n = 1584). Structural modeling predicted that mutations or deletions at or near the FCS significantly alter the cleavage loop structure and would presumably affect furin binding. Taken together, our results show that Q677H and FCS point mutations are prevalent and may have various biological effects on the circulating variants. Therefore, we recommend urgent monitoring and surveillance of the investigated mutations, as well as laboratory assessment of their pathogenicity and transmissibility.


Asunto(s)
COVID-19/epidemiología , Furina/metabolismo , Polimorfismo Genético , SARS-CoV-2/genética , Glicoproteína de la Espiga del Coronavirus/química , Secuencia de Aminoácidos , Animales , Sitios de Unión , COVID-19/transmisión , COVID-19/virología , Quirópteros/virología , Monitoreo Epidemiológico , Euterios/virología , Evolución Molecular , Furina/química , Expresión Génica , Humanos , Modelos Moleculares , Unión Proteica , Conformación Proteica en Hélice alfa , Conformación Proteica en Lámina beta , Dominios y Motivos de Interacción de Proteínas , Proteolisis , SARS-CoV-2/química , SARS-CoV-2/clasificación , SARS-CoV-2/metabolismo , Glicoproteína de la Espiga del Coronavirus/genética , Glicoproteína de la Espiga del Coronavirus/metabolismo
19.
Arch Virol ; 166(9): 2551-2561, 2021 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-34259914

RESUMEN

The aim of this study was to identify and validate a sensitive, high-throughput, and cost-effective SARS-CoV-2 real-time RT-PCR assay to be used as a surveillance and diagnostic tool for SARS-CoV-2 in a university surveillance program. We conducted a side-by-side clinical evaluation of a newly developed SARS-CoV-2 multiplex assay (EZ-SARS-CoV-2 Real-Time RT-PCR) with the commercial TaqPath COVID-19 Combo Kit, which has an Emergency Use Authorization from the FDA. The EZ-SARS-CoV-2 RT-PCR incorporates two assays targeting the SARS-CoV-2 N gene, an internal control targeting the human RNase P gene, and a PCR inhibition control in a single reaction. Nasopharyngeal (NP) and anterior nares (AN) swabs were tested as individuals and pools with both assays and in the ABI 7500 Fast and the QuantStudio 5 detection platforms. The analytical sensitivity of the EZ-SARS-CoV-2 RT-PCR assay was 250 copies/ml or approximately 1.75 genome copy equivalents per reaction. The clinical performance of the EZ-SARS-CoV-2 assay was evaluated using NP and AN samples tested in other laboratories. The diagnostic sensitivity of the assay ranged between 94 and 96% across the detection platforms, and the diagnostic specificity was 94.06%. The positive predictive value was 94%, and the negative predictive value ranged from 94 to 96%. Pooling five NP or AN specimens yielded 93% diagnostic sensitivity. The overall agreement between these SARS-CoV-2 RT-PCR assays was high, supported by a Cohen's kappa value of 0.93. The EZ-SARS-CoV-2 RT-PCR assay performance attributes of high sensitivity and specificity with AN sample matrix and pooled upper respiratory samples support its use in a high-throughput surveillance testing program.


Asunto(s)
Prueba de Ácido Nucleico para COVID-19/métodos , COVID-19/diagnóstico , Proteínas de la Nucleocápside de Coronavirus/genética , Reacción en Cadena de la Polimerasa Multiplex/métodos , ARN Viral/genética , SARS-CoV-2/genética , COVID-19/epidemiología , COVID-19/virología , Prueba de Ácido Nucleico para COVID-19/economía , Prueba de Ácido Nucleico para COVID-19/instrumentación , Monitoreo Epidemiológico , Expresión Génica , Humanos , Reacción en Cadena de la Polimerasa Multiplex/economía , Reacción en Cadena de la Polimerasa Multiplex/instrumentación , Cavidad Nasal/virología , Nasofaringe/virología , Fosfoproteínas/genética , Reproducibilidad de los Resultados , Sensibilidad y Especificidad , Manejo de Especímenes/métodos , Carga Viral
20.
R I Med J (2013) ; 104(7): 16-20, 2021 Sep 01.
Artículo en Inglés | MEDLINE | ID: mdl-34279520

RESUMEN

COVID-19 is a worldwide public health emergency caused by SARS-CoV-2. Genomic surveillance of SARS-CoV-2 emerging variants is important for pandemic monitoring and informing public health responses. Through an interstate academic-public health partnership, we established Rhode Island's capacity to sequence SARS-CoV-2 genomes and created a systematic surveillance program to monitor the prevalence of SARS-CoV-2 variants in the state. We describe circulating SARS-CoV-2 lineages in Rhode Island; provide a timeline for the emerging and expanding contribution of variants of concern (VOC) and variants of interest (VOI), from their first introduction to their eventual predominance over other lineages; and outline the frequent identification of known adaptively beneficial spike protein mutations that appear to have independently arisen in non-VOC/non-VOI lineages. Overall, the described Rhode Island- centric genomic surveillance initiative provides a valuable perspective on SARS-CoV-2 in the state and contributes data of interest for future epidemiological studies and state-to-state comparisons.


Asunto(s)
COVID-19/virología , SARS-CoV-2/genética , COVID-19/epidemiología , Monitoreo Epidemiológico , Variación Genética , Genómica , Humanos , Pandemias , Vigilancia de la Población , Rhode Island/epidemiología , SARS-CoV-2/aislamiento & purificación
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