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We used nasopharyngeal swab samples of patients with a symptomatic (n = 82) or asymp-tomatic (n = 20) coronavirus disease 2019 (COVID-19) diagnosis to assess the ability of antigen detection tests to infer active (potentially transmissible) or inactive (potentially non-transmissible) infection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Using the subgenomic RNA (sgRNA) as an active replication marker of SARS-CoV-2, 48 (76.2%), 56 (88.9%), and 63 (100%) of 63 samples with sgRNA positive results tested positive with the SD BIOSENSOR STANDARD Q COVID-19 Ag (Standard Q), the SD BIOSENSOR STANDARD F COVID-19 Ag FIA (Standard F), or the Fujirebio LUMIPULSE G SARS-CoV-2 Ag (Lumipulse) assay, respectively. Conversely, 37 (94.9%), 29 (74.4%), and 7 (17.9%) of 39 samples with sgRNA negative results tested negative with Standard Q, Standard F, or Lumipulse, respectively. Stratifying results by the number of days of symptoms before testing revealed that most antigen positive/sgRNA positive results were among samples tested at 2–7 days regardless of the assay used. Conversely, most antigen negative/sgRNA negative results were among samples tested at 16–30 days only when Standard Q or Standard F were used. In conclusion, based on our findings, a negative antigen test, especially with the Lumipulse assay, or a positive antigen test, especially with the Standard F assay, may suggest, respectively, the absence or presence of replication-competent SARS-CoV-2.

BACKGROUND: While the role of bacteria as an etiological factor triggering relapse in inflammatory bowel disease (IBD) has been studied extensively, little is known of the role of enteric viruses. We aimed to prospectively study the prevalence and risk factors for common enteropathogenic viruses in IBD patients in relation to disease activity. METHODS: IBD patients visiting the outpatient clinic of the Maastricht University Medical Center were included in a prospective cohort with a follow-up of 1 year. Every 3 months and during relapses, fecal samples, demographic, and clinical data were collected and disease activity was scored. A fecal sample from patients at baseline (Crohn's disease [CD] n = 170, ulcerative colitis [UC] n = 116) and an additional sample from a subgroup with changing disease activity during follow-up (CD n = 57, UC n = 31) were analyzed for the presence of rotavirus, norovirus GI and GII, human astrovirus, and adenovirus using quantitative polymerase chain reaction (qPCR). RESULTS: Overall viral pathogen detection, defined by the detection of at least one of the studied viruses, at baseline was 5.2% and differed neither between CD (6.5%) or UC patients (3.4%) (P = 0.20), nor between active disease (4.7%) and remission (5.5%) (P = 0.79). Within the subgroup of patients with changing disease activity no association was found between overall viral pathogen detection and disease activity (P = 0.39). Using multivariate logistic regression, age, gender, disease subtype, disease activity, medication, and season of sampling were not associated with overall viral pathogen detection. CONCLUSIONS: Enteropathogenic viruses are not frequently observed in a consecutive cohort of IBD patients and are not a common trigger for active disease in daily clinical practice. (Inflamm Bowel Dis 2012;).

BACKGROUND: While the role of bacteria as an etiological factor triggering relapse in inflammatory bowel disease (IBD) has been studied extensively, little is known of the role of enteric viruses. We aimed to prospectively study the prevalence and risk factors for common enteropathogenic viruses in IBD patients in relation to disease activity. METHODS: IBD patients visiting the outpatient clinic of the Maastricht University Medical Center were included in a prospective cohort with a follow-up of 1 year. Every 3 months and during relapses, fecal samples, demographic, and clinical data were collected and disease activity was scored. A fecal sample from patients at baseline (Crohn's disease [CD] n = 170, ulcerative colitis [UC] n = 116) and an additional sample from a subgroup with changing disease activity during follow-up (CD n = 57, UC n = 31) were analyzed for the presence of rotavirus, norovirus GI and GII, human astrovirus, and adenovirus using quantitative polymerase chain reaction (qPCR). RESULTS: Overall viral pathogen detection, defined by the detection of at least one of the studied viruses, at baseline was 5.2% and differed neither between CD (6.5%) or UC patients (3.4%) (P = 0.20), nor between active disease (4.7%) and remission (5.5%) (P = 0.79). Within the subgroup of patients with changing disease activity no association was found between overall viral pathogen detection and disease activity (P = 0.39). Using multivariate logistic regression, age, gender, disease subtype, disease activity, medication, and season of sampling were not associated with overall viral pathogen detection. CONCLUSIONS: Enteropathogenic viruses are not frequently observed in a consecutive cohort of IBD patients and are not a common trigger for active disease in daily clinical practice. (Inflamm Bowel Dis 2012;).

