Communicable Diseases, Emerging ; genetics ; Genomics ; Humans

The rapid development of sequencing technology brings the explosive growth of pathogen genetic data. The combination of genomic data and phylogenetic method is being used to elaborate the origin and evolution of pathogens, the time and space distribution and parameter changes in the prevalence process, and how phenotypes like antigen, virulence, and resistance change over time. This method is also being used to predict pathogen transmission trends. In this study, we described the aim of phylogeny and the process of the phylogenetic construction method. We elaborated the advantages and disadvantages and scope of application of tree-building methods including distance-based, maximum parsimony, maximum likelihood and bayesian methods. We have reviewed the application and the estimation methods of major epidemiological parameters of phylodynamics and phylogeography in domestic and foreign studies. We concluded that the time- and location-scaled phylogenetic trees are increasingly used for outbreak investigation and routine surveillance of infectious diseases.
Bayes Theorem ; Communicable Diseases/genetics* ; Epidemiologic Studies ; Genomics ; Humans ; Phylogeny

A large number of studies have demonstrated that mRNA vaccine has been characterized as a technique with good safety, strong immunogenicity and high developmental potential, which makes it have broad prospects in immunotherapy. In recent years, the stability and in vivo delivery efficiency of mRNA vaccines have been largely addressed by the progresses in mRNA engineering and delivery innovation. And some mRNA vaccines are now clinical approved or in preclinical trials. Here, we summarize current knowledge on the research advances, technology, and application in major infectious diseases in humans and animals of mRNA vaccines, with the aim to provide a reference for improving the development of novel mRNA vaccines.
Animals ; Humans ; Communicable Diseases ; Vaccines, Synthetic/genetics* ; mRNA Vaccines

Alternative splicing (AS) is an evolutionarily conserved mechanism that removes introns and ligates exons to generate mature messenger RNAs (mRNAs), extremely improving the richness of transcriptome and proteome. Both mammal hosts and pathogens require AS to maintain their life activities, and inherent physiological heterogeneity between mammals and pathogens makes them adopt different ways to perform AS. Mammals and fungi conduct a two-step transesterification reaction by spliceosomes to splice each individual mRNA (named cis -splicing). Parasites also use spliceosomes to splice, but this splicing can occur among different mRNAs (named trans -splicing). Bacteria and viruses directly hijack the host's splicing machinery to accomplish this process. Infection-related changes are reflected in the spliceosome behaviors and the characteristics of various splicing regulators (abundance, modification, distribution, movement speed, and conformation), which further radiate to alterations in the global splicing profiles. Genes with splicing changes are enriched in immune-, growth-, or metabolism-related pathways, highlighting approaches through which hosts crosstalk with pathogens. Based on these infection-specific regulators or AS events, several targeted agents have been developed to fight against pathogens. Here, we summarized recent findings in the field of infection-related splicing, including splicing mechanisms of pathogens and hosts, splicing regulation and aberrant AS events, as well as emerging targeted drugs. We aimed to systemically decode host-pathogen interactions from a perspective of splicing. We further discussed the current strategies of drug development, detection methods, analysis algorithms, and database construction, facilitating the annotation of infection-related splicing and the integration of AS with disease phenotype.
Animals ; Alternative Splicing/genetics* ; RNA Splicing ; Spliceosomes/metabolism* ; RNA, Messenger/metabolism* ; Communicable Diseases/genetics* ; Mammals/metabolism*

Messenger RNA (mRNA) vaccines emerge as promising vaccines to prevent infectious diseases. Compared with traditional vaccines, mRNA vaccines present numerous advantages, such as high potency, safe administration, rapid production potentials, and cost-effective manufacturing. In 2020, two COVID-19 vaccines (BNT162b2 and mRNA-1273) were approved by the Food and Drug Administration (FDA). The two vaccines showed high efficiency in combating COVID-19, which indicates the great advantages of mRNA technology in developing vaccines against emergent infectious diseases. Here, we summarize the type, immune mechanisms, modification methods of mRNA vaccines, and their applications in preventing infectious diseases. Current challenges and future perspectives in developing mRNA vaccines are also discussed.
United States ; Humans ; mRNA Vaccines ; BNT162 Vaccine ; COVID-19 Vaccines/genetics* ; Communicable Diseases ; RNA, Messenger/genetics*

