Ye Qiu

Coxsackievirus A16 (CVA16) is one of the major pathogens responsible for hand, foot, and mouth disease (HFMD), for which no specific antiviral therapy is currently available. Neochlorogenic acid (NCGA) and chlorogenic acid (CGA) are a pair of chiral isomers with highly similar chemical structures. While the antiviral activity of CGA has been extensively investigated, that of NCGA remains largely unexplored. In our study, we found that NCGA exhibited antiviral activity against CVA16, whereas CGA was completely inactive. Notably, NCGA also displayed extremely low cytotoxicity, and its antiviral efficacy was further confirmed in vivo. We further identified RNA-binding motif protein 24 (RBM24) as a host factor involved in the antiviral effect of NCGA against CVA16, as its knockdown attenuated the antiviral activity of NCGA. Collectively, our findings not only identify a novel natural product against CVA16 but also provide clues for the discovery of host factors involved in CVA16 infection.

Helicobacter pylori is a carcinogenic pathogen with a high gastric cancer risk. The rapid emergence of antibiotic resistance severely compromises treatment efficacy. However current conventional approaches fail to capture early molecular events preceding detectable resistance. Here, we used a gradient intermittent antibiotic exposure model to simulate stepwise resistance evolution and longitudinally acquired single‐cell Raman spectra across adaptive cycles. By integrating two‐dimensional correlation Raman spectroscopy (2D‐COS), we resolved the temporal sequence of molecular alterations during the phenotypic silent window. The earliest responses involved adjustments of pre‐existing biomass structures. Specifically, symmetric CH ₂ and CH ₃ vibrations changed first, reflecting membrane lipid and protein conformational shifts, followed by carbohydrate backbone and alkyl vibrations indicating initial metabolic adjustments. During a structural reorganization phase, amide III shifted earlier than amide I, suggesting protein conformational adjustment precedes content increase, while lipid chain vibration emerged concurrently. Subsequently, nucleic acid base and pyrimidine ring vibrations increased, culminating in the C‐D band representing newly synthesized biomass accumulation. This sequential cascade reveals that structural adaptation occurs prior to metabolic activation. Our work provides a detailed molecular basis for resistance evolution within the silent window and highlights single‐cell Raman‐based metabolic profiling for early detection.

Enterovirus alphacoxsackie (EV-A) is a highly diverse viral species containing at least 25 serotypes with diverse biological and clinical characteristics. EV-A can cause diseases ranging from asymptomatic infections to severe neurological disorders, as well as mucocutaneous diseases such as hand, foot, and mouth disease. 2A, a cysteine protease expressed by EV-A, plays critical roles in virus–host interactions. Although 2A orthologs of different EV-A serotypes share consistent protease-catalytic motifs and cleavage patterns, they show functional diversity in interacting with cellular proteins, probably due to distinct protease-independent activities determined by the single amino acid polymorphisms (SAPs) among different 2A orthologs. However, routine sequence alignment and phylogenetic analysis can hardly identify the key SAP sites (kSAPs) contributing to the functional variance, mainly due to the high conservation of the proteins and the unequal weight of SAPs in determining protein function. Herein, we developed Single Amino Acid Polymorphism Statistics (SAAPS), an information-entropy (IE)-based algorithmic pipeline, to identify the functional kSAPs of EV-A 2A. The core principle of the algorithm is that the IE of the kSAPs can be neither too low (highly conserved sites not leading to variance) nor too high (random neutral mutations). Using SAAPS, we identified 56 kSAPs from 2A of 25 EV-A serotypes. Based on the kSAPs, the 2As can be clustered into three major groups with a few outliers, which was distinct from the clustering generated by phylogenetic analysis using the whole amino acid sequences. Functional verification with transcriptomic profiles of HEK-293T cells expressing different 2A variants revealed closer alignment of kSAP clustering than phylogenetic clustering. Notably, EV-A89, an outlier identified by kSAP clustering but not phylogenetic clustering, showed a unique expression pattern with an altered shift in the molecular weight, which suggested that it was related to three SAPs identified by SAAPS. This study presents SAAPS as a useful tool for prioritizing functionally relevant SAPs to guide mechanistic discovery and can be applied to highly conserved proteins like EV-A 2A.

Enterovirus alphacoxsackie (EV-A) is a highly diverse viral species containing at least 25 serotypes of viruses which show distinct infectivity and pathogenicity. Increasing studies show that EV-A protease 2A plays critical roles in virus-host interactions. Although 2A is usually considered as a non-structural protein highly conserved among different EV-A serotypes, its orthologs of different EV-A serotypes harbor abundant single amino acid polymorphisms (SAPs), probably contributing to the variance of infectivity and patho-genicity of EV-As. However, the SAP profile of EV-A 2A and its functional impacts have been poorly understood, mainly due to the unequal contribution to protein function of dif-ferent SAP sites. Herein, we developed Single Amino Acid Polymorphism Statistics (SAAPS), an information-entropy-based algorithmic pipeline, to identify key SAP sites (kSAPs) related to functional variance of EV-A 2A. As the result, we identified 56 kSAPs from 2A of 25 EV-A serotypes. Based on the kSAPs, the 2As can be clustered into three major groups with a few outliers, which was distinct from the clustering generated by phylogenetic analysis using the whole amino acid sequences. Functional verification with transcriptomic profiles of HEK-293T cells expressing different 2A variants revealed better phenotypic matching of kSAP-based clustering than that of phylogenetic clustering. No-tably, EV-A89, an outlier identified by kSAP clustering but not phylogenetic clustering, showed unique expressing and self-cleavage patterns which were not observed in other 2As. These findings demonstrated the good performance of SAAPS and functional SAP profile of EVA 2As, contributing to the understanding of the variance of EV-A infectivity and pathogenicity.

