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Background: The rapid emergence and global dissemination of the Omicron variant of SARS-CoV-2 have posed formidable challenges in public health. This scenario underscores the urgent need for an enhanced understanding of Omicron's pathophysiological mechanisms to guide clinical management and shape public health strategies. Our study is aimed at deciphering the intricate molecular mechanisms underlying Omicron infections, particularly focusing on the identification of specific biomarkers. Methods: This investigation employed a robust and systematic approach, initially encompassing 15 Omicron-infected patients and an equal number of healthy controls, followed by a validation cohort of 20 individuals per group. The study's methodological framework included a comprehensive multi-omics analysis that integrated proteomics and metabolomics, augmented by extensive bioinformatics. Proteomic exploration was conducted via an advanced Ultra-High-Performance Liquid Chromatography (UHPLC) system linked with mass spectrometry. Concurrently, metabolomic profiling was executed using an Ultra-Performance Liquid Chromatography (UPLC) system. The bioinformatics component, fundamental to this research, entailed an exhaustive analysis of protein–protein interactions, pathway enrichment, and metabolic network dynamics, utilizing state-of-the-art tools such as the STRING database and Cytoscape software, ensuring a holistic interpretation of the data. Results: Our proteomic inquiry identified eight notably dysregulated proteins (THBS1, ACTN1, ACTC1, POTEF, ACTB, TPM4, VCL, ICAM1) in individuals infected with the Omicron variant. These proteins play critical roles in essential physiological processes, especially within the coagulation cascade and hemostatic mechanisms, suggesting their significant involvement in the pathogenesis of Omicron infection. Complementing these proteomic insights, metabolomic analysis discerned 146 differentially expressed metabolites, intricately associated with pivotal metabolic pathways such as tryptophan metabolism, retinol metabolism, and steroid hormone biosynthesis. This comprehensive metabolic profiling sheds light on the systemic implications of Omicron infection, underscoring profound alterations in metabolic equilibrium. Conclusions: This study substantially enriches our comprehension of the physiological ramifications induced by the Omicron variant, with a particular emphasis on the pivotal roles of coagulation and platelet pathways in disease pathogenesis. The discovery of these specific biomarkers illuminates their potential as critical targets for diagnostic and therapeutic strategies, providing invaluable insights for the development of tailored treatments and enhancing patient care in the dynamic context of the ongoing pandemic. [ABSTRACT FROM AUTHOR]

Background: The rapid emergence and global dissemination of the Omicron variant of SARS-CoV-2 have posed formidable challenges in public health. This scenario underscores the urgent need for an enhanced understanding of Omicron's pathophysiological mechanisms to guide clinical management and shape public health strategies. Our study is aimed at deciphering the intricate molecular mechanisms underlying Omicron infections, particularly focusing on the identification of specific biomarkers. Methods: This investigation employed a robust and systematic approach, initially encompassing 15 Omicron-infected patients and an equal number of healthy controls, followed by a validation cohort of 20 individuals per group. The study's methodological framework included a comprehensive multi-omics analysis that integrated proteomics and metabolomics, augmented by extensive bioinformatics. Proteomic exploration was conducted via an advanced Ultra-High-Performance Liquid Chromatography (UHPLC) system linked with mass spectrometry. Concurrently, metabolomic profiling was executed using an Ultra-Performance Liquid Chromatography (UPLC) system. The bioinformatics component, fundamental to this research, entailed an exhaustive analysis of protein–protein interactions, pathway enrichment, and metabolic network dynamics, utilizing state-of-the-art tools such as the STRING database and Cytoscape software, ensuring a holistic interpretation of the data. Results: Our proteomic inquiry identified eight notably dysregulated proteins (THBS1, ACTN1, ACTC1, POTEF, ACTB, TPM4, VCL, ICAM1) in individuals infected with the Omicron variant. These proteins play critical roles in essential physiological processes, especially within the coagulation cascade and hemostatic mechanisms, suggesting their significant involvement in the pathogenesis of Omicron infection. Complementing these proteomic insights, metabolomic analysis discerned 146 differentially expressed metabolites, intricately associated with pivotal metabolic pathways such as tryptophan metabolism, retinol metabolism, and steroid hormone biosynthesis. This comprehensive metabolic profiling sheds light on the systemic implications of Omicron infection, underscoring profound alterations in metabolic equilibrium. Conclusions: This study substantially enriches our comprehension of the physiological ramifications induced by the Omicron variant, with a particular emphasis on the pivotal roles of coagulation and platelet pathways in disease pathogenesis. The discovery of these specific biomarkers illuminates their potential as critical targets for diagnostic and therapeutic strategies, providing invaluable insights for the development of tailored treatments and enhancing patient care in the dynamic context of the ongoing pandemic. [ABSTRACT FROM AUTHOR]