Introduction of double-stranded RNA (dsRNA) into some cells or organisms results in degradation of its homologous mRNA, a process called RNA interference (RNAi). The dsRNAs are processed into short interfering RNAs (siRNAs) that subsequently bind to the RNA-induced silencing complex (RISC), causing degradation of target mRNAs. Because of this sequence-specific ability to silence target genes, RNAi has been extensively used to study gene functions and has the potential to control disease pathogens or vectors. With this promise of RNAi to control pathogens and vectors, this paper reviews the current status of RNAi in protozoans, animal parasitic helminths and disease-transmitting vectors, such as insects. Many pathogens and vectors cause severe parasitic diseases in tropical regions and it is difficult to control once the host has been invaded. Intracellularly, RNAi can be highly effective in impeding parasitic development and proliferation within the host. To fully realize its potential as a means to control tropical diseases, appropriate delivery methods for RNAi should be developed, and possible off-target effects should be minimized for specific gene suppression. RNAi can also be utilized to reduce vector competence to interfere with disease transmission, as genes critical for pathogenesis of tropical diseases are knockdowned via RNAi.
Animals ; Communicable Diseases/*genetics/*parasitology ; Helminths/*genetics/metabolism ; Humans ; Insect Vectors/*genetics/metabolism ; Protozoa/*genetics/physiology ; *RNA Interference ; *Tropical Climate

Introduction of double-stranded RNA (dsRNA) into some cells or organisms results in degradation of its homologous mRNA, a process called RNA interference (RNAi). The dsRNAs are processed into short interfering RNAs (siRNAs) that subsequently bind to the RNA-induced silencing complex (RISC), causing degradation of target mRNAs. Because of this sequence-specific ability to silence target genes, RNAi has been extensively used to study gene functions and has the potential to control disease pathogens or vectors. With this promise of RNAi to control pathogens and vectors, this paper reviews the current status of RNAi in protozoans, animal parasitic helminths and disease-transmitting vectors, such as insects. Many pathogens and vectors cause severe parasitic diseases in tropical regions and it is difficult to control once the host has been invaded. Intracellularly, RNAi can be highly effective in impeding parasitic development and proliferation within the host. To fully realize its potential as a means to control tropical diseases, appropriate delivery methods for RNAi should be developed, and possible off-target effects should be minimized for specific gene suppression. RNAi can also be utilized to reduce vector competence to interfere with disease transmission, as genes critical for pathogenesis of tropical diseases are knockdowned via RNAi.
Animals ; Communicable Diseases/*genetics/*parasitology ; Helminths/*genetics/metabolism ; Humans ; Insect Vectors/*genetics/metabolism ; Protozoa/*genetics/physiology ; *RNA Interference ; *Tropical Climate

Communicable Diseases ; genetics ; Genetic Diseases, Inborn ; genetics ; Genetic Testing ; Genotype ; Genotyping Techniques ; Humans ; Molecular Diagnostic Techniques ; Precision Medicine ; methods ; trends

An individual may be at increased risk of acquiring an infectious disease either because of inherent host factors, such as age and illness, or environmental factors, manipulations performed as part of medical practice, or a combination of both factors. Among the exogenaus causes, especially the mode of airborne transmission in hospital infection, the authors observed the effects of UV-254 nm light on air contaminants in the intensive care unit by performing colony counts and Gram stain. The mechanism of action of UV-254 nm light on air contaminants is known to be the destruction of the microbial genetic material such as RNA and/or DNA. The results of reducing the air contaminants through the UV-254 nm light in the intensive care unit show the destruction of a broad spectrum of pathogenic and opportunistic microorganisms as follows: 1) The UV-254 nm light was most effective in crowded conditions of the intensive care unit. 2) The effect was begun from one hour after exposure of the UV-254 nm light device, and low colony counts were maintained constantly up to the 12th day. 3) Among the microorganisms, the device especially reduced the colony counts of staphylococcus species.
Communicable Diseases ; Cross Infection ; DNA ; Genetics, Microbial ; Intensive Care Units ; RNA ; Staphylococcus

Infectious diseases are an enormous public health burden and a growing threat to human health worldwide. Emerging or classic recurrent pathogens, or pathogens with resistant traits, challenge our ability to diagnose and control infectious diseases. Nanopore sequencing technology has the potential to enhance our ability to diagnose, interrogate, and track infectious diseases due to the unrestricted read length and system portability. This review focuses on the application of nanopore sequencing technology in the clinical diagnosis of infectious diseases and includes the following: (i) a brief introduction to nanopore sequencing technology and Oxford Nanopore Technologies (ONT) sequencing platforms; (ii) strategies for nanopore-based sequencing technologies; and (iii) applications of nanopore sequencing technology in monitoring emerging pathogenic microorganisms, molecular detection of clinically relevant drug-resistance genes, and characterization of disease-related microbial communities. Finally, we discuss the current challenges, potential opportunities, and future outlook for applying nanopore sequencing technology in the diagnosis of infectious diseases.
Communicable Diseases/diagnosis* ; High-Throughput Nucleotide Sequencing ; Humans ; Microbiota/genetics* ; Nanopore Sequencing ; Sequence Analysis, DNA ; Technology