The importance of fecal nucleic acid detection in patients with coronavirus disease (COVID‐19): A systematic review and meta‐analysis

Zhou, Jinqiu; Liu, Gongxiang; Huang, Xiaoli; Gan, Hu

doi:10.1002/jmv.27652

Cited by 16 publications

(15 citation statements)

References 73 publications

(209 reference statements)

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“…In this study, both the tissue-specificity and expression volume restrictions were applied to facilitate identification of the most prominent interactions between host miRNAs and the viral genomes. First, the scope of the study was limited to the lungs and colon tissues as the two main sites of SARS-CoV-2 replication in the human body [15]. Second, we aimed to analyzed only those miRNA species that represent the top 95% of the miRNAome for their tissue type [37], with the following rationale.…”

Section: Resultsmentioning

confidence: 99%

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miRNA binding pressure channels evolution of SARS-CoV-2 genomes

Zhiyanov

Shkurnikov

Nersisyan

et al. 2023

Preprint

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In somatic cells, microRNAs (miRNAs) bind to the genomes of RNA viruses and influence their translation and replication. Here we demonstrate that a significant number of miRNA binding sites locate in the NSP4 region of the SARS-CoV-2 genome, and the intestinal human miRNAs exert evolutionary pressure on this region. Notably, in infected cells, NSP4 promotes the formation of double-membrane vesicles, which serve as the scaffolds for replication-transcriptional complexes and protect viral RNA from intracellular destruction. In three years of selection, the loss of many miRNA binding sites, in particular, those within the NSP4, has shaped the SARS-CoV-2 genomes to promote the descendants of the BA.2 variants as the dominant strains and define current momentum of the pandemics.

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Section: Resultsmentioning

confidence: 99%

“…In humans, the SARS-CoV-2 virus predominantly replicates in the type 2 alveocytes of the lung. In addition, significant clinical data indicate the presence of the virus in the intestinal epithelium, which expresses both ACE2 and TMPRSS2 [15]. Moreover, intestinal viral persistence is commonly detected.…”

Section: Introductionmentioning

confidence: 99%

miRNA binding pressure channels evolution of SARS-CoV-2 genomes

Zhiyanov

Shkurnikov

Nersisyan

et al. 2023

Preprint

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“…The previous studies on faecal viral shedding of COVID-19 cases mainly focused on the ancestral variant, and the proportion of faecal viral shedding of the ancestral variant was 21% to 59%. [24][25][26][27][28][29][30] We conducted the study with a sample size of over 1,000 infected cases, which provided valuable information for the utility of wastewater surveillance. In total, 82•4% (n=1,011) of participants had samples collected during the acute period, indicating that wastewater surveillance by Omicron was a reliable approach to monitor infection trends.…”

Section: Discussionmentioning

confidence: 99%

Longitudinal wastewater surveillance addressed public health priorities during the transition from “dynamic COVID-zero” to “opening up” in China: a population-based study

et al. 2023

Preprint

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Background Wastewater surveillance provides real-time, cost-effective monitoring of SARS-CoV-2 transmission. We developed the first city-level wastewater warning system in mainland China, located in Shenzhen. Our study aimed to reveal cryptic transmissions under the "dynamic COVID-zero" policy and characterize the dynamics of the infected population and variant prevalence, and then guide the allocation of medical resources during the transition to "opening up" in China. Methods In this population-based study, a total of 1,204 COVID-19 cases were enrolled to evaluate the contribution of Omicron variant-specific faecal shedding rates in wastewater. After that, wastewater samples from up to 334 sites distributed in communities and port areas in two districts of Shenzhen covering 1.74 million people were tested daily to evaluate the sensitivity and specificity of this approach and were validated against daily SARS-CoV-2 screening. After the public health policy was switched to "opening up" in December 7, 2022, we conducted wastewater surveillance at wastewater treatment plants and pump stations covering 3.55 million people to estimate infected populations using model prediction and detect the relative abundance of SARS-CoV-2 lineages using wastewater sequencing. Findings In total, 82.4% of SARS-CoV-2 Omicron cases tested positive for faecal viral RNA within the first four days after the diagnosis, which was far more than the proportion of the ancestral variant. A total of 27,759 wastewater samples were detected from July 26 to November 30 in 2022, showing a sensitivity of 73.8% and a specificity of 99.8%. We further found that wastewater surveillance played roles in providing early warnings and revealing cryptic transmissions in two communities. Based on the above results, we employed a prediction model to monitor the daily number of infected individuals in Shenzhen during the transition to "opening up" in China, with over 80% of the population infected in both Futian District and Nanshan District. Notably, the prediction of the daily number of hospital admission was consistent with the actual number. Further sequencing revealed that the Omicron subvariant BA.5.2.48 accounted for the most abundant SARS-CoV-2 RNA in wastewater, and BF.7.14 and BA.5.2.49 ranked second and third, respectively, which was consistent with the clinical sequencing. Interpretation This study provides a scalable solution for wastewater surveillance of SARS-CoV-2 to provide real-time monitoring of the new variants, infected populations and facilitate the precise prediction of hospital admission. This novel framework could be a One Health system for the surveillance of other infectious and emerging pathogens with faecal shedding and antibiotic resistance genes in the future. Funding Sanming Project of Medicine in Shenzhen, Shenzhen Key Medical Discipline Construction Fund.

