Test on stool samples improves the diagnosis of hospitalized patients: Detection of SARS-CoV-2 genomic and subgenomic RNA

Moreira, Luiz Vinícius Leão; Luna, Luciano Kleber de Souza; Barbosa, Gabriela; Perosa, Ana Helena; Chaves, Ana Paula Cunha; Conte, D.; Carvalho, Joseane Mayara Almeida; Bellei, Nancy

doi:10.1016/j.jinf.2020.11.034

Cited by 18 publications

(20 citation statements)

References 10 publications

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“…Moreover, in contrast to the data reported by Alexandersen et al [ 17 ], who reported that the relative abundance of subgenomic RNAs may be more related to the sample’s quality and storage before the laboratory assay than to the actual stage of infection, we can emphasize that the persistence of sgN RNAs might be considered as a candidate biomarker of the active viral load, regardless of the pre-analytical conditions and analytical diagnostic kit. It is noteworthy that sgN was reported as the most expressed transcript in other sample types, like stool [ 19 ]; the authors of this research concluded that the detection of sgN and s gE improves the diagnosis of COVID-19, particularly in patients who are suspected of being infected but with negative results in the upper respiratory tract. Although the setting of this study [ 19 ] is different, we can agree with the authors’ conclusion, which emphasized the role of these subgenomic transcripts.…”

Section: Discussionmentioning

confidence: 98%

“…It is noteworthy that sgN was reported as the most expressed transcript in other sample types, like stool [ 19 ]; the authors of this research concluded that the detection of sgN and s gE improves the diagnosis of COVID-19, particularly in patients who are suspected of being infected but with negative results in the upper respiratory tract. Although the setting of this study [ 19 ] is different, we can agree with the authors’ conclusion, which emphasized the role of these subgenomic transcripts. Our preliminary findings, although they were confirmed on a group of eighty-eight samples, should be deepened on larger cohorts, particularly to confirm the diagnostic potential of the sgN target in terms of the prediction of higher and active viral loads.…”

Section: Discussionmentioning

confidence: 98%

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SARS-CoV-2 Subgenomic N (sgN) Transcripts in Oro-Nasopharyngeal Swabs Correlate with the Highest Viral Load, as Evaluated by Five Different Molecular Methods

et al. 2021

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The COVID-19 pandemic has forced diagnostic laboratories to focus on the early diagnostics of SARS-CoV-2. The positivity of a molecular test cannot respond to the question regarding the viral capability to replicate, spread, and give different clinical effects. Despite the fact that some targets are covered by commercially-available assays, the identification of new biomarkers is desired in order to improve the quality of the information given by these assays. Therefore, since the subgenomic transcripts (sgN and sgE) are considered markers of viral activity, we evaluated these subgenomic transcripts in relation to the genomic amplification obtained using five different commercial CE-IVD tools. Methods: Five CE-IVD kits were compared in terms of their capability to detect both synthetic SARS-CoV-2 viral constructs (spiked in TMB or PBS medium) and targets (N, E, RdRp and Orf1ab genes) in twenty COVID-19–positive patients’ swabs. The sgN and sgE were assayed by real-time RT-qPCR and digital PCR. Results: None of the diagnostic kits missed the viral target genes when they were applied to targets spiked in TMB or PBS (at dilutions ranging from 100 pg to 0.1 pg). Nevertheless, once they were applied to RNA extracted from the patients’ swabs, the superimposability ranged from 50% to 100%, regardless of the extraction procedure. The sgN RNA transcript was detected only in samples with a higher viral load (Ct ≤ 22.5), while sgE was within all of the Ct ranges. Conclusions: The five kits show variable performances depending on the assay layout. It is worthy of note that the detection of the sgN transcript is associated with a higher viral load, thus representing a new marker of early and more severe infection.

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Section: Discussionmentioning

confidence: 98%

Section: Discussionmentioning

confidence: 98%

SARS-CoV-2 Subgenomic N (sgN) Transcripts in Oro-Nasopharyngeal Swabs Correlate with the Highest Viral Load, as Evaluated by Five Different Molecular Methods

et al. 2021

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“…It is evident that the ratio of positive samples among patients in different studies varied greatly from 0 to 100% and 0 to 50% in stool and urine samples, respectively (Table S1). The presence of SARS-CoV-2 in stool and urine samples could be related to the swallowing of respiratory secretions from the upper respiratory tract or residues of infected antigen-presenting immune cells, or, more likely, due to virus replication in gastrointestinal epithelial cells or tubular epithelium [45] , [46] , [47] . Furthermore, the shedding magnitude detected in urine and stool samples varied from 10-10 4 copies/mL in urine samples and 10-10 8 copies/g in stool samples (Table S1).…”

Section: Key Uncertainties For Estimating Sars-cov-2 Prevalence‘mentioning

confidence: 99%

Uncertainties in estimating SARS-CoV-2 prevalence by wastewater-based epidemiology

Zhang

Shi

et al. 2021

Chemical Engineering Journal

173

139

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“…The tissue homogenate/ swab specimens were used for RNA extraction. MagMAX™ Viral/Pathogen Nucleic Acid Isolation Kit was used for viral RNA extraction and real-time RT-PCR was performed for E gene of SARS-CoV-2 and for N gene for the sub genomic (sg) RNA detection using the published primers [13, 14].…”

Section: Methodsmentioning

confidence: 99%

SARS-CoV-2 Delta variant pathogenesis and host response in Syrian hamsters

Mohandas

Yadav

Shete

et al. 2021

Preprint

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B.1.617 lineage is becoming a dominant SARS-CoV-2 lineage worldwide and was the dominant lineage reported in second COVID-19 wave in India, which necessitated studying the properties of the variant. We evaluated the pathogenicity and virus shedding of B.1.617.2 (Delta) and B.1.617.3 lineage of SARS-CoV-2 and compared with that of B.1, an early virus isolate with D614G mutation in Syrian hamster model. Viral load, antibody response and lung disease were studied. No significant difference in the virus shedding pattern was observed among these variants studied. A significantly high SARS-CoV-2 sub genomic RNA could be detected in the respiratory tract of hamsters infected with Delta variant for 14 days. Delta variant induced lung disease of moderate severity in 40% of infected animals. The neutralizing capability of the B.1, Delta and B.1.617.3 variant infected animals were found significantly lower with the B.1.351 (Beta variant). The findings of the study support the attributed disease severity and the increased transmission potential of the Delta variant.

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Test on stool samples improves the diagnosis of hospitalized patients: Detection of SARS-CoV-2 genomic and subgenomic RNA

Cited by 18 publications

References 10 publications

SARS-CoV-2 Subgenomic N (sgN) Transcripts in Oro-Nasopharyngeal Swabs Correlate with the Highest Viral Load, as Evaluated by Five Different Molecular Methods

SARS-CoV-2 Subgenomic N (sgN) Transcripts in Oro-Nasopharyngeal Swabs Correlate with the Highest Viral Load, as Evaluated by Five Different Molecular Methods

Uncertainties in estimating SARS-CoV-2 prevalence by wastewater-based epidemiology

SARS-CoV-2 Delta variant pathogenesis and host response in Syrian hamsters

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