Rhizomania is a viral disease, caused by beet necrotic yellow vein furovirus (BNYVV), which was detected in Spanish sugar beets in 1988, it being focused on the Castilla y León region. BNYVV has five RNA fragments with specific functions, and the different composition and proportion of RNA in the virions allow their separation and the characterization of their activities during the development of the disease. Thirty–six samples of sugar beet rootlets and frozen pulps from three different sugar beet zones of Castilla y León were analyzed by DAS-ELISA and Immunocapture-Reverse Transcription-Polymerase Chain Reaction (IC-RT-PCR) using specific primers. The identity of the cDNA products was confirmed by nested- PCR and restriction fragment length polymorphism (RFLP). The uniformity of the patterns obtained by RFLP analyses with nine endonucleases showed the existence of a unique strain of BNYVV in 80,000 Ha of crop surface which could be explained by a recent arrival of the rhizomania disease to this region. The isolates studied were more similar to type A, which has been previously described in BNYVV, but a nonexpected cleavage site for this molecular group was observed with endonuclease Hinc II on the RNA-2 IC-RT-PCR product (nt 2133–3293) in the thirty–six Spanish samples and also in a North American strain taken as reference. The use of frozen pulps obtained as a previous step to the industrial extraction of sugar avoids problems due to erratic distribution of the virus in the roots, provides repetitive results for a particular sample, and facilitates epidemiological and distributional studies on rhizomania disease.

Rhizomania is a viral disease, caused by beet necrotic yellow vein furovirus (BNYVV), which was detected in Spanish sugar beets in 1988, it being focused on the Castilla y León region. BNYVV has five RNA fragments with specific functions, and the different composition and proportion of RNA in the virions allow their separation and the characterization of their activities during the development of the disease. Thirty–six samples of sugar beet rootlets and frozen pulps from three different sugar beet zones of Castilla y León were analyzed by DAS-ELISA and Immunocapture-Reverse Transcription-Polymerase Chain Reaction (IC-RT-PCR) using specific primers. The identity of the cDNA products was confirmed by nested- PCR and restriction fragment length polymorphism (RFLP). The uniformity of the patterns obtained by RFLP analyses with nine endonucleases showed the existence of a unique strain of BNYVV in 80,000 Ha of crop surface which could be explained by a recent arrival of the rhizomania disease to this region. The isolates studied were more similar to type A, which has been previously described in BNYVV, but a nonexpected cleavage site for this molecular group was observed with endonuclease Hinc II on the RNA-2 IC-RT-PCR product (nt 2133–3293) in the thirty–six Spanish samples and also in a North American strain taken as reference. The use of frozen pulps obtained as a previous step to the industrial extraction of sugar avoids problems due to erratic distribution of the virus in the roots, provides repetitive results for a particular sample, and facilitates epidemiological and distributional studies on rhizomania disease.

Virus-contaminated soft fruits or vegetables are increasingly identified as causes of foodborne viral illness. Noroviruses and hepatitis A virus are the most common pathogens in viral infections transmitted by these kinds of foods. To improve microbiological detection and monitoring and to increase insights into the contribution of fruits and vegetables to foodborne viral transmission, sensitive, reliable, and standardized methods are needed. More studies on virus detection methods for foods are being published, but validated consensus protocols are not yet available. In this paper, different methodologies are reviewed critically. The use of process controls and internal amplification controls is discussed.