Bats (Chiroptera) are a taxonomic group of immense biological and ecological importance. They are primary reservoirs and carriers of various zoonotic viruses. Endogenous retroviruses (ERVs) originate from ancient retroviruses invading the host, and ERV-derived sequences can function as regulatory elements which influence gene expression and contribute to both physiological and pathological processes. However, ERVs and ERV-like elements (ERVLEs) carried by bats have not been fully characterized. In this study, we systematically explored the ERVs in 61 bat species and identified 10,352 bat-ERVs and 5,884 bat-ERVLEs sequences, and these sequences covered 3 major virus genera and included 7 groups related to human ERVs in the subfamily Orthoretrovirinae. In particular, a relatively intact endogenous deltaretrovirus sequence was identified in Molossus molossus. Additionally, 358 bat-ERV and 33 bat-ERVLE were identified as recombinants. The integration time of bat-ERVs was estimated to be concentrated in the last 10 to 40 million years, indicating their role in shaping the bat genome during the long-term co-evolution of virus and host. Furthermore, carnivorous bats tended to have more relatively complete and younger ERVs compared to herbivorous bats. According to bat transcriptomes, we found that 1,385 bat-ERVs and 197 bat-ERVLEs had transcriptional potential in 20 different tissues of 25 bats, implying that bat-ERVs harboured actively expressed genes with potential functions. In summary, we comprehensively characterized bat-ERVs in terms of their evolution, types and potential functions, providing foundational data and a new perspective for further research on bat-ERVs.

The prevalence of the Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an important transition in the epidemic of coronavirus disease 2019 (COVID-19). Compared with other SARS-CoV-2 variants, Omicron and its subvariants exhibit decreased pathogenicity, thus contributing to the moderation of the epidemic. However, the mechanism underlying such changes is not fully understood. NSP5 is a SARS-CoV-2-encoded protease that counteracts antiviral immunity, and the P132H mutation of NSP5 is present exclusively in Omicron and its subvariants. In this study, we found that this mutation solely relieved cytopathogenicity and reduced the viral replication during SARS-CoV-2 infection. Further studies suggested that P132H blocked the NSP5-mediated degradation of MAVS by impairing the K136-linked ubiquitination of MAVS, thus restoring the IFN-β activation inhibited by NSP5. Structural analysis in silico suggested that P132H disrupted multiple hydrogen bonds between NSP5 and UbcH5b, an E2 ubiquitin-conjugating enzyme required for K136 ubiquitination. In summary, our results provide a potential mechanism explaining the decreased pathogenicity of the Omicron variant of SARS-CoV-2.

Viruses circulating in small mammals possess the potential to infect humans. Tree shrews are a group of small mammals inhabiting widely in forests and plantations, but studies on viruses in tree shrews are quite limited. Herein, viral metagenomic sequencing was employed to detect the virome in the tissue and swab samples from seventy-six tree shrews that we collected in Yunnan Province. As the results, genomic fragments belonging to eighteen viral families were identified, thirteen of which contain mammalian viruses. Through polymerase chain reaction (PCR) and Sanger sequencing, twelve complete genomes were determined, including five parvoviruses, three torque teno viruses (TTVs), two adenoviruses, one pneumovirus, and one hepacivirus, together with three partial genomes, including two hepatitis E virus and one paramyxovirus. Notably, the three TTVs, named TSTTV-HNU1, TSTTV-HNU2, and TSTTV-HNU3, may compose a new genus within the family Anelloviridae. Notably, TSParvoV-HNU5, one of the tree shrew parvoviruses detected, was likely to be a recombination of two murine viruses. Divergence time estimation further revealed the potential cross-species-transmission history of the tree shrew pneumovirus TSPenV-HNU1. Our study provides a comprehensive exploration of viral diversity in wild tree shrews, significantly enhancing our understanding of their role as natural virus reservoirs.

The membrane protein (M), a key structural protein of SARS‐CoV‐2 that regulates virus assembly and morphogenesis, is involved in the pathological processes of multiple organ damage and metabolic disorders. This study aims to elucidate the mechanisms of M‐mediated host ferroptosis and lipid accumulation during SARS‐CoV‐2 infection. Here, we detected that M protein enhances cellular sensitivity to ferroptosis. Additionally, we uncovered the pivotal role of perilipin‐2 and sterol regulatory element‐binding protein 1 in M‐induced lipid accumulation. Xanthohumol, a cost‐effective and orally available diacylglycerol acyltransferase inhibitor, alleviated triglyceride and total cholesterol accumulation, thereby counteracting the M‐induced ferroptosis. Furthermore, we identified that the mitochondrial import inner membrane translocase subunit TIM23 and the mitochondrial import receptor subunit TOM20 homolog contribute to M‐induced mitochondrial dysfunction. Notably, inhibiting lipid synthesis effectively reduced mitochondrial reactive oxygen species and transmembrane potential, indicating a cross‐talk between lipid and ferro metabolic pathways. Mechanistically, glutathione peroxidase 4 (GPX4) interacts with SARS‐CoV‐2 M, leading to its subsequent degradation by the Membrane Associated Ring‐CH‐Type Finger 1 (MARCHF1) ubiquitin ligase. M‐GPX4 interaction occurs at the R72 residue, which may represent a potential therapeutic target against SARS‐CoV‐2 infection. M modulates lipid accumulation and further impairs mitochondrial functions, ultimately resulting in ferroptosis through MARCHF1‐GPX4 axis. Disrupting host‐virus interactions along this pathway may provide a therapeutic strategy for SARS‐CoV‐2 infection.