The emergence of the novel GII.17 Kawasaki 2014 norovirus variant raising the interest of the public, has replaced GII.4 as the predominant cause of noroviruses outbreaks in East Asia during 2014–2015. Antigenic variation of the capsid protein is considered as one of the key mechanisms of norovirus evolution. In this study, we screened a panel of GII.17 mutants. First, we produced norovirus P proteins using cell-free protein synthesis (CFPS) system, comparing the results to pure proteins expressed in a cell-based system. Next, we determined the binding capability of specific monoclonal antibody (mAb) 2D11 using a unique set of wild-type GII.17 strains. Results of the EIA involving a panel of mutant cell-free proteins indicated that Q298 was the key residue within loop 1. These data highlighted the essential residues in the linear antibody binding characteristics of novel GII.17. Furthermore, it supported the CFPS as a promising tool for rapidly screening mutants via the scalable expression of norovirus P proteins. [ABSTRACT FROM AUTHOR]

Background: Human noroviruses are one of the main causes of foodborne illnesses and represent a serious public health concern. Rapid and sensitive assays for human norovirus detection are undoubtedly necessary for clinical diagnosis, especially in regions without more sophisticated equipment.Method: The rapid reverse transcription recombinase-aided amplification (RT-RAA) is a fast, robust and isothermal nucleic acid detection method based on enzyme reaction. This method can complete the sample detection at 39 °C in 30 min. In this study, we successfully established a rapid reverse transcription recombinase-aided amplification (RT-RAA) assay for the detection of human norovirus GII.4 and applied this assay to clinical samples, as well as comparison with commercial reverse transcription real-time fluorescence quantitative PCR (RT-qPCR).Results: At 95% probability, the detection sensitivity of RT-RAA was 3.425 log10 genomic copies (LGC)/reaction. Moreover, no cross-reaction was observed with other norovirus genogroups and other common foodborne viruses. Stool samples were examined by RT-RAA and reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR). Compared of RT-qPCR, kappa values for human norovirus detection with RT-RAA were 0.894 (p < 0.001), indicating that both assays were in agreement.Conclusion: This RT-RAA assay provides a rapid, specific, and sensitive assay for human norovirus detection and is suitable for clinical testing. [ABSTRACT FROM AUTHOR]

Human sapovirus is regarded as an important viral agent for acute diarrhea worldwide. GII.8, a recently reported genotype, has been detected in a few countries and regions. In this study, we obtained the first genome sequence of a sapovirus GII.8 strain isolated in mainland China, and comprehensively analyzed the genetic diversity and evolutionary process of this genotype. The viral genome of the new GII.8 Guangzhou strain GZ2014-L231 comprised 7433 nucleotides, including two ORFs. Pairwise alignments of the new genome with representative sequences of different genotypes showed inconsistent homology between different protein-encoding regions, of which NS1 and VP2 were found as the variable proteins, and NS3, NS5, and NS6/7 were found as the conserved ones. Compared with other reported GII.8 genomes, the Guangzhou strain introduced 34 new nucleotide changes and one new amino acid change. Phylogenetic analysis based on full-length VP1 sequences demonstrated that 11 GII.8 strains could be divided into 4 clusters A-D, with 88 SNP and 10 SAP spots occurred during their evolutionary process. The Guangzhou strain has higher homology with seven GII.8 strain detected after 2014, especially the US and Peruvian strains of 2015/2016, which have the identical VP1 amino acid sequences. Using a Bayesian coalescent method based on VP1 sequences, GII.8 was predicted to emerge in 2001 with the evolution rate of 1.45 × 10−3 nucleotide substitutions/site/year (strict clock). In summary, the data in this study not only provided reference data from mainland China for sapovirus researches in future, but also firstly described the evolutionary process of the GII.8 genotype. • The first genome sequence of GII.8 SaV from mainland China was obtained and analyzed. • The new Guangzhou genome employed 34 new SNP and one new SAP. • NS1 and VP2 were found as the variable proteins in the SaV genome. • GII.8 SaV could be further divided into four clusters based on the capsid VP1. • TMRCA and evolution rate for the capsid VP1 gene of GII.8 SaV was estimated. [ABSTRACT FROM AUTHOR]

