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Viral co-infections, in which a host is infected with multiple viruses simultaneously, are common in the human population. Human viral co-infections can lead to complex interactions between the viruses and the host immune system, affecting the clinical outcome and posing challenges for treatment. Understanding the types, mechanisms, impacts, and identification methods of human viral co-infections is crucial for the prevention and control of viral diseases. In this review, we first introduce the significance of studying human viral co-infections and summarize the current research progress and gaps in this field. We then classify human viral co-infections into four types based on the pathogenic properties and species of the viruses involved. Next, we discuss the molecular mechanisms of viral co-infections, focusing on virus–virus interactions, host immune responses, and clinical manifestations. We also summarize the experimental and computational methods for the identification of viral co-infections, emphasizing the latest advances in high-throughput sequencing and bioinformatics approaches. Finally, we highlight the challenges and future directions in human viral co-infection research, aiming to provide new insights and strategies for the prevention, control, diagnosis, and treatment of viral diseases. This review provides a comprehensive overview of the current knowledge and future perspectives on human viral co-infections and underscores the need for interdisciplinary collaboration to address this complex and important topic. [ABSTRACT FROM AUTHOR]

NMR serves as an important technique for probing rock pore space, such as pore structure characterization, fluid identification, and petrophysical property testing, due to the reusability of cores, convenience in sample processing, and time efficiency in laboratory tests. In practice, NMR signal collection is normally achieved through polarized nuclei relaxation which releases crucial relaxation messages for result interpretation. The impetus of this work is to help engineers and researchers with petroleum background obtain new insights into NMR principals and extend existing methodologies for characterization of unconventional formations. This article first gives a brief description of the development history of relaxation theories and models for porous media. Then, the widely used NMR techniques for characterizing petrophysical properties and pore structures are presented. Meanwhile, limitations and deficiencies of them are summarized. Finally, future work on improving these insufficiencies and approaches of enhancement applicability for NMR technologies are discussed. [ABSTRACT FROM AUTHOR]

Graphical abstract Abstract A nanostructured porous carbon (NPC) is prepared by using a facile physical activation method, with nitrogen-doped graphene nanoribbon aerogel and carbon dioxide as a precursor and an activating agent, respectively. The morphology, porosity parameters, and chemical properties of the as-prepared NPC have been revealed by using various characterization methods, including scanning electron microscopy, nitrogen sorption analysis, and X-ray photoelectron spectroscopy (XPS). The NPC with a moderate nitrogen content (5.1 atom % on the basis of XPS analysis) retains the sponge-like morphology of nitrogen-doped graphene nanoribbon aerogel, shows a high Brunauer–Emmett–Teller specific surface area (1380 m2 g−1), and possesses hierarchically porous structures. Based on its excellent properties such as high porosity, conductive network, and nitrogen-doping, NPC as a superior host is used to fabricate a sulfur-based cathode for lithium–sulfur batteries. The high specific surface area and the pore volume of NPC not only allow uniform distribution of sulfur in an amorphous form, but also help to alleviate the shuttle effect of polysulfides. As a result, the as-obtained cathode exhibits a good rate capability and cycling stability. [ABSTRACT FROM AUTHOR]

The Co 3 (PO 4) 2.8 H 2 O nanozyme was in situ synthesized through direct reaction between cobalt (Ⅱ) and phosphate, and its peroxidase-like activity was studied in the presence of hydrogen peroxide (H 2 O 2) using a chromogenic substrate 3, 3′, 5, 5′ - tetramethylbenzidine (TMB). The effects of pH value, temperature, and incubation time on the conversion of TMB to oxidized TMB (oxTMB) catalyzed by Co 3 (PO 4) 2.8 H 2 O in the presence of H 2 O 2 were optimized. The peroxidase-like activity of Co 3 (PO 4) 2.8 H 2 O conforms to the Michaelis-Menten kinetics, and its Michaelis constant (K m) is 0.073 mM, showing a higher H 2 O 2 affinity than natural horseradish peroxidase (HRP) and some other peroxidase nanozymes. The mechanism exploration experiment confirmed that the hydroxyl radical (•OH) is the main active species in the catalytic reaction of Co 3 (PO 4) 2.8 H 2 O. Finally, based on the inherent peroxidase-like activity of Co 3 (PO 4) 2.8 H 2 O, a simple colorimetric detection method for H 2 O 2 was established, with a linear range of 15.0 − 100.0 μM and a detection limit of 4.385 μM. The method was applied to the determination of H 2 O 2 in milk samples with the spiked recovery of 90.2%− 106.2%. This study reports a novel nanozyme that can be easily produced in situ, which is exempt from the harsh, cumbersome, and time-consuming synthesis and purification procedures. In addition, the H 2 O 2 colorimetric detection method based on the nanozyme has the advantages of low cost, convenient, high sensitivity, and good selectivity. [Display omitted] • A novel nanozyme Co 3 (PO 4) 2.8 H 2 O of excellent catalytic activity is discovered. • This peroxidase-mimic nanozyme is in situ synthesized rapidly. • The hydroxyl radical is the major active specie in the catalytic reaction. • A sensitive colorimetric method for hydrogen peroxide determination is established. [ABSTRACT FROM AUTHOR]