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“…However, recovered patients showed detectable SARS-CoV-2 RNA in feces regardless of their symptoms. The digestive tract might be an important organ to excreting the virus ( Galanopoulos et al., 2021 ; Zhou et al., 2022 ). The possibility of fecal-oral transmission remains to be revealed.…”

Section: Discussionmentioning

confidence: 99%

“…This was consistent with our findings, and prolonged fecal virus shedding might be a noteworthy source of transmission even after the respiratory virus has been cleared. The excretion of SARS-CoV-2 in stools might increase the risk of environmental contamination and facilitate viral spread among the general population through fecal-oral transmission ( Arslan et al., 2020 ; Zhou et al., 2022 ). The concentration of SARS-CoV-2 RNA in feces was estimated to be 10 4 -10 8 per gram ( Bar-On et al., 2020 ).…”

Section: Discussionmentioning

confidence: 99%

Characteristics of COVID-19 Patients With SARS-CoV-2 Positivity in Feces

Shi

Zhu

et al. 2022

Front. Cell. Infect. Microbiol.

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BackgroundSARS-CoV-2 is highly contagious and poses a great threat to epidemic control and prevention. The possibility of fecal-oral transmission has attracted increasing concern. However, viral shedding in feces has not been completely investigated.MethodsThis study retrospectively reviewed 97 confirmed coronavirus disease 2019 (COVID-19) patients hospitalized at the First Affiliated Hospital, School of Medicine, Zhejiang University, from January 19 to February 17, 2020. SARS-CoV-2 RNA in samples of sputum, nasopharyngeal or throat swabs, bronchoalveolar lavage and feces was detected by real-time reverse transcription polymerase chain reaction (RT–PCR). Clinical characteristics and parameters were compared between groups to determine whether fecal RNA was positive.ResultsThirty-four (35.1%) of the patients showed detectable SARS-CoV-2 RNA in feces, and 63 (64.9%) had negative detection results. The median time of viral shedding in feces was approximately 25 days, with the maximum time reaching 33 days. Prolonged fecal-shedding patients showed longer hospital stays. Those patients for whom fecal viral positivity persisted longer than 3 weeks also had lower plasma B-cell counts than those patients in the non-prolonged group [70.5 (47.3-121.5) per μL vs. 186.5 (129.3-376.0) per μL, P = 0.023]. Correlation analysis found that the duration of fecal shedding was positively related to the duration of respiratory viral shedding (R = 0.70, P < 0.001) and negatively related to peripheral B-cell counts (R = -0.44, P < 0.05).ConclusionsCOVID-19 patients who shed SARS-CoV-2 RNA in feces presented similar clinical characteristics and outcomes as those who did not shed SARS-CoV-2 RNA in feces. The prolonged presence of SARS-CoV-2 nucleic acids in feces was highly correlated with the prolonged shedding of SARS-CoV-2 RNA in the respiratory tract and with lower plasma B-cell counts.

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The importance of fecal nucleic acid detection in patients with coronavirus disease (COVID‐19): A systematic review and meta‐analysis

Cited by 16 publications

References 73 publications

miRNA binding pressure channels evolution of SARS-CoV-2 genomes

miRNA binding pressure channels evolution of SARS-CoV-2 genomes

Longitudinal wastewater surveillance addressed public health priorities during the transition from “dynamic COVID-zero” to “opening up” in China: a population-based study

Characteristics of COVID-19 Patients With SARS-CoV-2 Positivity in Feces

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