Key message: Overexpression of grapevine VvABF2 gene could enhance osmotic stress tolerance in Arabidopsis thaliana but fully required for ABA signaling. The abscisic acid (ABA)-dependent AREB/ABF-SnRK2 pathway has been demonstrated to play a pivotal role in response to osmotic stress in model plants. However, its function in other specific species, for example grapevine, has not been fully characterized. In this study, grapevine (Vitis vinifera L.) ABSCISIC ACID RESPONSE ELEMENT-BINDING FACTOR2 (VvABF2), a homologous gene of AREB/ABFs form Arabidopsis, was isolated and constitutively expressed in Arabidopsis under the control of the cauliflower mosaic virus 35S promoter. The VvABF2 transgenic Arabidopsis plants showed to be more sensitive to exogenous ABA compared to wild type plants and exhibited significant osmotic tolerance, like polyethylene glycol (PEG) and drought but fully required ABA for signaling. This fact was further confirmed by its downstream gene expression assays. In addition, the determination of ROS antioxidant enzymes (including SOD, POD and CAT) and the MDA of transgenic lines indicated that overexpression of VvABF2 in Arabidopsis significantly increased ROS scavenging ability and thereby reduced the cell membrane damage, which might be ABA-independent. Our results provide evidence that VvABF2 has a similar function to the Arabidopsis homolog in response to osmotic stresses, and that there is a similar ancestral function of this gene in ABA-dependent response to stresses in grapevine. [ABSTRACT FROM AUTHOR]

• VP2 in GII.4 NoV variants exhibits a hypervariable region and shows a similar evolutionary process to VP1. • VP2 in GII.4 NoV variants is found to interact with VP1 in a time-ordered, variant-dependent manner. • The residues of 131-160, 171-180 in the hypervariable region of VP2 are responsible for interaction and evolution. Norovirus is a leading cause of viral gastroenteritis outbreaks worldwide, with GII.4 responsible for the majority of infections. Minor capsid protein VP2 has been found to have functions such as stabilizing virus particles, and VP2 is one of the highly variable proteins of norovirus, similar to major capsid protein VP1. However, whether the variation of VP2 is functionally driven still remains unclear. In this study, VP2 showed a higher evolutionary rate (2.642×10−3 substitutions/site/year) than VP1 (1.587×10−3 substitutions/site/year), and a hypervariable region in VP2 in a serial of norovirus GII.4 over the past 50 years had been observed. Notably, the high variation of VP2 was not haphazard. The evolutionary process of VP2 is similar to that of VP1 with comparable topologies when the phylogenetic trees were constructed. Moreover, VP2 was found to interact with VP1 among epidemic variants of GII.4 using the yeast two-hybrid experiments. The results of interactions were grouped into time-adjacent (e.g. Ancestral-VP1 plus US95-VP2) and non-adjacent (e.g. Ancestral-VP1 plus Sydney-VP2) according to the epochal chronologically based prevalence of GII.4 norovirus. Interestingly, the interaction of the former group was significantly stronger than that of the latter group (P =0.0001). Furthermore, the interaction regions on VP2 (residues 131-160 and 171-180) were mapped to the hypervariable region. And these interaction regions did show an important role in the evolutionary process of VP2, which was consistent with that of VP1. In summary, the minor capsid protein VP2 of GII.4 noroviruses had shown the epochal coevolution with VP1 based on their interactions over the past 50 years. The findings of this study provided valuable information for further understanding and completing the evolutionary mechanism of norovirus. [ABSTRACT FROM AUTHOR]

Norovirus is a major cause of acute gastroenteritis worldwide. Like the major capsid protein (VP1), the minor capsid protein (VP2) also contains a hypervariable domain. Generally, a hypervariable domain is functionally driven. However, many functions of VP2 remain unknown and worth exploring. Without sufficient sequences and an available crystallographic model, it is difficult to explore VP2's mysteries. As a helper of stabilizing and coordinating the formation of virus-like particles (VLPs), we asked whether VP2 interacted with the major capsid protein (VP1) in GII.17 and if so, what the key interaction residues were. Here, we reported cross-interaction among four strains represented four clusters of GII.17, and the VP1 interaction domain of VP2 (174-179aa) was found. However, the VP1 interaction domain of VP2 was not universal in different clusters of GII.17. VP2 might evolve in a different pattern from VP1. Additionally, in contrast to previous reports, we found that VP2 localized in the cytoplasm. More possibilities of VP2 should be further explored. • Unlike the covariation of GII.4, cross-interactions are confirmed in four clusters of GII.17. • In the epidemic GII.17 strain, residues of 174–179 of VP2 are responsible for interacting with VP1. • The evolutionary pattern of VP2 might be different from VP1 and other possibilities of VP2 should be explored. [ABSTRACT FROM AUTHOR]