The SARS-CoV-2 genomic data continue to grow, providing valuable information for researchers and public health officials. Genomic analysis of these data sheds light on the transmission and evolution of the virus. To aid in SARS-CoV-2 genomic analysis, many web resources have been developed to store, collate, analyze, and visualize the genomic data. This review summarizes web resources used for the SARS-CoV-2 genomic epidemiology, covering data management and sharing, genomic annotation, analysis, and variant tracking. The challenges and further expectations for these web resources are also discussed. Finally, we highlight the importance and need for continued development and improvement of related web resources to effectively track the spread and understand the evolution of the virus. [ABSTRACT FROM AUTHOR]

Being in the epicenter of the COVID-19 pandemic, our lab tested 193,054 specimens for SARS-CoV-2 RNA by diagnostic multiplex reverse transcription polymerase chain reaction (mRT-PCR) starting in March 2020, of which 17,196 specimens resulted positive. To investigate the dynamics of virus molecular evolution and epidemiology, whole genome amplification (WGA) and Next Generation Sequencing (NGS) were performed on 9516 isolates. 7586 isolates with a high quality were further analyzed for the mutation frequency and spectrum. Lastly, we evaluated the utility of the mRT-PCR detection pattern among 26 reinfected patients with repeat positive testing three months after testing negative from the initial infection. Our results show a continuation of the genetic divergence in viral genomes. Furthermore, our results indicate that independent mutations in the primer and probe regions of the nucleocapsid gene amplicon and envelope gene amplicon accumulate over time. Some of these mutations correlate with the changes of detection pattern of viral targets of mRT-PCR. Our data highlight the significance of a continuous genetic divergence on a gene amplification-based assay, the value of the mRT-PCR detection pattern for complementing the clinical diagnosis of reinfection, and the potential for WGA and NGS to identify mutation hotspots throughout the entire viral genome to optimize the design of the PCR-based gene amplification assay. [ABSTRACT FROM AUTHOR]

The chemo‐regulation abilities of chemotherapeutic medications are appealing to address the low immunogenicity, immunosuppressive lactate microenvironment, and adaptive immune resistance of colorectal cancer. In this work, the proteolysis targeting chimera (PROTAC) of BRD4 (dBET57) is found to downregulate colorectal cancer glycolysis through the transcription inhibition of c‐Myc, which also inhibits the expression of programmed death ligand 1 (PD‐L1) to reverse immune evasion and avoid adaptive immune resistance. Based on this, self‐delivery nano‐PROTACs (designated as DdLD NPs) are further fabricated by the self‐assembly of doxorubicin (DOX) and dBET57 with the assistance of DSPE‐PEG2000. DdLD NPs can improve the stability, intracellular delivery, and tumor targeting accumulation of DOX and dBET57. Meanwhile, the chemotherapeutic effect of DdLD NPs can efficiently destroy colorectal cancer cells to trigger a robust immunogenic cell death (ICD). More importantly, the chemo‐regulation effects of DdLD NPs can inhibit colorectal cancer glycolysis to reduce the lactate production, and downregulate the PD‐L1 expression through BRD4 degradation. Taking advantages of the chemotherapy and chemo‐regulation ability, DdLD NPs systemically activated the antitumor immunity to suppress the primary and metastatic colorectal cancer progression without inducing any systemic side effects. Such self‐delivery nano‐PROTACs may provide a new insight for chemotherapy‐enabled tumor immunotherapy. [ABSTRACT FROM AUTHOR]