The worldwide response towards the acute gastroenteritis epidemic was well known, but the absence of an updated systematic review of global norovirus epidemiology in cases of gastroenteritis existed. We aimed to conduct and update a systematic review and meta-analysis of studies assessing norovirus prevalence among gastroenteritis patients worldwide. Four databases (PubMed, EMBASE, Cochrane Library, and Web of Science) were searched for epidemiological papers from 2014 to 2021 which applied the PCR method to access the prevalence of norovirus in acute gastroenteritis patients more than a full year. Statistical analysis was conducted using R-4.0.0 software. A total of 405 records with 842, 926 cases were included. The pooled prevalence of norovirus was 16% (95%CI 15, 17). Children under 5 years old were at a higher risk with norovirus. A higher prevalence was seen in South America (22%, 95% CI 18, 27), while other continents showed a similar result with the overall prevalence of norovirus. No association was found between national income level and norovirus prevalence. A gradient of decreasing prevalence was noticed from community (20%, 95% CI 16, 24) to outpatients (18%, 95% CI 16, 20) to hospital setting (included both in- and outpatients, 17%, 95% CI 16, 19) to inpatients (15%, 95% CI 13, 17). Norovirus were associated with 16% acute gastroenteritis globally. To fully understand the prevalence of norovirus worldwide, the continual surveillance of norovirus epidemics was required. • The pooled global prevalence of norovirus among acute gastroenteritis was 16% over the last 20 years. • The infection rate stayed the same compared to the last decade. • Norovirus should be included in continuous surveillance worldwide, especially in low-incoming countries. [ABSTRACT FROM AUTHOR]

Norovirus is a leading cause of viral gastroenteritis outbreaks worldwide. Histo-blood group antigens (HBGAs) are important host attachment factors in susceptibility to norovirus. In this study, the association of FUT2 gene, which participates in the biosynthesis of HBGAs, with norovirus infection has been investigated. All relevant studies on the associations of FUT2 gene with norovirus were retrieved from PubMed, Web of Science, Embase, and Cochrane Library databases. Odds ratios (ORs) and 95% confidence interval (CI) were used to analyze the extracted data. I 2 statistic, sensitivity analysis and publication bias analysis were used to confirm the findings. Subgroup analyses were performed for races, genotypes, development degree of the countries, publication years, age and setting when heterogeneity was recorded. Twenty studies including 4066 participants were included for the meta-analysis. This analysis showed that there is a significant association between FUT2 gene and norovirus infection (OR = 3.02, 95%CI = 2.00–4.55, P < 0.001). Additionally, the ORs of norovirus infection among Chinese (OR = 4.49, 95%CI = 2.37–8.50, P < 0.001) were higher than those among Caucasian (OR = 3.23, 95%CI = 2.20–4.74, P < 0.001). The meta-analysis suggested that FUT2 gene is associated with susceptibility to norovirus infection. • The association of non-sense mutation in FUT2 gene and norovirus infection was systematically evaluated. • Individuals with functional FUT2 gene were more vulnerable to norovirus infection. • The secretory status was significantly associated with the clinical symptoms of norovirus infection. [ABSTRACT FROM AUTHOR]

Noroviruses are the primary cause of gastroenteritis and foodborne diseases, affecting millions of individuals annually worldwide. Oysters are frequently associated with norovirus outbreaks. Hence, inexpensive and simple norovirus detection methods are important to detect and contain foodborne illness outbreaks. The objective of this study is to develop a high-efficient concentrated pretreatment method for reverse transcriptase quantitative real-time polymerase chain reaction (RT-qPCR) detection. Based on the existing ISO/TS 15216-2:2013 standard (ISO/TS 15216-2., 2013), four methods are compared for recovery of norovirus from spiked digestive tissue of oysters. A method is found to be the most efficient based on protease K method of increasing buffer volume and PEG precipitation method. The recovery rate and amplification efficiency approached 11.07 ± 0.09% and 124.12 ± 5.99%, respectively, being 7-fold that of the original ISO/TS 15216-2:2013 method. This method serves as a rapid (1.5h) sample concentration tool with a limit of detection as low as 7.05 × 103 copies. Thirty-eight oyster samples from an aquatic products market in Guangzhou are tested using this method, and noroviruses are detected in 13 samples. This method is an effective extension of the existing ISO/TS 15216-2:2013 standard and it is potentially applicable for detecting norovirus contamination in oysters. • PEG precipitation with proteinase K treatment was performed to detect NoV in independent oysters. • This method had a higher recovery rate than the standard ISO/TS 15216-2:2013 method. • This method had a better amplification efficiency upon RT-qPCR-based monitoring. [ABSTRACT FROM AUTHOR]