Background: Identifying polymorphism clades on phylogenetic trees could help detect punctual mutations that are associated with viral functions. With visualization tools coloring the tree, it is easy to visually find clades where most sequences have the same polymorphism state. However, with the fast accumulation of viral sequences, a computational tool to automate this process is urgently needed. Results: Here, by implementing a branch-and-bound-like search method, we developed an R package named sitePath to identify polymorphism clades automatically. Based on the identified polymorphism clades, fixed and parallel mutations could be inferred. Furthermore, sitePath also integrated visualization tools to generate figures of the calculated results. In an example with the influenza A virus H3N2 dataset, the detected fixed mutations coincide with antigenic shift mutations. The highly specificity and sensitivity of sitePath in finding fixed mutations were achieved for a range of parameters and different phylogenetic tree inference software. Conclusions: The result suggests that sitePath can identify polymorphism clades per site. The clustering of sequences on a phylogenetic tree can be used to infer fixed and parallel mutations. High-quality figures of the calculated results could also be generated by sitePath. [ABSTRACT FROM AUTHOR]

Early identification of adaptive mutations could provide timely help for the control and prevention of the COVID-19 pandemic. The fast accumulation of SARS-CoV-2 sequencing data provides important support, while also raising a great challenge for the recognition of adaptive mutations. Here, we proposed a computational strategy to detect potentially adaptive mutations from their fixed and parallel patterns in the phylogenetic trajectory. We found that the biological meanings of fixed substitution and parallel mutation are highly complementary, and can reasonably be integrated as a fixed and parallel (paraFix) mutation, to identify potentially adaptive mutations. Tracking the dynamic evolution of SARS-CoV-2, 37 sites in spike protein were identified as having experienced paraFix mutations. Interestingly, 70% (26/37) of them have already been experimentally confirmed as adaptive mutations. Moreover, most of the mutations could be inferred as paraFix mutations one month earlier than when they became regionally dominant. Overall, we believe that the concept of paraFix mutations will help researchers to identify potentially adaptive mutations quickly and accurately, which will provide invaluable clues for disease control and prevention. [ABSTRACT FROM AUTHOR]

In this study, the cobalt carbonate (CoCO 3) was in situ prepared using cobalt (Ⅱ) and carbonate at room temperature, and the intrinsic peroxidase-like activity of CoCO 3 was demonstrated for the first time through the oxidation of chromogenic substrate 3, 3', 5, 5' - tetramethylbenzidine (TMB) in the presence of hydrogen peroxide (H 2 O 2). The effects of pH, reaction temperature, and incubation time on the catalytic activity of CoCO 3 were studied. Under the optimal reaction conditions, the Michaelis constant (K m) of CoCO 3 to H 2 O 2 is 0.443 mM, which is lower than that of natural horseradish peroxidase and the previously reported peroxidase mimics. Furthermore, the mechanism exploration experiments confirm that the catalytic activity of CoCO 3 is mainly attributed to the hydroxyl radical (•OH). Finally, based on the outstanding peroxidase-like activity of CoCO 3 , a colorimetric sensor for the detection of H 2 O 2 , glucose, and ascorbic acid (AA) was developed, which shows satisfactory selectivity and recovery. In addition, the total antioxidant capacity of three types of tea, dried lemon, three kinds of fresh fruit juice, and vitamin C tablet were determined. In short, this study reports a novel in situ generated CoCO 3 , which can be prepared rapidly at room temperature, eliminating the harsh, cumbersome, and time-consuming synthesis and purification process. The developed sensor based on the newly found excellent peroxidase-like activity of in situ prepared CoCO 3 for the determination of H 2 O 2 , glucose, and AA is fast, simple, low cost, and high sensitivity. [Display omitted] • The excellent peroxidase-like activity of CoCO 3 is firstly investigated. • The CoCO 3 is in situ prepared of rapidity and simplicity. • The hydroxyl radical (•OH) is the major active specie in the catalytic reaction. • The nanozyme has preferable kinetics with a low K m value towards substrate H 2 O 2. • A colorimetric detection platform for H 2 O 2 , glucose, and ascorbic acid is developed. [ABSTRACT FROM AUTHOR]